Pair your accounts.

Export articles to Mendeley

Get article recommendations from ACS based on references in your Mendeley library.

Pair your accounts.

Export articles to Mendeley

Get article recommendations from ACS based on references in your Mendeley library.

You’ve supercharged your research process with ACS and Mendeley!

STEP 1:
Click to create an ACS ID

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

MENDELEY PAIRING EXPIRED
Your Mendeley pairing has expired. Please reconnect
ACS Publications. Most Trusted. Most Cited. Most Read
Reversible Covalent Inhibition─Desired Covalent Adduct Formation by Mass Action
More

OR SEARCH CITATIONS

My Activity
Publications

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:ACS Chem. Biol. 2024, 19, 4, 824-838
  • Open Access
Review

Reversible Covalent Inhibition─Desired Covalent Adduct Formation by Mass Action
Click to copy article linkArticle link copied!

Open PDF

ACS Chemical Biology

Cite this: ACS Chem. Biol. 2024, 19, 4, 824–838
Click to copy citationCitation copied!
https://doi.org/10.1021/acschembio.3c00805
Published April 3, 2024

Copyright © 2024 The Authors. Published by American Chemical Society. This publication is licensed under

CC-BY-NC-ND 4.0 .

Abstract

Click to copy section linkSection link copied!
High Resolution Image
Download MS PowerPoint Slide

Covalent inhibition has seen a resurgence in the last several years. Although long-plagued by concerns of off-target effects due to nonspecific reactions leading to covalent adducts, there has been success in developing covalent inhibitors, especially within the field of anticancer therapy. Covalent inhibitors can have an advantage over noncovalent inhibitors since the formation of a covalent adduct may serve as an additional mode of selectivity due to the intrinsic reactivity of the target protein that is absent in many other proteins. Unfortunately, many covalent inhibitors form irreversible adducts with off-target proteins, which can lead to considerable side-effects. By designing the inhibitor to form reversible covalent adducts, one can leverage competing on/off kinetics in complex formation by taking advantage of the law of mass action. Although covalent adducts do form with off-target proteins, the reversible nature of inhibition prevents accumulation of the off-target adduct, thus limiting side-effects. In this perspective, we outline important characteristics of reversible covalent inhibitors, including examples and a guide for inhibitor development.

This publication is licensed under

CC-BY-NC-ND 4.0 .
  • cc licence
  • by licence
  • nc licence
  • nd licence
Copyright © 2024 The Authors. Published by American Chemical Society

Subjects

what are subjects

Special Issue

Published as part of ACS Chemical Biology virtual special issue “Exploring Covalent Modulators in Drug Discovery and Chemical Biology”.

Introduction

Click to copy section linkSection link copied!
Covalent inhibition is an effective way to limit the function of an enzyme. This mechanism has been leveraged by many organisms to limit the growth of competitors vying for resources (e.g., beta-lactams from the fungal genus Penicillium) (1) or to fight infections (e.g., itaconate from mammalian macrophages (2)). The warheads of these covalent inhibitors are sometimes obvious, such as the strained ring of beta-lactams or the α,β-unsaturated carboxylic acid of itaconic acid, while some have subtle mechanisms of covalent inhibition that are not apparent by looking at the functional groups of the inhibitor (e.g., 3-nitropropionate as an inhibitor of isocitrate lyase (3) or wortmannin as a phosphoinositide-3 kinase inhibitor (4)) (Figure 1). The presence of numerous different covalent mechanisms of inhibition in nature suggests that the benefits of producing reactive electrophilic chemicals as a means of survival are, on the whole, more favorable than the potential off-target effects they may cause.

Figure 1

Figure 1. Structures of Penicillin G, 3-nitropropionate, itaconate, and wortmannin are examples of natural product covalent inhibitors with their covalent adducts.

High Resolution Image
Download MS PowerPoint Slide
In drug-development, we aim to minimize the extent of side-effects and maximize the therapeutic potential of drugs. Since covalent inhibitors typically contain electrophilic groups, there was considerable concern about indiscriminate reactivity, since that typically meant irreversible inhibition of enzymes (and off-target proteins) which could lead to severe side-effects. (5) Additionally, compounds (or groups within the compound) that upon metabolism bear reactive groups have been avoided for concern of toxicity. (6) Furthermore, concerns about drug–protein adducts or degradation products leading to immune activation (e.g., allergic reaction) have limited the desire to design covalent inhibitors. (7) Consequently, the gold standard for drug-development was in reversible (i.e., noncovalent) inhibitors. (5) Despite this, there have been numerous drugs approved and still in use that are covalent inhibitors, or are prodrugs which are metabolized to become the active inhibitor (such as omeprazole). (8) Additionally, many noncovalent inhibitors have been removed from the market due to toxicity. As such, the well-warranted concerns of covalent inhibition can be overcome with diligence toward expected hurdles and clever design.

Design of Noncovalent and Covalent Inhibitors

Click to copy section linkSection link copied!
The approach for developing noncovalent inhibitors (NCIs) is to design compounds that strongly bind to our target protein, bind significantly weaker to other proteins, and rely on dynamic equilibria leading to the most thermodynamically stable product (i.e., drug binding to intended target). This relies on the law of mass action, which describes the equilibrium of reactants as a function of their concentrations and activities. Indeed, this has been thoroughly described with a discussion of assumptions and models. (9) However, this still leads to unanticipated issues in drug-development for side-effects since small molecules bind to numerous different proteins and enzymes, even if there is little homology in structures. (10) This suggests that there needs to be additional mechanisms of discrimination to prefer binding of the target protein and limit off-target binding. Despite previously addressed concerns, there are advantages available to covalent inhibitors that are not found in NCIs. Indeed, leveraging these advantages has led to a resurgence of covalent inhibitors. (5) One such advantage is the prolonged residence time of the inhibitor in the target protein. (11) A second is the ability to inhibit “undruggable” targets. (12) Some characteristics of “undruggable” targets include those with an “extended or shallow pocket, or no pocket at all” and targets that engage in protein–protein interactions (PPI). (12) RCIs have seen success in inhibiting such “undruggable” targets such as Mcl-1 (which engaged in PPI) wherein a surface lysine residue forms a covalent adduct with the arylboronic acid of the RCI, which interferes in complex formation. (13) Additionally, RCIs have been successful in engaging with targets for which it may not be possible to develop NCIs that discriminate between highly homologous active sites of different enzymes (e.g., KRAS inhibitors). (14) A third is the 2-fold mode for protein selectivity: one as binding in the same fashion as NCIs, and two by forming a bond with a reactive amino acid residue to deactivate the target either by suicide inhibition─irreversible deactivation of the catalytic residues─or increased binding affinity due to forming a covalent adduct resulting in strong competitive inhibition. The incorporation of a covalent warhead improves the “stickiness” of the inhibitor for the target protein. The reaction between the inhibitor and target may be irreversible or reversible. As the name suggests, irreversible covalent inhibitors (ICIs) form covalent adducts that permanently alter the target, which is akin to adhering the inhibitor to the target with glue. Conversely, reversible covalent inhibitors (RCIs) form covalent adducts that do not permanently alter the target, analogous to sticking the inhibitor to the target with Velcro. This is summarized in Figure 2, where NCIs have a single binding equilibrium with on and off kinetics, while ICIs and RCIs have two steps, the second of which is the covalent adduct formation. In ICIs, this second step is inactivation, whereas in RCIs, this second step is also in equilibrium.

Figure 2

Figure 2. Schematic of NCI, ICI, and RCI inhibition with descriptions of the equilibrium or inactivation constants (Mons et al.). Adapted from ref (15). Available under a CC-BY 4.0 license. Copyright 2024 Elma Mons, Sander Roet, Robbert Q. Kim, Monique P. C. Mulder.

High Resolution Image
Download MS PowerPoint Slide

Incorporating the law of mass action into drug design

Click to copy section linkSection link copied!
By accepting off-target engagements as inevitable, we can introduce functionality into inhibitors that can address off-target issues. A method of doing this is to deliberately introduce functionality that reduces the level of target binding. Specifically, by designing a covalent inhibitor whose reaction kinetics allow for reversibility, permanent modification of off-target adducts can be mitigated. ICIs will react with unintended targets, which then results in off-target effects. The irreversible nature of ICIs results in permanent modification of the unintended target, which will persist until it is degraded. On the other hand, RCIs contain electrophilic warheads that have good reversible reaction kinetics allows for off-target reactions to occur, but then reverses to liberate the inhibitor. Ideally, an inhibitor would be designed for the target specifically in which it should have strong binding kinetics for the target, and weak binding kinetics for the formation of off-target covalent adducts. It is possible to design an inhibitor to have good on-target engagement, but it is not possible to design an inhibitor that has poor off-target engagement. By incorporating a mechanism of disengagement with off-target proteins, it is expected that off-target covalent inhibition diminishes over time. Conceptually, this suggests considering reaction equilibria, or on/off kinetics which returns us to the law of mass action. By deliberately considering the reaction kinetics with off-target proteins and reaction kinetics with the target protein, we can consider the formation of the desired “product” (inhibitor–target protein adduct) as a result of a series of kinetic equilibria.
Simplified, an RCI may reversibly react with many other substrates, but since the formation of desired product is highly favored, the result of all equilibria eventually leads to the formation of the desired product (Figure 3).

Figure 3

Figure 3. Inhibitor is in equilibrium with many enzymes, including the target enzyme. Since the inhibitor–target complex is greatly favored, this will shift the equilibria of the off-target interactions away from the off-target complexes with the inhibitor as described by Le Chatalier’s principle. Over time, the inhibitor–target complex will be the predominant site of the RCI.

High Resolution Image
Download MS PowerPoint Slide
This binding affinity should contribute more to Ki* (* designates a covalent adduct) than the propensity of adduct formation in order to favor formation of the intended inhibitor–target complex over off-target complexes. Additionally, it is worth noting that since Ki* are in terms of enzyme concentration, direct comparison of Ki* between the target protein or enzyme and off-target proteins or enzymes may be misleading since expression levels may differ by orders of magnitude. The overall steady-state equilibrium constant Ki* and target residence time (τ) is described in Figure 4. (15)

Figure 4

Figure 4. The observed equilibrium of a covalent inhibitor is the product of the binding equilibrium constant and the reaction equilibrium constant.

High Resolution Image
Download MS PowerPoint Slide
Since the goal in designing an inhibitor is for the compound to interact with the target enzyme to prevent substrate turnover, it is important not only for the inhibitor to bind strongly but to occupy the enzyme for a prolonged period to prevent substrate binding. Additionally, since we are considering steady-state kinetics with all other nucleophiles our inhibitor may form adducts with, the Ki* should be minimized and τ should be maximized. A comprehensive review and tutorial performing kinetic experiments with covalent inhibitors has been described by Mons et al. (15)

Modeling in covalent inhibitor design

Click to copy section linkSection link copied!
As interest in developing covalent inhibitors has increased in recent years, so has computational modeling to better understand and predict reactivity and selectivity. (16) Density Functional Theory (DFT) is a particularly helpful tool to assess the reactivity of electrophile and protein nucleophilicity to predict covalent reactions, such as a reaction between a kinase serine and a covalent inhibitor. (17) It is important to know if the target of interest is amenable to covalent inhibition before spending extensive efforts on synthesis and protein purification to learn that the nucleophilic residue (e.g., a catalytic serine) does not react sufficiently well with the warhead chosen for the inhibitor. Molecular modeling can allow for the incorporation of the appropriate warhead prior to embarking on synthetic efforts. (18) Indeed, Plescia et al., through computational modeling and kinetic experiments, found that a boronic acid warhead was more well-suited for inhibition of prolyl oligopeptidase than the typical nitrile warhead. (18) Recently, there have been increased efforts in designing models to describe the necessary conditions for reversible covalent inhibition to occur. Masuda et al. used the Gibbs free energy of hydrolytic water molecules to interrogate the expected rate of reaction for hydrolysis of the covalent adduct. Despite using training set and test set compounds that would more appropriately be described as competitive substrates, the model still provides useful information demonstrating that (intuitively) both the lower Gibbs free energy of water and the increased activation energy for bond-cleavage lead to a slower reverse reaction of the covalent adduct. In their work, the entropic component of the Gibbs free energy equation (-TΔS) correlates well with kcat, suggesting that their model utilizing the Gibbs free energy of water and the activation energy of covalent–adduct bond cleavage may be effective parameters by which to discriminate covalent inhibitors. (19) Efforts by Chatterjee et al. have been to probe free energy perturbations using quantum mechanics/molecular mechanics (QM/MM) calculations to predict binding affinities and binding kinetics for warheads and their target enzymes. They found that using this approach, when covalent binding was 5.5 kcal/mol stronger than noncovalent binding, selectivity could be predicted by the relative free binding energy of the covalent state. (16) An extensive review on the details of covalent inhibition modeling (irreversible and reversible) has recently been published by Awoonor-Williams et al. (20) Additionally, Scarpino et al. have described detailed protocols for screening large libraries of warheads with selected enzyme targets to model binding mode predictions, single-warhead virtual screening, and multiwarhead virtual screening. (21) For further reading, a detailed review of the application of computational methodologies to covalent inhibitor design has been described by De Cesco et al. (17)

Chemical characteristics of reversible covalent warheads

Click to copy section linkSection link copied!
There have been numerous reversible covalent warheads developed to mediate the off-target effects found in ICIs. (22) The warhead should be selected for its reactivity for the intended amino acid to react with, as different warheads have different reactivities to different amino acids (23) in addition to well-modeled predictions of how reactive the warhead is for the intended amino acids. (24) Jackson et al. have a highly thorough review of α,β-unsaturated carbonyls with thiols. (25) As expected, stronger Michael-acceptors such as α,β-unsaturated aldehydes, ketones, esters, and acid chlorides react quite rapidly, whereas α,β-unsaturated amides and carboxylic acids react significantly less so. The substituents of the amides do greatly affect the reactivity with thiols in which an N-(2-pyridyl) substituent has a half-life with glutathione of approximately 8 min, whereas an N-methyl substituent has a half-life of approximately 17 h. (25) Mechanistic studies performed by the Keillor group on model acrylamide substrates found that the nucleophilicity of the thiolate in question was not a significant contributor to reaction rates. (26,27) Combined, this suggests that when targeting cysteine residues, the intrinsic reactivity is dictated by the electrophile being designed. This is not to advocate neglect of the nature of the cysteine residues being targeted. For example, the reactivity of catalytic cysteine residues can be enhanced through methods such as “desolvation,” which destabilizes the thiolate anion and thus increases its nucleophilicity. (28) Nuances into the reactivity of cysteine residues are thoroughly reviewed by Parvez et al. (29)
Extensive efforts have been made by the Taunton group in tuning the reversibility and the residence times of RCIs. Using the cyano-acrylamide group warhead as a model, Krishnan et al. changed the amide into a variety of heteroaromatic groups. (30) They had then plotted the computed proton affinity of the α-carbanion (relative difference from the parent cyano-acrylamide) versus the rate of elimination. They found a linear relationship in which the greater the proton-affinity, the slower the rate of elimination. (30) This provides evidence of an intuitive assumption in which more acidic protons (lower pKa and lower proton affinity) in the α-position would lead to a more rapid elimination. Therefore, covalent adducts would be less stable, and lead to greater reversibility. (30) Additionally, there can be steric contributions that limit the accessibility of the acidic α-protons, which then reduces the rate of elimination. (31) In efforts to tune residence time, Bradshaw et al. introduced substitutions at the β-position of the cyanoacrylamides. The introduction of bulky β-substitutions did not affect greatly affect inhibition of their enzyme target, but could extend the residence time from minutes to days. (32) By tuning the reactivity of the warhead, the reverse reactivity (elimination), and the residence time, RCIs can mimic the on-target benefits of ICIs while circumventing issues associated with off-target reactivity.
Although not as thoroughly characterized as substituted acrylamides, tunability of boronates and nitriles have been described with postulating that varying the boronate pKa may be optimized for target engagement, (33) and that increasing the electron withdrawing groups bound to the nitrile improves electrophilicity (and therefore reactivity). (34)
Despite many warheads not having as much depth for kinetic and mechanistic studies for tuning reactivity for the purpose of designing RCIs, there are many that have been designed to leverage reactivity toward a particular target amino acid residue, such as cysteine, serine/threonine, or lysine, as seen in Figure 5. The examples include reversible warheads for cysteine such as α-cyanocarbonyls (35) or other α-substituted alkenes with good electron withdrawing groups, (30,36) nitriles, (37) aldehydes, (38) and dihaloacetamides (39) (although the halogens are lost, and the equilibrium is between the free cysteine and 2-oxoacetamide), and thiomethyltetrazines; (40) reversible warheads for serine/threonine include α-oxo-amides (41) and boronic acids; (42) and reactive amines such as lysines and N-terminus amines react with aldehydes to form stabilized imines, (43) either by a neighboring hydrogen bond donor, or through subsequent formation of a stable diazaborine. (44) Example compounds for each of these warheads can be seen in Figure 6. The incorporation of reversible warheads into drug design has led to numerous successes (22) with selected examples highlighting the advantages RCIs have over ICIs, and situations where RCIs are particularly effective.

Figure 5

Figure 5. Nucleophilic residues reacting with electrophilic warheads in equilibrium with their covalent-adduct products, with the electrophilic warheads highlighted in red.

High Resolution Image
Download MS PowerPoint Slide

Figure 6

Figure 6. Examples of reversible covalent inhibitors with their electrophilic warheads are highlighted in red.

High Resolution Image
Download MS PowerPoint Slide

Biochemical analysis of reversible covalent warheads

Click to copy section linkSection link copied!
After designing and synthesizing the RCIs, validating their reversibility, determining activity, measuring residence time, and evaluating off-target effects require numerous techniques. Confirming reversibility is a relatively easy to address. Using nuclear magnetic resonance (NMR) techniques, the chemical signal for adducts versus the unbound RCI may be quite distinct. By diluting the NMR sample of the covalent adduct, the system equilibrates which reduces the adduct concentration, providing greater unbound RCI. (45) Additionally, the Kd can also be determined through this method if the adduct or RCI has distinct UV/vis spectroscopic signals. (45) Mass spectrometry (MS) can also provide evidence for reversibility in which the covalent adduct is injected into the mass spectrometer, but over the course of the MS experiment, dissociation occurs and the molecular ion of the inhibitor, (31) or the native protein is liberated and observed on the MS spectrum. (46) Competitive inhibition assays utilizing bioluminescent resonance energy transfer (BRET) have also been used in combination with washout experiments in which the protein was saturated with the RCI, then a fluorescent tracer was introduced which replaced the RCI, demonstrating reversibility and binding kinetics of the RCI. (46) Additionally, degradation or denaturation of the RCI-protein adduct followed by recovery of the RCI provides further evidence for reversibility. (32)
The residence time of RCIs can be measured through fluorescence competition assays in vitro or through pharmacokinetic/pharmacodynamic (PK/PD) analyses. Bradshaw et al.─in their efforts to tune residence times of RCIs─they measured the residence time in cells via competition assays in which they incubated Bruton tyrosine kinase (BTK) with an inhibitor followed by washing to removed excess inhibitor, then incubated with a fluorescently labeled inhibitor. Measuring the fluorescence of the labeled inhibitor over time then is used to determine the residence time, and % of BTK bound over time. (32) Residence time measurements in vivo can be performed by dosing an animal model with the RCI, then harvesting the spleen at certain time points (e.g., 1, 12, and 24 h) followed by competition with an irreversible fluorescent probe and measuring the percent occupancy of the RCI. (35)
Evaluating off-target effects is particularly important considering the concerns of toxicity for covalent inhibitors. (6) Classical methods of determining what proteins were forming adducts with the covalent inhibitors involved incubation with a radiolabeled inhibitor, followed by gel chromatography, electrophoresis, excision from the gel and submitted to Edman sequencing to identify the amino acid-inhibitor adduct. (6,47,48) More modern methods include MS methodologies in which a protein of interest is analyzed after isolation (e.g., chromatography, electrophoresis) (49) for covalent modification (without protein digestion if sites of modification are known, after digestion if unknown). (49) Chemical proteomics is another method to probe the off-target reactivity of a covalent inhibitor. By tagging the RCI with a label (e.g., affinity, fluorescent, or radioactive) the adduct may be isolated and analyzed (such as purification from affinity columns using affinity labels, or excising from gels using fluorescent or radioactive labels). (50) These screens have been used to identify target compounds in drug discovery, but could also be applied to identify off-target proteins. (50) Similar principles have been applied to find reactive lysine and cysteine residues. (51−53) It is important to recognize that the presence of a covalent adduct does not necessarily mean that there is an adverse effect associated with it. Identifying off-target adducts can provide evidence to support hypotheses associated with side-effects, but the role of the off-target adduct must be explored further if unknown. (49)
Global stress responses in cells may also result from covalent inhibitors. This may be caused by reactivity with glutathione, which can cause electrophilic stress responses in cells. (54) Performing competition reactions of the protein target and glutathione with RCIs (31) in addition to monitoring for glutathione depletion in cells (55,56) can provide helpful information on the effect of RCIs on electrophilic stress in cells. Furthermore, covalent inhibitors may induce misfolding of proteins which could lead to a global protein misfolding profiles and responses. (57,58)
Additionally, T-cell activation due to chemically reactive intermediates are not necessarily identifiable through MS methods. (49) These can occur via the formation of drug haptens (covalent adducts of proteins) which subsequently induce T-cell-mediated drug-hypersensitivity reactions. (59) Additionally, there may be covalent interactions with the T-cell receptor or human leukocyte antigen (HLA) peptides which ultimately results in a T-cell response. (59) β-lactams are known to form haptens, which are responsible for penicillin allergies. (60) Unfortunately, drug-hypersensitivity reactions cannot be predicted, and remains an active field of research to critical antigens responsible for T-cell activation with respect to drug–protein adducts (59) or the nuances of T-cell activation with major histocompatibility complexes associated with drug-peptide adducts. (61)

Development of highly selective JAK3 inhibitors

Click to copy section linkSection link copied!
Janus kinases (JAK) are critical regulatory enzymes that mediate cell signaling responses, especially within the secretion of cytokine signals which are implicated in immune responses. (62) In humans, there are four subtypes (JAK1, JAK2, JAK3, and TYK2), each having high similarity. (63) Consequently, developing highly selective drugs to modulate the activity of one JAK over another is extremely challenging. Clinical success has been observed in developing pan-JAK inhibitors, with the FDA approval of tofacitinib, but the effects of inhibiting multiple JAKs is unclear, especially since different JAKs play diverse roles in immune health. (63) Goedken et al. aimed to leverage a unique cysteine residue on JAK3 (Cys909), which would confer unique reactivity relative to JAK1, JAK2, and TYR2 (which contain serine at the equivalent position) which makes covalent inhibition a particularly attractive approach. (63,64) Using a small collection of newly developed ICI (1–3), a known JAK3 inhibitor thought to be an ICI (4), and two previously known noncovalent JAK3 inhibitors (5 and 6) (Figure 7), Goedken et al. characterized and determined that the newly developed ICIs had excellent activity (low nM) and selectivity (>500×) for JAK3 versus other JAK kinases. (63) Additionally, for other highly similar kinases with cysteine residues at the equivalent position as JAK3, there was also high selectivity (>100×). (63) Although compounds 1–3 were found to have good IC50 values in vitro, this obscures the problem that if the covalent warhead were to react off-target before reaching JAK3, the result would be an off-target, irreversible adduct that could lead to adverse effects. By building off of the work done targeting Cys909 of JAK3, Forster et al. developed new inhibitors using the same tricyclic scaffold (7), but making modifications in which the covalent warhead was replaced with a cyano-acrylamide group, which is a good reversible Michael-acceptor (Figure 6). (46,65) The cyano-acrylamide containing compounds were validated to be reversible inhibitors using washout experiments utilizing BRET in addition to MS where adduct dissociation was observed. (46) Direct comparisons of the Michael-acceptors (9 and 10) versus their saturated equivalents (11 and 12) were made, and it was found that there was a general trend of a higher IC50 (upward of 4× higher for the saturated compounds). (66) This suggests that there are significant noncovalent interactions that the compounds are making with the target enzyme. Forester et al. found that their acrylamide-containing compounds (5 and 8, which form irreversible adducts) had good activity (292 nM and 22 pM), but low selectivity between the different JAK kinases, whereas the cyano-acrylamide-containing compounds (13 and 14, which form reversible adducts) also had good activity (127 pM and 154 pM) in addition to having high selectivity for JAK3 versus JAK1, JAK2, and TYR2 ranging from 400× to 5800× selectivity. (46) In an in vitro assay for selective inhibition of JAK3, the pan-JAK kinase inhibitor (5) was found to inhibit multiple JAK kinases, whereas the RCIs were found to be selective for JAK3. (46) The next generation of the JAK3 RCIs was to optimize the compound for selectivity, activity, and explore structure–activity relationships (SAR). (66) Significant efforts went into modifications at the position of the Michael-acceptor. The next steps for these inhibitors have been to improve pharmacokinetics and metabolic stability utilizing the cyano-acrylamide warhead. (67)

Figure 7

Figure 7. Examples of JAK3 inhibitors with covalent warheads are highlighted in red.

High Resolution Image
Download MS PowerPoint Slide

Development of Bruton Tyrosine Kinase inhibitors for immune diseases

Click to copy section linkSection link copied!
BTK is a critical enzyme in immune regulatory responses related to antibody signaling and immune cell recruitment and is expressed in most hematopoietic cells. (68) BTK is critical in signaling cascades in B cells, including the activation of NF-κB, (69) which is essential for regulating B cell activation and development. (70) Dysregulation of the BTK signaling pathway can lead to constitutive activation of NF-κB, and subsequent “addiction” to NF-κB by many cancer types. (71) Consequently, BTK is a particularly important therapeutic target for immune system diseases such as mantle cell lymphoma, chronic lymphocytic leukemia, Waldenstrom macroglobulinemia, marginal zone lymphoma, and chronic graft-versus-host disease, for which BTK inhibitors have been approved or are in development. (35) BTK contains a cysteine residue where analogous enzymes contain a serine, allowing for reactivity-based selectivity, which makes for a good candidate for covalent inhibition. (12) Ibrutinib, acalabrutinib, zanubrutinib, and tirabrutinib (Figure 8) are all approved drugs that inhibit BTK through an irreversible reaction with Cys481. (72−75) These drugs are highly potent inhibitors with low to subnanomolar IC50 values against BTK. (75,76) Despite their high potencies for BTK, kinases that have analogous cysteine residues to Cys481 are also prone to irreversible inhibition. Selectivity indices for ibrutinib show low to modest selectivity for BTK versus a panel of other related tyrosine kinases (0.36–117× selectivity), the second-generation BTK inhibitors acalabrutinib and tirabrutinib have greater selectivity generally, but still modest (0.88 to >8000×). (75) Due to the irreversible nature of the binding, potent off-target inhibition can lead to side-effects including atrial fibrillation, diarrhea, and bleeding significant enough to discontinue treatment (upward of 20–25% of patients). (77−80) Langrish et al. describe the reversible BTK inhibitor rilzabrutinib’s biochemical and safety profile. (35) Rilzabrutinib (Figure 8) contains a cyano-acrylamide group that serves as the reversible warhead and was validated to be an RCI by recovery of the inhibitor following BTK-adduct digestion by trypsin in addition to quantifying the kon (5.1 ± 2.1 × 104 M–1 s–1) and the koff (1.2 ± 0.1 × 10–6 s–1). (35) It was evaluated against 251 kinases from diverse families, with 6 (including BTK) having inhibition at >90% at 1 μM. (35) Residence time of rilzabrutinib was compared for 5 of these kinases, and only BTK was found to have an occupancy rate of over 80% during a 24-h incubation (35) suggesting that despite potent binding of rilzabrutinib to other kinases, it will dissociate from the off-target kinases better than BTK, suggesting that side-effects related to off-target binding may be limited due to low residence time. Langrish et al. performed a series of assays to evaluate the on- and off-target effects of rilzabrutinib. They determined that it had low cytotoxicity (>16,000 nM) in non BTK-expressing cell lines, did not inhibit T-cell receptor-induced activation or calcium flux-induced activation of T-cells (>5000 nM), and did not interfere in EGFR signaling. (35) Additionally, unlike ibrutinib, rilzabrutinib does not reduce normal platelet aggregation (35) which leads to normal clotting (which is a significant problem with ibrutinib). (77,78) Langrish et al. also found that there was durable inhibition of BTK in rats where BTK occupancy was ∼90% after 14 h, while the serum concentration of rilzabrutinib had fallen to <3 ng/mL (compared to nearly 500 ng/mL after 1 h) at 40 mg/kg dosing. This suggests that short exposure time and low systemic exposure is required for effective inhibition which reduces the chance of side-effects. (35) Rilzabrutinib is currently being evaluated in Phase III trials for adults and adolescents with persistent or chronic immune thrombocytopenia, and numerous Phase II clinical trials for immune disorders such as warm autoimmune hemolytic anemia, atopic dermatitis, asthma, IgG4-related disease, chronic spontaneous urticaria, and immune thrombocytopenia. (81)

Figure 8

Figure 8. Clinically approved irreversible covalent inhibitors for BTK: ibrutinib, Zanubrutinib, acalabrutinib, and tirabrutinib, and a reversible covalent inhibitor for BTK in clinical trials: rilzabrutinib. The covalent warhead is highlighted in red.

High Resolution Image
Download MS PowerPoint Slide

Development of inhibitors for proteases

Click to copy section linkSection link copied!
Proteases fall into seven categories based on their catalytic residues: aspartic, cysteine, serine, metallo, threonine, glutamic, and asparagine. (82) These proteases are found across all domains of life. As a consequence, the effort to inhibit proteases has been applied in anticancer, antimicrobial, hypertension, type 2 diabetes, Alzheimer’s disease, nonalcoholic fatty liver disease, and fibrosis therapies. (83) Since protease categories are mechanistically discrete due to their catalytic residues, RCIs are an effective tool for selective inhibition. Clinical success has been seen with RCI inhibition (22) including bortezomib and ixazomib (threonine protease inhibitors), (84) boceprevir, saxaglibtin, and telaprevir (serine protease inhibitors), (85−87) and nirmatrelvir (cysteine protease inhibitor). (88) A recent example for the development of a cysteine protease inhibitor was performed by Ma et al. (31) to treat enterovirus 71 (EV 71)─one of the causative agents of hand, foot, and mouth disease. (89) Ma et al. aimed to synthesize an inhibitor for the 3C protease with steady-state kinetics (i.e., rate of reaction and elimination of covalent warhead) residence time of the inhibitor as explicit parameters to tune in designing the optimal cysteine protease inhibitor (Figure 9). (31) Using the scaffold of rupintrivir (an ICI for human rhinovirus, which is a homologue of EV71), modifications were made to improve selectivity for EV71 3C protease, resulting in α-ketoamide (90) (15) and aldehyde-based (91) (16) warheads.

Figure 9

Figure 9. Compound optimization for the EV71 cPro enzyme. The covalent warhead is highlighted in red.

High Resolution Image
Download MS PowerPoint Slide
These warheads were likely responsible for poor potency due to off-target reactivity and to address these issues, Ma et al. introduced the cyano-acrylamide group, and modified the amide substitutions to tune reactivity, reversibility, and selectivity. (31) The reversibility of the series of compounds were validated by MS, through fitting kinetic data, and measuring enzyme activity after dialysis. When the covalent adduct was submitted to MS experimentation, the spectra showed both the adduct and the free protease, suggesting reversibility. Different inhibitors were found to have different ratios of the adduct to free enzyme, suggesting different rates of the reverse reaction. The fitting of the kinetic data supported a two-step mechanism, and the dialysis experiments showed that the enzyme would recover activity with increased dialysis time, suggesting that the RCI was disengaging with the protease. (31) All of these supported that the cyano-acrylamide inhibitors behave as RCIs.
To screen the SAR, Ma et al. made many modifications to the warhead. By introducing an α,β-unsaturated ester (17) or amide (18), they found moderate inactivation of 3C protease, and poor EC50 values (>100 000 nM). Introducing halogens as α-substituents to the conjugated esters (19 and 20) led to medium to high-nanomolar Ki* and EC50 values but with highly cytotoxic activity (100% at 100 μM). Substituting the halogens with a nitrile removed cytotoxicity and reduced the Ki* and EC50 values to low to midnanomolar potencies for the cyano-acrylamide (21) and cyano-acrylate ester (22) containing compounds. Interestingly, tertiary amides (such as 21) led to increased inhibitory activity compared to the secondary amides, likely due to steric shielding of the acidic α-proton, which allows for a decreased rate reverse reaction, which would increase residency time. This observation was consistent with the MS data, in which the bulky tertiary amides did not dissociate as much as the secondary amide.
Importantly, competition assays of 21 with 5 mM additions of nonenzymatic nucleophiles such as glutathione, ethanolamine, and lysine were performed. Glutathione modestly affects the in vitro inhibitor activity for cyano-acrylamides. Although the authors did not expect that there would be a significant change in cellular glutathione depletion due to the high potency of the compounds, and their reversible reactivity, the experiments supporting this claim were absent. Finally, in determining selectivity of the inhibitors, the compounds were screened for activity against chymotrypsin (serine protease), cathepsin K (cysteine protease), and calpain-1 (cysteine protease). None of the compounds evaluated had reactivity toward chymotrypsin, suggesting good selectivity for cysteine proteases (as expected considering serine is a poor Michael-donor), and only one compound had >50% inhibition of cathepsin K, while no compounds had >50% inhibition of calpain-1. (31) This is in contrast with analogous inhibitors that utilized aldehyde and cyanohydrin warheads, which had high degrees of inhibition for both cathepsin K and calpain-1 demonstrating that the nature of the warhead significantly reduces off-target activity. Although the screen provided good preliminary evidence of selectivity for the viral cysteine protease, the counterscreen against human proteases is by no means comprehensive, and the experiment would greatly benefit by incorporating more of the other cathepsins, which differ greatly in their amino acid recognition sequences and would therefore differ in their susceptibility to inhibition.

General considerations for developing reversible covalent inhibitors

Click to copy section linkSection link copied!
To develop an effective RCI, some considerations need to be made. There must be a covalent warhead within the designed inhibitor, there must be some selectivity of the covalent warhead for a particular nucleophile, the covalent adduct must be reversible, and the drug must have good binding affinity to the desired target. A framework for designing an optimal reversible covalent inhibitor is described below, in which the assumption is that a good reversible covalent inhibitor has a universal set of characteristics. These steps are summarized in Figure 10.
1)

Before embarking on a program to develop an RCI for your target of choice, perform computational analyses and in silico modeling to ensure that there is a suitable nucleophile to target (e.g., serine, threonine, lysine, cysteine, N-terminus amine). Computational evidence can help support design of the RCI with the appropriate warhead (18) but is not strictly necessary for a successful drug discovery program (especially if there is little high quality structural data with which to work). There have been many works discussing the theoretical frameworks of modeling covalent inhibitors (92) as well as experimental modeling using QM, QM/MM, or QM/MM coupled with molecular dynamics approaches. (16,93−96)

2)

The Law of Mass Action describes the state of products and reactants at equilibrium. Even though the equilibrium may ultimately favor the formation of desired products, the kinetics of desired adduct formation may be prohibitively slow under conditions amenable to therapeutic usage. Conversely, the reverse reaction for off-target effects may be thermodynamically favored, but if the kinetics of dissociation are slow, then the off-target effects may be significant since there may be a long-residence time of the inhibitor and the off-target enzyme, which leads to no functional difference between reversible inhibition and irreversible inhibition on the time scale of cellular stress response. Although slow off-kinetics improve residence time, faster rates may be more suited in certain circumstances. (32) Extensive reviews on slow-binding kinetics and residence time have previously been written concerning drug-design. (11,97−99) Since the intention for developing reversible covalent inhibitors is to reduce off-target effects by taking advantage of reversible kinetics, the residence times of the inhibitor with its on- and off-target enzymes should be optimized. (35,46) These experiments were performed both in the development of the BTK inhibitor rilzabrutinib (35) and JAK3 RCIs. (46)

3)

The binding kinetics of the inhibitor match that of reversible covalent inhibitors. There has been extensive work in characterizing different mechanisms of enzymatic inhibition with kinetic descriptions. (15) A step-by-step guide for the synthesis and biochemical characterization of reversible inhibitors was well-described by Frühauf et al. for histone deacetylase 4 (HDAC4). (100) This should be able to serve as a good starting point for spectroscopic experiments to biochemically characterize the inhibitor. Alternative methods for demonstrating reversible covalent inhibition have been performed by washing followed by tracer treatment (JAK3 inhibitors), (46) using inhibitor recovery after trypsin digest (rilzabrutinib), (35) and combination of steady-state kinetics and biomolecular mass spectrometry (EV71 C3 protease inhibitors). (31)

4)

There should not be a prolonged buildup of the inhibitor–glutathione adduct. This tripeptide is highly abundant in cells (upward of 10 mM) (101) and is intimately involved in redox metabolism (102−104) and electrophilic stress (54) within the cell. Therefore, there must be high reversibility with glutathione in order to not induce a global electrophilic stress response. Assays to be performed to address this issue include competition experiments, in which the intended enzyme and glutathione are coincubated with the reversible covalent inhibitor (31) and glutathione depletion experiments. (55,56) As described above, in the development of the EV71 C3 protease inhibitors, competition with noncovalent nucleophiles such as GSH were performed. (31)

5)

There should be a minimal effect on cellular stress responses. Covalent inhibition of an enzyme may lead to misfolding of the protein. (57,58) If this is nonspecific, this may lead to global protein misfolding stress responses. Examinations of protein profiles can be performed as previously described, (57) and comparisons with efforts to probe reactive residues of the proteome (51−53,105,106) to ensure limited off-target activity. Additionally, the compound should not induce electrophilic stress responses in the cell. (107,108) By incorporating experiments that assess global stress responses, a greater degree of confidence can be made toward knowing that the reversible covalent inhibitor is, indeed, not having obvious off-target effects within the cell.

