ACS Publications. Most Trusted. Most Cited. Most Read
Discovery and Mechanism of SARS-CoV-2 Main Protease Inhibitors
More

OR SEARCH CITATIONS

My Activity
Publications

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Med. Chem. 2022, 65, 4, 2866-2879
  • Open Access
Article

Discovery and Mechanism of SARS-CoV-2 Main Protease Inhibitors
Click to copy article linkArticle link copied!

  • Sarah Huff
    Sarah Huff
    Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    More by Sarah Huff
  • Indrasena Reddy Kummetha
    Indrasena Reddy Kummetha
    Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    More by Indrasena Reddy Kummetha
  • Shashi Kant Tiwari
    Shashi Kant Tiwari
    Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    More by Shashi Kant Tiwari
  • Matthew B. Huante
    Matthew B. Huante
    Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, United States
    More by Matthew B. Huante
  • Alex E. Clark
    Alex E. Clark
    Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    More by Alex E. Clark
  • Shaobo Wang
    Shaobo Wang
    Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    More by Shaobo Wang
  • William Bray
    William Bray
    Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    More by William Bray
  • Davey Smith
    Davey Smith
    Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    More by Davey Smith
  • Aaron F. Carlin
    Aaron F. Carlin
    Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    More by Aaron F. Carlin
    Orcidhttps://orcid.org/0000-0002-1669-8066
  • Mark Endsley
    Mark Endsley
    Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, United States
    More by Mark Endsley
  • Tariq M. Rana*
    Tariq M. Rana
    Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    *Email: [email protected]
    More by Tariq M. Rana
    Orcidhttps://orcid.org/0000-0001-9558-5766
Open PDFSupporting Information (2)

Journal of Medicinal Chemistry

Cite this: J. Med. Chem. 2022, 65, 4, 2866–2879
Click to copy citationCitation copied!
https://doi.org/10.1021/acs.jmedchem.1c00566
Published September 27, 2021

Copyright © 2021 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

The emergence of a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents an urgent public health crisis. Without available targeted therapies, treatment options remain limited for COVID-19 patients. Using medicinal chemistry and rational drug design strategies, we identify a 2-phenyl-1,2-benzoselenazol-3-one class of compounds targeting the SARS-CoV-2 main protease (Mpro). FRET-based screening against recombinant SARS-CoV-2 Mpro identified six compounds that inhibit proteolysis with nanomolar IC50 values. Preincubation dilution experiments and molecular docking determined that the inhibition of SARS-CoV-2 Mpro can occur by either covalent or noncovalent mechanisms, and lead E04 was determined to inhibit Mpro competitively. Lead E24 inhibited viral replication with a nanomolar EC50 value (844 nM) in SARS-CoV-2-infected Vero E6 cells and was further confirmed to impair SARS-CoV-2 replication in human lung epithelial cells and human-induced pluripotent stem cell-derived 3D lung organoids. Altogether, these studies provide a structural framework and mechanism of Mpro inhibition that should facilitate the design of future COVID-19 treatments.

This publication is licensed under

CC-BY-NC-ND 4.0 .
  • cc licence
  • by licence
  • nc licence
  • nd licence
Copyright © 2021 The Authors. Published by American Chemical Society

Subjects

what are subjects

SPECIAL ISSUE

This article is part of the COVID-19 special issue.

Introduction

Click to copy section linkSection link copied!
Emergent β-coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, for which there is a great need for a new targeted treatment. SARS-CoV-2 produces a spike protein that binds to host cell receptor ACE2 for entry. (1,2) Upon entry, the positive genomic RNA of SARS-CoV-2 will attach directly to the host ribosome and translate two large polyproteins, which are then processed by proteolysis into components for packaging new virions. This proteolysis is controlled by two protease enzymes, the coronavirus main protease (Mpro) and the papain-like protease (PLpro). (2−6) An RNA-dependent RNA polymerase (RdRp) is also required to replicate the RNA genome. (2,7) As all four of these proteins are essential for viral replication, they are considered attractive drug targets for treating coronaviruses. Of these, Mpro has been widely called the virus’ “Achilles Heel” and is considered one of the most attractive targets for drug development against SARS-CoV-2. The main protease is an established drug target for similar (+)-ssRNA viruses such as HIV and hepatitis C, (8−14) although to date there are no approved therapies targeting SARS-CoV-2’s main protease.
Some early studies have identified crystal structures of potential small-molecule binders of SARS-CoV-2 Mpro, which are predominately peptide-based scaffolds. (15−20) Jin et al. determined the first crystal structure of Mpro in complex with the peptide inhibitor N3. (15) Additional crystal structures of two rationally designed covalent peptide inhibitors, 11a and 11b, were reported shortly thereafter by Dai et al. (16) Two additional reports demonstrated that the feline coronavirus drug GC376 also inhibits Mpro and prevents viral replication in infected Vero cells. (17,20) Like 11a and 11b, GC376 is a peptide inhibitor that covalently modifies active site Cys 145. Several nonpeptide small molecules have also been shown to inhibit Mpro proteolysis in vitro, including the organoselenium compound ebselen; however, to date there is only limited knowledge of their mechanism of action and the cell-based evaluation of small molecules. (15,19) At this time, most studies targeting Mpro are focused on screening existing compounds, and there has been little interest in further developing early hits using medicinal chemistry and rational drug design approaches. In this study, we sought to determine if such approaches could be applied to address the following questions: (1) can rational drug design and medicinal chemistry be used to improve the potencies of identified Mpro inhibitors? (2) Can an enzymatic mechanism of inhibition be established for rationally designed Mpro inhibitors? (3) Can rationally designed compounds inhibit viral replication in vitro? Finally, (4) how do rationally designed Mpro inhibitors compare to existing treatments such as remdesivir?
To address these questions, we used the structure of the organoselenium compound ebselen as the basis for the rational design of improved Mpro inhibitors. In silico docking at the SARS-CoV-2 Mpro active site identified a class of 2-phenyl-1,2-benzoselenazol-3-one inhibitors with nanomolar proteolytic activities against recombinant SARS-CoV-2 Mpro and improved physicochemical properties relative to those of their parent compound ebselen. Steady-state enzyme kinetics was used to determine that ebselen and its analogue E04 are competitive inhibitors of Mpro, and 2-phenyl-1,2-benzoselenazol-3-one inhibitors may follow either a noncovalent or reversible covalent mechanism. These compounds were also determined to show potent antiviral effects in multiple SARS-CoV-2-infected cell lines, with leads E24 and E25 reporting inhibitory activities comparable or better to that of the clinical antiviral treatment remdesivir (EC50(E24) = 0.8 ± 0.3 μM, EC50(E25) = 2.0 ± 1.1 μM, and EC50(remdesivir) = 1.8 ± 1.3 μM). Furthermore, E24 was found to reduce viral replication in both Calu-3 human lung epithelial cells (EC50(E24) = 1.3 ± 0.8 μM) and human iPSC-derived lung organoids infected with SARS-CoV-2.

Results

Click to copy section linkSection link copied!

Identification of the 2-Phenyl-1,2-benzoselenazol-3-one Class of SARS-CoV-2 Mpro Inhibitors

Recently, a study showed that the organoselenium compound ebselen was able to bind SARS-CoV-2 Mpro and inhibit proteolytic activity. (15) While it was determined that ebselen could partially covalently modify Mpro, the binding site was not identified. Using this information as a starting point, we sought to model ebselen in the active site of Mpro to determine if organoselenium compounds could be rationally designed to target the catalytic site. Docking was performed in the Schrödinger software suite. (21−23) A crystal structure of the SARS-CoV-2 Mpro bound to N3 (PDB ID 6UL7) was used to generate the docking grid as a 15 Å cube centered on the ligand N3. As observed in Figure 1A, the active site of Mpro is expected to accommodate ebselen. Ebselen is predicted to bind in close proximity to catalytic His 41 and Cys 145, with the benzoisoselenazole ring forming π–π stacking interactions with catalytic His 41. Binding is further stabilized by a hydrogen bond between the carbonyl oxygen atom of ebselen and Glu 166. These results are consistent with a recently reported crystal structure of SARS-CoV-2 Mpro in complex with ebselen, which indicates that it primarily binds to the catalytic site of the enzyme and forms a selenyl sulfide bond with Cys 145; this was further confirmed by LC/MRM-MS. (24)

Figure 1

Figure 1. Docking poses of ebselen and 2-phenyl-1,2-benzoselenazol-3-one analogues. (A) Docking pose of ebselen bound to the catalytic site of SARS-CoV-2 Mpro. A hydrogen bond is present between the carbonyl oxygen atom of E01 and Glu 166. The benzoisoselenazole ring forms π–π stacking interactions with catalytic His 41. (B) Docking pose of E19 bound to the catalytic site of SARS-CoV-2 Mpro. A hydrogen bond is present between the carbonyl oxygen atom of E19 and Glu 166. The benzoisoselenazole ring forms π–π stacking interactions with catalytic His 41. The chlorine atom of E19 forms a halogen bond interaction with Gly 143. (C) Docking pose of E20 bound to the catalytic site of SARS-CoV-2 Mpro. π–π stacking interactions are present between the benzoisoselenazole ring of E20 and catalytic His 41. A hydrogen bond is present between the carbonyl oxygen atom of E20 and Glu 166. (D) Docking pose of E25 bound to the catalytic site of SARS-CoV-2 Mpro. A hydrogen bond is present between the carbonyl oxygen atom of E25 and Glu 166. π–π stacking interactions are present between the benzoisoselenazole ring of E25 and catalytic His 41. The nitrile group was observed to accept a hydrogen bond from Cys 44.

High Resolution Image
Download MS PowerPoint Slide
A series of 2-phenyl-1,2-benzoselenazol-3-one analogues was designed with substitutions primarily focused on the N-phenyl moiety. Substitutions included halogens (F, Cl, and Br) and hydrophobic groups (CH3, CF3, SCH3, OCH3, and CH2CH3) as well as several lipophilic replacements of the phenyl moiety. Potential inhibitors were docked and ranked by their docking score. The docking poses of prospective analogues were evaluated for interactions with catalytic residues His 41 and Cys 145; compounds that were expected to form strong hydrogen bonds or π-interactions with these residues were prioritized for synthesis. Docking poses for ebselen and three of its analogues can be found in Figure 1. As observed in Figure 1 B, E19 is able to maintain the interactions with Glu 166 and catalytic His 41 that were observed for ebselen, while the p-chloro substituent group forms an additional halogen bond with the amide backbone of Gly 143. Similarly, the m-cyano group of E25 is able to accept a hydrogen bond from Cys 44 while maintaining the interactions of the parent compound with His 41 and Glu 166 (Figure 1 A and D). In Figure 1 C, E20 is expected to maintain the core interactions of the parent structure with His 41 and Glu 166, while m,m-dichloro substitutions occupy a larger region of the binding pocket to increase the entropy of the binding interaction. Docking poses for select additional compounds may be found in the Supporting Information (Figure S1).
A total of 30 2-phenyl-1,2-benzoselenazol-3-one compounds were selected for synthesis according to Scheme 1 (Figure 1 E). Analogues were synthesized from commercially available acid chlorides and anilines in two steps. Nucleophilic acyl substitution in the presence of triethylamine yielded intermediate 3. Ring closure to form the benzoisoselenazole ring proceeded in the presence of NaSeOtBu with selenium powder and sodium tert-butoxide in DMF to produce the final product. In total, 30 compounds were prepared according to this scheme, purified by column chromatography (hexane/ethyl acetate 70:30), and characterized by NMR and HRMS prior to the biological evaluation.

Scheme 1

Scheme 1. Synthesis of Ebselen Analogues
High Resolution Image
Download MS PowerPoint Slide

The 2-Phenyl-1,2-benzoselenazol-3-one Class of Compounds Are Potent Inhibitors of Recombinant Mpro

To determine if the 2-phenyl-1,2-benzoselenazol-3-one class of rationally designed compounds was also able to inhibit protease activity of SARS-CoV-2 Mpro, a FRET assay adapted from Muramatsu et al. (25) was used to assess the inhibitory potency of the compounds against SARS-CoV-2 Mpro at 10 μM. Ebselen was included as a positive control. (15) Of the 30 analogues tested, 22 inhibited Mpro proteolytic activity by >50%, while eight compounds showed no inhibition at this concentration. Full dose–response curves were generated for compounds showing >50% inhibition at 10 μM (Table 1). The IC50 of ebselen was observed to be 0.33 μM, which was similar to the previously reported value of 0.67 μM. (15) Most 2-phenyl-1,2-benzoselenazol-3-one analogues reported IC50 values between 1 and 7.4 μM. Compounds E04, E07, E19, E20, and E25 reported submicromolar IC50 valuess ranging from 0.38 to 0.90 μM (Table 1). Additional reports have identified two peptide inhibitors, 11a and 11b, that were designed to inhibit the main protease with more potent IC50 values (0.053 and 0.040 μM, respectively); (16) however, the observed IC50 valuess for compounds E04, E07, E19, E20, and E25 are similar in range to that reported for the feline coronavirus drug GC376 (0.19 ± 0.04 μM). (17) In general, meta-substitution of the N-phenyl moiety was favorable. Two of the most potent compounds, E19 and E20, featured a meta-substituted chlorobenzene, and the most potent analogue, E25, featured a meta-cyano group. As observed in Figure 1 B, the p-chloro substitution of E19 is positioned such that it can form a halogen bond with the amide backbone of Gly 143, while the 1,2-benzisoselenazole ring forms π–π interactions with catalytic His 41 and a hydrogen bond to Glu 166. In Figure 1 D, the m-cyano group of E25 is able to accept a hydrogen bond from Cys 44 while maintaining the core interactions with the 1,2-benzisoselenazole ring, π–π interactions with catalytic His 41, and a hydrogen bond to Glu 166. In both these examples, meta-substitution could enable additional favorable interactions with the binding site that are not supported by ortho- or para-substitution. In general, para-substitution of the N-phenyl ring was tolerated, with most IC50 values in the micromolar range, while ortho-substitution was generally unfavorable. Compound E15 featured the only variation to the 1,2-benzisoselenazole ring, a methoxy group at the C6 position. As observed in Figure 1 A, the 1,2-benzisoselenazole ring of ebselen is expected to form π–π interactions with catalytic His 41 and a hydrogen bond to Glu 166, with the C6 position oriented toward His 41. The addition of the methoxy group at this position is likely to impair the π–π interactions expected with catalytic His 41 and could reposition the compound within the binding site such that the hydrogen bond to Glu 166 is weaker. This substitution was observed to reduce the potency against SARS-CoV-2 Mpro by ∼20× relative to that of ebselen.
Table 1. Structures, Docking Scores, and In Vitro Data Summary of 2-Phenyl-1,2-benzoselenazol-3-one Analogues

2-Phenyl-1,2-benzoselenazol-3-one Inhibitors Can Inhibit Mpro Covalently or Noncovalently

The selenium atom of ebselen is capable of forming a selenylsulfide bond (−Se–S−); (26−29) in Singh et al., the substitution of the Se atom with S or the mutation of the target active site Cys was observed to decrease inhibition. (29) In most cases, proteins covalently modified by ebselen may be rescued by the sulfhydryl reducing agents glutathione (GSH) and dithiothreitol (DTT). Previously, Jin et al. reported that ebselen was able to partially modify Mpro Cys residues and concluded that ebselen could inhibit Mpro by both covalent and noncovalent mechanisms. (15) To determine if 2-phenyl-1,2-benzoselenazol-3-one analogs were also able to covalently modify the active site of SARS-CoV-2 Mpro, we performed a preincubation dilution experiment where SARS-CoV-2 Mpro was incubated with 10 μM inhibitor for 30 min prior to 10× dilution with the reaction buffer. Upon dilution, rapidly reversible inhibitors dissociate from the enzyme active site, and the resulting activity is proportional to that observed for the final inhibitor concentration, in this case 1 μM. If the inhibitor dissociation is slow, then the enzyme–inhibitor complexes formed at high concentrations will persist after dilution and the resulting activity will instead be proportional to the initial concentration of 10 μM. The concentration range of 10 and 1 μM was selected as all compounds tested in this experiment showed full enzymatic inhibition at 10 μM and some activity at 1 μM, typically between 15 and 50% wt activity. As previous reports have indicated that the covalent modification of Cys residues by ebselen is sensitive to reversal by reducing agents such as DTT or glutathione, we removed DTT from the assay buffer for these experiments.
The effect of dilution on the reaction rate of SARS-CoV-2 Mpro preincubated with a 10 μM concentration of compounds E01 (ebselen), E04, E07, E19, E20, and E25 can be observed in Figure 2. The effect of the simultaneous addition of the substrate and either 1 or 10 μM inhibitor on the rate of SARS-CoV-2 Mpro was included for each inhibitor as a comparison. As seen in Figure 2 A, C, and E, dilution of the protease-inhibitor reaction mixture did not alter the reaction rate when Mpro was incubated with ebselen, E07, or E20, indicating that these compounds likely inhibit Mpro by covalent modification. However, the dilution of Mpro treated with compounds E04 and E19 did result in a reaction rate similar to that observed for a 1 μM concentration of the undiluted compound, indicating that these analogues are rapidly reversible inhibitors of SARS-CoV-2 Mpro (Figure 2 B and D). Interestingly, the dilution of the Mpro/E25 reaction mixture did show some recovery of the enzymatic activity but not a complete recovery comparable to the activity observed for Mpro treated with 1 μM E25 without dilution (Figure 2 F). These results could suggest that the covalent modification of Mpro was incomplete in the 30 min preincubation period. To determine if Mpro inhibition by 2-phenyl-1,2-benzoselenazol-3-one analogues is sensitive to reducing agents, the experiment was repeated with the presence of 1 mM DTT in the assay buffer. Under these conditions, the dilution of the reaction mixtures was sufficient to recover the enzymatic activity, suggesting that any covalent adduct formed with Mpro Cys residues was reduced such that the enzyme–inhibitor complex dissociated. These results indicate that while ebselen and some 2-phenyl-1,2-benzoselenazol-3-one analogues are able to covalently modify active Mpro Cys residues, this covalent modification is reversible in a reducing environment. It is also possible that 2-phenyl-1,2-benzoselenazol-3-one analogues can inhibit Mpro noncovalently, as observed for compounds E04 and E20.

Figure 2

Figure 2. Ebselen and its analogues can covalently modify SARS-CoV-2 Mpro in the absence of reducing agents. (A) Ebselen is a reversible covalent inhibitor of SARS-CoV-2 Mpro. The product formation over time was reduced by approximately 65% by 1 μM ebselen (red) and by 89% by 10 μM ebselen (purple) relative to that with the DMSO control (black) when added simultaneously with the fluorogenic substrate. Upon 10× dilution in an assay buffer without DTT, the product formation of SARS-CoV-2 Mpro preincubated with 10 μM ebselen (green) was reduced by 91%, which is comparable to an undiluted concentration of 10 μM. When diluted in the presence of DTT, the product formation of SARS-CoV-2 Mpro preincubated with 10 μM of ebselen (blue) was reduced by 53% relative to that with the DMSO control, similar to that observed for a final concentration of 1 μM. These data indicate that ebselen can covalently modify SARS-CoV-2 Mpro, although this modification is reversible in the presence of strong reducing agents. (B) Compound E04 is a rapidly reversible inhibitor of SARS-CoV-2 Mpro. Upon 10× dilution, the product formation of SARS-CoV-2 Mpro preincubated with 10 μM E04 in the absence of DTT (green) was reduced by 48% relative to that with the DMSO control, similar to that observed for a final concentration of 1 μM E04 (44% inhibition), while the simultaneous addition of the substrate and 10 μM E04 reduced the product formation by 86%. Similar results were observed for SARS-CoV-2 Mpro preincubated with 10 μM E04 in the presence of DTT (blue, 43% inhibition). (C) Compound E07 is a reversible covalent inhibitor of SARS-CoV-2 Mpro. (D) Compound E19 is a rapidly reversible inhibitor of SARS-CoV-2 Mpro. (E) Compound E20 is a reversible covalent inhibitor of SARS-CoV-2 Mpro. (F) Compound E25 is a reversible covalent inhibitor of SARS-CoV-2 Mpro. Upon 10× dilution, the product formation of SARS-CoV-2 Mpro preincubated with 10 μM E25 in the absence of DTT (green) was reduced by 64% relative to that with the DMSO control. The simultaneous addition of the substrate and 10 μM 25 reduced product formation by 94%, while the simultaneous addition of the substrate and 1 μM E25 reduced product formation by 29%. These data suggest that while E25 may covalently modify SARS-CoV-2 Mpro, the formation of the covalent adduct was incomplete after 30 min of incubation.

High Resolution Image
Download MS PowerPoint Slide

2-Phenyl-1,2-benzoselenazol-3-one Inhibitor E04 and Ebselen Are Competitive Inhibitors of Mpro

The mechanism of Mpro inhibition by ebselen and E04 was further characterized by steady-state enzyme kinetics (Figure 3). The reaction rates of untreated (wild-type) Mpro at varying substrate concentrations and Mpro in the presence of 0.5, 1, 5, and 10 μM E01 and E04 were determined, and the data were globally fit to a generalized mixed-model equation as described in the Inhibition Mechanism section. In this mechanism, the binding of the inhibitor to the ES complex is described by αKi, where Ki is the dissociation constant. An value of α ≫ 1 provided a better fit of the data for both inhibitors, suggesting a weak binding to the ES complex and a preference for the free enzyme. A plot of the reaction velocity versus the substrate concentration shows that when Mpro is treated with either ebselen or E04, Vmax recovers to that observed for wild-type Mpro at substrate concentrations of 30 μM (Figure 3 A and C). A double-reciprocal plot shows that for both compounds Km is dependent on [I] while Vmax remains consistent (Figure 3 B and D). These results indicate that ebselen and E04 are likely competitive inhibitors of Mpro.

Figure 3

Figure 3. Ebselen and E04 are competitive inhibitors of the SARS-CoV-2 main protease. (A) Mpro exposed to varying concentrations of ebselen reached a common Vmax at 30 μM substrate (B) All ebselen conditions converge on a common y-intercept, indicating that Vmax is independent of the inhibitor concentration, which is consistent with a competitive mechanism of inhibition. (C) Mpro exposed to varying concentrations of E04 reached a common Vmax at 30 μM substrate (D) All E04 conditions converge on a common y-intercept, indicating that Vmax is independent of the inhibitor concentration, which is consistent with a competitive mechanism of inhibition. (E) Antiviral activity of select compounds. Vero E6 cells were pretreated with varying doses of the compound, then infected with SARS-CoV-2 to a multiplicity of infection (MOI) of 0.01. After 72 h, cell proliferation was determined. Remdesivir is included as a positive control (EC50 = 1.8 ± 1.3 μM).

High Resolution Image
Download MS PowerPoint Slide

2-Phenyl-1,2-benzoselenazol-3-one Analogues Are Potent Antiviral Agents In Vitro

To determine if 2-phenyl-1,2-benzoselenazol-3-oneanalogues were able to impair SARS-CoV-2 replication, the compounds were screened against infected Vero E6 cells at doses ranging from 20 to 0.1 μM to determine the cellular EC50 value (Figures 3 E and S2 and Table 2). Briefly, cells were pretreated with compound for 1 h, then infected with SARS-CoV-2 (USA_WA01/2020) at a multiplicity of infection (MOI) of 0.01 for 1.5 h. Cells were washed, the compounds were reapplied, and cells were then incubated for 72 h prior to recording cthe ell proliferation. As a virus infection reduces cell proliferation and leads to cell death, only those compounds that show increased cell survival relative to that of the DMSO negative control are considered to have antiviral activity. In this way, compounds that are likely to be cytotoxic to Vero E6 cells at the concentrations tested are excluded as potential hits. Ebselen and remdesivir were included as positive controls. The antiviral activity of each compound is reported in Table 1. Most compounds reported EC50 valuess in the micromolar range, and compounds E18, E21, and E25 showed antiviral potencies similar to that of remdesivir (Tables 1 and 2 and Figure 3 E). The most potent compound, E24, showed a nanomolar antiviral potency (EC50 = 0.84 ± 0.3 μM). This is within range of the most potent Mpro inhibitors reported to date, including the rationally designed peptidyl inhibitors 11a and 11b (EC50 = 0.53 ± 0.01 and 0.72 ± 0.09 μM, respectively) (16) and the feline coronavirus drug GC376 (EC50 = 0.92 μM). (17) Interestingly, all three of these inhibitors are peptides that contain a similar warhead for the covalent modification of active site Cys 145. We demonstrated that the 2-phenyl-1,2-benzoselenazol-3-one class of inhibitors may inhibit Mpro either covalently or noncovalently (Figure 2).
Table 2. Antiviral Activity and logD Values of Select 2-Phenyl-1,2-benzoselenazol-3-one Analoguesa
compoundantiviral EC50 (μM)logD pH 7.4compoundantiviral EC50 (μM)logD pH 7.4
ebselen>200.92remdesivir1.8 ± 1.2ND
E0411.2 ± 1.33.19E2018.2 ± 3.61.67
E0726.5 ± 1.20.85E215.2 ± 1.81.46
E186.5 ± 2.02.87E240.8 ± 0.33.18
E1917.4 ± 3.51.53E252.0 ± 1.11.45
a

ND, not determined.

For some compounds, the potencies of the 2-phenyl-1,2-benzoselenazol-3-one analogues were reduced in the Vero cell assay relative to those in the FRET assay using recombinant Mpro. For example, while E04, E19, E20, and E25 reported nanomolar IC50 valuess against recombinant Mpro (IC50 = 0.38–0.90 μM), their EC50 valuess in the antiviral assay were in the micromolar range (2.0–18.2 μM). As these compounds are not expected to prevent viral entry into the cells, their antiviral potency will be a function of a variety of factors, including cell membrane permeability, efflux rate, and cellular metabolic pathways. The antiviral assays were also conducted over a 72 h incubation period, while the FRET assay was performed in a 1 h time frame, further complicating a direct comparison of potencies across these two assay systems. As observed in the preincubation dilution assays, many of the 2-phenyl-1,2-benzoselenazol-3-one analogues are sensitive to reducing agents, and their inhibitory potency could be affected by intracellular reducing mechanisms. While the exact potencies varied, in general compounds that were inactive against recombinant Mpro were also inactive in the Vero E6 cell antiviral assays.

2-Phenyl-1,2-benzoselenazol-3-one Compounds Show Improved LogD Values Relative to Ebselen

LogD values were also determined for ebselen and 2-phenyl-1,2-benzoselenazol-3-onecompounds E04, E07, E18, E19, E20, E21, E24, and E25 (Table 2). Meta-analyses of pharmaceutical drug development projects have identified the importance of logD in identifying compounds that are more likely to feature favorable clearance rates and membrane permeabilities; one such study found that compounds with a molecular weight of 350 g/mol and a logD of 1.5 had a 25% success rate of being advanced to clinical trials. (30−34) By analyzing the logD values for these analogues at this stage, we are able to predict which compounds are most likely to show favorable pharmacokinetic properties in future in vivo models. We may also determine if logD optimization can be useful in refining these compounds as antiviral agents prior to an in vivo study. As observed in Table 2, logD values are generally in the ideal range for most orally available drugs (Table 2, entries1–3). (30−33) Furthermore, logD values were broadly observed to correlate with the antiviral activity, where compounds with higher logD values (E18, and E24) showed greater antiviral potencies than those with low logD values (E07, E19, and E20). These data indicate that the logD value is a critical parameter for optimizing the antiviral potencies of these compounds.

2-Phenyl-1,2-benzoselenazol-3-one Analogues Show Antiviral Properties in Human Lung Cells

To further confirm the antiviral properties observed in the Vero E6 cell assay, four compounds were selected foran additional evaluation in human lung epithelial cells. Ebselen and remdesivir were both included as positive controls. As before, Calu-3 cells were pretreated with 0.1–20 μM concentrations of the compound for 1 h prior to infection with SARS-CoV-2 (USA_WA01/2020; MOI = 0.1) for 1.5 h. Cells were washed, the compounds were reapplied, and cells were then incubated for 24 h prior to the isolation and quantification of intracellular and supernatant viral RNA by RT-qPCR. Table 3 lists the antiviral EC50 values of ebselen, remdesivir, E04, E18, E21, and E24 in Calu-3 cells.
Table 3. Antiviral Activity of Select 2-Phenyl-1,2-benzoselenazol-3-one Analogues in Calu-3 Cells
compoundEC50 (μM)compoundEC50 (μM)
ebselen5.0 ± 4.0remdesivir0.8 ± 0.6
E042.8 ± 1.3E2115.7 ± 4.3
E188.8 ± 5.4E241.3 ± 0.8
In this model, remdesivir appears to be slightly more potent than in the Vero E6 cell proliferation assays (EC50 = 0.8 ± 0.6 and 1.8 ± 1.2 μM, respectively); interestingly, this slight improvement in potency in human cell models was also observed for remdesivir by Dittmer et al. (35) and Jang et al. (36) in Calu-3 cells and by Choi et al. (37) in hESC- and hiPSC-derived cardiomyocytes. The difference in potency could be due to the variations in experimental conditions, including the cell lines and infection rates. Additionally, a recent comparison of commonly used cell models for SARS-CoV-2 antiviral assays by Dittmer et al. indicated that entry mechanisms vary for Calu-3 and Vero cells, where entry in Calu-3 cells was pH-independent and relied on transmembrane protease serine 2 (TMPRSS2) and entry to Vero cells was reliant upon acid-dependent endosomal proteases and low pH levels. (35) These variations in entry mechanisms resulted in significant alterations in the drug efficacy, particularly for compounds that targeted host proteases. (35) However, compounds that target the virus directly, like remdesivir, should remain active across cell types. As our 2-phenyl-1,2-benzoselenazol-3-one analogues target the SARS-CoV-2 main protease, we expected to retain antiviral activity for these compounds as well.
In Calu-3, ebselen had an EC50 of 5.0 μM, which is in the range of reported EC50 values observed by Vero E6 cell proliferation assays. (24) Of the remaining 2-phenyl-1,2-benzoselenazol-3-one analogues, E18 and E24 had EC50 values consistent with those observed in Vero E6 cells (E18 EC50 = 8.8 ± 5.4 μM; E24 EC50 = 1.3 ± 0.8 μM). E04 showed a marked improvement in potency, with a fourfold reduction in EC50 in Calu-3 cells (2.8 ± 1.3 μM) versus that in Vero E6 (11.2 ± 1.3 μM). E21, however, showed a threefold reduction in potency Calu-3 cells (EC50 = 15.7 ± 4.3 μM) relative to that in Vero E6 (EC50 = 5.2 ± 1.8 μM). This difference in potency observed for E04 and E21 could be due to changes in either the compound permeability or stability in various cells and culture conditions. Importantly, all compounds remained active antivirals in human lung epithelial cells, indicating that the antiviral properties of the analogues are robust across assay systems and relevant to human models.

Compound E24 Reduces SARS-CoV-2 Viral Infection in Human Lung Organoids

The most potent compound from our antiviral screens, E24, was evaluated in a lung organoid model derived from human-induced pluripotent stem cells (iPSC). Human iPSC-derived lung 3D organoids were generated as described by Tiwari et al. (38) Organoids were characterized as containing epithelial cells, alveolar types 1 and 2, and a high expression of both ACE2 and TMPRSS2 and were verified to permit SARS-CoV-2 infection as described previously. (38−40) Organoids were pretreated with 5 μM E24 for 2 h and infected with SARS-CoV-2 at MOI = 2 for 2 h at 37 °C. Then, the cells were washed, and a fresh medium was added. At 72 h postinfection, both intracellular viral RNA and viral RNA from the supernatant were isolated and quantified by RT-qPCR. As shown in Figure 4, E24 treatment reduced viral RNA levels by ∼50% in both the supernatant and intracellular fractions with no observable toxicity toward the organoids. These data confirm that E24 can impair the viral replication of SARS-CoV-2 in human lung organoids.

Figure 4

Figure 4. E24 inhibits SARS-CoV-2 replication in infected human iPSC-derived lung organoids. Sixty-day-old lung organoids were infected with the SARS-CoV-2 USA-WA1/2020 virus at a MOI of 2, and viral RNAs from (A) supernatant and (B) cellular fractions were quantified after 72 h of infection. Mean ± SEM of n = 3 organoids cultured and infected in different wells, *p < 0.05 by Student’s t-test.

High Resolution Image
Download MS PowerPoint Slide

Discussion and Conclusions

Click to copy section linkSection link copied!
In this study, we sought to apply medicinal chemistry and rational drug design approaches to the SARS-CoV-2 main protease to address the following specific goals: (1) to improve potency of early Mpro screening hits, (2) to establish an enzymatic mechanism of inhibition, (3) to rationally design compounds with potent antiviral activity, and (4) to compare rationally designed compounds against existing early SARS-CoV-2 antivirals. With this approach, we have identified a class of 2-phenyl-1,2-benzoselenazol-3-one compounds showing nanomolar potencies against recombinant SARS-CoV-2 Mpro and improved lipophilicities relative to the early Mpro inhibitor ebselen. Using steady-state enzyme kinetics, we were able to establish that some 2-phenyl-1,2-benzoselenazol-3-one compounds inhibit Mpro noncovalently, suggesting they are less likely to suffer from target promiscuity than covalent modifiers such as ebselen. Furthermore, lead compound E04 was found to inhibit Mpro through a competitive mechanism of inhibition, indicating that nonpeptidyl small molecules may bind to the active site of Mpro to inhibit proteolysis. Additionally, 2-phenyl-1,2-benzoselenazol-3-one compounds were determined to inhibit SARS-CoV-2 viral replication in infected Vero E6 and Calu-3 cells with comparable potencies to that of the clinical treatment remdesivir. The further evaluation of lead E24 in iPSC-derived human lung organoids confirmed that E24 was able to significantly reduce viral RNA levels in both supernatant and intracellular fractions at a 5 μM dose.
Ebselen is known to be a promiscuous protease inhibitor capable of binding a variety of viral proteases, including SARS-CoV-2 Mpro and PLpro, EV-A71 2Apro and 3Cpro, and EV-D68 2Apro and 3Cpro. (41,42) At this stage, it is unknown if the 2-phenyl-1,2-benzoselenazol-3-one analogues presented in this study are also able to bind and inhibit additional proteases such as the SARS-CoV-2 papain-like protease (PLpro), which cleaves nonstructural protein 1 (nsp1), nonstructural protein 2 (nsp2), and nonstructural protein 3 (nsp3) of the viral polyprotein. PLpro has been identified as a promising drug target for SARS-CoV-2 both for its essential role in promoting viral replication and also for its ability to promote immune escape by cleaving the host ubiquitin-like interferon-stimulated gene 15 protein (ISG15), a key regulator of the host innate immune response. (43−46) Without further studies to characterize the selectivity index of the 2-phenyl-1,2-benzoselenazol-3-one inhibitors, we cannot say if the antiviral activity observed in both the Vero E6 and Calu-3 assays and the human iPSC-derived lung organoids is due to the inhibition of Mpro, PLpro, or a combination of both. Additionally, while the mechanism of action has been evaluated for some benzoisoselenazole compounds in vitro, it remains unclear if the compounds are covalent or noncovalent modifiers intracellularly. Tandem MS/MS experiments to verify covalent modification at the active site should be completed prior to advancing these compounds as leads for clinical development. However, we believe that while E24 shows promise as a Mpro inhibitor, and the potency can be further optimized prior to establishing the selectivity and intracellular mechanism of action of this class of inhibitors.
While future studies are needed to determine toxicity and efficacy of the 2-phenyl-1,2-benzoselenazol-3-one class of compounds in animal models, these findings could potentially be relevant to the development of Mpro-targeted clinical candidates for the treatment of COVID-19.

Experimental Section

Click to copy section linkSection link copied!

In Silico Modeling of Ebselen Analogues with Schrödinger

In silico modeling of ebselen analogs was performed using the Glide docking module of the Schrödinger 11.5 modeling software suite. A crystal structure of the SARS-CoV-2 pro bound to N3 (PDB ID 6UL7) was first refined using Prime. (15,47,48) The optimized potentials for liquid simulations (OPLS) all-atom force field and the surface generalized born (SGB) continuum solution model were used to optimize and minimize the crystal structure, respectively. The docking grid was generated as a 15 Å cube centered on N3 (x = −14, y = 17.7, and z = 67.1). Ligprep was used to generate a minimized 3D structure for all antiviral compounds using the OPLS 2001 force field. Docking was performed with Glide XP. (21−23) Compounds were ranked by their docking score, and the docking poses were evaluated for interactions with key residues such as the catalytic dyad His 41 and Cys 145.

