1
|
Zhang K, Eldin P, Ciesla JH, Briant L, Lentini JM, Ramos J, Cobb J, Munger J, Fu D. Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease. eLife 2024; 12:RP90316. [PMID: 38814682 PMCID: PMC11139479 DOI: 10.7554/elife.90316] [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] [Indexed: 05/31/2024] Open
Abstract
Nonstructural protein 5 (Nsp5) is the main protease of SARS-CoV-2 that cleaves viral polyproteins into individual polypeptides necessary for viral replication. Here, we show that Nsp5 binds and cleaves human tRNA methyltransferase 1 (TRMT1), a host enzyme required for a prevalent post-transcriptional modification in tRNAs. Human cells infected with SARS-CoV-2 exhibit a decrease in TRMT1 protein levels and TRMT1-catalyzed tRNA modifications, consistent with TRMT1 cleavage and inactivation by Nsp5. Nsp5 cleaves TRMT1 at a specific position that matches the consensus sequence of SARS-CoV-2 polyprotein cleavage sites, and a single mutation within the sequence inhibits Nsp5-dependent proteolysis of TRMT1. The TRMT1 cleavage fragments exhibit altered RNA binding activity and are unable to rescue tRNA modification in TRMT1-deficient human cells. Compared to wild-type human cells, TRMT1-deficient human cells infected with SARS-CoV-2 exhibit reduced levels of intracellular viral RNA. These findings provide evidence that Nsp5-dependent cleavage of TRMT1 and perturbation of tRNA modification patterns contribute to the cellular pathogenesis of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Kejia Zhang
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| | - Patrick Eldin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de MontpellierMontpellierFrance
| | - Jessica H Ciesla
- Department of Biochemistry and Biophysics, University of Rochester Medical CenterRochesterUnited States
| | - Laurence Briant
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de MontpellierMontpellierFrance
| | - Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| | - Jillian Ramos
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| | - Justin Cobb
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester Medical CenterRochesterUnited States
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| |
Collapse
|
2
|
Le UNP, Chang YJ, Lu CH, Chen Y, Su WC, Chao ST, Baltina LA, Petrova SF, Li SR, Hung MC, Lai MMC, Baltina LA, Lin CW. Glycyrrhizic acid conjugates with amino acid methyl esters target the main protease, exhibiting antiviral activity against wild-type and nirmatrelvir-resistant SARS-CoV-2 variants. Antiviral Res 2024:105920. [PMID: 38821317 DOI: 10.1016/j.antiviral.2024.105920] [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: 04/02/2024] [Revised: 05/10/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
COVID-19 pandemic is predominantly caused by SARS-CoV-2, with its main protease, Mpro, playing a pivotal role in viral replication and serving as a potential target for inhibiting different variants. In this study, potent Mpro inhibitors were identified from glycyrrhizic acid (GL) derivatives with amino acid methyl/ethyl esters. Out of the 17 derivatives semisynthesized, Compounds 2, 6, 9, and 15, with methionine methyl esters, D-tyrosine methyl esters, glutamic acid methyl esters, and methionines in the carbohydrate moiety, respectively, significantly inhibited wild-type SARS-CoV-2 Mpro-mediated proteolysis, with IC50 values ranging from 0.06 μM to 0.84 μM. They also demonstrated efficacy in inhibiting trans-cleavage by mutant Mpro variants (Mpro_P132H, Mpro_E166V, Mpro_P168A, Mpro_Q189I), with IC50 values ranging from 0.05 to 0.92 μM, surpassing nirmatrelvir (IC50: 1.17∼152.9 μM). Molecular modeling revealed stronger interactions with Valine166 in the structural complex of Mpro_E166V with the compounds compared to nirmatrelvir. Moreover, these compounds efficiently inhibited the post-entry viral processes of wild-type SARS-CoV-2 single-round infectious particles (SRIPs), mitigating viral cytopathic effects and reducing replicon-driven GFP reporter signals, as well as in vitro infectivity of wild-type, Mpro_E166V, and Mpro_Q189I SRIPs, with EC50 values ranging from 0.02 to 0.53 μM. However, nirmatrelvir showed a significant decrease in inhibiting the replication of mutant SARS-CoV-2 SRIPs carrying Mpro_E166V (EC50: > 20 μM) and Mpro_Q189I (EC50: 13.2 μM) compared to wild-type SRIPs (EC50: 0.06 μM). Overall, this study identifies four GL derivatives as promising lead compounds for developing treatments against various SARS-CoV-2 strains, including Omicron, and nirmatrelvir-resistant variants.
Collapse
Affiliation(s)
- Uyen Nguyen Phuong Le
- Graduate Institute of Biological Science and Technology, China Medical University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Yu-Jen Chang
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung, Taiwan
| | - Chih-Hao Lu
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung, Taiwan; Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan; Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yeh Chen
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Wen-Chi Su
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Shao-Ting Chao
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Lia A Baltina
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences
| | - Svetlana F Petrova
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences
| | - Sin-Rong Li
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 404327, Taiwan
| | - Mien-Chie Hung
- Research Center for Cancer Biology, China Medical University, Taichung 404327, Taiwan; Center for Molecular Medicine, China Medical University Hospital, Taichung 404327, Taiwan
| | - Michael M C Lai
- Institute of Molecular Biology, Academia Sinica, Taipei 115201, Taiwan
| | - Lidia A Baltina
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences.
| | - Cheng-Wen Lin
- Graduate Institute of Biological Science and Technology, China Medical University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan; The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan.
| |
Collapse
|
3
|
Evans D, Sheraz S, Lau A. SARS-CoV-2 3CLPro Dihedral Angles Reveal Allosteric Signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595309. [PMID: 38826232 PMCID: PMC11142162 DOI: 10.1101/2024.05.22.595309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
In allosteric proteins, identifying the pathways that signals take from allosteric ligand-binding sites to enzyme active sites or binding pockets and interfaces remains challenging. This avenue of research is motivated by the goals of understanding particular macromolecular systems of interest and creating general methods for their study. An especially important protein that is the subject of many investigations in allostery is the SARS-CoV-2 main protease (Mpro), which is necessary for coronaviral replication. It is both an attractive drug target and, due to intense interest in it for the development of pharmaceutical compounds, a gauge of the state-of-the-art approaches in studying protein inhibition. Here we develop a computational method for characterizing protein allostery and use it to study Mpro. We propose a role of the protein's C-terminal tail in allosteric modulation and warn of unintuitive traps that can plague studies of the role of protein dihedrals angles in transmitting allosteric signals.