6)

Beyond effective target engagement, a significant consideration in developing covalent inhibitors is the effect on immune cells. Immune cells are highly sensitive to electrophilic stresses, which can cause either immunostimulatory or immunosuppressive effects. (109) As such, assaying your inhibitor against B cells, T cells, and macrophages to determine whether the inhibitor causes an expression and secretion of pro-inflammatory or anti-inflammatory cytokines is important to avoid potential complications of immune activation.

Figure 10

Figure 10. Summarized activities for each parameter that are important in the design of a reversible covalent inhibitor.

High Resolution Image
Download MS PowerPoint Slide

Conclusion and future directions for reversible covalent inhibitors

Click to copy section linkSection link copied!
There has been a resurgence of covalent inhibitor development in recent years. Technology has improved to be able to interrogate many of the concerns that come with covalent inhibition in drug design. In an effort to profit off of the benefits of covalent inhibition (potent on-target activity via chemical deactivation of the target) while allaying concerns about covalent inhibition (indiscriminate reactivity with nucleophiles in serum or cytosol), one can develop RCIs. This approach leverages the law of mass action, in which the equilibrium of a series of reactions depends on their activities and concentrations. The consequence of this is that at steady-state, the concentration of the products (e.g., a covalent adduct of the target protein) will be dependent upon the equilibrium of all other side-reactions. By designing a strongly binding inhibitor, equilibrium will ultimately lead to inhibition of the desired target with off-target inhibition being disfavored. Although off-target binding will occur, the reversibility of the covalent-adduct will limit the phenotypic consequences of off-target binding. We anticipate that like the examples above wherein moving from irreversible covalent inhibition to reversible covalent inhibition, significant off-target effects were circumvented, leading to potentially a significantly safer drug; the adoption of reversible covalent inhibition will lead to promising drugs with few significant side-effects due to off-target reactivity. Although the focus of this perspective has been in drug-design and enzyme inhibition, reversible covalent adducts have been utilized in cell imaging, (110) and in material science (albeit under the name of dynamic covalent bonds). (111) Future directions for the field will include improving modeling to accurately identify sufficiently nucleophilic noncatalytic residues for adduct-formation, improved rules or guidelines for reactivity and reversibility of reactions of nonacrylamide warheads, and develop robust, easy-to-perform assays to detect unintended immune responses from electrophilic stress. Additionally, discovery of new warheads is always welcome, especially if they can be easily modified with fluorophores or radiolabels to track localization either within cells or within the body.

Author Information

Click to copy section linkSection link copied!
  • Corresponding Author
  • Authors
    • Disha Patel - Department of Chemistry, Brock University, St. Catharines, Ontario L2S 3A1, Canada
    • Zil E Huma - Department of Chemistry, Brock University, St. Catharines, Ontario L2S 3A1, Canada
  • Author Contributions

    Authors contributed equally to this work. D.P, Z.H, and D.D wrote the manuscript; Z.H and D.D. prepared the figures; all the authors proofread and approved the final submitted manuscript.

  • Notes
    The authors declare no competing financial interest.

Acknowledgments

Click to copy section linkSection link copied!

D.D. acknowledges start-up funds provided by Brock University. We thank F. Hammerer and N. Häggman for their discussions and insights.

Keywords

Click to copy section linkSection link copied!
Covalent adduct

a complex that forms from a covalent bond between the inhibitor and a nucleophilic amino acid

Covalent warhead

an electrophilic functional group that reacts with a nucleophilic amino acid

Glutathione

a three-amino-acid molecule (γ-glutamine-cysteine-glycine) that is involved in oxidative stress responses

Irreversible covalent inhibitor

a small molecular that binds with a therapeutic target (such as a protein) which forms a permanent covalent bond

Noncovalent inhibitor

a small molecular that binds with a therapeutic target (such as a protein) which does not form a covalent bond

Nontarget

the unintended biomolecule to which inhibitors bind

Protease

an enzyme that hydrolyses amides of proteins or polypeptides

Residence time

the amount of time that an inhibitor occupies the binding site of a protein

Reversible covalent inhibitor

a small molecular that binds with a therapeutic target (such as a protein) which forms a nonpermanent covalent bond

Target

the intended biomolecule to which inhibitors bind.

References

Click to copy section linkSection link copied!

This article references 111 other publications.