SARS-CoV-2 Main Protease Protein Expression and Purification

The GST-tagged SARS-CoV-2 main protease was expressed in Escherichia coli BL21 competent cells (New England Biolabs), which were transformed with the pET41b plasmid by heat shock and spread on a lysogeny broth (LB) kanamycin agar plate and then incubated overnight at 37 °C. Next, 2–3 colonies were picked and transferred to 5 mL of LB medium treated with kanamycin (0.5 mg/mL final concentration), then grown overnight with shaking at 37 °C. The overnight culture was then transferred to 2 L of the LB kanamycin medium and incubated at 37 °C until OD = 0.8. The culture was cooled at 4 °C for 20 min, induced with 0.5 mM isopropyl β-d-1-thiogalactopyranoside (IPTG), then grown with shaking at 16 °C. Cell pellets were collected by centrifugation (5000 g for 10 min at 4 °C), and the supernatant was discarded. The pellets were resuspended in lysis buffer (50 mM Tris-HCl pH 7.5, 500 mM NaCl, 1.0% Triton x-100, 0.5 mM EDTA, 1× complete protease inhibitor cocktail, and 1 mM β-mercaptoethanol in RNase-free water; 6 mL per gram) with DNase 1 (5 U/mL, RNase-free) and incubated at 4 °C for 1 h, then sonicated. The suspension was centrifuged at 10 000 g for 20 min, and the supernatant was transferred to a glutathione sepharose affinity resin column that had been pre-equilibrized with lysis buffer. The supernatant was incubated with the affinity resin column at 4 °C for 2 h with end-over-end rotation. After incubation, the column was washed with 5 bed volumes of lysis buffer, 3 × 5 bed volumes of wash buffer (50 mM Tris-HCl pH 7.5, 500 mM NaCl, 0.1% Triton x-100, 0.5 mM EDTA, 1× complete protease inhibitor cocktail, and 1 mM β-mercaptoethanol in RNase-free water), and 5 bed volumes of pre-elution buffer (50 mM Tris-HCl pH 7.5 and 100 mM NaCl in RNase-free water). The protease was eluted with elution buffer (50 mM Tris-HCl pH 7.5, 100 mM NaCl, and 40 mM glutathione in RNase-free water) and collected in 1 mL fractions until no further protein was collected (3–5 bed volumes total). The purity of the fractions was determined by SDS-page, and fractions of the purified protein were collected and concentrated to 2 mg/mL. The GST-tagged purified protein was incubated with TEV protease at 37 °C for 4 h to obtain the untagged SARS-CoV-2 protease. Excess GST and GST-TEV protease were removed by glutathione sepharose affinity column purification. The untagged proteases were eluted in 50 mM Tris-HCl pH 7.5 and 100 mM NaCl in RNase-free water. The purity of the fractions was determined by SDS-page, and fractions of purified protein were collected and concentrated to 5 μM. The protein solutions were transferred to a Slyde-A-Lyzer dialysis cassette (20 000 MWCO, Thermo Scientific) and dialyzed overnight at 4 °C against dialysis buffer (50 mM Tris-HCl pH 7.4, 200 mM NaCl, 1 mM EDTA, and 1 mM DTT in RNase-free water).

FRET Protease Activity Assay

The activity of the SARS-CoV-2 main proteases was determined using a fluorescence resonance energy transfer (FRET) assay adapted from Muramatsu et al. (25) The fluorogenic peptide Dabcyl-Val-Asn-Ser-Thr-Leu-Gln-Ser-Gly-Leu-Arg-Lys-EDANS was used as a substrate (AnaSpec Inc.). All reactions were performed in a black 96-well plate with 200 μL of assay buffer (50 mM Tris-HCl pH 7.4, 200 mM NaCl, 1 mM EDTA, and 1 mM DTT in RNase-free water), 25 nM SARS-CoV-2 protease, and 3 μM substrate. Ebselen analogs were screened at a concentration of 10 μM. All inhibitors were dissolved in DMSO and added to a final concentration of 0.2% DMSO. Fluorescent readings were normalized to 200 μL of assay buffer with 3 μM substrate and 10 μM inhibitor with a final concentration of 0.2% DMSO. Cleavage between the Gln and Ser residues was monitored by a BioTek Synergy plate reader with excitation at 380 nm and emission at 485 nm every 10 min for 1 h. The relative rate for wild-type protease, and each inhibitor concentration was averaged from three assay results. The relative reaction rates were normalized to the wild-type protease, and the relative activity was reported as a percentage of the wild-type protease activity in Table 1.
Additionally, dose–response curves were generated for compounds that showed significant inhibition at 10 μM using the assay conditions described above. The dose–response curve for ebselen (E01) was also generated as a positive control. Inhibitors were screened at six concentrations ranging from 0.100 to 10 μM. As before, cleavage between the Gln and Ser residues was monitored by a BioTek Synergy plate reader with excitation at 380 nm and emission at 485 nm every 10 min for 1 h. The relative rates for the wild-type protease and each inhibitor concentration were averaged from three assay results. The relative reaction rates were normalized to the wild-type protease, and dose–response curves were plotted in GraphPad Prism 6.
To determine if the ebselen analogs were covalent or rapid reversible inhibitors of SARS-CoV-2 Mpro, preincubation dilution experiments were performed. In assay buffer, 250 nM protease was incubated on ice for 30 min with 10 μM ebselen (E01), E04, E07, E19, E20, or E25. The reaction mixture was then diluted 10-fold with assay buffer, and the fluorogenic peptide substrate was added to a final concentration of 3 μM. The experiment was also repeated with assay buffer free of DTT to determine the effects of the reducing agent on the mechanism of inhibition. For each compound, the rate of product formation after preincubation and dilution was compared to the rate of product formation for Mpro with 0.2% DMSO, 1 μM compound, and 10 μM compound without dilution.

Inhibition Mechanism

The reaction velocities observed over a range of substrate (1.5, 3, 4.5, 6, 9, 15, 22.5, and 30 μM) and inhibitor concentrations (0, 0.5, 1, 5, and 10 μM) for either ebselen or E04 were globally fit to a generalized mixed-model of inhibition represented by the following equilibrium reaction scheme. This mechanism allows for inhibitor binding to both the free enzyme and the enzyme–substrate complex with varying affinity to be described by the following rate equation:
The term Ki describes the affinity of the inhibitor for free enzyme. The mechanism can be evaluated by the term α. When α approaches 1, the inhibitor is considered noncompetitive, and when α approaches infinity, the inhibitor is considered competitive.
(2)

logD Measurements

logD values were measured at pH 7.4 by the shake-flask method according to the literature. (49,50)

Antiviral Assays

Approximately 2 × 104 Vero E6 cells (ATCC) were plated in 100 μL of DMEM (Gibco) supplemented with 10% serum in each well of a 96-well flat bottom plate and allowed to adhere overnight. Cells were pretreated with 0.10–20 μM test compound in 100 μL of the same medium for 1 h, washed, and infected with SARS-CoV-2 (USA_WA01/2020 (World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch)) in 50 μL of medium at 0.01 MOI for 1.5 h. Cells were then washed, test compounds were reapplied at 0.10–20 μM in 100 μL of medium, and incubated at 37 °C in 5% CO2 for 72 h. Following incubation, 10 μL of room temperature WST8 reagent was added to each well, mixed, and incubated for an additional 3 h at 37 °C and 5% CO2. The OD at 460 nm was read on a BioTek plate reader.
For antiviral assays in Calu-3 human lung cells, approximately 1.5 × 105 Calu-3 cells (ATCC) were plated in 500 μL of EMEM (Gibco) supplemented with 10% FBS, 2 mM l-glutamine, and 1% penicillin/streptomycin in each well of 24-well flat bottom plates and allowed to adhere overnight. Cells were pretreated with 0.10–20 μM test compound in DMSO (0.2% final v/v) of the same medium for 1 h, washed, and infected with SARS-CoV-2 (USA_WA01/2020) in a reduced serum medium (2–3%) at 0.1 MOI for 1.5 h. Cells were then washed with PBS, and test compounds reapplied at 0.10–20 μM in 500 μL of the medium and incubated at 37 °C in 5% CO2 for 24 h. At 24 h postinfection, the supernatant and infected cells were collected and lysed using TRIzol, and RNA was extracted using a Direct-zol RNA Kit (Zymo) and quantified by RT-qPCR using SARS-CoV-2 N primers as previously described. (38−40) The primers are as follows: forward, CACATTGGCACCCGCAATC; reverse, GAGGAACGAGAAGAGGCTTG.

Lung Organoid Infection and Treatment with E24

Human iPSC-derived lung organoids were generated using previously published methods and characterized by the expression of ACE2, TMPRSS2, and alveolar cell epithelial markers (SFTPC, SFTPB, and HOPX). The 60D differentiated lung organoids were pretreated with 5 μM E24 for 2 h and infected with SARS-CoV-2 as described previously. (38) The SARS-CoV-2 isolate USA-WA1/2020 was obtained from BEI Resources. SARS-CoV-2 was propagated, and infectious units quantified by plaque assay using Vero E6 cells. Human iPSC-derived lung organoids, were infected with SARS-CoV-2 at MOI = 2 for 2 h at 37 °C. Then, cells were washed, and fresh medium was added. At 72 h post infection, the supernatant and infected organoids were collected and lysed using TRIzol, and RNA was extracted using a Direct-zol RNA kit (Zymo) and quantified by RT-qPCR using SARS-CoV-2 N primers.

General Procedure for the Synthesis of Compounds E01–30

A one-necked round-bottomed flask was fitted with a reflux condenser and a magnetic stirrer. The flask was charged with the corresponding SM 3 (1 mmol), followed by the addition of Se powder (5 mmol) and tBuONa (2 mmol). The reaction mixture was left to stir at 130 °C for 12 h. After the completion of reaction, the reaction mixture was diluted with excess water and extracted with ethyl acetate. The organic layer was separate and concentrated under reduced pressure. The crude material was purified by column chromatography (hexane/ethyl acetate 70:30) to yield compounds E01–30 as solids.

Compound Characterization

The Supporting Information provides a detailed description of the solvent purification and general methods for synthesis and purification of each analogue. All compounds were purified by column chromatography and characterized by 1H and 13C NMR and HRMS. Purity was determined by HPLC at >90% for all compounds, and spectra can be found in the Supporting Information.

2-Phenylbenzo[d][1,2]selenazol-3(2H)-one (E01)

1H NMR (600 MHz, CDCl3) δ 8.17 (d, J = 7.8 Hz, 1H), 7.72 (t, J = 7.8 Hz, 1H), 7.69 (dd, J = 8.4, 2.8 Hz, 3H), 7.52 (td, J = 6.2, 1.3 Hz, 1H), 7.48 (t, J = 8.4 Hz, 2H), 7.33 (dd, J = 14.1, 6.6 Hz, 1H). 13C NMR (151 MHz, CDCl3) δ 165.8, 139.2, 137.7, 132.6, 132.6, 129.5, 129.4, 127.6, 126.8, 126.6, 125.5, 125.5, 123.8. HRMS (ESI): m/z calculated for C13H9NOSe 274.9849, found 275.9927 [M + H]+. Purity >99%.

2-(4-Fluorophenyl)benzo[d][1,2]selenazol-3(2H)-one (E02)

1H NMR (600 MHz, CDCl3) δ 8.11 (d, J = 7.8 Hz, 1H), 7.68–7.64 (m, 2H), 7.57 (dd, J = 8.6, 4.8 Hz, 2H), 7.48 (t, J = 6.6 Hz, 1H), 7.12 (t, J = 8.5 Hz, 2H). 13C NMR (151 MHz, CDCl3) δ 165.9, 161.9, 160.3, 137.7, 134.9, 132.7, 129.5, 127.7, 127.1, 126.7, 123.9, 116.3, 116.2. HRMS (ESI): m/z calculated for C13H8FNOSe 292.9755, found 293.9831[M + H]+. Purity >99%.

2-(2-(Methylthio)phenyl)benzo[d][1,2]selenazol-3(2H)-one (E03)

1H NMR (600 MHz, CDCl3) δ 8.19 (d, J = 7.8 Hz, 1H), 7.75–7.68 (m, 2H), 7.52 (t, J = 7.3 Hz, 1H), 7.47–7.41 (m, 2H), 7.37 (d, J = 8.0 Hz, 1H), 7.28 (t, J = 7.6 Hz, 1H), 2.48 (s, 3H). 13C NMR (151 MHz, CDCl3) δ 165.9, 138.8, 138.5, 134.8, 132.0, 129.4, 129.0, 129.0, 125.8, 125.7, 125.5, 125.0, 123.5, 14.6. HRMS (ESI): m/z calculated for C14H11NOSSe 320.9727, found 321.9805 [M + H]+. Purity >98%.

2-(4-(Trifluoromethyl)phenyl)benzo[d][1,2]selenazol-3(2H)-one (E04)

1H NMR (600 MHz, CDCl3) δ 8.13 (d, J = 7.8 Hz, 1H), 7.81 (d, J = 8.4 Hz, 2H), 7.70–7.67 (m, 4H), 7.49 (ddd, J = 8.0, 5.6, 2.6 Hz, 1H). 13C NMR (151 MHz, CDCl3) δ 167.0, 137.3, 133.2, 133.2, 129.7, 129.7, 127.4, 127.0, 127.0, 126.7, 126.6, 124.9, 123.9, 123.9. HRMS (ESI): m/z calculated for C14H8F3NOSe 342.9723, found 343.9798 [M + H]+. Purity >98%.

2-(3,4-Dimethylphenyl)benzo[d][1,2]selenazol-3(2H)-one (E05)

1H NMR (600 MHz, CDCl3) δ 8.16 (d, J = 7.6 Hz, 1H), 7.69 (dt, J = 7.9, 7.3 Hz, 2H), 7.51 (t, J = 7.3 Hz, 1H), 7.45 (s, 1H), 7.36 (d, J = 8.0 Hz, 1H), 7.23 (d, J = 8.0 Hz, 1H), 2.35 (s, 3H), 2.32 (s, 3H). 13C NMR (151 MHz, CDCl3) δ 165.8, 137.8, 137.8, 136.6, 135.8, 132.4, 130.4, 129.4, 127.6, 126.8, 126.5, 123.8, 123.1, 19.9, 19.5. HRMS (ESI): m/z calculated for C15H13NOSe 303.0162, found 304.0240 [M + H]+. Purity >98%.

2-(4-Fluorobenzyl)benzo[d][1,2]selenazol-3(2H)-one (E06)

1H NMR (600 MHz, CDCl3) δ 8.13 (d, J = 7.8 Hz, 1H), 7.63 (t, J = 6.4 Hz, 2H), 7.48 (td, J = 8.0, 4.2 Hz, 1H), 7.39 (dd, J = 8.0, 5.5 Hz, 2H), 7.10 (t, J = 8.5 Hz, 2H), 5.03 (s, 2H). 13C NMR (151 MHz, CDCl3) δ 167.3, 163.6, 161.0, 138.1, 133.2, 132.3, 130.5, 130.4, 129.1, 126.5, 124.2, 116.09, 115.9, 48.0. HRMS (ESI): m/z calculated for C14H10FNOSe 306.9912, found 307.9988 [M + H]+. Purity >99%.

2-(2,4-Dimethoxybenzyl)benzo[d][1,2]selenazol-3(2H)-one (E07)

1H NMR (600 MHz, CDCl3) δ 8.04 (d, J = 7.9 Hz, 1H), 7.54–7.51 (m, 2H), 7.39 (qd, J = 5.8, 3.0 Hz, 1H), 7.32 (d, J = 8.2 Hz, 1H), 6.46 (dt, J = 8.2, 2.2 Hz, 2H), 4.96 (s, 2H), 3.87 (d, J = 6.7 Hz, 3H), 3.81 (s, 3H). 13C NMR (151 MHz, CDCl3) δ 167.0, 161.3, 158.7, 138.5, 131.9, 131.7, 128.7, 127.9, 126.0, 123.8, 118.2, 104.4, 98.6, 55.5, 55.5, 43.2. HRMS (ESI): m/z calculated for C16H15NO3Se 349.0217, found 350.0296 [M + H]+. Purity >98%.

2-(2-Fluorophenyl)benzo[d][1,2]selenazol-3(2H)-one (E08)

1H NMR (600 MHz, CDCl3) δ 8.19 (d, J = 7.8 Hz, 1H), 7.72 (d, J = 8.2 Hz, 2H), 7.55 (ddd, J = 8.0, 5.6, 2.6 Hz, 2H), 7.45–7.39 (m, 1H), 7.30–7.23 (m, 2H). 13C NMR (151 MHz, CDCl3) δ 166.6, 159.2, 157.5, −139.1, 132.8, 130.3, 130.1, 130.0, 129.6, 126.6, 124.8, 124.1, 117.1. HRMS (ESI): m/z calculated for C13H8FNOSe 292.9755, found 293.9834 [M + H]+. Purity >99%.

2-(4-(Trifluoromethyl)benzyl)benzo[d][1,2]selenazol-3(2H)-one (E09)

1H NMR (600 MHz, CDCl3) δ 8.15 (d, J = 7.8 Hz, 1H), 7.69–7.65 (m, 4H), 7.51 (t, J = 8.1 Hz, 3H), 5.13 (s, 2H). 13C NMR (151 MHz, CDCl3) δ 167.5, 137.8, 132.5, 129.3, 129.3, 128.7, 128.7, 126.9, 126.6, 126.6, 126.0, 126.0, 124.2, 124.2, 48.1. HRMS (ESI): m/z calculated for C15H10F3NOSe 356.9880, found 357.9957 [M + H]+. Purity >99%.

2-(4-Fluoro-2-(trifluoromethyl)phenyl)benzo[d][1,2]selenazol-3(2H)-one (E10)

1H NMR (600 MHz, CDCl3) δ 8.28 (d, J = 3.5 Hz, 1H), 8.05 (s, 1H), 7.79 (d, J = 7.8 Hz, 1H), 7.64 (d, J = 7.5 Hz, 1H), 7.51–7.47 (m, 1H), 7.44–7.40 (m, 2H). 13C NMR (151 MHz, CDCl3) δ 166.4, 160.1, 135.2, 133.7, 132.3, 132.2, 130.9, 127.7, 127.3, 127.1, 126.6, 120.1, 119.9, 113.8. HRMS (ESI): m/z calculated for C14H7F4NOSe 360.9629, found 361.9704 [M + H]+. Purity >90%.

2-(2,6-Difluorophenyl)benzo[d][1,2]selenazol-3(2H)-one (E11)

1H NMR (600 MHz, CDCl3) δ 8.15 (d, J = 7.7 Hz, 1H), 7.82 (d, J = 7.4 Hz, 1H), 7.74 (s, 1H), 7.472 (d, J = 7.0 Hz, 1H), 7.38 (m, 1H), 7.06 (m, 2H). 13C NMR (151 MHz, CDCl3) δ 169.7, 166.7, 139.6, 133.5, 133.0, 132.2, 130.4, 129.7, 129.1, 126.6, 124.2, 112.5, 112.3. HRMS (ESI): m/z calculated for C13H7F2NOSe 310.9661, found 311.9737 [M + H]+. Purity >90%.

2-(4-Methoxybenzyl)benzo[d][1,2]selenazol-3(2H)-one (E12)

1H NMR (600 MHz, CDCl3) δ 8.12 (d, J = 7.8 Hz, 1H), 7.61 (d, J = 3.6 Hz, 2H), 7.50–7.45 (m, 1H), 7.35 (dt, J = 8.6, 2.1 Hz, 2H), 6.94 (dt, J = 8.6, 1.9 Hz, 2H), 5.00 (s, 2H), 3.86 (d, J = 6.4 Hz, 3H). 13C NMR (151 MHz, CDCl3) δ 167.1, 159.7, 138.2, 131.9, 130.2, 130.2, 129.4, 128.9, 127.8, 126.2, 124.0, 114.2, 114.2, 55.4, 48.3. HRMS (ESI): m/z calculated for C15H13NO2Se 319.0112, found 320.0190 [M + H]+. Purity >99%.

2-(4-Chloro-2-(trifluoromethoxy)phenyl)benzo[d][1,2]selenazol-3(2H)-one (E13)

1H NMR (600 MHz, CDCl3) δ 8.54 (d, J = 8.8 Hz, 1H), 8.18 (s, 1H), 7.78 (d, J = 7.8 Hz, 1H), 7.64 (dd, J = 7.6, 1.1 Hz, 1H), 7.48 (td, J = 7.7, 1.4 Hz, 1H), 7.42 (dd, J = 7.5, 0.6 Hz, 1H), 7.37–7.35 (m, 1H). 13C NMR (151 MHz, CDCl3) δ 166.0, 138.6, 135.4, 133.3, 132.4, 132.3, 129.6, 129.0, 127.8, 127.4, 127.3, 122.9, 120.8, 46.0. HRMS (ESI): m/z calculated for C14H7ClF3NO2Se 392.9283, found 393.9352 [M + H]+. Purity >95%.

2-(5-Chloro-2-methoxyphenyl)benzo[d][1,2]selenazol-3(2H)-one (E14)

1H NMR (600 MHz, CDCl3) δ 8.17 (d, J = 7.4 Hz, 1H), 7.70 (t, J = 5.9 Hz, 2H), 7.56 (d, J = 2.4 Hz, 1H), 7.53–7.49 (m, 1H), 7.39–7.35 (m, 1H), 6.99 (d, J = 8.9 Hz, 1H), 3.89 (s, 3H). 13C NMR (151 MHz, CDCl3) δ 166.8, 154.1, 139.2, 132.6, 129.9, 129.5, 129.5, 127.9, 126.4, 126.1, 125.5, 123.9, 113.4, 56.3. HRMS (ESI): m/z calculated for C14H10ClNO2Se 338.9565, found 339.9641 [M + H]+. Purity >93%.

2-(4-Chlorophenyl)benzo[d][1,2]selenazol-3(2H)-one (E15)

1H NMR (600 MHz, (CD3)2SO) δ 8.08 (d, J = 8.0 Hz, 1H), 7.91 (dd, J = 7.8, 1.4 Hz, 2H), 7.68 (t, J = 7.7 Hz, 1H), 7.48 (t, J = 7.4 Hz, 1H), 7.36 (t, J = 8.2 Hz, 1H), 7.31 (t, J = 2.3 Hz, 1H), 7.16 (dd, J = 7.8, 1.2 Hz, 1H), 6.86 (dd, J = 8.3, 2.5 Hz, 1H), 3.79 (s, 3H). 13C NMR (151 MHz, (CD3)2SO) δ 165.0, 159.7, 140.9, 138.9, 132.3, 130.0, 128.6, 128.0, 126.3, 125.8, 116.7, 111.4, 110.4, 55.3. HRMS (ESI): m/z calculated for C14H11NO2Se 304.9955, found 309.3315 [M + H]+. Purity >90%.

2-(5-Fluoro-2-methoxyphenyl)benzo[d][1,2]selenazol-3(2H)-one (E16)

1H NMR (600 MHz, CDCl3) δ 8.12 (d, J = 7.7 Hz, 1H), 7.66–7.63 (m, 2H), 7.45 (ddd, J = 8.1, 5.7, 2.4 Hz, 1H), 7.33 (dd, J = 8.7, 2.8 Hz, 1H), 7.05 (td, J = 8.5, 3.1 Hz, 1H), 6.94 (dd, J = 9.0, 4.8 Hz, 1H), 3.84 (s, 3H). 13C NMR (151 MHz, CDCl3) δ 166.3, 156.6, 155.0, 151.9, 140.8, 132.7, 132.5, 128.2, 127.4 126.2, 116.7, 115.3, 114.0, 56.6. HRMS (ESI): m/z calculated for C14H10FNO2Se 322.9861, found 323.9937 [M + H]+. Purity >99%.

2-(4-Fluoro-2-methoxyphenyl)benzo[d][1,2]selenazol-3(2H)-one (E17)

1H NMR (600 MHz, CD3OD) δ 8.07 (d, J = 8.0 Hz, 1H), 7.86 (d, J = 7.3 Hz, 1H), 7.67 (ddd, J = 8.3, 7.2, 1.5 Hz, 1H), 7.46 (td, J = 7.5, 1.0 Hz, 1H), 7.37 (dd, J = 8.6, 6.4 Hz, 1H), 7.11 (dd, J = 11.0, 2.6 Hz, 1H), 6.85 (td, J = 8.4, 2.7 Hz, 1H), 3.78 (s, 3H). 13C NMR (151 MHz, CD3OD) δ 166.3, 140.9, 132.5, 131.5, 128.3, 127.6, 126.4, 126.4, 107.3, 107.1, 101.4, 101.3, 56.7, 36.3. HRMS (ESI): m/z calculated for C14H10FNO2Se 322.9861, found 323.9938 [M + H]+. Purity >95%.

2-(4-Ethylphenyl)benzo[d][1,2]selenazol-3(2H)-one (E18)

1H NMR (600 MHz, CDCl3) δ 8.12 (d, J = 7.7 Hz, 1H), 7.67–7.63 (m, 2H), 7.52 (dt, J = 8.2, 2.1 Hz, 2H), 7.47 (ddd, J = 7.9, 6.4, 1.8 Hz, 1H), 7.26 (d, J = 8.2 Hz, 2H), 2.67 (q, J = 7.6 Hz, 2H), 1.26 (t, J = 7.6 Hz, 3H). 13C NMR (151 MHz, CDCl3) δ 165.8, 143.2, 137.8, 136.6, 132.5, 129.4, 128.8, 128.8, 127.6, 126.5, 125.6, 125.6, 123.8, 28.5, 15.6. HRMS (ESI): m/z calculated for C15H13NOSe 303.0162, found 304.0240 [M + H]+. Purity >99%.

2-(3-Chlorophenyl)benzo[d][1,2]selenazol-3(2H)-one (E19)

1H NMR (600 MHz, CDCl3 + CD3OD) δ 7.92 (d, J = 7.6 Hz, 1H), 7.69 (d, J = 8.0 Hz, 1H), 7.53 (dt, J = 8.2, 1.6 Hz, 2H), 7.35 (dd, J = 8.0, 1.1 Hz, 1H), 7.34 (t, J = 7.0 Hz, 1H), 7.24 (d, J = 8.0 Hz, 1H), 7.14 (ddd, J = 7.2, 4.0, 3.2 Hz, 1H). 13C NMR (151 MHz, CDCl3) δ 166.4, 140.1, 138.6, 134.7, 132.7, 130.2, 128.8, 127.3, 126.8, 126.5, 125.5, 124.3, 123.5. HRMS (ESI): m/z calculated for C13H8ClNOSe 308.9460, found 309.9536 [M + H]+. Purity >98%.

2-(3,5-Dichlorophenyl)benzo[d][1,2]selenazol-3(2H)-one (E20)

1H NMR (600 MHz, (CD3)2SO) δ 8.11–8.06 (m, 2H), 7.91 (d, J = 2.2 Hz, 1H), 7.69 (t, J = 7.6 Hz, 2H), 7.58 (dd, J = 8.3, 2.7 Hz, 1H), 7.48 (t, J = 7.5 Hz, 1H). 13C NMR (151 MHz, (CD3)2SO) δ 166.4, 140.1, 138.6, 134.7, 132.7, 130.2, 128.8, 127.3, 126.8, 126.5, 125.5, 124.3, 123.54. HRMS (ESI): m/z calculated for C13H7Cl2NOSe 342.9070, found 344.2213 [M + H]+. Purity >95%.

2-(4-Bromophenyl)benzo[d][1,2]selenazol-3(2H)-one (E21)

1H NMR (600 MHz, CD3OD + CDCl3) δ 8.12 (d, J = 7.9 Hz, 1H), 7.90 (dd, J = 7.8, 1.4 Hz, 1H), 7.69 (ddd, J = 8.3, 7.2, 1.4, Hz, 1H), 7.64 (s, 4H), 7.48 (td, J = 7.5, 1.1 Hz, 1H). 13C NMR (151 MHz, CDCl3) δ 165.1, 139.3, 138.6, 132.4, 132.0, 132.0, 128.5, 128.0, 126.4, 126.4, 126.4, 126.1, 117.8. HRMS (ESI): m/z calculated for C13H8BrNOSe 352.8954, found 353.9028 [M + H]+. Purity >95%.

2-(p-Tolyl)benzo[d][1,2]selenazol-3(2H)-one (E22)

1H NMR (600 MHz,(CD3)2SO) δ 8.11 (d, J = 8.1 Hz, 1H), 7.789 (dd, J = 7.8, 1.4 Hz, 1H), 7.67 (t, J = 7.4 Hz, 1H), 7.51 (d, J = 8.1 Hz, 1H), 7.47 (t, J = 7.2 Hz, 2H), 7.25 (d, J = 8.1 Hz, 2H), 2.32 (s, 3H). 13C NMR (151 MHz, (CD3)2SO) δ 164.9, 138.8, 137.1, 135.3, 132.1, 129.6, 129.6, 128.6, 127.9, 126.2, 125.9, 124.7, 124.7, 20.6. HRMS (ESI): m/z calculated for C14H11NOSe 289.0006, found 290.0087 [M + H]+. Purity >96%.

2-(o-Tolyl)benzo[d][1,2]selenazol-3(2H)-one (E23)

1H NMR (600 MHz, CDCl3) δ 8.18 (d, J = 7.8 Hz, 1H), 7.74 (t, J = 7.2 Hz, 1H), 7.70 (t, J = 7.5 Hz, 1H), 7.53 (t, J = 7.5 Hz, 1H), 7.38–7.34 (m, 3H), 7.32 (d, J = 5.5 Hz, 1H), 2.29 (s, 3H). 13C NMR (151 MHz, CDCl3) δ 166.2, 139.1, 139.1, 137.7, 136.8, 132.4, 131.3, 129.4, 129.2, 129.1, 126.9, 126.5, 124.2, 18.3. HRMS (ESI): m/z calculated for C14H11NOSe 289.0006, found 290.0086 [M + H]+. Purity >98%.

2-(3-(Trifluoromethyl)phenyl)benzo[d][1,2]selenazol-3(2H)-one (E24)

1H NMR (600 MHz, CDCl3) δ 8.13 (d, J = 7.9 Hz, 1H), 7.95 (s, 1H), 7.84 (d, J = 7.8 Hz, 1H), 7.68 (d, J = 4.2 Hz, 2H), 7.56 (t, J = 7.8 Hz, 1H), 7.53 (d, J = 7.9 Hz, 1H), 7.49 (ddd, J = 8.0, 4.8, 3.4 Hz, 1H). 13C NMR (151 MHz, CDCl3) δ 166.0, 139.9, 137.4, 133.1, 130.1, 129.7, 128.6, 127.0, 127.0, 124.0, 123.4, 123.3, 122.2, 122.2. HRMS (ESI): m/z calculated for C14H8F3NOSe 342.9723, found 343.9800 [M + H]+. Purity >99%.

3-(3-Oxobenzo[d][1,2]selenazol-2(3H)-yl)benzonitrile (E25)

1H NMR (600 MHz, CDCl3) δ 8.15 (dt, J = 7.8, 1.1 Hz,1H), 7.78 (dd, J = 7.8, 1.4 Hz, 1H), 7.73–7.65 (m, 3H), 7.55 (dd, J = 8.1, 1.1 Hz, 1H), 7.50 (tdd, J = 6.1, 4.6, 2.9 Hz, 2H). 13C NMR (151 MHz, CDCl3) δ 166.5, 140.9, 138.6, 134.0, 133.8, 133.2, 129.9, 129.9, 128.7, 126.9, 125.4, 124.1, 116.1, 113.4. HRMS (ESI): m/z calculated for C14H8N2OSe 299.9802, found 300.9880 [M + H]+. Purity >98%.

2-(3-Methoxyphenyl)benzo[d][1,2]selenazol-3(2H)-one (E26)

1H NMR (600 MHz, CDCl3) δ 8.11 (d, J = 7.8 Hz, 1H), 7.65 (ddd, J = 10.0, 9.1, 4.4 Hz, 2H), 7.46 (ddd, J = 8.0, 6.8, 1.4 Hz, 1H), 7.360–7.28 (m, 2H), 7.16 (ddd, J = 7.9, 2.1, 0.9 Hz,1H), 6.83 (dd, J = 8.1, 2.3 Hz, 1H), 3.84 (s, 3H). 13C NMR (151 MHz, CDCl3) δ 165.8, 160.3, 140.3, 137.82, 132.7, 130.1, 129.5, 127.8, 126.7, 123.8, 117.6, 113.0, 111.0, 55.6. HRMS (ESI): m/z calculated for C14H11NO2Se 304.9955, found 306.0034 [M + H]+. Purity >99%.

2-(4-Methoxyphenyl)benzo[d][1,2]selenazol-3(2H)-one (E27)

1H NMR (600 MHz, CDCl3) δ 8.10 (d, J = 7.7 Hz, 1H), 7.64 (ddd, J = 12.3, 9.0, 4.5 Hz, 2H), 7.49 (d, J = 2. Hz, 1 H), 7.47 (td, J = 6.87, 1.1 Hz, 2H), 6.95 (dt, J = 8.9, 2.2 Hz, 2H), 3.83 (s, 3H). 13C NMR (151 MHz, CDCl3) δ 166.1, 158.5, 138.0, 132.4, 131.7, 129.3, 127.5, 127.3, 126.5, 123.9, 123.9, 114.5 114.5, 55.4. HRMS (ESI): m/z calculated for C14H11NO2Se 304.9955, found 306.0035 [M + H]+. Purity >99%.

2-Heptylbenzo[d][1,2]selenazol-3(2H)-one (E28)

1H NMR (600 MHz, CDCl3) δ 8.03 (d, J = 7.8 Hz, 1H), 7.63 (d, J = 7.9 Hz, 1H), 7.57 (td, J = 7.6, 1.4 Hz, 1H), 7.41 (t, J = 7.4 Hz, 1H), 3.84 (t, J = 7.3 Hz, 2H), 1.75–68 (m, 2H), 1.42–1.21 (m, 8H), 0.87 (t, J = 7.0 Hz, 3H). 13C NMR (151 MHz, CDCl3) δ 167.1, 137.6, 131.9, 128.9, 127.6, 126.3, 124.0, 44.8, 31.9, 30.4, 28.9, 26.3, 22.8, 14.1. HRMS (ESI): m/z calculated for C14H19NOSe 297.0632, found 298.0711 [M + H]+. Purity >98%.

2-Octylbenzo[d][1,2]selenazol-3(2H)-one (E29)

1H NMR (600 MHz, CDCl3) δ 8.04 (d, J = 7.8 Hz, 1H), 7.63 (dt, J = 8.0, 0.9 Hz, 1H), 7.57 (td, J = 7.1, 1.3 Hz, 1H), 7.42 (t, J = 7.2 Hz, 1H), 3.851 (t, J = 7.15 Hz, 2H), 1.72 (m, J = 2H), 1.43–1.27 (m, 4H), 1.29–1.25 (m, 2H), 1.27–1.20 (m, 4 H), 0.87 (t, J = 7.0 Hz, 3H). 13C NMR (151 MHz, CDCl3) δ 167.1, 137.7, 131.8, 128.9, 127.7, 126.2, 123.8, 44.9, 31.8, 30.7, 29.3, 29.1, 26.6, 22.6, 14.1. HRMS (ESI): m/z calculated for C15H21NOSe 311.0788, found 312.0868 [M + H]+. Purity >98%.

2-Pentylbenzo[d][1,2]selenazol-3(2H)-one (E30)

1H NMR (600 MHz, CDCl3) δ 8.04 (d, J = 7.8 Hz, 1H), 7.63 (d, J = 7.9 Hz, 1H), 7.57 (td, J = 7.7, 1.1 Hz, 1H), 7.42 (t, J = 7.5 Hz, 1H), 3.84 (t, J = 7.3 Hz, 2H), 1.72 (m, 2H), 1.37 (dd, J = 8.7, 5.5 Hz, 4H), 0.90 (t, J = 6.7 Hz, 3H). 13C NMR (151 MHz, CDCl3) δ 167.3, 137.7, 131.9, 128.9, 127.7, 126.2, 124.0, 44.9, 30.3, 28.8, 22.4, 14.0. HRMS (ESI): m/z calculated for C12H15NOSe 269.0319, found 270.0398 [M + H]+. Purity >99%.

Supporting Information

Click to copy section linkSection link copied!

The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jmedchem.1c00566.

  • Molecular formula strings(CSV)

  • Expanded synthetic methods and spectra for E01–30, structures and reported activities for known SARS-CoV-2 main protease inhibitors, docking poses, and individual antiviral dose–response curves for select compounds

    (PDF)

Terms & Conditions

Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

Author Information

Click to copy section linkSection link copied!
  • Corresponding Author
    • Tariq M. Rana - Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States;  Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States;  Orcidhttps://orcid.org/0000-0001-9558-5766;  Email: [email protected]
  • Authors
    • Sarah Huff - Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    • Indrasena Reddy Kummetha - Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    • Shashi Kant Tiwari - Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    • Matthew B. Huante - Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, United States
    • Alex E. Clark - Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    • Shaobo Wang - Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    • William Bray - Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    • Davey Smith - Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
    • Aaron F. Carlin - Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States;  Orcidhttps://orcid.org/0000-0002-1669-8066
    • Mark Endsley - Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, United States
  • Author Contributions

    These authors contributed equally to this work. S.H. and I.R.K. designed and performed the experiments, analyzed the data, and wrote the manuscript; S.K.T., M.B.H., A.E.C., S.W., W.B., and M.E. performed experiments and analysis; D.S. provided resources; A.C. gave advice in experimental plans and performed experiments; T.M.R. conceived of and planned the project and participated in experimental design, data analysis, data interpretation, and manuscript writing.

  • Notes
    The authors declare the following competing financial interest(s): T.M.R. is a founder of ViRx Pharmaceuticals and has an equity interest in the company. The terms of this arrangement have been reviewed and approved by the University of California San Diego in accordance with its conflict of interest policies.

Acknowledgments

Click to copy section linkSection link copied!

We thank the Rao Zihe and Yang Haitao laboratories of ShanghaiTech University for providing the coordinates of the SARS-CoV-2 Mpro crystal structure (PDB ID 6UL7). We thank members of the Rana lab for helpful discussions and advice. This work was supported by a T32 fellowship from the National Cancer Institute of the National Institutes of Health (award no. T32CA121938 to S.H.), a Career Award for Medical Scientists from the Burroughs Wellcome Fund (USA), a grant from the National Institutes of Health USA (K08 AI130381) to A.F.C., the John and Mary Tu Foundation (USA), a CIRM award to T.M.R., and in part by grants from the National Institutes of Health (USA) (CA177322, DA039562, DA049524, and AI125103).

ABBREVIATONS

Click to copy section linkSection link copied!
ACE2

angiotensin-converting enzyme 2

COVID-19

coronavirus disease 2019

iPSC

induced pluripotent stem cells

ISG15

interferon-stimulated gene 15

MOI

multiplicity of infection

Mpro

main protease

nsp1

nonstructural protein 1

nsp2

nonstructural protein 2

nsp3

nonstructural protein 3

OPLS

optimized potentials for liquid simulations

PLpro

papain-like protease

RT-qPCR

real-time quantitative reverse transcription PCR

RdRp

RNA-dependent RNA polymerase

SARS-CoV-2

severe acute respiratory syndrome coronavirus 2

SGB

surface generalized born

(+)ssRNA

positive-sense single-stranded RNA

TMPRSS2

transmembrane protease serine 2

References

Click to copy section linkSection link copied!