Collapse
|
4
|
Breidenbach J, Voget R, Si Y, Hingst A, Claff T, Sylvester K, Wolf V, Krasniqi V, Useini A, Sträter N, Ogura Y, Kawaguchi A, Müller CE, Gütschow M. Macrocyclic Azapeptide Nitriles: Structure-Based Discovery of Potent SARS-CoV-2 Main Protease Inhibitors as Antiviral Drugs. J Med Chem 2024. [PMID: 38753594 DOI: 10.1021/acs.jmedchem.4c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Given the crucial role of the main protease (Mpro) in the replication cycle of SARS-CoV-2, this viral cysteine protease constitutes a high-profile drug target. We investigated peptidomimetic azapeptide nitriles as auspicious, irreversibly acting inhibitors of Mpro. Our systematic approach combined an Mpro active-site scanning by combinatorially assembled azanitriles with structure-based design. Encouraged by the bioactive conformation of open-chain inhibitors, we conceptualized the novel chemotype of macrocyclic azanitriles whose binding mode was elucidated by cocrystallization. This strategy provided a favorable entropic contribution to target binding and resulted in the development of the extraordinarily potent Mpro inhibitor 84 with an IC50 value of 3.23 nM and a second-order rate constant of inactivation, kinac/Ki, of 448,000 M-1s-1. The open-chain Mpro inhibitor 58, along with the macrocyclic compounds 83 and 84, a broad-spectrum anticoronaviral agent, demonstrated the highest antiviral activity with EC50 values in the single-digit micromolar range. Our findings are expected to promote the future development of peptidomimetic Mpro inhibitors as anti-SARS-CoV-2 agents.
Collapse
Affiliation(s)
- Julian Breidenbach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Rabea Voget
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Yaoyao Si
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Alexandra Hingst
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Tobias Claff
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Katharina Sylvester
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Valentina Wolf
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Vesa Krasniqi
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Abibe Useini
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Yukino Ogura
- Department of Infection Biology, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, 305-8575 Tsukuba, Ibaraki, Japan
| | - Atsushi Kawaguchi
- Department of Infection Biology, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, 305-8575 Tsukuba, Ibaraki, Japan
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| |
Collapse
|
5
|
Taefehshokr N, Lac A, Vrieze AM, Dickson BH, Guo PN, Jung C, Blythe EN, Fink C, Aktar A, Dikeakos JD, Dekaban GA, Heit B. SARS-CoV-2 NSP5 antagonizes MHC II expression by subverting histone deacetylase 2. J Cell Sci 2024; 137:jcs262172. [PMID: 38682259 DOI: 10.1242/jcs.262172] [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: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024] Open
Abstract
SARS-CoV-2 interferes with antigen presentation by downregulating major histocompatibility complex (MHC) II on antigen-presenting cells, but the mechanism mediating this process is unelucidated. Herein, analysis of protein and gene expression in human antigen-presenting cells reveals that MHC II is downregulated by the SARS-CoV-2 main protease, NSP5. This suppression of MHC II expression occurs via decreased expression of the MHC II regulatory protein CIITA. CIITA downregulation is independent of the proteolytic activity of NSP5, and rather, NSP5 delivers HDAC2 to the transcription factor IRF3 at an IRF-binding site within the CIITA promoter. Here, HDAC2 deacetylates and inactivates the CIITA promoter. This loss of CIITA expression prevents further expression of MHC II, with this suppression alleviated by ectopic expression of CIITA or knockdown of HDAC2. These results identify a mechanism by which SARS-CoV-2 limits MHC II expression, thereby delaying or weakening the subsequent adaptive immune response.
Collapse
Affiliation(s)
- Nima Taefehshokr
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Alex Lac
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Angela M Vrieze
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Brandon H Dickson
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Peter N Guo
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Catherine Jung
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Eoin N Blythe
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Corby Fink
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Amena Aktar
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Gregory A Dekaban
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Bryan Heit
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| |
Collapse
|
6
|
M L SP, Kumari S, Martinek TA, M ES. De novo design of potential peptide analogs against the main protease of Omicron variant using in silico studies. Phys Chem Chem Phys 2024; 26:14006-14017. [PMID: 38683190 DOI: 10.1039/d4cp01199f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
SARS-CoV-2 and its variants are crossing the immunity barrier induced through vaccination. Recent Omicron sub-variants are highly transmissible and have a low mortality rate. Despite the low severity of Omicron variants, these new variants are known to cause acute post-infectious syndromes. Nowadays, novel strategies to develop new potential inhibitors for SARS-CoV-2 and other Omicron variants have gained prominence. For viral replication and survival the main protease of SARS-CoV-2 plays a vital role. Peptide-like inhibitors that mimic the substrate peptide have already proved to be effective in inhibiting the Mpro of SARS-CoV-2 variants. Our systematic canonical amino acid point mutation analysis on the native peptide has revealed various ways to improve the native peptide of the main protease. Multi mutation analysis has led us to identify and design potent peptide-analog inhibitors that act against the Mpro of the Omicron sub-variants. Our in-depth analysis of all-atom molecular dynamics studies has paved the way to characterize the atomistic behavior of Mpro in Omicron variants. Our goal is to develop potent peptide-analogs that could be therapeutically effective against Omicron and its sub-variants.
Collapse
Affiliation(s)
- Stanly Paul M L
- Institute of Pharmaceutical Analysis, University of Szeged, Eotvos u. 6, G-6720 Szeged, Hungary.
| | - Sonia Kumari
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, S.A.S. Nagar, Mohali 160062, India.
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary.
| | - Elizabeth Sobhia M
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, S.A.S. Nagar, Mohali 160062, India.
| |
Collapse
|
7
|
Azevedo PHRDA, Camargo PG, Constant LEC, Costa SDS, Silva CS, Rosa AS, Souza DDC, Tucci AR, Ferreira VNS, Oliveira TKF, Borba NRR, Rodrigues CR, Albuquerque MG, Dias LRS, Garrett R, Miranda MD, Allonso D, Lima CHDS, Muri EMF. Statine-based peptidomimetic compounds as inhibitors for SARS-CoV-2 main protease (SARS-CoV‑2 Mpro). Sci Rep 2024; 14:8991. [PMID: 38637583 PMCID: PMC11026380 DOI: 10.1038/s41598-024-59442-4] [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: 10/26/2023] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
COVID-19 is a multisystemic disease caused by the SARS-CoV-2 airborne virus, a member of the Coronaviridae family. It has a positive sense single-stranded RNA genome and encodes two non-structural proteins through viral cysteine-proteases processing. Blocking this step is crucial to control virus replication. In this work, we reported the synthesis of 23 statine-based peptidomimetics to determine their ability to inhibit the main protease (Mpro) activity of SARS-CoV-2. Among the 23 peptidomimetics, 15 compounds effectively inhibited Mpro activity by 50% or more, while three compounds (7d, 8e, and 9g) exhibited maximum inhibition above 70% and IC50 < 1 µM. Compounds 7d, 8e, and 9g inhibited roughly 80% of SARS-CoV-2 replication and proved no cytotoxicity. Molecular docking simulations show putative hydrogen bond and hydrophobic interactions between specific amino acids and these inhibitors. Molecular dynamics simulations further confirmed the stability and persisting interactions in Mpro's subsites, exhibiting favorable free energy binding (ΔGbind) values. These findings suggest the statine-based peptidomimetics as potential therapeutic agents against SARS-CoV-2 by targeting Mpro.