  1. 1
    Fleming, A. On the Antibacterial Action of Cultures of a Penicillium, with Special Reference to Their Use in the Isolation of B. Influenzae. 1929. Bull. World Health Organ. 2001, 79 (8), 780– 790
    Google Scholar
    1
    On the antibacterial action of cultures of a penicillium, with special reference to their use in the isolation of B. influenzae. 1929
    Fleming A
    Bulletin of the World Health Organization (2001), 79 (8), 780-90 ISSN:0042-9686.
    There is no expanded citation for this reference.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BD3MvpslCisA%253D%253D&md5=3c01ee5f9da7a862f0bd23359d039371
  2. 2
    Duncan, D.; Auclair, K. Itaconate: An Antimicrobial Metabolite of Macrophages. Can. J. Chem. 2022, 100 (2), 104– 113,  DOI: 10.1139/cjc-2021-0117
    Google Scholar
    There is no corresponding record for this reference.
  3. 3
    Ray, S.; Kreitler, D. F.; Gulick, A. M.; Murkin, A. S. The Nitro Group as a Masked Electrophile in Covalent Enzyme Inhibition. ACS Chem. Biol. 2018, 13 (6), 1470– 1473,  DOI: 10.1021/acschembio.8b00225
    Google Scholar
    3
    The nitro group as a masked electrophile in covalent enzyme inhibition
    Ray, Sneha; Kreitler, Dale F.; Gulick, Andrew M.; Murkin, Andrew S.
    ACS Chemical Biology (2018), 13 (6), 1470-1473CODEN: ACBCCT; ISSN:1554-8929. (American Chemical Society)
    We report the unprecedented reaction between a nitroalkane and an active-site cysteine residue to yield a thiohydroximate adduct. Structural and kinetic evidence suggests the nitro group is activated by conversion to its nitronic acid tautomer within the active site. The nitro group, therefore, shows promise as a masked electrophile in the design of covalent inhibitors targeting binding pockets with appropriately placed cysteine and general acid residues.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXpsl2nsLc%253D&md5=d2dc8f255fd7e5f7537c57a0c5a3343e
  4. 4
    Yuan, H.; Barnes, K. R.; Weissleder, R.; Cantley, L.; Josephson, L. Covalent Reactions of Wortmannin under Physiological Conditions. Chem. Biol. 2007, 14 (3), 321– 328,  DOI: 10.1016/j.chembiol.2007.02.007
    Google Scholar
    There is no corresponding record for this reference.
  5. 5
    De Vita, E. 10 Years into the Resurgence of Covalent Drugs. Future Med. Chem. 2021, 13 (2), 193– 210,  DOI: 10.4155/fmc-2020-0236
    Google Scholar
    5
    10 years into the resurgence of covalent drugs
    De Vita Elena
    Future medicinal chemistry (2021), 13 (2), 193-210 ISSN:.
    In the first decade of targeted covalent inhibition, scientists have successfully reversed the previous trend that had impeded the use of covalent inhibition in drug development. Successes in the clinic, mainly in the field of kinase inhibitors, are existing proof that safe covalent inhibitors can be designed and employed to develop effective treatments. The case of KRASG12C covalent inhibitors entering clinical trials in 2019 has been among the hottest topics discussed in drug discovery, raising expectations for the future of the field. In this perspective, an overview of the milestones hit with targeted covalent inhibitors, as well as the promise and the needs of current research, are presented. While recent results have confirmed the potential that was foreseen, many questions remain unexplored in this branch of precision medicine.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BB3szjt1ertQ%253D%253D&md5=71ac37667e2f40fa3f6de36c07fea9ec
  6. 6
    Baillie, T. A. Drug-Protein Adducts: Past, Present, and Future. Med. Chem. Res. 2020, 29 (7), 1093– 1104,  DOI: 10.1007/s00044-020-02567-8
    Google Scholar
    There is no corresponding record for this reference.
  7. 7
    Potashman, M. H.; Duggan, M. E. Covalent Modifiers: An Orthogonal Approach to Drug Design. J. Med. Chem. 2009, 52 (5), 1231– 1246,  DOI: 10.1021/jm8008597
    Google Scholar
    7
    Covalent Modifiers: An Orthogonal Approach to Drug Design
    Potashman, Michele H.; Duggan, Mark E.
    Journal of Medicinal Chemistry (2009), 52 (5), 1231-1246CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    A review. In this article we review a variety of examples in which therapeutic targets are covalently bound by small-mol. drugs or by compds. in advanced clin. development. The covalent interactions can be either reversible or irreversible, depending on the reaction partners.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhs1Sltbw%253D&md5=f8380d5a1cdd8638ad2a1e0405d25267
  8. 8
    Boike, L.; Henning, N. J.; Nomura, D. K. Advances in Covalent Drug Discovery. Nat. Rev. Drug Discovery 2022, 21 (12), 881– 898,  DOI: 10.1038/s41573-022-00542-z
    Google Scholar
    8
    Advances in covalent drug discovery
    Boike, Lydia; Henning, Nathaniel J.; Nomura, Daniel K.
    Nature Reviews Drug Discovery (2022), 21 (12), 881-898CODEN: NRDDAG; ISSN:1474-1776. (Nature Portfolio)
    A review. Covalent drugs have been used to treat diseases for more than a century, but tools that facilitate the rational design of covalent drugs have emerged more recently. The purposeful addn. of reactive functional groups to existing ligands can enable potent and selective inhibition of target proteins, as demonstrated by the covalent epidermal growth factor receptor (EGFR) and Bruton's tyrosine kinase (BTK) inhibitors used to treat various cancers. Moreover, the identification of covalent ligands through 'electrophile-first' approaches has also led to the discovery of covalent drugs, such as covalent inhibitors for KRAS(G12C) and SARS-CoV-2 main protease. In particular, the discovery of KRAS(G12C) inhibitors validates the use of covalent screening technologies, which have become more powerful and widespread over the past decade. Chemoproteomics platforms have emerged to complement covalent ligand screening and assist in ligand discovery, selectivity profiling and target identification. This Review showcases covalent drug discovery milestones with emphasis on the lessons learned from these programs and how an evolving toolbox of covalent drug discovery techniques facilitates success in this field.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38Xit1Clt7nE&md5=b41441b3a7bc5f2e87bedf243fa43faa
  9. 9
    Kenakin, T. The Mass Action Equation in Pharmacology. Br. J. Clin. Pharmacol. 2016, 81 (1), 41– 51,  DOI: 10.1111/bcp.12810
    Google Scholar
    There is no corresponding record for this reference.
  10. 10
    Pottel, J.; Levit, A.; Korczynska, M.; Fischer, M.; Shoichet, B. K. The Recognition of Unrelated Ligands by Identical Proteins. ACS Chem. Biol. 2018, 13 (9), 2522– 2533,  DOI: 10.1021/acschembio.8b00443
    Google Scholar
    There is no corresponding record for this reference.
  11. 11
    Knockenhauer, K. E.; Copeland, R. A. The Importance of Binding Kinetics and Drug-Target Residence Time in Pharmacology. Br. J. Pharmacol. 2023, 1– 14,  DOI: 10.1111/bph.16104
    Google Scholar
    There is no corresponding record for this reference.
  12. 12
    Zhang, G.; Zhang, J.; Gao, Y.; Li, Y.; Li, Y. Strategies for Targeting Undruggable Targets. Expert Opin. Drug Discovery 2022, 17 (1), 55– 69,  DOI: 10.1080/17460441.2021.1969359
    Google Scholar
    12
    Strategies for targeting undruggable targets
    Zhang Gong; Zhang Juan; Gao Yuting; Li Yangfeng; Li Yizhou; Li Yizhou
    Expert opinion on drug discovery (2022), 17 (1), 55-69 ISSN:.
    INTRODUCTION: Undruggable targets refer to clinically meaningful therapeutic targets that are 'difficult to drug' or 'yet to be drugged' via traditional approaches. Featuring characteristics of lacking defined ligand-binding pockets, non-catalytic protein-protein interaction functional modes and less-investigated 3D structures, these undruggable targets have been targeted with novel therapeutic entities developed with the progress of unconventional drug discovery approaches, such as targeted degradation molecules and display technologies. AREA COVERED: This review first presents the concept of 'undruggable' exemplified by RAS and other targets. Next, detailed strategies are illustrated in two aspects: innovation of therapeutic entities and development of unconventional drug discovery technologies. Finally, case studies covering typical undruggable targets (Bcl-2, p53, and RAS) are depicted to further demonstrate the feasibility of the strategies and entities above. EXPERT OPINION: Targeting the undruggable expands the scope of therapeutically reachable targets. Consequently, it represents the drug discovery frontier. Biomedical studies are capable of dissecting disease mechanisms, thus broadening the list of undruggable targets. Encouraged by the recent approval of the KRAS inhibitor Sotorasib, we believe that merging multiple discovery approaches and exploiting various novel therapeutic entities would pave the way for dealing with more 'undruggable' targets in the future.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BB2crgvFelug%253D%253D&md5=20ebb3e7bd0c80af87802eea43a05dfa
  13. 13
    Akçay, G.; Belmonte, M. A.; Aquila, B.; Chuaqui, C.; Hird, A. W.; Lamb, M. L.; Rawlins, P. B.; Su, N.; Tentarelli, S.; Grimster, N. P.; Su, Q. Inhibition of Mcl-1 through Covalent Modification of a Noncatalytic Lysine Side Chain. Nat. Chem. Biol. 2016, 12 (11), 931– 936,  DOI: 10.1038/nchembio.2174
    Google Scholar
    13
    Inhibition of Mcl-1 through covalent modification of a noncatalytic lysine side chain
    Akcay, Gizem; Belmonte, Matthew A.; Aquila, Brian; Chuaqui, Claudio; Hird, Alexander W.; Lamb, Michelle L.; Rawlins, Philip B.; Su, Nancy; Tentarelli, Sharon; Grimster, Neil P.; Su, Qibin
    Nature Chemical Biology (2016), 12 (11), 931-936CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
    Targeted covalent inhibition of disease-assocd. proteins has become a powerful methodol. in the field of drug discovery, leading to the approval of new therapeutics. Nevertheless, current approaches are often limited owing to their reliance on a cysteine residue to generate the covalent linkage. Here the authors used aryl boronic acid carbonyl warheads to covalently target a noncatalytic lysine side chain, and generated to the knowledge the first reversible covalent inhibitors for Mcl-1, a protein-protein interaction (PPI) target that has proven difficult to inhibit via traditional medicinal chem. strategies. These covalent binders exhibited improved potency in comparison to noncovalent congeners, as demonstrated in biochem. and cell-based assays. The authors identified Lys234 as the residue involved in covalent modification, via point mutation. The covalent binders discovered in this study will serve as useful starting points for the development of Mcl-1 therapeutics and probes to interrogate Mcl-1-dependent biol. phenomena.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsVKqtb3P&md5=bda5720579a9b5e6027632d2cffba2e1
  14. 14
    Huang, L.; Guo, Z.; Wang, F.; Fu, L. KRAS Mutation: From Undruggable to Druggable in Cancer. Signal Transduct. Target. Ther. 2021, 6 (1), 386,  DOI: 10.1038/s41392-021-00780-4
    Google Scholar
    14
    KRAS mutation: from undruggable to druggable in cancer
    Huang Lamei; Guo Zhixing; Wang Fang; Fu Liwu
    Signal transduction and targeted therapy (2021), 6 (1), 386 ISSN:.
    Cancer is the leading cause of death worldwide, and its treatment and outcomes have been dramatically revolutionised by targeted therapies. As the most frequently mutated oncogene, Kirsten rat sarcoma viral oncogene homologue (KRAS) has attracted substantial attention. The understanding of KRAS is constantly being updated by numerous studies on KRAS in the initiation and progression of cancer diseases. However, KRAS has been deemed a challenging therapeutic target, even "undruggable", after drug-targeting efforts over the past four decades. Recently, there have been surprising advances in directly targeted drugs for KRAS, especially in KRAS (G12C) inhibitors, such as AMG510 (sotorasib) and MRTX849 (adagrasib), which have obtained encouraging results in clinical trials. Excitingly, AMG510 was the first drug-targeting KRAS (G12C) to be approved for clinical use this year. This review summarises the most recent understanding of fundamental aspects of KRAS, the relationship between the KRAS mutations and tumour immune evasion, and new progress in targeting KRAS, particularly KRAS (G12C). Moreover, the possible mechanisms of resistance to KRAS (G12C) inhibitors and possible combination therapies are summarised, with a view to providing the best regimen for individualised treatment with KRAS (G12C) inhibitors and achieving truly precise treatment.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BB2cfivFanug%253D%253D&md5=05a5959689e63910ecf752595d4407ff
  15. 15
    Mons, E.; Roet, S.; Kim, R. Q.; Mulder, M. P. C. A Comprehensive Guide for Assessing Covalent Inhibition in Enzymatic Assays Illustrated with Kinetic Simulations. Curr. Protoc. 2022, 2 (6), e419  DOI: 10.1002/cpz1.419
    Google Scholar
    15
    A Comprehensive Guide for Assessing Covalent Inhibition in Enzymatic Assays Illustrated with Kinetic Simulations
    Mons, Elma; Roet, Sander; Kim, Robbert Q.; Mulder, Monique P. C.
    Current Protocols (2022), 2 (6), e419CODEN: CPURDB; ISSN:2691-1299. (John Wiley & Sons, Inc.)
    Covalent inhibition has become more accepted in the past two decades, as illustrated by the clin. approval of several irreversible inhibitors designed to covalently modify their target. Elucidation of the structure-activity relationship and potency of such inhibitors requires a detailed kinetic evaluation. Here, we elucidate the relationship between the exptl. read-out and the underlying inhibitor binding kinetics. Interactive kinetic simulation scripts are employed to highlight the effects of in vitro enzyme activity assay conditions and inhibitor binding mode, thereby showcasing which assumptions and corrections are crucial. Four stepwise protocols to assess the biochem. potency of (ir)reversible covalent enzyme inhibitors targeting a nucleophilic active site residue are included, with accompanying data anal. tailored to the covalent binding mode. Together, this will serve as a guide to make an educated decision regarding the most suitable method to assess covalent inhibition potency.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XitF2ksrrF&md5=1ffa766bb1fc413a27c47d458a3f54e7
  16. 16
    Chatterjee, P.; Botello-Smith, W. M.; Zhang, H.; Qian, L.; Alsamarah, A.; Kent, D.; Lacroix, J. J.; Baudry, M.; Luo, Y. Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?. J. Am. Chem. Soc. 2017, 139 (49), 17945– 17952,  DOI: 10.1021/jacs.7b08938
    Google Scholar
    16
    Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?
    Chatterjee, Payal; Botello-Smith, Wesley M.; Zhang, Han; Qian, Li; Alsamarah, Abdelaziz; Kent, David; Lacroix, Jerome J.; Baudry, Michel; Luo, Yun
    Journal of the American Chemical Society (2017), 139 (49), 17945-17952CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Reversible covalent inhibitors have many clin. advantages over noncovalent or irreversible covalent drugs. However, apart from selecting a warhead, substantial efforts in design and synthesis are needed to optimize noncovalent interactions to improve target-selective binding. Computational prediction of binding affinity for reversible covalent inhibitors presents a unique challenge since the binding process consists of multiple steps, which are not necessarily independent of each other. In this study, the authors lay out the relation between relative binding free energy and the overall reversible covalent binding affinity using a two-state binding model. To prove the concept, the authors employed free energy perturbation (FEP) coupled with λ-exchange mol. dynamics method to calc. the binding free energy of a series of α-ketoamide analogs relative to a common warhead scaffold, in both noncovalent and covalent binding states, and for two highly homologous proteases, calpain-1 and calpain-2. The authors conclude that covalent binding state alone, in general, can be used to predict reversible covalent binding selectivity. However, exceptions may exist. Therefore, the authors also discuss the conditions under which the noncovalent binding step is no longer negligible and propose to combine the relative FEP calcns. with a single QM/MM calcn. of warhead to predict the binding affinity and binding kinetics. The FEP calcns. also revealed that covalent and noncovalent binding states of an inhibitor do not necessarily exhibit the same selectivity. Thus, investigating both binding states, as well as the kinetics will provide extremely useful information for optimizing reversible covalent inhibitors.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhslyrs7bI&md5=e6a38ff570134e956eb43bd4a874ca55
  17. 17
    De Cesco, S.; Kurian, J.; Dufresne, C.; Mittermaier, A. K.; Moitessier, N. Covalent Inhibitors Design and Discovery. Eur. J. Med. Chem. 2017, 138, 96– 114,  DOI: 10.1016/j.ejmech.2017.06.019
    Google Scholar
    17
    Covalent inhibitors design and discovery
    De Cesco, Stephane; Kurian, Jerry; Dufresne, Caroline; Mittermaier, Anthony K.; Moitessier, Nicolas
    European Journal of Medicinal Chemistry (2017), 138 (), 96-114CODEN: EJMCA5; ISSN:0223-5234. (Elsevier Masson SAS)
    In the history of therapeutics, covalent drugs occupy a very distinct category. While representing a significant fraction of the drugs on the market, very few have been deliberately designed to interact covalently with their biol. target. In this review, the prevalence of covalent drugs will first be briefly covered, followed by an introduction to their mechanisms of action and more detailed discussions of their discovery and the development of safe and efficient covalent enzyme inhibitors. All stages of a drug discovery program will be covered, from target considerations to lead optimization, strategies to tune reactivity and computational methods. The goal of this article is to provide an overview of the field and to outline good practices that are needed for the proper assessment and development of covalent inhibitors as well as a good understanding of the potential and limitations of current computational methods for the design of covalent drugs.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtVKhsLrI&md5=551c9a9c4bd69d4ad4d9156c315d5a94
  18. 18
    Plescia, J.; De Cesco, S.; Patrascu, M. B.; Kurian, J.; Di Trani, J.; Dufresne, C.; Wahba, A. S.; Janmamode, N.; Mittermaier, A. K.; Moitessier, N. Integrated Synthetic, Biophysical, and Computational Investigations of Covalent Inhibitors of Prolyl Oligopeptidase and Fibroblast Activation Protein α. J. Med. Chem. 2019, 62 (17), 7874– 7884,  DOI: 10.1021/acs.jmedchem.9b00642
    Google Scholar
    There is no corresponding record for this reference.
  19. 19
    Masuda, Y.; Yoshida, T.; Yamaotsu, N.; Hirono, S. Linear Discriminant Analysis for the in Silico Discovery of Mechanism-Based Reversible Covalent Inhibitors of a Serine Protease: Application of Hydration Thermodynamics Analysis and Semi-Empirical Molecular Orbital Calculation. Chem. Pharm. Bull. (Tokyo) 2018, 66 (4), 399– 409,  DOI: 10.1248/cpb.c17-00854
    Google Scholar
    There is no corresponding record for this reference.
  20. 20
    Awoonor-Williams, E.; Walsh, A. G.; Rowley, C. N. Modeling Covalent-Modifier Drugs. Biochim. Biophys. Acta Proteins Proteomics 2017, 1865 (11), 1664– 1675,  DOI: 10.1016/j.bbapap.2017.05.009
    Google Scholar
    20
    Modeling covalent-modifier drugs
    Awoonor-Williams, Ernest; Walsh, Andrew G.; Rowley, Christopher N.
    Biochimica et Biophysica Acta, Proteins and Proteomics (2017), 1865 (11_Part_B), 1664-1675CODEN: BBAPBW; ISSN:1570-9639. (Elsevier B.V.)
    A review. In this review, we present a summary of how computer modeling has been used in the development of covalent-modifier drugs. Covalent-modifier drugs bind by forming a chem. bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly. Computer modeling is widely used in drug discovery, but different computational methods must be used to model covalent modifiers because of the chem. bonds formed. Structural and bioinformatic anal. has identified sites of modification that could yield selectivity for a chosen target. Docking methods, which are used to rank binding poses of large sets of inhibitors, have been augmented to support the formation of protein-ligand bonds and are now capable of predicting the binding pose of covalent modifiers accurately. The pKa's of amino acids can be calcd. in order to assess their reactivity towards electrophiles. QM/MM methods have been used to model the reaction mechanisms of covalent modification. The continued development of these tools will allow computation to aid in the development of new covalent-modifier drugs. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXotVOrtbo%253D&md5=ac579900da99ea005d0d562b53a1bca2
  21. 21
    Scarpino, A.; Ferenczy, G. G.; Keserű, G. M. Binding Mode Prediction and Virtual Screening Applications by Covalent Docking. Methods Mol. Biol. Clifton NJ. 2021, 2266, 73– 88,  DOI: 10.1007/978-1-0716-1209-5_4
    Google Scholar
    There is no corresponding record for this reference.
  22. 22
    Faridoon; Ng, R.; Zhang, G.; Li, J. J. An Update on the Discovery and Development of Reversible Covalent Inhibitors. Med. Chem. Res. Int. J. Rapid Commun. Des. Mech. Action Biol. Act. Agents 2023, 32 (6), 1039– 1062,  DOI: 10.1007/s00044-023-03065-3
    Google Scholar
    22
    An update on the discovery and development of reversible covalent inhibitors
    Faridoon; Ng, Raymond; Zhang, Guiping; Li, Jie Jack
    Medicinal Chemistry Research (2023), 32 (6), 1039-1062CODEN: MCREEB; ISSN:1054-2523. (Springer)
    A review. Small mol. drugs that covalently bind irreversibly to their target proteins have several advantages over conventional reversible inhibitors. They include increased duration of action, less-frequent drug dosing, reduced pharmacokinetic sensitivity, and the potential to target intractable shallow binding sites. Despite these advantages, the key challenges of irreversible covalent drugs are their potential for off-target toxicities and immunogenicity risks. Incorporating reversibility into covalent drugs would lead to less off-target toxicity by forming reversible adducts with off-target proteins and thus reducing the risk of idiosyncratic toxicities caused by the permanent modification of proteins, which leads to higher levels of potential haptens. Herein, we systematically review electrophilic warheads employed during the development of reversible covalent drugs. We hope the structural insights of electrophilic warheads would provide helpful information to medicinal chemists and aid in designing covalent drugs with better on-target selectivity and improved safety.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXovFKlurc%253D&md5=2f6664586b401207cbe840a4d50cee32
  23. 23
    Martin, J. S.; MacKenzie, C. J.; Fletcher, D.; Gilbert, I. H. Characterising Covalent Warhead Reactivity. Bioorg. Med. Chem. 2019, 27 (10), 2066– 2074,  DOI: 10.1016/j.bmc.2019.04.002
    Google Scholar
    23
    Characterising covalent warhead reactivity
    Martin, James S.; MacKenzie, Claire J.; Fletcher, Daniel; Gilbert, Ian H.
    Bioorganic & Medicinal Chemistry (2019), 27 (10), 2066-2074CODEN: BMECEP; ISSN:0968-0896. (Elsevier B.V.)
    Many drugs currently used are covalent inhibitors and irreversibly inhibit their targets. Most of these were discovered through serendipity. Covalent inhibitions can have many advantages from a pharmacokinetic perspective. However, until recently most organizations have shied away from covalent compd. design due to fears of non-specific inhibition of off-target proteins leading to toxicity risks. However, there has been a renewed interest in covalent modifiers as potential drugs, as it possible to get highly selective compds. It is therefore important to know how reactive a warhead is and to be able to select the least reactive warhead possible to avoid toxicity. A robust NMR based assay was developed and used to measure the reactivity of a variety of covalent warheads against serine and cysteine - the two most common targets for covalent drugs. A selection of these warheads also had their reactivity measured against threonine, tyrosine, lysine, histidine and arginine to better understand our ability to target non-traditional residues. The reactivity was also measured at various pHs to assess what effect the environment in the active site would have on these reactions. The reactivity of a covalent modifier was found to be very dependent on the amino acid residue.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXntVGgsbo%253D&md5=487334d8d0a8b03d0a25d6d87c1b4329
  24. 24
    Péczka, N.; Orgován, Z.; Ábrányi-Balogh, P.; Keserű, G. M. Electrophilic Warheads in Covalent Drug Discovery: An Overview. Expert Opin. Drug Discovery 2022, 17 (4), 413– 422,  DOI: 10.1080/17460441.2022.2034783
    Google Scholar
    There is no corresponding record for this reference.
  25. 25
    Jackson, P. A.; Widen, J. C.; Harki, D. A.; Brummond, K. M. Covalent Modifiers: A Chemical Perspective on the Reactivity of α,β-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions. J. Med. Chem. 2017, 60 (3), 839– 885,  DOI: 10.1021/acs.jmedchem.6b00788
    Google Scholar
    25
    Covalent Modifiers: A Chemical Perspective on the Reactivity of α,β-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions
    Jackson, Paul A.; Widen, John C.; Harki, Daniel A.; Brummond, Kay M.
    Journal of Medicinal Chemistry (2017), 60 (3), 839-885CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    A review. Although Michael acceptors display a potent and broad spectrum of bioactivity, they have largely been ignored in drug discovery because of their presumed indiscriminate reactivity. As such, a dearth of information exists relevant to the thiol reactivity of natural products and their analogs possessing this moiety. In the midst of recently approved acrylamide-contg. drugs, it is clear that a good understanding of the hetero-Michael addn. reaction and the relative reactivities of biol. thiols with Michael acceptors under physiol. conditions is needed for the design and use of these compds. as biol. tools and potential therapeutics. This Perspective provides information that will contribute to this understanding, such as kinetics of thiol addn. reactions, bioactivities, as well as steric and electronic factors that influence the electrophilicity and reversibility of Michael acceptors. This Perspective is focused on α,β-unsatd. carbonyls given their preponderance in bioactive natural products.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitV2rtbnM&md5=36d3be5bf688c4e4a8cf4bcf42073009
  26. 26
    Watt, S. K. I.; Charlebois, J. G.; Rowley, C. N.; Keillor, J. W. A Mechanistic Study of Thiol Addition to N-Phenylacrylamide. Org. Biomol. Chem. 2022, 20 (45), 8898– 8906,  DOI: 10.1039/D2OB01369J
    Google Scholar
    There is no corresponding record for this reference.
  27. 27
    Watt, S. K. I.; Charlebois, J. G.; Rowley, C. N.; Keillor, J. W. A Mechanistic Study of Thiol Addition to N-Acryloylpiperidine. Org. Biomol. Chem. 2023, 21 (10), 2204– 2212,  DOI: 10.1039/D2OB02223K
    Google Scholar
    There is no corresponding record for this reference.
  28. 28
    Lohman, D. C.; Edwards, D. R.; Wolfenden, R. Catalysis by Desolvation: The Catalytic Prowess of SAM-Dependent Halide-Alkylating Enzymes. J. Am. Chem. Soc. 2013, 135 (39), 14473– 14475,  DOI: 10.1021/ja406381b
    Google Scholar
    28
    Catalysis by desolvation: The catalytic prowess of SAM-dependent halide-alkylating enzymes
    Lohman, Danielle C.; Edwards, David R.; Wolfenden, Richard
    Journal of the American Chemical Society (2013), 135 (39), 14473-14475CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    In the biol. fixation of halide ions, several enzymes have been found to catalyze alkyl transfer from S-adenosylmethionine (SAM) to halide ions. It proved possible to measure the rates of reaction of the trimethylsulfonium ion with I-, Br-, Cl-, F-, HO-, and H2O in water at elevated temps. Comparison of the resulting 2nd-order rate consts., extrapolated to 25°, with values of kcat/Km reported for fluorinase and chlorinase indicated that these enzymes enhanced the rates of alkyl halide formation by factors of 2 × 1015- and 1 × 1017-fold, resp. These rate enhancements, achieved without the assistance of cofactors, metal ions, or general acid-base catalysis, were the largest that have been reported for an enzyme that acts on 2 substrates.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsVGjtLzN&md5=f7d0c69687c776310dda4facf967db64
  29. 29
    Parvez, S.; Long, M. J. C.; Poganik, J. R.; Aye, Y. Redox Signaling by Reactive Electrophiles and Oxidants. Chem. Rev. 2018, 118 (18), 8798– 8888,  DOI: 10.1021/acs.chemrev.7b00698
    Google Scholar
    29
    Redox Signaling by Reactive Electrophiles and Oxidants
    Parvez, Saba; Long, Marcus J. C.; Poganik, Jesse R.; Aye, Yimon
    Chemical Reviews (Washington, DC, United States) (2018), 118 (18), 8798-8888CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
    A review. The concept of cell signaling in the context of non-enzyme-assisted protein modifications by reactive electrophilic and oxidative species, broadly known as redox signaling, is a uniquely complex topic that has been approached from numerous different and multidisciplinary angles. The authors' review reflects on 5 aspects crit. for understanding how Nature harnesses these non-canonical post-translational modifications to coordinate distinct cellular activities: (1) specific players and their generation; (2) physicochem. properties; (3) mechanisms of action; (4) methods of interrogation; and (5) functional roles in health and disease. Emphasis is primarily placed on the latest progress in the field, but several aspects of classical work likely forgotten/lost are also recollected. For researchers with interests in getting into the field, this review is anticipated to function as a primer. For the expert, the aim is to stimulate thought and discussion about fundamentals of redox signaling mechanisms, and nuances of specificity/selectivity and timing in this sophisticated yet fascinating arena at the crossroads of chem. and biol.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsFyjurnI&md5=2cc16400a3dcab3bac28c25132595c7a
  30. 30
    Krishnan, S.; Miller, R. M.; Tian, B.; Mullins, R. D.; Jacobson, M. P.; Taunton, J. Design of Reversible, Cysteine-Targeted Michael Acceptors Guided by Kinetic and Computational Analysis. J. Am. Chem. Soc. 2014, 136 (36), 12624– 12630,  DOI: 10.1021/ja505194w
    Google Scholar
    30
    Design of Reversible, Cysteine-Targeted Michael Acceptors Guided by Kinetic and Computational Analysis
    Krishnan, Shyam; Miller, Rand M.; Tian, Boxue; Mullins, R. Dyche; Jacobson, Matthew P.; Taunton, Jack
    Journal of the American Chemical Society (2014), 136 (36), 12624-12630CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Electrophilic probes that covalently modify a cysteine thiol often show enhanced pharmacol. potency and selectivity. Although reversible Michael acceptors have been reported, the structural requirements for reversibility are poorly understood. Here, we report a novel class of acrylonitrile-based Michael acceptors, activated by aryl or heteroaryl electron-withdrawing groups. We demonstrate that thiol adducts of these acrylonitriles undergo β-elimination at rates that span more than 3 orders of magnitude. These rates correlate inversely with the computed proton affinity of the corresponding carbanions, enabling the intrinsic reversibility of the thiol-Michael reaction to be tuned in a predictable manner. We apply these principles to the design of new reversible covalent kinase inhibitors with improved properties. A cocrystal structure of one such inhibitor reveals specific noncovalent interactions between the 1,2,4-triazole activating group and the kinase. Our exptl. and computational study enables the design of new Michael acceptors, expanding the palette of reversible, cysteine-targeted electrophiles.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsVWrtbvK&md5=de052bac07c8920cb807c05f71f4f95d
  31. 31
    Ma, Y.; Li, L.; He, S.; Shang, C.; Sun, Y.; Liu, N.; Meek, T. D.; Wang, Y.; Shang, L. Application of Dually Activated Michael Acceptor to the Rational Design of Reversible Covalent Inhibitor for Enterovirus 71 3C Protease. J. Med. Chem. 2019, 62 (13), 6146– 6162,  DOI: 10.1021/acs.jmedchem.9b00387
    Google Scholar
    31
    Application of Dually Activated Michael Acceptor to the Rational Design of Reversible Covalent Inhibitor for Enterovirus 71 3C Protease
    Ma, Yuying; Li, Linfeng; He, Shuai; Shang, Chengyou; Sun, Yang; Liu, Ning; Meek, Thomas D.; Wang, Yaxin; Shang, Luqing
    Journal of Medicinal Chemistry (2019), 62 (13), 6146-6162CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    Targeted covalent inhibitors (TCIs) have attracted growing attention from the pharmaceutical industry in recent decades because they have potential advantages in terms of efficacy, selectivity, and safety. TCIs have recently evolved into a new version with reversibility that can be systematically modulated. This feature may diminish the risk of haptenization and help optimize the drug-target residence time as needed. The enteroviral 3C protease (3Cpro) is a valuable therapeutic target, but the development of 3Cpro inhibitors is far from satisfactory. Therefore, we aimed to apply a reversible TCI approach to the design of novel 3Cpro inhibitors. The introduction of various substituents onto the α-carbon of classical Michael acceptors yielded inhibitors bearing several classes of warheads. Using steady-state kinetics and biomol. mass spectrometry, we confirmed the mode of reversible covalent inhibition and elucidated the mechanism by which the potency and reversibility were affected by electronic and steric factors. This research produced several potent inhibitors with good selectivity and suitable reversibility; moreover, it validated the reversible TCI approach in the field of viral infection, suggesting broader applications in the design of reversible covalent inhibitors for other proteases.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtFGqsLjI&md5=2de757026f2542bff8092060a72107a5
  32. 32
    Bradshaw, J. M.; McFarland, J. M.; Paavilainen, V. O.; Bisconte, A.; Tam, D.; Phan, V. T.; Romanov, S.; Finkle, D.; Shu, J.; Patel, V.; Ton, T.; Li, X.; Loughhead, D. G.; Nunn, P. A.; Karr, D. E.; Gerritsen, M. E.; Funk, J. O.; Owens, T. D.; Verner, E.; Brameld, K. A.; Hill, R. J.; Goldstein, D. M.; Taunton, J. Prolonged and Tunable Residence Time Using Reversible Covalent Kinase Inhibitors. Nat. Chem. Biol. 2015, 11 (7), 525– 531,  DOI: 10.1038/nchembio.1817
    Google Scholar
    32
    Prolonged and tunable residence time using reversible covalent kinase inhibitors
    Bradshaw, J. Michael; McFarland, Jesse M.; Paavilainen, Ville O.; Bisconte, Angelina; Tam, Danny; Phan, Vernon T.; Romanov, Sergei; Finkle, David; Shu, Jin; Patel, Vaishali; Ton, Tony; Li, Xiaoyan; Loughhead, David G.; Nunn, Philip A.; Karr, Dane E.; Gerritsen, Mary E.; Funk, Jens Oliver; Owens, Timothy D.; Verner, Erik; Brameld, Ken A.; Hill, Ronald J.; Goldstein, David M.; Taunton, Jack
    Nature Chemical Biology (2015), 11 (7), 525-531CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
    Drugs with prolonged on-target residence times often show superior efficacy, yet general strategies for optimizing drug-target residence time are lacking. Here the authors made progress toward this elusive goal by targeting a noncatalytic cysteine in Bruton's tyrosine kinase (BTK) with reversible covalent inhibitors. Using an inverted orientation of the cysteine-reactive cyanoacrylamide electrophile, the authors identified potent and selective BTK inhibitors that demonstrated biochem. residence times spanning from minutes to 7 d. An inverted cyanoacrylamide with prolonged residence time in vivo remained bound to BTK for more than 18 h after clearance from the circulation. The inverted cyanoacrylamide strategy was further used to discover fibroblast growth factor receptor (FGFR) kinase inhibitors with residence times of several days, demonstrating the generalizability of the approach. Targeting of noncatalytic cysteines with inverted cyanoacrylamides may serve as a broadly applicable platform that facilitates 'residence time by design', the ability to modulate and improve the duration of target engagement in vivo.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFeju7%252FE&md5=85a73d9ecd62695d03166f7009c68dd8
  33. 33
    Zhou, J.; Stapleton, P.; Xavier-Junior, F. H.; Schatzlein, A.; Haider, S.; Healy, J.; Wells, G. Triazole-Substituted Phenylboronic Acids as Tunable Lead Inhibitors of KPC-2 Antibiotic Resistance. Eur. J. Med. Chem. 2022, 240, 114571,  DOI: 10.1016/j.ejmech.2022.114571
    Google Scholar
    There is no corresponding record for this reference.
  34. 34
    Ehmke, V.; Quinsaat, J. E. Q.; Rivera-Fuentes, P.; Heindl, C.; Freymond, C.; Rottmann, M.; Brun, R.; Schirmeister, T.; Diederich, F. Tuning and Predicting Biological Affinity: Aryl Nitriles as Cysteine Protease Inhibitors. Org. Biomol. Chem. 2012, 10 (30), 5764– 5768,  DOI: 10.1039/c2ob00034b
    Google Scholar
    34
    Tuning and predicting biological affinity: aryl nitriles as cysteine protease inhibitors
    Ehmke, Veronika; Quinsaat, Jose Enrico Q.; Rivera-Fuentes, Pablo; Heindl, Cornelia; Freymond, Celine; Rottmann, Matthias; Brun, Reto; Schirmeister, Tanja; Diederich, Francois
    Organic & Biomolecular Chemistry (2012), 10 (30), 5764-5768CODEN: OBCRAK; ISSN:1477-0520. (Royal Society of Chemistry)
    A series of aryl nitrile-based ligands were prepd. to investigate the effect of their electrophilicity on the affinity against the cysteine proteases rhodesain and human cathepsin L. D. functional theory calcns. provided relative reactivities of the nitriles, enabling prediction of their biol. affinity and cytotoxicity and a clear structure-activity relationship.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtVSlsr3J&md5=45858b629d24a54b72cd7e3b7ba15e5b
  35. 35
    Langrish, C. L.; Bradshaw, J. M.; Francesco, M. R.; Owens, T. D.; Xing, Y.; Shu, J.; LaStant, J.; Bisconte, A.; Outerbridge, C.; White, S. D.; Hill, R. J.; Brameld, K. A.; Goldstein, D. M.; Nunn, P. A. Preclinical Efficacy and Anti-Inflammatory Mechanisms of Action of the Bruton Tyrosine Kinase Inhibitor Rilzabrutinib for Immune-Mediated Disease. J. Immunol. Baltim. Md 1950 2021, 206 (7), 1454– 1468,  DOI: 10.4049/jimmunol.2001130
    Google Scholar
    There is no corresponding record for this reference.
  36. 36
    Jung, S.; Fuchs, N.; Johe, P.; Wagner, A.; Diehl, E.; Yuliani, T.; Zimmer, C.; Barthels, F.; Zimmermann, R. A.; Klein, P.; Waigel, W.; Meyr, J.; Opatz, T.; Tenzer, S.; Distler, U.; Räder, H.-J.; Kersten, C.; Engels, B.; Hellmich, U. A.; Klein, J.; Schirmeister, T. Fluorovinylsulfones and -Sulfonates as Potent Covalent Reversible Inhibitors of the Trypanosomal Cysteine Protease Rhodesain: Structure-Activity Relationship, Inhibition Mechanism, Metabolism, and In Vivo Studies. J. Med. Chem. 2021, 64 (16), 12322– 12358,  DOI: 10.1021/acs.jmedchem.1c01002
    Google Scholar
    36
    Fluorovinylsulfones and -Sulfonates as Potent Covalent Reversible Inhibitors of the Trypanosomal Cysteine Protease Rhodesain: Structure-Activity Relationship, Inhibition Mechanism, Metabolism, and In Vivo Studies
    Jung, Sascha; Fuchs, Natalie; Johe, Patrick; Wagner, Annika; Diehl, Erika; Yuliani, Tri; Zimmer, Collin; Barthels, Fabian; Zimmermann, Robert A.; Klein, Philipp; Waigel, Waldemar; Meyr, Jessica; Opatz, Till; Tenzer, Stefan; Distler, Ute; Raeder, Hans-Joachim; Kersten, Christian; Engels, Bernd; Hellmich, Ute A.; Klein, Jochen; Schirmeister, Tanja
    Journal of Medicinal Chemistry (2021), 64 (16), 12322-12358CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    Rhodesain is a major cysteine protease of Trypanosoma brucei rhodesiense, a pathogen causing Human African Trypanosomiasis, and a validated drug target. Recently, we reported the development of α-halovinylsulfones as a new class of covalent reversible cysteine protease inhibitors. Here, α-fluorovinylsulfones/-sulfonates were optimized for rhodesain based on mol. modeling approaches. I (X = F), the most potent and selective inhibitor in the series, shows a single-digit nanomolar affinity and high selectivity toward mammalian cathepsins B and L. Enzymic diln. assays and MS expts. indicate that I (X = F) is a slow-tight binder (Ki = 3 nM). Furthermore, the nonfluorinated I (X = H) shows favorable metab. and biodistribution by accumulation in mice brain tissue after i.p. and oral administration. The highest antitrypanosomal activity was obsd. for inhibitors with an N-terminal 2,3-dihydrobenzo[b][1,4]dioxine group and a 4-Me-Phe residue in P2 with nanomolar EC50 values (0.14/0.80μM). The different mechanisms of reversible and irreversible inhibitors were explained using QM/MM calcns. and MD simulations.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhslCitbvM&md5=322d56630ffe7e55bfd42ba0f8d62e97
  37. 37
    Feral, A.; Martin, A. R.; Desfoux, A.; Amblard, M.; Vezenkov, L. L. Covalent-Reversible Peptide-Based Protease Inhibitors. Design, Synthesis, and Clinical Success Stories. Amino Acids 2023, 55, 1775– 1800,  DOI: 10.1007/s00726-023-03286-1
    Google Scholar
    There is no corresponding record for this reference.
  38. 38
    Fairhurst, R. A.; Knoepfel, T.; Buschmann, N.; Leblanc, C.; Mah, R.; Todorov, M.; Nimsgern, P.; Ripoche, S.; Niklaus, M.; Warin, N.; Luu, V. H.; Madoerin, M.; Wirth, J.; Graus-Porta, D.; Weiss, A.; Kiffe, M.; Wartmann, M.; Kinyamu-Akunda, J.; Sterker, D.; Stamm, C.; Adler, F.; Buhles, A.; Schadt, H.; Couttet, P.; Blank, J.; Galuba, I.; Trappe, J.; Voshol, J.; Ostermann, N.; Zou, C.; Berghausen, J.; Del Rio Espinola, A.; Jahnke, W.; Furet, P. Discovery of Roblitinib (FGF401) as a Reversible-Covalent Inhibitor of the Kinase Activity of Fibroblast Growth Factor Receptor 4. J. Med. Chem. 2020, 63 (21), 12542– 12573,  DOI: 10.1021/acs.jmedchem.0c01019
