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Rational Design of Ligands with Optimized Residence TimeClick to copy article linkArticle link copied!
- Paolo Carloni*Paolo Carloni*[email protected]Computational Biomedicine, Institute for Neuroscience and Medicine, INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, GermanyFaculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52062 Aachen, GermanyMore by Paolo Carloni
- Giulia RossettiGiulia RossettiComputational Biomedicine, Institute for Neuroscience and Medicine, INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, GermanyJuelich Supercomputing Center (JSC), Forschungszentrum Jülich GmbH, 52428 Jülich, GermanyDepartment of Neurology, Faculty of Medicine, RWTH Aachen, 52074 Aachen, GermanyMore by Giulia Rossetti
- Christa E. MüllerChrista E. MüllerPharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, GermanyMore by Christa E. Müller
ACS Pharmacology & Translational Science
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Abstract
Residence time (RT) refers to the duration that a drug remains bound to its target, affecting its efficacy and pharmacokinetic properties. RTs are key factors in drug design, yet the structure-based design of ligands with desired RTs is still in its infancy. Here, we propose that a combination of cutting-edge molecular dynamics-based methods with classical computer-aided ligand design can help identify ligands that bind not only with high affinity to their target receptors but also with the required residence time to fully exert their beneficial action without causing undesired side effects.
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The kinetics of drug unbinding from proteins is a critical factor influencing drug efficacy. (1−3) Drug–protein target residence time (RT), defined as the reciprocal of a drug’s dissociation rate constant koff (RT = 1/koff), is gaining recognition as a crucial parameter for determining clinical efficacy. (4) Drugs with relatively long residence times (e.g., of minutes to hours at 37 °C) often show prolonged pharmacodynamic effects (5) and, in some cases, reduced toxicity, which is beneficial for designing more effective therapeutics. (6) A long residence time is desired for many drugs, e.g., those targeting chronic diseases such as cancer. (7) Recently, there has even been an upsurge in the development of infinite residence time covalent drugs for cancer, infection, and other indications. (8) Long residence times mean that drugs are still active even when they are no longer in circulation. (7) On the other hand, a drug with a short residence time may in some cases offer advantages such as a reduced risk of prolonged side effects, easier dosage adjustment, and faster reversibility of its effects. (9)
Unfortunately, to elucidate how small changes in drugs’ chemical structures can have profound effects on their RTs has in most cases remained speculative or elusive. It would clearly be of great importance to design drugs that are optimized not only for initial binding affinity but also for prolonged action at the protein target site. This could be achieved by focusing on high free energy intermediates along ligand unbinding pathways, which in turn can be predicted by a vast arsenal of powerful computational tools, and then tested experimentally. Indeed, to rationally design drugs with improved residence times, one must know the structural determinants of the transition state associated with the protein–ligand complex during the unbinding process. This represents the highest free energy configuration along the unbinding pathway, where the ligand is in a transient, less-stable position as it detaches from its target. Ligands that stabilize the intermediate states occurring during dissociation of the ligand from its target are expected to display prolonged RTs. While experimental techniques usually do not reveal the structural details of the transition states, a variety of computer simulation approaches effectively predict the kinetics of drug unbinding at the molecular level and provide a quantitative estimate of the residence time: (10−12) (i) Very long molecular dynamics (MD) simulations on dedicated machines such as Anton (https://www.deshawresearch.com/) have described this process at the molecular level, and (ii) techniques like infrequent metadynamics, Gaussian Accelerated MD, scaled MD, and dissipation-corrected targeted MD apply biasing potentials to reduce the free energy barriers that slow down dissociation events. These biases artificially accelerate the unbinding process, allowing faster sampling of dissociation events. Correction terms are then used to convert the biased dissociation rates into unbiased residence time estimates. Figure 1 shows an application using one of these methods (infrequent metadynamics) on a neuronal receptor of high medical relevance, the muscarinic receptor M2. (13) (iii) Methods like weighted ensemble and milestoning focus on generating an ensemble of unbiased trajectories by restarting simulations from specific configurations that are more likely to lead to unbinding. This approach increases the probability of observing the dissociation events without directly applying biasing forces, offering a rigorous way to compute unbinding kinetics. (iv) Markov State Models (MSMs), by analyzing molecular simulation data, provide insights into the metastable states of a system and the transition rates between them. MSMs help describe the complex conformational landscape of protein–ligand systems, offering a detailed understanding of both the binding and unbinding processes. Within the limitations associated with the force field used, (13) one can choose any of these methods to bridge the gap between experimental kinetic data and the detailed molecular mechanisms that underlie drug–target interactions. By stabilizing the transition states of known ligands by chemical modification, one may identify new ligands with longer residence times. Small changes in the interactions that stabilize this transition state can have a significant impact on the rate of dissociation.