This article references 50 other publications.

  1. 1
    Li, F.; Li, W.; Farzan, M.; Harrison, S. C. Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science 2005, 309 (5742), 1864– 1868,  DOI: 10.1126/science.1116480
    Google Scholar
    1
    Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed with Receptor
    Li, Fang; Li, Wenhui; Farzan, Michael; Harrison, Stephen C.
    Science (Washington, DC, United States) (2005), 309 (5742), 1864-1868CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    The spike protein (S) of SARS coronavirus (SARS-CoV) attaches the virus to its cellular receptor, angiotensin-converting enzyme 2 (ACE2). A defined receptor-binding domain (RBD) on S mediates this interaction. The crystal structure at 2.9 angstrom resoln. of the RBD bound with the peptidase domain of human ACE2 shows that the RBD presents a gently concave surface, which cradles the N-terminal lobe of the peptidase. The at. details at the interface between the two proteins clarify the importance of residue changes that facilitate efficient cross-species infection and human-to-human transmission. The structure of the RBD suggests ways to make truncated disulfide-stabilized RBD variants for use in the design of coronavirus vaccines.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXpvFCisLw%253D&md5=0a7ac2fb7a76c97979d859c0489c682f
  2. 2
    Phan, T. Novel coronavirus: From discovery to clinical diagnostics. Infect., Genet. Evol. 2020, 79, 104211,  DOI: 10.1016/j.meegid.2020.104211
    Google Scholar
    2
    Novel coronavirus: From discovery to clinical diagnostics
    Phan, Tung
    Infection, Genetics and Evolution (2020), 79 (), 104211CODEN: IGENCN; ISSN:1567-1348. (Elsevier B.V.)
    A novel coronavirus designated as 2019-nCoV first appeared in Wuhan, China in late Dec. 2019. Dozens of people died in China, and thousands of people infected as 2019-nCoV continues to spread around the world. We have described the discovery, emergence, genomic characteristics, and clin. diagnostics of 2019-nCoV.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitFOit7g%253D&md5=3cb3ef734c4f4f85479d8b55a2daf94c
  3. 3
    Pillaiyar, T.; Manickam, M.; Namasivayam, V.; Hayashi, Y.; Jung, S. H. An Overview of Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy. J. Med. Chem. 2016, 59 (14), 6595– 628,  DOI: 10.1021/acs.jmedchem.5b01461
    Google Scholar
    3
    An Overview of Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy
    Pillaiyar, Thanigaimalai; Manickam, Manoj; Namasivayam, Vigneshwaran; Hayashi, Yoshio; Jung, Sang-Hun
    Journal of Medicinal Chemistry (2016), 59 (14), 6595-6628CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    Severe acute respiratory syndrome (SARS) is caused by a newly emerged coronavirus that infected more than 8000 individuals and resulted in more than 800 (10-15%) fatalities in 2003. The causative agent of SARS has been identified as a novel human coronavirus (SARS-CoV), and its viral protease, SARS-CoV 3CLpro, has been shown to be essential for replication and has hence been recognized as a potent drug target for SARS infection. Currently, there is no effective treatment for this epidemic despite the intensive research that has been undertaken since 2003 (over 3500 publications). This perspective focuses on the status of various efficacious anti-SARS-CoV 3CLpro chemotherapies discovered during the last 12 years (2003-2015) from all sources, including lab. synthetic methods, natural products, and virtual screening. We describe here mainly peptidomimetic and small mol. inhibitors of SARS-CoV 3CLpro. Attempts have been made to provide a complete description of the structural features and binding modes of these inhibitors under many conditions.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XisVyns7c%253D&md5=6ce37076204280f64a7f362633fcee1a
  4. 4
    Ziebuhr, J.; Snijder, E. J.; Gorbalenya, A. E. Virus-encoded proteinases and proteolytic processing in the Nidovirales. J. Gen. Virol. 2000, 81 (4), 853– 879,  DOI: 10.1099/0022-1317-81-4-853
    Google Scholar
    4
    Virus-encoded proteinases and proteolytic processing in the nidovirales
    Ziebuhr, John; Snijder, Eric J.; Gorbalenya, Alexander E.
    Journal of General Virology (2000), 81 (4), 853-879CODEN: JGVIAY; ISSN:0022-1317. (Society for General Microbiology)
    A review with 128 refs. The review is organized into five main sections. In the first section nidovirus proteinases are introduced and classified into main and accessory proteinases. In the next two sections a brief overview of two classes of nidovirus proteinases is presented and, in this context, the coronavirus and arterivirus enzymes are compared to each other and to the prototypic proteinases. This is followed by a detailed description of the nidovirus proteinases themselves. The review is concluded by two sections that describe the regulatory role of the proteinases during virus replication and then give an outline of future perspectives concerning nidovirus proteinases.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXisVektLg%253D&md5=5293084b82548029518d57e401eccc3e
  5. 5
    Báez-Santos, Y. M.; St. John, S. E.; Mesecar, A. D. The SARS-coronavirus papain-like protease: Structure, function and inhibition by designed antiviral compounds. Antiviral Res. 2015, 115, 21– 38,  DOI: 10.1016/j.antiviral.2014.12.015
    Google Scholar
    5
    The SARS-coronavirus papain-like protease: Structure, function and inhibition by designed antiviral compounds
    Baez-Santos, Yahira M.; St. John, Sarah E.; Mesecar, Andrew D.
    Antiviral Research (2015), 115 (), 21-38CODEN: ARSRDR; ISSN:0166-3542. (Elsevier B.V.)
    A review. Over 10 years have passed since the deadly human coronavirus that causes severe acute respiratory syndrome (SARS-CoV) emerged from the Guangdong Province of China. Despite the fact that the SARS-CoV pandemic infected over 8500 individuals, claimed over 800 lives and cost billions of dollars in economic loss worldwide, there still are no clin. approved antiviral drugs, vaccines or monoclonal antibody therapies to treat SARS-CoV infections. The recent emergence of the deadly human coronavirus that causes Middle East respiratory syndrome (MERS-CoV) is a sobering reminder that new and deadly coronaviruses can emerge at any time with the potential to become pandemics. Therefore, the continued development of therapeutic and prophylactic countermeasures to potentially deadly coronaviruses is warranted. The coronaviral proteases, papain-like protease (PLpro) and 3C-like protease (3CLpro), are attractive antiviral drug targets because they are essential for coronaviral replication. Although the primary function of PLpro and 3CLpro are to process the viral polyprotein in a coordinated manner, PLpro has the addnl. function of stripping ubiquitin and ISG15 from host-cell proteins to aid coronaviruses in their evasion of the host innate immune responses. Therefore, targeting PLpro with antiviral drugs may have an advantage in not only inhibiting viral replication but also inhibiting the dysregulation of signaling cascades in infected cells that may lead to cell death in surrounding, uninfected cells. This review provides an up-to-date discussion on the SARS-CoV papain-like protease including a brief overview of the SARS-CoV genome and replication followed by a more in-depth discussion on the structure and catalytic mechanism of SARS-CoV PLpro, the multiple cellular functions of SARS-CoV PLpro, the inhibition of SARS-CoV PLpro by small mol. inhibitors, and the prospect of inhibiting papain-like protease from other coronaviruses. This paper forms part of a series of invited articles in Antiviral Research on "From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.".
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXmtVOnsw%253D%253D&md5=fcdde62e05b499546c73f3014ea521ad
  6. 6
    Lee, T. W.; Cherney, M. M.; Huitema, C.; Liu, J.; James, K. E.; Powers, J. C.; Eltis, L. D.; James, M. N. Crystal structures of the main peptidase from the SARS coronavirus inhibited by a substrate-like aza-peptide epoxide. J. Mol. Biol. 2005, 353 (5), 1137– 1151,  DOI: 10.1016/j.jmb.2005.09.004
    Google Scholar
    6
    Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide
    Lee, Ting-Wai; Cherney, Maia M.; Huitema, Carly; Liu, Jie; James, Karen Ellis; Powers, James C.; Eltis, Lindsay D.; James, Michael N. G.
    Journal of Molecular Biology (2005), 353 (5), 1137-1151CODEN: JMOBAK; ISSN:0022-2836. (Elsevier B.V.)
    The main peptidase (Mpro) from the coronavirus (CoV) causing severe acute respiratory syndrome (SARS) is one of the most attractive mol. targets for the development of anti-SARS agents. We report the irreversible inhibition of SARS-CoV Mpro by an aza-peptide epoxide (APE; kinact/Ki=1900(±400) M-1 s-1). The crystal structures of the Mpro:APE complex in the space groups C2 and P212121 revealed the formation of a covalent bond between the catalytic Cys145 Sγ atom of the peptidase and the epoxide C3 atom of the inhibitor, substantiating the mode of action of this class of cysteine-peptidase inhibitors. The aza-peptide component of APE binds in the substrate-binding regions of Mpro in a substrate-like manner, with excellent structural and chem. complementarity. In addn., the crystal structure of unbound Mpro in the space group C2 revealed that the "N-fingers" (N-terminal residues 1 to 7) of both protomers of Mpro are well defined and the substrate-binding regions of both protomers are in the catalytically competent conformation at the crystn. pH of 6.5, contrary to the previously detd. crystal structures of unbound Mpro in the space group P21.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXhtFKms7nL&md5=ba0e5fbad36bfc3d259c9221d451ef60
  7. 7
    Xu, X.; Liu, Y.; Weiss, S.; Arnold, E.; Sarafianos, S. G.; Ding, J. Molecular model of SARS coronavirus polymerase: implications for biochemical functions and drug design. Nucleic Acids Res. 2003, 31 (24), 7117– 7130,  DOI: 10.1093/nar/gkg916
    Google Scholar
    7
    Molecular model of SARS coronavirus polymerase: implications for biochemical functions and drug design
    Xu, Xiang; Liu, Yunqing; Weiss, Susan; Arnold, Eddy; Sarafianos, Stefan G.; Ding, Jianping
    Nucleic Acids Research (2003), 31 (24), 7117-7130CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)
    The causative agent of severe acute respiratory syndrome (SARS) is a previously unidentified coronavirus, SARS-CoV. The RNA-dependent RNA polymerase (RdRp) of SARS-CoV plays a pivotal role in viral replication and is a potential target for anti-SARS therapy. There is a lack of structural or biochem. data on any coronavirus polymerase. To provide insights into the structure and function of SARS-CoV RdRp, we have located its conserved motifs that are shared by all RdRps, and built a three-dimensional model of the catalytic domain. The structural model permits us to discuss the potential functional roles of the conserved motifs and residues in replication and their potential interactions with inhibitors of related enzymes. We predict the following important structural attributes for potential anti-SARS-CoV RdRp nucleotide analog inhibitors: hydrogen-bonding capability for the 2' and 3' groups of the sugar ring and C3' endo sugar puckering, and the absence of a hydrophobic binding pocket for non-nucleoside analog inhibitors similar to those obsd. in hepatitis C virus RdRp and human immunodeficiency virus type 1 reverse transcriptase. We propose that the clin. obsd. resistance of SARS to ribavirin is probably due to perturbation of the conserved motif A that controls rNTP binding and fidelity of polymn. Our results suggest that designing anti-SARS therapies can benefit from successful experiences in design of other antiviral drugs. This work should also provide guidance for future biochem. expts.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXps1Siu7Y%253D&md5=1c63b9eb468d4b067d4efb3136e18e66
  8. 8
    De Clercq, E.; Li, G. Approved Antiviral Drugs over the Past 50 Years. Clin. Microbiol. Rev. 2016, 29 (3), 695– 747,  DOI: 10.1128/CMR.00102-15
    Google Scholar
    8
    Approved Antiviral Drugs over the Past 50 Years
    De Clercq Erik; Li Guangdi
    Clinical microbiology reviews (2016), 29 (3), 695-747 ISSN:.
    Since the first antiviral drug, idoxuridine, was approved in 1963, 90 antiviral drugs categorized into 13 functional groups have been formally approved for the treatment of the following 9 human infectious diseases: (i) HIV infections (protease inhibitors, integrase inhibitors, entry inhibitors, nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, and acyclic nucleoside phosphonate analogues), (ii) hepatitis B virus (HBV) infections (lamivudine, interferons, nucleoside analogues, and acyclic nucleoside phosphonate analogues), (iii) hepatitis C virus (HCV) infections (ribavirin, interferons, NS3/4A protease inhibitors, NS5A inhibitors, and NS5B polymerase inhibitors), (iv) herpesvirus infections (5-substituted 2'-deoxyuridine analogues, entry inhibitors, nucleoside analogues, pyrophosphate analogues, and acyclic guanosine analogues), (v) influenza virus infections (ribavirin, matrix 2 protein inhibitors, RNA polymerase inhibitors, and neuraminidase inhibitors), (vi) human cytomegalovirus infections (acyclic guanosine analogues, acyclic nucleoside phosphonate analogues, pyrophosphate analogues, and oligonucleotides), (vii) varicella-zoster virus infections (acyclic guanosine analogues, nucleoside analogues, 5-substituted 2'-deoxyuridine analogues, and antibodies), (viii) respiratory syncytial virus infections (ribavirin and antibodies), and (ix) external anogenital warts caused by human papillomavirus infections (imiquimod, sinecatechins, and podofilox). Here, we present for the first time a comprehensive overview of antiviral drugs approved over the past 50 years, shedding light on the development of effective antiviral treatments against current and emerging infectious diseases worldwide.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2s%252Fos12htA%253D%253D&md5=1d25d961c1c6a72d6bc4634041bbb6fe
  9. 9
    Kanters, S.; Socias, M. E.; Paton, N. I.; Vitoria, M.; Doherty, M.; Ayers, D.; Popoff, E.; Chan, K.; Cooper, D. A.; Wiens, M. O.; Calmy, A.; Ford, N.; Nsanzimana, S.; Mills, E. J. Comparative efficacy and safety of second-line antiretroviral therapy for treatment of HIV/AIDS: A systematic review and network meta-analysis. Lancet HIV 2017, 4 (10), e433– e441,  DOI: 10.1016/S2352-3018(17)30109-1
    Google Scholar
    There is no corresponding record for this reference.
  10. 10
    Deeks, E. D. Darunavir: a review of its use in the management of HIV-1 infection. Drugs 2014, 74 (1), 99– 125,  DOI: 10.1007/s40265-013-0159-3
    Google Scholar
    10
    Darunavir: A Review of Its Use in the Management of HIV-1 Infection
    Deeks, Emma D.
    Drugs (2014), 74 (1), 99-125CODEN: DRUGAY; ISSN:0012-6667. (Springer International Publishing AG)
    A review. The latest HIV-1 protease inhibitor (PI) darunavir (Prezista®) has a high genetic barrier to resistance development and is active against wild-type HIV and HIV strains no longer susceptible to some older PIs. Ritonavir-boosted darunavir, as a component of antiretroviral therapy (ART), is indicated for the treatment of HIV-1 infection in adult and paediatric patients (aged ≥3 years), with or without treatment experience (details vary depending on region of approval). Several open-label or partially-blinded trials have evaluated the efficacy of ritonavir-boosted darunavir ART regimens for up to 192 wk in these settings. In treatment-naive adults, once-daily boosted darunavir was no less effective in establishing virol. suppression than once- or twice-daily boosted lopinavir, yet was more effective at maintaining suppression long term. Moreover, treatment-experienced adults with no darunavir resistance-assocd. mutations (RAMs) had no less effective viral load suppression with once-daily than with twice-daily boosted darunavir. In treatment-experienced adults, including some with multiple major PI RAMs, twice-daily boosted darunavir was more effective than twice-daily boosted lopinavir or boosted control PIs in reducing viral load, and provided virol. benefit as part of a salvage regimen in those with few remaining treatment options. Boosted darunavir also reduced viral load when administered once-daily in treatment-naive adolescents or twice-daily in treatment-experienced children and adolescents. Boosted darunavir is generally well tolerated, with gastrointestinal disturbances and lipid abnormalities among the most common tolerability issues. It has a lipid profile more favorable than that of boosted lopinavir in terms of total cholesterol and triglyceride changes and, when administered once daily, its lipid effects are generally similar to those of boosted atazanavir. Thus, boosted darunavir is a useful option for the ART regimens of adult and paediatric patients with HIV-1 infection.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXptFajuw%253D%253D&md5=b5f8e515fd0c0ce64d97b0c126c18ce4
  11. 11
    la Porte, C. J. Saquinavir, the pioneer antiretroviral protease inhibitor. Expert Opin. Drug Metab. Toxicol. 2009, 5 (10), 1313– 1322,  DOI: 10.1517/17425250903273160
    Google Scholar
    11
    Saquinavir, the pioneer antiretroviral protease inhibitor
    La Porte, Charles J. L.
    Expert Opinion on Drug Metabolism & Toxicology (2009), 5 (10), 1313-1322CODEN: EODMAP; ISSN:1742-5255. (Informa Healthcare)
    A review. Background: The treatment of HIV infection underwent a major change in 1995 when saquinavir was the first protease inhibitor introduced into the market. This drug made the use of combination therapy in the treatment of HIV possible and increased the success rate of treatment. Objective: This article will review recent literature on saquinavir to define its current role in HIV treatment, among the newer antiretroviral drugs. Methods: Scientific literature and conference presentations were evaluated for relevant information pertaining to saquinavir. Results/conclusions: Although underused, saquinavir has good efficacy and tolerability when compared to other protease inhibitors. The film-coated tablet formulation improved pill burden. Saquinavir still has potential in the treatment of adults, children and pregnant women.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtFCgsrfM&md5=337b9225b09c6cabc0a87f41272b1ede
  12. 12
    Heo, Y. A.; Deeks, E. D. Sofosbuvir/Velpatasvir/Voxilaprevir: A Review in Chronic Hepatitis C. Drugs 2018, 78 (5), 577– 587,  DOI: 10.1007/s40265-018-0895-5
    Google Scholar
    12
    Sofosbuvir/Velpatasvir/Voxilaprevir: A Review in Chronic Hepatitis C
    Heo, Young-A.; Deeks, Emma D.
    Drugs (2018), 78 (5), 577-587CODEN: DRUGAY; ISSN:0012-6667. (Springer International Publishing AG)
    A fixed-dose combination of the hepatitis C virus (HCV) NS5B polymerase inhibitor sofosbuvir, the HCV NS5A inhibitor velpatasvir and the HCV NS3/4A protease inhibitor voxilaprevir (sofosbuvir/velpatasvir/voxilaprevir; Vosevi) is approved in the EU for the treatment of chronic HCV genotype 1, 2, 3, 4, 5 or 6 infection in adults. In the phase III POLARIS trials, in patients who had HCV genotype 1-6 infection with or without compensated cirrhosis, overall rates of sustained virol. response at 12 wk post-treatment (SVR12) with sofosbuvir/velpatasvir/voxilaprevir were high after 8 wk of treatment in direct-acting antiviral (DAA)-naive patients and 12 wk of treatment in DAA-experienced patients. However, 8 wk of sofosbuvir/velpatasvir/voxilaprevir was inferior to 12 wk of sofosbuvir/velpatasvir in cirrhotic or non-cirrhotic DAA-naive patients with HCV genotype 1, 2, 4, 5 or 6 infection and non-cirrhotic DAA-naive patients with HCV genotype 3 infection, mostly due to an insufficient treatment period. Sofosbuvir/velpatasvir/voxilaprevir was generally well tolerated, with most adverse events being of mild or moderate intensity. The most common adverse events included headache, fatigue, nausea and diarrhoea. In conclusion, sofosbuvir/velpatasvir/voxilaprevir is an important and effective option for the treatment of HCV genotype 1-6 infection in adults, esp. those who have previously failed a DAA therapy with or without an HCV NS5A inhibitor.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXkslGjt7k%253D&md5=d4557e43a321ca3a9a30d996ac5f77ba
  13. 13
    Sanford, M. Simeprevir: a review of its use in patients with chronic hepatitis C virus infection. Drugs 2015, 75 (2), 183– 196,  DOI: 10.1007/s40265-014-0341-2
    Google Scholar
    13
    Simeprevir: A Review of Its Use in Patients with Chronic Hepatitis C Virus Infection
    Sanford, Mark
    Drugs (2015), 75 (2), 183-196CODEN: DRUGAY; ISSN:0012-6667. (Springer International Publishing AG)
    A review. Simeprevir (Olysio; Galexos; Sovriad) is an orally-administered NS3/4A protease inhibitor for use in combined drug regimens against chronic hepatitis C virus (HCV) infection. This article reviews studies relevant to the EU simeprevir label. In proof-of-concept studies, simeprevir had potent antiviral activity against all HCV genotypes, except genotype 3. In trials in patients with chronic HCV genotype 1 infection, week-12 sustained virol. response (SVR12) rates in treatment-naive patients and prior relapsers were significantly higher with simeprevir plus peginterferon-α/ribavirin (PR) [79-89 %] than with placebo plus PR (36-62 %). In prior partial/null responders, the SVR12 rate with simeprevir plus PR (54 %) was noninferior to that with telaprevir plus PR (55 %). Simeprevir plus PR was also efficacious in patients with HCV genotype 1/HIV-1 co-infection. In prior null responders without severe liver fibrosis (cohort 1) and treatment-naive patients with severe liver fibrosis (cohort 2) treated with simeprevir plus sofosbuvir, the SVR12 rate for the two cohorts combined was 92 %. In patients with chronic HCV genotype 4 infection, the SVR12 rates with simeprevir plus PR were 83, 87 and 40 % in treatment-naive patients, prior relapsers and prior null responders, resp. Grade 3-4 adverse event, serious adverse event and treatment withdrawal rates with simeprevir plus PR were similar to those with placebo plus PR. Skin rashes with simeprevir were mostly mild or moderate; serious photosensitivity reactions occur, but are rare. Simeprevir is efficacious and generally well tolerated in patients with chronic HCV genotypes 1 and 4 infection. Studies of simeprevir in interferon-free regimens and in other subpopulations with HCV infections will be of interest.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXitVCnt7k%253D&md5=20ef9a811518a120a68eb79241f0d735
  14. 14
    Chopp, S.; Vanderwall, R.; Hult, A.; Klepser, M. Simeprevir and sofosbuvir for treatment of hepatitis C infection. Am. J. Health-Syst. Pharm. 2015, 72 (17), 1445– 1455,  DOI: 10.2146/ajhp140290
    Google Scholar
    14
    Simeprevir and sofosbuvir for treatment of hepatitis C infection
    Chopp, Shelby; Vanderwall, Rebecca; Hult, Amanda; Klepser, Michael
    American Journal of Health-System Pharmacy (2015), 72 (17), 1445-1455CODEN: AHSPEK; ISSN:1079-2082. (American Society of Health-System Pharmacists)
    Purpose. The pharmacol., pharmacokinetics, efficacy, safety, costs, and place in therapy of simeprevir and sofosbuvir in the management of hepatitis C virus (HCV) infection are reviewed. Summary. Sofosbuvir and simeprevir are classified as direct-acting agents because they target specific proteins essential to the replication of HCV. Phase III trials demonstrated that simeprevir in combination with peginterferon alfa and ribavirin was superior to placebo combined with peginterferon alfa and ribavirin in achieving a sustained virol. response in both treatment-naive patients and patients who relapsed after treatment with peginterferon alfa-2a or alfa-2b and ribavirin. Q80K polymorphism substantially decreases the efficacy of simeprevir. Clin. trials revealed that sofosbuvir in combination with ribavirin was superior to peginterferon plus ribavirin against HCV genotype 2 infection and as effective as peginterferon plus ribavirin against HCV genotype 3 infection. These findings were significant because they demonstrated the effectiveness of an anti-HCV regimen that did not include peginterferon alfa. Sofosbuvir has much better adverse-effect and drug interaction profiles than previous hepatitis C antiviral agents. Both simeprevir and sofosbuvir are approved for the treatment of chronic hepatitis C in combination with other antiviral medications. Simeprevir has been approved specifically for patients infected with HCV genotype 1 with compensated liver disease (including cirrhosis) in combination with peginterferon alfa-2a or alfa-2b and ribavirin. Sofosbuvir has shown efficacy in HCV genotypes 1-4. Conclusion. Simeprevir and sofasbuvir have advantages in response rates and convenient dosage forms and frequency compared with other HCV treatments; however, they are more expensive than previous HCV therapies.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XmtFGgt7k%253D&md5=b8e2a8a629e121eeba1b7bb37a5fa5e6
  15. 15
    Jin, Z.; Du, X.; Xu, Y.; Deng, Y.; Liu, M.; Zhao, Y.; Zhang, B.; Li, X.; Zhang, L.; Peng, C.; Duan, Y.; Yu, J.; Wang, L.; Yang, K.; Liu, F.; Jiang, R.; Yang, X.; You, T.; Liu, X.; Yang, X.; Bai, F.; Liu, H.; Liu, X.; Guddat, L. W.; Xu, W.; Xiao, G.; Qin, C.; Shi, Z.; Jiang, H.; Rao, Z.; Yang, H. Structure of M(pro) from COVID-19 virus and discovery of its inhibitors. Nature 2020, 582, 289– 293,  DOI: 10.1038/s41586-020-2223-y
    Google Scholar
    15
    Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors
    Jin, Zhenming; Du, Xiaoyu; Xu, Yechun; Deng, Yongqiang; Liu, Meiqin; Zhao, Yao; Zhang, Bing; Li, Xiaofeng; Zhang, Leike; Peng, Chao; Duan, Yinkai; Yu, Jing; Wang, Lin; Yang, Kailin; Liu, Fengjiang; Jiang, Rendi; Yang, Xinglou; You, Tian; Liu, Xiaoce; Yang, Xiuna; Bai, Fang; Liu, Hong; Liu, Xiang; Guddat, Luke W.; Xu, Wenqing; Xiao, Gengfu; Qin, Chengfeng; Shi, Zhengli; Jiang, Hualiang; Rao, Zihe; Yang, Haitao
    Nature (London, United Kingdom) (2020), 582 (7811), 289-293CODEN: NATUAS; ISSN:0028-0836. (Nature Research)
    Abstr.: A new coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the etiol. agent responsible for the 2019-2020 viral pneumonia outbreak of coronavirus disease 2019 (COVID-19). Currently, there are no targeted therapeutic agents for the treatment of this disease, and effective treatment options remain very limited. Here, we describe the results of a program that aimed to rapidly discover lead compds. for clin. use, by combining structure-assisted drug design, virtual drug screening and high-throughput screening. This program focused on identifying drug leads that target main protease (Mpro) of SARS-CoV-2: Mpro is a key enzyme of coronaviruses and has a pivotal role in mediating viral replication and transcription, making it an attractive drug target for SARS-CoV-2. We identified a mechanism-based inhibitor (N3) by computer-aided drug design, and then detd. the crystal structure of Mpro of SARS-CoV-2 in complex with this compd. Through a combination of structure-based virtual and high-throughput screening, we assayed more than 10,000 compds.-including approved drugs, drug candidates in clin. trials and other pharmacol. active compds.-as inhibitors of Mpro. Six of these compds. inhibited Mpro, showing half-maximal inhibitory concn. values that ranged from 0.67 to 21.4μM. One of these compds. (ebselen) also exhibited promising antiviral activity in cell-based assays. Our results demonstrate the efficacy of our screening strategy, which can lead to the rapid discovery of drug leads with clin. potential in response to new infectious diseases for which no specific drugs or vaccines are available.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhtVyhsrrO&md5=b84f350fe9ce1109485df6caf814ba82
  16. 16
    Dai, W.; Zhang, B.; Jiang, X. M.; Su, H.; Li, J.; Zhao, Y.; Xie, X.; Jin, Z.; Peng, J.; Liu, F.; Li, C.; Li, Y.; Bai, F.; Wang, H.; Cheng, X.; Cen, X.; Hu, S.; Yang, X.; Wang, J.; Liu, X.; Xiao, G.; Jiang, H.; Rao, Z.; Zhang, L. K.; Xu, Y.; Yang, H.; Liu, H. Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science 2020, 368 (6497), 1331– 1335,  DOI: 10.1126/science.abb4489
    Google Scholar
    16
    Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease
    Dai, Wenhao; Zhang, Bing; Jiang, Xia-Ming; Su, Haixia; Li, Jian; Zhao, Yao; Xie, Xiong; Jin, Zhenming; Peng, Jingjing; Liu, Fengjiang; Li, Chunpu; Li, You; Bai, Fang; Wang, Haofeng; Cheng, Xi; Cen, Xiaobo; Hu, Shulei; Yang, Xiuna; Wang, Jiang; Liu, Xiang; Xiao, Gengfu; Jiang, Hualiang; Rao, Zihe; Zhang, Lei-Ke; Xu, Yechun; Yang, Haitao; Liu, Hong
    Science (Washington, DC, United States) (2020), 368 (6497), 1331-1335CODEN: SCIEAS; ISSN:1095-9203. (American Association for the Advancement of Science)
    SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the etiol. agent responsible for the global COVID-19 (coronavirus disease 2019) outbreak. The main protease of SARS-CoV-2, Mpro, is a key enzyme that plays a pivotal role in mediating viral replication and transcription. We designed and synthesized two lead compds. (11a and 11b) targeting Mpro. Both exhibited excellent inhibitory activity and potent anti-SARS-CoV-2 infection activity. The x-ray crystal structures of SARS-CoV-2 Mpro in complex with 11a or 11b, both detd. at a resoln. of 1.5 angstroms, showed that the aldehyde groups of 11a and 11b are covalently bound to cysteine 145 of Mpro. Both compds. showed good pharmacokinetic properties in vivo, and 11a also exhibited low toxicity, which suggests that these compds. are promising drug candidates.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXht1alsrzL&md5=ec87c340410edb919d2584a2b4d33e1a
  17. 17
    Vuong, W.; Khan, M. B.; Fischer, C.; Arutyunova, E.; Lamer, T.; Shields, J.; Saffran, H. A.; McKay, R. T.; van Belkum, M. J.; Joyce, M. A.; Young, H. S.; Tyrrell, D. L.; Vederas, J. C.; Lemieux, M. J. Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication. Nat. Commun. 2020, 11 (1), 4282,  DOI: 10.1038/s41467-020-18096-2
    Google Scholar
    17
    Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication
    Vuong, Wayne; Khan, Muhammad Bashir; Fischer, Conrad; Arutyunova, Elena; Lamer, Tess; Shields, Justin; Saffran, Holly A.; McKay, Ryan T.; van Belkum, Marco J.; Joyce, Michael A.; Young, Howard S.; Tyrrell, D. Lorne; Vederas, John C.; Lemieux, M. Joanne
    Nature Communications (2020), 11 (1), 4282CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)
    The main protease, Mpro (or 3CLpro) in SARS-CoV-2 is a viable drug target because of its essential role in the cleavage of the virus polypeptide. Feline infectious peritonitis, a fatal coronavirus infection in cats, was successfully treated previously with a prodrug GC376, a dipeptide-based protease inhibitor. We show the prodrug and its parent GC373, are effective inhibitors of the Mpro from both SARS-CoV and SARS-CoV-2 with IC50 values in the nanomolar range. Crystal structures of SARS-CoV-2 Mpro with these inhibitors have a covalent modification of the nucleophilic Cys145. NMR anal. reveals that inhibition proceeds via reversible formation of a hemithioacetal. GC373 and GC376 are potent inhibitors of SARS-CoV-2 replication in cell culture. They are strong drug candidates for the treatment of human coronavirus infections because they have already been successful in animals. The work here lays the framework for their use in human trials for the treatment of COVID-19.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhslWqtbzN&md5=c06d2dc9a65ae289505fe120d41d8885
  18. 18
    Zhang, L.; Lin, D.; Sun, X.; Curth, U.; Drosten, C.; Sauerhering, L.; Becker, S.; Rox, K.; Hilgenfeld, R. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors. Science 2020, 368 (6489), 409– 412,  DOI: 10.1126/science.abb3405
    Google Scholar
    18
    Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors
    Zhang, Linlin; Lin, Daizong; Sun, Xinyuanyuan; Curth, Ute; Drosten, Christian; Sauerhering, Lucie; Becker, Stephan; Rox, Katharina; Hilgenfeld, Rolf
    Science (Washington, DC, United States) (2020), 368 (6489), 409-412CODEN: SCIEAS; ISSN:1095-9203. (American Association for the Advancement of Science)
    The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a global health emergency. An attractive drug target among coronaviruses is the main protease (Mpro, also called 3CLpro) because of its essential role in processing the polyproteins that are translated from the viral RNA. We report the x-ray structures of the unliganded SARS-CoV-2 Mpro and its complex with an α-ketoamide inhibitor. This was derived from a previously designed inhibitor but with the P3-P2 amide bond incorporated into a pyridone ring to enhance the half-life of the compd. in plasma. On the basis of the unliganded structure, we developed the lead compd. into a potent inhibitor of the SARS-CoV-2 Mpro. The pharmacokinetic characterization of the optimized inhibitor reveals a pronounced lung tropism and suitability for administration by the inhalative route.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXnslKrtL8%253D&md5=9ac417c20f54c3327f9de9088b512d52
  19. 19
    Jin, Z.; Zhao, Y.; Sun, Y.; Zhang, B.; Wang, H.; Wu, Y.; Zhu, Y.; Zhu, C.; Hu, T.; Du, X.; Duan, Y.; Yu, J.; Yang, X.; Yang, X.; Yang, K.; Liu, X.; Guddat, L. W.; Xiao, G.; Zhang, L.; Yang, H.; Rao, Z. Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur. Nat. Struct. Mol. Biol. 2020, 27 (6), 529– 532,  DOI: 10.1038/s41594-020-0440-6
    Google Scholar
    19
    Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur
    Jin, Zhenming; Zhao, Yao; Sun, Yuan; Zhang, Bing; Wang, Haofeng; Wu, Yan; Zhu, Yan; Zhu, Chen; Hu, Tianyu; Du, Xiaoyu; Duan, Yinkai; Yu, Jing; Yang, Xiaobao; Yang, Xiuna; Yang, Kailin; Liu, Xiang; Guddat, Luke W.; Xiao, Gengfu; Zhang, Leike; Yang, Haitao; Rao, Zihe
    Nature Structural & Molecular Biology (2020), 27 (6), 529-532CODEN: NSMBCU; ISSN:1545-9993. (Nature Research)
    Abstr.: The antineoplastic drug carmofur is shown to inhibit the SARS-CoV-2 main protease (Mpro). Here, the X-ray crystal structure of Mpro in complex with carmofur reveals that the carbonyl reactive group of carmofur is covalently bound to catalytic Cys145, whereas its fatty acid tail occupies the hydrophobic S2 subsite. Carmofur inhibits viral replication in cells (EC50 = 24.30μM) and is a promising lead compd. to develop new antiviral treatment for COVID-19.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXovVOrtLY%253D&md5=28c7bed4e4154935e6909a53015bf64c
  20. 20
    Fu, L.; Ye, F.; Feng, Y.; Yu, F.; Wang, Q.; Wu, Y.; Zhao, C.; Sun, H.; Huang, B.; Niu, P.; Song, H.; Shi, Y.; Li, X.; Tan, W.; Qi, J.; Gao, G. F. Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease. Nat. Commun. 2020, 11 (1), 4417,  DOI: 10.1038/s41467-020-18233-x
    Google Scholar
    20
    Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease
    Fu, Lifeng; Ye, Fei; Feng, Yong; Yu, Feng; Wang, Qisheng; Wu, Yan; Zhao, Cheng; Sun, Huan; Huang, Baoying; Niu, Peihua; Song, Hao; Shi, Yi; Li, Xuebing; Tan, Wenjie; Qi, Jianxun; Gao, George Fu
    Nature Communications (2020), 11 (1), 4417CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)
    Abstr.: COVID-19 was declared a pandemic on March 11 by WHO, due to its great threat to global public health. The coronavirus main protease (Mpro, also called 3CLpro) is essential for processing and maturation of the viral polyprotein, therefore recognized as an attractive drug target. Here we show that a clin. approved anti-HCV drug, Boceprevir, and a pre-clin. inhibitor against feline infectious peritonitis (corona) virus (FIPV), GC376, both efficaciously inhibit SARS-CoV-2 in Vero cells by targeting Mpro. Moreover, combined application of GC376 with Remdesivir, a nucleotide analog that inhibits viral RNA dependent RNA polymerase (RdRp), results in sterilizing additive effect. Further structural anal. reveals binding of both inhibitors to the catalytically active side of SARS-CoV-2 protease Mpro as main mechanism of inhibition. Our findings may provide crit. information for the optimization and design of more potent inhibitors against the emerging SARS-CoV-2 virus.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhvVSmsr3F&md5=273b11d16241499f15103885be398b23
  21. 21
    Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47 (7), 1739– 1749,  DOI: 10.1021/jm0306430
    Google Scholar
    21
    Glide: A new approach for rapid, accurate docking and scoring. 1. method and assessment of docking accuracy
    Friesner, Richard A.; Banks, Jay L.; Murphy, Robert B.; Halgren, Thomas A.; Klicic, Jasna J.; Mainz, Daniel T.; Repasky, Matthew P.; Knoll, Eric H.; Shelley, Mee; Perry, Jason K.; Shaw, David E.; Francis, Perry; Shenkin, Peter S.
    Journal of Medicinal Chemistry (2004), 47 (7), 1739-1749CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    A review. Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand. In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses. The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose. Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms. Docking accuracy is assessed by redocking ligands from 282 cocrystd. PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose. Errors in geometry for the top-ranked pose are less than 1 Å in nearly half of the cases and are greater than 2 Å in only about one-third of them. Comparisons to published data on rms deviations show that Glide is nearly twice as accurate as GOLD and more than twice as accurate as FlexX for ligands having up to 20 rotatable bonds. Glide is also found to be more accurate than the recently described Surflex method.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhsFyit74%253D&md5=8cc2f0022318b12dd972e9c493375bf9
  22. 22
    Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 2004, 47 (7), 1750– 1759,  DOI: 10.1021/jm030644s
    Google Scholar
    22
    Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
    Halgren, Thomas A.; Murphy, Robert B.; Friesner, Richard A.; Beard, Hege S.; Frye, Leah L.; Pollard, W. Thomas; Banks, Jay L.
    Journal of Medicinal Chemistry (2004), 47 (7), 1750-1759CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    A review. Glide's ability to identify active compds. in a database screen is characterized by applying Glide to a diverse set of nine protein receptors. In many cases, two, or even three, protein sites are employed to probe the sensitivity of the results to the site geometry. To make the database screens as realistic as possible, the screens use sets of "druglike" decoy ligands that have been selected to be representative of what we believe is likely to be found in the compd. collection of a pharmaceutical or biotechnol. company. Results are presented for releases 1.8, 2.0, and 2.5 of Glide. The comparisons show that av. measures for both "early" and "global" enrichment for Glide 2.5 are 3 times higher than for Glide 1.8 and more than 2 times higher than for Glide 2.0 because of better results for the least well-handled screens. This improvement in enrichment stems largely from the better balance of the more widely parametrized GlideScore 2.5 function and the inclusion of terms that penalize ligand-protein interactions that violate established principles of phys. chem., particularly as it concerns the exposure to solvent of charged protein and ligand groups. Comparisons to results for the thymidine kinase and estrogen receptors published by Rognan and co-workers (J. Med. Chem. 2000, 43, 4759-4767) show that Glide 2.5 performs better than GOLD 1.1, FlexX 1.8, or DOCK 4.01.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhsFyit78%253D&md5=33d68dd968e65626b449df61e44e37be
  23. 23
    Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C.; Mainz, D. T. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 2006, 49 (21), 6177– 6196,  DOI: 10.1021/jm051256o
    Google Scholar
    23
    Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes
    Friesner, Richard A.; Murphy, Robert B.; Repasky, Matthew P.; Frye, Leah L.; Greenwood, Jeremy R.; Halgren, Thomas A.; Sanschagrin, Paul C.; Mainz, Daniel T.
    Journal of Medicinal Chemistry (2006), 49 (21), 6177-6196CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    A novel scoring function to est. protein-ligand binding affinities has been developed and implemented as the Glide 4.0 XP scoring function and docking protocol. In addn. to unique water desolvation energy terms, protein-ligand structural motifs leading to enhanced binding affinity are included:(1) hydrophobic enclosure where groups of lipophilic ligand atoms are enclosed on opposite faces by lipophilic protein atoms, (2) neutral-neutral single or correlated hydrogen bonds in a hydrophobically enclosed environment, and (3) five categories of charged-charged hydrogen bonds. The XP scoring function and docking protocol have been developed to reproduce exptl. binding affinities for a set of 198 complexes (RMSDs of 2.26 and 1.73 kcal/mol over all and well-docked ligands, resp.) and to yield quality enrichments for a set of fifteen screens of pharmaceutical importance. Enrichment results demonstrate the importance of the novel XP mol. recognition and water scoring in sepg. active and inactive ligands and avoiding false positives.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XpvVGmurg%253D&md5=ea428c82ead0d8c27f8c1a7b694a1edf
  24. 24
    Amporndanai, K.; Meng, X.; Shang, W.; Jin, Z.; Rogers, M.; Zhao, Y.; Rao, Z.; Liu, Z. J.; Yang, H.; Zhang, L.; O’Neill, P. M.; Samar Hasnain, S. Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives. Nat. Commun. 2021, 12 (1), 3061,  DOI: 10.1038/s41467-021-23313-7
    Google Scholar
    24
    Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives
    Amporndanai, Kangsa; Meng, Xiaoli; Shang, Weijuan; Jin, Zhenmig; Rogers, Michael; Zhao, Yao; Rao, Zihe; Liu, Zhi-Jie; Yang, Haitao; Zhang, Leike; O'Neill, Paul M.; Samar Hasnain, S.
    Nature Communications (2021), 12 (1), 3061CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)
    Abstr.: The SARS-CoV-2 pandemic has triggered global efforts to develop therapeutics. The main protease of SARS-CoV-2 (Mpro), crit. for viral replication, is a key target for therapeutic development. An organoselenium drug called ebselen has been demonstrated to have potent Mpro inhibition and antiviral activity. We have examd. the binding modes of ebselen and its deriv. in Mpro via high resoln. co-crystallog. and investigated their chem. reactivity via mass spectrometry. Stronger Mpro inhibition than ebselen and potent ability to rescue infected cells were obsd. for a no. of derivs. A free selenium atom bound with cysteine of catalytic dyad has been revealed in crystallog. structures of Mpro with ebselen and MR6-31-2 suggesting hydrolysis of the enzyme bound organoselenium covalent adduct and formation of a phenolic byproduct, confirmed by mass spectrometry. The target engagement with selenation mechanism of inhibition suggests wider therapeutic applications of these compds. against SARS-CoV-2 and other zoonotic beta-corona viruses.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhtFyntbvK&md5=08fe8105502a0bd2aec4879d78280716
  25. 25
    Muramatsu, T.; Takemoto, C.; Kim, Y. T.; Wang, H.; Nishii, W.; Terada, T.; Shirouzu, M.; Yokoyama, S. SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity. Proc. Natl. Acad. Sci. U. S. A. 2016, 113 (46), 12997– 13002,  DOI: 10.1073/pnas.1601327113
    Google Scholar
    25
    SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity
    Muramatsu, Tomonari; Takemoto, Chie; Kim, Yong-Tae; Wang, Hongfei; Nishii, Wataru; Terada, Takaho; Shirouzu, Mikako; Yokoyama, Shigeyuki
    Proceedings of the National Academy of Sciences of the United States of America (2016), 113 (46), 12997-13002CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
    The 3C-like protease (3CLpro) of severe acute respiratory syndrome coronavirus (SARS-CoV) cleaves 11 sites in the polyproteins, including its own N- and C-terminal autoprocessing sites, by recognizing P4-P1 and P1'. In this study, we detd. the crystal structure of 3CLpro with the C-terminal prosequence and the catalytic-site C145A mutation, in which the enzyme binds the C-terminal prosequence of another mol. Surprisingly, Phe at the P3' position [Phe(P3')] is snugly accommodated in the S3' pocket. Mutations of Phe(P3') impaired the C-terminal autoprocessing, but did not affect N-terminal autoprocessing. This difference was ascribed to the P2 residue, Phe(P2) and Leu(P2), in the C- and N-terminal sites, as follows. The S3' subsite is formed by Phe(P2)-induced conformational changes of 3CLpro and the direct involvement of Phe(P2) itself. In contrast, the N-terminal prosequence with Leu(P2) does not cause such conformational changes for the S3' subsite formation. In fact, the mutation of Phe(P2) to Leu in the C-terminal autoprocessing site abolishes the dependence on Phe(P3'). These mechanisms explain why Phe is required at the P3' position when the P2 position is occupied by Phe rather than Leu, which reveals a type of subsite cooperativity. Moreover, the peptide consisting of P4-P1 with Leu(P2) inhibits protease activity, whereas that with Phe(P2) exhibits a much smaller inhibitory effect, because Phe(P3') is missing. Thus, this subsite cooperativity likely exists to avoid the autoinhibition of the enzyme by its mature C-terminal sequence, and to retain the efficient C-terminal autoprocessing by the use of Phe(P2).
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhslKnu7%252FP&md5=f82749f292da1066e3eb4717dcbc66f2
  26. 26
    Sarma, B. K.; Mugesh, G. Antioxidant activity of the anti-inflammatory compound ebselen: a reversible cyclization pathway via selenenic and seleninic acid intermediates. Chem. - Eur. J. 2008, 14 (34), 10603– 10614,  DOI: 10.1002/chem.200801258
    Google Scholar
    26
    Antioxidant activity of the anti-inflammatory compound ebselen: a reversible cyclization pathway via selenenic and seleninic acid intermediates
    Sarma, Bani Kanta; Mugesh, Govindasamy
    Chemistry - A European Journal (2008), 14 (34), 10603-10614CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
    A revised mechanism that accounts for the glutathione peroxidase (GPx)-like catalytic activity of the organoselenium compd. ebselen (2-phenyl-1,2-benzisoselenazol-3(2H)-one) is described. The reaction of ebselen with H2O2 yields seleninic acid 2-PhNHC(O)C6H4SeO2H as the only oxidized product. The X- ray crystal structure of the seleninic acid shows that the Se atom is involved in a noncovalent interaction with the carbonyl O atom. In the presence of excess PhSH, the Se-N bond in ebselen is readily cleaved by the thiol to produce the corresponding selenenyl sulfide 2-PhNHC(O)C6H4SeSPh. The selenenyl sulfide thus produced undergoes a disproportionation in the presence of H2O2 to produce the diselenide, which upon reaction with H2O2, produces a mixt. of selenenic and seleninic acids. The addn. of thiol to the mixt. contg. selenenic and seleninic acids gives the selenenyl sulfide. When the concn. of the thiol is relatively low in the reaction mixt., the selenenic acid undergoes a rapid cyclization to produce ebselen. The seleninic acid, however, reacts with the diselenide to produce ebselen as the final product. DFT calcns. show that the cyclization of selenenic acids to the corresponding selenenyl amides is more favored than that of sulfenic acids to the corresponding sulfenyl amides. The regeneration of ebselen under a variety of conditions protects the Se moiety from irreversible inactivation, which may be responsible for the biol. activities of ebselen.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhsV2rsLfI&md5=6a82b84de2f8fddc7f2ac90cd62e0b15
  27. 27
    Haenen, G. R.; De Rooij, B. M.; Vermeulen, N. P.; Bast, A. Mechanism of the reaction of ebselen with endogenous thiols: Dihydrolipoate is a better cofactor than glutathione in the peroxidase activity of ebselen. Mol. Pharmacol. 1990, 37 (3), 412– 422
    Google Scholar
    27