    Google Scholar
    38
    Discovery of Roblitinib (FGF401) as a Reversible-Covalent Inhibitor of the Kinase Activity of Fibroblast Growth Factor Receptor 4
    Fairhurst, Robin A.; Knoepfel, Thomas; Buschmann, Nicole; Leblanc, Catherine; Mah, Robert; Todorov, Milen; Nimsgern, Pierre; Ripoche, Sebastien; Niklaus, Michel; Warin, Nicolas; Luu, Van Huy; Madoerin, Mario; Wirth, Jasmin; Graus-Porta, Diana; Weiss, Andreas; Kiffe, Michael; Wartmann, Markus; Kinyamu-Akunda, Jacqueline; Sterker, Dario; Stamm, Christelle; Adler, Flavia; Buhles, Alexandra; Schadt, Heiko; Couttet, Philippe; Blank, Jutta; Galuba, Inga; Trappe, Jorg; Voshol, Johannes; Ostermann, Nils; Zou, Chao; Berghausen, Jorg; Del Rio Espinola, Alberto; Jahnke, Wolfgang; Furet, Pascal
    Journal of Medicinal Chemistry (2020), 63 (21), 12542-12573CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    FGF19 signaling through the FGFR4/β-klotho receptor complex has been shown to be a key driver of growth and survival in a subset of hepatocellular carcinomas, making selective FGFR4 inhibition an attractive treatment opportunity. A kinome-wide sequence alignment highlighted a poorly conserved cysteine residue within the FGFR4 ATP-binding site at position 552, two positions beyond the gate-keeper residue. Several strategies for targeting this cysteine to identify FGFR4 selective inhibitor starting points are summarized which made use of both rational and unbiased screening approaches. The optimization of a 2-formylquinoline amide hit series is described in which the aldehyde makes a hemithioacetal reversible-covalent interaction with cysteine 552. Key challenges addressed during the optimization are improving the FGFR4 potency, metabolic stability, and soly. leading ultimately to the highly selective first-in-class clin. candidate roblitinib.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhvVeru77E&md5=94bfa1740e9cac34d0ceac67bc9181a7
  39. 39
    Shindo, N.; Fuchida, H.; Sato, M.; Watari, K.; Shibata, T.; Kuwata, K.; Miura, C.; Okamoto, K.; Hatsuyama, Y.; Tokunaga, K.; Sakamoto, S.; Morimoto, S.; Abe, Y.; Shiroishi, M.; Caaveiro, J. M. M.; Ueda, T.; Tamura, T.; Matsunaga, N.; Nakao, T.; Koyanagi, S.; Ohdo, S.; Yamaguchi, Y.; Hamachi, I.; Ono, M.; Ojida, A. Selective and Reversible Modification of Kinase Cysteines with Chlorofluoroacetamides. Nat. Chem. Biol. 2019, 15 (3), 250– 258,  DOI: 10.1038/s41589-018-0204-3
    Google Scholar
    39
    Selective and reversible modification of kinase cysteines with chlorofluoroacetamides
    Shindo, Naoya; Fuchida, Hirokazu; Sato, Mami; Watari, Kosuke; Shibata, Tomohiro; Kuwata, Keiko; Miura, Chizuru; Okamoto, Kei; Hatsuyama, Yuji; Tokunaga, Keisuke; Sakamoto, Seiichi; Morimoto, Satoshi; Abe, Yoshito; Shiroishi, Mitsunori; Caaveiro, Jose M. M.; Ueda, Tadashi; Tamura, Tomonori; Matsunaga, Naoya; Nakao, Takaharu; Koyanagi, Satoru; Ohdo, Shigehiro; Yamaguchi, Yasuchika; Hamachi, Itaru; Ono, Mayumi; Ojida, Akio
    Nature Chemical Biology (2019), 15 (3), 250-258CODEN: NCBABT; ISSN:1552-4450. (Nature Research)
    Irreversible inhibition of disease-assocd. proteins with small mols. is a powerful approach for achieving increased and sustained pharmacol. potency. Here, we introduce α-chlorofluoroacetamide (CFA) as a novel warhead of targeted covalent inhibitor (TCI). Despite weak intrinsic reactivity, CFA-appended quinazoline showed high reactivity toward Cys797 of epidermal growth factor receptor (EGFR). In cells, CFA-quinazoline showed higher target specificity for EGFR than the corresponding Michael acceptors in a wide concn. range (0.1-10 μM). The cysteine adduct of the CFA deriv. was susceptible to hydrolysis and reversibly yielded intact thiol but was stable in solvent-sequestered ATP-binding pocket of EGFR. This environment-dependent hydrolysis can potentially reduce off-target protein modification by CFA-based drugs. Oral administration of CFA quinazoline, (2R)-1-(2-chloro-2-fluoroacetyl)-N-[4-[(3-chloro-4-fluorophenyl)amino]-7-[3-(4-morpholinyl)-propoxy]quinazolin-6-yl]pyrrolidine-2-carboxamide [2226257-92-5] (NS-062, compd. 51) significantly suppressed tumor growth in a mouse xenograft model. Further, CFA-appended pyrazolopyrimidine irreversibly inhibited Bruton's tyrosine kinase with higher target specificity. These results demonstrate the utility of CFA as a new class warheads for TCI.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXlvFSgur4%253D&md5=f6c8886d540ea26a8abecd950feba913
  40. 40
    Tallon, A. M.; Xu, Y.; West, G. M.; Am Ende, C. W.; Fox, J. M. Thiomethyltetrazines Are Reversible Covalent Cysteine Warheads Whose Dynamic Behavior Can Be “Switched Off” via Bioorthogonal Chemistry Inside Live Cells. J. Am. Chem. Soc. 2023, 145 (29), 16069– 16080,  DOI: 10.1021/jacs.3c04444
    Google Scholar
    There is no corresponding record for this reference.
  41. 41
    Ingiliz, P.; Rockstroh, J. K. HIV-HCV Co-Infection Facing HCV Protease Inhibitor Licensing: Implications for Clinicians. Liver Int. Off. J. Int. Assoc. Study Liver 2012, 32 (8), 1194– 1199,  DOI: 10.1111/j.1478-3231.2012.02796.x
    Google Scholar
    There is no corresponding record for this reference.
  42. 42
    Teicher, B. A.; Tomaszewski, J. E. Proteasome Inhibitors. Biochem. Pharmacol. 2015, 96 (1), 1– 9,  DOI: 10.1016/j.bcp.2015.04.008
    Google Scholar
    There is no corresponding record for this reference.
  43. 43
    Metcalf, B.; Chuang, C.; Dufu, K.; Patel, M. P.; Silva-Garcia, A.; Johnson, C.; Lu, Q.; Partridge, J. R.; Patskovska, L.; Patskovsky, Y.; Almo, S. C.; Jacobson, M. P.; Hua, L.; Xu, Q.; Gwaltney, S. L.; Yee, C.; Harris, J.; Morgan, B. P.; James, J.; Xu, D.; Hutchaleelaha, A.; Paulvannan, K.; Oksenberg, D.; Li, Z. Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin. ACS Med. Chem. Lett. 2017, 8 (3), 321– 326,  DOI: 10.1021/acsmedchemlett.6b00491
    Google Scholar
    43
    Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin
    Metcalf, Brian; Chuang, Chihyuan; Dufu, Kobina; Patel, Mira P.; Silva-Garcia, Abel; Johnson, Carl; Lu, Qing; Partridge, James R.; Patskovska, Larysa; Patskovsky, Yury; Almo, Steven C.; Jacobson, Matthew P.; Hua, Lan; Xu, Qing; Gwaltney, Stephen L.; Yee, Calvin; Harris, Jason; Morgan, Bradley P.; James, Joyce; Xu, Donghong; Hutchaleelaha, Athiwat; Paulvannan, Kumar; Oksenberg, Donna; Li, Zhe
    ACS Medicinal Chemistry Letters (2017), 8 (3), 321-326CODEN: AMCLCT; ISSN:1948-5875. (American Chemical Society)
    The authors report the discovery of a new potent allosteric effector of sickle cell Hb, GBT440 I, that increases the affinity of Hb for oxygen and consequently inhibits its polymn. when subjected to hypoxic conditions. Unlike earlier allosteric activators that bind covalently to Hb in a 2:1 stoichiometry, I binds with a 1:1 stoichiometry. Compd. I is orally bioavailable and partitions highly and favorably into the red blood cell with a RBC/plasma ratio of ∼150. This partitioning onto the target protein is anticipated to allow therapeutic concns. to be achieved in the red blood cell at low plasma concns. I is in Phase 2 clin. trials for the treatment of sickle cell disease (NCT02285088).
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsFWqur0%253D&md5=63766931fdf731c68fd284cf86cc77d0
  44. 44
    Reja, R. M.; Wang, W.; Lyu, Y.; Haeffner, F.; Gao, J. Lysine-Targeting Reversible Covalent Inhibitors with Long Residence Time. J. Am. Chem. Soc. 2022, 144 (3), 1152– 1157,  DOI: 10.1021/jacs.1c12702
    Google Scholar
    44
    Lysine-Targeting Reversible Covalent Inhibitors with Long Residence Time
    Reja, Rahi M.; Wang, Wenjian; Lyu, Yuhan; Haeffner, Fredrik; Gao, Jianmin
    Journal of the American Chemical Society (2022), 144 (3), 1152-1157CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    We report a new reversible lysine conjugation that features a novel diazaborine product and much slowed dissocn. kinetics in comparison to the previously known iminoboronate chem. Incorporating the diazaborine-forming warhead RMR1 to a peptide ligand gives potent and long-acting reversible covalent inhibitors of the staphylococcal sortase. The efficacy of sortase inhibition is demonstrated via biochem. and cell-based assays. A comparative study of RMR1 and an iminoboronate-forming warhead highlights the significance and potential of modulating bond dissocn. kinetics in achieving long-acting reversible covalent inhibitors.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38Xht1egs7s%253D&md5=962dedfe735ef240b3430dfd74cdf5cb
  45. 45
    Serafimova, I. M.; Pufall, M. A.; Krishnan, S.; Duda, K.; Cohen, M. S.; Maglathlin, R. L.; McFarland, J. M.; Miller, R. M.; Frödin, M.; Taunton, J. Reversible Targeting of Noncatalytic Cysteines with Chemically Tuned Electrophiles. Nat. Chem. Biol. 2012, 8 (5), 471– 476,  DOI: 10.1038/nchembio.925
    Google Scholar
    45
    Reversible targeting of noncatalytic cysteines with chemically tuned electrophiles
    Serafimova, Iana M.; Pufall, Miles A.; Krishnan, Shyam; Duda, Katarzyna; Cohen, Michael S.; Maglathlin, Rebecca L.; McFarland, Jesse M.; Miller, Rand M.; Froedin, Morten; Taunton, Jack
    Nature Chemical Biology (2012), 8 (5), 471-476CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
    Targeting noncatalytic cysteine residues with irreversible acrylamide-based inhibitors is a powerful approach for enhancing pharmacol. potency and selectivity. Nevertheless, concerns about off-target modification motivate the development of reversible cysteine-targeting strategies. Here we show that electron-deficient olefins, including acrylamides, can be tuned to react with cysteine thiols in a rapidly reversible manner. Installation of a nitrile group increased the olefins' intrinsic reactivity, but, paradoxically, eliminated the formation of irreversible adducts. Incorporation of these electrophiles into a noncovalent kinase-recognition scaffold produced slowly dissocg., covalent inhibitors of the p90 ribosomal protein S6 kinase RSK2. A cocrystal structure revealed specific noncovalent interactions that stabilize the complex by positioning the electrophilic carbon near the targeted cysteine. Disruption of these interactions by protein unfolding or proteolysis promoted instantaneous cleavage of the covalent bond. Our results establish a chem.-based framework for engineering sustained covalent inhibition without accumulating permanently modified proteins and peptides.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XkvVKitrw%253D&md5=6455a9a029714beb317286f71ac1326b
  46. 46
    Forster, M.; Chaikuad, A.; Bauer, S. M.; Holstein, J.; Robers, M. B.; Corona, C. R.; Gehringer, M.; Pfaffenrot, E.; Ghoreschi, K.; Knapp, S.; Laufer, S. A. Selective JAK3 Inhibitors with a Covalent Reversible Binding Mode Targeting a New Induced Fit Binding Pocket. Cell Chem. Biol. 2016, 23 (11), 1335– 1340,  DOI: 10.1016/j.chembiol.2016.10.008
    Google Scholar
    46
    Selective JAK3 Inhibitors with a Covalent Reversible Binding Mode Targeting a New Induced Fit Binding Pocket
    Forster, Michael; Chaikuad, Apirat; Bauer, Silke M.; Holstein, Julia; Robers, Matthew B.; Corona, Cesear R.; Gehringer, Matthias; Pfaffenrot, Ellen; Ghoreschi, Kamran; Knapp, Stefan; Laufer, Stefan A.
    Cell Chemical Biology (2016), 23 (11), 1335-1340CODEN: CCBEBM; ISSN:2451-9448. (Cell Press)
    Janus kinases (JAKs) are a family of cytoplasmatic tyrosine kinases that are attractive targets for the development of anti-inflammatory drugs given their roles in cytokine signaling. One question regarding JAKs and their inhibitors that remains under intensive debate is whether JAK inhibitors should be isoform selective. Since JAK3 functions are restricted to immune cells, an isoform-selective inhibitor for JAK3 could be esp. valuable to achieve clin. more useful and precise effects. However, the high degree of structural conservation makes isoform-selective targeting a challenging task. Here, we present picomolar inhibitors with unprecedented kinome-wide selectivity for JAK3. Selectivity was achieved by concurrent covalent reversible targeting of a JAK3-specific cysteine residue and a ligand-induced binding pocket. We confirmed that in vitro activity and selectivity translate well into the cellular environment and suggest that our inhibitors are powerful tools to elucidate JAK3-specific functions.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvVeqsLrJ&md5=348c5b5fbfa91fd02fa21d984620ea16
  47. 47
    Dietze, E. C.; Schäfer, A.; Omichinski, J. G.; Nelson, S. D. Inactivation of Glyceraldehyde-3-Phosphate Dehydrogenase by a Reactive Metabolite of Acetaminophen and Mass Spectral Characterization of an Arylated Active Site Peptide. Chem. Res. Toxicol. 1997, 10 (10), 1097– 1103,  DOI: 10.1021/tx970090u
    Google Scholar
    47
    Inactivation of glyceraldehyde-3-phosphate dehydrogenase by a reactive metabolite of acetaminophen and mass spectral characterization of an arylated active site peptide
    Dietze E C; Schafer A; Omichinski J G; Nelson S D
    Chemical research in toxicology (1997), 10 (10), 1097-103 ISSN:0893-228X.
    Acetaminophen (4'-hydroxyacetanilide, APAP) is a widely used analgesic and antipyretic drug that can cause hepatic necrosis under some circumstances via cytochrome P450-mediated oxidation to a reactive metabolite, N-acetyl-p-benzoquinone imine (NAPQI). Although the mechanism of hepatocellular injury caused by APAP is not fully understood, it is known that NAPQI forms covalent adducts with several hepatocellular proteins. Reported here is the identification of one of these proteins as glyceraldehyde-3-phosphate dehydrogenase [GAPDH, D-glyceraldehyde-3-phosphate: NAD+ oxidoreductase (phosphorylating), EC 1.2.1.12]. Two hours after the administration of hepatotoxic doses of [14C]APAP to mice, at a time prior to overt cell damage, hepatocellular GAPDH activity was significantly decreased concurrent with the formation of a 14C-labeled GAPDH adduct. A nonhepatotoxic regioisomer of APAP, 3'-hydroxyacetanilide (AMAP), was found to decrease GAPDH activity to a lesser extent than APAP, and radiolabel from [14C]AMAP bound to a lesser extent to GAPDH at a time when its overall binding to hepatocellular proteins was almost equivalent to that of APAP. In order to determine the nature of the covalent adduct between GAPDH and APAP, its major reactive and toxic metabolite, NAPQI, was incubated with purified porcine muscle GAPDH. Microsequencing analysis and fast atom bombardment mass spectrometry (FAB-MS) with collision-induced dissociation (CID) were used to characterize one of the adducts as APAP bound to the cysteinyl sulfhydryl group of Cys-149 in the active site peptide of GAPDH.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADyaK1c%252FgvFSgtQ%253D%253D&md5=9f71f1d99f6cdbc647091eacb12e6fee
  48. 48
    Rombach, E. M.; Hanzlik, R. P. Identification of a Rat Liver Microsomal Esterase as a Target Protein for Bromobenzene Metabolites. Chem. Res. Toxicol. 1998, 11 (3), 178– 184,  DOI: 10.1021/tx970076h
    Google Scholar
    48
    Identification of a Rat Liver Microsomal Esterase as a Target Protein for Bromobenzene Metabolites
    Rombach, Elizabeth M.; Hanzlik, Robert P.
    Chemical Research in Toxicology (1998), 11 (3), 178-184CODEN: CRTOEC; ISSN:0893-228X. (American Chemical Society)
    To identify proteins targeted by bromobenzene metabolites, we incubated [14C]bromobenzene in vitro with liver microsomes from phenobarbital-induced rats under conditions which typically led to covalent binding of 2-4 nmol equiv of bromobenzene/mg of protein. Microsomal proteins were solubilized with detergent, sepd. by chromatog. and electrophoresis, and analyzed for 14C by phosphorimaging of stained blots. Much of the radioactivity was assocd. with several bands of proteins of ∼50-60 kDa, plus another prominent band around 70 kDa, but labeling d. appeared to vary considerably overall. A major radiolabeled protein was purified by preparative electrophoresis and submitted to automated Edman microsequencing. Its N-terminal sequence was found to correspond to that of a known rat liver microsomal carboxylesterase (E.C. 3.1.1.1) previously identified as a target for reactive metabolites of halothane. The extent to which covalent modification of this protein by reactive metabolites contributes to the prodn. of hepatotoxic effects remains to be detd.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXhslarsLc%253D&md5=1367c196a23344bf587b9d346bc5e7d1
  49. 49
    Tailor, A.; Waddington, J. C.; Meng, X.; Park, B. K. Mass Spectrometric and Functional Aspects of Drug-Protein Conjugation. Chem. Res. Toxicol. 2016, 29 (12), 1912– 1935,  DOI: 10.1021/acs.chemrestox.6b00147
    Google Scholar
    49
    Mass Spectrometric and Functional Aspects of Drug-Protein Conjugation
    Tailor, Arun; Waddington, James C.; Meng, Xiaoli; Park, B. Kevin
    Chemical Research in Toxicology (2016), 29 (12), 1912-1935CODEN: CRTOEC; ISSN:0893-228X. (American Chemical Society)
    A review. The covalent binding of drugs (metabolites) to proteins to form drug-protein adducts can have an adverse effect on the body. These adducts are thought to be responsible for idiosyncratic drug reactions including severe drug hypersensitivity reactions. Major advances in proteomics technol. have allowed for the identification and quantification of target proteins for certain drugs. Human serum albumin (HSA) and Hb have been identified as accessible targets, and potential biomarkers for drug-protein adducts formation, for numerous drugs (metabolites) including β-lactam antibiotics, reactive drug metabolites such as quinone imines (acetaminophen) and acyl glucuronides (diclofenac), and covalent inhibitors (neratinib). For example, MS/MS anal. of plasma samples from patients taking flucloxacillin revealed that flucloxacillin and its 5-hydroxymethyl metabolite formed covalent adducts with lysine residues on albumin via opening of the β-lactam ring. Other proteins such as P 450 and keratin are also potential targets for covalent binding. However, for most drugs, the properties of these target proteins including their location, their quantity, the timing of conjugate generation, and their biol. function are not well understood. In this review, currently available proteomic technologies including MS/MS anal. to identify antigens, precise location of modifications, and the immunol. consequence of hapten-protein complex are illustrated. Moving forward, identification of the nature of the antigenic determinants that trigger immune responses to drug protein adducts will increase the authors' ability to predict idiosyncratic toxicity for a given compd.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsFymu7fI&md5=488bc6cacaf831918db1c28c2f70aa8c
  50. 50
    Jeffery, D. A.; Bogyo, M. Chemical Proteomics and Its Application to Drug Discovery. Curr. Opin. Biotechnol. 2003, 14 (1), 87– 95,  DOI: 10.1016/S0958-1669(02)00010-1
    Google Scholar
    50
    Chemical proteomics and its application to drug discovery
    Jeffery, Douglas A.; Bogyo, Matthew
    Current Opinion in Biotechnology (2003), 14 (1), 87-95CODEN: CUOBE3; ISSN:0958-1669. (Elsevier Science Ltd.)
    A review with refs. The completion of the human genome sequencing project has provided a flood of new information that is likely to change the way scientists approach the study of complex biol. systems. A major challenge lies in translating this information into new and better ways to treat human disease. The multidisciplinary science of chem. proteomics can be used to distill this flood of new information. This approach makes use of synthetic small mols. that can be used to covalently modify a set of related enzymes and subsequently allow their purifn. and/or identification as valid drug targets. Furthermore, such methods enable rapid biochem. anal. and small-mol. screening of targets thereby accelerating the often difficult process of target validation and drug discovery.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXps1WmtQ%253D%253D&md5=9d77283dcea8e41a994dbcd4d14b382b
  51. 51
    Weerapana, E.; Wang, C.; Simon, G. M.; Richter, F.; Khare, S.; Dillon, M. B. D.; Bachovchin, D. A.; Mowen, K.; Baker, D.; Cravatt, B. F. Quantitative Reactivity Profiling Predicts Functional Cysteines in Proteomes. Nature 2010, 468 (7325), 790– 795,  DOI: 10.1038/nature09472
    Google Scholar
    51
    Quantitative reactivity profiling predicts functional cysteines in proteomes
    Weerapana, Eranthie; Wang, Chu; Simon, Gabriel M.; Richter, Florian; Khare, Sagar; Dillon, Myles B. D.; Bachovchin, Daniel A.; Mowen, Kerri; Baker, David; Cravatt, Benjamin F.
    Nature (London, United Kingdom) (2010), 468 (7325), 790-795CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
    Cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochem. functions. The absence of a consensus sequence that defines functional cysteines in proteins has hindered their discovery and characterization. Here we describe a proteomics method to profile quant. the intrinsic reactivity of cysteine residues en masse directly in native biol. systems. Hyper-reactivity was a rare feature among cysteines and it was found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. Hyper-reactive cysteines were identified in several proteins of uncharacterized function, including a residue conserved across eukaryotic phylogeny that we show is required for yeast viability and is involved in iron-sulfur protein biogenesis. We also demonstrate that quant. reactivity profiling can form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhsVGhsr%252FI&md5=277e436e7a8f4dfff0b548bce52ac40d
  52. 52
    Backus, K. M.; Correia, B. E.; Lum, K. M.; Forli, S.; Horning, B. D.; González-Páez, G. E.; Chatterjee, S.; Lanning, B. R.; Teijaro, J. R.; Olson, A. J.; Wolan, D. W.; Cravatt, B. F. Proteome-Wide Covalent Ligand Discovery in Native Biological Systems. Nature 2016, 534 (7608), 570– 574,  DOI: 10.1038/nature18002
    Google Scholar
    52
    Proteome-wide covalent ligand discovery in native biological systems
    Backus, Keriann M.; Correia, Bruno E.; Lum, Kenneth M.; Forli, Stefano; Horning, Benjamin D.; Gonzalez-Paez, Gonzalo E.; Chatterjee, Sandip; Lanning, Bryan R.; Teijaro, John R.; Olson, Arthur J.; Wolan, Dennis W.; Cravatt, Benjamin F.
    Nature (London, United Kingdom) (2016), 534 (7608), 570-574CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
    Small mols. are powerful tools for investigating protein function and can serve as leads for new therapeutics. Most human proteins, however, lack small-mol. ligands, and entire protein classes are considered 'undruggable'. Fragment-based ligand discovery can identify small-mol. probes for proteins that have proven difficult to target using high-throughput screening of complex compd. libraries. Although reversibly binding ligands are commonly pursued, covalent fragments provide an alternative route to small-mol. probes, including those that can access regions of proteins that are difficult to target through binding affinity alone. Here we report a quant. anal. of cysteine-reactive small-mol. fragments screened against thousands of proteins in human proteomes and cells. Covalent ligands were identified for >700 cysteines found in both druggable proteins and proteins deficient in chem. probes, including transcription factors, adaptor/scaffolding proteins, and uncharacterized proteins. Among the atypical ligand-protein interactions discovered were compds. that react preferentially with pro- (inactive) caspases. We used these ligands to distinguish extrinsic apoptosis pathways in human cell lines vs. primary human T cells, showing that the former is largely mediated by caspase-8 while the latter depends on both caspase-8 and -10. Fragment-based covalent ligand discovery provides a greatly expanded portrait of the ligandable proteome and furnishes compds. that can illuminate protein functions in native biol. systems.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtVSksbnN&md5=6fab087c042de735f8a5931e9f5b946c
  53. 53
    Abbasov, M. E.; Kavanagh, M. E.; Ichu, T.-A.; Lazear, M. R.; Tao, Y.; Crowley, V. M.; Am Ende, C. W.; Hacker, S. M.; Ho, J.; Dix, M. M.; Suciu, R.; Hayward, M. M.; Kiessling, L. L.; Cravatt, B. F. A Proteome-Wide Atlas of Lysine-Reactive Chemistry. Nat. Chem. 2021, 13 (11), 1081– 1092,  DOI: 10.1038/s41557-021-00765-4
    Google Scholar
    53
    A proteome-wide atlas of lysine-reactive chemistry
    Abbasov, Mikail E.; Kavanagh, Madeline E.; Ichu, Taka-Aki; Lazear, Michael R.; Tao, Yongfeng; Crowley, Vincent M.; am Ende, Christopher W.; Hacker, Stephan M.; Ho, Jordan; Dix, Melissa M.; Suciu, Radu; Hayward, Matthew M.; Kiessling, Laura L.; Cravatt, Benjamin F.
    Nature Chemistry (2021), 13 (11), 1081-1092CODEN: NCAHBB; ISSN:1755-4330. (Nature Portfolio)
    Recent advances in chem. proteomics have begun to characterize the reactivity and ligandability of lysines on a global scale. Yet, only a limited diversity of aminophilic electrophiles have been evaluated for interactions with the lysine proteome. Here, we report an in-depth profiling of >30 uncharted aminophilic chemotypes that greatly expands the content of ligandable lysines in human proteins. Aminophilic electrophiles showed disparate proteomic reactivities that range from selective interactions with a handful of lysines to, for a set of dicarboxaldehyde fragments, remarkably broad engagement of the covalent small-mol.-lysine interactions captured by the entire library. We used these latter 'scout' electrophiles to efficiently map ligandable lysines in primary human immune cells under stimulatory conditions. Finally, we show that aminophilic compds. perturb diverse biochem. functions through site-selective modification of lysines in proteins, including protein-RNA interactions implicated in innate immune responses. These findings support the broad potential of covalent chem. for targeting functional lysines in the human proteome.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvF2ju7rJ&md5=90e566b7a65ebfca5108a1c44f06f575
  54. 54
    Hayes, J. D.; Flanagan, J. U.; Jowsey, I. R. Glutathione Transferases. Annu. Rev. Pharmacol. Toxicol. 2005, 45, 51– 88,  DOI: 10.1146/annurev.pharmtox.45.120403.095857
    Google Scholar
    54
    Glutathione transferases
    Hayes, John D.; Flanagan, Jack U.; Jowsey, Ian R.
    Annual Review of Pharmacology and Toxicology (2005), 45 (), 51-88, 1 plateCODEN: ARPTDI; ISSN:0362-1642. (Annual Reviews Inc.)
    A review. The authors describe the 3 mammalian glutathione S-transferase (GST) families, namely cytosolic, mitochondrial, and microsomal GSTs, the latter now designated MAPEG (Membrane-Assocd. Proteins in Eicosanoid and Glutathione metab.). In addn. to detoxifying electrophilic xenobiotics, such as chem. carcinogens, environmental pollutants, and antitumor agents, these GSTs inactivate endogenous α,β-unsatd. aldehydes, quinones, epoxides, and hydroperoxides formed as secondary metabolites during oxidative stress. These enzymes are also intimately involved in the biosynthesis of leukotrienes, prostaglandins, testosterone, and progesterone, as well as the degrdn. of tyrosine. Among their substrates, GSTs conjugate the signaling mols., 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2) and 4-hydroxynonenal, with glutathione, and consequently they antagonize expression of genes trans-activated by peroxisome proliferator-activated receptor γ (PPARγ) and nuclear factor-erythroid 2 p45-related factor 2 (Nrf2). Through metab. of 15d-PGJ2, GST may enhance gene expression driven by nuclear factor-κB (NF-κB). Cytosolic human GST exhibit genetic polymorphisms and this variation can increase susceptibility to carcinogenesis and inflammatory disease. Polymorphisms in human MAPEG are assocd. with alterations in lung function and increased risk of myocardial infarction and stroke. Targeted disruption of murine genes has demonstrated that cytosolic GST isoenzymes are broadly cytoprotective, whereas MAPEG proteins have pro-inflammatory activities. Furthermore, knockout of mouse GSTA4 and GSTZ1 leads to overexpression of transferases in the Alpha, Mu, and Pi classes, an observation suggesting they are part of an adaptive mechanism that responds to endogenous chem. cues such as 4-hydroxynonenal and tyrosine degrdn. products. Consistent with this hypothesis, the promoters of cytosolic GST and MAPEG genes contain antioxidant response elements through which they are transcriptionally activated during exposure to Michael reaction acceptors and oxidative stress.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXisVWjtrk%253D&md5=c74f17b1381f046770a7f6faf5c51291
  55. 55
    Jiang, X.; Zhou, Q.; Du, B.; Li, S.; Huang, Y.; Chi, Z.; Lee, W. M.; Yu, M.; Zheng, J. Noninvasive Monitoring of Hepatic Glutathione Depletion through Fluorescence Imaging and Blood Testing. Sci. Adv. 2021, 7 (8), eabd9847  DOI: 10.1126/sciadv.abd9847
    Google Scholar
    There is no corresponding record for this reference.
  56. 56
    Jeffries, R. E.; Gomez, S. M.; Macdonald, J. M.; Gamcsik, M. P. Direct Detection of Glutathione Biosynthesis, Conjugation, Depletion and Recovery in Intact Hepatoma Cells. Int. J. Mol. Sci. 2022, 23 (9), 4733,  DOI: 10.3390/ijms23094733
    Google Scholar
    There is no corresponding record for this reference.
  57. 57
    Quanrud, G. M.; Lyu, Z.; Balamurugan, S. V.; Canizal, C.; Wu, H.-T.; Genereux, J. C. Cellular Exposure to Chloroacetanilide Herbicides Induces Distinct Protein Destabilization Profiles. ACS Chem. Biol. 2023, 18 (7), 1661– 1676,  DOI: 10.1021/acschembio.3c00338
    Google Scholar
    There is no corresponding record for this reference.
  58. 58
    Julio, A. R.; Shikwana, F.; Truong, C.; Burton, N. R.; Dominguez, E.; Turmon, A. C.; Cao, J.; Backus, K. Pervasive Aggregation and Depletion of Host and Viral Proteins in Response to Cysteine-Reactive Electrophilic Compounds. BioRxiv , November 1, 2023.  DOI: 10.1101/2023.10.30.564067 .
    Google Scholar
    There is no corresponding record for this reference.
  59. 59
    Adair, K.; Meng, X.; Naisbitt, D. J. Drug Hapten-Specific T-Cell Activation: Current Status and Unanswered Questions. Proteomics 2021, 21 (17–18), e2000267  DOI: 10.1002/pmic.202000267
    Google Scholar
    There is no corresponding record for this reference.
  60. 60
    Weltzien, H. U.; Padovan, E. Molecular Features of Penicillin Allergy. J. Invest. Dermatol. 1998, 110 (3), 203– 206,  DOI: 10.1046/j.1523-1747.1998.00122.x
    Google Scholar
    There is no corresponding record for this reference.
  61. 61
    Pirmohamed, M.; Ostrov, D. A.; Park, B. K. New Genetic Findings Lead the Way to a Better Understanding of Fundamental Mechanisms of Drug Hypersensitivity. J. Allergy Clin. Immunol. 2015, 136 (2), 236– 244,  DOI: 10.1016/j.jaci.2015.06.022
    Google Scholar
    There is no corresponding record for this reference.
  62. 62
    Agashe, R. P.; Lippman, S. M.; Kurzrock, R. JAK: Not Just Another Kinase. Mol. Cancer Ther. 2022, 21 (12), 1757– 1764,  DOI: 10.1158/1535-7163.MCT-22-0323
    Google Scholar
    There is no corresponding record for this reference.
  63. 63
    Goedken, E. R.; Argiriadi, M. A.; Banach, D. L.; Fiamengo, B. A.; Foley, S. E.; Frank, K. E.; George, J. S.; Harris, C. M.; Hobson, A. D.; Ihle, D. C.; Marcotte, D.; Merta, P. J.; Michalak, M. E.; Murdock, S. E.; Tomlinson, M. J.; Voss, J. W. Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol. J. Biol. Chem. 2015, 290 (8), 4573– 4589,  DOI: 10.1074/jbc.M114.595181
    Google Scholar
    63
    Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol
    Goedken, Eric R.; Argiriadi, Maria A.; Banach, David L.; Fiamengo, Bryan A.; Foley, Sage E.; Frank, Kristine E.; George, Jonathan S.; Harris, Christopher M.; Hobson, Adrian D.; Ihle, David C.; Marcotte, Douglas; Merta, Philip J.; Michalak, Mark E.; Murdock, Sara E.; Tomlinson, Medha J.; Voss, Jeffrey W.
    Journal of Biological Chemistry (2015), 290 (8), 4573-4589CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
    The action of Janus kinases (JAKs) is required for multiple cytokine signaling pathways, and as such, JAK inhibitors hold promise for treatment of autoimmune disorders, including rheumatoid arthritis, inflammatory bowel disease, and psoriasis. However, due to high similarity in the active sites of the four members (Jak1, Jak2, Jak3, and Tyk2), developing selective inhibitors within this family is challenging. We have designed and characterized substituted, tricyclic Jak3 inhibitors that selectively avoid inhibition of the other JAKs. This is accomplished through a covalent interaction between an inhibitor contg. a terminal electrophile and an active site cysteine (Cys-909). We found that these ATP competitive compds. are irreversible inhibitors of Jak3 enzyme activity in vitro. They possess high selectivity against other kinases and can potently (IC50 < 100 nm) inhibit Jak3 activity in cell-based assays. These results suggest irreversible inhibitors of this class may be useful selective agents, both as tools to probe Jak3 biol. and potentially as therapies for autoimmune diseases.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXjsF2lsLY%253D&md5=4d99cf5b13fd05df5c4abc197c1fe284
  64. 64
    Chen, C.; Lu, D.; Sun, T.; Zhang, T. JAK3 Inhibitors for the Treatment of Inflammatory and Autoimmune Diseases: A Patent Review (2016-Present). Expert Opin. Ther. Pat. 2022, 32 (3), 225– 242,  DOI: 10.1080/13543776.2022.2023129
    Google Scholar
    There is no corresponding record for this reference.
  65. 65
    Shindo, N.; Ojida, A. Recent Progress in Covalent Warheads for in Vivo Targeting of Endogenous Proteins. Bioorg. Med. Chem. 2021, 47, 116386,  DOI: 10.1016/j.bmc.2021.116386
    Google Scholar
    65
    Recent progress in covalent warheads for in vivo targeting of endogenous proteins
    Shindo, Naoya; Ojida, Akio
    Bioorganic & Medicinal Chemistry (2021), 47 (), 116386CODEN: BMECEP; ISSN:0968-0896. (Elsevier B.V.)
    Covalent drugs exert potent and durable activity by chem. modification of the endogenous target protein in vivo. To maximize the pharmacol. efficacy while alleviating the risk of toxicity due to nonspecific off-target reactions, current covalent drug discovery focuses on the development of targeted covalent inhibitors (TCIs), wherein a reactive group (warhead) is strategically incorporated onto a reversible ligand of the target protein to facilitate specific covalent engagement. Various aspects of warheads, such as intrinsic reactivity, chemoselectivity, mode of reaction, and reversibility of the covalent engagement, would affect the target selectivity of TCIs. Although TCIs clin. approved to date largely rely on Michael acceptor-type electrophiles for cysteine targeting, a wide array of novel warheads have been devised and tested in TCI development in recent years. In this short review, we provide an overview of recent progress in chem. for selective covalent targeting of proteins and their applications in TCI designs.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXitVSrtrjL&md5=d746f5fd8ac5778e1b23e8ef678ceec6
  66. 66
    Forster, M.; Chaikuad, A.; Dimitrov, T.; Döring, E.; Holstein, J.; Berger, B.-T.; Gehringer, M.; Ghoreschi, K.; Müller, S.; Knapp, S.; Laufer, S. A. Development, Optimization, and Structure-Activity Relationships of Covalent-Reversible JAK3 Inhibitors Based on a Tricyclic Imidazo[5,4- d]Pyrrolo[2,3- b]Pyridine Scaffold. J. Med. Chem. 2018, 61 (12), 5350– 5366,  DOI: 10.1021/acs.jmedchem.8b00571
    Google Scholar
    66
    Development, Optimization, and Structure-Activity Relationships of Covalent-Reversible JAK3 Inhibitors Based on a Tricyclic Imidazo[5,4-d]pyrrolo[2,3-b]pyridine Scaffold
    Forster, Michael; Chaikuad, Apirat; Dimitrov, Teodor; Doering, Eva; Holstein, Julia; Berger, Benedict-Tilman; Gehringer, Matthias; Ghoreschi, Kamran; Mueller, Susanne; Knapp, Stefan; Laufer, Stefan A.
    Journal of Medicinal Chemistry (2018), 61 (12), 5350-5366CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    Janus kinases are major drivers of immune signaling and have been the focus of anti-inflammatory drug discovery for more than a decade. Because of the invariable colocalization of JAK1 and JAK3 at cytokine receptors, the question if selective JAK3 inhibition is sufficient to effectively block downstream signaling has been highly controversial. Recently, we discovered the covalent-reversible JAK3 inhibitor FM-381 (23) featuring high isoform and kinome selectivity. Crystallog. revealed that this inhibitor induces an unprecedented binding pocket by interactions of a nitrile substituent with arginine residues in JAK3. Herein, we describe detailed structure-activity relationships necessary for induction of the arginine pocket and the impact of this structural change on potency, isoform selectivity, and efficacy in cellular models. Furthermore, we evaluated the stability of this novel inhibitor class in in vitro metabolic assays and were able to demonstrate an adequate stability of key compd. 23 for in vivo use.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtVGjsrbN&md5=8acdec137df746f854bbee75a10d5f70
  67. 67
    Laux, J.; Forster, M.; Riexinger, L.; Schwamborn, A.; Guezguez, J.; Pokoj, C.; Kudolo, M.; Berger, L. M.; Knapp, S.; Schollmeyer, D.; Guse, J.; Burnet, M.; Laufer, S. A. Pharmacokinetic Optimization of Small Molecule Janus Kinase 3 Inhibitors to Target Immune Cells. ACS Pharmacol. Transl. Sci. 2022, 5 (8), 573– 602,  DOI: 10.1021/acsptsci.2c00054
    Google Scholar
    67
    Pharmacokinetic Optimization of Small Molecule Janus Kinase 3 Inhibitors to Target Immune Cells
    Laux, Julian; Forster, Michael; Riexinger, Laura; Schwamborn, Anna; Guezguez, Jamil; Pokoj, Christina; Kudolo, Mark; Berger, Lena M.; Knapp, Stefan; Schollmeyer, Dieter; Guse, Jan; Burnet, Michael; Laufer, Stefan A.
    ACS Pharmacology & Translational Science (2022), 5 (8), 573-602CODEN: APTSFN; ISSN:2575-9108. (American Chemical Society)
    Modulation of Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling is a promising method of treating autoimmune diseases, and the profound potency of clin. compds. makes this mode of action particularly attractive. Other questions that remain unanswered also include: What is the ideal selectivity between JAK1 and JAK3. Which cells are most relevant to JAK blockade. And what is the ideal tissue distribution pattern for addressing specific autoimmune conditions. We hypothesized that JAK3 selectivity is most relevant to low-dose clin. effects and interleukin-10 (IL-10) stimulation in particular, that immune cells are the most important compartment, and that distribution to inflamed tissue is the most important pharmacokinetic characteristic for in vivo disease modification. To test these hypotheses, we prepd. modified derivs. of JAK3 specific inhibitors that target C909 near the ATP binding site based on FM-381, first reported in 2016; a compd. class that was hitherto limited in uptake and exposure in vivo. These limits appear to be due to metabolic instability of side groups binding in the selectivity pocket. We identified derivs. with improved stability and tissue exposure. Conjugation to macrolide scaffolds with medium chain linkers was sufficient to stabilize the compds. and improve transport to organs while maintaining JAK3 affinity. These conjugates are inflammation targeted JAK3 inhibitors with long tissue half-lives and high exposure to activated immune cells.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38Xhsl2nur7M&md5=31a71f1a28ac2893f116b25e3972fc36
  68. 68
    Burger, J. A. Bruton Tyrosine Kinase Inhibitors: Present and Future. Cancer J. 2019, 25 (6), 386– 393,  DOI: 10.1097/PPO.0000000000000412
    Google Scholar
    68
    Bruton Tyrosine Kinase Inhibitors: Present and Future
    Burger, Jan A.
    Cancer Journal (Philadelphia, PA, United States) (2019), 25 (6), 386-393CODEN: CAJOCB; ISSN:1528-9117. (Lippincott Williams & Wilkins)
    A review. Bruton tyrosine kinase (BTK) is a nonreceptor tyrosine kinase that plays a central role in the signal transduction of the B-cell antigen receptor and other cell surface receptors, both in normal and malignant B lymphocytes. B-cell antigen receptor signaling is activated in secondary lymphatic organs and drives the proliferation of malignant B cells, including chronic lymphocytic leukemia (CLL) cells. During the last 10 years, BTK inhibitors (BTKis) are increasingly replacing chemotherapy-based regimen, esp. in patients with CLL and mantle cell lymphoma (MCL). Bruton tyrosine kinase inhibitors are particularly active in patients with CLL and MCL, but also received approval for Waldenstroem macroglobulinemia, small lymphocytic lymphoma, marginal zone lymphoma, and chronic graft-vs.-host disease. Current clin. practice is continuous long-term administration of BTKi, which can be complicated by adverse effects or the development of drug resistance. Alternatives to long-term use of BTKi are being developed, such as combination therapies, permitting for limited duration therapy. Second-generation BTKis are under development, which differ from ibrutinib, the first-in-class BTKi, in their specificity for BTK, and therefore may differentiate themselves from ibrutinib in terms of adverse effects or efficacy.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXitlOms7zM&md5=574551611f4a8f843cf1ce2cd0db1697
  69. 69
    Khan, W. N. Regulation of B Lymphocyte Development and Activation by Bruton’s Tyrosine Kinase. Immunol. Res. 2001, 23 (2–3), 147– 156,  DOI: 10.1385/IR:23:2-3:147
    Google Scholar
    There is no corresponding record for this reference.
  70. 70
    Guldenpfennig, C.; Teixeiro, E.; Daniels, M. NF-kB’s Contribution to B Cell Fate Decisions. Front. Immunol. 2023, 14, 1214095,  DOI: 10.3389/fimmu.2023.1214095