Collapse
Affiliation(s)
- Pedro Henrique R de A Azevedo
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, 24241-000, Brazil
| | - Priscila G Camargo
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Larissa E C Constant
- Laboratório de Biotecnologia e Bioengenharia Tecidual, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Stephany da S Costa
- Laboratório de Biotecnologia e Bioengenharia Tecidual, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Celimar Sinézia Silva
- Laboratório de Biotecnologia e Bioengenharia Tecidual, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Alice S Rosa
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Daniel D C Souza
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Amanda R Tucci
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Vivian N S Ferreira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Thamara Kelcya F Oliveira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Nathalia R R Borba
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Carlos R Rodrigues
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Magaly G Albuquerque
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Luiza R S Dias
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, 24241-000, Brazil
| | - Rafael Garrett
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Milene D Miranda
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Diego Allonso
- Laboratório de Biotecnologia e Bioengenharia Tecidual, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Camilo Henrique da S Lima
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil.
| | - Estela Maris F Muri
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, 24241-000, Brazil.
| |
Collapse
|
8
|
Mohebbi A, Eskandarzadeh M, Zangi H, Fatehi M. In silico study of alkaloids with quercetin nucleus for inhibition of SARS-CoV-2 protease and receptor cell protease. PLoS One 2024; 19:e0298201. [PMID: 38626042 PMCID: PMC11020608 DOI: 10.1371/journal.pone.0298201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/21/2024] [Indexed: 04/18/2024] Open
Abstract
Covid-19 disease caused by the deadly SARS-CoV-2 virus is a serious and threatening global health issue declared by the WHO as an epidemic. Researchers are studying the design and discovery of drugs to inhibit the SARS-CoV-2 virus due to its high mortality rate. The main Covid-19 virus protease (Mpro) and human transmembrane protease, serine 2 (TMPRSS2) are attractive targets for the study of antiviral drugs against SARS-2 coronavirus. Increasing consumption of herbal medicines in the community and a serious approach to these drugs have increased the demand for effective herbal substances. Alkaloids are one of the most important active ingredients in medicinal plants that have wide applications in the pharmaceutical industry. In this study, seven alkaloid ligands with Quercetin nucleus for the inhibition of Mpro and TMPRSS2 were studied using computational drug design including molecular docking and molecular dynamics simulation (MD). Auto Dock software was used to evaluate molecular binding energy. Three ligands with the most negative docking score were selected to be entered into the MD simulation procedure. To evaluate the protein conformational changes induced by tested ligands and calculate the binding energy between the ligands and target proteins, GROMACS software based on AMBER03 force field was used. The MD results showed that Phyllospadine and Dracocephin-A form stable complexes with Mpro and TMPRSS2. Prolinalin-A indicated an acceptable inhibitory effect on Mpro, whereas it resulted in some structural instability of TMPRSS2. The total binding energies between three ligands, Prolinalin-A, Phyllospadine and Dracocephin-A and two proteins MPro and TMRPSS2 are (-111.235 ± 15.877, - 75.422 ± 11.140), (-107.033 ± 9.072, -84.939 ± 10.155) and (-102.941 ± 9.477, - 92.451 ± 10.539), respectively. Since the binding energies are at a minimum, this indicates confirmation of the proper binding of the ligands to the proteins. Regardless of some Prolinalin-A-induced TMPRSS2 conformational changes, it may properly bind to TMPRSS2 binding site due to its acceptable binding energy. Therefore, these three ligands can be promising candidates for the development of drugs to treat infections caused by the SARS-CoV-2 virus.
Collapse
Affiliation(s)
- Ali Mohebbi
- Department of Chemical Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Marzieh Eskandarzadeh
- Research Committee of Faculty of Pharmacy, Lorestan University of Medical Science, Khorramabad, Iran
| | - Hanieh Zangi
- Department of Chemical Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Marzie Fatehi
- Department of Chemical Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| |
Collapse
|
9
|
Yang M, Lin L, Flaumenhaft R. Protocol to identify flavonoid antagonists of the SARS-CoV-2 main protease. STAR Protoc 2024; 5:102990. [PMID: 38583157 PMCID: PMC11002865 DOI: 10.1016/j.xpro.2024.102990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/12/2024] [Accepted: 03/14/2024] [Indexed: 04/09/2024] Open
Abstract
Flavonoids are naturally occurring metabolites of plants that can inhibit the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro), which is required for viral replication. Here, we present a protocol to identify flavonoid antagonists of the SARS-CoV-2 Mpro. We describe steps for the expression and purification of Mpro and a kinetic enzymatic assay for Mpro activity using a dequenching fluorescence resonance energy transfer peptide substrate. We then detail procedures for using this enzymatic assay to test flavonoid antagonism and reversible inhibition. For complete details on the use and execution of this protocol, please refer to Lin et al.1.
Collapse
Affiliation(s)
- Moua Yang
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115, USA.
| | - Lin Lin
- College of Materials and Chemical Engineering, Minjiang University, Fuzhuo Institute of Oceanography, Fuzhuo, China
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
10
|
Lewandowski EM, Zhang X, Tan H, Jaskolka-Brown A, Kohaal N, Frazier A, Madsen JJ, Jacobs LMC, Wang J, Chen Y. Distal Protein-Protein Interactions Contribute to SARS-CoV-2 Main Protease Substrate Binding and Nirmatrelvir Resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587566. [PMID: 38617221 PMCID: PMC11014590 DOI: 10.1101/2024.04.01.587566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
SARS-CoV-2 main protease, M pro , is responsible for the processing of the viral polyproteins into individual proteins, including the protease itself. M pro is a key target of anti-COVID-19 therapeutics such as nirmatrelvir (the active component of Paxlovid). Resistance mutants identified clinically and in viral passage assays contain a combination of active site mutations (e.g. E166V, E166A, L167F), which reduce inhibitor binding and enzymatic activity, and non-active site mutations (e.g. P252L, T21I, L50F), which restore the fitness of viral replication. Although the mechanism of resistance for the active site mutations is apparent, the role of the non-active site mutations in fitness rescue remains elusive. In this study, we use the model system of a M pro triple mutant (L50F/E166A/L167F) that confers not only nirmatrelvir drug resistance but also a similar fitness of replication compared to the wild-type both in vitro and in vivo. By comparing peptide and full-length M pro protein as substrates, we demonstrate that the binding of M pro substrate involves more than residues in the active site. In particular, L50F and other non-active site mutations can enhance the M pro dimer-dimer interactions and help place the nsp5-6 substrate at the enzyme catalytic center. The structural and enzymatic activity data of M pro L50F, L50F/E166A/L167F, and others underscore the importance of considering the whole substrate protein in studying M pro and substrate interactions, and offers important insights into M pro function, resistance development, and inhibitor design.