    Mechanism of the reaction of ebselen with endogenous thiols: dihydrolipoate is a better cofactor than glutathione in the peroxidase activity of ebselen
    Haenen, Guido R. M. M.; De Rooij, Ben M.; Vermeulen, Nico P. E.; Bast, Aalt
    Molecular Pharmacology (1990), 37 (3), 412-22CODEN: MOPMA3; ISSN:0026-895X.
    The therapeutic effect of ebselen has been linked to its peroxidase activity. In the present study, the peroxidase activity of ebselen toward H2O2 with the endogenous thiols GSH and dihydrolipoate [L(SH)2] as cofactors was detd. When GSH was used, peroxide removal was described by a ter uni ping pong mechanism with Dalziel coeffs. for GSH and H2O2 of 0.165 and 0.081 mM min, resp. When L(SH)2 was used, peroxidase activity was independent of the concn. of L(SH)2, in the concn. range studied (5 μM to 2 mM) and peroxide removal was only dependent on the concn. of H2O2 and ebselen, with the second-order rate const. being 12.3 mM-1 min-1. To elucidate the difference between GSH and L(SH)2, the mol. mechanism of the peroxidase activity of ebselen was investigated, using UV spectrophotometry, HPLC, 77Se NMR, and mass spectrometry. GSH was found to react quickly with ebselen to give a selenenyl sulfide, an adduct of GSH to ebselen. Subsequently, the GSH-selenenyl sulfide is converted into the diselenide of ebselen. Finally the diselenide reacts with a peroxide and ebselen is regenerated. The formation by GSH of the diselenide from the GSH-selenenyl sulfide of ebselen is slow and linearly dependent on the concn. of free thiol; however, no net consumption of GSH was obsd. Furthermore, it is likely that a selenol is an intermediate in diselenide formation. After reaction between ebselen and L(SH)2 the diselenide of ebselen was immediately detected. The fast formation of the diselenide with L(SH)2 vs. the slow formation of the diselenide with GSH accounts for our observation that L(SH)2 is a better cofactor than GSH in the peroxidase activity of ebselen. These results suggest that the interaction between ebselen and L(SH)2 might be of major importance in the mechanism by which ebselen exerts its therapeutic effect.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK3cXhvFWlsrg%253D&md5=ce9215a47abfe5cd650595c67a39c9c7
  28. 28
    Wagner, G.; Schuch, G.; Akerboom, T. P.; Sies, H. Transport of ebselen in plasma and its transfer to binding sites in the hepatocyte. Biochem. Pharmacol. 1994, 48 (6), 1137– 1144,  DOI: 10.1016/0006-2952(94)90150-3
    Google Scholar
    28
    Transport of ebselen in plasma and its transfer to binding sites in the hepatocyte
    Wagner, Gunter; Schuch, Gunter; Akerboom, Theodorus P. M.; Sies, Helmut
    Biochemical Pharmacology (1994), 48 (6), 1137-44CODEN: BCPCA6; ISSN:0006-2952.
    In vivo transport in plasma and in vitro transfer of ebselen to binding sits in the hepatocyte were studied. More than 90% of i.v. administered ebselen in mouse plasma is bound by selenium-sulfur bonds to reactive thiols in serum albumin. In in vitro expts. the uptake of [14C]-ebselen from a complex prepd. with bovine serum albumin (BSA) was detd. in isolated perfused rat liver. Radioactive ebselen metabolites were excreted into bile. In isolated hepatocytes, radioactivity was bound to all subcellular organelles. Ebselen is transferred from the BSA complex to membrane-assocd. proteins after reductive cleavage of the Se-S bond effected by endogenous protein thiols. In contrast, when proteins were sepd. by dialysis membranes, ebselen transfer from its BSA complex occurred only in the presence of externally added reductants. Among the physiol. reductants tested, ebselen release from the BSA complex was highest with glutathione (75%) and lowest with ascorbic acid (less than 10%). Quant. release of ebselen from its BSA complex was only achieved by the combined action of reductant, notably 2-mercaptoethanol, and guanidine thiocyanate, suggesting that ebselen interacts with proteins by covalent Se-S bonds as well as by ionic charge interactions.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2cXmt1WjsL8%253D&md5=78392c5dbfaa4f9e7a5476146b852a55
  29. 29
    Singh, N.; Halliday, A. C.; Thomas, J. M.; Kuznetsova, O. V.; Baldwin, R.; Woon, E. C.; Aley, P. K.; Antoniadou, I.; Sharp, T.; Vasudevan, S. R.; Churchill, G. C. A safe lithium mimetic for bipolar disorder. Nat. Commun. 2013, 4, 1332,  DOI: 10.1038/ncomms2320
    Google Scholar
    29
    A safe lithium mimetic for bipolar disorder
    Singh Nisha; Halliday Amy C; Thomas Justyn M; Kuznetsova Olga V; Baldwin Rhiannon; Woon Esther C Y; Aley Parvinder K; Antoniadou Ivi; Sharp Trevor; Vasudevan Sridhar R; Churchill Grant C
    Nature communications (2013), 4 (), 1332 ISSN:.
    Lithium is the most effective mood stabilizer for the treatment of bipolar disorder, but it is toxic at only twice the therapeutic dosage and has many undesirable side effects. It is likely that a small molecule could be found with lithium-like efficacy but without toxicity through target-based drug discovery; however, therapeutic target of lithium remains equivocal. Inositol monophosphatase is a possible target but no bioavailable inhibitors exist. Here we report that the antioxidant ebselen inhibits inositol monophosphatase and induces lithium-like effects on mouse behaviour, which are reversed with inositol, consistent with a mechanism involving inhibition of inositol recycling. Ebselen is part of the National Institutes of Health Clinical Collection, a chemical library of bioavailable drugs considered clinically safe but without proven use. Therefore, ebselen represents a lithium mimetic with the potential both to validate inositol monophosphatase inhibition as a treatment for bipolar disorder and to serve as a treatment itself.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC3s3nvVSqsw%253D%253D&md5=682e37608458f5d24a55405d07a0e5b4
  30. 30
    Johnson, T. W.; Dress, K. R.; Edwards, M. Using the Golden Triangle to optimize clearance and oral absorption. Bioorg. Med. Chem. Lett. 2009, 19 (19), 5560– 5564,  DOI: 10.1016/j.bmcl.2009.08.045
    Google Scholar
    30
    Using the Golden Triangle to optimize clearance and oral absorption
    Johnson, Ted W.; Dress, Klaus R.; Edwards, Martin
    Bioorganic & Medicinal Chemistry Letters (2009), 19 (19), 5560-5564CODEN: BMCLE8; ISSN:0960-894X. (Elsevier B.V.)
    The Golden Triangle is a visualization tool developed from in vitro permeability, in vitro clearance and computational data designed to aid medicinal chemists in achieving metabolically stable, permeable and potent drug candidates. Classifying compds. as permeable and stable and plotting mol. wt. (MW) vs. octanol:buffer (pH 7.4) distribution coeffs. (log D) or estd. octanol:buffer (pH 7.4) distribution coeffs. (elog D) reveals useful trends. Anal. of at least 2 orthogonal trends, such as permeability and clearance, can be extremely effective in balancing and optimizing multiple properties. In addn., mol. wt. and log D impact potency-efficiency calcns., allowing potency, clearance and permeability to be optimized simultaneously.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtFaktbfE&md5=3cfed1288ec451eb4419f1db753ae4b4
  31. 31
    Johnson, T. W.; Gallego, R. A.; Edwards, M. P. Lipophilic Efficiency as an Important Metric in Drug Design. J. Med. Chem. 2018, 61 (15), 6401– 6420,  DOI: 10.1021/acs.jmedchem.8b00077
    Google Scholar
    31
    Lipophilic Efficiency as an Important Metric in Drug Design
    Johnson, Ted W.; Gallego, Rebecca A.; Edwards, Martin P.
    Journal of Medicinal Chemistry (2018), 61 (15), 6401-6420CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    A review. Lipophilic efficiency (LipE) is an important metric that has been increasingly applied in drug discovery medicinal chem. lead optimization programs. In this perspective, using literature drug discovery examples, we discuss the concept of rigorously applying LipE to guide medicinal chem. lead optimization toward drug candidates with potential for superior in vivo efficacy and safety, esp. when guided by physiochem. property-based optimization (PPBO). Also highlighted are examples of small structural modifications such as addn. of single atoms, small functional groups, and cyclizations that produce large increases in LipE. Understanding the factors that may contribute to LipE changes through anal. of ligand-protein crystal structures and using structure-based drug design (SBDD) to increase LipE by design is also discussed. Herein we advocate for use of LipE anal. coupled with PPBO and SBDD as an efficient mechanism for drug design.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXmsVahsbg%253D&md5=29f38880914fa75c33be3a640ace4309
  32. 32
    Hopkins, A. L.; Keseru, G. M.; Leeson, P. D.; Rees, D. C.; Reynolds, C. H. The role of ligand efficiency metrics in drug discovery. Nat. Rev. Drug Discovery 2014, 13 (2), 105– 121,  DOI: 10.1038/nrd4163
    Google Scholar
    32
    The role of ligand efficiency metrics in drug discovery
    Hopkins, Andrew L.; Keserue, Gyoergy M.; Leeson, Paul D.; Rees, David C.; Reynolds, Charles H.
    Nature Reviews Drug Discovery (2014), 13 (2), 105-121CODEN: NRDDAG; ISSN:1474-1776. (Nature Publishing Group)
    A review. The judicious application of ligand or binding efficiency metrics, which quantify the mol. properties required to obtain binding affinity for a drug target, is gaining traction in the selection and optimization of fragments, hits and leads. Retrospective anal. of recently marketed oral drugs shows that they frequently have highly optimized ligand efficiency values for their targets. Optimizing ligand efficiency metrics based on both mol. mass and lipophilicity, when set in the context of the specific target, has the potential to ameliorate the inflation of these properties that has been obsd. in current medicinal chem. practice, and to increase the quality of drug candidates.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhs1SmtLk%253D&md5=344030e59f499180f79d311302a27532
  33. 33
    Raymer, B.; Bhattacharya, S. K. Lead-like Drugs: A Perspective. J. Med. Chem. 2018, 61 (23), 10375– 10384,  DOI: 10.1021/acs.jmedchem.8b00407
    Google Scholar
    33
    Lead-like Drugs: A Perspective
    Raymer, Brian; Bhattacharya, Samit K.
    Journal of Medicinal Chemistry (2018), 61 (23), 10375-10384CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    Lead-like drugs, or drugs below mol. wt. 300, are an important and sometimes overlooked component of the current pharmacopeia and contemporary medicinal chem. practice. To examine the recent state-of-the-art in lead-like drug discovery, we surveyed recent drug approvals from 2011 to 2017 and top 200 prescribed medications, as well as provide case studies on recently approved lead-like drugs. Many of these recent drugs are close analogs of previously known drugs or natural substrates, with a key focus of their medicinal chem. optimization being the choice of a low mol. wt. starting point and maintaining low mol. wt. during the optimization. However, the identification of low mol. wt. starting points may be limited by the availability of suitable low mol. wt. screening sets. To increase the discovery rate of lead-like drugs, we suggest an increased focus on inclusion and prosecution of lead-like starting points in screening libraries.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtl2is73O&md5=e9fc17d69c7d671459fdaf77d6721829
  34. 34
    Weiss, M. M.; Dineen, T. A.; Marx, I. E.; Altmann, S.; Boezio, A.; Bregman, H.; Chu-Moyer, M.; DiMauro, E. F.; Feric Bojic, E.; Foti, R. S.; Gao, H.; Graceffa, R.; Gunaydin, H.; Guzman-Perez, A.; Huang, H.; Huang, L.; Jarosh, M.; Kornecook, T.; Kreiman, C. R.; Ligutti, J.; La, D. S.; Lin, M. J.; Liu, D.; Moyer, B. D.; Nguyen, H. N.; Peterson, E. A.; Rose, P. E.; Taborn, K.; Youngblood, B. D.; Yu, V.; Fremeau, R. T., Jr. Sulfonamides as Selective NaV1.7 Inhibitors: Optimizing Potency and Pharmacokinetics While Mitigating Metabolic Liabilities. J. Med. Chem. 2017, 60 (14), 5969– 5989,  DOI: 10.1021/acs.jmedchem.6b01851
    Google Scholar
    34
    Sulfonamides as Selective NaV1.7 Inhibitors: Optimizing Potency and Pharmacokinetics While Mitigating Metabolic Liabilities
    Weiss, Matthew M.; Dineen, Thomas A.; Marx, Isaac E.; Altmann, Steven; Boezio, Alessandro; Bregman, Howard; Chu-Moyer, Margaret; DiMauro, Erin F.; Feric Bojic, Elma; Foti, Robert S.; Gao, Hua; Graceffa, Russell; Gunaydin, Hakan; Guzman-Perez, Angel; Huang, Hongbing; Huang, Liyue; Jarosh, Michael; Kornecook, Thomas; Kreiman, Charles R.; Ligutti, Joseph; La, Daniel S.; Lin, Min-Hwa Jasmine; Liu, Dong; Moyer, Bryan D.; Nguyen, Hanh N.; Peterson, Emily A.; Rose, Paul E.; Taborn, Kristin; Youngblood, Beth D.; Yu, Violeta; Fremeau, Robert T.
    Journal of Medicinal Chemistry (2017), 60 (14), 5969-5989CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
    Several reports have recently emerged regarding the identification of heteroarylsulfonamides as NaV1.7 inhibitors that demonstrate high levels of selectivity over other NaV isoforms. The optimization of a series of internal NaV1.7 leads that address a no. of metabolic liabilities including bioactivation, PXR activation, as well as CYP3A4 induction and inhibition led to the identification of potent and selective inhibitors that demonstrated favorable pharmacokinetic profiles and were devoid of the aforementioned liabilities. The key to achieving this within a series prone to transporter-mediated clearance was the identification of a small range of optimal cLogD values and the discovery of subtle PXR SAR that was not lipophilicity dependent. This enabled the identification of compd. 20, which was advanced into a target engagement pharmacodynamic model where it exhibited robust reversal of histamine-induced scratching bouts in mice.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXktFOmtbw%253D&md5=6333a6b936e48f9d18cf9df10ea12853
  35. 35
    Dittmar, M.; Lee, J. S.; Whig, K.; Segrist, E.; Li, M.; Kamalia, B.; Castellana, L.; Ayyanathan, K.; Cardenas-Diaz, F. L.; Morrisey, E. E.; Truitt, R.; Yang, W.; Jurado, K.; Samby, K.; Ramage, H.; Schultz, D. C.; Cherry, S. Drug repurposing screens reveal cell-type-specific entry pathways and FDA-approved drugs active against SARS-Cov-2. Cell Rep. 2021, 35 (1), 108959,  DOI: 10.1016/j.celrep.2021.108959
    Google Scholar
    35
    Drug repurposing screens reveal cell-type-specific entry pathways and FDA-approved drugs active against SARS-Cov-2
    Dittmar, Mark; Lee, Jae Seung; Whig, Kanupriya; Segrist, Elisha; Li, Minghua; Kamalia, Brinda; Castellana, Lauren; Ayyanathan, Kasirajan; Cardenas-Diaz, Fabian L.; Morrisey, Edward E.; Truitt, Rachel; Yang, Wenli; Jurado, Kellie; Samby, Kirandeep; Ramage, Holly; Schultz, David C.; Cherry, Sara
    Cell Reports (2021), 35 (1), 108959CODEN: CREED8; ISSN:2211-1247. (Cell Press)
    There is an urgent need for antivirals to treat the newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To identify new candidates, we screen a repurposing library of ~ 3,000 drugs. Screening in Vero cells finds few antivirals, while screening in human Huh7.5 cells validates 23 diverse antiviral drugs. Extending our studies to lung epithelial cells, we find that there are major differences in drug sensitivity and entry pathways used by SARS-CoV-2 in these cells. Entry in lung epithelial Calu-3 cells is pH independent and requires TMPRSS2, while entry in Vero and Huh7.5 cells requires low pH and triggering by acid-dependent endosomal proteases. Moreover, we find nine drugs are antiviral in respiratory cells, seven of which have been used in humans, and three are US Food and Drug Administration (FDA) approved, including cyclosporine. We find that the antiviral activity of cyclosporine is targeting Cyclophilin rather than calcineurin, revealing essential host targets that have the potential for rapid clin. implementation.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXnsVWju7w%253D&md5=52eaa65b358385380f995e46d3c7703d
  36. 36
    Jang, W. D.; Jeon, S.; Kim, S.; Lee, S. Y. Drugs repurposed for COVID-19 by virtual screening of 6,218 drugs and cell-based assay. Proc. Natl. Acad. Sci. U. S. A. 2021, 118 (30), e2024302118  DOI: 10.1073/pnas.2024302118
    Google Scholar
    36
    Drugs repurposed for COVID-19 by virtual screening of 6,218 drugs and cell-based assay
    Jang, Woo Dae; Jeon, Sangeun; Kim, Seungtaek; Lee, Sang Yup
    Proceedings of the National Academy of Sciences of the United States of America (2021), 118 (30), e2024302118CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
    The COVID-19 pandemic caused by SARS-CoV-2 is an unprecedentedly significant health threat, prompting the need for rapidly developing antiviral drugs for the treatment. Drug repurposing is currently 1 of the most tangible options for rapidly developing drugs for emerging and reemerging viruses. In general, drug repurposing starts with virtual screening of approved drugs employing various computational methods. However, the actual hit rate of virtual screening is very low, and most of the predicted compds. are false positives. Here, we developed a strategy for virtual screening with much reduced false positives through incorporating predocking filtering based on shape similarity and postdocking filtering based on interaction similarity. We applied this advanced virtual screening approach to repurpose 6218 approved and clin. trial drugs for COVID-19. All 6218 compds. were screened against main protease and RNA-dependent RNA polymerase of SARS-CoV-2, resulting in 15 and 23 potential repurposed drugs, resp. Among them, 7 compds. can inhibit SARS-CoV-2 replication in Vero cells. Three of these drugs, emodin, omipalisib, and tipifarnib, show anti-SARS-CoV-2 activities in human lung cells, Calu-3. Notably, the activity of omipalisib is 200-fold higher than that of remdesivir in Calu-3. Furthermore, 3 drug combinations, omipalisib/remdesivir, tipifarnib/omipalisib, and tipifarnib/remdesivir, show strong synergistic effects in inhibiting SARS-CoV-2. Such drug combination therapy improves antiviral efficacy in SARS-CoV-2 infection and reduces the risk of each drug's toxicity. The drug repurposing strategy reported here will be useful for rapidly developing drugs for treating COVID-19 and other viruses.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhs1KmsbjN&md5=d37de60099bc07ebf242e4a17132e153
  37. 37
    Choi, S. W.; Shin, J. S.; Park, S. J.; Jung, E.; Park, Y. G.; Lee, J.; Kim, S. J.; Park, H. J.; Lee, J. H.; Park, S. M.; Moon, S. H.; Ban, K.; Go, Y. Y. Antiviral activity and safety of remdesivir against SARS-CoV-2 infection in human pluripotent stem cell-derived cardiomyocytes. Antiviral Res. 2020, 184, 104955,  DOI: 10.1016/j.antiviral.2020.104955
    Google Scholar
    37
    Antiviral activity and safety of remdesivir against SARS-CoV-2 infection in human pluripotent stem cell-derived cardiomyocytes
    Choi, Seong Woo; Shin, Jin Soo; Park, Soon-Jung; Jung, Eunhye; Park, Yun-Gwi; Lee, Jiho; Kim, Sung Joon; Park, Hun-Jun; Lee, Jung-Hoon; Park, Sung-Min; Moon, Sung-Hwan; Ban, Kiwon; Go, Yun Young
    Antiviral Research (2020), 184 (), 104955CODEN: ARSRDR; ISSN:0166-3542. (Elsevier B.V.)
    Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is considered as the most significant global public health crisis of the century. Several drug candidates have been suggested as potential therapeutic options for COVID-19, including remdesivir, currently the only authorized drug for use under an Emergency Use Authorization. However, there is only limited information regarding the safety profiles of the proposed drugs, in particular drug-induced cardiotoxicity. Here, we evaluated the antiviral activity and cardiotoxicity of remdesivir using cardiomyocytes-derived from human pluripotent stem cells (hPSC-CMs) as an alternative source of human primary cardiomyocytes (CMs). In this study, remdesivir exhibited up to 60-fold higher antiviral activity in hPSC-CMs compared to Vero E6 cells; however, it also induced moderate cardiotoxicity in these cells. To gain further insight into the drug-induced arrhythmogenic risk, we assessed QT interval prolongation and automaticity of remdesivir-treated hPSC-CMs using a multielectrode array (MEA). As a result, the data indicated a potential risk of QT prolongation when remdesivir is used at concns. higher than the estd. peak plasma concn. Therefore, we conclude that close monitoring of the electrocardiog./QT interval should be advised in SARS-CoV-2-infected patients under remdesivir medication, in particular individuals with pre-existing heart conditions.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitl2nsbfJ&md5=2a4723ae20790ada7df5ecabe730a2bd
  38. 38
    Tiwari, S. K.; Wang, S.; Smith, D.; Carlin, A. F.; Rana, T. M. Revealing Tissue-Specific SARS-CoV-2 Infection and Host Responses using Human Stem Cell-Derived Lung and Cerebral Organoids. Stem Cell Rep. 2021, 16 (3), 437– 445,  DOI: 10.1016/j.stemcr.2021.02.005
    Google Scholar
    38
    Revealing tissue-specific SARS-CoV-2 infection and host responses using human stem cell-derived lung and cerebral organoids
    Tiwari, Shashi Kant; Wang, Shaobo; Smith, Davey; Carlin, Aaron F.; Rana, Tariq M.
    Stem Cell Reports (2021), 16 (3), 437-445CODEN: SCRTFL; ISSN:2213-6711. (Cell Press)
    COVID-19 is a transmissible respiratory disease caused by a novel coronavirus, SARS-CoV-2, and has become a global health emergency. There is an urgent need for robust and practical in vitro model systems to investigate viral pathogenesis. Here, we generated human induced pluripotent stem cell (iPSC)-derived lung organoids (LORGs), cerebral organoids (CORGs), neural progenitor cells (NPCs), neurons, and astrocytes. LORGs contg. epithelial cells, alveolar types 1 and 2, highly express ACE2 and TMPRSS2 and are permissive to SARS-CoV-2 infection. SARS-CoV-2 infection induces interferons, cytokines, and chemokines and activates crit. inflammasome pathway genes. Spike protein inhibitor, EK1 peptide, and TMPRSS2 inhibitors (camostat/nafamostat) block viral entry in LORGs. Conversely, CORGs, NPCs, astrocytes, and neurons express low levels of ACE2 and TMPRSS2 and correspondingly are not highly permissive to SARS-CoV-2 infection. Infection in neuronal cells activates TLR3/7, OAS2, complement system, and apoptotic genes. These findings will aid in understanding COVID-19 pathogenesis and facilitate drug discovery.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXls1ersbw%253D&md5=e12410b74f51084672e12fab3eb5230e
  39. 39
    Li, N.; Hui, H.; Bray, B.; Gonzalez, G. M.; Zeller, M.; Anderson, K. G.; Knight, R.; Smith, D.; Wang, Y.; Carlin, A. F.; Rana, T. M. METTL3 regulates viral m6A RNA modification and host cell innate immune responses during SARS-CoV-2 infection. Cell Rep. 2021, 35 (6), 109091,  DOI: 10.1016/j.celrep.2021.109091
    Google Scholar
    39
    METTL3 regulates viral m6A RNA modification and host cell innate immune responses during SARS-CoV-2 infection
    Li, Na; Hui, Hui; Bray, Bill; Gonzalez, Gwendolyn Michelle; Zeller, Mark; Anderson, Kristian G.; Knight, Rob; Smith, Davey; Wang, Yinsheng; Carlin, Aaron F.; Rana, Tariq M.
    Cell Reports (2021), 35 (6), 109091CODEN: CREED8; ISSN:2211-1247. (Cell Press)
    It is urgent and important to understand the relationship of the widespread severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) with host immune response and study the underlining mol. mechanism. N6-methylation of adenosine (m6A) in RNA regulates many physiol. and disease processes. Here, we investigate m6A modification of the SARS-CoV-2 gene in regulating the host cell innate immune response. Our data show that the SARS-CoV-2 virus has m6A modifications that are enriched in the 3' end of the viral genome. We find that depletion of the host cell m6A methyltransferase METTL3 decreases m6A levels in SARS-CoV-2 and host genes, and m6A redn. in viral RNA increases RIG-I binding and subsequently enhances the downstream innate immune signaling pathway and inflammatory gene expression. METTL3 expression is reduced and inflammatory genes are induced in patients with severe coronavirus disease 2019 (COVID-19). These findings will aid in the understanding of COVID-19 pathogenesis and the design of future studies regulating innate immunity for COVID-19 treatment.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhtVShu7zP&md5=938ee9a0e2de397723df26374d4e2612
  40. 40
    Wang, S.; Li, W.; Hui, H.; Tiwari, S. K.; Zhang, Q.; Croker, B. A.; Rawlings, S.; Smith, D.; Carlin, A. F.; Rana, T. M. Cholesterol 25-Hydroxylase inhibits SARS-CoV-2 and other coronaviruses by depleting membrane cholesterol. EMBO J. 2020, 39 (21), e106057  DOI: 10.15252/embj.2020106057
    Google Scholar
    40
    Cholesterol 25-Hydroxylase inhibits SARS-CoV-2 and other coronaviruses by depleting membrane cholesterol
    Wang, Shaobo; Li, Wanyu; Hui, Hui; Tiwari, Shashi Kant; Zhang, Qiong; Croker, Ben A.; Rawlings, Stephen; Smith, Davey; Carlin, Aaron F.; Rana, Tariq M.
    EMBO Journal (2020), 39 (21), e106057CODEN: EMJODG; ISSN:0261-4189. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2 and has spread across the globe. SARS-CoV-2 is a highly infectious virus with no vaccine or antiviral therapy available to control the pandemic; therefore, it is crucial to understand the mechanisms of viral pathogenesis and the host immune responses to SARS-CoV-2. SARS-CoV-2 is a new member of the betacoronavirus genus like other closely related viruses including SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Both SARS-CoV and MERS-CoV have caused serious outbreaks and epidemics in the past 18 yr. We report that 1 of the interferon-stimulated genes (ISGs), cholesterol 25-hydroxylase (CH25H), is induced by SARS-CoV-2 infection in vitro and in COVID-19-infected patients. CH25H converts cholesterol to 25-hydroxycholesterol (25HC) and 25HC shows broad anti-coronavirus activity by blocking membrane fusion. Furthermore, 25HC inhibits USA-WA1/2020 SARS-CoV-2 infection in lung epithelial cells and viral entry in human lung organoids. Mechanistically, 25HC inhibits viral membrane fusion by activating the ER-localized acyl-CoA:cholesterol acyltransferase (ACAT) which leads to the depletion of accessible cholesterol from the plasma membrane. Altogether, our results shed light on a potentially broad antiviral mechanism by 25HC through depleting accessible cholesterol on the plasma membrane to suppress virus-cell fusion. Since 25HC is a natural product with no known toxicity at effective concns., it provides a potential therapeutic candidate for COVID-19 and emerging viral diseases in the future.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhvFyisbvL&md5=7b37216366d03b329695f0703c5e96df
  41. 41
    Ma, C.; Hu, Y.; Townsend, J. A.; Lagarias, P. I.; Marty, M. T.; Kolocouris, A.; Wang, J. Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors. ACS Pharmacol Transl Sci. 2020, 3 (6), 1265– 1277,  DOI: 10.1021/acsptsci.0c00130
    Google Scholar
    41
    Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors
    Ma, Chunlong; Hu, Yanmei; Townsend, Julia Alma; Lagarias, Panagiotis I.; Marty, Michael Thomas; Kolocouris, Antonios; Wang, Jun
    ACS Pharmacology & Translational Science (2020), 3 (6), 1265-1277CODEN: APTSFN; ISSN:2575-9108. (American Chemical Society)
    Among the drug targets being investigated for SARS-CoV-2, the viral main protease (Mpro) is one of the most extensively studied. Mpro is a cysteine protease that hydrolyzes the viral polyprotein at more than 11 sites. It is highly conserved and has a unique substrate preference for glutamine in the P1 position. Therefore, Mpro inhibitors are expected to have broad-spectrum antiviral activity and a high selectivity index. Structurally diverse compds. have been reported as Mpro inhibitors. In this study, we investigated the mechanism of action of six previously reported Mpro inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12, using a consortium of techniques including FRET-based enzymic assay, thermal shift assay, native mass spectrometry, cellular antiviral assays, and mol. dynamics simulations. Collectively, the results showed that the inhibition of Mpro by these six compds. is nonspecific and that the inhibition is abolished or greatly reduced with the addn. of reducing reagent 1,4-dithiothreitol (DTT). Without DTT, these six compds. inhibit not only Mpro but also a panel of viral cysteine proteases including SARS-CoV-2 papain-like protease and 2Apro and 3Cpro from enterovirus A71 (EV-A71) and EV-D68. However, none of the compds. inhibits the viral replication of EV-A71 or EV-D68, suggesting that the enzymic inhibition potency IC50 values obtained in the absence of DTT cannot be used to faithfully predict their cellular antiviral activity. Overall, we provide compelling evidence suggesting that these six compds. are nonspecific SARS-CoV-2 Mpro inhibitors and urge the scientific community to be stringent with hit validation.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitVajsrjK&md5=29d0e69db20f681ed4ef7cddd153cc6d
  42. 42
    Weglarz-Tomczak, E.; Tomczak, J. M.; Talma, M.; Burda-Grabowska, M.; Giurg, M.; Brul, S. Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2. Sci. Rep. 2021, 11 (1), 3640,  DOI: 10.1038/s41598-021-83229-6
    Google Scholar
    42
    Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2
    Weglarz-Tomczak, Ewelina; Tomczak, Jakub M.; Talma, Michal; Burda-Grabowska, Malgorzata; Giurg, Miroslaw; Brul, Stanley
    Scientific Reports (2021), 11 (1), 3640CODEN: SRCEC3; ISSN:2045-2322. (Nature Research)
    An efficient treatment against a COVID-19 disease, caused by the novel coronavirus SARS-CoV-2 (CoV2), remains a challenge. The papain-like protease (PLpro) from the human coronavirus is a protease that plays a crit. role in virus replication. Moreover, CoV2 uses this enzyme to modulate the host's immune system to its own benefit. Therefore, it represents a highly promising target for the development of antiviral drugs. We used Approx. Bayesian Computation tools, mol. modeling and enzyme activity studies to identify highly active inhibitors of the PLpro. We discovered organoselenium compds., ebselen and its structural analogs, as a novel approach for inhibiting the activity of PLproCoV2. Furthermore, we identified, for the first time, inhibitors of PLproCoV2 showing potency in the nanomolar range. Moreover, we found a difference between PLpro from SARS and CoV2 that can be correlated with the diverse dynamics of their replication, and, putatively to disease progression.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXktVOntbY%253D&md5=bb905ef94cebd529c4fc53d196adc5a4
  43. 43
    Freitas, B. T.; Durie, I. A.; Murray, J.; Longo, J. E.; Miller, H. C.; Crich, D.; Hogan, R. J.; Tripp, R. A.; Pegan, S. D. Characterization and Noncovalent Inhibition of the Deubiquitinase and deISGylase Activity of SARS-CoV-2 Papain-Like Protease. ACS Infect. Dis. 2020, 6 (8), 2099– 2109,  DOI: 10.1021/acsinfecdis.0c00168
    Google Scholar
    43
    Characterization and Noncovalent Inhibition of the Deubiquitinase and deISGylase Activity of SARS-CoV-2 Papain-Like Protease
    Freitas, Brendan T.; Durie, Ian A.; Murray, Jackelyn; Longo, Jaron E.; Miller, Holden C.; Crich, David; Hogan, Robert Jeff; Tripp, Ralph A.; Pegan, Scott D.
    ACS Infectious Diseases (2020), 6 (8), 2099-2109CODEN: AIDCBC; ISSN:2373-8227. (American Chemical Society)
    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent for COVID-19, is a novel human betacoronavirus that is rapidly spreading worldwide. The outbreak currently includes over 3.7 million cases and 260,000 fatalities. As a betacoronavirus, SARS-CoV-2 encodes for a papain-like protease (PLpro) that is likely responsible for cleavage of the coronavirus (CoV) viral polypeptide. The PLpro is also responsible for suppression of host innate immune responses by virtue of its ability to reverse host ubiquitination and ISGylation events. Here, the biochem. activity of SARS-CoV-2 PLpro against ubiquitin (Ub) and interferon-stimulated gene product 15 (ISG15) substrates is evaluated, revealing that the protease has a marked redn. in its ability to process K48 linked Ub substrates compared to its counterpart in SARS-CoV. Addnl., its substrate activity more closely mirrors that of the PLpro from the Middle East respiratory syndrome coronavirus and prefers ISG15s from certain species including humans. Addnl., naphthalene based PLpro inhibitors are shown to be effective at halting SARS-CoV-2 PLpro activity as well as SARS-CoV-2 replication.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXpslylsbs%253D&md5=314ea59a92d60345f982e78e31e5b569
  44. 44
    Shin, D.; Mukherjee, R.; Grewe, D.; Bojkova, D.; Baek, K.; Bhattacharya, A.; Schulz, L.; Widera, M.; Mehdipour, A. R.; Tascher, G.; Geurink, P. P.; Wilhelm, A.; van der Heden van Noort, G. J.; Ovaa, H.; Muller, S.; Knobeloch, K. P.; Rajalingam, K.; Schulman, B. A.; Cinatl, J.; Hummer, G.; Ciesek, S.; Dikic, I. Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 2020, 587 (7835), 657– 662,  DOI: 10.1038/s41586-020-2601-5
    Google Scholar
    44
    Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity
    Shin, Donghyuk; Mukherjee, Rukmini; Grewe, Diana; Bojkova, Denisa; Baek, Kheewoong; Bhattacharya, Anshu; Schulz, Laura; Widera, Marek; Mehdipour, Ahmad Reza; Tascher, Georg; Geurink, Paul P.; Wilhelm, Alexander; van der Heden van Noort, Gerbrand J.; Ovaa, Huib; Mueller, Stefan; Knobeloch, Klaus-Peter; Rajalingam, Krishnaraj; Schulman, Brenda A.; Cinatl, Jindrich; Hummer, Gerhard; Ciesek, Sandra; Dikic, Ivan
    Nature (London, United Kingdom) (2020), 587 (7835), 657-662CODEN: NATUAS; ISSN:0028-0836. (Nature Research)
    The papain-like protease PLpro is an essential coronavirus enzyme that is required for processing viral polyproteins to generate a functional replicase complex and enable viral spread. PLpro is also implicated in cleaving proteinaceous post-translational modifications on host proteins as an evasion mechanism against host antiviral immune responses. We perform biochem., structural, and functional characterization of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PLpro (SCoV2-PLpro) and outline differences with SARS-CoV PLpro (SCoV-PLpro) in regulation of host interferon and NF-κB pathways. SCoV2-PLpro and SCoV-PLpro share 83% sequence identity but exhibit different host substrate preferences; SCoV2-PLpro preferentially cleaves the ubiquitin-like interferon-stimulated gene 15 protein (ISG15), whereas SCoV-PLpro predominantly targets ubiquitin chains. The crystal structure of SCoV2-PLpro in complex with ISG15 reveals distinctive interactions with the N-terminal ubiquitin-like domain of ISG15, highlighting the high affinity and specificity of these interactions. Furthermore, upon infection, SCoV2-PLpro contributes to the cleavage of ISG15 from interferon responsive factor 3 (IRF3) and attenuates type I interferon responses. Notably, inhibition of SCoV2-PLpro with GRL-0617 impairs the virus-induced cytopathogenic effect, maintains the antiviral interferon pathway and reduces viral replication in infected cells. These results highlight a potential dual therapeutic strategy in which targeting of SCoV2-PLpro can suppress SARS-CoV-2 infection and promote antiviral immunity.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitVSqu7nP&md5=d6e55cd2e91c4a55f19abf2652973aab
  45. 45
    Klemm, T.; Ebert, G.; Calleja, D. J; Allison, C. C; Richardson, L. W; Bernardini, J. P; Lu, B. G.; Kuchel, N. W; Grohmann, C.; Shibata, Y.; Gan, Z. Y.; Cooney, J. P; Doerflinger, M.; Au, A. E; Blackmore, T. R; Heden van Noort, G. J; Geurink, P. P; Ovaa, H.; Newman, J.; Riboldi-Tunnicliffe, A.; Czabotar, P. E; Mitchell, J. P; Feltham, R.; Lechtenberg, B. C; Lowes, K. N; Dewson, G.; Pellegrini, M.; Lessene, G.; Komander, D. Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2. EMBO J. 2020, 39 (18), e106275  DOI: 10.15252/embj.2020106275
    Google Scholar
    45
    Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2
    Klemm, Theresa; Ebert, Gregor; Calleja, Dale J.; Allison, Cody C.; Richardson, Lachlan W.; Bernardini, Jonathan P.; Lu, Bernadine G. C.; Kuchel, Nathan W.; Grohmann, Christoph; Shibata, Yuri; Gan, Zhong Yan; Cooney, James P.; Doerflinger, Marcel; Au, Amanda E.; Blackmore, Timothy R.; van der Heden van Noort, Gerbrand J.; Geurink, Paul P.; Ovaa, Huib; Newman, Janet; Riboldi-Tunnicliffe, Alan; Czabotar, Peter E.; Mitchell, Jeffrey P.; Feltham, Rebecca; Lechtenberg, Bernhard C.; Lowes, Kym N.; Dewson, Grant; Pellegrini, Marc; Lessene, Guillaume; Komander, David
    EMBO Journal (2020), 39 (18), e106275CODEN: EMJODG; ISSN:0261-4189. (Wiley-VCH Verlag GmbH & Co. KGaA)
    The SARS-CoV-2 coronavirus encodes an essential papain-like protease domain as part of its non-structural protein (nsp)-3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin-like ISG15 protein modifications as well as, with lower activity, Lys48-linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin-binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clin. compds. against SARS2 PLpro identified no compds. that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non-covalent small mol. SARS PLpro inhibitors also target SARS2 PLpro, prevent self-processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS-CoV-2 infection model.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhs1KgsrbE&md5=3d6a13fc99f05c4fdd6666e8fa72bbd7
  46. 46
    Liu, G.; Lee, J.-H.; Parker, Z. M.; Acharya, D.; Chiang, J. J.; van Gent, M.; Riedl, W.; Davis-Gardner, M. E.; Wies, E.; Chiang, C.; Gack, M. U. ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity. Nature Microbiology 2021, 6, 467– 478,  DOI: 10.1038/s41564-021-00884-1
    Google Scholar
    46
    ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity
    Liu, GuanQun; Lee, Jung-Hyun; Parker, Zachary M.; Acharya, Dhiraj; Chiang, Jessica J.; van Gent, Michiel; Riedl, William; Davis-Gardner, Meredith E.; Wies, Effi; Chiang, Cindy; Gack, Michaela U.
    Nature Microbiology (2021), 6 (4), 467-478CODEN: NMAICH; ISSN:2058-5276. (Nature Research)
    Abstr.: Activation of the RIG-I-like receptors, retinoic-acid inducible gene I (RIG-I) and melanoma differentiation-assocd. protein 5 (MDA5), establishes an antiviral state by upregulating interferon (IFN)-stimulated genes (ISGs). Among these is ISG15, the mechanistic roles of which in innate immunity still remain enigmatic. In the present study, we report that ISG15 conjugation is essential for antiviral IFN responses mediated by the viral RNA sensor MDA5. ISGylation of the caspase activation and recruitment domains of MDA5 promotes its oligomerization and thereby triggers activation of innate immunity against a range of viruses, including coronaviruses, flaviviruses and picornaviruses. The ISG15-dependent activation of MDA5 is antagonized through direct de-ISGylation mediated by the papain-like protease of SARS-CoV-2, a recently emerged coronavirus that has caused the COVID-19 pandemic. Our work demonstrates a crucial role for ISG15 in the MDA5-mediated antiviral response, and also identifies a key immune evasion mechanism of SARS-CoV-2, which may be targeted for the development of new antivirals and vaccines to combat COVID-19.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXms1Onsbs%253D&md5=a74cf2f655bfac4c2e8516b0f9f0f4e0
  47. 47
    Jacobson, M. P.; Friesner, R. A.; Xiang, Z.; Honig, B. On the role of the crystal environment in determining protein side-chain conformations. J. Mol. Biol. 2002, 320 (3), 597– 608,  DOI: 10.1016/S0022-2836(02)00470-9
    Google Scholar
    47
    On the Role of the Crystal Environment in Determining Protein Side-chain Conformations
    Jacobson, Matthew P.; Friesner, Richard A.; Xiang, Zhexin; Honig, Barry
    Journal of Molecular Biology (2002), 320 (3), 597-608CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Science Ltd.)
    The role of crystal packing in detg. the obsd. conformations of amino acid side-chains in protein crystals is investigated by (1) anal. of a database of proteins that have been crystd. in different unit cells (space group or unit cell dimensions) and (2) theor. predictions of side-chain conformations with the crystal environment explicitly represented. Both of these approaches indicate that the crystal environment plays an important role in detg. the conformations of polar side-chains on the surfaces of proteins. Inclusion of the crystal environment permits a more sensitive measurement of the achievable accuracy of side-chain prediction programs, when validating against structures obtained by x-ray crystallog. Our side-chain prediction program uses an all-atom force field and a Generalized Born model of solvation and is thus capable of modeling simple packing effects (i.e. van der Waals interactions), electrostatic effects, and desolvation, which are all important mechanisms by which the crystal environment impacts obsd. side-chain conformations. Our results are also relevant to the understanding of changes in side-chain conformation that may result from ligand docking and protein-protein assocn., insofar as the results reveal how side-chain conformations change in response to their local environment.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XltVKmu70%253D&md5=006de6bd2d0f233ab32d6798dc1a3fbc
  48. 48
    Jacobson, M. P.; Pincus, D. L.; Rapp, C. S.; Day, T. J.; Honig, B.; Shaw, D. E.; Friesner, R. A. A hierarchical approach to all-atom protein loop prediction. Proteins: Struct., Funct., Genet. 2004, 55 (2), 351– 367,  DOI: 10.1002/prot.10613
    Google Scholar
    48
    A hierarchical approach to all-atom protein loop prediction
    Jacobson, Matthew P.; Pincus, David L.; Rapp, Chaya S.; Day, Tyler J. F.; Honig, Barry; Shaw, David E.; Friesner, Richard A.
    Proteins: Structure, Function, and Bioinformatics (2004), 55 (2), 351-367CODEN: PSFBAF ISSN:. (Wiley-Liss, Inc.)
    The application of all-atom force fields (and explicit or implicit solvent models) to protein homol.-modeling tasks such as side-chain and loop prediction remains challenging both because of the expense of the individual energy calcns. and because of the difficulty of sampling the rugged all-atom energy surface. Here the authors address this challenge for the problem of loop prediction through the development of numerous new algorithms, with an emphasis on multiscale and hierarchical techniques. As a first step in evaluating the performance of the authors' loop prediction algorithm, the authors have applied it to the problem of reconstructing loops in native structures; the authors also explicitly include crystal packing to provide a fair comparison with crystal structures. In brief, large nos. of loops are generated by using a dihedral angle-based buildup procedure followed by iterative cycles of clustering, side-chain optimization, and complete energy minimization of selected loop structures. The authors evaluate this method by the largest test set yet used for validation of a loop prediction method, with a total of 833 loops ranging from 4 to 12 residues in length. Av./median backbone root-mean-square deviations (RMSDs) to the native structures (superimposing the body of the protein, not the loop itself) are 0.42/0.24 Å for 5 residue loops, 1.00/0.44 Å for 8 residue loops, and 2.47/1.83 Å for 11 residue loops. Median RMSDs are substantially lower than the avs. because of a small no. of outliers; the causes of these failures are examd. in some detail, and many can be attributed to errors in assignment of protonation states of titratable residues, omission of ligands from the simulation, and, in a few cases, probable errors in the exptl. detd. structures. When these obvious problems in the data sets are filtered out, av. RMSDs to the native structures improve to 0.43 Å for 5 residue loops, 0.84 Å for 8 residue loops, and 1.63 Å for 11 residue loops. In the vast majority of cases, the method locates energy min. that are lower than or equal to that of the minimized native loop, thus indicating that sampling rarely limits prediction accuracy. The overall results are, to the authors' knowledge, the best reported to date, and the authors attribute this success to the combination of an accurate all-atom energy function, efficient methods for loop buildup and side-chain optimization, and, esp. for the longer loops, the hierarchical refinement protocol.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXjtFKhsrc%253D&md5=e0eff655eeefb30ea00ae041ea9099c8
  49. 49
    Donovan, S. F.; Pescatore, M. C. Method for measuring the logarithm of the octanol-water partition coefficient by using short octadecyl-poly(vinyl alcohol) high-performance liquid chromatography columns. J. Chromatogr A 2002, 952 (1–2), 47– 61,  DOI: 10.1016/S0021-9673(02)00064-X
    Google Scholar
    49
    Method for measuring the logarithm of the octanol-water partition coefficient by using short octadecyl-poly(vinyl alcohol) high-performance liquid chromatography columns
    Donovan, Stephen F.; Pescatore, Mark C.
    Journal of Chromatography A (2002), 952 (1-2), 47-61CODEN: JCRAEY; ISSN:0021-9673. (Elsevier Science B.V.)
    A simple, quick, versatile and inexpensive HPLC method to est. the logarithm of the octanol-water partition coeff. (log Pow) employing a methanol-water gradient and a short octadecyl-poly(vinyl alc.) (ODP) column is described. This method is different from published HPLC-based log Pow methods because it uses retention times from a rapid methanol-water gradient to directly generate log Pow ests., rather than from a series of isocratic mixts. extrapolated to 100% water. These HPLC log Pow values have good precision and correlate well with traditional shake-flask log Pow values. If necessary, the log Pow detn. (including replications) can easily be carried out using only a milligram of sample. By suppressing ionization of acids and bases by the use of a buffer in the aq. phase, the method can measure the log Pow of neutral org. mols. at any pH between 2 and 13. The method can be used with impure material and is rapid, 7 min per run and 4 min equilibration; it lends itself to and has been utilized for high-throughput hydrophobicity detns. (we have now carried out thousands of HPLC log Pow measurements by this method).
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XisV2gs7s%253D&md5=4c4aa02a23c1a496d3a9107d43329629
  50. 50
    Box, K.; Bevan, C.; Comer, J.; Hill, A.; Allen, R.; Reynolds, D. High-throughput measurement of pKa values in a mixed-buffer linear pH gradient system. Anal. Chem. 2003, 75 (4), 883– 892,  DOI: 10.1021/ac020329y
    Google Scholar
    50
    High-Throughput Measurement of pKa Values in a Mixed-Buffer Linear pH Gradient System
    Box, Karl; Bevan, Christopher; Comer, John; Hill, Alan; Allen, Ruth; Reynolds, Derek
    Analytical Chemistry (2003), 75 (4), 883-892CODEN: ANCHAM; ISSN:0003-2700. (American Chemical Society)
    A procedure is described for measuring pKa values in a short time, e.g., 4 min/assay. Samples, as 10 mM solns., are prepd. in DMSO in 96-well plates. A flowing pH gradient is produced by mixing two buffer solns. contg. mixts. of weak acids and bases that do not absorb significantly in the UV above 250 nm. The sample soln. is dild. with water and then injected directly into the flowing gradient, which then passes through a diode array spectrophotometer measuring in the UV wavelength range. The buffer has been formulated so that its acid-base titrn. curve is linear over a wide pH range, such that the pH of the gradient is a linear function of time. The soln. pH in the measurement flow cell is therefore proportional to the time elapsed since the start of gradient generation. The sample's pKa values are calcd. from the change in UV absorbance at multiple wavelengths as a function of pH. The pKa values of 71 drugs have been measured, and results compare well with values measured by pH-metric or traditional UV methods. Rules are suggested for the rapid inspection of data and the choice of method for the calcn. of pKa from the data.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXjt1yksg%253D%253D&md5=4050d66a7c92550c1efd346e76c392d9

