1
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Oneto A, Hamwi GA, Schäkel L, Krüger N, Sylvester K, Petry M, Shamleh RA, Pillaiyar T, Claff T, Schiedel AC, Sträter N, Gütschow M, Müller CE. Nonpeptidic Irreversible Inhibitors of SARS-CoV-2 Main Protease with Potent Antiviral Activity. J Med Chem 2024. [PMID: 39146284 DOI: 10.1021/acs.jmedchem.4c00535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
SARS-CoV-2 infections pose a high risk for vulnerable patients. In this study, we designed benzoic acid halopyridyl esters bearing a variety of substituents as irreversible inhibitors of the main viral protease (Mpro). Altogether, 55 benzoyl chloro/bromo-pyridyl esters were synthesized, with broad variation of the substitution pattern on the benzoyl moiety. A workflow was employed for multiparametric optimization, including Mpro inhibition assays of SARS-CoV-2 and related pathogenic coronaviruses, the duration of enzyme inhibition, the compounds' stability versus glutathione, cytotoxicity, and antiviral activity. Several compounds showed IC50 values in the low nanomolar range, kinact/Ki values of >100,000 M-1 s-1 and high antiviral activity. High-resolution X-ray cocrystal structures indicated an important role of ortho-fluorobenzoyl substitution, forming a water network that stabilizes the inhibitor-bound enzyme. The most potent antiviral compound was the p-ethoxy-o-fluorobenzoyl chloropyridyl ester (PSB-21110, 29b, MW 296 g/mol; EC50 2.68 nM), which may serve as a lead structure for broad-spectrum anticoronaviral therapeutics.
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Affiliation(s)
- Angelo Oneto
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Ghazl Al Hamwi
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Laura Schäkel
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Nadine Krüger
- Platform Infection Models, German Primate Center, Leibniz Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
| | - Katharina Sylvester
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Marvin Petry
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Rasha Abu Shamleh
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Thanigaimalai Pillaiyar
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Tobias Claff
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Anke C Schiedel
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Norbert Sträter
- Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, Leipzig 04103, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany
- PharmaCenter Bonn, University of Bonn, Brühler Straße 7, Bonn D-53121, Germany
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2
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Ciaglia T, Vestuto V, Di Sarno V, Musella S, Smaldone G, Di Matteo F, Napolitano V, Miranda MR, Pepe G, Basilicata MG, Novi S, Capolupo I, Bifulco G, Campiglia P, Gomez-Monterrey I, Snoeck R, Andrei G, Manfra M, Ostacolo C, Lauro G, Bertamino A. Peptidomimetics as potent dual SARS-CoV-2 cathepsin-L and main protease inhibitors: In silico design, synthesis and pharmacological characterization. Eur J Med Chem 2024; 266:116128. [PMID: 38232463 DOI: 10.1016/j.ejmech.2024.116128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024]
Abstract
In this paper we present the design, synthesis, and biological evaluation of a new series of peptidomimetics acting as potent anti-SARS-CoV-2 agents. Starting from our previously described Main Protease (MPro) and Papain Like Protease (PLPro) dual inhibitor, CV11, here we disclose its high inhibitory activity against cathepsin L (CTSL) (IC50 = 19.80 ± 4.44 nM), an emerging target in SARS-CoV-2 infection machinery. An in silico design, inspired by the structure of CV11, led to the development of a library of peptidomimetics showing interesting activities against CTSL and Mpro, allowing us to trace the chemical requirements for the binding to both enzymes. The screening in Vero cells infected with 5 different SARS-CoV-2 variants of concerns, highlighted sub-micromolar activities for most of the synthesized compounds (13, 15, 16, 17 and 31) in agreement with the enzymatic inhibition assays results. The compounds showed lack of activity against several different RNA viruses except for the 229E and OC43 human coronavirus strains, also characterized by a cathepsin-L dependent release into the host cells. The most promising derivatives were also evaluated for their chemical and metabolic in-vitro stability, with derivatives 15 and 17 showing a suitable profile for further preclinical characterization.
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Affiliation(s)
- Tania Ciaglia
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Vincenzo Vestuto
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Veronica Di Sarno
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Simona Musella
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Gerardina Smaldone
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Francesca Di Matteo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Valeria Napolitano
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Maria Rosaria Miranda
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Giacomo Pepe
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | | | - Sara Novi
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Ilaria Capolupo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy; European Biomedical Research Institute (EBRIS), Via S. De Renzi 50, 84125, Salerno, Italy
| | - Isabel Gomez-Monterrey
- Department of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131, Naples, Italy
| | - Robert Snoeck
- Rega Institute for Medical Research, Department of Microbiology, Immunology, and Transplantation, KU Leuven, BE-3000, Leuven, Belgium
| | - Graciela Andrei
- Rega Institute for Medical Research, Department of Microbiology, Immunology, and Transplantation, KU Leuven, BE-3000, Leuven, Belgium
| | - Michele Manfra
- Department of Science, University of Basilicata, Via Dell'Ateneo Lucano 10, 85100, Potenza, Italy
| | - Carmine Ostacolo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy.
| | - Alessia Bertamino
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy.