Collapse
|
11
|
Ruiz-Moreno AJ, Cedillo-González R, Cordova-Bahena L, An Z, Medina-Franco JL, Velasco-Velázquez MA. Consensus Pharmacophore Strategy For Identifying Novel SARS-Cov-2 M pro Inhibitors from Large Chemical Libraries. J Chem Inf Model 2024; 64:1984-1995. [PMID: 38472094 DOI: 10.1021/acs.jcim.3c01439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main Protease (Mpro) is an enzyme that cleaves viral polyproteins translated from the viral genome and is critical for viral replication. Mpro is a target for anti-SARS-CoV-2 drug development, and multiple Mpro crystals complexed with competitive inhibitors have been reported. In this study, we aimed to develop an Mpro consensus pharmacophore as a tool to expand the search for inhibitors. We generated a consensus model by aligning and summarizing pharmacophoric points from 152 bioactive conformers of SARS-CoV-2 Mpro inhibitors. Validation against a library of conformers from a subset of ligands showed that our model retrieved poses that reproduced the crystal-binding mode in 77% of the cases. Using models derived from a consensus pharmacophore, we screened >340 million compounds. Pharmacophore-matching and chemoinformatics analyses identified new potential Mpro inhibitors. The candidate compounds were chemically dissimilar to the reference set, and among them, demonstrating the relevance of our model. We evaluated the effect of 16 candidates on Mpro enzymatic activity finding that seven have inhibitory activity. Three compounds (1, 4, and 5) had IC50 values in the midmicromolar range. The Mpro consensus pharmacophore reported herein can be used to identify compounds with improved activity and novel chemical scaffolds against Mpro. The method developed for its generation is provided as an open-access code (https://github.com/AngelRuizMoreno/ConcensusPharmacophore) and can be applied to other pharmacological targets.
Collapse
Affiliation(s)
- Angel J Ruiz-Moreno
- School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Raziel Cedillo-González
- School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Graduate Program in Biochemical Sciences, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Luis Cordova-Bahena
- School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Consejo Nacional de Humanidades, Ciencias y Tecnología, Mexico City 03940, Mexico
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - José L Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Marco A Velasco-Velázquez
- School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, United States
| |
Collapse
|
12
|
Nguyen HH, Tufts J, Minh DDL. On Inactivation of the Coronavirus Main Protease. J Chem Inf Model 2024; 64:1644-1656. [PMID: 38423522 PMCID: PMC10936523 DOI: 10.1021/acs.jcim.3c01518] [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: 10/05/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
A deeper understanding of the inactive conformations of the coronavirus main protease (MPro) could inform the design of allosteric drugs. Based on extensive molecular dynamics simulations, we built a Markov State Model to investigate structural changes that can inactivate the SARS-CoV-2 MPro. In a subset of structures, one subunit of the homodimer assumes an inactive conformation that resembles an inactive crystal structure. However, contradicting the widely held half-of-sites activity hypothesis, the most populated enzyme structures have two active subunits. We then used transition path theory (TPT) and the Jensen-Shannon Divergence (JSD) to pinpoint residues involved in the inactivation process. A π stack between Phe140 and His163 is a key feature that can distinguish active and inactive conformations of MPro. Each subunit has unique inactive conformations stabilized by π stacking interactions involving residues Phe140, Tyr118, His163, and His172, a hydrogen bonding network centered around His163 and His172, and a modified network of interactions in the dimer interface. The importance of these residues in maintaining an active structure explains the sensitivity of enzymatic activity to site-directed mutagenesis.
Collapse
Affiliation(s)
- Hong Ha Nguyen
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Jim Tufts
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - David D. L. Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| |
Collapse
|
13
|
Barton LS, Callahan JF, Cantizani J, Concha NO, Cotillo Torrejon I, Goodwin NC, Joshi-Pangu A, Kiesow TJ, McAtee JJ, Mellinger M, Nixon CJ, Padrón-Barthe L, Patterson JR, Pearson ND, Pouliot JJ, Rendina AR, Buitrago Santanilla A, Schneck JL, Sanz O, Thalji RK, Ward P, Williams SP, King BW. Exploration of the P1 residue in 3CL protease inhibitors leading to the discovery of a 2-tetrahydrofuran P1 replacement. Bioorg Med Chem 2024; 100:117618. [PMID: 38309201 DOI: 10.1016/j.bmc.2024.117618] [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: 10/18/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
The virally encoded 3C-like protease (3CLpro) is a well-validated drug target for the inhibition of coronaviruses including Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Most inhibitors of 3CLpro are peptidomimetic, with a γ-lactam in place of Gln at the P1 position of the pseudopeptide chain. An effort was pursued to identify a viable alternative to the γ-lactam P1 mimetic which would improve physicochemical properties while retaining affinity for the target. Discovery of a 2-tetrahydrofuran as a suitable P1 replacement that is a potent enzymatic inhibitor of 3CLpro in SARS-CoV-2 virus is described herein.
Collapse
Affiliation(s)
- Linda S Barton
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States.