Figure 1
Figure 1. The residence time of a ligand (here the molecule iperoxo) unbinding from its target receptor (the transmembrane G protein-coupled muscarinic receptor M2), as investigated by metadynamics simulations. (13) Top: Simulation setup. Bottom: The simulation explores the bound state and three different intermediate states (State A-C), along with the transition states among them. TS 2 is the state at the highest free energy. Taken from ref (13).
A drug design protocol for ligands with improved residence times could thus involve the following steps: (i) Determining which amino acid residues and noncovalent interactions are most critical for stabilizing the ligand during the transition state (TS 2 in Figure 1). (ii) Based on the knowledge of the transition state structure, designing new ligands or modifying existing ones to enhance their interactions with the protein during the intermediate state. This might involve adding or modifying functional groups on the ligand to better interact with specific residues or to form new bonds that stabilize the transition state. The predictions could be tested experimentally by chemical synthesis of the ligands, followed by kinetic assays. Techniques like X-ray crystallography (14) and cryo-electron microscopy (15) might be further used to capture structural snapshots of the transition state analogs.
In conclusion, transition state design is a powerful concept that can lead to the development of drugs with longer-lasting effects, greater target selectivity, and reduced off-target interactions, and thus less side effects and decreased toxicity. Collaborative efforts are required by computational and medicinal chemists involving associated disciplines such as structural biology and pharmacology. If these efforts are made, we can soon expect concrete results in this field by academic and industrial laboratories all over the world.
Author Information
- Giulia Rossetti - Computational Biomedicine, Institute for Neuroscience and Medicine, INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany; Juelich Supercomputing Center (JSC), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany; Department of Neurology, Faculty of Medicine, RWTH Aachen, 52074 Aachen, Germany;
https://orcid.org/0000-0002-2032-4630 - Christa E. Müller - PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany;https://orcid.org/0000-0002-0013-6624
References
This article references 15 other publications.
- 1Voss, J. H.; Crüsemann, M.; Bartling, C. R. O.; Kehraus, S.; Inoue, A.; König, G. M.; Strømgaard, K.; Müller, C. E. Structure-affinity and structure-residence time relationships of macrocyclic Gαq protein inhibitors. iScience 2023, 26, 106492 DOI: 10.1016/j.isci.2023.106492Google Scholar1Structure-affinity and structure-residence time relationships of macrocyclic Gαq protein inhibitorsVoss, Jan H.; Cruesemann, Max; Bartling, Christian R. O.; Kehraus, Stefan; Inoue, Asuka; Koenig, Gabriele M.; Stroemgaard, Kristian; Mueller, Christa E.iScience (2023), 26 (4), 106492CODEN: ISCICE; ISSN:2589-0042. (Elsevier B.V.)The macrocyclic depsipeptides YM-254890 (YM) and FR900359 (FR) are potent inhibitors of G αq/11 proteins. They are important pharmacol. tools and have potential as therapeutic drugs. The hydrogenated, tritium-labeled YM and FR derivs. display largely different residence times despite similar structures. In the present study we established a competition-assocn. binding assay to det. the dissocn. kinetics of unlabeled Gq protein inhibitors. Structure-affinity and structure-residence time relationships were analyzed. Small structural modifications had a large impact on residence time. YM and FR exhibited 4- to 10-fold higher residence times than their hydrogenated derivs. While FR showed pseudo-irreversible binding, YM displayed much faster dissocn. from its target. The iso-Pr anchor present in FR and some derivs. was essential for slow dissocn. These data provide a basis for future drug design toward modulating residence times of macrocyclic Gq protein inhibitors, which has been recognized as a crucial determinant for therapeutic outcome.
- 2Voss, J. H.; Nagel, J.; Rafehi, M.; Guixà-González, R.; Malfacini, D.; Patt, J.; Kehraus, S.; Inoue, A.; König, G. M.; Kostenis, E.; Deupi, X.; Namasivayam, V.; Müller, C. E. Unraveling binding mechanism and kinetics of macrocyclic Gαq protein inhibitors. Pharmacol. Res. 2021, 173, 105880 DOI: 10.1016/j.phrs.2021.105880Google Scholar2Unraveling binding mechanism and kinetics of macrocyclic Gαq protein inhibitorsVoss, Jan H.; Nagel, Jessica; Rafehi, Muhammad; Guixa-Gonzalez, Ramon; Malfacini, Davide; Patt, Julian; Kehraus, Stefan; Inoue, Asuka; Koenig, Gabriele M.; Kostenis, Evi; Deupi, Xavier; Namasivayam, Vigneshwaran; Mueller, Christa E.Pharmacological Research (2021), 173 (), 105880CODEN: PHMREP; ISSN:1043-6618. (Elsevier Ltd.)G proteins represent intracellular switches that transduce signals relayed from G protein-coupled receptors. The structurally related macrocyclic depsipeptides FR900359 (FR) and YM-254890 (YM) are potent, selective inhibitors of the Gαq protein family. We recently discovered that radiolabeled FR and YM display strongly divergent residence times, which translates into significantly longer antiasthmatic effects of FR. The present study is aimed at investigating the mol. basis for this obsd. disparity. Based on docking studies, we mutated amino acid residues of the Gαq protein predicted to interact with FR or YM, and recombinantly expressed the mutated Gαq proteins in cells in which the native Gαq proteins had been knocked out by CRISPR-Cas9. Both radioligands showed similar assocn. kinetics, and their binding followed a conformational selection mechanism, which was rationalized by mol. dynamics simulation studies. Several mutations of amino acid residues near the putative binding site of the "lipophilic anchors" of FR, esp. those predicted to interact with the iso-Pr group present in FR but not in YM, led to dramatically accelerated dissocn. kinetics. Our data indicate that the long residence time of FR depends on lipophilic interactions within its binding site. The obsd. structure-kinetic relationships point to a complex binding mechanism of FR, which likely involves snap-lock- or dowel-like conformational changes of either ligand or protein, or both. These exptl. data will be useful for the design of compds. with a desired residence time, a parameter that has now been recognized to be of utmost importance in drug development.