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3
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Albani S, Costanzi E, Hoang GL, Kuzikov M, Frings M, Ansari N, Demitri N, Nguyen TT, Rizzi V, Schulz JB, Bolm C, Zaliani A, Carloni P, Storici P, Rossetti G. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. J Chem Inf Model 2024; 64:892-904. [PMID: 38051605 PMCID: PMC10865365 DOI: 10.1021/acs.jcim.3c01497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
Many homodimeric enzymes tune their functions by exploiting either negative or positive cooperativity between subunits. In the SARS-CoV-2 Main protease (Mpro) homodimer, the latter has been suggested by symmetry in most of the 500 reported protease/ligand complex structures solved by macromolecular crystallography (MX). Here we apply the latter to both covalent and noncovalent ligands in complex with Mpro. Strikingly, our experiments show that the occupation of both active sites of the dimer originates from an excess of ligands. Indeed, cocrystals obtained using a 1:1 ligand/protomer stoichiometry lead to single occupation only. The empty binding site exhibits a catalytically inactive geometry in solution, as suggested by molecular dynamics simulations. Thus, Mpro operates through negative cooperativity with the asymmetric activity of the catalytic sites. This allows it to function with a wide range of substrate concentrations, making it resistant to saturation and potentially difficult to shut down, all properties advantageous for the virus' adaptability and resistance.
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Affiliation(s)
- Simone Albani
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- Faculty
of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen 52062, Germany
| | - Elisa Costanzi
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Gia Linh Hoang
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
| | - Maria Kuzikov
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
- Constructor University, School of Science, Campus Ring 1, Bremen 28759, Germany
| | - Marcus Frings
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Narjes Ansari
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Nicola Demitri
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Toan T. Nguyen
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Valerio Rizzi
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1206 Genève, Switzerland
| | - Jörg B. Schulz
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
| | - Carsten Bolm
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg 22525, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
| | - Paolo Carloni
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Paola Storici
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Giulia Rossetti
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich, Jülich 52425, Germany
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4
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van Huizen M, Vendrell XM, de Gruyter HLM, Boomaars-van der Zanden AL, van der Meer Y, Snijder EJ, Kikkert M, Myeni SK. The Main Protease of Middle East Respiratory Syndrome Coronavirus Induces Cleavage of Mitochondrial Antiviral Signaling Protein to Antagonize the Innate Immune Response. Viruses 2024; 16:256. [PMID: 38400032 PMCID: PMC10892576 DOI: 10.3390/v16020256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial antiviral signaling protein (MAVS) is a crucial signaling adaptor in the sensing of positive-sense RNA viruses and the subsequent induction of the innate immune response. Coronaviruses have evolved multiple mechanisms to evade this response, amongst others, through their main protease (Mpro), which is responsible for the proteolytic cleavage of the largest part of the viral replicase polyproteins pp1a and pp1ab. Additionally, it can cleave cellular substrates, such as innate immune signaling factors, to dampen the immune response. Here, we show that MAVS is cleaved in cells infected with Middle East respiratory syndrome coronavirus (MERS-CoV), but not in cells infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This cleavage was independent of cellular negative feedback mechanisms that regulate MAVS activation. Furthermore, MERS-CoV Mpro expression induced MAVS cleavage upon overexpression and suppressed the activation of the interferon-β (IFN-β) and nuclear factor-κB (NF-κB) response. We conclude that we have uncovered a novel mechanism by which MERS-CoV downregulates the innate immune response, which is not observed among other highly pathogenic coronaviruses.