| | - James F Callahan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Juan Cantizani
- GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Nestor O Concha
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | | | - Nicole C Goodwin
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Amruta Joshi-Pangu
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Terry J Kiesow
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Jeff J McAtee
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Mark Mellinger
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Christopher J Nixon
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | | | - Jaclyn R Patterson
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Neil D Pearson
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Jeffrey J Pouliot
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Alan R Rendina
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | | | - Jessica L Schneck
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Olalla Sanz
- GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Reema K Thalji
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Paris Ward
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Shawn P Williams
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Bryan W King
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Zhang K, Eldin P, Ciesla JH, Briant L, Lentini JM, Ramos J, Cobb J, Munger J, Fu D. Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.10.527147. [PMID: 37502865 PMCID: PMC10370084 DOI: 10.1101/2023.02.10.527147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Nonstructural protein 5 (Nsp5) is the main protease of SARS-CoV-2 that cleaves viral polyproteins into individual polypeptides necessary for viral replication. Here, we show that Nsp5 binds and cleaves human tRNA methyltransferase 1 (TRMT1), a host enzyme required for a prevalent post-transcriptional modification in tRNAs. Human cells infected with SARS-CoV-2 exhibit a decrease in TRMT1 protein levels and TRMT1-catalyzed tRNA modifications, consistent with TRMT1 cleavage and inactivation by Nsp5. Nsp5 cleaves TRMT1 at a specific position that matches the consensus sequence of SARS-CoV-2 polyprotein cleavage sites, and a single mutation within the sequence inhibits Nsp5-dependent proteolysis of TRMT1. The TRMT1 cleavage fragments exhibit altered RNA binding activity and are unable to rescue tRNA modification in TRMT1-deficient human cells. Compared to wildtype human cells, TRMT1-deficient human cells infected with SARS-CoV-2 exhibit reduced levels of intracellular viral RNA. These findings provide evidence that Nsp5-dependent cleavage of TRMT1 and perturbation of tRNA modification patterns contribute to the cellular pathogenesis of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Kejia Zhang
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Patrick Eldin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Jessica H. Ciesla
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Laurence Briant
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Jenna M. Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Justin Cobb
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| |
Collapse
|
16
|
Funk LM, Poschmann G, Rabe von Pappenheim F, Chari A, Stegmann KM, Dickmanns A, Wensien M, Eulig N, Paknia E, Heyne G, Penka E, Pearson AR, Berndt C, Fritz T, Bazzi S, Uranga J, Mata RA, Dobbelstein M, Hilgenfeld R, Curth U, Tittmann K. Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design. Nat Commun 2024; 15:411. [PMID: 38195625 PMCID: PMC10776599 DOI: 10.1038/s41467-023-44621-0] [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: 12/03/2022] [Accepted: 12/21/2023] [Indexed: 01/11/2024] Open
Abstract
Besides vaccines, the development of antiviral drugs targeting SARS-CoV-2 is critical for preventing future COVID outbreaks. The SARS-CoV-2 main protease (Mpro), a cysteine protease with essential functions in viral replication, has been validated as an effective drug target. Here, we show that Mpro is subject to redox regulation in vitro and reversibly switches between the enzymatically active dimer and the functionally dormant monomer through redox modifications of cysteine residues. These include a disulfide-dithiol switch between the catalytic cysteine C145 and cysteine C117, and generation of an allosteric cysteine-lysine-cysteine SONOS bridge that is required for structural stability under oxidative stress conditions, such as those exerted by the innate immune system. We identify homo- and heterobifunctional reagents that mimic the redox switching and inhibit Mpro activity. The discovered redox switches are conserved in main proteases from other coronaviruses, e.g. MERS-CoV and SARS-CoV, indicating their potential as common druggable sites.
Collapse
Affiliation(s)
- Lisa-Marie Funk
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Fabian Rabe von Pappenheim
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Ashwin Chari
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Kim M Stegmann
- Institute of Molecular Oncology, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Antje Dickmanns
- Institute of Molecular Oncology, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Marie Wensien
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Nora Eulig
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Elham Paknia
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Gabi Heyne
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Elke Penka
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Arwen R Pearson
- Institute for Nanostructure and Solid-State Physics, Hamburg Centre for Ultrafast Imaging, Hamburg University, HARBOR, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Carsten Berndt
- Department of Neurology, Medical Faculty, Heinrich-Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Tobias Fritz
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Sophia Bazzi
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Jon Uranga
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Ricardo A Mata
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Rolf Hilgenfeld
- Institute for Biochemistry, Lübeck University, Ratzeburger Allee 160, 23562, Lübeck, Germany
- German Center for Infection Research, Hamburg - Lübeck-Borstel-Riems Site, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany.
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany.
| |
Collapse
|
17
|
Mizuno A, Nakayoshi T, Kato K, Kurimoto E, Oda A. Computational Estimation of Residues Involving Resistance to the SARS-CoV-2 Main Protease Inhibitor Ensitrelvir Based on Virtual Alanine Scan of the Active Site. Biol Pharm Bull 2024; 47:967-977. [PMID: 38763751 DOI: 10.1248/bpb.b24-00031] [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] [Indexed: 05/21/2024]
Abstract
Ensitrelvir is a noncovalent inhibitor of the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2. Acquisition of drug resistance in virus-derived proteins is a serious therapeutic concern, and drug resistance occurs due to amino acid mutations. In this study, we computationally constructed 24 mutants, in which one residue around the active site was replaced with alanine and performed molecular dynamics simulations to the complex of Mpro and ensitrelvir to predict the residues involved in drug resistance. We evaluated the changes in the entire protein structure and ligand configuration in each of these mutants and estimated which residues were involved in ensitrelvir recognition. This method is called a virtual alanine scan. In nine mutants (S1A, T26A, H41A, M49A, L141A, H163A, E166A, V186A, and R188A), although the entire protein structure and catalytic dyad (cysteine (Cys)145 and histidine (His)41) were not significantly moved, the ensitrelvir configuration changed. Thus, it is considered that these mutants did not recognize ensitrelvir while maintaining Mpro enzymatic activities, and Ser1, Thr26, His41, Met49, Leu141, His163, Glu166, Val186, and Arg188 may be related to ensitrelvir resistance. The ligand shift noted in M49A was similar to that observed in M49I, which has been shown to be experimentally ensitrelvir resistant. These findings suggest that our research approach can predict mutations that incite drug resistance.
Collapse
Affiliation(s)
| | - Tomoki Nakayoshi
- Faculty of Pharmacy, Meijo University
- Graduate School of Information Sciences, Hiroshima City University
| | - Koichi Kato
- Faculty of Pharmacy, Meijo University
- Faculty of Pharmaceutical Sciences, Shonan University of Medical Sciences
| | | | - Akifumi Oda
- Faculty of Pharmacy, Meijo University
- Institute for Protein Research, Osaka University
| |
Collapse
|
18
|
Khan MT, Ali A, Wei X, Nadeem T, Muhammad S, Al-Sehemi AG, Wei D. Inhibitory effect of thymoquinone from Nigella sativa against SARS-CoV-2 main protease. An in-silico study. BRAZ J BIOL 2024; 84:e250667. [DOI: 10.1590/1519-6984.25066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 01/24/2022] [Indexed: 11/21/2022] Open
Abstract
Abstract Nigella sativa is known for the safety profile, containing a wealth of useful antiviral compounds. The main protease (Mpro, 3CLpro) of severe acute respiratory syndrome 2 (SARS-CoV-2) is being considered as one of the most attractive viral target, processing the polyproteins during viral pathogenesis and replication. In the current investigation we analyzed the potency of active component, thymoquinone (TQ) of Nigella sativa against SARS-CoV-2 Mpro. The structures of TQ and Mpro was retrieved from PubChem (CID10281) and Protein Data Bank (PDB ID 6MO3) respectively. The Mpro and TQ were docked and the complex was subjected to molecular dynamic (MD) simulations for a period 50ns. Protein folding effect was analyzed using radius of gyration (Rg) while stability and flexibility was measured, using root means square deviations (RMSD) and root means square fluctuation (RMSF) respectively. The simulation results shows that TQ is exhibiting good binding activity against SARS-CoV-2 Mpro, interacting many residues, present in the active site (His41, Cys145) and also the Glu166, facilitating the pocket shape. Further, experimental approaches are needed to validate the role of TQ against virus infection. The TQ is interfering with pocket maintaining residues as well as active site of virus Mpro which may be used as a potential inhibitor against SARS-CoV-2 for better management of COVID-19.