    Google Scholar
    There is no corresponding record for this reference.
  71. 71
    Staudt, L. M. Oncogenic Activation of NF-kappaB. Cold Spring Harb. Perspect. Biol. 2010, 2 (6), a000109,  DOI: 10.1101/cshperspect.a000109
    Google Scholar
    There is no corresponding record for this reference.
  72. 72
    Small Molecules in Oncology; Martens, U. M., Ed.; Recent Results in Cancer Research Series; Springer: Berlin, Heidelberg, 2014; Vol. 201.  DOI: 10.1007/978-3-642-54490-3 .
    Google Scholar
    There is no corresponding record for this reference.
  73. 73
    Wu, J.; Zhang, M.; Liu, D. Acalabrutinib (ACP-196): A Selective Second-Generation BTK Inhibitor. J. Hematol. Oncol.J. Hematol Oncol 2016, 9, 21,  DOI: 10.1186/s13045-016-0250-9
    Google Scholar
    73
    Acalabrutinib (ACP-196): a selective second-generation BTK inhibitor
    Wu, Jingjing; Zhang, Mingzhi; Liu, Delong
    Journal of Hematology & Oncology (2016), 9 (), 21/1-21/4CODEN: JHOOAO; ISSN:1756-8722. (BioMed Central Ltd.)
    More and more targeted agents become available for B cell malignancies with increasing precision and potency. The first-in-class Bruton's tyrosine kinase (BTK) inhibitor, ibrutinib, has been in clin. use for the treatment of chronic lymphocytic leukemia, mantle cell lymphoma, and Waldenstrom's macroglobulinemia. More selective BTK inhibitors (ACP-196, ONO/GS-4059, BGB-3111, CC-292) are being explored. Acalabrutinib (ACP-196) is a novel irreversible second-generation BTK inhibitor that was shown to be more potent and selective than ibrutinib. This review summarized the preclin. research and clin. data of acalabrutinib.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXis1eisrw%253D&md5=a6a8f9b9236abe7ef1054a41e1c71e5a
  74. 74
    Guo, Y.; Liu, Y.; Hu, N.; Yu, D.; Zhou, C.; Shi, G.; Zhang, B.; Wei, M.; Liu, J.; Luo, L.; Tang, Z.; Song, H.; Guo, Y.; Liu, X.; Su, D.; Zhang, S.; Song, X.; Zhou, X.; Hong, Y.; Chen, S.; Cheng, Z.; Young, S.; Wei, Q.; Wang, H.; Wang, Q.; Lv, L.; Wang, F.; Xu, H.; Sun, H.; Xing, H.; Li, N.; Zhang, W.; Wang, Z.; Liu, G.; Sun, Z.; Zhou, D.; Li, W.; Liu, L.; Wang, L.; Wang, Z. Discovery of Zanubrutinib (BGB-3111), a Novel, Potent, and Selective Covalent Inhibitor of Bruton’s Tyrosine Kinase. J. Med. Chem. 2019, 62 (17), 7923– 7940,  DOI: 10.1021/acs.jmedchem.9b00687
    Google Scholar
    74
    Discovery of Zanubrutinib (BGB-3111), a Novel, Potent, and Selective Covalent Inhibitor of Bruton's Tyrosine Kinase
    Guo, Yunhang; Liu, Ye; Hu, Nan; Yu, Desheng; Zhou, Changyou; Shi, Gongyin; Zhang, Bo; Wei, Min; Liu, Junhua; Luo, Lusong; Tang, Zhiyu; Song, Huipeng; Guo, Yin; Liu, Xuesong; Su, Dan; Zhang, Shuo; Song, Xiaomin; Zhou, Xing; Hong, Yuan; Chen, Shuaishuai; Cheng, Zhenzhen; Young, Steve; Wei, Qiang; Wang, Haisheng; Wang, Qiuwen; Lv, Lei; Wang, Fan; Xu, Haipeng; Sun, Hanzi; Xing, Haimei; Li, Na; Zhang, Wei; Wang, Zhongbo; Liu, Guodong; Sun, Zhijian; Zhou, Dongping; Li, Wei; Liu, Libin; Wang, Lai; Wang, Zhiwei
    Journal of Medicinal Chemistry (2019), 62 (17), 7923-7940CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    Aberrant activation of Bruton's tyrosine kinase (BTK) plays an important role in pathogenesis of B-cell lymphomas, suggesting that inhibition of BTK is useful in the treatment of hematol. malignancies. The discovery of a more selective on-target covalent BTK inhibitor is of high value. Herein, we disclose the discovery and preclin. characterization of a potent, selective, and irreversible BTK inhibitor as our clin. candidate by using in vitro potency, selectivity, pharmacokinetics (PK), and in vivo pharmacodynamic for prioritizing compds. Compd. BGB-3111 (31a, Zanubrutinib) demonstrates (i) potent activity against BTK and excellent selectivity over other TEC, EGFR and Src family kinases, (ii) desirable ADME, excellent in vivo pharmacodynamic in mice and efficacy in OCI-LY10 xenograft models.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsFSku7bP&md5=5cdb551d296e60eb1e82b03b7a0384ee
  75. 75
    Liclican, A.; Serafini, L.; Xing, W.; Czerwieniec, G.; Steiner, B.; Wang, T.; Brendza, K. M.; Lutz, J. D.; Keegan, K. S.; Ray, A. S.; Schultz, B. E.; Sakowicz, R.; Feng, J. Y. Biochemical Characterization of Tirabrutinib and Other Irreversible Inhibitors of Bruton’s Tyrosine Kinase Reveals Differences in on - and off - Target Inhibition. Biochim. Biophys. Acta Gen. Subj. 2020, 1864 (4), 129531,  DOI: 10.1016/j.bbagen.2020.129531
    Google Scholar
    There is no corresponding record for this reference.
  76. 76
    Tam, C. S.; Muñoz, J. L.; Seymour, J. F.; Opat, S. Zanubrutinib: Past, Present, and Future. Blood Cancer J. 2023, 13 (1), 141,  DOI: 10.1038/s41408-023-00902-x
    Google Scholar
    There is no corresponding record for this reference.
  77. 77
    Estupiñán, H. Y.; Berglöf, A.; Zain, R.; Smith, C. I. E. Comparative Analysis of BTK Inhibitors and Mechanisms Underlying Adverse Effects. Front. Cell Dev. Biol. 2021, 9, 630942,  DOI: 10.3389/fcell.2021.630942
    Google Scholar
    77
    Comparative Analysis of BTK Inhibitors and Mechanisms Underlying Adverse Effects
    Estupinan H Yesid; Berglof Anna; Zain Rula; Smith C I Edvard; Estupinan H Yesid; Zain Rula
    Frontiers in cell and developmental biology (2021), 9 (), 630942 ISSN:2296-634X.
    The cytoplasmic protein-tyrosine kinase BTK plays an essential role for differentiation and survival of B-lineage cells and, hence, represents a suitable drug target. The number of BTK inhibitors (BTKis) in the clinic has increased considerably and currently amounts to at least 22. First-in-class was ibrutinib, an irreversible binder forming a covalent bond to a cysteine in the catalytic region of the kinase, for which we have identified 228 active trials listed at ClinicalTrials.gov. Next-generation inhibitors, acalabrutinib and zanubrutinib, are approved both in the United States and in Europe, and zanubrutinib also in China, while tirabrutinib is currently only registered in Japan. In most cases, these compounds have been used for the treatment of B-lymphocyte tumors. However, an increasing number of trials instead addresses autoimmunity and inflammation in multiple sclerosis, rheumatoid arthritis, pemphigus and systemic lupus erythematosus with the use of either irreversibly binding inhibitors, e.g., evobrutinib and tolebrutinib, or reversibly binding inhibitors, like fenebrutinib. Adverse effects (AEs) have predominantly implicated inhibition of other kinases with a BTKi-binding cysteine in their catalytic domain. Analysis of the reported AEs suggests that ibrutinib-associated atrial fibrillation is caused by binding to ERBB2/HER2 and ERBB4/HER4. However, the binding pattern of BTKis to various additional kinases does not correlate with the common assumption that skin manifestations and diarrhoeas are off-target effects related to EGF receptor inhibition. Moreover, dermatological toxicities, diarrhoea, bleedings and invasive fungal infections often develop early after BTKi treatment initiation and subsequently subside. Conversely, cardiovascular AEs, like hypertension and various forms of heart disease, often persist.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BB3sfjtlCrtg%253D%253D&md5=c559e266e46358b280c7835a9574d965
  78. 78
    Mato, A. R.; Nabhan, C.; Thompson, M. C.; Lamanna, N.; Brander, D. M.; Hill, B.; Howlett, C.; Skarbnik, A.; Cheson, B. D.; Zent, C.; Pu, J.; Kiselev, P.; Goy, A.; Claxton, D.; Isaac, K.; Kennard, K. H.; Timlin, C.; Landsburg, D.; Winter, A.; Nasta, S. D.; Bachow, S. H.; Schuster, S. J.; Dorsey, C.; Svoboda, J.; Barr, P.; Ujjani, C. S. Toxicities and Outcomes of 616 Ibrutinib-Treated Patients in the United States: A Real-World Analysis. Haematologica 2018, 103 (5), 874– 879,  DOI: 10.3324/haematol.2017.182907
    Google Scholar
    There is no corresponding record for this reference.
  79. 79
    Sharman, J. P.; Black-Shinn, J. L.; Clark, J.; Bitman, B. Understanding Ibrutinib Treatment Discontinuation Patterns for Chronic Lymphocytic Leukemia. Blood 2017, 130 (Supplement 1), 4060,  DOI: 10.1182/blood.V130.Suppl_1.4060.4060
    Google Scholar
    There is no corresponding record for this reference.
  80. 80
    Winqvist, M.; Andersson, P.-O.; Asklid, A.; Karlsson, K.; Karlsson, C.; Lauri, B.; Lundin, J.; Mattsson, M.; Norin, S.; Sandstedt, A.; Rosenquist, R.; Späth, F.; Hansson, L.; Österborg, A. for the Swedish CLL Group. Long-Term Real-World Results of Ibrutinib Therapy in Patients with Relapsed or Refractory Chronic Lymphocytic Leukemia: 30-Month Follow up of the Swedish Compassionate Use Cohort. Haematologica 2019, 104 (5), e208– e210,  DOI: 10.3324/haematol.2018.198820
    Google Scholar
    There is no corresponding record for this reference.
  81. 81
    ClinicalTrials.gov. Rilzabrutinib. https://clinicaltrials.gov/search?intr=Rilzabrutinib (accessed 2023–11–28).
    Google Scholar
    There is no corresponding record for this reference.
  82. 82
    Oda, K. New Families of Carboxyl Peptidases: Serine-Carboxyl Peptidases and Glutamic Peptidases. J. Biochem. (Tokyo) 2012, 151 (1), 13– 25,  DOI: 10.1093/jb/mvr129
    Google Scholar
    There is no corresponding record for this reference.
  83. 83
    Ćwilichowska, N.; Świderska, K. W.; Dobrzyń, A.; Drąg, M.; Poręba, M. Diagnostic and Therapeutic Potential of Protease Inhibition. Mol. Aspects Med. 2022, 88, 101144,  DOI: 10.1016/j.mam.2022.101144
    Google Scholar
    There is no corresponding record for this reference.
  84. 84
    Manasanch, E. E.; Orlowski, R. Z. Proteasome Inhibitors in Cancer Therapy. Nat. Rev. Clin. Oncol. 2017, 14 (7), 417– 433,  DOI: 10.1038/nrclinonc.2016.206
    Google Scholar
    84
    Proteasome inhibitors in cancer therapy
    Manasanch, Elisabet E.; Orlowski, Robert Z.
    Nature Reviews Clinical Oncology (2017), 14 (7), 417-433CODEN: NRCOAA; ISSN:1759-4774. (Nature Publishing Group)
    The ubiquitin proteasome pathway was discovered in the 1980s to be a central component of the cellular protein-degrdn. machinery with essential functions in homeostasis, which include preventing the accumulation of misfolded or deleterious proteins. Cancer cells produce proteins that promote both cell survival and proliferation, and/or inhibit mechanisms of cell death. This notion set the stage for preclin. testing of proteasome inhibitors as a means to shift this fine equil. towards cell death. Since the late 1990s, clin. trials have been conducted for a variety of malignancies, leading to regulatory approvals of proteasome inhibitors to treat multiple myeloma and mantle-cell lymphoma. First-generation and second-generation proteasome inhibitors can elicit deep initial responses in patients with myeloma, for whom these drugs have dramatically improved outcomes, but relapses are frequent and acquired resistance to treatment eventually emerges. In addn., promising preclin. data obtained with proteasome inhibitors in models of solid tumors have not been confirmed in the clinic, indicating the importance of primary resistance. Investigation of the mechanisms of resistance is, therefore, essential to further maximize the utility of this class of drugs in the era of personalized medicine. Herein, we discuss the advances and challenges resulting from the introduction of proteasome inhibitors into the clinic.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsFGlsbg%253D&md5=7246069f357a4cc9449f822c57767811
  85. 85
    Flint, M.; Mullen, S.; Deatly, A. M.; Chen, W.; Miller, L. Z.; Ralston, R.; Broom, C.; Emini, E. A.; Howe, A. Y. M. Selection and Characterization of Hepatitis C Virus Replicons Dually Resistant to the Polymerase and Protease Inhibitors HCV-796 and Boceprevir (SCH 503034). Antimicrob. Agents Chemother. 2009, 53 (2), 401– 411,  DOI: 10.1128/AAC.01081-08
    Google Scholar
    There is no corresponding record for this reference.
  86. 86
    Augeri, D. J.; Robl, J. A.; Betebenner, D. A.; Magnin, D. R.; Khanna, A.; Robertson, J. G.; Wang, A.; Simpkins, L. M.; Taunk, P.; Huang, Q.; Han, S.-P.; Abboa-Offei, B.; Cap, M.; Xin, L.; Tao, L.; Tozzo, E.; Welzel, G. E.; Egan, D. M.; Marcinkeviciene, J.; Chang, S. Y.; Biller, S. A.; Kirby, M. S.; Parker, R. A.; Hamann, L. G. Discovery and Preclinical Profile of Saxagliptin (BMS-477118): A Highly Potent, Long-Acting, Orally Active Dipeptidyl Peptidase IV Inhibitor for the Treatment of Type 2 Diabetes. J. Med. Chem. 2005, 48 (15), 5025– 5037,  DOI: 10.1021/jm050261p
    Google Scholar
    86
    Discovery and Preclinical Profile of Saxagliptin (BMS-477118): A Highly Potent, Long-Acting, Orally Active Dipeptidyl Peptidase IV Inhibitor for the Treatment of Type 2 Diabetes
    Augeri, David J.; Robl, Jeffrey A.; Betebenner, David A.; Magnin, David R.; Khanna, Ashish; Robertson, James G.; Wang, Aiying; Simpkins, Ligaya M.; Taunk, Prakash; Huang, Qi; Han, Song-Ping; Abboa-Offei, Benoni; Cap, Michael; Xin, Li; Tao, Li; Tozzo, Effie; Welzel, Gustav E.; Egan, Donald M.; Marcinkeviciene, Jovita; Chang, Shu Y.; Biller, Scott A.; Kirby, Mark S.; Parker, Rex A.; Hamann, Lawrence G.
    Journal of Medicinal Chemistry (2005), 48 (15), 5025-5037CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    Efforts to further elucidate structure-activity relationships (SAR) within the authors previously disclosed series of β-quaternary amino acid linked L-cis-4,5-methanoprolinenitrile dipeptidyl peptidase IV (DPP-IV) inhibitors led to the investigation of vinyl substitution at the β-position of α-cycloalkyl-substituted glycines. Despite poor systemic exposure, vinyl-substituted compds. showed extended duration of action in acute rat ex vivo plasma DPP-IV inhibition models. Oxygenated putative metabolites were prepd. and were shown to exhibit the potency and extended duration of action of their precursors in efficacy models measuring glucose clearance in Zuckerfa/fa rats. Extension of this approach to adamantylglycine-derived inhibitors led to the discovery of highly potent inhibitors, including hydroxyadamantyl compd. BMS-477118 (saxagliptin), a highly efficacious, stable, and long-acting DPP-IV inhibitor, which is currently undergoing clin. trials for treatment of type 2 diabetes.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXlsVeltb0%253D&md5=878355880133bb0ddd6bd14ecbf1d070
  87. 87
    Lin, K.; Perni, R. B.; Kwong, A. D.; Lin, C. VX-950, a Novel Hepatitis C Virus (HCV) NS3–4A Protease Inhibitor, Exhibits Potent Antiviral Activities in HCv Replicon Cells. Antimicrob. Agents Chemother. 2006, 50 (5), 1813– 1822,  DOI: 10.1128/AAC.50.5.1813-1822.2006
    Google Scholar
    There is no corresponding record for this reference.
  88. 88
    Focosi, D.; McConnell, S.; Shoham, S.; Casadevall, A.; Maggi, F.; Antonelli, G. Nirmatrelvir and COVID-19: Development, Pharmacokinetics, Clinical Efficacy, Resistance, Relapse, and Pharmacoeconomics. Int. J. Antimicrob. Agents 2023, 61 (2), 106708,  DOI: 10.1016/j.ijantimicag.2022.106708
    Google Scholar
    There is no corresponding record for this reference.
  89. 89
    Wen, W.; Qi, Z.; Wang, J. The Function and Mechanism of Enterovirus 71 (EV71) 3C Protease. Curr. Microbiol. 2020, 77 (9), 1968– 1975,  DOI: 10.1007/s00284-020-02082-4
    Google Scholar
    There is no corresponding record for this reference.
  90. 90
    Zeng, D.; Ma, Y.; Zhang, R.; Nie, Q.; Cui, Z.; Wang, Y.; Shang, L.; Yin, Z. Synthesis and Structure-Activity Relationship of α-Keto Amides as Enterovirus 71 3C Protease Inhibitors. Bioorg. Med. Chem. Lett. 2016, 26 (7), 1762– 1766,  DOI: 10.1016/j.bmcl.2016.02.039
    Google Scholar
    There is no corresponding record for this reference.
  91. 91
    Zhai, Y.; Ma, Y.; Ma, F.; Nie, Q.; Ren, X.; Wang, Y.; Shang, L.; Yin, Z. Structure-Activity Relationship Study of Peptidomimetic Aldehydes as Enterovirus 71 3C Protease Inhibitors. Eur. J. Med. Chem. 2016, 124, 559– 573,  DOI: 10.1016/j.ejmech.2016.08.064
    Google Scholar
    91
    Structure-activity relationship study of peptidomimetic aldehydes as enterovirus 71 3C protease inhibitors
    Zhai, Yangyang; Ma, Yuying; Ma, Fei; Nie, Quandeng; Ren, Xuejiao; Wang, Yaxin; Shang, Luqing; Yin, Zheng
    European Journal of Medicinal Chemistry (2016), 124 (), 559-573CODEN: EJMCA5; ISSN:0223-5234. (Elsevier Masson SAS)
    A series of peptidomimetic aldehydes were designed, synthesized, and evaluated for their biochem. activity against 3C protease (3Cpro) and anti-enterovirus 71 (EV71) activity in vitro. Mol. docking revealed that 5s (IC50 = 0.22 ± 0.07 μM, EC50 = 0.18 ± 0.05 μM) could bind well to the active site of EV71 3Cpro, which was consistent with the biol. data compared to ref. 5a (IC50 = 0.54 ± 0.02 μM, EC50 = 0.26 ± 0.07 μM). Structure and relationship study led to the discovery of aldehyde 5x (IC50 = 0.10 ± 0.02 μM, EC50 = 0.11 ± 0.07 μM), which exhibited the most potent 3Cpro inhibitory and antiviral activity.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsV2jurnN&md5=41cabd5d56ab0164e48cbd7806dbf2c7
  92. 92
    Luo, Y. L. Mechanism-Based and Computational-Driven Covalent Drug Design. J. Chem. Inf. Model. 2021, 61 (11), 5307– 5311,  DOI: 10.1021/acs.jcim.1c01278
    Google Scholar
    There is no corresponding record for this reference.
  93. 93
    Mihalovits, L. M.; Ferenczy, G. G.; Keserű, G. M. Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations. J. Chem. Inf. Model. 2020, 60 (12), 6579– 6594,  DOI: 10.1021/acs.jcim.0c00834
    Google Scholar
    93
    Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations
    Mihalovits, Levente M.; Ferenczy, Gyorgy G.; Keseru, Gyorgy M.
    Journal of Chemical Information and Modeling (2020), 60 (12), 6579-6594CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
    Covalent inhibitors have been gaining increased attention in drug discovery due to their beneficial properties such as long residence time, high biochem. efficiency, and specificity. Optimization of covalent inhibitors is a complex task that involves parallel monitoring of the noncovalent recognition elements and the covalent reactivity of the mols. to avoid potential idiosyncratic side effects. This challenge calls for special design protocols, including a variety of computational chem. methods. Covalent inhibition proceeds through multiple steps, and calcg. free energy changes of the subsequent binding events along the overall binding process would help us to better control the design of drug candidates. Inspired by the recent success of free energy calcns. on reversible binders, we developed a complex protocol to compute free energies related to the noncovalent and covalent binding steps with thermodn. integration and hybrid quantum mech./mol. mech. (QM/MM) potential of mean force (PMF) calcns., resp. In optimization settings, we examd. two therapeutically relevant proteins complexed with congeneric sets of irreversible cysteine targeting covalent inhibitors. In the selectivity paradigm, we studied the irreversible binding of covalent inhibitors to phylogenetically close targets by a mutational approach. The results of the calcns. are in good agreement with the exptl. free energy values derived from the inhibition and kinetic consts. (Ki and kinact) of the enzyme-inhibitor binding. The proposed method might be a powerful tool to predict the potency, selectivity, and binding mechanism of irreversible covalent inhibitors.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXisFSqu73N&md5=61ff455099a14db29ffd081cd3fd613e
  94. 94
    Mihalovits, L. M.; Ferenczy, G. G.; Keserű, G. M. The Role of Quantum Chemistry in Covalent Inhibitor Design. Int. J. Quantum Chem. 2022, 122 (8), e26768  DOI: 10.1002/qua.26768
    Google Scholar
    There is no corresponding record for this reference.
  95. 95
    Lonsdale, R.; Burgess, J.; Colclough, N.; Davies, N. L.; Lenz, E. M.; Orton, A. L.; Ward, R. A. Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity. J. Chem. Inf. Model. 2017, 57 (12), 3124– 3137,  DOI: 10.1021/acs.jcim.7b00553
    Google Scholar
    95
    Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity
    Lonsdale, Richard; Burgess, Jonathan; Colclough, Nicola; Davies, Nichola L.; Lenz, Eva M.; Orton, Alexandra L.; Ward, Richard A.
    Journal of Chemical Information and Modeling (2017), 57 (12), 3124-3137CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
    Targeted covalent inhibition is an established approach for increasing the potency and selectivity of potential drug candidates, as well as identifying potent and selective tool compds. for target validation studies. It is evident that identification of reversible recognition elements is essential for selective covalent inhibition, but this must also be achieved with the appropriate level of inherent reactivity of the reactive functionality (or "warhead"). Structural changes that increase or decrease warhead reactivity, guided by methods to predict the effect of those changes, have the potential to tune warhead reactivity and negate issues related to potency and/or toxicity. The half-life to adduct formation with glutathione (GSH t1/2) is a useful assay for measuring the reactivity of cysteine-targeting covalent warheads but is limited to synthesized mols. In this manuscript the authors assess the ability of several exptl. and computational approaches to predict GSH t1/2 for a range of cysteine targeting warheads, including a novel method based on pKa. Furthermore, matched mol. pairs anal. has been performed against the internal compd. collection, revealing structure-activity relationships between a selection of different covalent warheads. These observations and methods of prediction will be valuable in the design of new covalent inhibitors with desired levels of reactivity.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsl2gsLjF&md5=722e83699c58dee1009b87c8c31bdecc
  96. 96
    Oballa, R. M.; Truchon, J.-F.; Bayly, C. I.; Chauret, N.; Day, S.; Crane, S.; Berthelette, C. A Generally Applicable Method for Assessing the Electrophilicity and Reactivity of Diverse Nitrile-Containing Compounds. Bioorg. Med. Chem. Lett. 2007, 17 (4), 998– 1002,  DOI: 10.1016/j.bmcl.2006.11.044
    Google Scholar
    96
    A generally applicable method for assessing the electrophilicity and reactivity of diverse nitrile-containing compounds
    Oballa, Renata M.; Truchon, Jean-Francois; Bayly, Christopher I.; Chauret, Nathalie; Day, Stephen; Crane, Sheldon; Berthelette, Carl
    Bioorganic & Medicinal Chemistry Letters (2007), 17 (4), 998-1002CODEN: BMCLE8; ISSN:0960-894X. (Elsevier Ltd.)
    Nitrile-based inhibitors of cathepsin K have been known for some time and mechanism-of-action studies have demonstrated that cysteinyl proteases interact with nitriles in a reversible fashion. Three main classes of nitrile-contg. inhibitors have been published in the cathepsin K field: (i) cyanamides, (ii) arom. nitriles, and (iii) aminoacetonitriles. A computational approach was used to calc. the theor. reactivities of diverse nitriles and this was found to correlate with their extent of reactivity with free cysteine. Moreover, there is a tentative link between high reactivity with cysteine and the potential to lead to irreversible covalent binding to proteins.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXht12qtr4%253D&md5=b8fff00bdd6a746753f8f244d25b0cc8
  97. 97
    Copeland, R. A.; Pompliano, D. L.; Meek, T. D. Drug-Target Residence Time and Its Implications for Lead Optimization. Nat. Rev. Drug Discovery 2006, 5 (9), 730– 739,  DOI: 10.1038/nrd2082
    Google Scholar
    97
    Drug-target residence time and its implications for lead optimization
    Copeland, Robert A.; Pompliano, David L.; Meek, Thomas D.
    Nature Reviews Drug Discovery (2006), 5 (9), 730-739CODEN: NRDDAG; ISSN:1474-1776. (Nature Publishing Group)
    A review. Much of drug discovery today is predicated on the concept of selective targeting of particular bioactive macromols. by low-mol.-mass drugs. The binding of drugs to their macromol. targets is therefore seen as paramount for pharmacol. activity. In vitro assessment of drug-target interactions is classically quantified in terms of binding parameters such as IC50 or Kd. This article presents an alternative perspective on drug optimization in terms of drug-target binary complex residence time, as quantified by the dissociative half-life of the drug-target binary complex. We describe the potential advantages of long residence time in terms of duration of pharmacol. effect and target selectivity.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XptVCltro%253D&md5=60ede2301584b10ac4e8fa18e1e6d107
  98. 98
    Bernetti, M.; Masetti, M.; Rocchia, W.; Cavalli, A. Kinetics of Drug Binding and Residence Time. Annu. Rev. Phys. Chem. 2019, 70, 143– 171,  DOI: 10.1146/annurev-physchem-042018-052340
    Google Scholar
    98
    Kinetics of Drug Binding and Residence Time
    Bernetti, Mattia; Masetti, Matteo; Rocchia, Walter; Cavalli, Andrea
    Annual Review of Physical Chemistry (2019), 70 (), 143-171CODEN: ARPLAP; ISSN:0066-426X. (Annual Reviews)
    The kinetics of drug binding and unbinding is assuming an increasingly crucial role in the long, costly process of bringing a new medicine to patients. For example, the time a drug spends in contact with its biol. target is known as residence time (the inverse of the kinetic const. of the drug-target unbinding, 1/koff). Recent reports suggest that residence time could predict drug efficacy in vivo, perhaps even more effectively than conventional thermodn. parameters (free energy, enthalpy, entropy). There are many exptl. and computational methods for predicting drug-target residence time at an early stage of drug discovery programs. Here, we review and discuss the methodol. approaches to estg. drug binding kinetics and residence time. We first introduce the theor. background of drug binding kinetics from a physicochem. standpoint. We then analyze the recent literature in the field, starting from the exptl. methodologies and applications thereof and moving to theor. and computational approaches to the kinetics of drug binding and unbinding. We acknowledge the central role of mol. dynamics and related methods, which comprise a great no. of the computational methods and applications reviewed here. However, we also consider kinetic Monte Carlo. We conclude with the outlook that drug (un)binding kinetics may soon become a go/no go step in the discovery and development of new medicines.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXjsFSgsro%253D&md5=6016da9b20e539f43e627432018ae51b
  99. 99
    Ren, T.; Zhu, X.; Jusko, N. M.; Krzyzanski, W.; Jusko, W. J. Pharmacodynamic Model of Slow Reversible Binding and Its Applications in Pharmacokinetic/Pharmacodynamic Modeling: Review and Tutorial. J. Pharmacokinet. Pharmacodyn. 2022, 49 (5), 493– 510,  DOI: 10.1007/s10928-022-09822-y
    Google Scholar
    There is no corresponding record for this reference.
  100. 100
    Frühauf, A.; Wolff, B.; Schweipert, M.; Meyer-Almes, F.-J. Synthesis and Characterization of Reversible Covalent HDAC4 Inhibitors. Methods Mol. Biol. Clifton NJ. 2023, 2589, 207– 221,  DOI: 10.1007/978-1-0716-2788-4_14
    Google Scholar
    There is no corresponding record for this reference.
  101. 101
    Forman, H. J.; Zhang, H.; Rinna, A. Glutathione: Overview of Its Protective Roles, Measurement, and Biosynthesis. Mol. Aspects Med. 2009, 30 (1–2), 1– 12,  DOI: 10.1016/j.mam.2008.08.006
    Google Scholar
    101
    Glutathione: Overview of its protective roles, measurement, and biosynthesis
    Forman, Henry Jay; Zhang, Hongqiao; Rinna, Alessandra
    Molecular Aspects of Medicine (2009), 30 (1-2), 1-12CODEN: MAMED5; ISSN:0098-2997. (Elsevier B.V.)
    This review is the introduction to a special issue concerning, glutathione (GSH), the most abundant low mol. wt. thiol compd. synthesized in cells. GSH plays crit. roles in protecting cells from oxidative damage and the toxicity of xenobiotic electrophiles, and maintaining redox homeostasis. Here, the functions and GSH and the sources of oxidants and electrophiles, the elimination of oxidants by redn. and electrophiles by conjugation with GSH are briefly described. Methods of assessing GSH status in the cells are also described. GSH synthesis and its regulation are addressed along with therapeutic approaches for manipulating GSH content that have been proposed. The purpose here is to provide a brief overview of some of the important aspects of glutathione metab. as part of this special issue that will provide a more comprehensive review of the state of knowledge regarding this essential mol.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXltFelurY%253D&md5=c1b1aa2b03389bf1434af0762df78fe1
  102. 102
    Wu, G.; Fang, Y.-Z.; Yang, S.; Lupton, J. R.; Turner, N. D. Glutathione Metabolism and Its Implications for Health. J. Nutr. 2004, 134 (3), 489– 492,  DOI: 10.1093/jn/134.3.489
    Google Scholar
    102
    Glutathione metabolism and its implications for health
    Wu, Guoyao; Fang, Yun-Zhong; Yang, Sheng; Lupton, Joanne R.; Turner, Nancy D.
    Journal of Nutrition (2004), 134 (3), 489-492CODEN: JONUAI; ISSN:0022-3166. (American Society for Nutritional Sciences)
    A review. Glutathione (γ-glutamyl-cysteinyl-glycine; GSH) is the most abundant low-mol.-wt. thiol, and GSH/glutathione disulfide is the major redox couple in animal cells. The synthesis of GSH from glutamate, cysteine, and glycine is catalyzed sequentially by two cytosolic enzymes, γ-glutamylcysteine synthetase and GSH synthetase. Compelling evidence shows that GSH synthesis is regulated primarily by γ-glutamylcysteine synthetase activity, cysteine availability, and GSH feedback inhibition. Animal and human studies demonstrate that adequate protein nutrition is crucial for the maintenance of GSH homeostasis. In addn., enteral or parenteral cystine, methionine, N-acetyl-cysteine, and L-2-oxothiazolidine-4-carboxylate are effective precursors of cysteine for tissue GSH synthesis. Glutathione plays important roles in antioxidant defense, nutrient metab., and regulation of cellular events (including gene expression, DNA and protein synthesis, cell proliferation and apoptosis, signal transduction, cytokine prodn. and immune response, and protein glutathionylation). Glutathione deficiency contributes to oxidative stress, which plays a key role in aging and the pathogenesis of many diseases (including kwashiorkor, seizure, Alzheimer's disease, Parkinson's disease, liver disease, cystic fibrosis, sickle cell anemia, HIV, AIDS, cancer, heart attack, stroke, and diabetes). New knowledge of the nutritional regulation of GSH metab. is crit. for the development of effective strategies to improve health and to treat these diseases.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXitlCrurc%253D&md5=98f0af4f642d488fbfa0b4f43632512c
  103. 103
    Bansal, A.; Simon, M. C. Glutathione Metabolism in Cancer Progression and Treatment Resistance. J. Cell Biol. 2018, 217 (7), 2291– 2298,  DOI: 10.1083/jcb.201804161
    Google Scholar
    103
    Glutathione metabolism in cancer progression and treatment resistance
    Bansal, Ankita; Simon, M. Celeste
    Journal of Cell Biology (2018), 217 (7), 2291-2298CODEN: JCLBA3; ISSN:1540-8140. (Rockefeller University Press)
    Glutathione (GSH) is the most abundant antioxidant found in living organisms and has multiple functions, most of which maintain cellular redox homeostasis. GSH preserves sufficient levels of cysteine and detoxifies xenobiotics while also conferring therapeutic resistance to cancer cells. However, GSH metab. plays both beneficial and pathogenic roles in a variety of malignancies. It is crucial to the removal and detoxification of carcinogens, and alterations in this pathway can have a profound effect on cell survival. Excess GSH promotes tumor progression, where elevated levels correlate with increased metastasis. In this review, we discuss recent studies that focus on deciphering the role of GSH in tumor initiation and progression as well as mechanisms underlying how GSH imparts treatment resistance to growing cancers. Targeting GSH synthesis/utilization therefore represents a potential means of rendering tumor cells more susceptible to different treatment options such as chemotherapy and radiotherapy.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhvFGntb3N&md5=2d071bd5b51fa8628dd56a2ee683931d
  104. 104
    Bajic, V. P.; Van Neste, C.; Obradovic, M.; Zafirovic, S.; Radak, D.; Bajic, V. B.; Essack, M.; Isenovic, E. R. Glutathione “Redox Homeostasis” and Its Relation to Cardiovascular Disease. Oxid. Med. Cell. Longev. 2019, 2019, 5028181,  DOI: 10.1155/2019/5028181
    Google Scholar
    There is no corresponding record for this reference.
  105. 105
    Fu, L.; Li, Z.; Liu, K.; Tian, C.; He, J.; He, J.; He, F.; Xu, P.; Yang, J. A Quantitative Thiol Reactivity Profiling Platform to Analyze Redox and Electrophile Reactive Cysteine Proteomes. Nat. Protoc. 2020, 15 (9), 2891– 2919,  DOI: 10.1038/s41596-020-0352-2
    Google Scholar
    105
    A quantitative thiol reactivity profiling platform to analyze redox and electrophile reactive cysteine proteomes
    Fu, Ling; Li, Zongmin; Liu, Keke; Tian, Caiping; He, Jixiang; He, Jingyang; He, Fuchu; Xu, Ping; Yang, Jing
    Nature Protocols (2020), 15 (9), 2891-2919CODEN: NPARDW; ISSN:1750-2799. (Nature Research)
    Cysteine is unique among all protein-coding amino acids, owing to its intrinsically high nucleophilicity. The cysteinyl thiol group can be covalently modified by a broad range of redox mechanisms or by various electrophiles derived from exogenous or endogenous sources. Measuring the response of protein cysteines to redox perturbation or electrophiles is crit. for understanding the underlying mechanisms involved. Activity-based protein profiling based on thiol-reactive probes has been the method of choice for such analyses. We therefore adapted this approach and developed a new chemoproteomic platform, termed 'QTRP' (quant. thiol reactivity profiling), that relies on the ability of a com. available thiol-reactive probe IPM (2-iodo-N-(prop-2-yn-1-yl)acetamide) to covalently label, enrich and quantify the reactive cysteinome in cells and tissues. Here, we provide a detailed and updated workflow of QTRP that includes procedures for (i) labeling of the reactive cysteinome from cell or tissue samples (e.g., control vs. treatment) with IPM, (ii) processing the protein samples into tryptic peptides and tagging the probe-modified peptides with isotopically labeled azido-biotin reagents contg. a photo-cleavable linker via click chem. reaction, (iii) capturing biotin-conjugated peptides with streptavidin beads, (iv) identifying and quantifying the photo-released peptides by mass spectrometry (MS)-based shotgun proteomics and (v) interpreting MS data by a streamlined informatic pipeline using a proteomics software, pFind 3, and an automatic post-processing algorithm. We also exemplified here how to use QTRP for mining H2O2-sensitive cysteines and for detg. the intrinsic reactivity of cysteines in a complex proteome. We anticipate that this protocol should find broad applications in redox biol., chem. biol. and the pharmaceutical industry. The protocol for sample prepn. takes 3 d, whereas MS measurements and data analyses require 75 min and <30 min, resp., per sample.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsVWgt7bJ&md5=aebfe7aa84c68df1202c7f984b2672be
  106. 106
    Kuljanin, M.; Mitchell, D. C.; Schweppe, D. K.; Gikandi, A. S.; Nusinow, D. P.; Bulloch, N. J.; Vinogradova, E. V.; Wilson, D. L.; Kool, E. T.; Mancias, J. D.; Cravatt, B. F.; Gygi, S. P. Reimagining High-Throughput Profiling of Reactive Cysteines for Cell-Based Screening of Large Electrophile Libraries. Nat. Biotechnol. 2021, 39 (5), 630– 641,  DOI: 10.1038/s41587-020-00778-3
    Google Scholar
    106
    Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries
    Kuljanin, Miljan; Mitchell, Dylan C.; Schweppe, Devin K.; Gikandi, Ajami S.; Nusinow, David P.; Bulloch, Nathan J.; Vinogradova, Ekaterina V.; Wilson, David L.; Kool, Eric T.; Mancias, Joseph D.; Cravatt, Benjamin F.; Gygi, Steven P.
    Nature Biotechnology (2021), 39 (5), 630-641CODEN: NABIF9; ISSN:1087-0156. (Nature Portfolio)
    Current methods used for measuring amino acid side-chain reactivity lack the throughput needed to screen large chem. libraries for interactions across the proteome. Here we redesigned the work flow for activity-based protein profiling of reactive cysteine residues by using a smaller desthiobiotin-based probe, sample multiplexing, reduced protein starting amts. and software to boost data acquisition in real time on the mass spectrometer. Our method, streamlined cysteine activity-based protein profiling (SLC-ABPP), achieved a 42-fold improvement in sample throughput, corresponding to profiling library members at a depth of >8,000 reactive cysteine sites at 18 min per compd. We applied it to identify proteome-wide targets of covalent inhibitors to mutant Kirsten rat sarcoma (KRAS)G12C and Bruton's tyrosine kinase (BTK). In addn., we created a resource of cysteine reactivity to 285 electrophiles in three human cell lines, which includes >20,000 cysteines from >6,000 proteins per line. The goal of proteome-wide profiling of cysteine reactivity across thousand-member libraries under several cellular contexts is now within reach.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXkslSrug%253D%253D&md5=d256bc7ff87c75e4929fe4a6649242b4
  107. 107
    Yamamoto, M.; Kensler, T. W.; Motohashi, H. The KEAP1-NRF2 System: A Thiol-Based Sensor-Effector Apparatus for Maintaining Redox Homeostasis. Physiol. Rev. 2018, 98 (3), 1169– 1203,  DOI: 10.1152/physrev.00023.2017
    Google Scholar
    107
    The KEAP1-NRF2 system: a thiol-based sensor-effector apparatus for maintaining redox homeostasis
    Yamamoto, Masayuki; Kensler, Thomas W.; Motohashi, Hozumi
    Physiological Reviews (2018), 98 (3), 1169-1203CODEN: PHREA7; ISSN:1522-1210. (American Physiological Society)
    A review. The Kelch-like ECH-assocd. protein 1-NF-E2-related factor 2 (KEAP1-NRF2) system forms the major node of cellular and organismal defense against oxidative and electrophilic stresses of both exogenous and endogenous origins. KEAP1 acts as a cysteine thiol-rich sensor of redox insults, whereas NRF2 is a transcription factor that robustly transduces chem. signals to regulate a battery of cytoprotective genes. KEAP1 represses NRF2 activity under quiescent conditions, whereas NRF2 is liberated from KEAP1-mediated repression on exposure to stresses. The rapid inducibility of a response based on a derepression mechanism is an important feature of the KEAP1-NRF2 system. Recent studies have unveiled the complexities of the functional contributions of the KEAP1-NRF2 system and defined its broader involvement in biol. processes, including cell proliferation and differentiation, as well as cytoprotection. In this review, we describe historical milestones in the initial characterization of the KEAP1-NRF2 system and provide a comprehensive overview of the mol. mechanisms governing the functions of KEAP1 and NRF2, as well as their roles in physiol. and pathol. We also refer to the clin. significance of the KEAP1-NRF2 system as an important prophylactic and therapeutic target for various diseases, particularly aging-related disorders. We believe that controlled harnessing of the KEAP1-NRF2 system is a key to healthy aging and well-being in humans.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXkvFektrc%253D&md5=906947c8ad97c48f60e46bc44103664a
  108. 108
    Unoki, T.; Akiyama, M.; Kumagai, Y. Nrf2 Activation and Its Coordination with the Protective Defense Systems in Response to Electrophilic Stress. Int. J. Mol. Sci. 2020, 21 (2), 545,  DOI: 10.3390/ijms21020545
    Google Scholar
    There is no corresponding record for this reference.
  109. 109
    Backus, K. M.; Cao, J.; Maddox, S. M. Opportunities and Challenges for the Development of Covalent Chemical Immunomodulators. Bioorg. Med. Chem. 2019, 27 (15), 3421– 3439,  DOI: 10.1016/j.bmc.2019.05.050
    Google Scholar
    109
    Opportunities and challenges for the development of covalent chemical immunomodulators
    Backus, Keriann M.; Cao, Jian; Maddox, Sean M.
    Bioorganic & Medicinal Chemistry (2019), 27 (15), 3421-3439CODEN: BMECEP; ISSN:0968-0896. (Elsevier B.V.)
    A review. Compds. that react irreversibly with cysteines have reemerged as potent and selective tools for altering protein function, serving as chem. probes and even clin. approved drugs. The exquisite sensitivity of human immune cell signaling pathways to oxidative stress indicates the likely, yet still underexploited, general utility of covalent probes for selective chem. immunomodulation. Here, we provide an overview of immunomodulatory cysteines, including identification of electrophilic compds. available to label these residues. We focus our discussion on three protein classes essential for cell signaling, which span the 'druggability' spectrum from amenable to chem. probes (kinases), somewhat druggable (proteases), to inaccessible (phosphatases). Using existing inhibitors as a guide, we identify general strategies to guide the development of covalent probes for selected undruggable classes of proteins and propose the application of such compds. to alter immune cell functions.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtFOku73L&md5=fbec9cd36ed1c0f3e9dbacf4d613730b
  110. 110
    Lincoln, R.; Zhang, W.; Lovell, T. C.; Jodko-Piórecka, K.; Devlaminck, P. A.; Sakaya, A.; Van Kessel, A.; Cosa, G. Chemically Tuned, Reversible Fluorogenic Electrophile for Live Cell Nanoscopy. ACS Sens. 2022, 7 (1), 166– 174,  DOI: 10.1021/acssensors.1c01940
    Google Scholar
    There is no corresponding record for this reference.
  111. 111
    Zheng, S.; Liu, G. Polymeric Emissive Materials Based on Dynamic Covalent Bonds. Mol. Basel Switz. 2022, 27 (19), 6635,  DOI: 10.3390/molecules27196635
    Google Scholar
    There is no corresponding record for this reference.