- 3Schlegel, J. G.; Tahoun, M.; Seidinger, A.; Voss, J. H.; Kuschak, M.; Kehraus, S.; Schneider, M.; Matthey, M.; Fleischmann, B. K.; König, G. M.; Wenzel, D.; Müller, C. E. Macrocyclic Gq Protein Inhibitors FR900359 and/or YM-254890-Fit for Translation?. ACS Pharmacol. Transl. Sci. 2021, 4, 888– 897, DOI: 10.1021/acsptsci.1c00021Google Scholar3Macrocyclic Gq Protein Inhibitors FR900359 and/or YM-254890-Fit for Translation?Schlegel, Jonathan G.; Tahoun, Mariam; Seidinger, Alexander; Voss, Jan H.; Kuschak, Markus; Kehraus, Stefan; Schneider, Marion; Matthey, Michaela; Fleischmann, Bernd K.; Koenig, Gabriele M.; Wenzel, Daniela; Mueller, Christa E.ACS Pharmacology & Translational Science (2021), 4 (2), 888-897CODEN: APTSFN; ISSN:2575-9108. (American Chemical Society)Guanine nucleotide-binding proteins (G proteins) transduce extracellular signals received by G protein-coupled receptors (GPCRs) to intracellular signaling cascades. While GPCRs represent the largest class of drug targets, G protein inhibition has only recently been recognized as a novel strategy for treating complex diseases such as asthma, inflammation, and cancer. The structurally similar macrocyclic depsipeptides FR900359 (FR) and YM-254890 (YM) are potent selective inhibitors of the Gq subfamily of G proteins. FR and YM differ in two positions, FR being more lipophilic than YM. Both compds. are utilized as pharmacol. tools to block Gq proteins in vitro and in vivo. However, no detailed characterization of FR and YM has been performed, which is a prerequisite for the compds.' translation into clin. application. Here, we performed a thorough study of both compds.' physicochem., pharmacokinetic, and pharmacol. properties. Chem. stability was high across a large range of pH values, with FR being somewhat more stable than YM. Oral bioavailability and brain penetration of both depsipeptides were low. FR showed lower plasma protein binding and was metabolized significantly faster than YM by human and mouse liver microsomes. FR accumulated in lung after chronic intratracheal or i.p. application, while YM was more distributed to other organs. Most strikingly, the previously obsd. longer residence time of FR resulted in a significantly prolonged pharmacol. effect as compared to YM in a methacholine-induced bronchoconstriction mouse model. These results prove that changes within a mol. which seem marginal compared to its structural complexity can lead to crucial pharmacol. differences.
- 4Zhong, H.; Zhang, Z.; Chen, M.; Chen, Y.; Yang, C.; Xue, Y.; Xu, P.; Liu, H. Structural Basis for Long Residence Time c-Src Antagonist: Insights from Molecular Dynamics Simulations. Int. J. Mol. Sci. 2024, 25, 10477, DOI: 10.3390/ijms251910477Google ScholarThere is no corresponding record for this reference.
- 5Tonge, P. J. Drug-Target Kinetics in Drug Discovery. ACS Chem. Neurosci. 2018, 9, 29– 39, DOI: 10.1021/acschemneuro.7b00185Google Scholar5Drug-Target Kinetics in Drug DiscoveryTonge, Peter J.ACS Chemical Neuroscience (2018), 9 (1), 29-39CODEN: ACNCDM; ISSN:1948-7193. (American Chemical Society)A review. The development of therapies for the treatment of neurol. cancer faces a no. of major challenges including the synthesis of small mol. agents that can penetrate the blood brain barrier (BBB). Given the likelihood that in many cases drug exposure will be lower in the CNS than in systemic circulation, it follows that strategies should be employed that can sustain target engagement at low drug concn. Time dependent target occupancy is a function of both the drug and target concn. as well as the thermodn. and kinetic parameters that describe the binding reaction coordinate, and sustained target occupancy can be achieved through structural modifications that increase target (re)binding and/or that decrease the rate of drug dissocn. The discovery and deployment of compds. with optimized kinetic effects requires information on the structure-kinetic relationships that modulate the kinetics of binding, and the mol. factors that control the translation of drug-target kinetics to time-dependent drug activity in the disease state. This review first introduces the potential benefits of drug-target kinetics, such as the ability to delineate both thermodn. and kinetic selectivity, and then describes factors, such as target vulnerability, that impact the utility of kinetic selectivity. The review concludes with a description of a mechanistic PK/PD model that integrates drug-target kinetics into predictions of drug activity.