Collapse
Affiliation(s)
| | - A. Ali
- Shanghai Jiao Tong University, China
| | - X. Wei
- Shanghai Jiao Tong University, China
| | | | | | | | - Dongqing Wei
- Shanghai Jiao Tong University, China; Peng Cheng Laboratory, China
| |
Collapse
|
19
|
Ferraro S, Convertino I, Cappello E, Valdiserra G, Bonaso M, Tuccori M. Lessons learnt from the preclinical discovery and development of ensitrelvir as a COVID-19 therapeutic option. Expert Opin Drug Discov 2024; 19:9-20. [PMID: 37830361 DOI: 10.1080/17460441.2023.2267001] [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: 06/30/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023]
Abstract
INTRODUCTION The COVID-19 pandemic stimulated the development of several therapeutic tools with several degrees of success. Ensitrelvir, a protease inhibitor that blocks the replication of SARS-CoV-2, can reduce the viral load and the severity of symptoms in infected patients and become available for emergency use in Japan. Clinical trials showed a good tolerability profile although the potential for interactions with substrates, inhibitors, and inducers of CYP3A must be considered. The occurrence of resistance is also a matter of investigation. AREAS COVERED In this article, the authors describe the development of ensitrelvir starting from the identification of the molecule to the pre-clinical and clinical trials up to the post-authorization phase. EXPERT OPINION Ensitrelvir was developed in a late phase of the pandemic when the availability of patients that can be candidate to enter the clinical trial was limited with consequences for the possibility of assessing certain outcomes and for the robustness of results. Although the evidence about the benefits of ensitrelvir in COVID-19 is not questionable, the problems of interactions with other drugs, emerging resistant variants, the availability of alternative therapeutic options, costs, and accessibility will concur to its probable limited clinical use in the future.
Collapse
Affiliation(s)
- Sara Ferraro
- Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa Italy
| | - Irma Convertino
- Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa Italy
| | - Emiliano Cappello
- Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa Italy
| | - Giulia Valdiserra
- Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa Italy
| | - Marco Bonaso
- Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa Italy
| | - Marco Tuccori
- Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa Italy
- Unit of Adverse Drug Reaction Monitoring, University Hospital of Pisa, Pisa, Italy
| |
Collapse
|
20
|
Lombardo D, Musolino C, Chines V, Caminiti G, Palermo C, Cacciola I, Raffa G, Pollicino T. Assessing Genomic Mutations in SARS-CoV-2: Potential Resistance to Antiviral Drugs in Viral Populations from Untreated COVID-19 Patients. Microorganisms 2023; 12:2. [PMID: 38276171 PMCID: PMC10821222 DOI: 10.3390/microorganisms12010002] [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: 10/30/2023] [Revised: 12/09/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Naturally occurring SARS-CoV-2 variants mutated in genomic regions targeted by antiviral drugs have not been extensively studied. This study investigated the potential of the RNA-dependent RNA polymerase (RdRp) complex subunits and non-structural protein (Nsp)5 of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to accumulate natural mutations that could affect the efficacy of antiviral drugs. To this aim, SARS-CoV-2 genomic sequences isolated from 4155 drug-naive individuals from southern Italy were analyzed using the Illumina MiSeq platform. Sequencing of the 4155 samples showed the following viral variant distribution: 71.2% Delta, 22.2% Omicron, and 6.4% Alpha. In the Nsp12 sequences, we found 84 amino acid substitutions. The most common one was P323L, detected in 3777/4155 (91%) samples, with 2906/3777 (69.9%) also showing the G671S substitution in combination. Additionally, we identified 28, 14, and 24 different amino acid substitutions in the Nsp5, Nsp7, and Nsp8 genomic regions, respectively. Of note, the V186F and A191V substitutions, affecting residues adjacent to the active site of Nsp5 (the target of the antiviral drug Paxlovid), were found in 157/4155 (3.8%) and 3/4155 (0.07%) samples, respectively. In conclusion, the RdRp complex subunits and the Nsp5 genomic region exhibit susceptibility to accumulating natural mutations. This susceptibility poses a potential risk to the efficacy of antiviral drugs, as these mutations may compromise the drug ability to inhibit viral replication.
Collapse
Affiliation(s)
- Daniele Lombardo
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Cristina Musolino
- Department of Human Pathology, University Hospital of Messina, 98124 Messina, Italy;
| | - Valeria Chines
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Giuseppe Caminiti
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Claudia Palermo
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Irene Cacciola
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Giuseppina Raffa
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Teresa Pollicino
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| |
Collapse
|
21
|
Pérez-Vargas J, Worrall LJ, Olmstead AD, Ton AT, Lee J, Villanueva I, Thompson CAH, Dudek S, Ennis S, Smith JR, Shapira T, De Guzman J, Gang S, Ban F, Vuckovic M, Bielecki M, Kovacic S, Kenward C, Hong CY, Gordon DG, Levett PN, Krajden M, Leduc R, Boudreault PL, Niikura M, Paetzel M, Young RN, Cherkasov A, Strynadka NCJ, Jean F. A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants. Emerg Microbes Infect 2023; 12:2246594. [PMID: 37555275 PMCID: PMC10453993 DOI: 10.1080/22221751.2023.2246594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 08/10/2023]
Abstract
Antivirals with broad coronavirus activity are important for treating high-risk individuals exposed to the constantly evolving SARS-CoV-2 variants of concern (VOCs) as well as emerging drug-resistant variants. We developed and characterized a novel class of active-site-directed 3-chymotrypsin-like protease (3CLpro) inhibitors (C2-C5a). Our lead direct-acting antiviral (DAA), C5a, is a non-covalent, non-peptide with a dissociation constant of 170 nM against recombinant SARS-CoV-2 3CLpro. The compounds C2-C5a exhibit broad-spectrum activity against Omicron subvariants (BA.5, BQ.1.1, and XBB.1.5) and seasonal human coronavirus-229E infection in human cells. Notably, C5a has median effective concentrations of 30-50 nM against BQ.1.1 and XBB.1.5 in two different human cell lines. X-ray crystallography has confirmed the unique binding modes of C2-C5a to the 3CLpro, which can limit virus cross-resistance to emerging Paxlovid-resistant variants. We tested the effect of C5a with two of our newly discovered host-directed antivirals (HDAs): N-0385, a TMPRSS2 inhibitor, and bafilomycin D (BafD), a human vacuolar H+-ATPase [V-ATPase] inhibitor. We demonstrated a synergistic action of C5a in combination with N-0385 and BafD against Omicron BA.5 infection in human Calu-3 lung cells. Our findings underscore that a SARS-CoV-2 multi-targeted treatment for circulating Omicron subvariants based on DAAs (C5a) and HDAs (N-0385 or BafD) can lead to therapeutic benefits by enhancing treatment efficacy. Furthermore, the high-resolution structures of SARS-CoV-2 3CLpro in complex with C2-C5a will facilitate future rational optimization of our novel broad-spectrum active-site-directed 3C-like protease inhibitors.