Cited By

Click to copy section linkSection link copied!

This article is cited by 74 publications.

  1. Zhihao Gu, Yong Yan, Hanwen Liu, Di Wu, Hequan Yao, Kejiang Lin, Xuanyi Li. Discovery of Covalent Lead Compounds Targeting 3CL Protease with a Lateral Interactions Spiking Neural Network. Journal of Chemical Information and Modeling 2024, 64 (8) , 3047-3058. https://doi.org/10.1021/acs.jcim.3c01900
  2. Katarzyna Macegoniuk, Wojciech Tabor, Luca Mazzei, Michele Cianci, Mirosław Giurg, Kamila Olech, Małgorzata Burda-Grabowska, Rafał Kaleta, Agnieszka Grabowiecka, Artur Mucha, Stefano Ciurli, Łukasz Berlicki. Optimized Ebselen-Based Inhibitors of Bacterial Ureases with Nontypical Mode of Action. Journal of Medicinal Chemistry 2023, 66 (3) , 2054-2063. https://doi.org/10.1021/acs.jmedchem.2c01799
  3. Xi Feng, Lixia Pan, Zhiyu Qian, Dongyu Liu, Xin Guan, Li Feng, Bin Song, Xi Xu, Ninghua Tan, Yi Ma, Zhiyu Li, Zhe Wang, Jinlei Bian. Discovery of Selenium-Containing STING Agonists as Orally Available Antitumor Agents. Journal of Medicinal Chemistry 2022, 65 (22) , 15048-15065. https://doi.org/10.1021/acs.jmedchem.2c00634
  4. Gabriele La Monica, Alessia Bono, Antonino Lauria, Annamaria Martorana. Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure–Activity Relationship Insights and Evolution Perspectives. Journal of Medicinal Chemistry 2022, 65 (19) , 12500-12534. https://doi.org/10.1021/acs.jmedchem.2c01005
  5. Xin-Xin Liang, Xing-Jie Zhang, Ying-Xin Zhao, Jian Feng, Jie-Chun Zeng, Qiang-Qiang Shi, Joseph Sakah Kaunda, Xiao-Li Li, Wei-Guang Wang, Wei-Lie Xiao. Aspulvins A–H, Aspulvinone Analogues with SARS-CoV-2 Mpro Inhibitory and Anti-inflammatory Activities from an Endophytic Cladosporium sp.. Journal of Natural Products 2022, 85 (4) , 878-887. https://doi.org/10.1021/acs.jnatprod.1c01003
  6. Wei Hou, Hongtao Xu. Incorporating Selenium into Heterocycles and Natural Products─From Chemical Properties to Pharmacological Activities. Journal of Medicinal Chemistry 2022, 65 (6) , 4436-4456. https://doi.org/10.1021/acs.jmedchem.1c01859
  7. Nouri Neamati. Advances Toward COVID-19 Therapies Special Issue. Journal of Medicinal Chemistry 2022, 65 (4) , 2713-2715. https://doi.org/10.1021/acs.jmedchem.2c00178
  8. Abdelali Chihab, Nabil El Brahmi, Abdelmoula El Abbouchi, Abdelaziz El Alaoui, Mostapha Bousmina, Elmostafa El Fahime, Saïd El Kazzouli. Synthesis, characterization, proteolytic activity inhibition, ADMET prediction, and molecular docking studies of novel indole derivatives as potential SARS-CoV-2 protease inhibitors. Journal of Molecular Structure 2025, 1323 , 140707. https://doi.org/10.1016/j.molstruc.2024.140707
  9. Aditya Trivedi, Tushar Kushwaha, Ishani, Sudhanshu Vrati, Dharmender Gupta, Sarala Rani Kayampeta, Mohammad Khalid Parvez, Krishna Kishore Inampudi, Mohan Babu Appaiahgari, Deepak Sehgal. Psoralidin acts as a dual protease inhibitor against PL pro and M pro of SARS ‐ CoV ‐2. The FEBS Journal 2025, 67 https://doi.org/10.1111/febs.17380
  10. Nabeel Ahmed, Aimen Sajid, Taseer Ahmad, Muhammad Ajmal Shah, Abdul Jabbar Shah. Coumarins as potential inhibitors targeting SARS-CoV-2. 2025, 151-182. https://doi.org/10.1016/B978-0-443-18757-5.00006-2
  11. Ilma Shakeel, Aaliya Taiyab, Aanchal Rathi, Taj Mohammad, Md. Imtaiyaz Hassan. Insights into SARS-CoV-2 structure: Approaches and action of SARS-CoV-2 main protease inhibitor. 2025, 89-117. https://doi.org/10.1016/B978-0-443-19170-1.00037-1
  12. S. k. Erfanul Haque, Sukanta Bhadra, Nishith Kumar Pal. Exploring potential therapeutic candidates against COVID-19: a molecular docking study. Discover Molecules 2024, 1 (1) https://doi.org/10.1007/s44345-024-00005-5
  13. Kristine Mae H. Bonalos, Khent Primo Alcantara, Pornchai Rojsitthisak, Ross D. Vasquez. Comprehensive In silico and In vitro evaluation of Plectranthus amboinicus essential oil: A promising inhibitor of SARS-CoV-2 B.1.1.529 Omicron variant, proinflammatory biomarkers and diabetes-related enzymes. Industrial Crops and Products 2024, 222 , 119905. https://doi.org/10.1016/j.indcrop.2024.119905
  14. Luca Sancineto, Francesca Mangiavacchi, Agnieszka Dabrowska, Agata J. Pacuła-Miszewska, Magdalena Obieziurska-Fabisiak, Cecilia Scimmi, Veronica Ceccucci, Juan Kong, Yao Zhao, Gianluca Ciancaleoni, Vanessa Nascimento, Bruno Rizzuti, Marco Bortoli, Laura Orian, Anna Kula-Pacurar, Haitao Yang, Jacek Ścianowski, Ying Lei, Krzysztof Pyrc, Claudio Santi. New insights in the mechanism of the SARS-CoV-2 Mpro inhibition by benzisoselenazolones and diselenides. Scientific Reports 2024, 14 (1) https://doi.org/10.1038/s41598-024-75519-6
  15. Chunru Liu, Xiaoqing Dong, Pinghuang Liu, Xi Lin. Advances in porcine respiratory and intestinal organoids: status and potential application for virus infections. One Health Advances 2024, 2 (1) https://doi.org/10.1186/s44280-024-00052-0
  16. Md. Kaderi Kibria, Md. Ahad Ali, Md. Nurul Haque Mollah, . Exploring bacterial key genes and therapeutic agents for breast cancer among the Ghanaian female population: Insights from In Silico analyses. PLOS ONE 2024, 19 (11) , e0312493. https://doi.org/10.1371/journal.pone.0312493
  17. Mianling Yang, Myoung Kyu Lee, Shenghua Gao, Letian Song, Hye‐Yeon Jang, Inseong Jo, Chun‐Chiao Yang, Katharina Sylvester, Chunkyu Ko, Shuo Wang, Bing Ye, Kai Tang, Junyi Li, Manyu Gu, Christa E. Müller, Norbert Sträter, Xinyong Liu, Meehyein Kim, Peng Zhan. Miniaturized Modular Click Chemistry‐enabled Rapid Discovery of Unique SARS‐CoV‐2 M pro Inhibitors With Robust Potency and Drug‐like Profile. Advanced Science 2024, 11 (43) https://doi.org/10.1002/advs.202404884
  18. Asma Fatima, Anupriya M. Geethakumari, Wesam S. Ahmed, Kabir H. Biswas. A potential allosteric inhibitor of SARS-CoV-2 main protease (Mpro) identified through metastable state analysis. Frontiers in Molecular Biosciences 2024, 11 https://doi.org/10.3389/fmolb.2024.1451280
  19. Borwornlak Toopradab, Wanting Xie, Lian Duan, Kowit Hengphasatporn, Ryuhei Harada, Silpsiri Sinsulpsiri, Yasuteru Shigeta, Liyi Shi, Phornphimon Maitarad, Thanyada Rungrotmongkol. Machine learning-based QSAR and LB-PaCS-MD guided design of SARS-CoV-2 main protease inhibitors. Bioorganic & Medicinal Chemistry Letters 2024, 110 , 129852. https://doi.org/10.1016/j.bmcl.2024.129852
  20. Ying Kuan, Hsu-Feng Chu, Pang-Hung Hsu, Kai-Cheng Hsu, Ta-Hsien Lin, Chun-Hsiang Huang, Wei-Yi Chen. Disulfiram inhibits coronaviral main protease by conjugating to its substrate entry site. International Journal of Biological Macromolecules 2024, 276 , 133955. https://doi.org/10.1016/j.ijbiomac.2024.133955
  21. Christos Papaneophytou. Breaking the Chain: Protease Inhibitors as Game Changers in Respiratory Viruses Management. International Journal of Molecular Sciences 2024, 25 (15) , 8105. https://doi.org/10.3390/ijms25158105
  22. Lei Han, Bing Wang, Kunhui Sun, Muqadas Sitara, Meifang Li, Ping Wang, Ning Chen, Xie-an Yu, Jiangwei Tian. A SARS-CoV-2 M pro fluorescent sensor for exploring pharmacodynamic substances from traditional Chinese medicine. The Analyst 2024, 149 (13) , 3585-3595. https://doi.org/10.1039/D4AN00372A
  23. Ya-Qi Xiao, Jiao Long, Shuang-Shuang Zhang, Yuan-Yuan Zhu, Shuang-Xi Gu. Non-peptidic inhibitors targeting SARS-CoV-2 main protease: A review. Bioorganic Chemistry 2024, 147 , 107380. https://doi.org/10.1016/j.bioorg.2024.107380
  24. Hezha O. Rasul, Noel Vinay Thomas, Dlzar D. Ghafour, Bakhtyar K. Aziz, Guillermo Salgado M., L. H. Mendoza-Huizar, Lorena Gerli Candia. Searching possible SARS-CoV-2 main protease inhibitors in constituents from herbal medicines using in silico studies. Journal of Biomolecular Structure and Dynamics 2024, 42 (8) , 4234-4248. https://doi.org/10.1080/07391102.2023.2220040
  25. Vimal K. Jain, K. Indira Priyadarsini. Selenium compounds as promising antiviral agents. New Journal of Chemistry 2024, 48 (15) , 6534-6552. https://doi.org/10.1039/D3NJ05180C
  26. Hongtao Li, Meng Sun, Fuzhi Lei, Jinfeng Liu, Xixiang Chen, Yaqi Li, Ying Wang, Jiani Lu, Danmei Yu, Yueqiu Gao, Jianrong Xu, Hongzhuan Chen, Man Li, Zhigang Yi, Xiao He, Lili Chen. Methyl rosmarinate is an allosteric inhibitor of SARS-CoV-2 3 CL protease as a potential candidate against SARS-cov-2 infection. Antiviral Research 2024, 224 , 105841. https://doi.org/10.1016/j.antiviral.2024.105841
  27. Md. Kaderi Kibria, Md. Ahad Ali, Muhammad Yaseen, Imran Ahmad Khan, Mashooq Ahmad Bhat, Md. Ariful Islam, Rashidul Alam Mahumud, Md. Nurul Haque Mollah. Discovery of Bacterial Key Genes from 16S rRNA-Seq Profiles That Are Associated with the Complications of SARS-CoV-2 Infections and Provide Therapeutic Indications. Pharmaceuticals 2024, 17 (4) , 432. https://doi.org/10.3390/ph17040432
  28. Prabuddha Bhattacharya, Anirban Mandal. Identification of amentoflavone as a potent SARS-CoV-2 M pro inhibitor: a combination of computational studies and in vitro biological evaluation. Journal of Biomolecular Structure and Dynamics 2024, 266 , 1-19. https://doi.org/10.1080/07391102.2024.2304676
  29. Samuel J.M. Santos, Antoninho Valentini. In silico investigation of Komaroviquinone as a potential inhibitor of SARS-CoV-2 main protease (Mpro): Molecular docking, molecular dynamics, and QM/MM approaches. Journal of Molecular Graphics and Modelling 2024, 126 , 108662. https://doi.org/10.1016/j.jmgm.2023.108662
  30. Frank Eric Tatsing Foka, Hazel Tumelo Mufhandu, . Predictive Assessment of the Antiviral Properties of Imperata cylindrica against SARS‐CoV‐2. Advances in Virology 2024, 2024 (1) https://doi.org/10.1155/2024/8598708
  31. Seshadri Reddy Varikasuvu, Subodh Kumar, Munikumar Manne, Mona Lisa, Saurabh Varshney, Pratima Gupta, Ashoo Grover, Vanita Lal, Harminder Singh, Shiv Kumar Mudgal, Konda Venkata Nagaraju. Covid-19 Clinical Outcomes and N-Acetylcysteine (Covinac Study): A Grade Compliant Meta-Analysis of Randomized Controlled Trials, Molecular Docking, and Dynamics Simulations with Mpro of Sars-Cov-2. 2024https://doi.org/10.2139/ssrn.4679821
  32. Xiaoli Shen, Hao Zhang, Pengyin Zhang, Xuerui Zhao, Chang Liu, Jianan Ju, Aijun Liu, Song Wang. The Inhibitory Mechanism of Sars-Cov-2 by Small Molecules of the Condensed Amino Thiourea Scaffold Based on Molecular Dynamics Simulation. 2024https://doi.org/10.2139/ssrn.4961580
  33. Kailasam Saravana Mani, Sundarraj Rajamanikandan, Balakrishnan Prabha. Discovery, synthesis and in silico approach of pyrrolo [3,4- c ]pyrroles as SARS-CoV-2 m pro inhibitors. Journal of Biomolecular Structure and Dynamics 2023, 41 (22) , 13454-13465. https://doi.org/10.1080/07391102.2023.2174599
  34. Ssemuyiga Charles, Mulumba Pius Edgar, Rajani Kanta Mahapatra. Artificial intelligence based virtual screening study for competitive and allosteric inhibitors of the SARS-CoV-2 main protease. Journal of Biomolecular Structure and Dynamics 2023, 41 (24) , 15286-15304. https://doi.org/10.1080/07391102.2023.2188419
  35. Shengchao Zhou, Kun Wang, Ziwei Hu, Tao Chen, Yao Dong, Rongmei Gao, Mengyuan Wu, Yuhuan Li, Xingyue Ji. Design, synthesis, and structure-activity relationships of a novel class of quinazoline derivatives as coronavirus inhibitors. European Journal of Medicinal Chemistry 2023, 261 , 115831. https://doi.org/10.1016/j.ejmech.2023.115831
  36. Shailima Rampogu, Tae Sung Jung, Min Woo Ha, Keun Woo Lee. Repurposing and computational design of PARP inhibitors as SARS-CoV-2 inhibitors. Scientific Reports 2023, 13 (1) https://doi.org/10.1038/s41598-023-36342-7
  37. Sunyu Song, Yeseul Kim, Kiwoong Kwak, Hyeonmin Lee, Hyunjae Park, Young Bong Kim, Hee-Jung Lee, Lin-Woo Kang. The N-terminal peptide of the main protease of SARS-CoV-2, targeting dimer interface, inhibits its proteolytic activity. BMB Reports 2023, 56 (11) , 606-611. https://doi.org/10.5483/BMBRep.2023-0153
  38. Jie Liu, Liang Xu, Wenjing Guo, Zoe Li, Md Kamrul Hasan Khan, Weigong Ge, Tucker A Patterson, Huixiao Hong. Developing a SARS-CoV-2 main protease binding prediction random forest model for drug repurposing for COVID-19 treatment. Experimental Biology and Medicine 2023, 82 https://doi.org/10.1177/15353702231209413
  39. Kun Zhou, Daquan Chen. Conventional Understanding of SARS‐CoV‐2 M pro and Common Strategies for Developing Its Inhibitors. ChemBioChem 2023, 24 (22) https://doi.org/10.1002/cbic.202300301
  40. Navid Kaboudi, Nadine Krüger, Maryam Hamzeh‐Mivehroud. Development of novel ligands against SARS‐CoV‐2 M pro enzyme: an in silico and in vitro Study. Molecular Informatics 2023, 42 (11) https://doi.org/10.1002/minf.202300120
  41. Wandong Liu, Juan Wang, Suyun Wang, Kairui Yue, Yu Hu, Xiaochun Liu, Lihao Wang, Shengbiao Wan, Ximing Xu. Discovery of new non-covalent and covalent inhibitors targeting SARS-CoV-2 papain-like protease and main protease. Bioorganic Chemistry 2023, 140 , 106830. https://doi.org/10.1016/j.bioorg.2023.106830
  42. Xin Li, Yongcheng Song. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. European Journal of Medicinal Chemistry 2023, 260 , 115772. https://doi.org/10.1016/j.ejmech.2023.115772
  43. Jiaojiao Li, Lin Zhu, Zheng Qin, Zhengfu Li, Xun Gao, Jing Ji, Jinyang Shen. Discovery of Potential Compounds Against SARS-CoV-2 Based on 3CLpro/RdRp Dual-target: An In silico Approach. Letters in Drug Design & Discovery 2023, 20 (11) , 1846-1860. https://doi.org/10.2174/1570180819666220818145647
  44. Yinkai Duan, Haofeng Wang, Zhenghong Yuan, Haitao Yang. Structural biology of SARS-CoV-2 Mpro and drug discovery. Current Opinion in Structural Biology 2023, 82 , 102667. https://doi.org/10.1016/j.sbi.2023.102667
  45. Xiaojing Pang, Wei Xu, Yang Liu, Hua Li, Lixia Chen. The research progress of SARS-CoV-2 main protease inhibitors from 2020 to 2022. European Journal of Medicinal Chemistry 2023, 257 , 115491. https://doi.org/10.1016/j.ejmech.2023.115491
  46. Sabikeh Azimi, Muna S. Merza, Fatemeh Ghasemi, Hasan Ali Dhahi, Farid Baradarbarjastehbaf, Mehdi Moosavi, Pouya Ghamari Kargar, Christophe Len. Green and rapid and instrumental one-pot method for the synthesis of imidazolines having potential anti-SARS-CoV-2 main protease activity. Sustainable Chemistry and Pharmacy 2023, 34 , 101136. https://doi.org/10.1016/j.scp.2023.101136
  47. Andrea Citarella, Alessandro Dimasi, Davide Moi, Daniele Passarella, Angela Scala, Anna Piperno, Nicola Micale. Recent Advances in SARS-CoV-2 Main Protease Inhibitors: From Nirmatrelvir to Future Perspectives. Biomolecules 2023, 13 (9) , 1339. https://doi.org/10.3390/biom13091339
  48. Amanda Resende Tucci, Raquel Mello da Rosa, Alice Santos Rosa, Otávio Augusto Chaves, Vivian Neuza Santos Ferreira, Thamara Kelcya Fonseca Oliveira, Daniel Dias Coutinho Souza, Nathalia Roberto Resende Borba, Luciano Dornelles, Nayra Salazar Rocha, João Candido Pilar Mayer, João B. Teixeira da Rocha, Oscar Endrigo D. Rodrigues, Milene Dias Miranda. Antiviral Effect of 5′-Arylchalcogeno-3-aminothymidine Derivatives in SARS-CoV-2 Infection. Molecules 2023, 28 (18) , 6696. https://doi.org/10.3390/molecules28186696
  49. Tushar Saha, Shubhra Sinha, Rhodri Harfoot, Miguel E. Quiñones-Mateu, Shyamal C. Das. Spray-Dried Inhalable Microparticles Combining Remdesivir and Ebselen against SARS-CoV-2 Infection. Pharmaceutics 2023, 15 (9) , 2229. https://doi.org/10.3390/pharmaceutics15092229
  50. Swaraj Mohanty, Soumya Lipsa Rath, Poornima Sharma, Yasmin Ahmad. An Evidence of Drug Repurposing for COVID-19 Pandemic Based on In silico Investigation from Phenolic Derivatives of Silybum Marianum Against SARS-Cov-2 Proteins. OBM Genetics 2023, 07 (03) , 1-17. https://doi.org/10.21926/obm.genet.2303186
  51. Guilherme Wildner, Amanda Resende Tucci, Alessandro de Souza Prestes, Talise Muller, Alice dos Santos Rosa, Nathalia Roberto R. Borba, Vivian Neuza Ferreira, João Batista Teixeira Rocha, Milene Dias Miranda, Nilda Vargas Barbosa. Ebselen and Diphenyl Diselenide Inhibit SARS-CoV-2 Replication at Non-Toxic Concentrations to Human Cell Lines. Vaccines 2023, 11 (7) , 1222. https://doi.org/10.3390/vaccines11071222
  52. Hossein Mousavi, Behzad Zeynizadeh, Mehdi Rimaz. Green and efficient one-pot three-component synthesis of novel drug-like furo[2,3-d]pyrimidines as potential active site inhibitors and putative allosteric hotspots modulators of both SARS-CoV-2 MPro and PLPro. Bioorganic Chemistry 2023, 135 , 106390. https://doi.org/10.1016/j.bioorg.2023.106390
  53. Chamandi S. Dampalla, Matthew J. Miller, Yunjeong Kim, Alexandria Zabiegala, Harry Nhat Nguyen, Trent K. Madden, Hayden A. Thurman, Alexandra J. Machen, Anne Cooper, Lijun Liu, Kevin P. Battaile, Scott Lovell, Kyeong-Ok Chang, William C. Groutas. Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV). European Journal of Medicinal Chemistry 2023, 254 , 115376. https://doi.org/10.1016/j.ejmech.2023.115376
  54. Samson Afewerki, Thiago Domingues Stocco, André Diniz Rosa da Silva, André Sales Aguiar Furtado, Gustavo Fernandes de Sousa, Guillermo U. Ruiz-Esparza, Thomas J. Webster, Fernanda R. Marciano, Maria Strømme, Yu Shrike Zhang, Anderson Oliveira Lobo. In vitro high-content tissue models to address precision medicine challenges. Molecular Aspects of Medicine 2023, 91 , 101108. https://doi.org/10.1016/j.mam.2022.101108
  55. J. Jeya Vandana, Cassandra Manrique, Lauretta A. Lacko, Shuibing Chen. Human pluripotent-stem-cell-derived organoids for drug discovery and evaluation. Cell Stem Cell 2023, 30 (5) , 571-591. https://doi.org/10.1016/j.stem.2023.04.011
  56. Xuming Tang, Dongxiang Xue, Tuo Zhang, Benjamin E. Nilsson-Payant, Lucia Carrau, Xiaohua Duan, Miriam Gordillo, Adrian Y. Tan, Yunping Qiu, Jenny Xiang, Robert E. Schwartz, Benjamin R. tenOever, Todd Evans, Shuibing Chen. A multi-organoid platform identifies CIART as a key factor for SARS-CoV-2 infection. Nature Cell Biology 2023, 25 (3) , 381-389. https://doi.org/10.1038/s41556-023-01095-y
  57. Matteo Pavan, Stefano Moro. Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics. International Journal of Molecular Sciences 2023, 24 (5) , 4401. https://doi.org/10.3390/ijms24054401
  58. Luca Sancineto, Vanessa Nascimento. Chalcogen-containing Therapeutic Molecules. 2023, 592-602. https://doi.org/10.1039/BK9781839167386-00592
  59. Hongtao Xu, Wei Hou. Selenium-containing heterocycles. 2023, 915-930. https://doi.org/10.1016/B978-0-443-18611-0.00006-1
  60. Nasim Bakhtiyari, Sepideh Parvizpour, Yosef Masoudi-Sobhanzadeh, Ali Masoudi-Nejad. Computational-based strategies to deal with liver injuries induced by the repurposed drugs against SARS-CoV-2. Informatics in Medicine Unlocked 2023, 41 , 101336. https://doi.org/10.1016/j.imu.2023.101336
  61. Yong-Ming Yan, Xin Shen, Yan-Peng Li, Yong-Kai Cao, Jiao-Jiao Zhang, Yan Wang, Yong-Xian Cheng. Discovery of anti-SARS-CoV-2 agents from 38 Chinese patent drugs toward respiratory diseases <i>via</i> docking screening. Medicinal Plant Biology 2023, 2 (1) , 0-0. https://doi.org/10.48130/MPB-2023-0009
  62. Jiaojiao Zhang, Xin Shen, Yanpeng Li, Yongming Yan, Yan Wang, Yongxian Cheng. Discovery of anti-SARS-CoV-2 agents from commercially available flavor <i>via</i> docking screening. Medicinal Plant Biology 2023, 2 (1) , 0-0. https://doi.org/10.48130/MPB-2023-0010
  63. Kai Ni, Bo Che, Chongxin Yang, Youyuan Qin, Rong Gu, Chunhong Wang, Mingzhi Luo, Linhong Deng. Emerging toolset of three-dimensional pulmonary cell culture models for simulating lung pathophysiology towards mechanistic elucidation and therapeutic treatment of SARS-COV-2 infection. Frontiers in Pharmacology 2022, 13 https://doi.org/10.3389/fphar.2022.1033043
  64. Divya M. Teli, Bansari Patel, Mahesh T. Chhabria. Fragment-based design of SARS-CoV-2 Mpro inhibitors. Structural Chemistry 2022, 33 (6) , 2155-2168. https://doi.org/10.1007/s11224-022-02031-w
  65. Mahima Chauhan, Vijay Kumar Bhardwaj, Asheesh Kumar, Vinod Kumar, Pawan Kumar, M. Ghalib Enayathullah, Jessie Thomas, Joel George, Bokara Kiran Kumar, Rituraj Purohit, Arun Kumar, Sanjay Kumar. Theaflavin 3-gallate inhibits the main protease (Mpro) of SARS-CoV-2 and reduces its count in vitro. Scientific Reports 2022, 12 (1) https://doi.org/10.1038/s41598-022-17558-5
  66. Kunal Nepali, Ram Sharma, Sachin Sharma, Amandeep Thakur, Jing-Ping Liou. Beyond the vaccines: a glance at the small molecule and peptide-based anti-COVID19 arsenal. Journal of Biomedical Science 2022, 29 (1) https://doi.org/10.1186/s12929-022-00847-6
  67. Vijayan Ramachandran, Yanyun Liu, Qianying He, Andrew Tang, Patrick Ronaldson, Dominik Schenten, Rui Chang. Novel inhibitors against COVID-19 main protease suppressed viral infection. 2022https://doi.org/10.1101/2022.11.05.515305
  68. Kirsten McAulay, Alan Bilsland, Marta Bon. Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery. Pharmaceuticals 2022, 15 (11) , 1366. https://doi.org/10.3390/ph15111366
  69. Suhasini M. Iyengar, Kelly K. Barnsley, Hoang Yen Vu, Ian Jef A. Bongalonta, Alyssa S. Herrod, Jasmine A. Scott, Mary Jo Ondrechen. Identification and characterization of alternative sites and molecular probes for SARS-CoV-2 target proteins. Frontiers in Chemistry 2022, 10 https://doi.org/10.3389/fchem.2022.1017394
  70. Pushyaraga P. Venugopal, Omkar Singh, Debashree Chakraborty. Understanding the role of water on temperature-dependent structural modifications of SARS CoV-2 main protease binding sites. Journal of Molecular Liquids 2022, 363 , 119867. https://doi.org/10.1016/j.molliq.2022.119867
  71. Ly Hien Doan, Li-Wei Chu, Zi-Yi Huang, Anh Thuc Nguyen, Chia-Yin Lee, Chien-Ling Huang, Yu-Fen Chang, Wen-Yu Hsieh, Trang Thi Huyen Nguyen, Chao-Hsiung Lin, Chun-Li Su, Tsung-Hsien Chuang, Jin-Mei Lai, Feng-Sheng Wang, Chia-Jui Yang, Hui-Kang Liu, Yueh-Hsin Ping, Chi-Ying F. Huang. Virofree, an Herbal Medicine-Based Formula, Interrupts the Viral Infection of Delta and Omicron Variants of SARS-CoV-2. Frontiers in Pharmacology 2022, 13 https://doi.org/10.3389/fphar.2022.905197
  72. Nicola Gambacorta, Leonardo Caputo, Laura Quintieri, Linda Monaci, Fulvio Ciriaco, Orazio Nicolotti. Rational Discovery of Antiviral Whey Protein-Derived Small Peptides Targeting the SARS-CoV-2 Main Protease. Biomedicines 2022, 10 (5) , 1067. https://doi.org/10.3390/biomedicines10051067
  73. Supaphorn Seetaha, Phatcharin Khamplong, Panatda Wanaragthai, Thitinan Aiebchun, Siriluk Ratanabunyong, Sucheewin Krobthong, Yodying Yingchutrakul, Jatuporn Rattanasrisomporn, Kiattawee Choowongkomon. KERRA, Mixed Medicinal Plant Extracts, Inhibits SARS-CoV-2 Targets Enzymes and Feline Coronavirus. COVID 2022, 2 (5) , 621-632. https://doi.org/10.3390/covid2050046
  74. Zhonglei Wang, Liyan Yang. Broad‐spectrum prodrugs with anti‐SARS‐CoV‐2 activities: Strategies, benefits, and challenges. Journal of Medical Virology 2022, 94 (4) , 1373-1390. https://doi.org/10.1002/jmv.27517
  75. Yuling Han, Liuliu Yang, Lauretta A. Lacko, Shuibing Chen. Human organoid models to study SARS-CoV-2 infection. Nature Methods 2022, 19 (4) , 418-428. https://doi.org/10.1038/s41592-022-01453-y
  76. Guillem Macip, Pol Garcia-Segura, Júlia Mestres-Truyol, Bryan Saldivar-Espinoza, Gerard Pujadas, Santiago Garcia-Vallvé. A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet?. International Journal of Molecular Sciences 2022, 23 (1) , 259. https://doi.org/10.3390/ijms23010259
  77. Prasat Kittakoop, Dhanushka Darshana, Rapeepat Sangsuwan, Chulabhorn Mahidol. Alkaloids and Alkaloid-Like Compounds are Potential Scaffolds of Antiviral Agents against SARS-CoV-2 (COVID-19) Virus. HETEROCYCLES 2022, 105 (1) , 115. https://doi.org/10.3987/REV-22-SR(R)3
Download PDF
Go to Journal of Medicinal Chemistry
Get e-Alerts
Get e-Alerts