Cited By

Click to copy section linkSection link copied!

This article has not yet been cited by other publications.

Download PDF
Open PDF
Go to ACS Chemical Biology
Get e-Alerts
Get e-Alerts

ACS Chemical Biology

Cite this: ACS Chem. Biol. 2024, 19, 4, 824–838
Click to copy citationCitation copied!
https://doi.org/10.1021/acschembio.3c00805
Published April 3, 2024

Copyright © 2024 The Authors. Published by American Chemical Society. This publication is licensed under

CC-BY-NC-ND 4.0 .

Article Views

5985

Altmetric

-

Citations

-
Learn about these metrics

Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.

  • Abstract

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 1

    Figure 1. Structures of Penicillin G, 3-nitropropionate, itaconate, and wortmannin are examples of natural product covalent inhibitors with their covalent adducts.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 2

    Figure 2. Schematic of NCI, ICI, and RCI inhibition with descriptions of the equilibrium or inactivation constants (Mons et al.). Adapted from ref (15). Available under a CC-BY 4.0 license. Copyright 2024 Elma Mons, Sander Roet, Robbert Q. Kim, Monique P. C. Mulder.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 3

    Figure 3. Inhibitor is in equilibrium with many enzymes, including the target enzyme. Since the inhibitor–target complex is greatly favored, this will shift the equilibria of the off-target interactions away from the off-target complexes with the inhibitor as described by Le Chatalier’s principle. Over time, the inhibitor–target complex will be the predominant site of the RCI.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 4

    Figure 4. The observed equilibrium of a covalent inhibitor is the product of the binding equilibrium constant and the reaction equilibrium constant.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 5

    Figure 5. Nucleophilic residues reacting with electrophilic warheads in equilibrium with their covalent-adduct products, with the electrophilic warheads highlighted in red.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 6

    Figure 6. Examples of reversible covalent inhibitors with their electrophilic warheads are highlighted in red.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 7

    Figure 7. Examples of JAK3 inhibitors with covalent warheads are highlighted in red.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 8

    Figure 8. Clinically approved irreversible covalent inhibitors for BTK: ibrutinib, Zanubrutinib, acalabrutinib, and tirabrutinib, and a reversible covalent inhibitor for BTK in clinical trials: rilzabrutinib. The covalent warhead is highlighted in red.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 9

    Figure 9. Compound optimization for the EV71 cPro enzyme. The covalent warhead is highlighted in red.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 10

    Figure 10. Summarized activities for each parameter that are important in the design of a reversible covalent inhibitor.

    High Resolution Image
    Download MS PowerPoint Slide

  • References

    This article references 111 other publications.

