51
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Yang KS, Leeuwon SZ, Xu S, Liu WR. Evolutionary and Structural Insights about Potential SARS-CoV-2 Evasion of Nirmatrelvir. J Med Chem 2022; 65:8686-8698. [PMID: 35731933 PMCID: PMC9236210 DOI: 10.1021/acs.jmedchem.2c00404] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 12/15/2022]
Abstract
The U.S. FDA approval of PAXLOVID, a combination therapy of nirmatrelvir and ritonavir has significantly boosted our morale in fighting the COVID-19 pandemic. Nirmatrelvir is an inhibitor of the main protease (MPro) of SARS-CoV-2. Since many SARS-CoV-2 variants that resist vaccines and antibodies have emerged, a concern of acquired viral resistance to nirmatrelvir naturally arises. Here, possible mutations in MPro to confer viral evasion of nirmatrelvir are analyzed and discussed from both evolutionary and structural standpoints. The analysis indicates that those mutations will likely reside in the whole aa45-51 helical region and residues including M165, L167, P168, R188, and Q189. Relevant mutations have also been observed in existing SARS-CoV-2 samples. Implications of this analysis to the fight against future drug-resistant viral variants and the development of broad-spectrum antivirals are discussed as well.
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Affiliation(s)
- Kai S. Yang
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 7743, USA
| | - Sunshine Z. Leeuwon
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 7743, USA
| | - Shiqing Xu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 7743, USA
| | - Wenshe Ray Liu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 7743, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA
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52
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Dampalla CS, Rathnayake AD, Kankanamalage ACG, Kim Y, Perera KD, Nguyen HN, Miller MJ, Madden TK, Picard HR, Thurman HA, Kashipathy MM, Liu L, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease. J Med Chem 2022; 65:7818-7832. [PMID: 35638577 PMCID: PMC9172056 DOI: 10.1021/acs.jmedchem.2c00224] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Indexed: 12/22/2022]
Abstract
The worldwide impact of the ongoing COVID-19 pandemic on public health has made imperative the discovery and development of direct-acting antivirals aimed at targeting viral and/or host targets. SARS-CoV-2 3C-like protease (3CLpro) has emerged as a validated target for the discovery of SARS-CoV-2 therapeutics because of the pivotal role it plays in viral replication. We describe herein the structure-guided design of highly potent inhibitors of SARS-CoV-2 3CLpro that incorporate in their structure novel spirocyclic design elements aimed at optimizing potency by accessing new chemical space. Inhibitors of both SARS-CoV-2 3CLpro and MERS-CoV 3CLpro that exhibit nM potency and high safety indices have been identified. The mechanism of action of the inhibitors and the structural determinants associated with binding were established using high-resolution cocrystal structures.
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Affiliation(s)
- Chamandi S. Dampalla
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Athri D. Rathnayake
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | | | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Harry Nhat Nguyen
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Matthew J. Miller
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Trent K. Madden
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Hunter R. Picard
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Hayden A. Thurman
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | | | - Lijun Liu
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, USA
| | | | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - William C. Groutas
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
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53
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Malla TR, Brewitz L, Muntean DG, Aslam H, Owen CD, Salah E, Tumber A, Lukacik P, Strain-Damerell C, Mikolajek H, Walsh MA, Schofield CJ. Penicillin Derivatives Inhibit the SARS-CoV-2 Main Protease by Reaction with Its Nucleophilic Cysteine. J Med Chem 2022; 65:7682-7696. [PMID: 35549342 PMCID: PMC9115881 DOI: 10.1021/acs.jmedchem.1c02214] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Indexed: 12/05/2022]
Abstract
The SARS-CoV-2 main protease (Mpro) is a medicinal chemistry target for COVID-19 treatment. Given the clinical efficacy of β-lactams as inhibitors of bacterial nucleophilic enzymes, they are of interest as inhibitors of viral nucleophilic serine and cysteine proteases. We describe the synthesis of penicillin derivatives which are potent Mpro inhibitors and investigate their mechanism of inhibition using mass spectrometric and crystallographic analyses. The results suggest that β-lactams have considerable potential as Mpro inhibitors via a mechanism involving reaction with the nucleophilic cysteine to form a stable acyl-enzyme complex as shown by crystallographic analysis. The results highlight the potential for inhibition of viral proteases employing nucleophilic catalysis by β-lactams and related acylating agents.