Journal of Medicinal Chemistry

Cite this: J. Med. Chem. 2022, 65, 4, 2866–2879
Click to copy citationCitation copied!
https://doi.org/10.1021/acs.jmedchem.1c00566
Published September 27, 2021

Copyright © 2021 The Authors. Published by American Chemical Society. This publication is licensed under

CC-BY-NC-ND 4.0 .

Article Views

17k

Altmetric

-

Citations

74
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. Docking poses of ebselen and 2-phenyl-1,2-benzoselenazol-3-one analogues. (A) Docking pose of ebselen bound to the catalytic site of SARS-CoV-2 Mpro. A hydrogen bond is present between the carbonyl oxygen atom of E01 and Glu 166. The benzoisoselenazole ring forms π–π stacking interactions with catalytic His 41. (B) Docking pose of E19 bound to the catalytic site of SARS-CoV-2 Mpro. A hydrogen bond is present between the carbonyl oxygen atom of E19 and Glu 166. The benzoisoselenazole ring forms π–π stacking interactions with catalytic His 41. The chlorine atom of E19 forms a halogen bond interaction with Gly 143. (C) Docking pose of E20 bound to the catalytic site of SARS-CoV-2 Mpro. π–π stacking interactions are present between the benzoisoselenazole ring of E20 and catalytic His 41. A hydrogen bond is present between the carbonyl oxygen atom of E20 and Glu 166. (D) Docking pose of E25 bound to the catalytic site of SARS-CoV-2 Mpro. A hydrogen bond is present between the carbonyl oxygen atom of E25 and Glu 166. π–π stacking interactions are present between the benzoisoselenazole ring of E25 and catalytic His 41. The nitrile group was observed to accept a hydrogen bond from Cys 44.

    High Resolution Image
    Download MS PowerPoint Slide

    Scheme 1

    Scheme 1. Synthesis of Ebselen Analogues
    High Resolution Image
    Download MS PowerPoint Slide

    Figure 2

    Figure 2. Ebselen and its analogues can covalently modify SARS-CoV-2 Mpro in the absence of reducing agents. (A) Ebselen is a reversible covalent inhibitor of SARS-CoV-2 Mpro. The product formation over time was reduced by approximately 65% by 1 μM ebselen (red) and by 89% by 10 μM ebselen (purple) relative to that with the DMSO control (black) when added simultaneously with the fluorogenic substrate. Upon 10× dilution in an assay buffer without DTT, the product formation of SARS-CoV-2 Mpro preincubated with 10 μM ebselen (green) was reduced by 91%, which is comparable to an undiluted concentration of 10 μM. When diluted in the presence of DTT, the product formation of SARS-CoV-2 Mpro preincubated with 10 μM of ebselen (blue) was reduced by 53% relative to that with the DMSO control, similar to that observed for a final concentration of 1 μM. These data indicate that ebselen can covalently modify SARS-CoV-2 Mpro, although this modification is reversible in the presence of strong reducing agents. (B) Compound E04 is a rapidly reversible inhibitor of SARS-CoV-2 Mpro. Upon 10× dilution, the product formation of SARS-CoV-2 Mpro preincubated with 10 μM E04 in the absence of DTT (green) was reduced by 48% relative to that with the DMSO control, similar to that observed for a final concentration of 1 μM E04 (44% inhibition), while the simultaneous addition of the substrate and 10 μM E04 reduced the product formation by 86%. Similar results were observed for SARS-CoV-2 Mpro preincubated with 10 μM E04 in the presence of DTT (blue, 43% inhibition). (C) Compound E07 is a reversible covalent inhibitor of SARS-CoV-2 Mpro. (D) Compound E19 is a rapidly reversible inhibitor of SARS-CoV-2 Mpro. (E) Compound E20 is a reversible covalent inhibitor of SARS-CoV-2 Mpro. (F) Compound E25 is a reversible covalent inhibitor of SARS-CoV-2 Mpro. Upon 10× dilution, the product formation of SARS-CoV-2 Mpro preincubated with 10 μM E25 in the absence of DTT (green) was reduced by 64% relative to that with the DMSO control. The simultaneous addition of the substrate and 10 μM 25 reduced product formation by 94%, while the simultaneous addition of the substrate and 1 μM E25 reduced product formation by 29%. These data suggest that while E25 may covalently modify SARS-CoV-2 Mpro, the formation of the covalent adduct was incomplete after 30 min of incubation.

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 3

    Figure 3. Ebselen and E04 are competitive inhibitors of the SARS-CoV-2 main protease. (A) Mpro exposed to varying concentrations of ebselen reached a common Vmax at 30 μM substrate (B) All ebselen conditions converge on a common y-intercept, indicating that Vmax is independent of the inhibitor concentration, which is consistent with a competitive mechanism of inhibition. (C) Mpro exposed to varying concentrations of E04 reached a common Vmax at 30 μM substrate (D) All E04 conditions converge on a common y-intercept, indicating that Vmax is independent of the inhibitor concentration, which is consistent with a competitive mechanism of inhibition. (E) Antiviral activity of select compounds. Vero E6 cells were pretreated with varying doses of the compound, then infected with SARS-CoV-2 to a multiplicity of infection (MOI) of 0.01. After 72 h, cell proliferation was determined. Remdesivir is included as a positive control (EC50 = 1.8 ± 1.3 μM).

    High Resolution Image
    Download MS PowerPoint Slide

    Figure 4

    Figure 4. E24 inhibits SARS-CoV-2 replication in infected human iPSC-derived lung organoids. Sixty-day-old lung organoids were infected with the SARS-CoV-2 USA-WA1/2020 virus at a MOI of 2, and viral RNAs from (A) supernatant and (B) cellular fractions were quantified after 72 h of infection. Mean ± SEM of n = 3 organoids cultured and infected in different wells, *p < 0.05 by Student’s t-test.

    High Resolution Image
    Download MS PowerPoint Slide

  • References

    This article references 50 other publications.