- 6Bernetti, 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-042018-052340Google Scholar6Kinetics of Drug Binding and Residence TimeBernetti, Mattia; Masetti, Matteo; Rocchia, Walter; Cavalli, AndreaAnnual 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.
- 7Copeland, R. A. The drug-target residence time model: a 10-year retrospective. Nat. Rev. Drug Discovery 2016, 15, 87– 95, DOI: 10.1038/nrd.2015.18Google Scholar7The drug-target residence time model: a 10-year retrospectiveCopeland, Robert A.Nature Reviews Drug Discovery (2016), 15 (2), 87-95CODEN: NRDDAG; ISSN:1474-1776. (Nature Publishing Group)The drug-target residence time model was first introduced in 2006 and has been broadly adopted across the chem. biol., biotechnol. and pharmaceutical communities. While traditional in vitro methods view drug-target interactions exclusively in terms of equil. affinity, the residence time model takes into account the conformational dynamics of target macromols. that affect drug binding and dissocn. The key tenet of this model is that the lifetime (or residence time) of the binary drug-target complex, and not the binding affinity per se, dictates much of the in vivo pharmacol. activity. Here, this model is revisited and key applications of it over the past 10 years are highlighted.
- 8De Vita, E. 10 years into the resurgence of covalent drugs. Future Med. Chem. 2021, 13, 193– 210, DOI: 10.4155/fmc-2020-0236Google Scholar810 years into the resurgence of covalent drugsDe Vita ElenaFuture 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.
- 9van der Velden, W. J. C.; Heitman, L. H.; Rosenkilde, M. M. Perspective: Implications of Ligand-Receptor Binding Kinetics for Therapeutic Targeting of G Protein-Coupled Receptors. ACS Pharmacol. Transl. Sci. 2020, 3, 179– 189, DOI: 10.1021/acsptsci.0c00012Google Scholar9Perspective: Implications of Ligand-Receptor Binding Kinetics for Therapeutic Targeting of G Protein-Coupled Receptorsvan der Velden, Wijnand J. C.; Heitman, Laura H.; Rosenkilde, Mette M.ACS Pharmacology & Translational Science (2020), 3 (2), 179-189CODEN: APTSFN; ISSN:2575-9108. (American Chemical Society)A review. The concept of ligand-receptor binding kinetics has been broadly applied in drug development pipelines focusing on G protein-coupled receptors (GPCRs). The ligand residence time (RT) for a receptor describes how long a ligand-receptor complex exists, and is defined as the reciprocal of the dissocn. rate const. (koff). RT has turned out to be a valuable parameter for GPCR researchers focusing on drug development as a good predictor of in vivo efficacy. The pos. correlation between RT and in vivo efficacy has been established for several drugs targeting class A GPCRs (e.g., the neurokinin-1 receptor (NK1R), the β2 adrenergic receptor (β2AR), and the muscarinic 3 receptor (M3R)) and for drugs targeting class B1 (e.g., the glucagon-like peptide 1 receptor (GLP-1R)). Recently, the assocn. rate const. (kon) has gained similar attention as another parameter affecting in vivo efficacy. In the current perspective, we address the importance of studying ligand-receptor binding kinetics for therapeutic targeting of GPCRs, with an emphasis on how binding kinetics can be altered by subtle mol. changes in the ligands and/or the receptors and how such changes affect treatment outcome. Moreover, we speculate on the impact of binding kinetic parameters for functional selectivity and sustained receptor signaling from endosomal compartments; phenomena that have gained increasing interest in attempts to improve therapeutic targeting of GPCRs.
- 10Ahmad, K.; Rizzi, A.; Capelli, R.; Mandelli, D.; Lyu, W.; Carloni, P. Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective. Front. Mol. Biosci. 2022, 9, 899805 DOI: 10.3389/fmolb.2022.899805Google Scholar10Enhanced-sampling simulations for the estimation of ligand binding kinetics: current status and perspectiveAhmad, Katya; Rizzi, Andrea; Capelli, Riccardo; Mandelli, Davide; Lyu, Wenping; Carloni, PaoloFrontiers in Molecular Biosciences (2022), 9 (), 899805CODEN: FMBRBS; ISSN:2296-889X. (Frontiers Media S.A.)A review. The dissocn. rate (koff) assocd. with ligand unbinding events from proteins is a parameter of fundamental importance in drug design. Here we review recent major advancements in mol. simulation methodologies for the prediction of koff. Next, we discuss the impact of the potential energy function models on the accuracy of calcd. koff values. Finally, we provide a perspective from high-performance computing and machine learning which might help improve such predictions.