Collapse
Affiliation(s)
- Jimena Pérez-Vargas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Andrea D. Olmstead
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Jaeyong Lee
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Ivan Villanueva
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Connor A. H. Thompson
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Svenja Dudek
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Jason R. Smith
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Tirosh Shapira
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Joshua De Guzman
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Shutong Gang
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Michael Bielecki
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Suzana Kovacic
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Calem Kenward
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Christopher Yee Hong
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Danielle G. Gordon
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Paul N. Levett
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Richard Leduc
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Robert N. Young
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - François Jean
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| |
Collapse
|
22
|
Kang KM, Jang Y, Lee SS, Jin MS, Jun CD, Kim M, Kim YC. Discovery of antiviral SARS-CoV-2 main protease inhibitors by structure-guided hit-to-lead optimization of carmofur. Eur J Med Chem 2023; 260:115720. [PMID: 37633203 DOI: 10.1016/j.ejmech.2023.115720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/25/2023] [Accepted: 08/10/2023] [Indexed: 08/28/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) has been targeted for the development of anti-SARS-CoV-2 agents against COVID-19 infection because Mpro processes essential viral polyproteins and plays a key role in SARS-CoV-2 replication. In this study, we report the development of novel SARS-CoV-2 Mpro inhibitors derived from carmofur, a previously identified compound that has shown moderate potency as a covalent inhibitor of SARS-CoV-2 Mpro. To employ a structure-guided drug design strategy, a putative intact binding mode of carmofur at catalytic active site of Mpro was initially predicted by docking simulation. Based on the predicted binding mode, a series of carmofur derivatives aiming to occupy the Mpro substrate binding regions were investigated for structure-activity relationship analysis. As a result, an indole-based derivative, speculated to interact with the S4 binding pocket, 21b (IC50 = 1.5 ± 0.1 μM) was discovered. Its structure was further modified and evaluated in silico by combining docking simulation, free energy perturbation calculation and subpocket interaction analysis to optimize the interactions at the S2 and S4 binding pockets. Among the newly designed novel derivatives, 21h and 21i showed the best inhibitory potencies against Mpro with IC50 values of 0.35 and 0.37 μM, respectively. Moreover, their antiviral activities were confirmed with EC50 values of 20-30 μM in the SARS-CoV-2-infected cell-based assay, suggesting that these novel Mpro inhibitors could be applied as potential lead compounds for the development of substantial anti-SARS-CoV-2 agents.
Collapse
Affiliation(s)
- Koon Mook Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Yejin Jang
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Sang Soo Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Mi Sun Jin
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Chang-Duk Jun
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea.
| | - Meehyein Kim
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea; Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
| | - Yong-Chul Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea.
| |
Collapse
|
23
|
Aniana A, Nashed NT, Ghirlando R, Coates L, Kneller DW, Kovalevsky A, Louis JM. Insights into the mechanism of SARS-CoV-2 main protease autocatalytic maturation from model precursors. Commun Biol 2023; 6:1159. [PMID: 37957287 PMCID: PMC10643566 DOI: 10.1038/s42003-023-05469-8] [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: 07/11/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
A critical step for SARS-CoV-2 assembly and maturation involves the autoactivation of the main protease (MProWT) from precursor polyproteins. Upon expression, a model precursor of MProWT mediates its own release at its termini rapidly to yield a mature dimer. A construct with an E290A mutation within MPro exhibits time dependent autoprocessing of the accumulated precursor at the N-terminal nsp4/nsp5 site followed by the C-terminal nsp5/nsp6 cleavage. In contrast, a precursor containing E290A and R298A mutations (MProM) displays cleavage only at the nsp4/nsp5 site to yield an intermediate monomeric product, which is cleaved at the nsp5/nsp6 site only by MProWT. MProM and the catalytic domain (MPro1-199) fused to the truncated nsp4 region also show time-dependent conversion in vitro to produce MProM and MPro1-199, respectively. The reactions follow first-order kinetics indicating that the nsp4/nsp5 cleavage occurs via an intramolecular mechanism. These results support a mechanism involving an N-terminal intramolecular cleavage leading to an increase in the dimer population and followed by an intermolecular cleavage at the C-terminus. Thus, targeting the predominantly monomeric MPro precursor for inhibition may lead to the identification of potent drugs for treatment.
Collapse
Affiliation(s)
- Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892-0520, USA
| | - Nashaat T Nashed
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892-0520, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892-0520, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
- New England Biolabs, 240 County Road, Ipswich, MA, 01938-2723, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, 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.
| |
Collapse
|
24
|
de Munnik M, Lithgow J, Brewitz L, Christensen KE, Bates RH, Rodriguez-Miquel B, Schofield CJ. αβ,α'β'-Diepoxyketones are mechanism-based inhibitors of nucleophilic cysteine enzymes. Chem Commun (Camb) 2023; 59:12859-12862. [PMID: 37815791 PMCID: PMC10601815 DOI: 10.1039/d3cc02932h] [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: 06/19/2023] [Accepted: 09/30/2023] [Indexed: 10/11/2023]
Abstract
Epoxides are an established class of electrophilic alkylating agents that react with nucleophilic protein residues. We report αβ,α'β'-diepoxyketones (DEKs) as a new type of mechanism-based inhibitors of nucleophilic cysteine enzymes. Studies with the L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis and the main protease from SARS-CoV-2 (Mpro) reveal that following epoxide ring opening by a nucleophilic cysteine, further reactions can occur, leading to irreversible alkylation.