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Affiliation(s)
- Tika R. Malla
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Dorian-Gabriel Muntean
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Hiba Aslam
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - C. David Owen
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Petra Lukacik
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Claire Strain-Damerell
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Halina Mikolajek
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Martin A. Walsh
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
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Li Petri G, Di Martino S, De Rosa M. Peptidomimetics: An Overview of Recent Medicinal Chemistry Efforts toward the Discovery of Novel Small Molecule Inhibitors. J Med Chem 2022; 65:7438-7475. [PMID: 35604326 DOI: 10.1021/acs.jmedchem.2c00123] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The use of peptides as therapeutics has often been associated with several drawbacks such as poor absorption, low stability to proteolytic digestion, and fast clearance. Peptidomimetics are developed by modifications of native peptides with the aim of obtaining molecules that are more suitable for clinical development and, for this reason, are widely used as tools in medicinal chemistry programs. The effort to disclose innovative peptidomimetic therapies is recurrent and constantly evolving as demonstrated by the new lead compounds in clinical trials. Synthetic strategies for the development of peptidomimetics have also been implemented with time. This perspective highlights some of the most recent efforts for the design and synthesis of peptidomimetic agents together with their biological evaluation toward a panel of targets.
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Affiliation(s)
| | | | - Maria De Rosa
- Drug Discovery Unit, Ri.MED Foundation, Palermo 90133, Italy
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55
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Kumar V, Kar S, De P, Roy K, Leszczynski J. Identification of potential antivirals against 3CLpro enzyme for the treatment of SARS-CoV-2: A multi-step virtual screening study. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:357-386. [PMID: 35380087 DOI: 10.1080/1062936x.2022.2055140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak is posing a serious public health threat worldwide in the form of COVD-19. Herein, we have performed two-dimensional quantitative structure-activity relationship (2D-QSAR) and three-dimensional pharmacophore modelling analysis employing inhibitors of 3-chymotrypsin-like protease (3CLpro), the leading protease that is crucial for the replication of SARS-CoV-2. The investigation aims to identify the important structural features responsible for the enzyme inhibition and the search for novel 3CLpro enzyme inhibitors as effective therapeutics for treating SARS-CoV-2. Furthermore, we carried out molecular docking studies using the most and least active compounds in the dataset, aiming to validate the contributions of various features as appeared in the QSAR models. Later, the stringently validated 2D-QSAR model was used to estimate the 3CLpro inhibitory activity of compounds from five chemical databases. Compounds with the significant predicted activity were then subjected to pharmacophore-based virtual screening to screen the top-rated compounds, which were then further subjected to molecular docking analysis, absorption, distribution, metabolism, excretion - toxicity (ADMET) profiling, and molecular dynamics (MD) simulation. The multi-step virtual screening analyses suggested that compounds CASAntiV-865453-58-3, CASAntiV-865453-40-3, and CASAntiV-2043031-84-9 could be used as effective therapeutic agents for the treatment of SARS-CoV-2.
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Affiliation(s)
- V Kumar
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Kar
- Department of Chemistry, Physics and Atmospheric Sciences interdisciplinary Center for Nontoxicity, Jackson State University, Jackson, MS, USA
| | - P De
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - K Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - J Leszczynski
- Department of Chemistry, Physics and Atmospheric Sciences interdisciplinary Center for Nontoxicity, Jackson State University, Jackson, MS, USA
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56
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High predictive QSAR models for predicting the SARS coronavirus main protease inhibition activity of ketone-based covalent inhibitors. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [PMCID: PMC8547569 DOI: 10.1007/s13738-021-02426-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this research, a dataset including 29 ketone-based covalent inhibitors with SARS-CoV-1 3CLpro inhibition activity was used to develop high predictive QSAR models. Twenty-two molecules were put in train set and seven molecules in test set. By using stepwise MLR method for molecules in train set, four molecular descriptors including Mor26p, Hy, GATS7p and Mor04v were selected to build QSAR models. MLR and ANN methods were used to create QSAR models for predicting the activity of molecules in both train and test sets. Both QSAR models were validated by calculating several statistical parameters. R2 values for the test set of MLR and ANN models were 0.93 and 0.95, respectively, and RMSE values for their test sets were 0.24 and 0.17, respectively. Other calculated statistical parameters (especially \documentclass[12pt]{minimal}
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\begin{document}$$Q_{F3}^{2}$$\end{document}QF32 parameter) show that created ANN model has more predictive power with respect to developed MLR model (with four descriptor). Calculated leverages for all molecules show that predicted pIC50 (by both QSAR models) for all molecules is acceptable, and drawn residuals plots show that there is no systematic error in building both QSAR modes. Also, based on developed MLR model, used molecular descriptors were interpreted.