- 11D’Arrigo, G.; Kokh, D. B.; Nunes-Alves, A.; Wade, R. C. Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD. Commun. Biol. 2024, 7, 1159, DOI: 10.1038/s42003-024-06880-5Google ScholarThere is no corresponding record for this reference.
- 12Paul, F.; Wehmeyer, C.; Abualrous, E. T.; Wu, H.; Crabtree, M. D.; Schöneberg, J.; Clarke, J.; Freund, C.; Weikl, T. R.; Noé, F. Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nat. Commun. 2017, 8, 1095, DOI: 10.1038/s41467-017-01163-6Google Scholar12Protein-peptide association kinetics beyond the seconds timescale from atomistic simulationsPaul Fabian; Wehmeyer Christoph; Abualrous Esam T; Wu Hao; Schoneberg Johannes; Noe Frank; Paul Fabian; Weikl Thomas R; Crabtree Michael D; Clarke Jane; Freund ChristianNature communications (2017), 8 (1), 1095 ISSN:.Understanding and control of structures and rates involved in protein ligand binding are essential for drug design. Unfortunately, atomistic molecular dynamics (MD) simulations cannot directly sample the excessively long residence and rearrangement times of tightly binding complexes. Here we exploit the recently developed multi-ensemble Markov model framework to compute full protein-peptide kinetics of the oncoprotein fragment (25-109)Mdm2 and the nano-molar inhibitor peptide PMI. Using this system, we report, for the first time, direct estimates of kinetics beyond the seconds timescale using simulations of an all-atom MD model, with high accuracy and precision. These results only require explicit simulations on the sub-milliseconds timescale and are tested against existing mutagenesis data and our own experimental measurements of the dissociation and association rates. The full kinetic model reveals an overall downhill but rugged binding funnel with multiple pathways. The overall strong binding arises from a variety of conformations with different hydrophobic contact surfaces that interconvert on the milliseconds timescale.
- 13Capelli, R.; Lyu, W.; Bolnykh, V.; Meloni, S.; Magnus, J.; Olsen, H.; Rothlisberger, U.; Parrinello, M.; Carloni, P. Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study. J. Phys. Chem. let. 2020, 11, 6373– 6381, DOI: 10.1021/acs.jpclett.0c00999Google ScholarThere is no corresponding record for this reference.
- 14Fieulaine, S.; Boularot, A.; Artaud, I.; Desmadril, M.; Dardel, F.; Meinnel, T.; Giglione, C. Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis. PLoS Biol. 2011, 9, e1001066 DOI: 10.1371/journal.pbio.1001066Google ScholarThere is no corresponding record for this reference.
- 15De, I.; Weidenhausen, J.; Concha, N.; Müller, C. W. Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy. PLoS One 2024, 19, e0307850 DOI: 10.1371/journal.pone.0307850Google ScholarThere is no corresponding record for this reference.
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Abstract
Figure 1
Figure 1. The residence time of a ligand (here the molecule iperoxo) unbinding from its target receptor (the transmembrane G protein-coupled muscarinic receptor M2), as investigated by metadynamics simulations. (13) Top: Simulation setup. Bottom: The simulation explores the bound state and three different intermediate states (State A-C), along with the transition states among them. TS 2 is the state at the highest free energy. Taken from ref (13).
References
This article references 15 other publications.
- 1Voss, J. H.; Crüsemann, M.; Bartling, C. R. O.; Kehraus, S.; Inoue, A.; König, G. M.; Strømgaard, K.; Müller, C. E. Structure-affinity and structure-residence time relationships of macrocyclic Gαq protein inhibitors. iScience 2023, 26, 106492 DOI: 10.1016/j.isci.2023.1064921Structure-affinity and structure-residence time relationships of macrocyclic Gαq protein inhibitorsVoss, Jan H.; Cruesemann, Max; Bartling, Christian R. O.; Kehraus, Stefan; Inoue, Asuka; Koenig, Gabriele M.; Stroemgaard, Kristian; Mueller, Christa E.iScience (2023), 26 (4), 106492CODEN: ISCICE; ISSN:2589-0042. (Elsevier B.V.)The macrocyclic depsipeptides YM-254890 (YM) and FR900359 (FR) are potent inhibitors of G αq/11 proteins. They are important pharmacol. tools and have potential as therapeutic drugs. The hydrogenated, tritium-labeled YM and FR derivs. display largely different residence times despite similar structures. In the present study we established a competition-assocn. binding assay to det. the dissocn. kinetics of unlabeled Gq protein inhibitors. Structure-affinity and structure-residence time relationships were analyzed. Small structural modifications had a large impact on residence time. YM and FR exhibited 4- to 10-fold higher residence times than their hydrogenated derivs. While FR showed pseudo-irreversible binding, YM displayed much faster dissocn. from its target. The iso-Pr anchor present in FR and some derivs. was essential for slow dissocn. These data provide a basis for future drug design toward modulating residence times of macrocyclic Gq protein inhibitors, which has been recognized as a crucial determinant for therapeutic outcome.