    1. 1
      Fleming, A. On the Antibacterial Action of Cultures of a Penicillium, with Special Reference to Their Use in the Isolation of B. Influenzae. 1929. Bull. World Health Organ. 2001, 79 (8), 780– 790
      1
      On the antibacterial action of cultures of a penicillium, with special reference to their use in the isolation of B. influenzae. 1929
      Fleming A
      Bulletin of the World Health Organization (2001), 79 (8), 780-90 ISSN:0042-9686.
      There is no expanded citation for this reference.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BD3MvpslCisA%253D%253D&md5=3c01ee5f9da7a862f0bd23359d039371
    2. 2
      Duncan, D.; Auclair, K. Itaconate: An Antimicrobial Metabolite of Macrophages. Can. J. Chem. 2022, 100 (2), 104– 113,  DOI: 10.1139/cjc-2021-0117
      There is no corresponding record for this reference.
    3. 3
      Ray, S.; Kreitler, D. F.; Gulick, A. M.; Murkin, A. S. The Nitro Group as a Masked Electrophile in Covalent Enzyme Inhibition. ACS Chem. Biol. 2018, 13 (6), 1470– 1473,  DOI: 10.1021/acschembio.8b00225
      3
      The nitro group as a masked electrophile in covalent enzyme inhibition
      Ray, Sneha; Kreitler, Dale F.; Gulick, Andrew M.; Murkin, Andrew S.
      ACS Chemical Biology (2018), 13 (6), 1470-1473CODEN: ACBCCT; ISSN:1554-8929. (American Chemical Society)
      We report the unprecedented reaction between a nitroalkane and an active-site cysteine residue to yield a thiohydroximate adduct. Structural and kinetic evidence suggests the nitro group is activated by conversion to its nitronic acid tautomer within the active site. The nitro group, therefore, shows promise as a masked electrophile in the design of covalent inhibitors targeting binding pockets with appropriately placed cysteine and general acid residues.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXpsl2nsLc%253D&md5=d2dc8f255fd7e5f7537c57a0c5a3343e
    4. 4
      Yuan, H.; Barnes, K. R.; Weissleder, R.; Cantley, L.; Josephson, L. Covalent Reactions of Wortmannin under Physiological Conditions. Chem. Biol. 2007, 14 (3), 321– 328,  DOI: 10.1016/j.chembiol.2007.02.007
      There is no corresponding record for this reference.
    5. 5
      De Vita, E. 10 Years into the Resurgence of Covalent Drugs. Future Med. Chem. 2021, 13 (2), 193– 210,  DOI: 10.4155/fmc-2020-0236
      5
      10 years into the resurgence of covalent drugs
      De Vita Elena
      Future medicinal chemistry (2021), 13 (2), 193-210 ISSN:.
      In the first decade of targeted covalent inhibition, scientists have successfully reversed the previous trend that had impeded the use of covalent inhibition in drug development. Successes in the clinic, mainly in the field of kinase inhibitors, are existing proof that safe covalent inhibitors can be designed and employed to develop effective treatments. The case of KRASG12C covalent inhibitors entering clinical trials in 2019 has been among the hottest topics discussed in drug discovery, raising expectations for the future of the field. In this perspective, an overview of the milestones hit with targeted covalent inhibitors, as well as the promise and the needs of current research, are presented. While recent results have confirmed the potential that was foreseen, many questions remain unexplored in this branch of precision medicine.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BB3szjt1ertQ%253D%253D&md5=71ac37667e2f40fa3f6de36c07fea9ec
    6. 6
      Baillie, T. A. Drug-Protein Adducts: Past, Present, and Future. Med. Chem. Res. 2020, 29 (7), 1093– 1104,  DOI: 10.1007/s00044-020-02567-8
      There is no corresponding record for this reference.
    7. 7
      Potashman, M. H.; Duggan, M. E. Covalent Modifiers: An Orthogonal Approach to Drug Design. J. Med. Chem. 2009, 52 (5), 1231– 1246,  DOI: 10.1021/jm8008597
      7
      Covalent Modifiers: An Orthogonal Approach to Drug Design
      Potashman, Michele H.; Duggan, Mark E.
      Journal of Medicinal Chemistry (2009), 52 (5), 1231-1246CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      A review. In this article we review a variety of examples in which therapeutic targets are covalently bound by small-mol. drugs or by compds. in advanced clin. development. The covalent interactions can be either reversible or irreversible, depending on the reaction partners.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhs1Sltbw%253D&md5=f8380d5a1cdd8638ad2a1e0405d25267
    8. 8
      Boike, L.; Henning, N. J.; Nomura, D. K. Advances in Covalent Drug Discovery. Nat. Rev. Drug Discovery 2022, 21 (12), 881– 898,  DOI: 10.1038/s41573-022-00542-z
      8
      Advances in covalent drug discovery
      Boike, Lydia; Henning, Nathaniel J.; Nomura, Daniel K.
      Nature Reviews Drug Discovery (2022), 21 (12), 881-898CODEN: NRDDAG; ISSN:1474-1776. (Nature Portfolio)
      A review. Covalent drugs have been used to treat diseases for more than a century, but tools that facilitate the rational design of covalent drugs have emerged more recently. The purposeful addn. of reactive functional groups to existing ligands can enable potent and selective inhibition of target proteins, as demonstrated by the covalent epidermal growth factor receptor (EGFR) and Bruton's tyrosine kinase (BTK) inhibitors used to treat various cancers. Moreover, the identification of covalent ligands through 'electrophile-first' approaches has also led to the discovery of covalent drugs, such as covalent inhibitors for KRAS(G12C) and SARS-CoV-2 main protease. In particular, the discovery of KRAS(G12C) inhibitors validates the use of covalent screening technologies, which have become more powerful and widespread over the past decade. Chemoproteomics platforms have emerged to complement covalent ligand screening and assist in ligand discovery, selectivity profiling and target identification. This Review showcases covalent drug discovery milestones with emphasis on the lessons learned from these programs and how an evolving toolbox of covalent drug discovery techniques facilitates success in this field.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38Xit1Clt7nE&md5=b41441b3a7bc5f2e87bedf243fa43faa
    9. 9
      Kenakin, T. The Mass Action Equation in Pharmacology. Br. J. Clin. Pharmacol. 2016, 81 (1), 41– 51,  DOI: 10.1111/bcp.12810
      There is no corresponding record for this reference.
    10. 10
      Pottel, J.; Levit, A.; Korczynska, M.; Fischer, M.; Shoichet, B. K. The Recognition of Unrelated Ligands by Identical Proteins. ACS Chem. Biol. 2018, 13 (9), 2522– 2533,  DOI: 10.1021/acschembio.8b00443
      There is no corresponding record for this reference.
    11. 11
      Knockenhauer, K. E.; Copeland, R. A. The Importance of Binding Kinetics and Drug-Target Residence Time in Pharmacology. Br. J. Pharmacol. 2023, 1– 14,  DOI: 10.1111/bph.16104
      There is no corresponding record for this reference.
    12. 12
      Zhang, G.; Zhang, J.; Gao, Y.; Li, Y.; Li, Y. Strategies for Targeting Undruggable Targets. Expert Opin. Drug Discovery 2022, 17 (1), 55– 69,  DOI: 10.1080/17460441.2021.1969359
      12
      Strategies for targeting undruggable targets
      Zhang Gong; Zhang Juan; Gao Yuting; Li Yangfeng; Li Yizhou; Li Yizhou
      Expert opinion on drug discovery (2022), 17 (1), 55-69 ISSN:.
      INTRODUCTION: Undruggable targets refer to clinically meaningful therapeutic targets that are 'difficult to drug' or 'yet to be drugged' via traditional approaches. Featuring characteristics of lacking defined ligand-binding pockets, non-catalytic protein-protein interaction functional modes and less-investigated 3D structures, these undruggable targets have been targeted with novel therapeutic entities developed with the progress of unconventional drug discovery approaches, such as targeted degradation molecules and display technologies. AREA COVERED: This review first presents the concept of 'undruggable' exemplified by RAS and other targets. Next, detailed strategies are illustrated in two aspects: innovation of therapeutic entities and development of unconventional drug discovery technologies. Finally, case studies covering typical undruggable targets (Bcl-2, p53, and RAS) are depicted to further demonstrate the feasibility of the strategies and entities above. EXPERT OPINION: Targeting the undruggable expands the scope of therapeutically reachable targets. Consequently, it represents the drug discovery frontier. Biomedical studies are capable of dissecting disease mechanisms, thus broadening the list of undruggable targets. Encouraged by the recent approval of the KRAS inhibitor Sotorasib, we believe that merging multiple discovery approaches and exploiting various novel therapeutic entities would pave the way for dealing with more 'undruggable' targets in the future.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BB2crgvFelug%253D%253D&md5=20ebb3e7bd0c80af87802eea43a05dfa
    13. 13
      Akçay, G.; Belmonte, M. A.; Aquila, B.; Chuaqui, C.; Hird, A. W.; Lamb, M. L.; Rawlins, P. B.; Su, N.; Tentarelli, S.; Grimster, N. P.; Su, Q. Inhibition of Mcl-1 through Covalent Modification of a Noncatalytic Lysine Side Chain. Nat. Chem. Biol. 2016, 12 (11), 931– 936,  DOI: 10.1038/nchembio.2174
      13
      Inhibition of Mcl-1 through covalent modification of a noncatalytic lysine side chain
      Akcay, Gizem; Belmonte, Matthew A.; Aquila, Brian; Chuaqui, Claudio; Hird, Alexander W.; Lamb, Michelle L.; Rawlins, Philip B.; Su, Nancy; Tentarelli, Sharon; Grimster, Neil P.; Su, Qibin
      Nature Chemical Biology (2016), 12 (11), 931-936CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
      Targeted covalent inhibition of disease-assocd. proteins has become a powerful methodol. in the field of drug discovery, leading to the approval of new therapeutics. Nevertheless, current approaches are often limited owing to their reliance on a cysteine residue to generate the covalent linkage. Here the authors used aryl boronic acid carbonyl warheads to covalently target a noncatalytic lysine side chain, and generated to the knowledge the first reversible covalent inhibitors for Mcl-1, a protein-protein interaction (PPI) target that has proven difficult to inhibit via traditional medicinal chem. strategies. These covalent binders exhibited improved potency in comparison to noncovalent congeners, as demonstrated in biochem. and cell-based assays. The authors identified Lys234 as the residue involved in covalent modification, via point mutation. The covalent binders discovered in this study will serve as useful starting points for the development of Mcl-1 therapeutics and probes to interrogate Mcl-1-dependent biol. phenomena.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsVKqtb3P&md5=bda5720579a9b5e6027632d2cffba2e1
    14. 14
      Huang, L.; Guo, Z.; Wang, F.; Fu, L. KRAS Mutation: From Undruggable to Druggable in Cancer. Signal Transduct. Target. Ther. 2021, 6 (1), 386,  DOI: 10.1038/s41392-021-00780-4
      14
      KRAS mutation: from undruggable to druggable in cancer
      Huang Lamei; Guo Zhixing; Wang Fang; Fu Liwu
      Signal transduction and targeted therapy (2021), 6 (1), 386 ISSN:.
      Cancer is the leading cause of death worldwide, and its treatment and outcomes have been dramatically revolutionised by targeted therapies. As the most frequently mutated oncogene, Kirsten rat sarcoma viral oncogene homologue (KRAS) has attracted substantial attention. The understanding of KRAS is constantly being updated by numerous studies on KRAS in the initiation and progression of cancer diseases. However, KRAS has been deemed a challenging therapeutic target, even "undruggable", after drug-targeting efforts over the past four decades. Recently, there have been surprising advances in directly targeted drugs for KRAS, especially in KRAS (G12C) inhibitors, such as AMG510 (sotorasib) and MRTX849 (adagrasib), which have obtained encouraging results in clinical trials. Excitingly, AMG510 was the first drug-targeting KRAS (G12C) to be approved for clinical use this year. This review summarises the most recent understanding of fundamental aspects of KRAS, the relationship between the KRAS mutations and tumour immune evasion, and new progress in targeting KRAS, particularly KRAS (G12C). Moreover, the possible mechanisms of resistance to KRAS (G12C) inhibitors and possible combination therapies are summarised, with a view to providing the best regimen for individualised treatment with KRAS (G12C) inhibitors and achieving truly precise treatment.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BB2cfivFanug%253D%253D&md5=05a5959689e63910ecf752595d4407ff
    15. 15
      Mons, E.; Roet, S.; Kim, R. Q.; Mulder, M. P. C. A Comprehensive Guide for Assessing Covalent Inhibition in Enzymatic Assays Illustrated with Kinetic Simulations. Curr. Protoc. 2022, 2 (6), e419  DOI: 10.1002/cpz1.419
      15
      A Comprehensive Guide for Assessing Covalent Inhibition in Enzymatic Assays Illustrated with Kinetic Simulations
      Mons, Elma; Roet, Sander; Kim, Robbert Q.; Mulder, Monique P. C.
      Current Protocols (2022), 2 (6), e419CODEN: CPURDB; ISSN:2691-1299. (John Wiley & Sons, Inc.)
      Covalent inhibition has become more accepted in the past two decades, as illustrated by the clin. approval of several irreversible inhibitors designed to covalently modify their target. Elucidation of the structure-activity relationship and potency of such inhibitors requires a detailed kinetic evaluation. Here, we elucidate the relationship between the exptl. read-out and the underlying inhibitor binding kinetics. Interactive kinetic simulation scripts are employed to highlight the effects of in vitro enzyme activity assay conditions and inhibitor binding mode, thereby showcasing which assumptions and corrections are crucial. Four stepwise protocols to assess the biochem. potency of (ir)reversible covalent enzyme inhibitors targeting a nucleophilic active site residue are included, with accompanying data anal. tailored to the covalent binding mode. Together, this will serve as a guide to make an educated decision regarding the most suitable method to assess covalent inhibition potency.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XitF2ksrrF&md5=1ffa766bb1fc413a27c47d458a3f54e7
    16. 16
      Chatterjee, P.; Botello-Smith, W. M.; Zhang, H.; Qian, L.; Alsamarah, A.; Kent, D.; Lacroix, J. J.; Baudry, M.; Luo, Y. Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?. J. Am. Chem. Soc. 2017, 139 (49), 17945– 17952,  DOI: 10.1021/jacs.7b08938
      16
      Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?
      Chatterjee, Payal; Botello-Smith, Wesley M.; Zhang, Han; Qian, Li; Alsamarah, Abdelaziz; Kent, David; Lacroix, Jerome J.; Baudry, Michel; Luo, Yun
      Journal of the American Chemical Society (2017), 139 (49), 17945-17952CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Reversible covalent inhibitors have many clin. advantages over noncovalent or irreversible covalent drugs. However, apart from selecting a warhead, substantial efforts in design and synthesis are needed to optimize noncovalent interactions to improve target-selective binding. Computational prediction of binding affinity for reversible covalent inhibitors presents a unique challenge since the binding process consists of multiple steps, which are not necessarily independent of each other. In this study, the authors lay out the relation between relative binding free energy and the overall reversible covalent binding affinity using a two-state binding model. To prove the concept, the authors employed free energy perturbation (FEP) coupled with λ-exchange mol. dynamics method to calc. the binding free energy of a series of α-ketoamide analogs relative to a common warhead scaffold, in both noncovalent and covalent binding states, and for two highly homologous proteases, calpain-1 and calpain-2. The authors conclude that covalent binding state alone, in general, can be used to predict reversible covalent binding selectivity. However, exceptions may exist. Therefore, the authors also discuss the conditions under which the noncovalent binding step is no longer negligible and propose to combine the relative FEP calcns. with a single QM/MM calcn. of warhead to predict the binding affinity and binding kinetics. The FEP calcns. also revealed that covalent and noncovalent binding states of an inhibitor do not necessarily exhibit the same selectivity. Thus, investigating both binding states, as well as the kinetics will provide extremely useful information for optimizing reversible covalent inhibitors.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhslyrs7bI&md5=e6a38ff570134e956eb43bd4a874ca55
    17. 17
      De Cesco, S.; Kurian, J.; Dufresne, C.; Mittermaier, A. K.; Moitessier, N. Covalent Inhibitors Design and Discovery. Eur. J. Med. Chem. 2017, 138, 96– 114,  DOI: 10.1016/j.ejmech.2017.06.019
      17
      Covalent inhibitors design and discovery
      De Cesco, Stephane; Kurian, Jerry; Dufresne, Caroline; Mittermaier, Anthony K.; Moitessier, Nicolas
      European Journal of Medicinal Chemistry (2017), 138 (), 96-114CODEN: EJMCA5; ISSN:0223-5234. (Elsevier Masson SAS)
      In the history of therapeutics, covalent drugs occupy a very distinct category. While representing a significant fraction of the drugs on the market, very few have been deliberately designed to interact covalently with their biol. target. In this review, the prevalence of covalent drugs will first be briefly covered, followed by an introduction to their mechanisms of action and more detailed discussions of their discovery and the development of safe and efficient covalent enzyme inhibitors. All stages of a drug discovery program will be covered, from target considerations to lead optimization, strategies to tune reactivity and computational methods. The goal of this article is to provide an overview of the field and to outline good practices that are needed for the proper assessment and development of covalent inhibitors as well as a good understanding of the potential and limitations of current computational methods for the design of covalent drugs.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtVKhsLrI&md5=551c9a9c4bd69d4ad4d9156c315d5a94
    18. 18
      Plescia, J.; De Cesco, S.; Patrascu, M. B.; Kurian, J.; Di Trani, J.; Dufresne, C.; Wahba, A. S.; Janmamode, N.; Mittermaier, A. K.; Moitessier, N. Integrated Synthetic, Biophysical, and Computational Investigations of Covalent Inhibitors of Prolyl Oligopeptidase and Fibroblast Activation Protein α. J. Med. Chem. 2019, 62 (17), 7874– 7884,  DOI: 10.1021/acs.jmedchem.9b00642
      There is no corresponding record for this reference.
    19. 19
      Masuda, Y.; Yoshida, T.; Yamaotsu, N.; Hirono, S. Linear Discriminant Analysis for the in Silico Discovery of Mechanism-Based Reversible Covalent Inhibitors of a Serine Protease: Application of Hydration Thermodynamics Analysis and Semi-Empirical Molecular Orbital Calculation. Chem. Pharm. Bull. (Tokyo) 2018, 66 (4), 399– 409,  DOI: 10.1248/cpb.c17-00854
      There is no corresponding record for this reference.
    20. 20
      Awoonor-Williams, E.; Walsh, A. G.; Rowley, C. N. Modeling Covalent-Modifier Drugs. Biochim. Biophys. Acta Proteins Proteomics 2017, 1865 (11), 1664– 1675,  DOI: 10.1016/j.bbapap.2017.05.009
      20
      Modeling covalent-modifier drugs
      Awoonor-Williams, Ernest; Walsh, Andrew G.; Rowley, Christopher N.
      Biochimica et Biophysica Acta, Proteins and Proteomics (2017), 1865 (11_Part_B), 1664-1675CODEN: BBAPBW; ISSN:1570-9639. (Elsevier B.V.)
      A review. In this review, we present a summary of how computer modeling has been used in the development of covalent-modifier drugs. Covalent-modifier drugs bind by forming a chem. bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly. Computer modeling is widely used in drug discovery, but different computational methods must be used to model covalent modifiers because of the chem. bonds formed. Structural and bioinformatic anal. has identified sites of modification that could yield selectivity for a chosen target. Docking methods, which are used to rank binding poses of large sets of inhibitors, have been augmented to support the formation of protein-ligand bonds and are now capable of predicting the binding pose of covalent modifiers accurately. The pKa's of amino acids can be calcd. in order to assess their reactivity towards electrophiles. QM/MM methods have been used to model the reaction mechanisms of covalent modification. The continued development of these tools will allow computation to aid in the development of new covalent-modifier drugs. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXotVOrtbo%253D&md5=ac579900da99ea005d0d562b53a1bca2
    21. 21
      Scarpino, A.; Ferenczy, G. G.; Keserű, G. M. Binding Mode Prediction and Virtual Screening Applications by Covalent Docking. Methods Mol. Biol. Clifton NJ. 2021, 2266, 73– 88,  DOI: 10.1007/978-1-0716-1209-5_4
      There is no corresponding record for this reference.
    22. 22
      Faridoon; Ng, R.; Zhang, G.; Li, J. J. An Update on the Discovery and Development of Reversible Covalent Inhibitors. Med. Chem. Res. Int. J. Rapid Commun. Des. Mech. Action Biol. Act. Agents 2023, 32 (6), 1039– 1062,  DOI: 10.1007/s00044-023-03065-3
      22
      An update on the discovery and development of reversible covalent inhibitors
      Faridoon; Ng, Raymond; Zhang, Guiping; Li, Jie Jack
      Medicinal Chemistry Research (2023), 32 (6), 1039-1062CODEN: MCREEB; ISSN:1054-2523. (Springer)
      A review. Small mol. drugs that covalently bind irreversibly to their target proteins have several advantages over conventional reversible inhibitors. They include increased duration of action, less-frequent drug dosing, reduced pharmacokinetic sensitivity, and the potential to target intractable shallow binding sites. Despite these advantages, the key challenges of irreversible covalent drugs are their potential for off-target toxicities and immunogenicity risks. Incorporating reversibility into covalent drugs would lead to less off-target toxicity by forming reversible adducts with off-target proteins and thus reducing the risk of idiosyncratic toxicities caused by the permanent modification of proteins, which leads to higher levels of potential haptens. Herein, we systematically review electrophilic warheads employed during the development of reversible covalent drugs. We hope the structural insights of electrophilic warheads would provide helpful information to medicinal chemists and aid in designing covalent drugs with better on-target selectivity and improved safety.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXovFKlurc%253D&md5=2f6664586b401207cbe840a4d50cee32
    23. 23
      Martin, J. S.; MacKenzie, C. J.; Fletcher, D.; Gilbert, I. H. Characterising Covalent Warhead Reactivity. Bioorg. Med. Chem. 2019, 27 (10), 2066– 2074,  DOI: 10.1016/j.bmc.2019.04.002
      23
      Characterising covalent warhead reactivity
      Martin, James S.; MacKenzie, Claire J.; Fletcher, Daniel; Gilbert, Ian H.
      Bioorganic & Medicinal Chemistry (2019), 27 (10), 2066-2074CODEN: BMECEP; ISSN:0968-0896. (Elsevier B.V.)
      Many drugs currently used are covalent inhibitors and irreversibly inhibit their targets. Most of these were discovered through serendipity. Covalent inhibitions can have many advantages from a pharmacokinetic perspective. However, until recently most organizations have shied away from covalent compd. design due to fears of non-specific inhibition of off-target proteins leading to toxicity risks. However, there has been a renewed interest in covalent modifiers as potential drugs, as it possible to get highly selective compds. It is therefore important to know how reactive a warhead is and to be able to select the least reactive warhead possible to avoid toxicity. A robust NMR based assay was developed and used to measure the reactivity of a variety of covalent warheads against serine and cysteine - the two most common targets for covalent drugs. A selection of these warheads also had their reactivity measured against threonine, tyrosine, lysine, histidine and arginine to better understand our ability to target non-traditional residues. The reactivity was also measured at various pHs to assess what effect the environment in the active site would have on these reactions. The reactivity of a covalent modifier was found to be very dependent on the amino acid residue.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXntVGgsbo%253D&md5=487334d8d0a8b03d0a25d6d87c1b4329
    24. 24
      Péczka, N.; Orgován, Z.; Ábrányi-Balogh, P.; Keserű, G. M. Electrophilic Warheads in Covalent Drug Discovery: An Overview. Expert Opin. Drug Discovery 2022, 17 (4), 413– 422,  DOI: 10.1080/17460441.2022.2034783
      There is no corresponding record for this reference.
    25. 25
      Jackson, P. A.; Widen, J. C.; Harki, D. A.; Brummond, K. M. Covalent Modifiers: A Chemical Perspective on the Reactivity of α,β-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions. J. Med. Chem. 2017, 60 (3), 839– 885,  DOI: 10.1021/acs.jmedchem.6b00788
      25
      Covalent Modifiers: A Chemical Perspective on the Reactivity of α,β-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions
      Jackson, Paul A.; Widen, John C.; Harki, Daniel A.; Brummond, Kay M.
      Journal of Medicinal Chemistry (2017), 60 (3), 839-885CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      A review. Although Michael acceptors display a potent and broad spectrum of bioactivity, they have largely been ignored in drug discovery because of their presumed indiscriminate reactivity. As such, a dearth of information exists relevant to the thiol reactivity of natural products and their analogs possessing this moiety. In the midst of recently approved acrylamide-contg. drugs, it is clear that a good understanding of the hetero-Michael addn. reaction and the relative reactivities of biol. thiols with Michael acceptors under physiol. conditions is needed for the design and use of these compds. as biol. tools and potential therapeutics. This Perspective provides information that will contribute to this understanding, such as kinetics of thiol addn. reactions, bioactivities, as well as steric and electronic factors that influence the electrophilicity and reversibility of Michael acceptors. This Perspective is focused on α,β-unsatd. carbonyls given their preponderance in bioactive natural products.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitV2rtbnM&md5=36d3be5bf688c4e4a8cf4bcf42073009
    26. 26
      Watt, S. K. I.; Charlebois, J. G.; Rowley, C. N.; Keillor, J. W. A Mechanistic Study of Thiol Addition to N-Phenylacrylamide. Org. Biomol. Chem. 2022, 20 (45), 8898– 8906,  DOI: 10.1039/D2OB01369J
      There is no corresponding record for this reference.
    27. 27
      Watt, S. K. I.; Charlebois, J. G.; Rowley, C. N.; Keillor, J. W. A Mechanistic Study of Thiol Addition to N-Acryloylpiperidine. Org. Biomol. Chem. 2023, 21 (10), 2204– 2212,  DOI: 10.1039/D2OB02223K
      There is no corresponding record for this reference.
    28. 28
      Lohman, D. C.; Edwards, D. R.; Wolfenden, R. Catalysis by Desolvation: The Catalytic Prowess of SAM-Dependent Halide-Alkylating Enzymes. J. Am. Chem. Soc. 2013, 135 (39), 14473– 14475,  DOI: 10.1021/ja406381b
      28
      Catalysis by desolvation: The catalytic prowess of SAM-dependent halide-alkylating enzymes
      Lohman, Danielle C.; Edwards, David R.; Wolfenden, Richard
      Journal of the American Chemical Society (2013), 135 (39), 14473-14475CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      In the biol. fixation of halide ions, several enzymes have been found to catalyze alkyl transfer from S-adenosylmethionine (SAM) to halide ions. It proved possible to measure the rates of reaction of the trimethylsulfonium ion with I-, Br-, Cl-, F-, HO-, and H2O in water at elevated temps. Comparison of the resulting 2nd-order rate consts., extrapolated to 25°, with values of kcat/Km reported for fluorinase and chlorinase indicated that these enzymes enhanced the rates of alkyl halide formation by factors of 2 × 1015- and 1 × 1017-fold, resp. These rate enhancements, achieved without the assistance of cofactors, metal ions, or general acid-base catalysis, were the largest that have been reported for an enzyme that acts on 2 substrates.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsVGjtLzN&md5=f7d0c69687c776310dda4facf967db64
    29. 29
      Parvez, S.; Long, M. J. C.; Poganik, J. R.; Aye, Y. Redox Signaling by Reactive Electrophiles and Oxidants. Chem. Rev. 2018, 118 (18), 8798– 8888,  DOI: 10.1021/acs.chemrev.7b00698
      29
      Redox Signaling by Reactive Electrophiles and Oxidants
      Parvez, Saba; Long, Marcus J. C.; Poganik, Jesse R.; Aye, Yimon
      Chemical Reviews (Washington, DC, United States) (2018), 118 (18), 8798-8888CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
      A review. The concept of cell signaling in the context of non-enzyme-assisted protein modifications by reactive electrophilic and oxidative species, broadly known as redox signaling, is a uniquely complex topic that has been approached from numerous different and multidisciplinary angles. The authors' review reflects on 5 aspects crit. for understanding how Nature harnesses these non-canonical post-translational modifications to coordinate distinct cellular activities: (1) specific players and their generation; (2) physicochem. properties; (3) mechanisms of action; (4) methods of interrogation; and (5) functional roles in health and disease. Emphasis is primarily placed on the latest progress in the field, but several aspects of classical work likely forgotten/lost are also recollected. For researchers with interests in getting into the field, this review is anticipated to function as a primer. For the expert, the aim is to stimulate thought and discussion about fundamentals of redox signaling mechanisms, and nuances of specificity/selectivity and timing in this sophisticated yet fascinating arena at the crossroads of chem. and biol.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsFyjurnI&md5=2cc16400a3dcab3bac28c25132595c7a
    30. 30
      Krishnan, S.; Miller, R. M.; Tian, B.; Mullins, R. D.; Jacobson, M. P.; Taunton, J. Design of Reversible, Cysteine-Targeted Michael Acceptors Guided by Kinetic and Computational Analysis. J. Am. Chem. Soc. 2014, 136 (36), 12624– 12630,  DOI: 10.1021/ja505194w
      30
      Design of Reversible, Cysteine-Targeted Michael Acceptors Guided by Kinetic and Computational Analysis
      Krishnan, Shyam; Miller, Rand M.; Tian, Boxue; Mullins, R. Dyche; Jacobson, Matthew P.; Taunton, Jack
      Journal of the American Chemical Society (2014), 136 (36), 12624-12630CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Electrophilic probes that covalently modify a cysteine thiol often show enhanced pharmacol. potency and selectivity. Although reversible Michael acceptors have been reported, the structural requirements for reversibility are poorly understood. Here, we report a novel class of acrylonitrile-based Michael acceptors, activated by aryl or heteroaryl electron-withdrawing groups. We demonstrate that thiol adducts of these acrylonitriles undergo β-elimination at rates that span more than 3 orders of magnitude. These rates correlate inversely with the computed proton affinity of the corresponding carbanions, enabling the intrinsic reversibility of the thiol-Michael reaction to be tuned in a predictable manner. We apply these principles to the design of new reversible covalent kinase inhibitors with improved properties. A cocrystal structure of one such inhibitor reveals specific noncovalent interactions between the 1,2,4-triazole activating group and the kinase. Our exptl. and computational study enables the design of new Michael acceptors, expanding the palette of reversible, cysteine-targeted electrophiles.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsVWrtbvK&md5=de052bac07c8920cb807c05f71f4f95d
    31. 31
      Ma, Y.; Li, L.; He, S.; Shang, C.; Sun, Y.; Liu, N.; Meek, T. D.; Wang, Y.; Shang, L. Application of Dually Activated Michael Acceptor to the Rational Design of Reversible Covalent Inhibitor for Enterovirus 71 3C Protease. J. Med. Chem. 2019, 62 (13), 6146– 6162,  DOI: 10.1021/acs.jmedchem.9b00387
      31
      Application of Dually Activated Michael Acceptor to the Rational Design of Reversible Covalent Inhibitor for Enterovirus 71 3C Protease
      Ma, Yuying; Li, Linfeng; He, Shuai; Shang, Chengyou; Sun, Yang; Liu, Ning; Meek, Thomas D.; Wang, Yaxin; Shang, Luqing
      Journal of Medicinal Chemistry (2019), 62 (13), 6146-6162CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      Targeted covalent inhibitors (TCIs) have attracted growing attention from the pharmaceutical industry in recent decades because they have potential advantages in terms of efficacy, selectivity, and safety. TCIs have recently evolved into a new version with reversibility that can be systematically modulated. This feature may diminish the risk of haptenization and help optimize the drug-target residence time as needed. The enteroviral 3C protease (3Cpro) is a valuable therapeutic target, but the development of 3Cpro inhibitors is far from satisfactory. Therefore, we aimed to apply a reversible TCI approach to the design of novel 3Cpro inhibitors. The introduction of various substituents onto the α-carbon of classical Michael acceptors yielded inhibitors bearing several classes of warheads. Using steady-state kinetics and biomol. mass spectrometry, we confirmed the mode of reversible covalent inhibition and elucidated the mechanism by which the potency and reversibility were affected by electronic and steric factors. This research produced several potent inhibitors with good selectivity and suitable reversibility; moreover, it validated the reversible TCI approach in the field of viral infection, suggesting broader applications in the design of reversible covalent inhibitors for other proteases.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtFGqsLjI&md5=2de757026f2542bff8092060a72107a5
    32. 32
      Bradshaw, J. M.; McFarland, J. M.; Paavilainen, V. O.; Bisconte, A.; Tam, D.; Phan, V. T.; Romanov, S.; Finkle, D.; Shu, J.; Patel, V.; Ton, T.; Li, X.; Loughhead, D. G.; Nunn, P. A.; Karr, D. E.; Gerritsen, M. E.; Funk, J. O.; Owens, T. D.; Verner, E.; Brameld, K. A.; Hill, R. J.; Goldstein, D. M.; Taunton, J. Prolonged and Tunable Residence Time Using Reversible Covalent Kinase Inhibitors. Nat. Chem. Biol. 2015, 11 (7), 525– 531,  DOI: 10.1038/nchembio.1817
      32
      Prolonged and tunable residence time using reversible covalent kinase inhibitors
      Bradshaw, J. Michael; McFarland, Jesse M.; Paavilainen, Ville O.; Bisconte, Angelina; Tam, Danny; Phan, Vernon T.; Romanov, Sergei; Finkle, David; Shu, Jin; Patel, Vaishali; Ton, Tony; Li, Xiaoyan; Loughhead, David G.; Nunn, Philip A.; Karr, Dane E.; Gerritsen, Mary E.; Funk, Jens Oliver; Owens, Timothy D.; Verner, Erik; Brameld, Ken A.; Hill, Ronald J.; Goldstein, David M.; Taunton, Jack
      Nature Chemical Biology (2015), 11 (7), 525-531CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
      Drugs with prolonged on-target residence times often show superior efficacy, yet general strategies for optimizing drug-target residence time are lacking. Here the authors made progress toward this elusive goal by targeting a noncatalytic cysteine in Bruton's tyrosine kinase (BTK) with reversible covalent inhibitors. Using an inverted orientation of the cysteine-reactive cyanoacrylamide electrophile, the authors identified potent and selective BTK inhibitors that demonstrated biochem. residence times spanning from minutes to 7 d. An inverted cyanoacrylamide with prolonged residence time in vivo remained bound to BTK for more than 18 h after clearance from the circulation. The inverted cyanoacrylamide strategy was further used to discover fibroblast growth factor receptor (FGFR) kinase inhibitors with residence times of several days, demonstrating the generalizability of the approach. Targeting of noncatalytic cysteines with inverted cyanoacrylamides may serve as a broadly applicable platform that facilitates 'residence time by design', the ability to modulate and improve the duration of target engagement in vivo.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFeju7%252FE&md5=85a73d9ecd62695d03166f7009c68dd8
    33. 33
      Zhou, J.; Stapleton, P.; Xavier-Junior, F. H.; Schatzlein, A.; Haider, S.; Healy, J.; Wells, G. Triazole-Substituted Phenylboronic Acids as Tunable Lead Inhibitors of KPC-2 Antibiotic Resistance. Eur. J. Med. Chem. 2022, 240, 114571,  DOI: 10.1016/j.ejmech.2022.114571
      There is no corresponding record for this reference.
    34. 34
      Ehmke, V.; Quinsaat, J. E. Q.; Rivera-Fuentes, P.; Heindl, C.; Freymond, C.; Rottmann, M.; Brun, R.; Schirmeister, T.; Diederich, F. Tuning and Predicting Biological Affinity: Aryl Nitriles as Cysteine Protease Inhibitors. Org. Biomol. Chem. 2012, 10 (30), 5764– 5768,  DOI: 10.1039/c2ob00034b
      34
      Tuning and predicting biological affinity: aryl nitriles as cysteine protease inhibitors
      Ehmke, Veronika; Quinsaat, Jose Enrico Q.; Rivera-Fuentes, Pablo; Heindl, Cornelia; Freymond, Celine; Rottmann, Matthias; Brun, Reto; Schirmeister, Tanja; Diederich, Francois
      Organic & Biomolecular Chemistry (2012), 10 (30), 5764-5768CODEN: OBCRAK; ISSN:1477-0520. (Royal Society of Chemistry)
      A series of aryl nitrile-based ligands were prepd. to investigate the effect of their electrophilicity on the affinity against the cysteine proteases rhodesain and human cathepsin L. D. functional theory calcns. provided relative reactivities of the nitriles, enabling prediction of their biol. affinity and cytotoxicity and a clear structure-activity relationship.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtVSlsr3J&md5=45858b629d24a54b72cd7e3b7ba15e5b
    35. 35
      Langrish, C. L.; Bradshaw, J. M.; Francesco, M. R.; Owens, T. D.; Xing, Y.; Shu, J.; LaStant, J.; Bisconte, A.; Outerbridge, C.; White, S. D.; Hill, R. J.; Brameld, K. A.; Goldstein, D. M.; Nunn, P. A. Preclinical Efficacy and Anti-Inflammatory Mechanisms of Action of the Bruton Tyrosine Kinase Inhibitor Rilzabrutinib for Immune-Mediated Disease. J. Immunol. Baltim. Md 1950 2021, 206 (7), 1454– 1468,  DOI: 10.4049/jimmunol.2001130
      There is no corresponding record for this reference.
    36. 36
      Jung, S.; Fuchs, N.; Johe, P.; Wagner, A.; Diehl, E.; Yuliani, T.; Zimmer, C.; Barthels, F.; Zimmermann, R. A.; Klein, P.; Waigel, W.; Meyr, J.; Opatz, T.; Tenzer, S.; Distler, U.; Räder, H.-J.; Kersten, C.; Engels, B.; Hellmich, U. A.; Klein, J.; Schirmeister, T. Fluorovinylsulfones and -Sulfonates as Potent Covalent Reversible Inhibitors of the Trypanosomal Cysteine Protease Rhodesain: Structure-Activity Relationship, Inhibition Mechanism, Metabolism, and In Vivo Studies. J. Med. Chem. 2021, 64 (16), 12322– 12358,  DOI: 10.1021/acs.jmedchem.1c01002
      36
      Fluorovinylsulfones and -Sulfonates as Potent Covalent Reversible Inhibitors of the Trypanosomal Cysteine Protease Rhodesain: Structure-Activity Relationship, Inhibition Mechanism, Metabolism, and In Vivo Studies
      Jung, Sascha; Fuchs, Natalie; Johe, Patrick; Wagner, Annika; Diehl, Erika; Yuliani, Tri; Zimmer, Collin; Barthels, Fabian; Zimmermann, Robert A.; Klein, Philipp; Waigel, Waldemar; Meyr, Jessica; Opatz, Till; Tenzer, Stefan; Distler, Ute; Raeder, Hans-Joachim; Kersten, Christian; Engels, Bernd; Hellmich, Ute A.; Klein, Jochen; Schirmeister, Tanja
      Journal of Medicinal Chemistry (2021), 64 (16), 12322-12358CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      Rhodesain is a major cysteine protease of Trypanosoma brucei rhodesiense, a pathogen causing Human African Trypanosomiasis, and a validated drug target. Recently, we reported the development of α-halovinylsulfones as a new class of covalent reversible cysteine protease inhibitors. Here, α-fluorovinylsulfones/-sulfonates were optimized for rhodesain based on mol. modeling approaches. I (X = F), the most potent and selective inhibitor in the series, shows a single-digit nanomolar affinity and high selectivity toward mammalian cathepsins B and L. Enzymic diln. assays and MS expts. indicate that I (X = F) is a slow-tight binder (Ki = 3 nM). Furthermore, the nonfluorinated I (X = H) shows favorable metab. and biodistribution by accumulation in mice brain tissue after i.p. and oral administration. The highest antitrypanosomal activity was obsd. for inhibitors with an N-terminal 2,3-dihydrobenzo[b][1,4]dioxine group and a 4-Me-Phe residue in P2 with nanomolar EC50 values (0.14/0.80μM). The different mechanisms of reversible and irreversible inhibitors were explained using QM/MM calcns. and MD simulations.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhslCitbvM&md5=322d56630ffe7e55bfd42ba0f8d62e97
    37. 37
      Feral, A.; Martin, A. R.; Desfoux, A.; Amblard, M.; Vezenkov, L. L. Covalent-Reversible Peptide-Based Protease Inhibitors. Design, Synthesis, and Clinical Success Stories. Amino Acids 2023, 55, 1775– 1800,  DOI: 10.1007/s00726-023-03286-1
      There is no corresponding record for this reference.
    38. 38
      Fairhurst, R. A.; Knoepfel, T.; Buschmann, N.; Leblanc, C.; Mah, R.; Todorov, M.; Nimsgern, P.; Ripoche, S.; Niklaus, M.; Warin, N.; Luu, V. H.; Madoerin, M.; Wirth, J.; Graus-Porta, D.; Weiss, A.; Kiffe, M.; Wartmann, M.; Kinyamu-Akunda, J.; Sterker, D.; Stamm, C.; Adler, F.; Buhles, A.; Schadt, H.; Couttet, P.; Blank, J.; Galuba, I.; Trappe, J.; Voshol, J.; Ostermann, N.; Zou, C.; Berghausen, J.; Del Rio Espinola, A.; Jahnke, W.; Furet, P. Discovery of Roblitinib (FGF401) as a Reversible-Covalent Inhibitor of the Kinase Activity of Fibroblast Growth Factor Receptor 4. J. Med. Chem. 2020, 63 (21), 12542– 12573,  DOI: 10.1021/acs.jmedchem.0c01019
      38
      Discovery of Roblitinib (FGF401) as a Reversible-Covalent Inhibitor of the Kinase Activity of Fibroblast Growth Factor Receptor 4
      Fairhurst, Robin A.; Knoepfel, Thomas; Buschmann, Nicole; Leblanc, Catherine; Mah, Robert; Todorov, Milen; Nimsgern, Pierre; Ripoche, Sebastien; Niklaus, Michel; Warin, Nicolas; Luu, Van Huy; Madoerin, Mario; Wirth, Jasmin; Graus-Porta, Diana; Weiss, Andreas; Kiffe, Michael; Wartmann, Markus; Kinyamu-Akunda, Jacqueline; Sterker, Dario; Stamm, Christelle; Adler, Flavia; Buhles, Alexandra; Schadt, Heiko; Couttet, Philippe; Blank, Jutta; Galuba, Inga; Trappe, Jorg; Voshol, Johannes; Ostermann, Nils; Zou, Chao; Berghausen, Jorg; Del Rio Espinola, Alberto; Jahnke, Wolfgang; Furet, Pascal
      Journal of Medicinal Chemistry (2020), 63 (21), 12542-12573CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      FGF19 signaling through the FGFR4/β-klotho receptor complex has been shown to be a key driver of growth and survival in a subset of hepatocellular carcinomas, making selective FGFR4 inhibition an attractive treatment opportunity. A kinome-wide sequence alignment highlighted a poorly conserved cysteine residue within the FGFR4 ATP-binding site at position 552, two positions beyond the gate-keeper residue. Several strategies for targeting this cysteine to identify FGFR4 selective inhibitor starting points are summarized which made use of both rational and unbiased screening approaches. The optimization of a 2-formylquinoline amide hit series is described in which the aldehyde makes a hemithioacetal reversible-covalent interaction with cysteine 552. Key challenges addressed during the optimization are improving the FGFR4 potency, metabolic stability, and soly. leading ultimately to the highly selective first-in-class clin. candidate roblitinib.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhvVeru77E&md5=94bfa1740e9cac34d0ceac67bc9181a7
    39. 39
      Shindo, N.; Fuchida, H.; Sato, M.; Watari, K.; Shibata, T.; Kuwata, K.; Miura, C.; Okamoto, K.; Hatsuyama, Y.; Tokunaga, K.; Sakamoto, S.; Morimoto, S.; Abe, Y.; Shiroishi, M.; Caaveiro, J. M. M.; Ueda, T.; Tamura, T.; Matsunaga, N.; Nakao, T.; Koyanagi, S.; Ohdo, S.; Yamaguchi, Y.; Hamachi, I.; Ono, M.; Ojida, A. Selective and Reversible Modification of Kinase Cysteines with Chlorofluoroacetamides. Nat. Chem. Biol. 2019, 15 (3), 250– 258,  DOI: 10.1038/s41589-018-0204-3
      39
      Selective and reversible modification of kinase cysteines with chlorofluoroacetamides
      Shindo, Naoya; Fuchida, Hirokazu; Sato, Mami; Watari, Kosuke; Shibata, Tomohiro; Kuwata, Keiko; Miura, Chizuru; Okamoto, Kei; Hatsuyama, Yuji; Tokunaga, Keisuke; Sakamoto, Seiichi; Morimoto, Satoshi; Abe, Yoshito; Shiroishi, Mitsunori; Caaveiro, Jose M. M.; Ueda, Tadashi; Tamura, Tomonori; Matsunaga, Naoya; Nakao, Takaharu; Koyanagi, Satoru; Ohdo, Shigehiro; Yamaguchi, Yasuchika; Hamachi, Itaru; Ono, Mayumi; Ojida, Akio
      Nature Chemical Biology (2019), 15 (3), 250-258CODEN: NCBABT; ISSN:1552-4450. (Nature Research)
      Irreversible inhibition of disease-assocd. proteins with small mols. is a powerful approach for achieving increased and sustained pharmacol. potency. Here, we introduce α-chlorofluoroacetamide (CFA) as a novel warhead of targeted covalent inhibitor (TCI). Despite weak intrinsic reactivity, CFA-appended quinazoline showed high reactivity toward Cys797 of epidermal growth factor receptor (EGFR). In cells, CFA-quinazoline showed higher target specificity for EGFR than the corresponding Michael acceptors in a wide concn. range (0.1-10 μM). The cysteine adduct of the CFA deriv. was susceptible to hydrolysis and reversibly yielded intact thiol but was stable in solvent-sequestered ATP-binding pocket of EGFR. This environment-dependent hydrolysis can potentially reduce off-target protein modification by CFA-based drugs. Oral administration of CFA quinazoline, (2R)-1-(2-chloro-2-fluoroacetyl)-N-[4-[(3-chloro-4-fluorophenyl)amino]-7-[3-(4-morpholinyl)-propoxy]quinazolin-6-yl]pyrrolidine-2-carboxamide [2226257-92-5] (NS-062, compd. 51) significantly suppressed tumor growth in a mouse xenograft model. Further, CFA-appended pyrazolopyrimidine irreversibly inhibited Bruton's tyrosine kinase with higher target specificity. These results demonstrate the utility of CFA as a new class warheads for TCI.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXlvFSgur4%253D&md5=f6c8886d540ea26a8abecd950feba913
    40. 40
      Tallon, A. M.; Xu, Y.; West, G. M.; Am Ende, C. W.; Fox, J. M. Thiomethyltetrazines Are Reversible Covalent Cysteine Warheads Whose Dynamic Behavior Can Be “Switched Off” via Bioorthogonal Chemistry Inside Live Cells. J. Am. Chem. Soc. 2023, 145 (29), 16069– 16080,  DOI: 10.1021/jacs.3c04444
      There is no corresponding record for this reference.
    41. 41
      Ingiliz, P.; Rockstroh, J. K. HIV-HCV Co-Infection Facing HCV Protease Inhibitor Licensing: Implications for Clinicians. Liver Int. Off. J. Int. Assoc. Study Liver 2012, 32 (8), 1194– 1199,  DOI: 10.1111/j.1478-3231.2012.02796.x
      There is no corresponding record for this reference.
    42. 42
      Teicher, B. A.; Tomaszewski, J. E. Proteasome Inhibitors. Biochem. Pharmacol. 2015, 96 (1), 1– 9,  DOI: 10.1016/j.bcp.2015.04.008
      There is no corresponding record for this reference.
    43. 43
      Metcalf, B.; Chuang, C.; Dufu, K.; Patel, M. P.; Silva-Garcia, A.; Johnson, C.; Lu, Q.; Partridge, J. R.; Patskovska, L.; Patskovsky, Y.; Almo, S. C.; Jacobson, M. P.; Hua, L.; Xu, Q.; Gwaltney, S. L.; Yee, C.; Harris, J.; Morgan, B. P.; James, J.; Xu, D.; Hutchaleelaha, A.; Paulvannan, K.; Oksenberg, D.; Li, Z. Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin. ACS Med. Chem. Lett. 2017, 8 (3), 321– 326,  DOI: 10.1021/acsmedchemlett.6b00491
      43
      Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin
      Metcalf, Brian; Chuang, Chihyuan; Dufu, Kobina; Patel, Mira P.; Silva-Garcia, Abel; Johnson, Carl; Lu, Qing; Partridge, James R.; Patskovska, Larysa; Patskovsky, Yury; Almo, Steven C.; Jacobson, Matthew P.; Hua, Lan; Xu, Qing; Gwaltney, Stephen L.; Yee, Calvin; Harris, Jason; Morgan, Bradley P.; James, Joyce; Xu, Donghong; Hutchaleelaha, Athiwat; Paulvannan, Kumar; Oksenberg, Donna; Li, Zhe
      ACS Medicinal Chemistry Letters (2017), 8 (3), 321-326CODEN: AMCLCT; ISSN:1948-5875. (American Chemical Society)
      The authors report the discovery of a new potent allosteric effector of sickle cell Hb, GBT440 I, that increases the affinity of Hb for oxygen and consequently inhibits its polymn. when subjected to hypoxic conditions. Unlike earlier allosteric activators that bind covalently to Hb in a 2:1 stoichiometry, I binds with a 1:1 stoichiometry. Compd. I is orally bioavailable and partitions highly and favorably into the red blood cell with a RBC/plasma ratio of ∼150. This partitioning onto the target protein is anticipated to allow therapeutic concns. to be achieved in the red blood cell at low plasma concns. I is in Phase 2 clin. trials for the treatment of sickle cell disease (NCT02285088).
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsFWqur0%253D&md5=63766931fdf731c68fd284cf86cc77d0
    44. 44
      Reja, R. M.; Wang, W.; Lyu, Y.; Haeffner, F.; Gao, J. Lysine-Targeting Reversible Covalent Inhibitors with Long Residence Time. J. Am. Chem. Soc. 2022, 144 (3), 1152– 1157,  DOI: 10.1021/jacs.1c12702
      44
      Lysine-Targeting Reversible Covalent Inhibitors with Long Residence Time
      Reja, Rahi M.; Wang, Wenjian; Lyu, Yuhan; Haeffner, Fredrik; Gao, Jianmin
      Journal of the American Chemical Society (2022), 144 (3), 1152-1157CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      We report a new reversible lysine conjugation that features a novel diazaborine product and much slowed dissocn. kinetics in comparison to the previously known iminoboronate chem. Incorporating the diazaborine-forming warhead RMR1 to a peptide ligand gives potent and long-acting reversible covalent inhibitors of the staphylococcal sortase. The efficacy of sortase inhibition is demonstrated via biochem. and cell-based assays. A comparative study of RMR1 and an iminoboronate-forming warhead highlights the significance and potential of modulating bond dissocn. kinetics in achieving long-acting reversible covalent inhibitors.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38Xht1egs7s%253D&md5=962dedfe735ef240b3430dfd74cdf5cb
    45. 45
      Serafimova, I. M.; Pufall, M. A.; Krishnan, S.; Duda, K.; Cohen, M. S.; Maglathlin, R. L.; McFarland, J. M.; Miller, R. M.; Frödin, M.; Taunton, J. Reversible Targeting of Noncatalytic Cysteines with Chemically Tuned Electrophiles. Nat. Chem. Biol. 2012, 8 (5), 471– 476,  DOI: 10.1038/nchembio.925
      45
      Reversible targeting of noncatalytic cysteines with chemically tuned electrophiles
      Serafimova, Iana M.; Pufall, Miles A.; Krishnan, Shyam; Duda, Katarzyna; Cohen, Michael S.; Maglathlin, Rebecca L.; McFarland, Jesse M.; Miller, Rand M.; Froedin, Morten; Taunton, Jack
      Nature Chemical Biology (2012), 8 (5), 471-476CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)
      Targeting noncatalytic cysteine residues with irreversible acrylamide-based inhibitors is a powerful approach for enhancing pharmacol. potency and selectivity. Nevertheless, concerns about off-target modification motivate the development of reversible cysteine-targeting strategies. Here we show that electron-deficient olefins, including acrylamides, can be tuned to react with cysteine thiols in a rapidly reversible manner. Installation of a nitrile group increased the olefins' intrinsic reactivity, but, paradoxically, eliminated the formation of irreversible adducts. Incorporation of these electrophiles into a noncovalent kinase-recognition scaffold produced slowly dissocg., covalent inhibitors of the p90 ribosomal protein S6 kinase RSK2. A cocrystal structure revealed specific noncovalent interactions that stabilize the complex by positioning the electrophilic carbon near the targeted cysteine. Disruption of these interactions by protein unfolding or proteolysis promoted instantaneous cleavage of the covalent bond. Our results establish a chem.-based framework for engineering sustained covalent inhibition without accumulating permanently modified proteins and peptides.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XkvVKitrw%253D&md5=6455a9a029714beb317286f71ac1326b
    46. 46
      Forster, M.; Chaikuad, A.; Bauer, S. M.; Holstein, J.; Robers, M. B.; Corona, C. R.; Gehringer, M.; Pfaffenrot, E.; Ghoreschi, K.; Knapp, S.; Laufer, S. A. Selective JAK3 Inhibitors with a Covalent Reversible Binding Mode Targeting a New Induced Fit Binding Pocket. Cell Chem. Biol. 2016, 23 (11), 1335– 1340,  DOI: 10.1016/j.chembiol.2016.10.008
      46
      Selective JAK3 Inhibitors with a Covalent Reversible Binding Mode Targeting a New Induced Fit Binding Pocket
      Forster, Michael; Chaikuad, Apirat; Bauer, Silke M.; Holstein, Julia; Robers, Matthew B.; Corona, Cesear R.; Gehringer, Matthias; Pfaffenrot, Ellen; Ghoreschi, Kamran; Knapp, Stefan; Laufer, Stefan A.
      Cell Chemical Biology (2016), 23 (11), 1335-1340CODEN: CCBEBM; ISSN:2451-9448. (Cell Press)
      Janus kinases (JAKs) are a family of cytoplasmatic tyrosine kinases that are attractive targets for the development of anti-inflammatory drugs given their roles in cytokine signaling. One question regarding JAKs and their inhibitors that remains under intensive debate is whether JAK inhibitors should be isoform selective. Since JAK3 functions are restricted to immune cells, an isoform-selective inhibitor for JAK3 could be esp. valuable to achieve clin. more useful and precise effects. However, the high degree of structural conservation makes isoform-selective targeting a challenging task. Here, we present picomolar inhibitors with unprecedented kinome-wide selectivity for JAK3. Selectivity was achieved by concurrent covalent reversible targeting of a JAK3-specific cysteine residue and a ligand-induced binding pocket. We confirmed that in vitro activity and selectivity translate well into the cellular environment and suggest that our inhibitors are powerful tools to elucidate JAK3-specific functions.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvVeqsLrJ&md5=348c5b5fbfa91fd02fa21d984620ea16
    47. 47
      Dietze, E. C.; Schäfer, A.; Omichinski, J. G.; Nelson, S. D. Inactivation of Glyceraldehyde-3-Phosphate Dehydrogenase by a Reactive Metabolite of Acetaminophen and Mass Spectral Characterization of an Arylated Active Site Peptide. Chem. Res. Toxicol. 1997, 10 (10), 1097– 1103,  DOI: 10.1021/tx970090u
      47
      Inactivation of glyceraldehyde-3-phosphate dehydrogenase by a reactive metabolite of acetaminophen and mass spectral characterization of an arylated active site peptide
      Dietze E C; Schafer A; Omichinski J G; Nelson S D
      Chemical research in toxicology (1997), 10 (10), 1097-103 ISSN:0893-228X.
      Acetaminophen (4'-hydroxyacetanilide, APAP) is a widely used analgesic and antipyretic drug that can cause hepatic necrosis under some circumstances via cytochrome P450-mediated oxidation to a reactive metabolite, N-acetyl-p-benzoquinone imine (NAPQI). Although the mechanism of hepatocellular injury caused by APAP is not fully understood, it is known that NAPQI forms covalent adducts with several hepatocellular proteins. Reported here is the identification of one of these proteins as glyceraldehyde-3-phosphate dehydrogenase [GAPDH, D-glyceraldehyde-3-phosphate: NAD+ oxidoreductase (phosphorylating), EC 1.2.1.12]. Two hours after the administration of hepatotoxic doses of [14C]APAP to mice, at a time prior to overt cell damage, hepatocellular GAPDH activity was significantly decreased concurrent with the formation of a 14C-labeled GAPDH adduct. A nonhepatotoxic regioisomer of APAP, 3'-hydroxyacetanilide (AMAP), was found to decrease GAPDH activity to a lesser extent than APAP, and radiolabel from [14C]AMAP bound to a lesser extent to GAPDH at a time when its overall binding to hepatocellular proteins was almost equivalent to that of APAP. In order to determine the nature of the covalent adduct between GAPDH and APAP, its major reactive and toxic metabolite, NAPQI, was incubated with purified porcine muscle GAPDH. Microsequencing analysis and fast atom bombardment mass spectrometry (FAB-MS) with collision-induced dissociation (CID) were used to characterize one of the adducts as APAP bound to the cysteinyl sulfhydryl group of Cys-149 in the active site peptide of GAPDH.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADyaK1c%252FgvFSgtQ%253D%253D&md5=9f71f1d99f6cdbc647091eacb12e6fee
    48. 48
      Rombach, E. M.; Hanzlik, R. P. Identification of a Rat Liver Microsomal Esterase as a Target Protein for Bromobenzene Metabolites. Chem. Res. Toxicol. 1998, 11 (3), 178– 184,  DOI: 10.1021/tx970076h
      48
      Identification of a Rat Liver Microsomal Esterase as a Target Protein for Bromobenzene Metabolites
      Rombach, Elizabeth M.; Hanzlik, Robert P.
      Chemical Research in Toxicology (1998), 11 (3), 178-184CODEN: CRTOEC; ISSN:0893-228X. (American Chemical Society)
      To identify proteins targeted by bromobenzene metabolites, we incubated [14C]bromobenzene in vitro with liver microsomes from phenobarbital-induced rats under conditions which typically led to covalent binding of 2-4 nmol equiv of bromobenzene/mg of protein. Microsomal proteins were solubilized with detergent, sepd. by chromatog. and electrophoresis, and analyzed for 14C by phosphorimaging of stained blots. Much of the radioactivity was assocd. with several bands of proteins of ∼50-60 kDa, plus another prominent band around 70 kDa, but labeling d. appeared to vary considerably overall. A major radiolabeled protein was purified by preparative electrophoresis and submitted to automated Edman microsequencing. Its N-terminal sequence was found to correspond to that of a known rat liver microsomal carboxylesterase (E.C. 3.1.1.1) previously identified as a target for reactive metabolites of halothane. The extent to which covalent modification of this protein by reactive metabolites contributes to the prodn. of hepatotoxic effects remains to be detd.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXhslarsLc%253D&md5=1367c196a23344bf587b9d346bc5e7d1
    49. 49
      Tailor, A.; Waddington, J. C.; Meng, X.; Park, B. K. Mass Spectrometric and Functional Aspects of Drug-Protein Conjugation. Chem. Res. Toxicol. 2016, 29 (12), 1912– 1935,  DOI: 10.1021/acs.chemrestox.6b00147
      49
      Mass Spectrometric and Functional Aspects of Drug-Protein Conjugation
      Tailor, Arun; Waddington, James C.; Meng, Xiaoli; Park, B. Kevin
      Chemical Research in Toxicology (2016), 29 (12), 1912-1935CODEN: CRTOEC; ISSN:0893-228X. (American Chemical Society)
      A review. The covalent binding of drugs (metabolites) to proteins to form drug-protein adducts can have an adverse effect on the body. These adducts are thought to be responsible for idiosyncratic drug reactions including severe drug hypersensitivity reactions. Major advances in proteomics technol. have allowed for the identification and quantification of target proteins for certain drugs. Human serum albumin (HSA) and Hb have been identified as accessible targets, and potential biomarkers for drug-protein adducts formation, for numerous drugs (metabolites) including β-lactam antibiotics, reactive drug metabolites such as quinone imines (acetaminophen) and acyl glucuronides (diclofenac), and covalent inhibitors (neratinib). For example, MS/MS anal. of plasma samples from patients taking flucloxacillin revealed that flucloxacillin and its 5-hydroxymethyl metabolite formed covalent adducts with lysine residues on albumin via opening of the β-lactam ring. Other proteins such as P 450 and keratin are also potential targets for covalent binding. However, for most drugs, the properties of these target proteins including their location, their quantity, the timing of conjugate generation, and their biol. function are not well understood. In this review, currently available proteomic technologies including MS/MS anal. to identify antigens, precise location of modifications, and the immunol. consequence of hapten-protein complex are illustrated. Moving forward, identification of the nature of the antigenic determinants that trigger immune responses to drug protein adducts will increase the authors' ability to predict idiosyncratic toxicity for a given compd.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsFymu7fI&md5=488bc6cacaf831918db1c28c2f70aa8c
    50. 50
      Jeffery, D. A.; Bogyo, M. Chemical Proteomics and Its Application to Drug Discovery. Curr. Opin. Biotechnol. 2003, 14 (1), 87– 95,  DOI: 10.1016/S0958-1669(02)00010-1
      50
      Chemical proteomics and its application to drug discovery
      Jeffery, Douglas A.; Bogyo, Matthew
      Current Opinion in Biotechnology (2003), 14 (1), 87-95CODEN: CUOBE3; ISSN:0958-1669. (Elsevier Science Ltd.)
      A review with refs. The completion of the human genome sequencing project has provided a flood of new information that is likely to change the way scientists approach the study of complex biol. systems. A major challenge lies in translating this information into new and better ways to treat human disease. The multidisciplinary science of chem. proteomics can be used to distill this flood of new information. This approach makes use of synthetic small mols. that can be used to covalently modify a set of related enzymes and subsequently allow their purifn. and/or identification as valid drug targets. Furthermore, such methods enable rapid biochem. anal. and small-mol. screening of targets thereby accelerating the often difficult process of target validation and drug discovery.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXps1WmtQ%253D%253D&md5=9d77283dcea8e41a994dbcd4d14b382b
    51. 51
      Weerapana, E.; Wang, C.; Simon, G. M.; Richter, F.; Khare, S.; Dillon, M. B. D.; Bachovchin, D. A.; Mowen, K.; Baker, D.; Cravatt, B. F. Quantitative Reactivity Profiling Predicts Functional Cysteines in Proteomes. Nature 2010, 468 (7325), 790– 795,  DOI: 10.1038/nature09472
      51
      Quantitative reactivity profiling predicts functional cysteines in proteomes
      Weerapana, Eranthie; Wang, Chu; Simon, Gabriel M.; Richter, Florian; Khare, Sagar; Dillon, Myles B. D.; Bachovchin, Daniel A.; Mowen, Kerri; Baker, David; Cravatt, Benjamin F.
      Nature (London, United Kingdom) (2010), 468 (7325), 790-795CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
      Cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochem. functions. The absence of a consensus sequence that defines functional cysteines in proteins has hindered their discovery and characterization. Here we describe a proteomics method to profile quant. the intrinsic reactivity of cysteine residues en masse directly in native biol. systems. Hyper-reactivity was a rare feature among cysteines and it was found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. Hyper-reactive cysteines were identified in several proteins of uncharacterized function, including a residue conserved across eukaryotic phylogeny that we show is required for yeast viability and is involved in iron-sulfur protein biogenesis. We also demonstrate that quant. reactivity profiling can form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhsVGhsr%252FI&md5=277e436e7a8f4dfff0b548bce52ac40d
    52. 52
      Backus, K. M.; Correia, B. E.; Lum, K. M.; Forli, S.; Horning, B. D.; González-Páez, G. E.; Chatterjee, S.; Lanning, B. R.; Teijaro, J. R.; Olson, A. J.; Wolan, D. W.; Cravatt, B. F. Proteome-Wide Covalent Ligand Discovery in Native Biological Systems. Nature 2016, 534 (7608), 570– 574,  DOI: 10.1038/nature18002
      52
      Proteome-wide covalent ligand discovery in native biological systems
      Backus, Keriann M.; Correia, Bruno E.; Lum, Kenneth M.; Forli, Stefano; Horning, Benjamin D.; Gonzalez-Paez, Gonzalo E.; Chatterjee, Sandip; Lanning, Bryan R.; Teijaro, John R.; Olson, Arthur J.; Wolan, Dennis W.; Cravatt, Benjamin F.
      Nature (London, United Kingdom) (2016), 534 (7608), 570-574CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
      Small mols. are powerful tools for investigating protein function and can serve as leads for new therapeutics. Most human proteins, however, lack small-mol. ligands, and entire protein classes are considered 'undruggable'. Fragment-based ligand discovery can identify small-mol. probes for proteins that have proven difficult to target using high-throughput screening of complex compd. libraries. Although reversibly binding ligands are commonly pursued, covalent fragments provide an alternative route to small-mol. probes, including those that can access regions of proteins that are difficult to target through binding affinity alone. Here we report a quant. anal. of cysteine-reactive small-mol. fragments screened against thousands of proteins in human proteomes and cells. Covalent ligands were identified for >700 cysteines found in both druggable proteins and proteins deficient in chem. probes, including transcription factors, adaptor/scaffolding proteins, and uncharacterized proteins. Among the atypical ligand-protein interactions discovered were compds. that react preferentially with pro- (inactive) caspases. We used these ligands to distinguish extrinsic apoptosis pathways in human cell lines vs. primary human T cells, showing that the former is largely mediated by caspase-8 while the latter depends on both caspase-8 and -10. Fragment-based covalent ligand discovery provides a greatly expanded portrait of the ligandable proteome and furnishes compds. that can illuminate protein functions in native biol. systems.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtVSksbnN&md5=6fab087c042de735f8a5931e9f5b946c
    53. 53
      Abbasov, M. E.; Kavanagh, M. E.; Ichu, T.-A.; Lazear, M. R.; Tao, Y.; Crowley, V. M.; Am Ende, C. W.; Hacker, S. M.; Ho, J.; Dix, M. M.; Suciu, R.; Hayward, M. M.; Kiessling, L. L.; Cravatt, B. F. A Proteome-Wide Atlas of Lysine-Reactive Chemistry. Nat. Chem. 2021, 13 (11), 1081– 1092,  DOI: 10.1038/s41557-021-00765-4
      53
      A proteome-wide atlas of lysine-reactive chemistry
      Abbasov, Mikail E.; Kavanagh, Madeline E.; Ichu, Taka-Aki; Lazear, Michael R.; Tao, Yongfeng; Crowley, Vincent M.; am Ende, Christopher W.; Hacker, Stephan M.; Ho, Jordan; Dix, Melissa M.; Suciu, Radu; Hayward, Matthew M.; Kiessling, Laura L.; Cravatt, Benjamin F.
      Nature Chemistry (2021), 13 (11), 1081-1092CODEN: NCAHBB; ISSN:1755-4330. (Nature Portfolio)
      Recent advances in chem. proteomics have begun to characterize the reactivity and ligandability of lysines on a global scale. Yet, only a limited diversity of aminophilic electrophiles have been evaluated for interactions with the lysine proteome. Here, we report an in-depth profiling of >30 uncharted aminophilic chemotypes that greatly expands the content of ligandable lysines in human proteins. Aminophilic electrophiles showed disparate proteomic reactivities that range from selective interactions with a handful of lysines to, for a set of dicarboxaldehyde fragments, remarkably broad engagement of the covalent small-mol.-lysine interactions captured by the entire library. We used these latter 'scout' electrophiles to efficiently map ligandable lysines in primary human immune cells under stimulatory conditions. Finally, we show that aminophilic compds. perturb diverse biochem. functions through site-selective modification of lysines in proteins, including protein-RNA interactions implicated in innate immune responses. These findings support the broad potential of covalent chem. for targeting functional lysines in the human proteome.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvF2ju7rJ&md5=90e566b7a65ebfca5108a1c44f06f575
    54. 54
      Hayes, J. D.; Flanagan, J. U.; Jowsey, I. R. Glutathione Transferases. Annu. Rev. Pharmacol. Toxicol. 2005, 45, 51– 88,  DOI: 10.1146/annurev.pharmtox.45.120403.095857
      54
      Glutathione transferases
      Hayes, John D.; Flanagan, Jack U.; Jowsey, Ian R.
      Annual Review of Pharmacology and Toxicology (2005), 45 (), 51-88, 1 plateCODEN: ARPTDI; ISSN:0362-1642. (Annual Reviews Inc.)
      A review. The authors describe the 3 mammalian glutathione S-transferase (GST) families, namely cytosolic, mitochondrial, and microsomal GSTs, the latter now designated MAPEG (Membrane-Assocd. Proteins in Eicosanoid and Glutathione metab.). In addn. to detoxifying electrophilic xenobiotics, such as chem. carcinogens, environmental pollutants, and antitumor agents, these GSTs inactivate endogenous α,β-unsatd. aldehydes, quinones, epoxides, and hydroperoxides formed as secondary metabolites during oxidative stress. These enzymes are also intimately involved in the biosynthesis of leukotrienes, prostaglandins, testosterone, and progesterone, as well as the degrdn. of tyrosine. Among their substrates, GSTs conjugate the signaling mols., 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2) and 4-hydroxynonenal, with glutathione, and consequently they antagonize expression of genes trans-activated by peroxisome proliferator-activated receptor γ (PPARγ) and nuclear factor-erythroid 2 p45-related factor 2 (Nrf2). Through metab. of 15d-PGJ2, GST may enhance gene expression driven by nuclear factor-κB (NF-κB). Cytosolic human GST exhibit genetic polymorphisms and this variation can increase susceptibility to carcinogenesis and inflammatory disease. Polymorphisms in human MAPEG are assocd. with alterations in lung function and increased risk of myocardial infarction and stroke. Targeted disruption of murine genes has demonstrated that cytosolic GST isoenzymes are broadly cytoprotective, whereas MAPEG proteins have pro-inflammatory activities. Furthermore, knockout of mouse GSTA4 and GSTZ1 leads to overexpression of transferases in the Alpha, Mu, and Pi classes, an observation suggesting they are part of an adaptive mechanism that responds to endogenous chem. cues such as 4-hydroxynonenal and tyrosine degrdn. products. Consistent with this hypothesis, the promoters of cytosolic GST and MAPEG genes contain antioxidant response elements through which they are transcriptionally activated during exposure to Michael reaction acceptors and oxidative stress.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXisVWjtrk%253D&md5=c74f17b1381f046770a7f6faf5c51291
    55. 55
      Jiang, X.; Zhou, Q.; Du, B.; Li, S.; Huang, Y.; Chi, Z.; Lee, W. M.; Yu, M.; Zheng, J. Noninvasive Monitoring of Hepatic Glutathione Depletion through Fluorescence Imaging and Blood Testing. Sci. Adv. 2021, 7 (8), eabd9847  DOI: 10.1126/sciadv.abd9847
      There is no corresponding record for this reference.
    56. 56
      Jeffries, R. E.; Gomez, S. M.; Macdonald, J. M.; Gamcsik, M. P. Direct Detection of Glutathione Biosynthesis, Conjugation, Depletion and Recovery in Intact Hepatoma Cells. Int. J. Mol. Sci. 2022, 23 (9), 4733,  DOI: 10.3390/ijms23094733
      There is no corresponding record for this reference.
    57. 57
      Quanrud, G. M.; Lyu, Z.; Balamurugan, S. V.; Canizal, C.; Wu, H.-T.; Genereux, J. C. Cellular Exposure to Chloroacetanilide Herbicides Induces Distinct Protein Destabilization Profiles. ACS Chem. Biol. 2023, 18 (7), 1661– 1676,  DOI: 10.1021/acschembio.3c00338
      There is no corresponding record for this reference.
    58. 58
      Julio, A. R.; Shikwana, F.; Truong, C.; Burton, N. R.; Dominguez, E.; Turmon, A. C.; Cao, J.; Backus, K. Pervasive Aggregation and Depletion of Host and Viral Proteins in Response to Cysteine-Reactive Electrophilic Compounds. BioRxiv , November 1, 2023.  DOI: 10.1101/2023.10.30.564067 .
      There is no corresponding record for this reference.
    59. 59
      Adair, K.; Meng, X.; Naisbitt, D. J. Drug Hapten-Specific T-Cell Activation: Current Status and Unanswered Questions. Proteomics 2021, 21 (17–18), e2000267  DOI: 10.1002/pmic.202000267
      There is no corresponding record for this reference.
    60. 60
      Weltzien, H. U.; Padovan, E. Molecular Features of Penicillin Allergy. J. Invest. Dermatol. 1998, 110 (3), 203– 206,  DOI: 10.1046/j.1523-1747.1998.00122.x
      There is no corresponding record for this reference.
    61. 61
      Pirmohamed, M.; Ostrov, D. A.; Park, B. K. New Genetic Findings Lead the Way to a Better Understanding of Fundamental Mechanisms of Drug Hypersensitivity. J. Allergy Clin. Immunol. 2015, 136 (2), 236– 244,  DOI: 10.1016/j.jaci.2015.06.022
      There is no corresponding record for this reference.
    62. 62
      Agashe, R. P.; Lippman, S. M.; Kurzrock, R. JAK: Not Just Another Kinase. Mol. Cancer Ther. 2022, 21 (12), 1757– 1764,  DOI: 10.1158/1535-7163.MCT-22-0323
      There is no corresponding record for this reference.
    63. 63
      Goedken, E. R.; Argiriadi, M. A.; Banach, D. L.; Fiamengo, B. A.; Foley, S. E.; Frank, K. E.; George, J. S.; Harris, C. M.; Hobson, A. D.; Ihle, D. C.; Marcotte, D.; Merta, P. J.; Michalak, M. E.; Murdock, S. E.; Tomlinson, M. J.; Voss, J. W. Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol. J. Biol. Chem. 2015, 290 (8), 4573– 4589,  DOI: 10.1074/jbc.M114.595181
      63
      Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol
      Goedken, Eric R.; Argiriadi, Maria A.; Banach, David L.; Fiamengo, Bryan A.; Foley, Sage E.; Frank, Kristine E.; George, Jonathan S.; Harris, Christopher M.; Hobson, Adrian D.; Ihle, David C.; Marcotte, Douglas; Merta, Philip J.; Michalak, Mark E.; Murdock, Sara E.; Tomlinson, Medha J.; Voss, Jeffrey W.
      Journal of Biological Chemistry (2015), 290 (8), 4573-4589CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
      The action of Janus kinases (JAKs) is required for multiple cytokine signaling pathways, and as such, JAK inhibitors hold promise for treatment of autoimmune disorders, including rheumatoid arthritis, inflammatory bowel disease, and psoriasis. However, due to high similarity in the active sites of the four members (Jak1, Jak2, Jak3, and Tyk2), developing selective inhibitors within this family is challenging. We have designed and characterized substituted, tricyclic Jak3 inhibitors that selectively avoid inhibition of the other JAKs. This is accomplished through a covalent interaction between an inhibitor contg. a terminal electrophile and an active site cysteine (Cys-909). We found that these ATP competitive compds. are irreversible inhibitors of Jak3 enzyme activity in vitro. They possess high selectivity against other kinases and can potently (IC50 < 100 nm) inhibit Jak3 activity in cell-based assays. These results suggest irreversible inhibitors of this class may be useful selective agents, both as tools to probe Jak3 biol. and potentially as therapies for autoimmune diseases.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXjsF2lsLY%253D&md5=4d99cf5b13fd05df5c4abc197c1fe284
    64. 64
      Chen, C.; Lu, D.; Sun, T.; Zhang, T. JAK3 Inhibitors for the Treatment of Inflammatory and Autoimmune Diseases: A Patent Review (2016-Present). Expert Opin. Ther. Pat. 2022, 32 (3), 225– 242,  DOI: 10.1080/13543776.2022.2023129
      There is no corresponding record for this reference.
    65. 65
      Shindo, N.; Ojida, A. Recent Progress in Covalent Warheads for in Vivo Targeting of Endogenous Proteins. Bioorg. Med. Chem. 2021, 47, 116386,  DOI: 10.1016/j.bmc.2021.116386
      65
      Recent progress in covalent warheads for in vivo targeting of endogenous proteins
      Shindo, Naoya; Ojida, Akio
      Bioorganic & Medicinal Chemistry (2021), 47 (), 116386CODEN: BMECEP; ISSN:0968-0896. (Elsevier B.V.)
      Covalent drugs exert potent and durable activity by chem. modification of the endogenous target protein in vivo. To maximize the pharmacol. efficacy while alleviating the risk of toxicity due to nonspecific off-target reactions, current covalent drug discovery focuses on the development of targeted covalent inhibitors (TCIs), wherein a reactive group (warhead) is strategically incorporated onto a reversible ligand of the target protein to facilitate specific covalent engagement. Various aspects of warheads, such as intrinsic reactivity, chemoselectivity, mode of reaction, and reversibility of the covalent engagement, would affect the target selectivity of TCIs. Although TCIs clin. approved to date largely rely on Michael acceptor-type electrophiles for cysteine targeting, a wide array of novel warheads have been devised and tested in TCI development in recent years. In this short review, we provide an overview of recent progress in chem. for selective covalent targeting of proteins and their applications in TCI designs.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXitVSrtrjL&md5=d746f5fd8ac5778e1b23e8ef678ceec6
    66. 66
      Forster, M.; Chaikuad, A.; Dimitrov, T.; Döring, E.; Holstein, J.; Berger, B.-T.; Gehringer, M.; Ghoreschi, K.; Müller, S.; Knapp, S.; Laufer, S. A. Development, Optimization, and Structure-Activity Relationships of Covalent-Reversible JAK3 Inhibitors Based on a Tricyclic Imidazo[5,4- d]Pyrrolo[2,3- b]Pyridine Scaffold. J. Med. Chem. 2018, 61 (12), 5350– 5366,  DOI: 10.1021/acs.jmedchem.8b00571
      66
      Development, Optimization, and Structure-Activity Relationships of Covalent-Reversible JAK3 Inhibitors Based on a Tricyclic Imidazo[5,4-d]pyrrolo[2,3-b]pyridine Scaffold
      Forster, Michael; Chaikuad, Apirat; Dimitrov, Teodor; Doering, Eva; Holstein, Julia; Berger, Benedict-Tilman; Gehringer, Matthias; Ghoreschi, Kamran; Mueller, Susanne; Knapp, Stefan; Laufer, Stefan A.
      Journal of Medicinal Chemistry (2018), 61 (12), 5350-5366CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      Janus kinases are major drivers of immune signaling and have been the focus of anti-inflammatory drug discovery for more than a decade. Because of the invariable colocalization of JAK1 and JAK3 at cytokine receptors, the question if selective JAK3 inhibition is sufficient to effectively block downstream signaling has been highly controversial. Recently, we discovered the covalent-reversible JAK3 inhibitor FM-381 (23) featuring high isoform and kinome selectivity. Crystallog. revealed that this inhibitor induces an unprecedented binding pocket by interactions of a nitrile substituent with arginine residues in JAK3. Herein, we describe detailed structure-activity relationships necessary for induction of the arginine pocket and the impact of this structural change on potency, isoform selectivity, and efficacy in cellular models. Furthermore, we evaluated the stability of this novel inhibitor class in in vitro metabolic assays and were able to demonstrate an adequate stability of key compd. 23 for in vivo use.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtVGjsrbN&md5=8acdec137df746f854bbee75a10d5f70
    67. 67
      Laux, J.; Forster, M.; Riexinger, L.; Schwamborn, A.; Guezguez, J.; Pokoj, C.; Kudolo, M.; Berger, L. M.; Knapp, S.; Schollmeyer, D.; Guse, J.; Burnet, M.; Laufer, S. A. Pharmacokinetic Optimization of Small Molecule Janus Kinase 3 Inhibitors to Target Immune Cells. ACS Pharmacol. Transl. Sci. 2022, 5 (8), 573– 602,  DOI: 10.1021/acsptsci.2c00054
      67
      Pharmacokinetic Optimization of Small Molecule Janus Kinase 3 Inhibitors to Target Immune Cells
      Laux, Julian; Forster, Michael; Riexinger, Laura; Schwamborn, Anna; Guezguez, Jamil; Pokoj, Christina; Kudolo, Mark; Berger, Lena M.; Knapp, Stefan; Schollmeyer, Dieter; Guse, Jan; Burnet, Michael; Laufer, Stefan A.
      ACS Pharmacology & Translational Science (2022), 5 (8), 573-602CODEN: APTSFN; ISSN:2575-9108. (American Chemical Society)
      Modulation of Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling is a promising method of treating autoimmune diseases, and the profound potency of clin. compds. makes this mode of action particularly attractive. Other questions that remain unanswered also include: What is the ideal selectivity between JAK1 and JAK3. Which cells are most relevant to JAK blockade. And what is the ideal tissue distribution pattern for addressing specific autoimmune conditions. We hypothesized that JAK3 selectivity is most relevant to low-dose clin. effects and interleukin-10 (IL-10) stimulation in particular, that immune cells are the most important compartment, and that distribution to inflamed tissue is the most important pharmacokinetic characteristic for in vivo disease modification. To test these hypotheses, we prepd. modified derivs. of JAK3 specific inhibitors that target C909 near the ATP binding site based on FM-381, first reported in 2016; a compd. class that was hitherto limited in uptake and exposure in vivo. These limits appear to be due to metabolic instability of side groups binding in the selectivity pocket. We identified derivs. with improved stability and tissue exposure. Conjugation to macrolide scaffolds with medium chain linkers was sufficient to stabilize the compds. and improve transport to organs while maintaining JAK3 affinity. These conjugates are inflammation targeted JAK3 inhibitors with long tissue half-lives and high exposure to activated immune cells.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38Xhsl2nur7M&md5=31a71f1a28ac2893f116b25e3972fc36
    68. 68
      Burger, J. A. Bruton Tyrosine Kinase Inhibitors: Present and Future. Cancer J. 2019, 25 (6), 386– 393,  DOI: 10.1097/PPO.0000000000000412
      68
      Bruton Tyrosine Kinase Inhibitors: Present and Future
      Burger, Jan A.
      Cancer Journal (Philadelphia, PA, United States) (2019), 25 (6), 386-393CODEN: CAJOCB; ISSN:1528-9117. (Lippincott Williams & Wilkins)
      A review. Bruton tyrosine kinase (BTK) is a nonreceptor tyrosine kinase that plays a central role in the signal transduction of the B-cell antigen receptor and other cell surface receptors, both in normal and malignant B lymphocytes. B-cell antigen receptor signaling is activated in secondary lymphatic organs and drives the proliferation of malignant B cells, including chronic lymphocytic leukemia (CLL) cells. During the last 10 years, BTK inhibitors (BTKis) are increasingly replacing chemotherapy-based regimen, esp. in patients with CLL and mantle cell lymphoma (MCL). Bruton tyrosine kinase inhibitors are particularly active in patients with CLL and MCL, but also received approval for Waldenstroem macroglobulinemia, small lymphocytic lymphoma, marginal zone lymphoma, and chronic graft-vs.-host disease. Current clin. practice is continuous long-term administration of BTKi, which can be complicated by adverse effects or the development of drug resistance. Alternatives to long-term use of BTKi are being developed, such as combination therapies, permitting for limited duration therapy. Second-generation BTKis are under development, which differ from ibrutinib, the first-in-class BTKi, in their specificity for BTK, and therefore may differentiate themselves from ibrutinib in terms of adverse effects or efficacy.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXitlOms7zM&md5=574551611f4a8f843cf1ce2cd0db1697
    69. 69
      Khan, W. N. Regulation of B Lymphocyte Development and Activation by Bruton’s Tyrosine Kinase. Immunol. Res. 2001, 23 (2–3), 147– 156,  DOI: 10.1385/IR:23:2-3:147
      There is no corresponding record for this reference.
    70. 70
      Guldenpfennig, C.; Teixeiro, E.; Daniels, M. NF-kB’s Contribution to B Cell Fate Decisions. Front. Immunol. 2023, 14, 1214095,  DOI: 10.3389/fimmu.2023.1214095
      There is no corresponding record for this reference.
    71. 71
      Staudt, L. M. Oncogenic Activation of NF-kappaB. Cold Spring Harb. Perspect. Biol. 2010, 2 (6), a000109,  DOI: 10.1101/cshperspect.a000109
      There is no corresponding record for this reference.
    72. 72
      Small Molecules in Oncology; Martens, U. M., Ed.; Recent Results in Cancer Research Series; Springer: Berlin, Heidelberg, 2014; Vol. 201.  DOI: 10.1007/978-3-642-54490-3 .
      There is no corresponding record for this reference.
    73. 73
      Wu, J.; Zhang, M.; Liu, D. Acalabrutinib (ACP-196): A Selective Second-Generation BTK Inhibitor. J. Hematol. Oncol.J. Hematol Oncol 2016, 9, 21,  DOI: 10.1186/s13045-016-0250-9
      73
      Acalabrutinib (ACP-196): a selective second-generation BTK inhibitor
      Wu, Jingjing; Zhang, Mingzhi; Liu, Delong
      Journal of Hematology & Oncology (2016), 9 (), 21/1-21/4CODEN: JHOOAO; ISSN:1756-8722. (BioMed Central Ltd.)
      More and more targeted agents become available for B cell malignancies with increasing precision and potency. The first-in-class Bruton's tyrosine kinase (BTK) inhibitor, ibrutinib, has been in clin. use for the treatment of chronic lymphocytic leukemia, mantle cell lymphoma, and Waldenstrom's macroglobulinemia. More selective BTK inhibitors (ACP-196, ONO/GS-4059, BGB-3111, CC-292) are being explored. Acalabrutinib (ACP-196) is a novel irreversible second-generation BTK inhibitor that was shown to be more potent and selective than ibrutinib. This review summarized the preclin. research and clin. data of acalabrutinib.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXis1eisrw%253D&md5=a6a8f9b9236abe7ef1054a41e1c71e5a
    74. 74
      Guo, Y.; Liu, Y.; Hu, N.; Yu, D.; Zhou, C.; Shi, G.; Zhang, B.; Wei, M.; Liu, J.; Luo, L.; Tang, Z.; Song, H.; Guo, Y.; Liu, X.; Su, D.; Zhang, S.; Song, X.; Zhou, X.; Hong, Y.; Chen, S.; Cheng, Z.; Young, S.; Wei, Q.; Wang, H.; Wang, Q.; Lv, L.; Wang, F.; Xu, H.; Sun, H.; Xing, H.; Li, N.; Zhang, W.; Wang, Z.; Liu, G.; Sun, Z.; Zhou, D.; Li, W.; Liu, L.; Wang, L.; Wang, Z. Discovery of Zanubrutinib (BGB-3111), a Novel, Potent, and Selective Covalent Inhibitor of Bruton’s Tyrosine Kinase. J. Med. Chem. 2019, 62 (17), 7923– 7940,  DOI: 10.1021/acs.jmedchem.9b00687
      74
      Discovery of Zanubrutinib (BGB-3111), a Novel, Potent, and Selective Covalent Inhibitor of Bruton's Tyrosine Kinase
      Guo, Yunhang; Liu, Ye; Hu, Nan; Yu, Desheng; Zhou, Changyou; Shi, Gongyin; Zhang, Bo; Wei, Min; Liu, Junhua; Luo, Lusong; Tang, Zhiyu; Song, Huipeng; Guo, Yin; Liu, Xuesong; Su, Dan; Zhang, Shuo; Song, Xiaomin; Zhou, Xing; Hong, Yuan; Chen, Shuaishuai; Cheng, Zhenzhen; Young, Steve; Wei, Qiang; Wang, Haisheng; Wang, Qiuwen; Lv, Lei; Wang, Fan; Xu, Haipeng; Sun, Hanzi; Xing, Haimei; Li, Na; Zhang, Wei; Wang, Zhongbo; Liu, Guodong; Sun, Zhijian; Zhou, Dongping; Li, Wei; Liu, Libin; Wang, Lai; Wang, Zhiwei
      Journal of Medicinal Chemistry (2019), 62 (17), 7923-7940CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      Aberrant activation of Bruton's tyrosine kinase (BTK) plays an important role in pathogenesis of B-cell lymphomas, suggesting that inhibition of BTK is useful in the treatment of hematol. malignancies. The discovery of a more selective on-target covalent BTK inhibitor is of high value. Herein, we disclose the discovery and preclin. characterization of a potent, selective, and irreversible BTK inhibitor as our clin. candidate by using in vitro potency, selectivity, pharmacokinetics (PK), and in vivo pharmacodynamic for prioritizing compds. Compd. BGB-3111 (31a, Zanubrutinib) demonstrates (i) potent activity against BTK and excellent selectivity over other TEC, EGFR and Src family kinases, (ii) desirable ADME, excellent in vivo pharmacodynamic in mice and efficacy in OCI-LY10 xenograft models.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsFSku7bP&md5=5cdb551d296e60eb1e82b03b7a0384ee
    75. 75
      Liclican, A.; Serafini, L.; Xing, W.; Czerwieniec, G.; Steiner, B.; Wang, T.; Brendza, K. M.; Lutz, J. D.; Keegan, K. S.; Ray, A. S.; Schultz, B. E.; Sakowicz, R.; Feng, J. Y. Biochemical Characterization of Tirabrutinib and Other Irreversible Inhibitors of Bruton’s Tyrosine Kinase Reveals Differences in on - and off - Target Inhibition. Biochim. Biophys. Acta Gen. Subj. 2020, 1864 (4), 129531,  DOI: 10.1016/j.bbagen.2020.129531
      There is no corresponding record for this reference.
    76. 76
      Tam, C. S.; Muñoz, J. L.; Seymour, J. F.; Opat, S. Zanubrutinib: Past, Present, and Future. Blood Cancer J. 2023, 13 (1), 141,  DOI: 10.1038/s41408-023-00902-x
      There is no corresponding record for this reference.
    77. 77
      Estupiñán, H. Y.; Berglöf, A.; Zain, R.; Smith, C. I. E. Comparative Analysis of BTK Inhibitors and Mechanisms Underlying Adverse Effects. Front. Cell Dev. Biol. 2021, 9, 630942,  DOI: 10.3389/fcell.2021.630942
      77
      Comparative Analysis of BTK Inhibitors and Mechanisms Underlying Adverse Effects
      Estupinan H Yesid; Berglof Anna; Zain Rula; Smith C I Edvard; Estupinan H Yesid; Zain Rula
      Frontiers in cell and developmental biology (2021), 9 (), 630942 ISSN:2296-634X.
      The cytoplasmic protein-tyrosine kinase BTK plays an essential role for differentiation and survival of B-lineage cells and, hence, represents a suitable drug target. The number of BTK inhibitors (BTKis) in the clinic has increased considerably and currently amounts to at least 22. First-in-class was ibrutinib, an irreversible binder forming a covalent bond to a cysteine in the catalytic region of the kinase, for which we have identified 228 active trials listed at ClinicalTrials.gov. Next-generation inhibitors, acalabrutinib and zanubrutinib, are approved both in the United States and in Europe, and zanubrutinib also in China, while tirabrutinib is currently only registered in Japan. In most cases, these compounds have been used for the treatment of B-lymphocyte tumors. However, an increasing number of trials instead addresses autoimmunity and inflammation in multiple sclerosis, rheumatoid arthritis, pemphigus and systemic lupus erythematosus with the use of either irreversibly binding inhibitors, e.g., evobrutinib and tolebrutinib, or reversibly binding inhibitors, like fenebrutinib. Adverse effects (AEs) have predominantly implicated inhibition of other kinases with a BTKi-binding cysteine in their catalytic domain. Analysis of the reported AEs suggests that ibrutinib-associated atrial fibrillation is caused by binding to ERBB2/HER2 and ERBB4/HER4. However, the binding pattern of BTKis to various additional kinases does not correlate with the common assumption that skin manifestations and diarrhoeas are off-target effects related to EGF receptor inhibition. Moreover, dermatological toxicities, diarrhoea, bleedings and invasive fungal infections often develop early after BTKi treatment initiation and subsequently subside. Conversely, cardiovascular AEs, like hypertension and various forms of heart disease, often persist.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BB3sfjtlCrtg%253D%253D&md5=c559e266e46358b280c7835a9574d965
    78. 78
      Mato, A. R.; Nabhan, C.; Thompson, M. C.; Lamanna, N.; Brander, D. M.; Hill, B.; Howlett, C.; Skarbnik, A.; Cheson, B. D.; Zent, C.; Pu, J.; Kiselev, P.; Goy, A.; Claxton, D.; Isaac, K.; Kennard, K. H.; Timlin, C.; Landsburg, D.; Winter, A.; Nasta, S. D.; Bachow, S. H.; Schuster, S. J.; Dorsey, C.; Svoboda, J.; Barr, P.; Ujjani, C. S. Toxicities and Outcomes of 616 Ibrutinib-Treated Patients in the United States: A Real-World Analysis. Haematologica 2018, 103 (5), 874– 879,  DOI: 10.3324/haematol.2017.182907
      There is no corresponding record for this reference.
    79. 79
      Sharman, J. P.; Black-Shinn, J. L.; Clark, J.; Bitman, B. Understanding Ibrutinib Treatment Discontinuation Patterns for Chronic Lymphocytic Leukemia. Blood 2017, 130 (Supplement 1), 4060,  DOI: 10.1182/blood.V130.Suppl_1.4060.4060
      There is no corresponding record for this reference.
    80. 80
      Winqvist, M.; Andersson, P.-O.; Asklid, A.; Karlsson, K.; Karlsson, C.; Lauri, B.; Lundin, J.; Mattsson, M.; Norin, S.; Sandstedt, A.; Rosenquist, R.; Späth, F.; Hansson, L.; Österborg, A. for the Swedish CLL Group. Long-Term Real-World Results of Ibrutinib Therapy in Patients with Relapsed or Refractory Chronic Lymphocytic Leukemia: 30-Month Follow up of the Swedish Compassionate Use Cohort. Haematologica 2019, 104 (5), e208– e210,  DOI: 10.3324/haematol.2018.198820
      There is no corresponding record for this reference.
    81. 81
      ClinicalTrials.gov. Rilzabrutinib. https://clinicaltrials.gov/search?intr=Rilzabrutinib (accessed 2023–11–28).
      There is no corresponding record for this reference.
    82. 82
      Oda, K. New Families of Carboxyl Peptidases: Serine-Carboxyl Peptidases and Glutamic Peptidases. J. Biochem. (Tokyo) 2012, 151 (1), 13– 25,  DOI: 10.1093/jb/mvr129
      There is no corresponding record for this reference.
    83. 83
      Ćwilichowska, N.; Świderska, K. W.; Dobrzyń, A.; Drąg, M.; Poręba, M. Diagnostic and Therapeutic Potential of Protease Inhibition. Mol. Aspects Med. 2022, 88, 101144,  DOI: 10.1016/j.mam.2022.101144
      There is no corresponding record for this reference.
    84. 84
      Manasanch, E. E.; Orlowski, R. Z. Proteasome Inhibitors in Cancer Therapy. Nat. Rev. Clin. Oncol. 2017, 14 (7), 417– 433,  DOI: 10.1038/nrclinonc.2016.206
      84
      Proteasome inhibitors in cancer therapy
      Manasanch, Elisabet E.; Orlowski, Robert Z.
      Nature Reviews Clinical Oncology (2017), 14 (7), 417-433CODEN: NRCOAA; ISSN:1759-4774. (Nature Publishing Group)
      The ubiquitin proteasome pathway was discovered in the 1980s to be a central component of the cellular protein-degrdn. machinery with essential functions in homeostasis, which include preventing the accumulation of misfolded or deleterious proteins. Cancer cells produce proteins that promote both cell survival and proliferation, and/or inhibit mechanisms of cell death. This notion set the stage for preclin. testing of proteasome inhibitors as a means to shift this fine equil. towards cell death. Since the late 1990s, clin. trials have been conducted for a variety of malignancies, leading to regulatory approvals of proteasome inhibitors to treat multiple myeloma and mantle-cell lymphoma. First-generation and second-generation proteasome inhibitors can elicit deep initial responses in patients with myeloma, for whom these drugs have dramatically improved outcomes, but relapses are frequent and acquired resistance to treatment eventually emerges. In addn., promising preclin. data obtained with proteasome inhibitors in models of solid tumors have not been confirmed in the clinic, indicating the importance of primary resistance. Investigation of the mechanisms of resistance is, therefore, essential to further maximize the utility of this class of drugs in the era of personalized medicine. Herein, we discuss the advances and challenges resulting from the introduction of proteasome inhibitors into the clinic.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsFGlsbg%253D&md5=7246069f357a4cc9449f822c57767811
    85. 85
      Flint, M.; Mullen, S.; Deatly, A. M.; Chen, W.; Miller, L. Z.; Ralston, R.; Broom, C.; Emini, E. A.; Howe, A. Y. M. Selection and Characterization of Hepatitis C Virus Replicons Dually Resistant to the Polymerase and Protease Inhibitors HCV-796 and Boceprevir (SCH 503034). Antimicrob. Agents Chemother. 2009, 53 (2), 401– 411,  DOI: 10.1128/AAC.01081-08
      There is no corresponding record for this reference.
    86. 86
      Augeri, D. J.; Robl, J. A.; Betebenner, D. A.; Magnin, D. R.; Khanna, A.; Robertson, J. G.; Wang, A.; Simpkins, L. M.; Taunk, P.; Huang, Q.; Han, S.-P.; Abboa-Offei, B.; Cap, M.; Xin, L.; Tao, L.; Tozzo, E.; Welzel, G. E.; Egan, D. M.; Marcinkeviciene, J.; Chang, S. Y.; Biller, S. A.; Kirby, M. S.; Parker, R. A.; Hamann, L. G. Discovery and Preclinical Profile of Saxagliptin (BMS-477118): A Highly Potent, Long-Acting, Orally Active Dipeptidyl Peptidase IV Inhibitor for the Treatment of Type 2 Diabetes. J. Med. Chem. 2005, 48 (15), 5025– 5037,  DOI: 10.1021/jm050261p
      86
      Discovery and Preclinical Profile of Saxagliptin (BMS-477118): A Highly Potent, Long-Acting, Orally Active Dipeptidyl Peptidase IV Inhibitor for the Treatment of Type 2 Diabetes
      Augeri, David J.; Robl, Jeffrey A.; Betebenner, David A.; Magnin, David R.; Khanna, Ashish; Robertson, James G.; Wang, Aiying; Simpkins, Ligaya M.; Taunk, Prakash; Huang, Qi; Han, Song-Ping; Abboa-Offei, Benoni; Cap, Michael; Xin, Li; Tao, Li; Tozzo, Effie; Welzel, Gustav E.; Egan, Donald M.; Marcinkeviciene, Jovita; Chang, Shu Y.; Biller, Scott A.; Kirby, Mark S.; Parker, Rex A.; Hamann, Lawrence G.
      Journal of Medicinal Chemistry (2005), 48 (15), 5025-5037CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      Efforts to further elucidate structure-activity relationships (SAR) within the authors previously disclosed series of β-quaternary amino acid linked L-cis-4,5-methanoprolinenitrile dipeptidyl peptidase IV (DPP-IV) inhibitors led to the investigation of vinyl substitution at the β-position of α-cycloalkyl-substituted glycines. Despite poor systemic exposure, vinyl-substituted compds. showed extended duration of action in acute rat ex vivo plasma DPP-IV inhibition models. Oxygenated putative metabolites were prepd. and were shown to exhibit the potency and extended duration of action of their precursors in efficacy models measuring glucose clearance in Zuckerfa/fa rats. Extension of this approach to adamantylglycine-derived inhibitors led to the discovery of highly potent inhibitors, including hydroxyadamantyl compd. BMS-477118 (saxagliptin), a highly efficacious, stable, and long-acting DPP-IV inhibitor, which is currently undergoing clin. trials for treatment of type 2 diabetes.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXlsVeltb0%253D&md5=878355880133bb0ddd6bd14ecbf1d070
    87. 87
      Lin, K.; Perni, R. B.; Kwong, A. D.; Lin, C. VX-950, a Novel Hepatitis C Virus (HCV) NS3–4A Protease Inhibitor, Exhibits Potent Antiviral Activities in HCv Replicon Cells. Antimicrob. Agents Chemother. 2006, 50 (5), 1813– 1822,  DOI: 10.1128/AAC.50.5.1813-1822.2006
      There is no corresponding record for this reference.
    88. 88
      Focosi, D.; McConnell, S.; Shoham, S.; Casadevall, A.; Maggi, F.; Antonelli, G. Nirmatrelvir and COVID-19: Development, Pharmacokinetics, Clinical Efficacy, Resistance, Relapse, and Pharmacoeconomics. Int. J. Antimicrob. Agents 2023, 61 (2), 106708,  DOI: 10.1016/j.ijantimicag.2022.106708
      There is no corresponding record for this reference.
    89. 89
      Wen, W.; Qi, Z.; Wang, J. The Function and Mechanism of Enterovirus 71 (EV71) 3C Protease. Curr. Microbiol. 2020, 77 (9), 1968– 1975,  DOI: 10.1007/s00284-020-02082-4
      There is no corresponding record for this reference.
    90. 90
      Zeng, D.; Ma, Y.; Zhang, R.; Nie, Q.; Cui, Z.; Wang, Y.; Shang, L.; Yin, Z. Synthesis and Structure-Activity Relationship of α-Keto Amides as Enterovirus 71 3C Protease Inhibitors. Bioorg. Med. Chem. Lett. 2016, 26 (7), 1762– 1766,  DOI: 10.1016/j.bmcl.2016.02.039
      There is no corresponding record for this reference.
    91. 91
      Zhai, Y.; Ma, Y.; Ma, F.; Nie, Q.; Ren, X.; Wang, Y.; Shang, L.; Yin, Z. Structure-Activity Relationship Study of Peptidomimetic Aldehydes as Enterovirus 71 3C Protease Inhibitors. Eur. J. Med. Chem. 2016, 124, 559– 573,  DOI: 10.1016/j.ejmech.2016.08.064
      91
      Structure-activity relationship study of peptidomimetic aldehydes as enterovirus 71 3C protease inhibitors
      Zhai, Yangyang; Ma, Yuying; Ma, Fei; Nie, Quandeng; Ren, Xuejiao; Wang, Yaxin; Shang, Luqing; Yin, Zheng
      European Journal of Medicinal Chemistry (2016), 124 (), 559-573CODEN: EJMCA5; ISSN:0223-5234. (Elsevier Masson SAS)
      A series of peptidomimetic aldehydes were designed, synthesized, and evaluated for their biochem. activity against 3C protease (3Cpro) and anti-enterovirus 71 (EV71) activity in vitro. Mol. docking revealed that 5s (IC50 = 0.22 ± 0.07 μM, EC50 = 0.18 ± 0.05 μM) could bind well to the active site of EV71 3Cpro, which was consistent with the biol. data compared to ref. 5a (IC50 = 0.54 ± 0.02 μM, EC50 = 0.26 ± 0.07 μM). Structure and relationship study led to the discovery of aldehyde 5x (IC50 = 0.10 ± 0.02 μM, EC50 = 0.11 ± 0.07 μM), which exhibited the most potent 3Cpro inhibitory and antiviral activity.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsV2jurnN&md5=41cabd5d56ab0164e48cbd7806dbf2c7
    92. 92
      Luo, Y. L. Mechanism-Based and Computational-Driven Covalent Drug Design. J. Chem. Inf. Model. 2021, 61 (11), 5307– 5311,  DOI: 10.1021/acs.jcim.1c01278
      There is no corresponding record for this reference.
    93. 93
      Mihalovits, L. M.; Ferenczy, G. G.; Keserű, G. M. Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations. J. Chem. Inf. Model. 2020, 60 (12), 6579– 6594,  DOI: 10.1021/acs.jcim.0c00834
      93
      Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations
      Mihalovits, Levente M.; Ferenczy, Gyorgy G.; Keseru, Gyorgy M.
      Journal of Chemical Information and Modeling (2020), 60 (12), 6579-6594CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
      Covalent inhibitors have been gaining increased attention in drug discovery due to their beneficial properties such as long residence time, high biochem. efficiency, and specificity. Optimization of covalent inhibitors is a complex task that involves parallel monitoring of the noncovalent recognition elements and the covalent reactivity of the mols. to avoid potential idiosyncratic side effects. This challenge calls for special design protocols, including a variety of computational chem. methods. Covalent inhibition proceeds through multiple steps, and calcg. free energy changes of the subsequent binding events along the overall binding process would help us to better control the design of drug candidates. Inspired by the recent success of free energy calcns. on reversible binders, we developed a complex protocol to compute free energies related to the noncovalent and covalent binding steps with thermodn. integration and hybrid quantum mech./mol. mech. (QM/MM) potential of mean force (PMF) calcns., resp. In optimization settings, we examd. two therapeutically relevant proteins complexed with congeneric sets of irreversible cysteine targeting covalent inhibitors. In the selectivity paradigm, we studied the irreversible binding of covalent inhibitors to phylogenetically close targets by a mutational approach. The results of the calcns. are in good agreement with the exptl. free energy values derived from the inhibition and kinetic consts. (Ki and kinact) of the enzyme-inhibitor binding. The proposed method might be a powerful tool to predict the potency, selectivity, and binding mechanism of irreversible covalent inhibitors.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXisFSqu73N&md5=61ff455099a14db29ffd081cd3fd613e
    94. 94
      Mihalovits, L. M.; Ferenczy, G. G.; Keserű, G. M. The Role of Quantum Chemistry in Covalent Inhibitor Design. Int. J. Quantum Chem. 2022, 122 (8), e26768  DOI: 10.1002/qua.26768
      There is no corresponding record for this reference.
    95. 95
      Lonsdale, R.; Burgess, J.; Colclough, N.; Davies, N. L.; Lenz, E. M.; Orton, A. L.; Ward, R. A. Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity. J. Chem. Inf. Model. 2017, 57 (12), 3124– 3137,  DOI: 10.1021/acs.jcim.7b00553
      95
      Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity
      Lonsdale, Richard; Burgess, Jonathan; Colclough, Nicola; Davies, Nichola L.; Lenz, Eva M.; Orton, Alexandra L.; Ward, Richard A.
      Journal of Chemical Information and Modeling (2017), 57 (12), 3124-3137CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
      Targeted covalent inhibition is an established approach for increasing the potency and selectivity of potential drug candidates, as well as identifying potent and selective tool compds. for target validation studies. It is evident that identification of reversible recognition elements is essential for selective covalent inhibition, but this must also be achieved with the appropriate level of inherent reactivity of the reactive functionality (or "warhead"). Structural changes that increase or decrease warhead reactivity, guided by methods to predict the effect of those changes, have the potential to tune warhead reactivity and negate issues related to potency and/or toxicity. The half-life to adduct formation with glutathione (GSH t1/2) is a useful assay for measuring the reactivity of cysteine-targeting covalent warheads but is limited to synthesized mols. In this manuscript the authors assess the ability of several exptl. and computational approaches to predict GSH t1/2 for a range of cysteine targeting warheads, including a novel method based on pKa. Furthermore, matched mol. pairs anal. has been performed against the internal compd. collection, revealing structure-activity relationships between a selection of different covalent warheads. These observations and methods of prediction will be valuable in the design of new covalent inhibitors with desired levels of reactivity.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsl2gsLjF&md5=722e83699c58dee1009b87c8c31bdecc
    96. 96
      Oballa, R. M.; Truchon, J.-F.; Bayly, C. I.; Chauret, N.; Day, S.; Crane, S.; Berthelette, C. A Generally Applicable Method for Assessing the Electrophilicity and Reactivity of Diverse Nitrile-Containing Compounds. Bioorg. Med. Chem. Lett. 2007, 17 (4), 998– 1002,  DOI: 10.1016/j.bmcl.2006.11.044
      96
      A generally applicable method for assessing the electrophilicity and reactivity of diverse nitrile-containing compounds
      Oballa, Renata M.; Truchon, Jean-Francois; Bayly, Christopher I.; Chauret, Nathalie; Day, Stephen; Crane, Sheldon; Berthelette, Carl
      Bioorganic & Medicinal Chemistry Letters (2007), 17 (4), 998-1002CODEN: BMCLE8; ISSN:0960-894X. (Elsevier Ltd.)
      Nitrile-based inhibitors of cathepsin K have been known for some time and mechanism-of-action studies have demonstrated that cysteinyl proteases interact with nitriles in a reversible fashion. Three main classes of nitrile-contg. inhibitors have been published in the cathepsin K field: (i) cyanamides, (ii) arom. nitriles, and (iii) aminoacetonitriles. A computational approach was used to calc. the theor. reactivities of diverse nitriles and this was found to correlate with their extent of reactivity with free cysteine. Moreover, there is a tentative link between high reactivity with cysteine and the potential to lead to irreversible covalent binding to proteins.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXht12qtr4%253D&md5=b8fff00bdd6a746753f8f244d25b0cc8
    97. 97
      Copeland, R. A.; Pompliano, D. L.; Meek, T. D. Drug-Target Residence Time and Its Implications for Lead Optimization. Nat. Rev. Drug Discovery 2006, 5 (9), 730– 739,  DOI: 10.1038/nrd2082
      97
      Drug-target residence time and its implications for lead optimization
      Copeland, Robert A.; Pompliano, David L.; Meek, Thomas D.
      Nature Reviews Drug Discovery (2006), 5 (9), 730-739CODEN: NRDDAG; ISSN:1474-1776. (Nature Publishing Group)
      A review. Much of drug discovery today is predicated on the concept of selective targeting of particular bioactive macromols. by low-mol.-mass drugs. The binding of drugs to their macromol. targets is therefore seen as paramount for pharmacol. activity. In vitro assessment of drug-target interactions is classically quantified in terms of binding parameters such as IC50 or Kd. This article presents an alternative perspective on drug optimization in terms of drug-target binary complex residence time, as quantified by the dissociative half-life of the drug-target binary complex. We describe the potential advantages of long residence time in terms of duration of pharmacol. effect and target selectivity.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XptVCltro%253D&md5=60ede2301584b10ac4e8fa18e1e6d107
    98. 98
      Bernetti, M.; Masetti, M.; Rocchia, W.; Cavalli, A. Kinetics of Drug Binding and Residence Time. Annu. Rev. Phys. Chem. 2019, 70, 143– 171,  DOI: 10.1146/annurev-physchem-042018-052340
      98
      Kinetics of Drug Binding and Residence Time
      Bernetti, Mattia; Masetti, Matteo; Rocchia, Walter; Cavalli, Andrea
      Annual Review of Physical Chemistry (2019), 70 (), 143-171CODEN: ARPLAP; ISSN:0066-426X. (Annual Reviews)
      The kinetics of drug binding and unbinding is assuming an increasingly crucial role in the long, costly process of bringing a new medicine to patients. For example, the time a drug spends in contact with its biol. target is known as residence time (the inverse of the kinetic const. of the drug-target unbinding, 1/koff). Recent reports suggest that residence time could predict drug efficacy in vivo, perhaps even more effectively than conventional thermodn. parameters (free energy, enthalpy, entropy). There are many exptl. and computational methods for predicting drug-target residence time at an early stage of drug discovery programs. Here, we review and discuss the methodol. approaches to estg. drug binding kinetics and residence time. We first introduce the theor. background of drug binding kinetics from a physicochem. standpoint. We then analyze the recent literature in the field, starting from the exptl. methodologies and applications thereof and moving to theor. and computational approaches to the kinetics of drug binding and unbinding. We acknowledge the central role of mol. dynamics and related methods, which comprise a great no. of the computational methods and applications reviewed here. However, we also consider kinetic Monte Carlo. We conclude with the outlook that drug (un)binding kinetics may soon become a go/no go step in the discovery and development of new medicines.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXjsFSgsro%253D&md5=6016da9b20e539f43e627432018ae51b
    99. 99
      Ren, T.; Zhu, X.; Jusko, N. M.; Krzyzanski, W.; Jusko, W. J. Pharmacodynamic Model of Slow Reversible Binding and Its Applications in Pharmacokinetic/Pharmacodynamic Modeling: Review and Tutorial. J. Pharmacokinet. Pharmacodyn. 2022, 49 (5), 493– 510,  DOI: 10.1007/s10928-022-09822-y
      There is no corresponding record for this reference.
    100. 100
      Frühauf, A.; Wolff, B.; Schweipert, M.; Meyer-Almes, F.-J. Synthesis and Characterization of Reversible Covalent HDAC4 Inhibitors. Methods Mol. Biol. Clifton NJ. 2023, 2589, 207– 221,  DOI: 10.1007/978-1-0716-2788-4_14
      There is no corresponding record for this reference.
    101. 101
      Forman, H. J.; Zhang, H.; Rinna, A. Glutathione: Overview of Its Protective Roles, Measurement, and Biosynthesis. Mol. Aspects Med. 2009, 30 (1–2), 1– 12,  DOI: 10.1016/j.mam.2008.08.006
      101
      Glutathione: Overview of its protective roles, measurement, and biosynthesis
      Forman, Henry Jay; Zhang, Hongqiao; Rinna, Alessandra
      Molecular Aspects of Medicine (2009), 30 (1-2), 1-12CODEN: MAMED5; ISSN:0098-2997. (Elsevier B.V.)
      This review is the introduction to a special issue concerning, glutathione (GSH), the most abundant low mol. wt. thiol compd. synthesized in cells. GSH plays crit. roles in protecting cells from oxidative damage and the toxicity of xenobiotic electrophiles, and maintaining redox homeostasis. Here, the functions and GSH and the sources of oxidants and electrophiles, the elimination of oxidants by redn. and electrophiles by conjugation with GSH are briefly described. Methods of assessing GSH status in the cells are also described. GSH synthesis and its regulation are addressed along with therapeutic approaches for manipulating GSH content that have been proposed. The purpose here is to provide a brief overview of some of the important aspects of glutathione metab. as part of this special issue that will provide a more comprehensive review of the state of knowledge regarding this essential mol.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXltFelurY%253D&md5=c1b1aa2b03389bf1434af0762df78fe1
    102. 102
      Wu, G.; Fang, Y.-Z.; Yang, S.; Lupton, J. R.; Turner, N. D. Glutathione Metabolism and Its Implications for Health. J. Nutr. 2004, 134 (3), 489– 492,  DOI: 10.1093/jn/134.3.489
      102
      Glutathione metabolism and its implications for health
      Wu, Guoyao; Fang, Yun-Zhong; Yang, Sheng; Lupton, Joanne R.; Turner, Nancy D.
      Journal of Nutrition (2004), 134 (3), 489-492CODEN: JONUAI; ISSN:0022-3166. (American Society for Nutritional Sciences)
      A review. Glutathione (γ-glutamyl-cysteinyl-glycine; GSH) is the most abundant low-mol.-wt. thiol, and GSH/glutathione disulfide is the major redox couple in animal cells. The synthesis of GSH from glutamate, cysteine, and glycine is catalyzed sequentially by two cytosolic enzymes, γ-glutamylcysteine synthetase and GSH synthetase. Compelling evidence shows that GSH synthesis is regulated primarily by γ-glutamylcysteine synthetase activity, cysteine availability, and GSH feedback inhibition. Animal and human studies demonstrate that adequate protein nutrition is crucial for the maintenance of GSH homeostasis. In addn., enteral or parenteral cystine, methionine, N-acetyl-cysteine, and L-2-oxothiazolidine-4-carboxylate are effective precursors of cysteine for tissue GSH synthesis. Glutathione plays important roles in antioxidant defense, nutrient metab., and regulation of cellular events (including gene expression, DNA and protein synthesis, cell proliferation and apoptosis, signal transduction, cytokine prodn. and immune response, and protein glutathionylation). Glutathione deficiency contributes to oxidative stress, which plays a key role in aging and the pathogenesis of many diseases (including kwashiorkor, seizure, Alzheimer's disease, Parkinson's disease, liver disease, cystic fibrosis, sickle cell anemia, HIV, AIDS, cancer, heart attack, stroke, and diabetes). New knowledge of the nutritional regulation of GSH metab. is crit. for the development of effective strategies to improve health and to treat these diseases.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXitlCrurc%253D&md5=98f0af4f642d488fbfa0b4f43632512c
    103. 103
      Bansal, A.; Simon, M. C. Glutathione Metabolism in Cancer Progression and Treatment Resistance. J. Cell Biol. 2018, 217 (7), 2291– 2298,  DOI: 10.1083/jcb.201804161
      103
      Glutathione metabolism in cancer progression and treatment resistance
      Bansal, Ankita; Simon, M. Celeste
      Journal of Cell Biology (2018), 217 (7), 2291-2298CODEN: JCLBA3; ISSN:1540-8140. (Rockefeller University Press)
      Glutathione (GSH) is the most abundant antioxidant found in living organisms and has multiple functions, most of which maintain cellular redox homeostasis. GSH preserves sufficient levels of cysteine and detoxifies xenobiotics while also conferring therapeutic resistance to cancer cells. However, GSH metab. plays both beneficial and pathogenic roles in a variety of malignancies. It is crucial to the removal and detoxification of carcinogens, and alterations in this pathway can have a profound effect on cell survival. Excess GSH promotes tumor progression, where elevated levels correlate with increased metastasis. In this review, we discuss recent studies that focus on deciphering the role of GSH in tumor initiation and progression as well as mechanisms underlying how GSH imparts treatment resistance to growing cancers. Targeting GSH synthesis/utilization therefore represents a potential means of rendering tumor cells more susceptible to different treatment options such as chemotherapy and radiotherapy.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhvFGntb3N&md5=2d071bd5b51fa8628dd56a2ee683931d
    104. 104
      Bajic, V. P.; Van Neste, C.; Obradovic, M.; Zafirovic, S.; Radak, D.; Bajic, V. B.; Essack, M.; Isenovic, E. R. Glutathione “Redox Homeostasis” and Its Relation to Cardiovascular Disease. Oxid. Med. Cell. Longev. 2019, 2019, 5028181,  DOI: 10.1155/2019/5028181
      There is no corresponding record for this reference.
    105. 105
      Fu, L.; Li, Z.; Liu, K.; Tian, C.; He, J.; He, J.; He, F.; Xu, P.; Yang, J. A Quantitative Thiol Reactivity Profiling Platform to Analyze Redox and Electrophile Reactive Cysteine Proteomes. Nat. Protoc. 2020, 15 (9), 2891– 2919,  DOI: 10.1038/s41596-020-0352-2
      105
      A quantitative thiol reactivity profiling platform to analyze redox and electrophile reactive cysteine proteomes
      Fu, Ling; Li, Zongmin; Liu, Keke; Tian, Caiping; He, Jixiang; He, Jingyang; He, Fuchu; Xu, Ping; Yang, Jing
      Nature Protocols (2020), 15 (9), 2891-2919CODEN: NPARDW; ISSN:1750-2799. (Nature Research)
      Cysteine is unique among all protein-coding amino acids, owing to its intrinsically high nucleophilicity. The cysteinyl thiol group can be covalently modified by a broad range of redox mechanisms or by various electrophiles derived from exogenous or endogenous sources. Measuring the response of protein cysteines to redox perturbation or electrophiles is crit. for understanding the underlying mechanisms involved. Activity-based protein profiling based on thiol-reactive probes has been the method of choice for such analyses. We therefore adapted this approach and developed a new chemoproteomic platform, termed 'QTRP' (quant. thiol reactivity profiling), that relies on the ability of a com. available thiol-reactive probe IPM (2-iodo-N-(prop-2-yn-1-yl)acetamide) to covalently label, enrich and quantify the reactive cysteinome in cells and tissues. Here, we provide a detailed and updated workflow of QTRP that includes procedures for (i) labeling of the reactive cysteinome from cell or tissue samples (e.g., control vs. treatment) with IPM, (ii) processing the protein samples into tryptic peptides and tagging the probe-modified peptides with isotopically labeled azido-biotin reagents contg. a photo-cleavable linker via click chem. reaction, (iii) capturing biotin-conjugated peptides with streptavidin beads, (iv) identifying and quantifying the photo-released peptides by mass spectrometry (MS)-based shotgun proteomics and (v) interpreting MS data by a streamlined informatic pipeline using a proteomics software, pFind 3, and an automatic post-processing algorithm. We also exemplified here how to use QTRP for mining H2O2-sensitive cysteines and for detg. the intrinsic reactivity of cysteines in a complex proteome. We anticipate that this protocol should find broad applications in redox biol., chem. biol. and the pharmaceutical industry. The protocol for sample prepn. takes 3 d, whereas MS measurements and data analyses require 75 min and <30 min, resp., per sample.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsVWgt7bJ&md5=aebfe7aa84c68df1202c7f984b2672be
    106. 106
      Kuljanin, M.; Mitchell, D. C.; Schweppe, D. K.; Gikandi, A. S.; Nusinow, D. P.; Bulloch, N. J.; Vinogradova, E. V.; Wilson, D. L.; Kool, E. T.; Mancias, J. D.; Cravatt, B. F.; Gygi, S. P. Reimagining High-Throughput Profiling of Reactive Cysteines for Cell-Based Screening of Large Electrophile Libraries. Nat. Biotechnol. 2021, 39 (5), 630– 641,  DOI: 10.1038/s41587-020-00778-3
      106
      Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries
      Kuljanin, Miljan; Mitchell, Dylan C.; Schweppe, Devin K.; Gikandi, Ajami S.; Nusinow, David P.; Bulloch, Nathan J.; Vinogradova, Ekaterina V.; Wilson, David L.; Kool, Eric T.; Mancias, Joseph D.; Cravatt, Benjamin F.; Gygi, Steven P.
      Nature Biotechnology (2021), 39 (5), 630-641CODEN: NABIF9; ISSN:1087-0156. (Nature Portfolio)
      Current methods used for measuring amino acid side-chain reactivity lack the throughput needed to screen large chem. libraries for interactions across the proteome. Here we redesigned the work flow for activity-based protein profiling of reactive cysteine residues by using a smaller desthiobiotin-based probe, sample multiplexing, reduced protein starting amts. and software to boost data acquisition in real time on the mass spectrometer. Our method, streamlined cysteine activity-based protein profiling (SLC-ABPP), achieved a 42-fold improvement in sample throughput, corresponding to profiling library members at a depth of >8,000 reactive cysteine sites at 18 min per compd. We applied it to identify proteome-wide targets of covalent inhibitors to mutant Kirsten rat sarcoma (KRAS)G12C and Bruton's tyrosine kinase (BTK). In addn., we created a resource of cysteine reactivity to 285 electrophiles in three human cell lines, which includes >20,000 cysteines from >6,000 proteins per line. The goal of proteome-wide profiling of cysteine reactivity across thousand-member libraries under several cellular contexts is now within reach.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXkslSrug%253D%253D&md5=d256bc7ff87c75e4929fe4a6649242b4
    107. 107
      Yamamoto, M.; Kensler, T. W.; Motohashi, H. The KEAP1-NRF2 System: A Thiol-Based Sensor-Effector Apparatus for Maintaining Redox Homeostasis. Physiol. Rev. 2018, 98 (3), 1169– 1203,  DOI: 10.1152/physrev.00023.2017
      107
      The KEAP1-NRF2 system: a thiol-based sensor-effector apparatus for maintaining redox homeostasis
      Yamamoto, Masayuki; Kensler, Thomas W.; Motohashi, Hozumi
      Physiological Reviews (2018), 98 (3), 1169-1203CODEN: PHREA7; ISSN:1522-1210. (American Physiological Society)
      A review. The Kelch-like ECH-assocd. protein 1-NF-E2-related factor 2 (KEAP1-NRF2) system forms the major node of cellular and organismal defense against oxidative and electrophilic stresses of both exogenous and endogenous origins. KEAP1 acts as a cysteine thiol-rich sensor of redox insults, whereas NRF2 is a transcription factor that robustly transduces chem. signals to regulate a battery of cytoprotective genes. KEAP1 represses NRF2 activity under quiescent conditions, whereas NRF2 is liberated from KEAP1-mediated repression on exposure to stresses. The rapid inducibility of a response based on a derepression mechanism is an important feature of the KEAP1-NRF2 system. Recent studies have unveiled the complexities of the functional contributions of the KEAP1-NRF2 system and defined its broader involvement in biol. processes, including cell proliferation and differentiation, as well as cytoprotection. In this review, we describe historical milestones in the initial characterization of the KEAP1-NRF2 system and provide a comprehensive overview of the mol. mechanisms governing the functions of KEAP1 and NRF2, as well as their roles in physiol. and pathol. We also refer to the clin. significance of the KEAP1-NRF2 system as an important prophylactic and therapeutic target for various diseases, particularly aging-related disorders. We believe that controlled harnessing of the KEAP1-NRF2 system is a key to healthy aging and well-being in humans.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXkvFektrc%253D&md5=906947c8ad97c48f60e46bc44103664a
    108. 108
      Unoki, T.; Akiyama, M.; Kumagai, Y. Nrf2 Activation and Its Coordination with the Protective Defense Systems in Response to Electrophilic Stress. Int. J. Mol. Sci. 2020, 21 (2), 545,  DOI: 10.3390/ijms21020545
      There is no corresponding record for this reference.
    109. 109
      Backus, K. M.; Cao, J.; Maddox, S. M. Opportunities and Challenges for the Development of Covalent Chemical Immunomodulators. Bioorg. Med. Chem. 2019, 27 (15), 3421– 3439,  DOI: 10.1016/j.bmc.2019.05.050
      109
      Opportunities and challenges for the development of covalent chemical immunomodulators
      Backus, Keriann M.; Cao, Jian; Maddox, Sean M.
      Bioorganic & Medicinal Chemistry (2019), 27 (15), 3421-3439CODEN: BMECEP; ISSN:0968-0896. (Elsevier B.V.)
      A review. Compds. that react irreversibly with cysteines have reemerged as potent and selective tools for altering protein function, serving as chem. probes and even clin. approved drugs. The exquisite sensitivity of human immune cell signaling pathways to oxidative stress indicates the likely, yet still underexploited, general utility of covalent probes for selective chem. immunomodulation. Here, we provide an overview of immunomodulatory cysteines, including identification of electrophilic compds. available to label these residues. We focus our discussion on three protein classes essential for cell signaling, which span the 'druggability' spectrum from amenable to chem. probes (kinases), somewhat druggable (proteases), to inaccessible (phosphatases). Using existing inhibitors as a guide, we identify general strategies to guide the development of covalent probes for selected undruggable classes of proteins and propose the application of such compds. to alter immune cell functions.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtFOku73L&md5=fbec9cd36ed1c0f3e9dbacf4d613730b
    110. 110
      Lincoln, R.; Zhang, W.; Lovell, T. C.; Jodko-Piórecka, K.; Devlaminck, P. A.; Sakaya, A.; Van Kessel, A.; Cosa, G. Chemically Tuned, Reversible Fluorogenic Electrophile for Live Cell Nanoscopy. ACS Sens. 2022, 7 (1), 166– 174,  DOI: 10.1021/acssensors.1c01940
      There is no corresponding record for this reference.
    111. 111
      Zheng, S.; Liu, G. Polymeric Emissive Materials Based on Dynamic Covalent Bonds. Mol. Basel Switz. 2022, 27 (19), 6635,  DOI: 10.3390/molecules27196635
      There is no corresponding record for this reference.