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57
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Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease. Nat Commun 2022; 13:2268. [PMID: 35477935 PMCID: PMC9046211 DOI: 10.1038/s41467-022-29915-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/07/2022] [Indexed: 11/08/2022] Open
Abstract
Emerging SARS-CoV-2 variants continue to threaten the effectiveness of COVID-19 vaccines, and small-molecule antivirals can provide an important therapeutic treatment option. The viral main protease (Mpro) is critical for virus replication and thus is considered an attractive drug target. We performed the design and characterization of three covalent hybrid inhibitors BBH-1, BBH-2 and NBH-2 created by splicing components of hepatitis C protease inhibitors boceprevir and narlaprevir, and known SARS-CoV-1 protease inhibitors. A joint X-ray/neutron structure of the Mpro/BBH-1 complex demonstrates that a Cys145 thiolate reaction with the inhibitor’s keto-warhead creates a negatively charged oxyanion. Protonation states of the ionizable residues in the Mpro active site adapt to the inhibitor, which appears to be an intrinsic property of Mpro. Structural comparisons of the hybrid inhibitors with PF-07321332 reveal unconventional F···O interactions of PF-07321332 with Mpro which may explain its more favorable enthalpy of binding. BBH-1, BBH-2 and NBH-2 exhibit comparable antiviral properties in vitro relative to PF-07321332, making them good candidates for further design of improved antivirals. Three covalent hybrid inhibitors of SARS-CoV-2 main protease (Mpro) have been designed and compared to Pfizer’s nirmatrelvir (PF-07321332), providing atomic and thermodynamic details of their binding to the enzyme, and antiviral potency.
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58
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Xu T, Xu M, Zhu W, Chen CZ, Zhang Q, Zheng W, Huang R. Efficient Identification of Anti-SARS-CoV-2 Compounds Using Chemical Structure- and Biological Activity-Based Modeling. J Med Chem 2022; 65:4590-4599. [PMID: 35275639 PMCID: PMC8936051 DOI: 10.1021/acs.jmedchem.1c01372] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Indexed: 12/12/2022]
Abstract
Identification of anti-SARS-CoV-2 compounds through traditional high-throughput screening (HTS) assays is limited by high costs and low hit rates. To address these challenges, we developed machine learning models to identify compounds acting via inhibition of the entry of SARS-CoV-2 into human host cells or the SARS-CoV-2 3-chymotrypsin-like (3CL) protease. The optimal classification models achieved good performance with area under the receiver operating characteristic curve (AUC-ROC) values of >0.78. Experimental validation showed that the best performing models increased the assay hit rate by 2.1-fold for viral entry inhibitors and 10.4-fold for 3CL protease inhibitors compared to those of the original drug repurposing screens. Twenty-two compounds showed potent (<5 μM) antiviral activities in a SARS-CoV-2 live virus assay. In conclusion, machine learning models can be developed and used as a complementary approach to HTS to expand compound screening capacities and improve the speed and efficiency of anti-SARS-CoV-2 drug discovery.