- 2Voss, J. H.; Nagel, J.; Rafehi, M.; Guixà-González, R.; Malfacini, D.; Patt, J.; Kehraus, S.; Inoue, A.; König, G. M.; Kostenis, E.; Deupi, X.; Namasivayam, V.; Müller, C. E. Unraveling binding mechanism and kinetics of macrocyclic Gαq protein inhibitors. Pharmacol. Res. 2021, 173, 105880 DOI: 10.1016/j.phrs.2021.1058802Unraveling binding mechanism and kinetics of macrocyclic Gαq protein inhibitorsVoss, Jan H.; Nagel, Jessica; Rafehi, Muhammad; Guixa-Gonzalez, Ramon; Malfacini, Davide; Patt, Julian; Kehraus, Stefan; Inoue, Asuka; Koenig, Gabriele M.; Kostenis, Evi; Deupi, Xavier; Namasivayam, Vigneshwaran; Mueller, Christa E.Pharmacological Research (2021), 173 (), 105880CODEN: PHMREP; ISSN:1043-6618. (Elsevier Ltd.)G proteins represent intracellular switches that transduce signals relayed from G protein-coupled receptors. The structurally related macrocyclic depsipeptides FR900359 (FR) and YM-254890 (YM) are potent, selective inhibitors of the Gαq protein family. We recently discovered that radiolabeled FR and YM display strongly divergent residence times, which translates into significantly longer antiasthmatic effects of FR. The present study is aimed at investigating the mol. basis for this obsd. disparity. Based on docking studies, we mutated amino acid residues of the Gαq protein predicted to interact with FR or YM, and recombinantly expressed the mutated Gαq proteins in cells in which the native Gαq proteins had been knocked out by CRISPR-Cas9. Both radioligands showed similar assocn. kinetics, and their binding followed a conformational selection mechanism, which was rationalized by mol. dynamics simulation studies. Several mutations of amino acid residues near the putative binding site of the "lipophilic anchors" of FR, esp. those predicted to interact with the iso-Pr group present in FR but not in YM, led to dramatically accelerated dissocn. kinetics. Our data indicate that the long residence time of FR depends on lipophilic interactions within its binding site. The obsd. structure-kinetic relationships point to a complex binding mechanism of FR, which likely involves snap-lock- or dowel-like conformational changes of either ligand or protein, or both. These exptl. data will be useful for the design of compds. with a desired residence time, a parameter that has now been recognized to be of utmost importance in drug development.
- 3Schlegel, J. G.; Tahoun, M.; Seidinger, A.; Voss, J. H.; Kuschak, M.; Kehraus, S.; Schneider, M.; Matthey, M.; Fleischmann, B. K.; König, G. M.; Wenzel, D.; Müller, C. E. Macrocyclic Gq Protein Inhibitors FR900359 and/or YM-254890-Fit for Translation?. ACS Pharmacol. Transl. Sci. 2021, 4, 888– 897, DOI: 10.1021/acsptsci.1c000213Macrocyclic Gq Protein Inhibitors FR900359 and/or YM-254890-Fit for Translation?Schlegel, Jonathan G.; Tahoun, Mariam; Seidinger, Alexander; Voss, Jan H.; Kuschak, Markus; Kehraus, Stefan; Schneider, Marion; Matthey, Michaela; Fleischmann, Bernd K.; Koenig, Gabriele M.; Wenzel, Daniela; Mueller, Christa E.ACS Pharmacology & Translational Science (2021), 4 (2), 888-897CODEN: APTSFN; ISSN:2575-9108. (American Chemical Society)Guanine nucleotide-binding proteins (G proteins) transduce extracellular signals received by G protein-coupled receptors (GPCRs) to intracellular signaling cascades. While GPCRs represent the largest class of drug targets, G protein inhibition has only recently been recognized as a novel strategy for treating complex diseases such as asthma, inflammation, and cancer. The structurally similar macrocyclic depsipeptides FR900359 (FR) and YM-254890 (YM) are potent selective inhibitors of the Gq subfamily of G proteins. FR and YM differ in two positions, FR being more lipophilic than YM. Both compds. are utilized as pharmacol. tools to block Gq proteins in vitro and in vivo. However, no detailed characterization of FR and YM has been performed, which is a prerequisite for the compds.' translation into clin. application. Here, we performed a thorough study of both compds.' physicochem., pharmacokinetic, and pharmacol. properties. Chem. stability was high across a large range of pH values, with FR being somewhat more stable than YM. Oral bioavailability and brain penetration of both depsipeptides were low. FR showed lower plasma protein binding and was metabolized significantly faster than YM by human and mouse liver microsomes. FR accumulated in lung after chronic intratracheal or i.p. application, while YM was more distributed to other organs. Most strikingly, the previously obsd. longer residence time of FR resulted in a significantly prolonged pharmacol. effect as compared to YM in a methacholine-induced bronchoconstriction mouse model. These results prove that changes within a mol. which seem marginal compared to its structural complexity can lead to crucial pharmacol. differences.