    1. 1
      Li, F.; Li, W.; Farzan, M.; Harrison, S. C. Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science 2005, 309 (5742), 1864– 1868,  DOI: 10.1126/science.1116480
      1
      Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed with Receptor
      Li, Fang; Li, Wenhui; Farzan, Michael; Harrison, Stephen C.
      Science (Washington, DC, United States) (2005), 309 (5742), 1864-1868CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
      The spike protein (S) of SARS coronavirus (SARS-CoV) attaches the virus to its cellular receptor, angiotensin-converting enzyme 2 (ACE2). A defined receptor-binding domain (RBD) on S mediates this interaction. The crystal structure at 2.9 angstrom resoln. of the RBD bound with the peptidase domain of human ACE2 shows that the RBD presents a gently concave surface, which cradles the N-terminal lobe of the peptidase. The at. details at the interface between the two proteins clarify the importance of residue changes that facilitate efficient cross-species infection and human-to-human transmission. The structure of the RBD suggests ways to make truncated disulfide-stabilized RBD variants for use in the design of coronavirus vaccines.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXpvFCisLw%253D&md5=0a7ac2fb7a76c97979d859c0489c682f
    2. 2
      Phan, T. Novel coronavirus: From discovery to clinical diagnostics. Infect., Genet. Evol. 2020, 79, 104211,  DOI: 10.1016/j.meegid.2020.104211
      2
      Novel coronavirus: From discovery to clinical diagnostics
      Phan, Tung
      Infection, Genetics and Evolution (2020), 79 (), 104211CODEN: IGENCN; ISSN:1567-1348. (Elsevier B.V.)
      A novel coronavirus designated as 2019-nCoV first appeared in Wuhan, China in late Dec. 2019. Dozens of people died in China, and thousands of people infected as 2019-nCoV continues to spread around the world. We have described the discovery, emergence, genomic characteristics, and clin. diagnostics of 2019-nCoV.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitFOit7g%253D&md5=3cb3ef734c4f4f85479d8b55a2daf94c
    3. 3
      Pillaiyar, T.; Manickam, M.; Namasivayam, V.; Hayashi, Y.; Jung, S. H. An Overview of Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy. J. Med. Chem. 2016, 59 (14), 6595– 628,  DOI: 10.1021/acs.jmedchem.5b01461
      3
      An Overview of Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy
      Pillaiyar, Thanigaimalai; Manickam, Manoj; Namasivayam, Vigneshwaran; Hayashi, Yoshio; Jung, Sang-Hun
      Journal of Medicinal Chemistry (2016), 59 (14), 6595-6628CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      Severe acute respiratory syndrome (SARS) is caused by a newly emerged coronavirus that infected more than 8000 individuals and resulted in more than 800 (10-15%) fatalities in 2003. The causative agent of SARS has been identified as a novel human coronavirus (SARS-CoV), and its viral protease, SARS-CoV 3CLpro, has been shown to be essential for replication and has hence been recognized as a potent drug target for SARS infection. Currently, there is no effective treatment for this epidemic despite the intensive research that has been undertaken since 2003 (over 3500 publications). This perspective focuses on the status of various efficacious anti-SARS-CoV 3CLpro chemotherapies discovered during the last 12 years (2003-2015) from all sources, including lab. synthetic methods, natural products, and virtual screening. We describe here mainly peptidomimetic and small mol. inhibitors of SARS-CoV 3CLpro. Attempts have been made to provide a complete description of the structural features and binding modes of these inhibitors under many conditions.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XisVyns7c%253D&md5=6ce37076204280f64a7f362633fcee1a
    4. 4
      Ziebuhr, J.; Snijder, E. J.; Gorbalenya, A. E. Virus-encoded proteinases and proteolytic processing in the Nidovirales. J. Gen. Virol. 2000, 81 (4), 853– 879,  DOI: 10.1099/0022-1317-81-4-853
      4
      Virus-encoded proteinases and proteolytic processing in the nidovirales
      Ziebuhr, John; Snijder, Eric J.; Gorbalenya, Alexander E.
      Journal of General Virology (2000), 81 (4), 853-879CODEN: JGVIAY; ISSN:0022-1317. (Society for General Microbiology)
      A review with 128 refs. The review is organized into five main sections. In the first section nidovirus proteinases are introduced and classified into main and accessory proteinases. In the next two sections a brief overview of two classes of nidovirus proteinases is presented and, in this context, the coronavirus and arterivirus enzymes are compared to each other and to the prototypic proteinases. This is followed by a detailed description of the nidovirus proteinases themselves. The review is concluded by two sections that describe the regulatory role of the proteinases during virus replication and then give an outline of future perspectives concerning nidovirus proteinases.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXisVektLg%253D&md5=5293084b82548029518d57e401eccc3e
    5. 5
      Báez-Santos, Y. M.; St. John, S. E.; Mesecar, A. D. The SARS-coronavirus papain-like protease: Structure, function and inhibition by designed antiviral compounds. Antiviral Res. 2015, 115, 21– 38,  DOI: 10.1016/j.antiviral.2014.12.015
      5
      The SARS-coronavirus papain-like protease: Structure, function and inhibition by designed antiviral compounds
      Baez-Santos, Yahira M.; St. John, Sarah E.; Mesecar, Andrew D.
      Antiviral Research (2015), 115 (), 21-38CODEN: ARSRDR; ISSN:0166-3542. (Elsevier B.V.)
      A review. Over 10 years have passed since the deadly human coronavirus that causes severe acute respiratory syndrome (SARS-CoV) emerged from the Guangdong Province of China. Despite the fact that the SARS-CoV pandemic infected over 8500 individuals, claimed over 800 lives and cost billions of dollars in economic loss worldwide, there still are no clin. approved antiviral drugs, vaccines or monoclonal antibody therapies to treat SARS-CoV infections. The recent emergence of the deadly human coronavirus that causes Middle East respiratory syndrome (MERS-CoV) is a sobering reminder that new and deadly coronaviruses can emerge at any time with the potential to become pandemics. Therefore, the continued development of therapeutic and prophylactic countermeasures to potentially deadly coronaviruses is warranted. The coronaviral proteases, papain-like protease (PLpro) and 3C-like protease (3CLpro), are attractive antiviral drug targets because they are essential for coronaviral replication. Although the primary function of PLpro and 3CLpro are to process the viral polyprotein in a coordinated manner, PLpro has the addnl. function of stripping ubiquitin and ISG15 from host-cell proteins to aid coronaviruses in their evasion of the host innate immune responses. Therefore, targeting PLpro with antiviral drugs may have an advantage in not only inhibiting viral replication but also inhibiting the dysregulation of signaling cascades in infected cells that may lead to cell death in surrounding, uninfected cells. This review provides an up-to-date discussion on the SARS-CoV papain-like protease including a brief overview of the SARS-CoV genome and replication followed by a more in-depth discussion on the structure and catalytic mechanism of SARS-CoV PLpro, the multiple cellular functions of SARS-CoV PLpro, the inhibition of SARS-CoV PLpro by small mol. inhibitors, and the prospect of inhibiting papain-like protease from other coronaviruses. This paper forms part of a series of invited articles in Antiviral Research on "From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.".
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXmtVOnsw%253D%253D&md5=fcdde62e05b499546c73f3014ea521ad
    6. 6
      Lee, T. W.; Cherney, M. M.; Huitema, C.; Liu, J.; James, K. E.; Powers, J. C.; Eltis, L. D.; James, M. N. Crystal structures of the main peptidase from the SARS coronavirus inhibited by a substrate-like aza-peptide epoxide. J. Mol. Biol. 2005, 353 (5), 1137– 1151,  DOI: 10.1016/j.jmb.2005.09.004
      6
      Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide
      Lee, Ting-Wai; Cherney, Maia M.; Huitema, Carly; Liu, Jie; James, Karen Ellis; Powers, James C.; Eltis, Lindsay D.; James, Michael N. G.
      Journal of Molecular Biology (2005), 353 (5), 1137-1151CODEN: JMOBAK; ISSN:0022-2836. (Elsevier B.V.)
      The main peptidase (Mpro) from the coronavirus (CoV) causing severe acute respiratory syndrome (SARS) is one of the most attractive mol. targets for the development of anti-SARS agents. We report the irreversible inhibition of SARS-CoV Mpro by an aza-peptide epoxide (APE; kinact/Ki=1900(±400) M-1 s-1). The crystal structures of the Mpro:APE complex in the space groups C2 and P212121 revealed the formation of a covalent bond between the catalytic Cys145 Sγ atom of the peptidase and the epoxide C3 atom of the inhibitor, substantiating the mode of action of this class of cysteine-peptidase inhibitors. The aza-peptide component of APE binds in the substrate-binding regions of Mpro in a substrate-like manner, with excellent structural and chem. complementarity. In addn., the crystal structure of unbound Mpro in the space group C2 revealed that the "N-fingers" (N-terminal residues 1 to 7) of both protomers of Mpro are well defined and the substrate-binding regions of both protomers are in the catalytically competent conformation at the crystn. pH of 6.5, contrary to the previously detd. crystal structures of unbound Mpro in the space group P21.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXhtFKms7nL&md5=ba0e5fbad36bfc3d259c9221d451ef60
    7. 7
      Xu, X.; Liu, Y.; Weiss, S.; Arnold, E.; Sarafianos, S. G.; Ding, J. Molecular model of SARS coronavirus polymerase: implications for biochemical functions and drug design. Nucleic Acids Res. 2003, 31 (24), 7117– 7130,  DOI: 10.1093/nar/gkg916
      7
      Molecular model of SARS coronavirus polymerase: implications for biochemical functions and drug design
      Xu, Xiang; Liu, Yunqing; Weiss, Susan; Arnold, Eddy; Sarafianos, Stefan G.; Ding, Jianping
      Nucleic Acids Research (2003), 31 (24), 7117-7130CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)
      The causative agent of severe acute respiratory syndrome (SARS) is a previously unidentified coronavirus, SARS-CoV. The RNA-dependent RNA polymerase (RdRp) of SARS-CoV plays a pivotal role in viral replication and is a potential target for anti-SARS therapy. There is a lack of structural or biochem. data on any coronavirus polymerase. To provide insights into the structure and function of SARS-CoV RdRp, we have located its conserved motifs that are shared by all RdRps, and built a three-dimensional model of the catalytic domain. The structural model permits us to discuss the potential functional roles of the conserved motifs and residues in replication and their potential interactions with inhibitors of related enzymes. We predict the following important structural attributes for potential anti-SARS-CoV RdRp nucleotide analog inhibitors: hydrogen-bonding capability for the 2' and 3' groups of the sugar ring and C3' endo sugar puckering, and the absence of a hydrophobic binding pocket for non-nucleoside analog inhibitors similar to those obsd. in hepatitis C virus RdRp and human immunodeficiency virus type 1 reverse transcriptase. We propose that the clin. obsd. resistance of SARS to ribavirin is probably due to perturbation of the conserved motif A that controls rNTP binding and fidelity of polymn. Our results suggest that designing anti-SARS therapies can benefit from successful experiences in design of other antiviral drugs. This work should also provide guidance for future biochem. expts.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXps1Siu7Y%253D&md5=1c63b9eb468d4b067d4efb3136e18e66
    8. 8
      De Clercq, E.; Li, G. Approved Antiviral Drugs over the Past 50 Years. Clin. Microbiol. Rev. 2016, 29 (3), 695– 747,  DOI: 10.1128/CMR.00102-15
      8
      Approved Antiviral Drugs over the Past 50 Years
      De Clercq Erik; Li Guangdi
      Clinical microbiology reviews (2016), 29 (3), 695-747 ISSN:.
      Since the first antiviral drug, idoxuridine, was approved in 1963, 90 antiviral drugs categorized into 13 functional groups have been formally approved for the treatment of the following 9 human infectious diseases: (i) HIV infections (protease inhibitors, integrase inhibitors, entry inhibitors, nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, and acyclic nucleoside phosphonate analogues), (ii) hepatitis B virus (HBV) infections (lamivudine, interferons, nucleoside analogues, and acyclic nucleoside phosphonate analogues), (iii) hepatitis C virus (HCV) infections (ribavirin, interferons, NS3/4A protease inhibitors, NS5A inhibitors, and NS5B polymerase inhibitors), (iv) herpesvirus infections (5-substituted 2'-deoxyuridine analogues, entry inhibitors, nucleoside analogues, pyrophosphate analogues, and acyclic guanosine analogues), (v) influenza virus infections (ribavirin, matrix 2 protein inhibitors, RNA polymerase inhibitors, and neuraminidase inhibitors), (vi) human cytomegalovirus infections (acyclic guanosine analogues, acyclic nucleoside phosphonate analogues, pyrophosphate analogues, and oligonucleotides), (vii) varicella-zoster virus infections (acyclic guanosine analogues, nucleoside analogues, 5-substituted 2'-deoxyuridine analogues, and antibodies), (viii) respiratory syncytial virus infections (ribavirin and antibodies), and (ix) external anogenital warts caused by human papillomavirus infections (imiquimod, sinecatechins, and podofilox). Here, we present for the first time a comprehensive overview of antiviral drugs approved over the past 50 years, shedding light on the development of effective antiviral treatments against current and emerging infectious diseases worldwide.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2s%252Fos12htA%253D%253D&md5=1d25d961c1c6a72d6bc4634041bbb6fe
    9. 9
      Kanters, S.; Socias, M. E.; Paton, N. I.; Vitoria, M.; Doherty, M.; Ayers, D.; Popoff, E.; Chan, K.; Cooper, D. A.; Wiens, M. O.; Calmy, A.; Ford, N.; Nsanzimana, S.; Mills, E. J. Comparative efficacy and safety of second-line antiretroviral therapy for treatment of HIV/AIDS: A systematic review and network meta-analysis. Lancet HIV 2017, 4 (10), e433– e441,  DOI: 10.1016/S2352-3018(17)30109-1
      There is no corresponding record for this reference.
    10. 10
      Deeks, E. D. Darunavir: a review of its use in the management of HIV-1 infection. Drugs 2014, 74 (1), 99– 125,  DOI: 10.1007/s40265-013-0159-3
      10
      Darunavir: A Review of Its Use in the Management of HIV-1 Infection
      Deeks, Emma D.
      Drugs (2014), 74 (1), 99-125CODEN: DRUGAY; ISSN:0012-6667. (Springer International Publishing AG)
      A review. The latest HIV-1 protease inhibitor (PI) darunavir (Prezista®) has a high genetic barrier to resistance development and is active against wild-type HIV and HIV strains no longer susceptible to some older PIs. Ritonavir-boosted darunavir, as a component of antiretroviral therapy (ART), is indicated for the treatment of HIV-1 infection in adult and paediatric patients (aged ≥3 years), with or without treatment experience (details vary depending on region of approval). Several open-label or partially-blinded trials have evaluated the efficacy of ritonavir-boosted darunavir ART regimens for up to 192 wk in these settings. In treatment-naive adults, once-daily boosted darunavir was no less effective in establishing virol. suppression than once- or twice-daily boosted lopinavir, yet was more effective at maintaining suppression long term. Moreover, treatment-experienced adults with no darunavir resistance-assocd. mutations (RAMs) had no less effective viral load suppression with once-daily than with twice-daily boosted darunavir. In treatment-experienced adults, including some with multiple major PI RAMs, twice-daily boosted darunavir was more effective than twice-daily boosted lopinavir or boosted control PIs in reducing viral load, and provided virol. benefit as part of a salvage regimen in those with few remaining treatment options. Boosted darunavir also reduced viral load when administered once-daily in treatment-naive adolescents or twice-daily in treatment-experienced children and adolescents. Boosted darunavir is generally well tolerated, with gastrointestinal disturbances and lipid abnormalities among the most common tolerability issues. It has a lipid profile more favorable than that of boosted lopinavir in terms of total cholesterol and triglyceride changes and, when administered once daily, its lipid effects are generally similar to those of boosted atazanavir. Thus, boosted darunavir is a useful option for the ART regimens of adult and paediatric patients with HIV-1 infection.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXptFajuw%253D%253D&md5=b5f8e515fd0c0ce64d97b0c126c18ce4
    11. 11
      la Porte, C. J. Saquinavir, the pioneer antiretroviral protease inhibitor. Expert Opin. Drug Metab. Toxicol. 2009, 5 (10), 1313– 1322,  DOI: 10.1517/17425250903273160
      11
      Saquinavir, the pioneer antiretroviral protease inhibitor
      La Porte, Charles J. L.
      Expert Opinion on Drug Metabolism & Toxicology (2009), 5 (10), 1313-1322CODEN: EODMAP; ISSN:1742-5255. (Informa Healthcare)
      A review. Background: The treatment of HIV infection underwent a major change in 1995 when saquinavir was the first protease inhibitor introduced into the market. This drug made the use of combination therapy in the treatment of HIV possible and increased the success rate of treatment. Objective: This article will review recent literature on saquinavir to define its current role in HIV treatment, among the newer antiretroviral drugs. Methods: Scientific literature and conference presentations were evaluated for relevant information pertaining to saquinavir. Results/conclusions: Although underused, saquinavir has good efficacy and tolerability when compared to other protease inhibitors. The film-coated tablet formulation improved pill burden. Saquinavir still has potential in the treatment of adults, children and pregnant women.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtFCgsrfM&md5=337b9225b09c6cabc0a87f41272b1ede
    12. 12
      Heo, Y. A.; Deeks, E. D. Sofosbuvir/Velpatasvir/Voxilaprevir: A Review in Chronic Hepatitis C. Drugs 2018, 78 (5), 577– 587,  DOI: 10.1007/s40265-018-0895-5
      12
      Sofosbuvir/Velpatasvir/Voxilaprevir: A Review in Chronic Hepatitis C
      Heo, Young-A.; Deeks, Emma D.
      Drugs (2018), 78 (5), 577-587CODEN: DRUGAY; ISSN:0012-6667. (Springer International Publishing AG)
      A fixed-dose combination of the hepatitis C virus (HCV) NS5B polymerase inhibitor sofosbuvir, the HCV NS5A inhibitor velpatasvir and the HCV NS3/4A protease inhibitor voxilaprevir (sofosbuvir/velpatasvir/voxilaprevir; Vosevi) is approved in the EU for the treatment of chronic HCV genotype 1, 2, 3, 4, 5 or 6 infection in adults. In the phase III POLARIS trials, in patients who had HCV genotype 1-6 infection with or without compensated cirrhosis, overall rates of sustained virol. response at 12 wk post-treatment (SVR12) with sofosbuvir/velpatasvir/voxilaprevir were high after 8 wk of treatment in direct-acting antiviral (DAA)-naive patients and 12 wk of treatment in DAA-experienced patients. However, 8 wk of sofosbuvir/velpatasvir/voxilaprevir was inferior to 12 wk of sofosbuvir/velpatasvir in cirrhotic or non-cirrhotic DAA-naive patients with HCV genotype 1, 2, 4, 5 or 6 infection and non-cirrhotic DAA-naive patients with HCV genotype 3 infection, mostly due to an insufficient treatment period. Sofosbuvir/velpatasvir/voxilaprevir was generally well tolerated, with most adverse events being of mild or moderate intensity. The most common adverse events included headache, fatigue, nausea and diarrhoea. In conclusion, sofosbuvir/velpatasvir/voxilaprevir is an important and effective option for the treatment of HCV genotype 1-6 infection in adults, esp. those who have previously failed a DAA therapy with or without an HCV NS5A inhibitor.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXkslGjt7k%253D&md5=d4557e43a321ca3a9a30d996ac5f77ba
    13. 13
      Sanford, M. Simeprevir: a review of its use in patients with chronic hepatitis C virus infection. Drugs 2015, 75 (2), 183– 196,  DOI: 10.1007/s40265-014-0341-2
      13
      Simeprevir: A Review of Its Use in Patients with Chronic Hepatitis C Virus Infection
      Sanford, Mark
      Drugs (2015), 75 (2), 183-196CODEN: DRUGAY; ISSN:0012-6667. (Springer International Publishing AG)
      A review. Simeprevir (Olysio; Galexos; Sovriad) is an orally-administered NS3/4A protease inhibitor for use in combined drug regimens against chronic hepatitis C virus (HCV) infection. This article reviews studies relevant to the EU simeprevir label. In proof-of-concept studies, simeprevir had potent antiviral activity against all HCV genotypes, except genotype 3. In trials in patients with chronic HCV genotype 1 infection, week-12 sustained virol. response (SVR12) rates in treatment-naive patients and prior relapsers were significantly higher with simeprevir plus peginterferon-α/ribavirin (PR) [79-89 %] than with placebo plus PR (36-62 %). In prior partial/null responders, the SVR12 rate with simeprevir plus PR (54 %) was noninferior to that with telaprevir plus PR (55 %). Simeprevir plus PR was also efficacious in patients with HCV genotype 1/HIV-1 co-infection. In prior null responders without severe liver fibrosis (cohort 1) and treatment-naive patients with severe liver fibrosis (cohort 2) treated with simeprevir plus sofosbuvir, the SVR12 rate for the two cohorts combined was 92 %. In patients with chronic HCV genotype 4 infection, the SVR12 rates with simeprevir plus PR were 83, 87 and 40 % in treatment-naive patients, prior relapsers and prior null responders, resp. Grade 3-4 adverse event, serious adverse event and treatment withdrawal rates with simeprevir plus PR were similar to those with placebo plus PR. Skin rashes with simeprevir were mostly mild or moderate; serious photosensitivity reactions occur, but are rare. Simeprevir is efficacious and generally well tolerated in patients with chronic HCV genotypes 1 and 4 infection. Studies of simeprevir in interferon-free regimens and in other subpopulations with HCV infections will be of interest.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXitVCnt7k%253D&md5=20ef9a811518a120a68eb79241f0d735
    14. 14
      Chopp, S.; Vanderwall, R.; Hult, A.; Klepser, M. Simeprevir and sofosbuvir for treatment of hepatitis C infection. Am. J. Health-Syst. Pharm. 2015, 72 (17), 1445– 1455,  DOI: 10.2146/ajhp140290
      14
      Simeprevir and sofosbuvir for treatment of hepatitis C infection
      Chopp, Shelby; Vanderwall, Rebecca; Hult, Amanda; Klepser, Michael
      American Journal of Health-System Pharmacy (2015), 72 (17), 1445-1455CODEN: AHSPEK; ISSN:1079-2082. (American Society of Health-System Pharmacists)
      Purpose. The pharmacol., pharmacokinetics, efficacy, safety, costs, and place in therapy of simeprevir and sofosbuvir in the management of hepatitis C virus (HCV) infection are reviewed. Summary. Sofosbuvir and simeprevir are classified as direct-acting agents because they target specific proteins essential to the replication of HCV. Phase III trials demonstrated that simeprevir in combination with peginterferon alfa and ribavirin was superior to placebo combined with peginterferon alfa and ribavirin in achieving a sustained virol. response in both treatment-naive patients and patients who relapsed after treatment with peginterferon alfa-2a or alfa-2b and ribavirin. Q80K polymorphism substantially decreases the efficacy of simeprevir. Clin. trials revealed that sofosbuvir in combination with ribavirin was superior to peginterferon plus ribavirin against HCV genotype 2 infection and as effective as peginterferon plus ribavirin against HCV genotype 3 infection. These findings were significant because they demonstrated the effectiveness of an anti-HCV regimen that did not include peginterferon alfa. Sofosbuvir has much better adverse-effect and drug interaction profiles than previous hepatitis C antiviral agents. Both simeprevir and sofosbuvir are approved for the treatment of chronic hepatitis C in combination with other antiviral medications. Simeprevir has been approved specifically for patients infected with HCV genotype 1 with compensated liver disease (including cirrhosis) in combination with peginterferon alfa-2a or alfa-2b and ribavirin. Sofosbuvir has shown efficacy in HCV genotypes 1-4. Conclusion. Simeprevir and sofasbuvir have advantages in response rates and convenient dosage forms and frequency compared with other HCV treatments; however, they are more expensive than previous HCV therapies.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XmtFGgt7k%253D&md5=b8e2a8a629e121eeba1b7bb37a5fa5e6
    15. 15
      Jin, Z.; Du, X.; Xu, Y.; Deng, Y.; Liu, M.; Zhao, Y.; Zhang, B.; Li, X.; Zhang, L.; Peng, C.; Duan, Y.; Yu, J.; Wang, L.; Yang, K.; Liu, F.; Jiang, R.; Yang, X.; You, T.; Liu, X.; Yang, X.; Bai, F.; Liu, H.; Liu, X.; Guddat, L. W.; Xu, W.; Xiao, G.; Qin, C.; Shi, Z.; Jiang, H.; Rao, Z.; Yang, H. Structure of M(pro) from COVID-19 virus and discovery of its inhibitors. Nature 2020, 582, 289– 293,  DOI: 10.1038/s41586-020-2223-y
      15
      Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors
      Jin, Zhenming; Du, Xiaoyu; Xu, Yechun; Deng, Yongqiang; Liu, Meiqin; Zhao, Yao; Zhang, Bing; Li, Xiaofeng; Zhang, Leike; Peng, Chao; Duan, Yinkai; Yu, Jing; Wang, Lin; Yang, Kailin; Liu, Fengjiang; Jiang, Rendi; Yang, Xinglou; You, Tian; Liu, Xiaoce; Yang, Xiuna; Bai, Fang; Liu, Hong; Liu, Xiang; Guddat, Luke W.; Xu, Wenqing; Xiao, Gengfu; Qin, Chengfeng; Shi, Zhengli; Jiang, Hualiang; Rao, Zihe; Yang, Haitao
      Nature (London, United Kingdom) (2020), 582 (7811), 289-293CODEN: NATUAS; ISSN:0028-0836. (Nature Research)
      Abstr.: A new coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the etiol. agent responsible for the 2019-2020 viral pneumonia outbreak of coronavirus disease 2019 (COVID-19). Currently, there are no targeted therapeutic agents for the treatment of this disease, and effective treatment options remain very limited. Here, we describe the results of a program that aimed to rapidly discover lead compds. for clin. use, by combining structure-assisted drug design, virtual drug screening and high-throughput screening. This program focused on identifying drug leads that target main protease (Mpro) of SARS-CoV-2: Mpro is a key enzyme of coronaviruses and has a pivotal role in mediating viral replication and transcription, making it an attractive drug target for SARS-CoV-2. We identified a mechanism-based inhibitor (N3) by computer-aided drug design, and then detd. the crystal structure of Mpro of SARS-CoV-2 in complex with this compd. Through a combination of structure-based virtual and high-throughput screening, we assayed more than 10,000 compds.-including approved drugs, drug candidates in clin. trials and other pharmacol. active compds.-as inhibitors of Mpro. Six of these compds. inhibited Mpro, showing half-maximal inhibitory concn. values that ranged from 0.67 to 21.4μM. One of these compds. (ebselen) also exhibited promising antiviral activity in cell-based assays. Our results demonstrate the efficacy of our screening strategy, which can lead to the rapid discovery of drug leads with clin. potential in response to new infectious diseases for which no specific drugs or vaccines are available.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhtVyhsrrO&md5=b84f350fe9ce1109485df6caf814ba82
    16. 16
      Dai, W.; Zhang, B.; Jiang, X. M.; Su, H.; Li, J.; Zhao, Y.; Xie, X.; Jin, Z.; Peng, J.; Liu, F.; Li, C.; Li, Y.; Bai, F.; Wang, H.; Cheng, X.; Cen, X.; Hu, S.; Yang, X.; Wang, J.; Liu, X.; Xiao, G.; Jiang, H.; Rao, Z.; Zhang, L. K.; Xu, Y.; Yang, H.; Liu, H. Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science 2020, 368 (6497), 1331– 1335,  DOI: 10.1126/science.abb4489
      16
      Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease
      Dai, Wenhao; Zhang, Bing; Jiang, Xia-Ming; Su, Haixia; Li, Jian; Zhao, Yao; Xie, Xiong; Jin, Zhenming; Peng, Jingjing; Liu, Fengjiang; Li, Chunpu; Li, You; Bai, Fang; Wang, Haofeng; Cheng, Xi; Cen, Xiaobo; Hu, Shulei; Yang, Xiuna; Wang, Jiang; Liu, Xiang; Xiao, Gengfu; Jiang, Hualiang; Rao, Zihe; Zhang, Lei-Ke; Xu, Yechun; Yang, Haitao; Liu, Hong
      Science (Washington, DC, United States) (2020), 368 (6497), 1331-1335CODEN: SCIEAS; ISSN:1095-9203. (American Association for the Advancement of Science)
      SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the etiol. agent responsible for the global COVID-19 (coronavirus disease 2019) outbreak. The main protease of SARS-CoV-2, Mpro, is a key enzyme that plays a pivotal role in mediating viral replication and transcription. We designed and synthesized two lead compds. (11a and 11b) targeting Mpro. Both exhibited excellent inhibitory activity and potent anti-SARS-CoV-2 infection activity. The x-ray crystal structures of SARS-CoV-2 Mpro in complex with 11a or 11b, both detd. at a resoln. of 1.5 angstroms, showed that the aldehyde groups of 11a and 11b are covalently bound to cysteine 145 of Mpro. Both compds. showed good pharmacokinetic properties in vivo, and 11a also exhibited low toxicity, which suggests that these compds. are promising drug candidates.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXht1alsrzL&md5=ec87c340410edb919d2584a2b4d33e1a
    17. 17
      Vuong, W.; Khan, M. B.; Fischer, C.; Arutyunova, E.; Lamer, T.; Shields, J.; Saffran, H. A.; McKay, R. T.; van Belkum, M. J.; Joyce, M. A.; Young, H. S.; Tyrrell, D. L.; Vederas, J. C.; Lemieux, M. J. Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication. Nat. Commun. 2020, 11 (1), 4282,  DOI: 10.1038/s41467-020-18096-2
      17
      Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication
      Vuong, Wayne; Khan, Muhammad Bashir; Fischer, Conrad; Arutyunova, Elena; Lamer, Tess; Shields, Justin; Saffran, Holly A.; McKay, Ryan T.; van Belkum, Marco J.; Joyce, Michael A.; Young, Howard S.; Tyrrell, D. Lorne; Vederas, John C.; Lemieux, M. Joanne
      Nature Communications (2020), 11 (1), 4282CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)
      The main protease, Mpro (or 3CLpro) in SARS-CoV-2 is a viable drug target because of its essential role in the cleavage of the virus polypeptide. Feline infectious peritonitis, a fatal coronavirus infection in cats, was successfully treated previously with a prodrug GC376, a dipeptide-based protease inhibitor. We show the prodrug and its parent GC373, are effective inhibitors of the Mpro from both SARS-CoV and SARS-CoV-2 with IC50 values in the nanomolar range. Crystal structures of SARS-CoV-2 Mpro with these inhibitors have a covalent modification of the nucleophilic Cys145. NMR anal. reveals that inhibition proceeds via reversible formation of a hemithioacetal. GC373 and GC376 are potent inhibitors of SARS-CoV-2 replication in cell culture. They are strong drug candidates for the treatment of human coronavirus infections because they have already been successful in animals. The work here lays the framework for their use in human trials for the treatment of COVID-19.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhslWqtbzN&md5=c06d2dc9a65ae289505fe120d41d8885
    18. 18
      Zhang, L.; Lin, D.; Sun, X.; Curth, U.; Drosten, C.; Sauerhering, L.; Becker, S.; Rox, K.; Hilgenfeld, R. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors. Science 2020, 368 (6489), 409– 412,  DOI: 10.1126/science.abb3405
      18
      Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors
      Zhang, Linlin; Lin, Daizong; Sun, Xinyuanyuan; Curth, Ute; Drosten, Christian; Sauerhering, Lucie; Becker, Stephan; Rox, Katharina; Hilgenfeld, Rolf
      Science (Washington, DC, United States) (2020), 368 (6489), 409-412CODEN: SCIEAS; ISSN:1095-9203. (American Association for the Advancement of Science)
      The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a global health emergency. An attractive drug target among coronaviruses is the main protease (Mpro, also called 3CLpro) because of its essential role in processing the polyproteins that are translated from the viral RNA. We report the x-ray structures of the unliganded SARS-CoV-2 Mpro and its complex with an α-ketoamide inhibitor. This was derived from a previously designed inhibitor but with the P3-P2 amide bond incorporated into a pyridone ring to enhance the half-life of the compd. in plasma. On the basis of the unliganded structure, we developed the lead compd. into a potent inhibitor of the SARS-CoV-2 Mpro. The pharmacokinetic characterization of the optimized inhibitor reveals a pronounced lung tropism and suitability for administration by the inhalative route.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXnslKrtL8%253D&md5=9ac417c20f54c3327f9de9088b512d52
    19. 19
      Jin, Z.; Zhao, Y.; Sun, Y.; Zhang, B.; Wang, H.; Wu, Y.; Zhu, Y.; Zhu, C.; Hu, T.; Du, X.; Duan, Y.; Yu, J.; Yang, X.; Yang, X.; Yang, K.; Liu, X.; Guddat, L. W.; Xiao, G.; Zhang, L.; Yang, H.; Rao, Z. Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur. Nat. Struct. Mol. Biol. 2020, 27 (6), 529– 532,  DOI: 10.1038/s41594-020-0440-6
      19
      Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur
      Jin, Zhenming; Zhao, Yao; Sun, Yuan; Zhang, Bing; Wang, Haofeng; Wu, Yan; Zhu, Yan; Zhu, Chen; Hu, Tianyu; Du, Xiaoyu; Duan, Yinkai; Yu, Jing; Yang, Xiaobao; Yang, Xiuna; Yang, Kailin; Liu, Xiang; Guddat, Luke W.; Xiao, Gengfu; Zhang, Leike; Yang, Haitao; Rao, Zihe
      Nature Structural & Molecular Biology (2020), 27 (6), 529-532CODEN: NSMBCU; ISSN:1545-9993. (Nature Research)
      Abstr.: The antineoplastic drug carmofur is shown to inhibit the SARS-CoV-2 main protease (Mpro). Here, the X-ray crystal structure of Mpro in complex with carmofur reveals that the carbonyl reactive group of carmofur is covalently bound to catalytic Cys145, whereas its fatty acid tail occupies the hydrophobic S2 subsite. Carmofur inhibits viral replication in cells (EC50 = 24.30μM) and is a promising lead compd. to develop new antiviral treatment for COVID-19.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXovVOrtLY%253D&md5=28c7bed4e4154935e6909a53015bf64c
    20. 20
      Fu, L.; Ye, F.; Feng, Y.; Yu, F.; Wang, Q.; Wu, Y.; Zhao, C.; Sun, H.; Huang, B.; Niu, P.; Song, H.; Shi, Y.; Li, X.; Tan, W.; Qi, J.; Gao, G. F. Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease. Nat. Commun. 2020, 11 (1), 4417,  DOI: 10.1038/s41467-020-18233-x
      20
      Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease
      Fu, Lifeng; Ye, Fei; Feng, Yong; Yu, Feng; Wang, Qisheng; Wu, Yan; Zhao, Cheng; Sun, Huan; Huang, Baoying; Niu, Peihua; Song, Hao; Shi, Yi; Li, Xuebing; Tan, Wenjie; Qi, Jianxun; Gao, George Fu
      Nature Communications (2020), 11 (1), 4417CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)
      Abstr.: COVID-19 was declared a pandemic on March 11 by WHO, due to its great threat to global public health. The coronavirus main protease (Mpro, also called 3CLpro) is essential for processing and maturation of the viral polyprotein, therefore recognized as an attractive drug target. Here we show that a clin. approved anti-HCV drug, Boceprevir, and a pre-clin. inhibitor against feline infectious peritonitis (corona) virus (FIPV), GC376, both efficaciously inhibit SARS-CoV-2 in Vero cells by targeting Mpro. Moreover, combined application of GC376 with Remdesivir, a nucleotide analog that inhibits viral RNA dependent RNA polymerase (RdRp), results in sterilizing additive effect. Further structural anal. reveals binding of both inhibitors to the catalytically active side of SARS-CoV-2 protease Mpro as main mechanism of inhibition. Our findings may provide crit. information for the optimization and design of more potent inhibitors against the emerging SARS-CoV-2 virus.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhvVSmsr3F&md5=273b11d16241499f15103885be398b23
    21. 21
      Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47 (7), 1739– 1749,  DOI: 10.1021/jm0306430
      21
      Glide: A new approach for rapid, accurate docking and scoring. 1. method and assessment of docking accuracy
      Friesner, Richard A.; Banks, Jay L.; Murphy, Robert B.; Halgren, Thomas A.; Klicic, Jasna J.; Mainz, Daniel T.; Repasky, Matthew P.; Knoll, Eric H.; Shelley, Mee; Perry, Jason K.; Shaw, David E.; Francis, Perry; Shenkin, Peter S.
      Journal of Medicinal Chemistry (2004), 47 (7), 1739-1749CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      A review. Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand. In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses. The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose. Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms. Docking accuracy is assessed by redocking ligands from 282 cocrystd. PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose. Errors in geometry for the top-ranked pose are less than 1 Å in nearly half of the cases and are greater than 2 Å in only about one-third of them. Comparisons to published data on rms deviations show that Glide is nearly twice as accurate as GOLD and more than twice as accurate as FlexX for ligands having up to 20 rotatable bonds. Glide is also found to be more accurate than the recently described Surflex method.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhsFyit74%253D&md5=8cc2f0022318b12dd972e9c493375bf9
    22. 22
      Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 2004, 47 (7), 1750– 1759,  DOI: 10.1021/jm030644s
      22
      Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
      Halgren, Thomas A.; Murphy, Robert B.; Friesner, Richard A.; Beard, Hege S.; Frye, Leah L.; Pollard, W. Thomas; Banks, Jay L.
      Journal of Medicinal Chemistry (2004), 47 (7), 1750-1759CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      A review. Glide's ability to identify active compds. in a database screen is characterized by applying Glide to a diverse set of nine protein receptors. In many cases, two, or even three, protein sites are employed to probe the sensitivity of the results to the site geometry. To make the database screens as realistic as possible, the screens use sets of "druglike" decoy ligands that have been selected to be representative of what we believe is likely to be found in the compd. collection of a pharmaceutical or biotechnol. company. Results are presented for releases 1.8, 2.0, and 2.5 of Glide. The comparisons show that av. measures for both "early" and "global" enrichment for Glide 2.5 are 3 times higher than for Glide 1.8 and more than 2 times higher than for Glide 2.0 because of better results for the least well-handled screens. This improvement in enrichment stems largely from the better balance of the more widely parametrized GlideScore 2.5 function and the inclusion of terms that penalize ligand-protein interactions that violate established principles of phys. chem., particularly as it concerns the exposure to solvent of charged protein and ligand groups. Comparisons to results for the thymidine kinase and estrogen receptors published by Rognan and co-workers (J. Med. Chem. 2000, 43, 4759-4767) show that Glide 2.5 performs better than GOLD 1.1, FlexX 1.8, or DOCK 4.01.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhsFyit78%253D&md5=33d68dd968e65626b449df61e44e37be
    23. 23
      Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C.; Mainz, D. T. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 2006, 49 (21), 6177– 6196,  DOI: 10.1021/jm051256o
      23
      Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes
      Friesner, Richard A.; Murphy, Robert B.; Repasky, Matthew P.; Frye, Leah L.; Greenwood, Jeremy R.; Halgren, Thomas A.; Sanschagrin, Paul C.; Mainz, Daniel T.
      Journal of Medicinal Chemistry (2006), 49 (21), 6177-6196CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      A novel scoring function to est. protein-ligand binding affinities has been developed and implemented as the Glide 4.0 XP scoring function and docking protocol. In addn. to unique water desolvation energy terms, protein-ligand structural motifs leading to enhanced binding affinity are included:(1) hydrophobic enclosure where groups of lipophilic ligand atoms are enclosed on opposite faces by lipophilic protein atoms, (2) neutral-neutral single or correlated hydrogen bonds in a hydrophobically enclosed environment, and (3) five categories of charged-charged hydrogen bonds. The XP scoring function and docking protocol have been developed to reproduce exptl. binding affinities for a set of 198 complexes (RMSDs of 2.26 and 1.73 kcal/mol over all and well-docked ligands, resp.) and to yield quality enrichments for a set of fifteen screens of pharmaceutical importance. Enrichment results demonstrate the importance of the novel XP mol. recognition and water scoring in sepg. active and inactive ligands and avoiding false positives.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XpvVGmurg%253D&md5=ea428c82ead0d8c27f8c1a7b694a1edf
    24. 24
      Amporndanai, K.; Meng, X.; Shang, W.; Jin, Z.; Rogers, M.; Zhao, Y.; Rao, Z.; Liu, Z. J.; Yang, H.; Zhang, L.; O’Neill, P. M.; Samar Hasnain, S. Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives. Nat. Commun. 2021, 12 (1), 3061,  DOI: 10.1038/s41467-021-23313-7
      24
      Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives
      Amporndanai, Kangsa; Meng, Xiaoli; Shang, Weijuan; Jin, Zhenmig; Rogers, Michael; Zhao, Yao; Rao, Zihe; Liu, Zhi-Jie; Yang, Haitao; Zhang, Leike; O'Neill, Paul M.; Samar Hasnain, S.
      Nature Communications (2021), 12 (1), 3061CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)
      Abstr.: The SARS-CoV-2 pandemic has triggered global efforts to develop therapeutics. The main protease of SARS-CoV-2 (Mpro), crit. for viral replication, is a key target for therapeutic development. An organoselenium drug called ebselen has been demonstrated to have potent Mpro inhibition and antiviral activity. We have examd. the binding modes of ebselen and its deriv. in Mpro via high resoln. co-crystallog. and investigated their chem. reactivity via mass spectrometry. Stronger Mpro inhibition than ebselen and potent ability to rescue infected cells were obsd. for a no. of derivs. A free selenium atom bound with cysteine of catalytic dyad has been revealed in crystallog. structures of Mpro with ebselen and MR6-31-2 suggesting hydrolysis of the enzyme bound organoselenium covalent adduct and formation of a phenolic byproduct, confirmed by mass spectrometry. The target engagement with selenation mechanism of inhibition suggests wider therapeutic applications of these compds. against SARS-CoV-2 and other zoonotic beta-corona viruses.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhtFyntbvK&md5=08fe8105502a0bd2aec4879d78280716
    25. 25
      Muramatsu, T.; Takemoto, C.; Kim, Y. T.; Wang, H.; Nishii, W.; Terada, T.; Shirouzu, M.; Yokoyama, S. SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity. Proc. Natl. Acad. Sci. U. S. A. 2016, 113 (46), 12997– 13002,  DOI: 10.1073/pnas.1601327113
      25
      SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity
      Muramatsu, Tomonari; Takemoto, Chie; Kim, Yong-Tae; Wang, Hongfei; Nishii, Wataru; Terada, Takaho; Shirouzu, Mikako; Yokoyama, Shigeyuki
      Proceedings of the National Academy of Sciences of the United States of America (2016), 113 (46), 12997-13002CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      The 3C-like protease (3CLpro) of severe acute respiratory syndrome coronavirus (SARS-CoV) cleaves 11 sites in the polyproteins, including its own N- and C-terminal autoprocessing sites, by recognizing P4-P1 and P1'. In this study, we detd. the crystal structure of 3CLpro with the C-terminal prosequence and the catalytic-site C145A mutation, in which the enzyme binds the C-terminal prosequence of another mol. Surprisingly, Phe at the P3' position [Phe(P3')] is snugly accommodated in the S3' pocket. Mutations of Phe(P3') impaired the C-terminal autoprocessing, but did not affect N-terminal autoprocessing. This difference was ascribed to the P2 residue, Phe(P2) and Leu(P2), in the C- and N-terminal sites, as follows. The S3' subsite is formed by Phe(P2)-induced conformational changes of 3CLpro and the direct involvement of Phe(P2) itself. In contrast, the N-terminal prosequence with Leu(P2) does not cause such conformational changes for the S3' subsite formation. In fact, the mutation of Phe(P2) to Leu in the C-terminal autoprocessing site abolishes the dependence on Phe(P3'). These mechanisms explain why Phe is required at the P3' position when the P2 position is occupied by Phe rather than Leu, which reveals a type of subsite cooperativity. Moreover, the peptide consisting of P4-P1 with Leu(P2) inhibits protease activity, whereas that with Phe(P2) exhibits a much smaller inhibitory effect, because Phe(P3') is missing. Thus, this subsite cooperativity likely exists to avoid the autoinhibition of the enzyme by its mature C-terminal sequence, and to retain the efficient C-terminal autoprocessing by the use of Phe(P2).
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhslKnu7%252FP&md5=f82749f292da1066e3eb4717dcbc66f2
    26. 26
      Sarma, B. K.; Mugesh, G. Antioxidant activity of the anti-inflammatory compound ebselen: a reversible cyclization pathway via selenenic and seleninic acid intermediates. Chem. - Eur. J. 2008, 14 (34), 10603– 10614,  DOI: 10.1002/chem.200801258
      26
      Antioxidant activity of the anti-inflammatory compound ebselen: a reversible cyclization pathway via selenenic and seleninic acid intermediates
      Sarma, Bani Kanta; Mugesh, Govindasamy
      Chemistry - A European Journal (2008), 14 (34), 10603-10614CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
      A revised mechanism that accounts for the glutathione peroxidase (GPx)-like catalytic activity of the organoselenium compd. ebselen (2-phenyl-1,2-benzisoselenazol-3(2H)-one) is described. The reaction of ebselen with H2O2 yields seleninic acid 2-PhNHC(O)C6H4SeO2H as the only oxidized product. The X- ray crystal structure of the seleninic acid shows that the Se atom is involved in a noncovalent interaction with the carbonyl O atom. In the presence of excess PhSH, the Se-N bond in ebselen is readily cleaved by the thiol to produce the corresponding selenenyl sulfide 2-PhNHC(O)C6H4SeSPh. The selenenyl sulfide thus produced undergoes a disproportionation in the presence of H2O2 to produce the diselenide, which upon reaction with H2O2, produces a mixt. of selenenic and seleninic acids. The addn. of thiol to the mixt. contg. selenenic and seleninic acids gives the selenenyl sulfide. When the concn. of the thiol is relatively low in the reaction mixt., the selenenic acid undergoes a rapid cyclization to produce ebselen. The seleninic acid, however, reacts with the diselenide to produce ebselen as the final product. DFT calcns. show that the cyclization of selenenic acids to the corresponding selenenyl amides is more favored than that of sulfenic acids to the corresponding sulfenyl amides. The regeneration of ebselen under a variety of conditions protects the Se moiety from irreversible inactivation, which may be responsible for the biol. activities of ebselen.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhsV2rsLfI&md5=6a82b84de2f8fddc7f2ac90cd62e0b15
    27. 27
      Haenen, G. R.; De Rooij, B. M.; Vermeulen, N. P.; Bast, A. Mechanism of the reaction of ebselen with endogenous thiols: Dihydrolipoate is a better cofactor than glutathione in the peroxidase activity of ebselen. Mol. Pharmacol. 1990, 37 (3), 412– 422
      27
      Mechanism of the reaction of ebselen with endogenous thiols: dihydrolipoate is a better cofactor than glutathione in the peroxidase activity of ebselen
      Haenen, Guido R. M. M.; De Rooij, Ben M.; Vermeulen, Nico P. E.; Bast, Aalt
      Molecular Pharmacology (1990), 37 (3), 412-22CODEN: MOPMA3; ISSN:0026-895X.