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Affiliation(s)
- Tuan Xu
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Miao Xu
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Wei Zhu
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Catherine Z Chen
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Qi Zhang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Wei Zheng
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Ruili Huang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
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59
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Yamane D, Onitsuka S, Re S, Isogai H, Hamada R, Hiramoto T, Kawanishi E, Mizuguchi K, Shindo N, Ojida A. Selective covalent targeting of SARS-CoV-2 main protease by enantiopure chlorofluoroacetamide. Chem Sci 2022; 13:3027-3034. [PMID: 35432850 PMCID: PMC8905997 DOI: 10.1039/d1sc06596c] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/15/2022] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has necessitated the development of antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main protease (Mpro) is a promising target for COVID-19 treatment. Here, we report an irreversible SARS-CoV-2 Mpro inhibitor possessing chlorofluoroacetamide (CFA) as a warhead for the covalent modification of Mpro. Ugi multicomponent reaction using chlorofluoroacetic acid enabled the rapid synthesis of dipeptidic CFA derivatives that identified 18 as a potent inhibitor of SARS-CoV-2 Mpro. Among the four stereoisomers, (R,R)-18 exhibited a markedly higher inhibitory activity against Mpro than the other isomers. Reaction kinetics and computational docking studies suggest that the R configuration of the CFA warhead is crucial for the rapid covalent inhibition of Mpro. Our findings highlight the prominent influence of the CFA chirality on the covalent modification of proteinous cysteines and provide the basis for improving the potency and selectivity of CFA-based covalent inhibitors.
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Affiliation(s)
- Daiki Yamane
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Satsuki Onitsuka
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Suyong Re
- Artificial Intelligence Center for Health and Biomedical Research, National Institute of Biomedical Innovation, Health and Nutrition 7-6-8 Saito-Asagi, Ibaraki Osaka 567-0085 Japan
| | - Hikaru Isogai
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Rui Hamada
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Tadanari Hiramoto
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Eiji Kawanishi
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research, National Institute of Biomedical Innovation, Health and Nutrition 7-6-8 Saito-Asagi, Ibaraki Osaka 567-0085 Japan
- Institute for Protein Research, Osaka University 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
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61
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Lu J, Chen SA, Khan MB, Brassard R, Arutyunova E, Lamer T, Vuong W, Fischer C, Young HS, Vederas JC, Lemieux MJ. Crystallization of Feline Coronavirus M pro With GC376 Reveals Mechanism of Inhibition. Front Chem 2022; 10:852210. [PMID: 35281564 PMCID: PMC8907848 DOI: 10.3389/fchem.2022.852210] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/01/2022] [Indexed: 12/28/2022] Open
Abstract
Coronaviruses infect a variety of hosts in the animal kingdom, and while each virus is taxonomically different, they all infect their host via the same mechanism. The coronavirus main protease (Mpro, also called 3CLpro), is an attractive target for drug development due to its essential role in mediating viral replication and transcription. An Mpro inhibitor, GC376, has been shown to treat feline infectious peritonitis (FIP), a fatal infection in cats caused by internal mutations in the feline enteric coronavirus (FECV). Recently, our lab demonstrated that the feline drug, GC373, and prodrug, GC376, are potent inhibitors of SARS-CoV-2 Mpro and solved the structures in complex with the drugs; however, no crystal structures of the FIP virus (FIPV) Mpro with the feline drugs have been published so far. Here, we present crystal structures of FIPV Mpro-GC373/GC376 complexes, revealing the inhibitors covalently bound to Cys144 in the active site, similar to SARS-CoV-2 Mpro. Additionally, GC376 has a higher affinity for FIPV Mpro with lower nanomolar Ki values compared to SARS-CoV and SARS-CoV-2 Mpro. We also show that improved derivatives of GC376 have higher potency for FIPV Mpro. Since GC373 and GC376 represent strong starting points for structure-guided drug design, determining the crystal structures of FIPV Mpro with these inhibitors are important steps in drug optimization and structure-based broad-spectrum antiviral drug discovery.