- 4Zhong, H.; Zhang, Z.; Chen, M.; Chen, Y.; Yang, C.; Xue, Y.; Xu, P.; Liu, H. Structural Basis for Long Residence Time c-Src Antagonist: Insights from Molecular Dynamics Simulations. Int. J. Mol. Sci. 2024, 25, 10477, DOI: 10.3390/ijms251910477There is no corresponding record for this reference.
- 5Tonge, P. J. Drug-Target Kinetics in Drug Discovery. ACS Chem. Neurosci. 2018, 9, 29– 39, DOI: 10.1021/acschemneuro.7b001855Drug-Target Kinetics in Drug DiscoveryTonge, Peter J.ACS Chemical Neuroscience (2018), 9 (1), 29-39CODEN: ACNCDM; ISSN:1948-7193. (American Chemical Society)A review. The development of therapies for the treatment of neurol. cancer faces a no. of major challenges including the synthesis of small mol. agents that can penetrate the blood brain barrier (BBB). Given the likelihood that in many cases drug exposure will be lower in the CNS than in systemic circulation, it follows that strategies should be employed that can sustain target engagement at low drug concn. Time dependent target occupancy is a function of both the drug and target concn. as well as the thermodn. and kinetic parameters that describe the binding reaction coordinate, and sustained target occupancy can be achieved through structural modifications that increase target (re)binding and/or that decrease the rate of drug dissocn. The discovery and deployment of compds. with optimized kinetic effects requires information on the structure-kinetic relationships that modulate the kinetics of binding, and the mol. factors that control the translation of drug-target kinetics to time-dependent drug activity in the disease state. This review first introduces the potential benefits of drug-target kinetics, such as the ability to delineate both thermodn. and kinetic selectivity, and then describes factors, such as target vulnerability, that impact the utility of kinetic selectivity. The review concludes with a description of a mechanistic PK/PD model that integrates drug-target kinetics into predictions of drug activity.
- 6Bernetti, 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-042018-0523406Kinetics of Drug Binding and Residence TimeBernetti, Mattia; Masetti, Matteo; Rocchia, Walter; Cavalli, AndreaAnnual 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.
- 7Copeland, R. A. The drug-target residence time model: a 10-year retrospective. Nat. Rev. Drug Discovery 2016, 15, 87– 95, DOI: 10.1038/nrd.2015.187The drug-target residence time model: a 10-year retrospectiveCopeland, Robert A.Nature Reviews Drug Discovery (2016), 15 (2), 87-95CODEN: NRDDAG; ISSN:1474-1776. (Nature Publishing Group)The drug-target residence time model was first introduced in 2006 and has been broadly adopted across the chem. biol., biotechnol. and pharmaceutical communities. While traditional in vitro methods view drug-target interactions exclusively in terms of equil. affinity, the residence time model takes into account the conformational dynamics of target macromols. that affect drug binding and dissocn. The key tenet of this model is that the lifetime (or residence time) of the binary drug-target complex, and not the binding affinity per se, dictates much of the in vivo pharmacol. activity. Here, this model is revisited and key applications of it over the past 10 years are highlighted.
- 8De Vita, E. 10 years into the resurgence of covalent drugs. Future Med. Chem. 2021, 13, 193– 210, DOI: 10.4155/fmc-2020-0236810 years into the resurgence of covalent drugsDe Vita ElenaFuture 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.