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Affiliation(s)
| | | | | | | | | | | | | | - Sebenzile K. Myeni
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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Haghir Ebrahim Abadi MH, Ghasemlou A, Bayani F, Sefidbakht Y, Vosough M, Mozaffari-Jovin S, Uversky VN. AI-driven covalent drug design strategies targeting main protease (m pro) against SARS-CoV-2: structural insights and molecular mechanisms. J Biomol Struct Dyn 2024:1-29. [PMID: 38287509 DOI: 10.1080/07391102.2024.2308769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024]
Abstract
The emergence of new SARS-CoV-2 variants has raised concerns about the effectiveness of COVID-19 vaccines. To address this challenge, small-molecule antivirals have been proposed as a crucial therapeutic option. Among potential targets for anti-COVID-19 therapy, the main protease (Mpro) of SARS-CoV-2 is important due to its essential role in the virus's life cycle and high conservation. The substrate-binding region of the core proteases of various coronaviruses, including SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), could be used for the generation of new protease inhibitors. Various drug discovery methods have employed a diverse range of strategies, targeting both monomeric and dimeric forms, including drug repurposing, integrating virtual screening with high-throughput screening (HTS), and structure-based drug design, each demonstrating varying levels of efficiency. Covalent inhibitors, such as Nirmatrelvir and MG-101, showcase robust and high-affinity binding to Mpro, exhibiting stable interactions confirmed by molecular docking studies. Development of effective antiviral drugs is imperative to address potential pandemic situations. This review explores recent advances in the search for Mpro inhibitors and the application of artificial intelligence (AI) in drug design. AI leverages vast datasets and advanced algorithms to streamline the design and identification of promising Mpro inhibitors. AI-driven drug discovery methods, including molecular docking, predictive modeling, and structure-based drug repurposing, are at the forefront of identifying potential candidates for effective antiviral therapy. In a time when COVID-19 potentially threat global health, the quest for potent antiviral solutions targeting Mpro could be critical for inhibiting the virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Fatemeh Bayani
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sina Mozaffari-Jovin
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
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6
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Tian L, Qiang T, Yang X, Gao Y, Zhai X, Kang K, Du C, Lu Q, Gao H, Zhang D, Xie X, Liang C. Development of de-novo coronavirus 3-chymotrypsin-like protease (3CL pro) inhibitors since COVID-19 outbreak: A strategy to tackle challenges of persistent virus infection. Eur J Med Chem 2024; 264:115979. [PMID: 38048696 DOI: 10.1016/j.ejmech.2023.115979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/30/2023] [Accepted: 11/18/2023] [Indexed: 12/06/2023]
Abstract
Although no longer a public health emergency of international concern, COVID-19 remains a persistent and critical health concern. The development of effective antiviral drugs could serve as the ultimate piece of the puzzle to curbing this global crisis. 3-chymotrypsin-like protease (3CLpro), with its substrate specificity mirroring that of the main picornavirus 3C protease and conserved across various coronaviruses, emerges as an ideal candidate for broad-spectrum antiviral drug development. Moreover, it holds the potential as a reliable contingency option to combat emerging SARS-CoV-2 variants. In this light, the approved drugs, promising candidates, and de-novo small molecule therapeutics targeting 3CLpro since the COVID-19 outbreak in 2020 are discussed. Emphasizing the significance of diverse structural characteristics in inhibitors, be they peptidomimetic or nonpeptidic, with a shared mission to minimize the risk of cross-resistance. Moreover, the authors propose an innovative optimization strategy for 3CLpro reversible covalent PROTACs, optimizing pharmacodynamics and pharmacokinetics to better prepare for potential future viral outbreaks.
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Affiliation(s)
- Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
| | - Xiuding Yang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Yue Gao
- College of Pharmacy, Jinan University, Guangzhou, 511436, PR China
| | - Xiaopei Zhai
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Xi'an, 710032, PR China
| | - Kairui Kang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Cong Du
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Qi Lu
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Hong Gao
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Shaanxi Pioneer Biotech Co., Ltd., Xi'an, 710021, PR China
| | - Dezhu Zhang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Xiaolin Xie
- Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Chengyuan Liang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
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7
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Purohit P, Panda M, Muya JT, Bandyopadhyay P, Meher BR. Theoretical insights into the binding interaction of Nirmatrelvir with SARS-CoV-2 Mpro mutants (C145A and C145S): MD simulations and binding free-energy calculation to understand drug resistance. J Biomol Struct Dyn 2023:1-20. [PMID: 37599474 DOI: 10.1080/07391102.2023.2248519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
Mpro, the main protease and a crucial enzyme in SARS-CoV-2 is the most fascinating molecular target for pharmacological treatment and is also liable for viral protein maturation. For antiviral therapy, no drugs have been approved clinically to date. Targeting the Mpro with a compound having inhibitory properties against it can hinder viral replication. The therapeutic potential of the antiviral compound Nirmatrelvir (NMV) against SARS-CoV-2 Mpro was investigated using a systematic approach of molecular docking, MD simulations, and binding free energy calculation based on the MM-GBSA method. NMV, a covalent inhibitor with a recently revealed chemical structure, is a promising oral antiviral clinical candidate with significant in vitro anti-SARS-CoV-2 action in third-phase clinical trials. To explore the therapeutic ability and possible drug resistance, the Mpro system was studied for WT and two of its primary mutants (C145A & C145S). The protein-ligand (Mpro/NMV) complexes were further examined through long MD simulations to check the possible drug resistance in the mutants. To understand the binding affinity, the MM-GBSA method was applied to the Mpro/NMV complexes. Moreover, PCA analysis confirms the detachment of the linker region from the major domains in C145S and C145A mutants allowing for conformational alterations in the active-site region. Based on the predicted biological activities and binding affinities of NMV to WT and mutant (C145A & C145S) Mpro, it can be stipulated that NMV may have conventional potency to act as an anti-viral agent against WT Mpro, while the catalytic-dyad mutations may show substantial mutation-induced drug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Jules Tshishimbi Muya
- Faculte of Science, Research Centre for Theoretical Chemistry and Physics in Central Africa, University of Kinshasa, Kinshasa, Congo
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
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