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Affiliation(s)
- Jimmy Lu
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Sizhu Amelia Chen
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | | | - Raelynn Brassard
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Tess Lamer
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Wayne Vuong
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Conrad Fischer
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Howard S. Young
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - M. Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
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62
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Stille JK, Tjutrins J, Wang G, Venegas FA, Hennecker C, Rueda AM, Sharon I, Blaine N, Miron CE, Pinus S, Labarre A, Plescia J, Burai Patrascu M, Zhang X, Wahba AS, Vlaho D, Huot MJ, Schmeing TM, Mittermaier AK, Moitessier N. Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL pro covalent inhibitors. Eur J Med Chem 2022; 229:114046. [PMID: 34995923 PMCID: PMC8665847 DOI: 10.1016/j.ejmech.2021.114046] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/17/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022]
Abstract
Severe diseases such as the ongoing COVID-19 pandemic, as well as the previous SARS and MERS outbreaks, are the result of coronavirus infections and have demonstrated the urgent need for antiviral drugs to combat these deadly viruses. Due to its essential role in viral replication and function, 3CLpro (main coronaviruses cysteine-protease) has been identified as a promising target for the development of antiviral drugs. Previously reported SARS-CoV 3CLpro non-covalent inhibitors were used as a starting point for the development of covalent inhibitors of SARS-CoV-2 3CLpro. We report herein our efforts in the design and synthesis of submicromolar covalent inhibitors when the enzymatic activity of the viral protease was used as a screening platform.
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Affiliation(s)
- Julia K Stille
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Jevgenijs Tjutrins
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Guanyu Wang
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Felipe A Venegas
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Christopher Hennecker
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Andrés M Rueda
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Itai Sharon
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler Montreal, QC, Canada, H3G 0B1
| | - Nicole Blaine
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Caitlin E Miron
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Sharon Pinus
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Anne Labarre
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Jessica Plescia
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Mihai Burai Patrascu
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Xiaocong Zhang
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Alexander S Wahba
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Danielle Vlaho
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - Mitchell J Huot
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler Montreal, QC, Canada, H3G 0B1
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8.
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8.
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63
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Kittakoop P, Darshana D, Sangsuwan R, Mahidol C. Alkaloids and Alkaloid-Like Compounds are Potential Scaffolds of Antiviral Agents against SARS-CoV-2 (COVID-19) Virus. HETEROCYCLES 2022. [DOI: 10.3987/rev-22-sr(r)3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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64
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Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Pujadas G, Garcia-Vallvé S. A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet? Int J Mol Sci 2021; 23:259. [PMID: 35008685 PMCID: PMC8745775 DOI: 10.3390/ijms23010259] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 01/01/2023] Open
Abstract
In this review, we collected 1765 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) M-pro inhibitors from the bibliography and other sources, such as the COVID Moonshot project and the ChEMBL database. This set of inhibitors includes only those compounds whose inhibitory capacity, mainly expressed as the half-maximal inhibitory concentration (IC50) value, against M-pro from SARS-CoV-2 has been determined. Several covalent warheads are used to treat covalent and non-covalent inhibitors separately. Chemical space, the variation of the IC50 inhibitory activity when measured by different methods or laboratories, and the influence of 1,4-dithiothreitol (DTT) are discussed. When available, we have collected the values of inhibition of viral replication measured with a cellular antiviral assay and expressed as half maximal effective concentration (EC50) values, and their possible relationship to inhibitory potency against M-pro is analyzed. Finally, the most potent covalent and non-covalent inhibitors that simultaneously inhibit the SARS-CoV-2 M-pro and the virus replication in vitro are discussed.
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Affiliation(s)
| | | | | | | | - Gerard Pujadas
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
| | - Santiago Garcia-Vallvé
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
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65
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Kneller DW, Li H, Galanie S, Phillips G, Labbé A, Weiss KL, Zhang Q, Arnould MA, Clyde A, Ma H, Ramanathan A, Jonsson CB, Head MS, Coates L, Louis JM, Bonnesen PV, Kovalevsky A. Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease. J Med Chem 2021; 64:17366-17383. [PMID: 34705466 PMCID: PMC8565456 DOI: 10.1021/acs.jmedchem.1c01475] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 02/08/2023]
Abstract
Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (Mpro) is an established drug target for the design of protease inhibitors. We performed a structure-activity relationship (SAR) study of noncovalent compounds that bind in the enzyme's substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of Mpro complexed with Mcule-5948770040 (compound 1), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1. In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on Mpro inhibition, showing that (1) maintaining correct geometry of an inhibitor's P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.