- 9van der Velden, W. J. C.; Heitman, L. H.; Rosenkilde, M. M. Perspective: Implications of Ligand-Receptor Binding Kinetics for Therapeutic Targeting of G Protein-Coupled Receptors. ACS Pharmacol. Transl. Sci. 2020, 3, 179– 189, DOI: 10.1021/acsptsci.0c000129Perspective: Implications of Ligand-Receptor Binding Kinetics for Therapeutic Targeting of G Protein-Coupled Receptorsvan der Velden, Wijnand J. C.; Heitman, Laura H.; Rosenkilde, Mette M.ACS Pharmacology & Translational Science (2020), 3 (2), 179-189CODEN: APTSFN; ISSN:2575-9108. (American Chemical Society)A review. The concept of ligand-receptor binding kinetics has been broadly applied in drug development pipelines focusing on G protein-coupled receptors (GPCRs). The ligand residence time (RT) for a receptor describes how long a ligand-receptor complex exists, and is defined as the reciprocal of the dissocn. rate const. (koff). RT has turned out to be a valuable parameter for GPCR researchers focusing on drug development as a good predictor of in vivo efficacy. The pos. correlation between RT and in vivo efficacy has been established for several drugs targeting class A GPCRs (e.g., the neurokinin-1 receptor (NK1R), the β2 adrenergic receptor (β2AR), and the muscarinic 3 receptor (M3R)) and for drugs targeting class B1 (e.g., the glucagon-like peptide 1 receptor (GLP-1R)). Recently, the assocn. rate const. (kon) has gained similar attention as another parameter affecting in vivo efficacy. In the current perspective, we address the importance of studying ligand-receptor binding kinetics for therapeutic targeting of GPCRs, with an emphasis on how binding kinetics can be altered by subtle mol. changes in the ligands and/or the receptors and how such changes affect treatment outcome. Moreover, we speculate on the impact of binding kinetic parameters for functional selectivity and sustained receptor signaling from endosomal compartments; phenomena that have gained increasing interest in attempts to improve therapeutic targeting of GPCRs.
- 10Ahmad, K.; Rizzi, A.; Capelli, R.; Mandelli, D.; Lyu, W.; Carloni, P. Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective. Front. Mol. Biosci. 2022, 9, 899805 DOI: 10.3389/fmolb.2022.89980510Enhanced-sampling simulations for the estimation of ligand binding kinetics: current status and perspectiveAhmad, Katya; Rizzi, Andrea; Capelli, Riccardo; Mandelli, Davide; Lyu, Wenping; Carloni, PaoloFrontiers in Molecular Biosciences (2022), 9 (), 899805CODEN: FMBRBS; ISSN:2296-889X. (Frontiers Media S.A.)A review. The dissocn. rate (koff) assocd. with ligand unbinding events from proteins is a parameter of fundamental importance in drug design. Here we review recent major advancements in mol. simulation methodologies for the prediction of koff. Next, we discuss the impact of the potential energy function models on the accuracy of calcd. koff values. Finally, we provide a perspective from high-performance computing and machine learning which might help improve such predictions.
- 11D’Arrigo, G.; Kokh, D. B.; Nunes-Alves, A.; Wade, R. C. Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD. Commun. Biol. 2024, 7, 1159, DOI: 10.1038/s42003-024-06880-5There is no corresponding record for this reference.
- 12Paul, F.; Wehmeyer, C.; Abualrous, E. T.; Wu, H.; Crabtree, M. D.; Schöneberg, J.; Clarke, J.; Freund, C.; Weikl, T. R.; Noé, F. Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nat. Commun. 2017, 8, 1095, DOI: 10.1038/s41467-017-01163-612Protein-peptide association kinetics beyond the seconds timescale from atomistic simulationsPaul Fabian; Wehmeyer Christoph; Abualrous Esam T; Wu Hao; Schoneberg Johannes; Noe Frank; Paul Fabian; Weikl Thomas R; Crabtree Michael D; Clarke Jane; Freund ChristianNature communications (2017), 8 (1), 1095 ISSN:.Understanding and control of structures and rates involved in protein ligand binding are essential for drug design. Unfortunately, atomistic molecular dynamics (MD) simulations cannot directly sample the excessively long residence and rearrangement times of tightly binding complexes. Here we exploit the recently developed multi-ensemble Markov model framework to compute full protein-peptide kinetics of the oncoprotein fragment (25-109)Mdm2 and the nano-molar inhibitor peptide PMI. Using this system, we report, for the first time, direct estimates of kinetics beyond the seconds timescale using simulations of an all-atom MD model, with high accuracy and precision. These results only require explicit simulations on the sub-milliseconds timescale and are tested against existing mutagenesis data and our own experimental measurements of the dissociation and association rates. The full kinetic model reveals an overall downhill but rugged binding funnel with multiple pathways. The overall strong binding arises from a variety of conformations with different hydrophobic contact surfaces that interconvert on the milliseconds timescale.
- 13Capelli, R.; Lyu, W.; Bolnykh, V.; Meloni, S.; Magnus, J.; Olsen, H.; Rothlisberger, U.; Parrinello, M.; Carloni, P. Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study. J. Phys. Chem. let. 2020, 11, 6373– 6381, DOI: 10.1021/acs.jpclett.0c00999There is no corresponding record for this reference.
- 14Fieulaine, S.; Boularot, A.; Artaud, I.; Desmadril, M.; Dardel, F.; Meinnel, T.; Giglione, C. Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis. PLoS Biol. 2011, 9, e1001066 DOI: 10.1371/journal.pbio.1001066There is no corresponding record for this reference.
- 15De, I.; Weidenhausen, J.; Concha, N.; Müller, C. W. Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy. PLoS One 2024, 19, e0307850 DOI: 10.1371/journal.pone.0307850There is no corresponding record for this reference.