      The therapeutic effect of ebselen has been linked to its peroxidase activity. In the present study, the peroxidase activity of ebselen toward H2O2 with the endogenous thiols GSH and dihydrolipoate [L(SH)2] as cofactors was detd. When GSH was used, peroxide removal was described by a ter uni ping pong mechanism with Dalziel coeffs. for GSH and H2O2 of 0.165 and 0.081 mM min, resp. When L(SH)2 was used, peroxidase activity was independent of the concn. of L(SH)2, in the concn. range studied (5 μM to 2 mM) and peroxide removal was only dependent on the concn. of H2O2 and ebselen, with the second-order rate const. being 12.3 mM-1 min-1. To elucidate the difference between GSH and L(SH)2, the mol. mechanism of the peroxidase activity of ebselen was investigated, using UV spectrophotometry, HPLC, 77Se NMR, and mass spectrometry. GSH was found to react quickly with ebselen to give a selenenyl sulfide, an adduct of GSH to ebselen. Subsequently, the GSH-selenenyl sulfide is converted into the diselenide of ebselen. Finally the diselenide reacts with a peroxide and ebselen is regenerated. The formation by GSH of the diselenide from the GSH-selenenyl sulfide of ebselen is slow and linearly dependent on the concn. of free thiol; however, no net consumption of GSH was obsd. Furthermore, it is likely that a selenol is an intermediate in diselenide formation. After reaction between ebselen and L(SH)2 the diselenide of ebselen was immediately detected. The fast formation of the diselenide with L(SH)2 vs. the slow formation of the diselenide with GSH accounts for our observation that L(SH)2 is a better cofactor than GSH in the peroxidase activity of ebselen. These results suggest that the interaction between ebselen and L(SH)2 might be of major importance in the mechanism by which ebselen exerts its therapeutic effect.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK3cXhvFWlsrg%253D&md5=ce9215a47abfe5cd650595c67a39c9c7
    28. 28
      Wagner, G.; Schuch, G.; Akerboom, T. P.; Sies, H. Transport of ebselen in plasma and its transfer to binding sites in the hepatocyte. Biochem. Pharmacol. 1994, 48 (6), 1137– 1144,  DOI: 10.1016/0006-2952(94)90150-3
      28
      Transport of ebselen in plasma and its transfer to binding sites in the hepatocyte
      Wagner, Gunter; Schuch, Gunter; Akerboom, Theodorus P. M.; Sies, Helmut
      Biochemical Pharmacology (1994), 48 (6), 1137-44CODEN: BCPCA6; ISSN:0006-2952.
      In vivo transport in plasma and in vitro transfer of ebselen to binding sits in the hepatocyte were studied. More than 90% of i.v. administered ebselen in mouse plasma is bound by selenium-sulfur bonds to reactive thiols in serum albumin. In in vitro expts. the uptake of [14C]-ebselen from a complex prepd. with bovine serum albumin (BSA) was detd. in isolated perfused rat liver. Radioactive ebselen metabolites were excreted into bile. In isolated hepatocytes, radioactivity was bound to all subcellular organelles. Ebselen is transferred from the BSA complex to membrane-assocd. proteins after reductive cleavage of the Se-S bond effected by endogenous protein thiols. In contrast, when proteins were sepd. by dialysis membranes, ebselen transfer from its BSA complex occurred only in the presence of externally added reductants. Among the physiol. reductants tested, ebselen release from the BSA complex was highest with glutathione (75%) and lowest with ascorbic acid (less than 10%). Quant. release of ebselen from its BSA complex was only achieved by the combined action of reductant, notably 2-mercaptoethanol, and guanidine thiocyanate, suggesting that ebselen interacts with proteins by covalent Se-S bonds as well as by ionic charge interactions.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2cXmt1WjsL8%253D&md5=78392c5dbfaa4f9e7a5476146b852a55
    29. 29
      Singh, N.; Halliday, A. C.; Thomas, J. M.; Kuznetsova, O. V.; Baldwin, R.; Woon, E. C.; Aley, P. K.; Antoniadou, I.; Sharp, T.; Vasudevan, S. R.; Churchill, G. C. A safe lithium mimetic for bipolar disorder. Nat. Commun. 2013, 4, 1332,  DOI: 10.1038/ncomms2320
      29
      A safe lithium mimetic for bipolar disorder
      Singh Nisha; Halliday Amy C; Thomas Justyn M; Kuznetsova Olga V; Baldwin Rhiannon; Woon Esther C Y; Aley Parvinder K; Antoniadou Ivi; Sharp Trevor; Vasudevan Sridhar R; Churchill Grant C
      Nature communications (2013), 4 (), 1332 ISSN:.
      Lithium is the most effective mood stabilizer for the treatment of bipolar disorder, but it is toxic at only twice the therapeutic dosage and has many undesirable side effects. It is likely that a small molecule could be found with lithium-like efficacy but without toxicity through target-based drug discovery; however, therapeutic target of lithium remains equivocal. Inositol monophosphatase is a possible target but no bioavailable inhibitors exist. Here we report that the antioxidant ebselen inhibits inositol monophosphatase and induces lithium-like effects on mouse behaviour, which are reversed with inositol, consistent with a mechanism involving inhibition of inositol recycling. Ebselen is part of the National Institutes of Health Clinical Collection, a chemical library of bioavailable drugs considered clinically safe but without proven use. Therefore, ebselen represents a lithium mimetic with the potential both to validate inositol monophosphatase inhibition as a treatment for bipolar disorder and to serve as a treatment itself.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC3s3nvVSqsw%253D%253D&md5=682e37608458f5d24a55405d07a0e5b4
    30. 30
      Johnson, T. W.; Dress, K. R.; Edwards, M. Using the Golden Triangle to optimize clearance and oral absorption. Bioorg. Med. Chem. Lett. 2009, 19 (19), 5560– 5564,  DOI: 10.1016/j.bmcl.2009.08.045
      30
      Using the Golden Triangle to optimize clearance and oral absorption
      Johnson, Ted W.; Dress, Klaus R.; Edwards, Martin
      Bioorganic & Medicinal Chemistry Letters (2009), 19 (19), 5560-5564CODEN: BMCLE8; ISSN:0960-894X. (Elsevier B.V.)
      The Golden Triangle is a visualization tool developed from in vitro permeability, in vitro clearance and computational data designed to aid medicinal chemists in achieving metabolically stable, permeable and potent drug candidates. Classifying compds. as permeable and stable and plotting mol. wt. (MW) vs. octanol:buffer (pH 7.4) distribution coeffs. (log D) or estd. octanol:buffer (pH 7.4) distribution coeffs. (elog D) reveals useful trends. Anal. of at least 2 orthogonal trends, such as permeability and clearance, can be extremely effective in balancing and optimizing multiple properties. In addn., mol. wt. and log D impact potency-efficiency calcns., allowing potency, clearance and permeability to be optimized simultaneously.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtFaktbfE&md5=3cfed1288ec451eb4419f1db753ae4b4
    31. 31
      Johnson, T. W.; Gallego, R. A.; Edwards, M. P. Lipophilic Efficiency as an Important Metric in Drug Design. J. Med. Chem. 2018, 61 (15), 6401– 6420,  DOI: 10.1021/acs.jmedchem.8b00077
      31
      Lipophilic Efficiency as an Important Metric in Drug Design
      Johnson, Ted W.; Gallego, Rebecca A.; Edwards, Martin P.
      Journal of Medicinal Chemistry (2018), 61 (15), 6401-6420CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      A review. Lipophilic efficiency (LipE) is an important metric that has been increasingly applied in drug discovery medicinal chem. lead optimization programs. In this perspective, using literature drug discovery examples, we discuss the concept of rigorously applying LipE to guide medicinal chem. lead optimization toward drug candidates with potential for superior in vivo efficacy and safety, esp. when guided by physiochem. property-based optimization (PPBO). Also highlighted are examples of small structural modifications such as addn. of single atoms, small functional groups, and cyclizations that produce large increases in LipE. Understanding the factors that may contribute to LipE changes through anal. of ligand-protein crystal structures and using structure-based drug design (SBDD) to increase LipE by design is also discussed. Herein we advocate for use of LipE anal. coupled with PPBO and SBDD as an efficient mechanism for drug design.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXmsVahsbg%253D&md5=29f38880914fa75c33be3a640ace4309
    32. 32
      Hopkins, A. L.; Keseru, G. M.; Leeson, P. D.; Rees, D. C.; Reynolds, C. H. The role of ligand efficiency metrics in drug discovery. Nat. Rev. Drug Discovery 2014, 13 (2), 105– 121,  DOI: 10.1038/nrd4163
      32
      The role of ligand efficiency metrics in drug discovery
      Hopkins, Andrew L.; Keserue, Gyoergy M.; Leeson, Paul D.; Rees, David C.; Reynolds, Charles H.
      Nature Reviews Drug Discovery (2014), 13 (2), 105-121CODEN: NRDDAG; ISSN:1474-1776. (Nature Publishing Group)
      A review. The judicious application of ligand or binding efficiency metrics, which quantify the mol. properties required to obtain binding affinity for a drug target, is gaining traction in the selection and optimization of fragments, hits and leads. Retrospective anal. of recently marketed oral drugs shows that they frequently have highly optimized ligand efficiency values for their targets. Optimizing ligand efficiency metrics based on both mol. mass and lipophilicity, when set in the context of the specific target, has the potential to ameliorate the inflation of these properties that has been obsd. in current medicinal chem. practice, and to increase the quality of drug candidates.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhs1SmtLk%253D&md5=344030e59f499180f79d311302a27532
    33. 33
      Raymer, B.; Bhattacharya, S. K. Lead-like Drugs: A Perspective. J. Med. Chem. 2018, 61 (23), 10375– 10384,  DOI: 10.1021/acs.jmedchem.8b00407
      33
      Lead-like Drugs: A Perspective
      Raymer, Brian; Bhattacharya, Samit K.
      Journal of Medicinal Chemistry (2018), 61 (23), 10375-10384CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      Lead-like drugs, or drugs below mol. wt. 300, are an important and sometimes overlooked component of the current pharmacopeia and contemporary medicinal chem. practice. To examine the recent state-of-the-art in lead-like drug discovery, we surveyed recent drug approvals from 2011 to 2017 and top 200 prescribed medications, as well as provide case studies on recently approved lead-like drugs. Many of these recent drugs are close analogs of previously known drugs or natural substrates, with a key focus of their medicinal chem. optimization being the choice of a low mol. wt. starting point and maintaining low mol. wt. during the optimization. However, the identification of low mol. wt. starting points may be limited by the availability of suitable low mol. wt. screening sets. To increase the discovery rate of lead-like drugs, we suggest an increased focus on inclusion and prosecution of lead-like starting points in screening libraries.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtl2is73O&md5=e9fc17d69c7d671459fdaf77d6721829
    34. 34
      Weiss, M. M.; Dineen, T. A.; Marx, I. E.; Altmann, S.; Boezio, A.; Bregman, H.; Chu-Moyer, M.; DiMauro, E. F.; Feric Bojic, E.; Foti, R. S.; Gao, H.; Graceffa, R.; Gunaydin, H.; Guzman-Perez, A.; Huang, H.; Huang, L.; Jarosh, M.; Kornecook, T.; Kreiman, C. R.; Ligutti, J.; La, D. S.; Lin, M. J.; Liu, D.; Moyer, B. D.; Nguyen, H. N.; Peterson, E. A.; Rose, P. E.; Taborn, K.; Youngblood, B. D.; Yu, V.; Fremeau, R. T., Jr. Sulfonamides as Selective NaV1.7 Inhibitors: Optimizing Potency and Pharmacokinetics While Mitigating Metabolic Liabilities. J. Med. Chem. 2017, 60 (14), 5969– 5989,  DOI: 10.1021/acs.jmedchem.6b01851
      34
      Sulfonamides as Selective NaV1.7 Inhibitors: Optimizing Potency and Pharmacokinetics While Mitigating Metabolic Liabilities
      Weiss, Matthew M.; Dineen, Thomas A.; Marx, Isaac E.; Altmann, Steven; Boezio, Alessandro; Bregman, Howard; Chu-Moyer, Margaret; DiMauro, Erin F.; Feric Bojic, Elma; Foti, Robert S.; Gao, Hua; Graceffa, Russell; Gunaydin, Hakan; Guzman-Perez, Angel; Huang, Hongbing; Huang, Liyue; Jarosh, Michael; Kornecook, Thomas; Kreiman, Charles R.; Ligutti, Joseph; La, Daniel S.; Lin, Min-Hwa Jasmine; Liu, Dong; Moyer, Bryan D.; Nguyen, Hanh N.; Peterson, Emily A.; Rose, Paul E.; Taborn, Kristin; Youngblood, Beth D.; Yu, Violeta; Fremeau, Robert T.
      Journal of Medicinal Chemistry (2017), 60 (14), 5969-5989CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)
      Several reports have recently emerged regarding the identification of heteroarylsulfonamides as NaV1.7 inhibitors that demonstrate high levels of selectivity over other NaV isoforms. The optimization of a series of internal NaV1.7 leads that address a no. of metabolic liabilities including bioactivation, PXR activation, as well as CYP3A4 induction and inhibition led to the identification of potent and selective inhibitors that demonstrated favorable pharmacokinetic profiles and were devoid of the aforementioned liabilities. The key to achieving this within a series prone to transporter-mediated clearance was the identification of a small range of optimal cLogD values and the discovery of subtle PXR SAR that was not lipophilicity dependent. This enabled the identification of compd. 20, which was advanced into a target engagement pharmacodynamic model where it exhibited robust reversal of histamine-induced scratching bouts in mice.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXktFOmtbw%253D&md5=6333a6b936e48f9d18cf9df10ea12853
    35. 35
      Dittmar, M.; Lee, J. S.; Whig, K.; Segrist, E.; Li, M.; Kamalia, B.; Castellana, L.; Ayyanathan, K.; Cardenas-Diaz, F. L.; Morrisey, E. E.; Truitt, R.; Yang, W.; Jurado, K.; Samby, K.; Ramage, H.; Schultz, D. C.; Cherry, S. Drug repurposing screens reveal cell-type-specific entry pathways and FDA-approved drugs active against SARS-Cov-2. Cell Rep. 2021, 35 (1), 108959,  DOI: 10.1016/j.celrep.2021.108959
      35
      Drug repurposing screens reveal cell-type-specific entry pathways and FDA-approved drugs active against SARS-Cov-2
      Dittmar, Mark; Lee, Jae Seung; Whig, Kanupriya; Segrist, Elisha; Li, Minghua; Kamalia, Brinda; Castellana, Lauren; Ayyanathan, Kasirajan; Cardenas-Diaz, Fabian L.; Morrisey, Edward E.; Truitt, Rachel; Yang, Wenli; Jurado, Kellie; Samby, Kirandeep; Ramage, Holly; Schultz, David C.; Cherry, Sara
      Cell Reports (2021), 35 (1), 108959CODEN: CREED8; ISSN:2211-1247. (Cell Press)
      There is an urgent need for antivirals to treat the newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To identify new candidates, we screen a repurposing library of ~ 3,000 drugs. Screening in Vero cells finds few antivirals, while screening in human Huh7.5 cells validates 23 diverse antiviral drugs. Extending our studies to lung epithelial cells, we find that there are major differences in drug sensitivity and entry pathways used by SARS-CoV-2 in these cells. Entry in lung epithelial Calu-3 cells is pH independent and requires TMPRSS2, while entry in Vero and Huh7.5 cells requires low pH and triggering by acid-dependent endosomal proteases. Moreover, we find nine drugs are antiviral in respiratory cells, seven of which have been used in humans, and three are US Food and Drug Administration (FDA) approved, including cyclosporine. We find that the antiviral activity of cyclosporine is targeting Cyclophilin rather than calcineurin, revealing essential host targets that have the potential for rapid clin. implementation.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXnsVWju7w%253D&md5=52eaa65b358385380f995e46d3c7703d
    36. 36
      Jang, W. D.; Jeon, S.; Kim, S.; Lee, S. Y. Drugs repurposed for COVID-19 by virtual screening of 6,218 drugs and cell-based assay. Proc. Natl. Acad. Sci. U. S. A. 2021, 118 (30), e2024302118  DOI: 10.1073/pnas.2024302118
      36
      Drugs repurposed for COVID-19 by virtual screening of 6,218 drugs and cell-based assay
      Jang, Woo Dae; Jeon, Sangeun; Kim, Seungtaek; Lee, Sang Yup
      Proceedings of the National Academy of Sciences of the United States of America (2021), 118 (30), e2024302118CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      The COVID-19 pandemic caused by SARS-CoV-2 is an unprecedentedly significant health threat, prompting the need for rapidly developing antiviral drugs for the treatment. Drug repurposing is currently 1 of the most tangible options for rapidly developing drugs for emerging and reemerging viruses. In general, drug repurposing starts with virtual screening of approved drugs employing various computational methods. However, the actual hit rate of virtual screening is very low, and most of the predicted compds. are false positives. Here, we developed a strategy for virtual screening with much reduced false positives through incorporating predocking filtering based on shape similarity and postdocking filtering based on interaction similarity. We applied this advanced virtual screening approach to repurpose 6218 approved and clin. trial drugs for COVID-19. All 6218 compds. were screened against main protease and RNA-dependent RNA polymerase of SARS-CoV-2, resulting in 15 and 23 potential repurposed drugs, resp. Among them, 7 compds. can inhibit SARS-CoV-2 replication in Vero cells. Three of these drugs, emodin, omipalisib, and tipifarnib, show anti-SARS-CoV-2 activities in human lung cells, Calu-3. Notably, the activity of omipalisib is 200-fold higher than that of remdesivir in Calu-3. Furthermore, 3 drug combinations, omipalisib/remdesivir, tipifarnib/omipalisib, and tipifarnib/remdesivir, show strong synergistic effects in inhibiting SARS-CoV-2. Such drug combination therapy improves antiviral efficacy in SARS-CoV-2 infection and reduces the risk of each drug's toxicity. The drug repurposing strategy reported here will be useful for rapidly developing drugs for treating COVID-19 and other viruses.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhs1KmsbjN&md5=d37de60099bc07ebf242e4a17132e153
    37. 37
      Choi, S. W.; Shin, J. S.; Park, S. J.; Jung, E.; Park, Y. G.; Lee, J.; Kim, S. J.; Park, H. J.; Lee, J. H.; Park, S. M.; Moon, S. H.; Ban, K.; Go, Y. Y. Antiviral activity and safety of remdesivir against SARS-CoV-2 infection in human pluripotent stem cell-derived cardiomyocytes. Antiviral Res. 2020, 184, 104955,  DOI: 10.1016/j.antiviral.2020.104955
      37
      Antiviral activity and safety of remdesivir against SARS-CoV-2 infection in human pluripotent stem cell-derived cardiomyocytes
      Choi, Seong Woo; Shin, Jin Soo; Park, Soon-Jung; Jung, Eunhye; Park, Yun-Gwi; Lee, Jiho; Kim, Sung Joon; Park, Hun-Jun; Lee, Jung-Hoon; Park, Sung-Min; Moon, Sung-Hwan; Ban, Kiwon; Go, Yun Young
      Antiviral Research (2020), 184 (), 104955CODEN: ARSRDR; ISSN:0166-3542. (Elsevier B.V.)
      Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is considered as the most significant global public health crisis of the century. Several drug candidates have been suggested as potential therapeutic options for COVID-19, including remdesivir, currently the only authorized drug for use under an Emergency Use Authorization. However, there is only limited information regarding the safety profiles of the proposed drugs, in particular drug-induced cardiotoxicity. Here, we evaluated the antiviral activity and cardiotoxicity of remdesivir using cardiomyocytes-derived from human pluripotent stem cells (hPSC-CMs) as an alternative source of human primary cardiomyocytes (CMs). In this study, remdesivir exhibited up to 60-fold higher antiviral activity in hPSC-CMs compared to Vero E6 cells; however, it also induced moderate cardiotoxicity in these cells. To gain further insight into the drug-induced arrhythmogenic risk, we assessed QT interval prolongation and automaticity of remdesivir-treated hPSC-CMs using a multielectrode array (MEA). As a result, the data indicated a potential risk of QT prolongation when remdesivir is used at concns. higher than the estd. peak plasma concn. Therefore, we conclude that close monitoring of the electrocardiog./QT interval should be advised in SARS-CoV-2-infected patients under remdesivir medication, in particular individuals with pre-existing heart conditions.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitl2nsbfJ&md5=2a4723ae20790ada7df5ecabe730a2bd
    38. 38
      Tiwari, S. K.; Wang, S.; Smith, D.; Carlin, A. F.; Rana, T. M. Revealing Tissue-Specific SARS-CoV-2 Infection and Host Responses using Human Stem Cell-Derived Lung and Cerebral Organoids. Stem Cell Rep. 2021, 16 (3), 437– 445,  DOI: 10.1016/j.stemcr.2021.02.005
      38
      Revealing tissue-specific SARS-CoV-2 infection and host responses using human stem cell-derived lung and cerebral organoids
      Tiwari, Shashi Kant; Wang, Shaobo; Smith, Davey; Carlin, Aaron F.; Rana, Tariq M.
      Stem Cell Reports (2021), 16 (3), 437-445CODEN: SCRTFL; ISSN:2213-6711. (Cell Press)
      COVID-19 is a transmissible respiratory disease caused by a novel coronavirus, SARS-CoV-2, and has become a global health emergency. There is an urgent need for robust and practical in vitro model systems to investigate viral pathogenesis. Here, we generated human induced pluripotent stem cell (iPSC)-derived lung organoids (LORGs), cerebral organoids (CORGs), neural progenitor cells (NPCs), neurons, and astrocytes. LORGs contg. epithelial cells, alveolar types 1 and 2, highly express ACE2 and TMPRSS2 and are permissive to SARS-CoV-2 infection. SARS-CoV-2 infection induces interferons, cytokines, and chemokines and activates crit. inflammasome pathway genes. Spike protein inhibitor, EK1 peptide, and TMPRSS2 inhibitors (camostat/nafamostat) block viral entry in LORGs. Conversely, CORGs, NPCs, astrocytes, and neurons express low levels of ACE2 and TMPRSS2 and correspondingly are not highly permissive to SARS-CoV-2 infection. Infection in neuronal cells activates TLR3/7, OAS2, complement system, and apoptotic genes. These findings will aid in understanding COVID-19 pathogenesis and facilitate drug discovery.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXls1ersbw%253D&md5=e12410b74f51084672e12fab3eb5230e
    39. 39
      Li, N.; Hui, H.; Bray, B.; Gonzalez, G. M.; Zeller, M.; Anderson, K. G.; Knight, R.; Smith, D.; Wang, Y.; Carlin, A. F.; Rana, T. M. METTL3 regulates viral m6A RNA modification and host cell innate immune responses during SARS-CoV-2 infection. Cell Rep. 2021, 35 (6), 109091,  DOI: 10.1016/j.celrep.2021.109091
      39
      METTL3 regulates viral m6A RNA modification and host cell innate immune responses during SARS-CoV-2 infection
      Li, Na; Hui, Hui; Bray, Bill; Gonzalez, Gwendolyn Michelle; Zeller, Mark; Anderson, Kristian G.; Knight, Rob; Smith, Davey; Wang, Yinsheng; Carlin, Aaron F.; Rana, Tariq M.
      Cell Reports (2021), 35 (6), 109091CODEN: CREED8; ISSN:2211-1247. (Cell Press)
      It is urgent and important to understand the relationship of the widespread severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) with host immune response and study the underlining mol. mechanism. N6-methylation of adenosine (m6A) in RNA regulates many physiol. and disease processes. Here, we investigate m6A modification of the SARS-CoV-2 gene in regulating the host cell innate immune response. Our data show that the SARS-CoV-2 virus has m6A modifications that are enriched in the 3' end of the viral genome. We find that depletion of the host cell m6A methyltransferase METTL3 decreases m6A levels in SARS-CoV-2 and host genes, and m6A redn. in viral RNA increases RIG-I binding and subsequently enhances the downstream innate immune signaling pathway and inflammatory gene expression. METTL3 expression is reduced and inflammatory genes are induced in patients with severe coronavirus disease 2019 (COVID-19). These findings will aid in the understanding of COVID-19 pathogenesis and the design of future studies regulating innate immunity for COVID-19 treatment.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhtVShu7zP&md5=938ee9a0e2de397723df26374d4e2612
    40. 40
      Wang, S.; Li, W.; Hui, H.; Tiwari, S. K.; Zhang, Q.; Croker, B. A.; Rawlings, S.; Smith, D.; Carlin, A. F.; Rana, T. M. Cholesterol 25-Hydroxylase inhibits SARS-CoV-2 and other coronaviruses by depleting membrane cholesterol. EMBO J. 2020, 39 (21), e106057  DOI: 10.15252/embj.2020106057
      40
      Cholesterol 25-Hydroxylase inhibits SARS-CoV-2 and other coronaviruses by depleting membrane cholesterol
      Wang, Shaobo; Li, Wanyu; Hui, Hui; Tiwari, Shashi Kant; Zhang, Qiong; Croker, Ben A.; Rawlings, Stephen; Smith, Davey; Carlin, Aaron F.; Rana, Tariq M.
      EMBO Journal (2020), 39 (21), e106057CODEN: EMJODG; ISSN:0261-4189. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2 and has spread across the globe. SARS-CoV-2 is a highly infectious virus with no vaccine or antiviral therapy available to control the pandemic; therefore, it is crucial to understand the mechanisms of viral pathogenesis and the host immune responses to SARS-CoV-2. SARS-CoV-2 is a new member of the betacoronavirus genus like other closely related viruses including SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Both SARS-CoV and MERS-CoV have caused serious outbreaks and epidemics in the past 18 yr. We report that 1 of the interferon-stimulated genes (ISGs), cholesterol 25-hydroxylase (CH25H), is induced by SARS-CoV-2 infection in vitro and in COVID-19-infected patients. CH25H converts cholesterol to 25-hydroxycholesterol (25HC) and 25HC shows broad anti-coronavirus activity by blocking membrane fusion. Furthermore, 25HC inhibits USA-WA1/2020 SARS-CoV-2 infection in lung epithelial cells and viral entry in human lung organoids. Mechanistically, 25HC inhibits viral membrane fusion by activating the ER-localized acyl-CoA:cholesterol acyltransferase (ACAT) which leads to the depletion of accessible cholesterol from the plasma membrane. Altogether, our results shed light on a potentially broad antiviral mechanism by 25HC through depleting accessible cholesterol on the plasma membrane to suppress virus-cell fusion. Since 25HC is a natural product with no known toxicity at effective concns., it provides a potential therapeutic candidate for COVID-19 and emerging viral diseases in the future.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhvFyisbvL&md5=7b37216366d03b329695f0703c5e96df
    41. 41
      Ma, C.; Hu, Y.; Townsend, J. A.; Lagarias, P. I.; Marty, M. T.; Kolocouris, A.; Wang, J. Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors. ACS Pharmacol Transl Sci. 2020, 3 (6), 1265– 1277,  DOI: 10.1021/acsptsci.0c00130
      41
      Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors
      Ma, Chunlong; Hu, Yanmei; Townsend, Julia Alma; Lagarias, Panagiotis I.; Marty, Michael Thomas; Kolocouris, Antonios; Wang, Jun
      ACS Pharmacology & Translational Science (2020), 3 (6), 1265-1277CODEN: APTSFN; ISSN:2575-9108. (American Chemical Society)
      Among the drug targets being investigated for SARS-CoV-2, the viral main protease (Mpro) is one of the most extensively studied. Mpro is a cysteine protease that hydrolyzes the viral polyprotein at more than 11 sites. It is highly conserved and has a unique substrate preference for glutamine in the P1 position. Therefore, Mpro inhibitors are expected to have broad-spectrum antiviral activity and a high selectivity index. Structurally diverse compds. have been reported as Mpro inhibitors. In this study, we investigated the mechanism of action of six previously reported Mpro inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12, using a consortium of techniques including FRET-based enzymic assay, thermal shift assay, native mass spectrometry, cellular antiviral assays, and mol. dynamics simulations. Collectively, the results showed that the inhibition of Mpro by these six compds. is nonspecific and that the inhibition is abolished or greatly reduced with the addn. of reducing reagent 1,4-dithiothreitol (DTT). Without DTT, these six compds. inhibit not only Mpro but also a panel of viral cysteine proteases including SARS-CoV-2 papain-like protease and 2Apro and 3Cpro from enterovirus A71 (EV-A71) and EV-D68. However, none of the compds. inhibits the viral replication of EV-A71 or EV-D68, suggesting that the enzymic inhibition potency IC50 values obtained in the absence of DTT cannot be used to faithfully predict their cellular antiviral activity. Overall, we provide compelling evidence suggesting that these six compds. are nonspecific SARS-CoV-2 Mpro inhibitors and urge the scientific community to be stringent with hit validation.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitVajsrjK&md5=29d0e69db20f681ed4ef7cddd153cc6d
    42. 42
      Weglarz-Tomczak, E.; Tomczak, J. M.; Talma, M.; Burda-Grabowska, M.; Giurg, M.; Brul, S. Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2. Sci. Rep. 2021, 11 (1), 3640,  DOI: 10.1038/s41598-021-83229-6
      42
      Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2
      Weglarz-Tomczak, Ewelina; Tomczak, Jakub M.; Talma, Michal; Burda-Grabowska, Malgorzata; Giurg, Miroslaw; Brul, Stanley
      Scientific Reports (2021), 11 (1), 3640CODEN: SRCEC3; ISSN:2045-2322. (Nature Research)
      An efficient treatment against a COVID-19 disease, caused by the novel coronavirus SARS-CoV-2 (CoV2), remains a challenge. The papain-like protease (PLpro) from the human coronavirus is a protease that plays a crit. role in virus replication. Moreover, CoV2 uses this enzyme to modulate the host's immune system to its own benefit. Therefore, it represents a highly promising target for the development of antiviral drugs. We used Approx. Bayesian Computation tools, mol. modeling and enzyme activity studies to identify highly active inhibitors of the PLpro. We discovered organoselenium compds., ebselen and its structural analogs, as a novel approach for inhibiting the activity of PLproCoV2. Furthermore, we identified, for the first time, inhibitors of PLproCoV2 showing potency in the nanomolar range. Moreover, we found a difference between PLpro from SARS and CoV2 that can be correlated with the diverse dynamics of their replication, and, putatively to disease progression.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXktVOntbY%253D&md5=bb905ef94cebd529c4fc53d196adc5a4
    43. 43
      Freitas, B. T.; Durie, I. A.; Murray, J.; Longo, J. E.; Miller, H. C.; Crich, D.; Hogan, R. J.; Tripp, R. A.; Pegan, S. D. Characterization and Noncovalent Inhibition of the Deubiquitinase and deISGylase Activity of SARS-CoV-2 Papain-Like Protease. ACS Infect. Dis. 2020, 6 (8), 2099– 2109,  DOI: 10.1021/acsinfecdis.0c00168
      43
      Characterization and Noncovalent Inhibition of the Deubiquitinase and deISGylase Activity of SARS-CoV-2 Papain-Like Protease
      Freitas, Brendan T.; Durie, Ian A.; Murray, Jackelyn; Longo, Jaron E.; Miller, Holden C.; Crich, David; Hogan, Robert Jeff; Tripp, Ralph A.; Pegan, Scott D.
      ACS Infectious Diseases (2020), 6 (8), 2099-2109CODEN: AIDCBC; ISSN:2373-8227. (American Chemical Society)
      Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent for COVID-19, is a novel human betacoronavirus that is rapidly spreading worldwide. The outbreak currently includes over 3.7 million cases and 260,000 fatalities. As a betacoronavirus, SARS-CoV-2 encodes for a papain-like protease (PLpro) that is likely responsible for cleavage of the coronavirus (CoV) viral polypeptide. The PLpro is also responsible for suppression of host innate immune responses by virtue of its ability to reverse host ubiquitination and ISGylation events. Here, the biochem. activity of SARS-CoV-2 PLpro against ubiquitin (Ub) and interferon-stimulated gene product 15 (ISG15) substrates is evaluated, revealing that the protease has a marked redn. in its ability to process K48 linked Ub substrates compared to its counterpart in SARS-CoV. Addnl., its substrate activity more closely mirrors that of the PLpro from the Middle East respiratory syndrome coronavirus and prefers ISG15s from certain species including humans. Addnl., naphthalene based PLpro inhibitors are shown to be effective at halting SARS-CoV-2 PLpro activity as well as SARS-CoV-2 replication.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXpslylsbs%253D&md5=314ea59a92d60345f982e78e31e5b569
    44. 44
      Shin, D.; Mukherjee, R.; Grewe, D.; Bojkova, D.; Baek, K.; Bhattacharya, A.; Schulz, L.; Widera, M.; Mehdipour, A. R.; Tascher, G.; Geurink, P. P.; Wilhelm, A.; van der Heden van Noort, G. J.; Ovaa, H.; Muller, S.; Knobeloch, K. P.; Rajalingam, K.; Schulman, B. A.; Cinatl, J.; Hummer, G.; Ciesek, S.; Dikic, I. Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 2020, 587 (7835), 657– 662,  DOI: 10.1038/s41586-020-2601-5
      44
      Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity
      Shin, Donghyuk; Mukherjee, Rukmini; Grewe, Diana; Bojkova, Denisa; Baek, Kheewoong; Bhattacharya, Anshu; Schulz, Laura; Widera, Marek; Mehdipour, Ahmad Reza; Tascher, Georg; Geurink, Paul P.; Wilhelm, Alexander; van der Heden van Noort, Gerbrand J.; Ovaa, Huib; Mueller, Stefan; Knobeloch, Klaus-Peter; Rajalingam, Krishnaraj; Schulman, Brenda A.; Cinatl, Jindrich; Hummer, Gerhard; Ciesek, Sandra; Dikic, Ivan
      Nature (London, United Kingdom) (2020), 587 (7835), 657-662CODEN: NATUAS; ISSN:0028-0836. (Nature Research)
      The papain-like protease PLpro is an essential coronavirus enzyme that is required for processing viral polyproteins to generate a functional replicase complex and enable viral spread. PLpro is also implicated in cleaving proteinaceous post-translational modifications on host proteins as an evasion mechanism against host antiviral immune responses. We perform biochem., structural, and functional characterization of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PLpro (SCoV2-PLpro) and outline differences with SARS-CoV PLpro (SCoV-PLpro) in regulation of host interferon and NF-κB pathways. SCoV2-PLpro and SCoV-PLpro share 83% sequence identity but exhibit different host substrate preferences; SCoV2-PLpro preferentially cleaves the ubiquitin-like interferon-stimulated gene 15 protein (ISG15), whereas SCoV-PLpro predominantly targets ubiquitin chains. The crystal structure of SCoV2-PLpro in complex with ISG15 reveals distinctive interactions with the N-terminal ubiquitin-like domain of ISG15, highlighting the high affinity and specificity of these interactions. Furthermore, upon infection, SCoV2-PLpro contributes to the cleavage of ISG15 from interferon responsive factor 3 (IRF3) and attenuates type I interferon responses. Notably, inhibition of SCoV2-PLpro with GRL-0617 impairs the virus-induced cytopathogenic effect, maintains the antiviral interferon pathway and reduces viral replication in infected cells. These results highlight a potential dual therapeutic strategy in which targeting of SCoV2-PLpro can suppress SARS-CoV-2 infection and promote antiviral immunity.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitVSqu7nP&md5=d6e55cd2e91c4a55f19abf2652973aab
    45. 45
      Klemm, T.; Ebert, G.; Calleja, D. J; Allison, C. C; Richardson, L. W; Bernardini, J. P; Lu, B. G.; Kuchel, N. W; Grohmann, C.; Shibata, Y.; Gan, Z. Y.; Cooney, J. P; Doerflinger, M.; Au, A. E; Blackmore, T. R; Heden van Noort, G. J; Geurink, P. P; Ovaa, H.; Newman, J.; Riboldi-Tunnicliffe, A.; Czabotar, P. E; Mitchell, J. P; Feltham, R.; Lechtenberg, B. C; Lowes, K. N; Dewson, G.; Pellegrini, M.; Lessene, G.; Komander, D. Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2. EMBO J. 2020, 39 (18), e106275  DOI: 10.15252/embj.2020106275
      45
      Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2
      Klemm, Theresa; Ebert, Gregor; Calleja, Dale J.; Allison, Cody C.; Richardson, Lachlan W.; Bernardini, Jonathan P.; Lu, Bernadine G. C.; Kuchel, Nathan W.; Grohmann, Christoph; Shibata, Yuri; Gan, Zhong Yan; Cooney, James P.; Doerflinger, Marcel; Au, Amanda E.; Blackmore, Timothy R.; van der Heden van Noort, Gerbrand J.; Geurink, Paul P.; Ovaa, Huib; Newman, Janet; Riboldi-Tunnicliffe, Alan; Czabotar, Peter E.; Mitchell, Jeffrey P.; Feltham, Rebecca; Lechtenberg, Bernhard C.; Lowes, Kym N.; Dewson, Grant; Pellegrini, Marc; Lessene, Guillaume; Komander, David
      EMBO Journal (2020), 39 (18), e106275CODEN: EMJODG; ISSN:0261-4189. (Wiley-VCH Verlag GmbH & Co. KGaA)
      The SARS-CoV-2 coronavirus encodes an essential papain-like protease domain as part of its non-structural protein (nsp)-3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin-like ISG15 protein modifications as well as, with lower activity, Lys48-linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin-binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clin. compds. against SARS2 PLpro identified no compds. that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non-covalent small mol. SARS PLpro inhibitors also target SARS2 PLpro, prevent self-processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS-CoV-2 infection model.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhs1KgsrbE&md5=3d6a13fc99f05c4fdd6666e8fa72bbd7
    46. 46
      Liu, G.; Lee, J.-H.; Parker, Z. M.; Acharya, D.; Chiang, J. J.; van Gent, M.; Riedl, W.; Davis-Gardner, M. E.; Wies, E.; Chiang, C.; Gack, M. U. ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity. Nature Microbiology 2021, 6, 467– 478,  DOI: 10.1038/s41564-021-00884-1
      46
      ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity
      Liu, GuanQun; Lee, Jung-Hyun; Parker, Zachary M.; Acharya, Dhiraj; Chiang, Jessica J.; van Gent, Michiel; Riedl, William; Davis-Gardner, Meredith E.; Wies, Effi; Chiang, Cindy; Gack, Michaela U.
      Nature Microbiology (2021), 6 (4), 467-478CODEN: NMAICH; ISSN:2058-5276. (Nature Research)
      Abstr.: Activation of the RIG-I-like receptors, retinoic-acid inducible gene I (RIG-I) and melanoma differentiation-assocd. protein 5 (MDA5), establishes an antiviral state by upregulating interferon (IFN)-stimulated genes (ISGs). Among these is ISG15, the mechanistic roles of which in innate immunity still remain enigmatic. In the present study, we report that ISG15 conjugation is essential for antiviral IFN responses mediated by the viral RNA sensor MDA5. ISGylation of the caspase activation and recruitment domains of MDA5 promotes its oligomerization and thereby triggers activation of innate immunity against a range of viruses, including coronaviruses, flaviviruses and picornaviruses. The ISG15-dependent activation of MDA5 is antagonized through direct de-ISGylation mediated by the papain-like protease of SARS-CoV-2, a recently emerged coronavirus that has caused the COVID-19 pandemic. Our work demonstrates a crucial role for ISG15 in the MDA5-mediated antiviral response, and also identifies a key immune evasion mechanism of SARS-CoV-2, which may be targeted for the development of new antivirals and vaccines to combat COVID-19.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXms1Onsbs%253D&md5=a74cf2f655bfac4c2e8516b0f9f0f4e0
    47. 47
      Jacobson, M. P.; Friesner, R. A.; Xiang, Z.; Honig, B. On the role of the crystal environment in determining protein side-chain conformations. J. Mol. Biol. 2002, 320 (3), 597– 608,  DOI: 10.1016/S0022-2836(02)00470-9
      47
      On the Role of the Crystal Environment in Determining Protein Side-chain Conformations
      Jacobson, Matthew P.; Friesner, Richard A.; Xiang, Zhexin; Honig, Barry
      Journal of Molecular Biology (2002), 320 (3), 597-608CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Science Ltd.)
      The role of crystal packing in detg. the obsd. conformations of amino acid side-chains in protein crystals is investigated by (1) anal. of a database of proteins that have been crystd. in different unit cells (space group or unit cell dimensions) and (2) theor. predictions of side-chain conformations with the crystal environment explicitly represented. Both of these approaches indicate that the crystal environment plays an important role in detg. the conformations of polar side-chains on the surfaces of proteins. Inclusion of the crystal environment permits a more sensitive measurement of the achievable accuracy of side-chain prediction programs, when validating against structures obtained by x-ray crystallog. Our side-chain prediction program uses an all-atom force field and a Generalized Born model of solvation and is thus capable of modeling simple packing effects (i.e. van der Waals interactions), electrostatic effects, and desolvation, which are all important mechanisms by which the crystal environment impacts obsd. side-chain conformations. Our results are also relevant to the understanding of changes in side-chain conformation that may result from ligand docking and protein-protein assocn., insofar as the results reveal how side-chain conformations change in response to their local environment.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XltVKmu70%253D&md5=006de6bd2d0f233ab32d6798dc1a3fbc
    48. 48
      Jacobson, M. P.; Pincus, D. L.; Rapp, C. S.; Day, T. J.; Honig, B.; Shaw, D. E.; Friesner, R. A. A hierarchical approach to all-atom protein loop prediction. Proteins: Struct., Funct., Genet. 2004, 55 (2), 351– 367,  DOI: 10.1002/prot.10613
      48
      A hierarchical approach to all-atom protein loop prediction
      Jacobson, Matthew P.; Pincus, David L.; Rapp, Chaya S.; Day, Tyler J. F.; Honig, Barry; Shaw, David E.; Friesner, Richard A.
      Proteins: Structure, Function, and Bioinformatics (2004), 55 (2), 351-367CODEN: PSFBAF ISSN:. (Wiley-Liss, Inc.)
      The application of all-atom force fields (and explicit or implicit solvent models) to protein homol.-modeling tasks such as side-chain and loop prediction remains challenging both because of the expense of the individual energy calcns. and because of the difficulty of sampling the rugged all-atom energy surface. Here the authors address this challenge for the problem of loop prediction through the development of numerous new algorithms, with an emphasis on multiscale and hierarchical techniques. As a first step in evaluating the performance of the authors' loop prediction algorithm, the authors have applied it to the problem of reconstructing loops in native structures; the authors also explicitly include crystal packing to provide a fair comparison with crystal structures. In brief, large nos. of loops are generated by using a dihedral angle-based buildup procedure followed by iterative cycles of clustering, side-chain optimization, and complete energy minimization of selected loop structures. The authors evaluate this method by the largest test set yet used for validation of a loop prediction method, with a total of 833 loops ranging from 4 to 12 residues in length. Av./median backbone root-mean-square deviations (RMSDs) to the native structures (superimposing the body of the protein, not the loop itself) are 0.42/0.24 Å for 5 residue loops, 1.00/0.44 Å for 8 residue loops, and 2.47/1.83 Å for 11 residue loops. Median RMSDs are substantially lower than the avs. because of a small no. of outliers; the causes of these failures are examd. in some detail, and many can be attributed to errors in assignment of protonation states of titratable residues, omission of ligands from the simulation, and, in a few cases, probable errors in the exptl. detd. structures. When these obvious problems in the data sets are filtered out, av. RMSDs to the native structures improve to 0.43 Å for 5 residue loops, 0.84 Å for 8 residue loops, and 1.63 Å for 11 residue loops. In the vast majority of cases, the method locates energy min. that are lower than or equal to that of the minimized native loop, thus indicating that sampling rarely limits prediction accuracy. The overall results are, to the authors' knowledge, the best reported to date, and the authors attribute this success to the combination of an accurate all-atom energy function, efficient methods for loop buildup and side-chain optimization, and, esp. for the longer loops, the hierarchical refinement protocol.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXjtFKhsrc%253D&md5=e0eff655eeefb30ea00ae041ea9099c8
    49. 49
      Donovan, S. F.; Pescatore, M. C. Method for measuring the logarithm of the octanol-water partition coefficient by using short octadecyl-poly(vinyl alcohol) high-performance liquid chromatography columns. J. Chromatogr A 2002, 952 (1–2), 47– 61,  DOI: 10.1016/S0021-9673(02)00064-X
      49
      Method for measuring the logarithm of the octanol-water partition coefficient by using short octadecyl-poly(vinyl alcohol) high-performance liquid chromatography columns
      Donovan, Stephen F.; Pescatore, Mark C.
      Journal of Chromatography A (2002), 952 (1-2), 47-61CODEN: JCRAEY; ISSN:0021-9673. (Elsevier Science B.V.)
      A simple, quick, versatile and inexpensive HPLC method to est. the logarithm of the octanol-water partition coeff. (log Pow) employing a methanol-water gradient and a short octadecyl-poly(vinyl alc.) (ODP) column is described. This method is different from published HPLC-based log Pow methods because it uses retention times from a rapid methanol-water gradient to directly generate log Pow ests., rather than from a series of isocratic mixts. extrapolated to 100% water. These HPLC log Pow values have good precision and correlate well with traditional shake-flask log Pow values. If necessary, the log Pow detn. (including replications) can easily be carried out using only a milligram of sample. By suppressing ionization of acids and bases by the use of a buffer in the aq. phase, the method can measure the log Pow of neutral org. mols. at any pH between 2 and 13. The method can be used with impure material and is rapid, 7 min per run and 4 min equilibration; it lends itself to and has been utilized for high-throughput hydrophobicity detns. (we have now carried out thousands of HPLC log Pow measurements by this method).
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XisV2gs7s%253D&md5=4c4aa02a23c1a496d3a9107d43329629
    50. 50
      Box, K.; Bevan, C.; Comer, J.; Hill, A.; Allen, R.; Reynolds, D. High-throughput measurement of pKa values in a mixed-buffer linear pH gradient system. Anal. Chem. 2003, 75 (4), 883– 892,  DOI: 10.1021/ac020329y
      50
      High-Throughput Measurement of pKa Values in a Mixed-Buffer Linear pH Gradient System
      Box, Karl; Bevan, Christopher; Comer, John; Hill, Alan; Allen, Ruth; Reynolds, Derek
      Analytical Chemistry (2003), 75 (4), 883-892CODEN: ANCHAM; ISSN:0003-2700. (American Chemical Society)
      A procedure is described for measuring pKa values in a short time, e.g., 4 min/assay. Samples, as 10 mM solns., are prepd. in DMSO in 96-well plates. A flowing pH gradient is produced by mixing two buffer solns. contg. mixts. of weak acids and bases that do not absorb significantly in the UV above 250 nm. The sample soln. is dild. with water and then injected directly into the flowing gradient, which then passes through a diode array spectrophotometer measuring in the UV wavelength range. The buffer has been formulated so that its acid-base titrn. curve is linear over a wide pH range, such that the pH of the gradient is a linear function of time. The soln. pH in the measurement flow cell is therefore proportional to the time elapsed since the start of gradient generation. The sample's pKa values are calcd. from the change in UV absorbance at multiple wavelengths as a function of pH. The pKa values of 71 drugs have been measured, and results compare well with values measured by pH-metric or traditional UV methods. Rules are suggested for the rapid inspection of data and the choice of method for the calcn. of pKa from the data.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXjt1yksg%253D%253D&md5=4050d66a7c92550c1efd346e76c392d9

  • Supporting Information

    Supporting Information

    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jmedchem.1c00566.

    • Molecular formula strings(CSV)

    • Expanded synthetic methods and spectra for E01–30, structures and reported activities for known SARS-CoV-2 main protease inhibitors, docking poses, and individual antiviral dose–response curves for select compounds

      (PDF)


    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.