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Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Hui Li
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Audrey Labbé
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Mark A. Arnould
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Austin Clyde
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Computer Science, University of Chicago, Chicago, IL 60615, USA
| | - Heng Ma
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Arvind Ramanathan
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60615
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Martha S. Head
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - Peter V. Bonnesen
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
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66
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Costanzi E, Kuzikov M, Esposito F, Albani S, Demitri N, Giabbai B, Camasta M, Tramontano E, Rossetti G, Zaliani A, Storici P. Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L. Int J Mol Sci 2021; 22:11779. [PMID: 34769210 PMCID: PMC8583849 DOI: 10.3390/ijms222111779] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022] Open
Abstract
After almost two years from its first evidence, the COVID-19 pandemic continues to afflict people worldwide, highlighting the need for multiple antiviral strategies. SARS-CoV-2 main protease (Mpro/3CLpro) is a recognized promising target for the development of effective drugs. Because single target inhibition might not be sufficient to block SARS-CoV-2 infection and replication, multi enzymatic-based therapies may provide a better strategy. Here we present a structural and biochemical characterization of the binding mode of MG-132 to both the main protease of SARS-CoV-2, and to the human Cathepsin-L, suggesting thus an interesting scaffold for the development of double-inhibitors. X-ray diffraction data show that MG-132 well fits into the Mpro active site, forming a covalent bond with Cys145 independently from reducing agents and crystallization conditions. Docking of MG-132 into Cathepsin-L well-matches with a covalent binding to the catalytic cysteine. Accordingly, MG-132 inhibits Cathepsin-L with nanomolar potency and reversibly inhibits Mpro with micromolar potency, but with a prolonged residency time. We compared the apo and MG-132-inhibited structures of Mpro solved in different space groups and we identified a new apo structure that features several similarities with the inhibited ones, offering interesting perspectives for future drug design and in silico efforts.
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Affiliation(s)
- Elisa Costanzi
- Elettra—Sincrotrone Trieste, 34149 Trieste, Italy; (E.C.); (N.D.); (B.G.)
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 22525 Hamburg, Germany; (M.K.); (A.Z.)
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, 28759 Bremen, Germany
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (F.E.); (M.C.); (E.T.)
| | - Simone Albani
- Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5) “Computational Biomedicine”, Forschungszentrum Jülich, 52425 Jülich, Germany; (S.A.); (G.R.)
- Department of Biology, Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Nicola Demitri
- Elettra—Sincrotrone Trieste, 34149 Trieste, Italy; (E.C.); (N.D.); (B.G.)
| | - Barbara Giabbai
- Elettra—Sincrotrone Trieste, 34149 Trieste, Italy; (E.C.); (N.D.); (B.G.)
| | - Marianna Camasta
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (F.E.); (M.C.); (E.T.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (F.E.); (M.C.); (E.T.)
| | - Giulia Rossetti
- Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5) “Computational Biomedicine”, Forschungszentrum Jülich, 52425 Jülich, Germany; (S.A.); (G.R.)
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, 52425 Jülich, Germany
- Department of Neurology, Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 22525 Hamburg, Germany; (M.K.); (A.Z.)
| | - Paola Storici
- Elettra—Sincrotrone Trieste, 34149 Trieste, Italy; (E.C.); (N.D.); (B.G.)
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67
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Bai B, Arutyunova E, Khan MB, Lu J, Joyce MA, Saffran HA, Shields JA, Kandadai AS, Belovodskiy A, Hena M, Vuong W, Lamer T, Young HS, Vederas JC, Tyrrell DL, Lemieux MJ, Nieman JA. Peptidomimetic nitrile warheads as SARS-CoV-2 3CL protease inhibitors. RSC Med Chem 2021; 12:1722-1730. [PMID: 34778773 PMCID: PMC8529539 DOI: 10.1039/d1md00247c] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Tragically, the death toll from the COVID-19 pandemic continues to rise, and with variants being observed around the globe new therapeutics, particularly direct-acting antivirals that are easily administered, are desperately needed. Studies targeting the SARS-CoV-2 3CL protease, which is critical for viral replication, with different peptidomimetics and warheads is an active area of research for development of potential drugs. To date, however, only a few publications have evaluated the nitrile warhead as a viral 3CL protease inhibitor, with only modest activity reported. This article describes our investigation of P3 4-methoxyindole peptidomimetic analogs with select P1 and P2 groups with a nitrile warhead that are potent inhibitors of SARS-CoV-2 3CL protease and demonstrate in vitro SARS-CoV-2 antiviral activity. A selectivity for SARS-CoV-2 3CL protease over human cathepsins B, S and L was also observed with the nitrile warhead, which was superior to that with the aldehyde warhead. A co-crystal structure with SARS-CoV-2 3CL protease and a reversibility study indicate that a reversible, thioimidate adduct is formed when the catalytic sulfur forms a covalent bond with the carbon of the nitrile. This effort also identified efflux as a property limiting antiviral activity of these compounds, and together with the positive attributes described these results provide insight for further drug development of novel nitrile peptidomimetics targeting SARS-CoV-2 3CL protease.
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Affiliation(s)
- Bing Bai
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
| | - Jimmy Lu
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Michael A Joyce
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Holly A Saffran
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Justin A Shields
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Appan Srinivas Kandadai
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Alexandr Belovodskiy
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Mostofa Hena
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Wayne Vuong
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Tess Lamer
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Howard S Young
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - D Lorne Tyrrell
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - James A Nieman
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
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68
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Wang Z, Yang L, Zhao XE. Co-crystallization and structure determination: An effective direction for anti-SARS-CoV-2 drug discovery. Comput Struct Biotechnol J 2021; 19:4684-4701. [PMID: 34426762 PMCID: PMC8373586 DOI: 10.1016/j.csbj.2021.08.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/29/2021] [Accepted: 08/17/2021] [Indexed: 01/18/2023] Open
Abstract
Safer and more-effective drugs are urgently needed to counter infections with the highly pathogenic SARS-CoV-2, cause of the COVID-19 pandemic. Identification of efficient inhibitors to treat and prevent SARS-CoV-2 infection is a predominant focus. Encouragingly, using X-ray crystal structures of therapeutically relevant drug targets (PLpro, Mpro, RdRp, and S glycoprotein) offers a valuable direction for anti-SARS-CoV-2 drug discovery and lead optimization through direct visualization of interactions. Computational analyses based primarily on MMPBSA calculations have also been proposed for assessing the binding stability of biomolecular structures involving the ligand and receptor. In this study, we focused on state-of-the-art X-ray co-crystal structures of the abovementioned targets complexed with newly identified small-molecule inhibitors (natural products, FDA-approved drugs, candidate drugs, and their analogues) with the assistance of computational analyses to support the precision design and screening of anti-SARS-CoV-2 drugs.
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Key Words
- 3CLpro, 3C-Like protease
- ACE2, angiotensin-converting enzyme 2
- COVID-19, coronavirus disease 2019
- Candidate drugs
- Co-crystal structures
- DyKAT, dynamic kinetic asymmetric transformation
- EBOV, Ebola virus
- EC50, half maximal effective concentration
- EMD, Electron Microscopy Data
- FDA, U.S. Food and Drug Administration
- FDA-approved drugs
- HCoV-229E, human coronavirus 229E
- HPLC, high-performance liquid chromatography
- IC50, half maximal inhibitory concentration
- MD, molecular dynamics
- MERS-CoV, Middle East respiratory syndrome coronavirus
- MMPBSA, molecular mechanics Poisson-Boltzmann surface area
- MTase, methyltransferase
- Mpro, main protease
- Natural products
- Nsp, nonstructural protein
- PDB, Protein Data Bank
- PLpro, papain-like protease
- RTP, ribonucleoside triphosphate
- RdRp, RNA-dependent RNA polymerase
- SAM, S-adenosylmethionine
- SARS-CoV, severe acute respiratory syndrome coronavirus
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SI, selectivity index
- Ugi-4CR, Ugi four-component reaction
- cryo-EM, cryo-electron microscopy
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Affiliation(s)
- Zhonglei Wang
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
| | - Liyan Yang
- School of Physics and Physical Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Xian-En Zhao
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
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