Collapse
Affiliation(s)
- Mariska de Munnik
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Jasper Lithgow
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Kirsten E Christensen
- Chemical Crystallography, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Robert H Bates
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Calle Severo Ochoa 2, Tres Cantos, Madrid, Spain
| | - Beatriz Rodriguez-Miquel
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Calle Severo Ochoa 2, Tres Cantos, Madrid, Spain
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| |
Collapse
|
25
|
Wralstad EC, Sayers J, Raines RT. Bayesian Inference Elucidates the Catalytic Competency of the SARS-CoV-2 Main Protease 3CL pro. Anal Chem 2023; 95:14981-14989. [PMID: 37750823 PMCID: PMC10662973 DOI: 10.1021/acs.analchem.3c02459] [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] [Indexed: 09/27/2023]
Abstract
The main protease of SARS-CoV-2, 3CLpro, is a dimeric enzyme that is indispensable to viral replication and presents an attractive opportunity for therapeutic intervention. Previous reports regarding the key properties of 3CLpro and its highly similar SARS-CoV homologue conflict dramatically. Values of the dimeric Kd and enzymic kcat/KM differ by 106- and 103-fold, respectively. Establishing a confident benchmark of the intrinsic capabilities of this enzyme is essential for combating the current pandemic as well as potential future outbreaks. Here, we use enzymatic methods to characterize the dimerization and catalytic efficiency of the authentic protease from SARS-CoV-2. Specifically, we use the rigor of Bayesian inference in a Markov Chain Monte Carlo analysis of progress curves to circumvent the limitations of traditional Michaelis-Menten initial rate analysis. We report that SARS-CoV-2 3CLpro forms a dimer at pH 7.5 that has Kd = 16 ± 4 nM and is capable of catalysis with kcat = 9.9 ± 1.5 s-1, KM = 0.23 ± 0.01 mM, and kcat/KM = (4.3 ± 0.7) × 104 M-1 s-1. We also find that enzymatic activity decreases substantially in solutions of high ionic strength, largely as a consequence of impaired dimerization. We conclude that 3CLpro is a more capable catalyst than appreciated previously, which has important implications for the design of antiviral therapeutic agents that target 3CLpro.
Collapse
Affiliation(s)
- Evans C Wralstad
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jessica Sayers
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
26
|
Duan Y, Wang H, Yuan Z, Yang H. Structural biology of SARS-CoV-2 M pro and drug discovery. Curr Opin Struct Biol 2023; 82:102667. [PMID: 37544112 DOI: 10.1016/j.sbi.2023.102667] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/10/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023]
Abstract
Since its outbreak in late 2019, the COVID-19 pandemic has drawn enormous attention worldwide as a consequence of being the most disastrous infectious disease in the past century. As one of the most immediately druggable targets of SARS-CoV-2, the main protease (Mpro) has been studied thoroughly. In this review, we provide a comprehensive summary of recent advances in structural studies of Mpro, which provide new knowledge about Mpro in terms of its biological function, structural characteristics, substrate specificity, and autocleavage process. We examine the remarkable strides made in targeting Mpro for drug discovery during the pandemic. We summarize insights into the current understanding of the structural features of Mpro and the discovery of existing Mpro-targeting drugs, illuminating pathways for the future development of anti-SARS-CoV-2 therapeutics.
Collapse
Affiliation(s)
- Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Haofeng Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Institute of Infectious Disease and Biosecurity, Shanghai Medical College of Fudan University, Shanghai, China.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Clinical Research and Trial Center, Shanghai, China.
| |
Collapse
|
27
|
Lin L, Chen DY, Scartelli C, Xie H, Merrill-Skoloff G, Yang M, Sun L, Saeed M, Flaumenhaft R. Plant flavonoid inhibition of SARS-CoV-2 main protease and viral replication. iScience 2023; 26:107602. [PMID: 37664626 PMCID: PMC10470319 DOI: 10.1016/j.isci.2023.107602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/15/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Plant-based flavonoids have been evaluated as inhibitors of β-coronavirus replication and as therapies for COVID-19 on the basis of their safety profile and widespread availability. The SARS-CoV-2 main protease (Mpro) has been implicated as a target for flavonoids in silico. Yet no comprehensive in vitro testing of flavonoid activity against SARS-CoV-2 Mpro has heretofore been performed. We screened 1,019 diverse flavonoids for their ability to inhibit SARS-CoV-2 Mpro. Multiple structure-activity relationships were identified among active compounds such as enrichment of galloylated flavonoids and biflavones, including multiple biflavone analogs of apigenin. In a cell-based SARS-CoV-2 replication assay, the most potent inhibitors were apigenin and the galloylated pinocembrin analog, pinocembrin 7-O-(3''-galloyl-4'',6''-(S)-hexahydroxydiphenoyl)-beta-D-glucose (PGHG). Molecular dynamic simulations predicted that PGHG occludes the S1 binding site via a galloyl group and induces a conformational change in Mpro. These studies will advance the development of plant-based flavonoids-including widely available natural products-to target β-coronaviruses.
Collapse
Affiliation(s)
- Lin Lin
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou Institute of Oceanography, Fuzhou, China
| | - Da-Yuan Chen
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Christina Scartelli
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Huanzhang Xie
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou Institute of Oceanography, Fuzhou, China
| | - Glenn Merrill-Skoloff
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Moua Yang
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lijun Sun
- Center for Drug Discovery and Translational Research, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Mohsan Saeed
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| |
Collapse
|
28
|
Ngo C, Fried W, Aliyari S, Feng J, Qin C, Zhang S, Yang H, Shanaa J, Feng P, Cheng G, Chen XS, Zhang C. Alkyne as a Latent Warhead to Covalently Target SARS-CoV-2 Main Protease. J Med Chem 2023; 66:12237-12248. [PMID: 37595260 PMCID: PMC10510381 DOI: 10.1021/acs.jmedchem.3c00810] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Indexed: 08/20/2023]
Abstract
There is an urgent need for improved therapy to better control the ongoing COVID-19 pandemic. The main protease Mpro plays a pivotal role in SARS-CoV-2 replications, thereby representing an attractive target for antiviral development. We seek to identify novel electrophilic warheads for efficient, covalent inhibition of Mpro. By comparing the efficacy of a panel of warheads installed on a common scaffold against Mpro, we discovered that the terminal alkyne could covalently modify Mpro as a latent warhead. Our biochemical and X-ray structural analyses revealed the irreversible formation of the vinyl-sulfide linkage between the alkyne and the catalytic cysteine of Mpro. Clickable probes based on the alkyne inhibitors were developed to measure target engagement, drug residence time, and off-target effects. The best alkyne-containing inhibitors potently inhibited SARS-CoV-2 infection in cell infection models. Our findings highlight great potentials of alkyne as a latent warhead to target cystine proteases in viruses and beyond.
Collapse
Affiliation(s)
- Chau Ngo
- Department
of Chemistry and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - William Fried
- Molecular
and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Saba Aliyari
- Department
of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Joshua Feng
- Department
of Chemistry and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Chao Qin
- Section
of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089, United States
| | - Shilei Zhang
- Department
of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Hanjing Yang
- Molecular
and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Jean Shanaa
- Department
of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Pinghui Feng
- Section
of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089, United States
| | - Genhong Cheng
- Department
of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Xiaojiang S. Chen
- Molecular
and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Chao Zhang
- Department
of Chemistry and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| |
Collapse
|
29
|
Mihalič F, Benz C, Kassa E, Lindqvist R, Simonetti L, Inturi R, Aronsson H, Andersson E, Chi CN, Davey NE, Överby AK, Jemth P, Ivarsson Y. Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets. Nat Commun 2023; 14:5636. [PMID: 37704626 PMCID: PMC10499821 DOI: 10.1038/s41467-023-41312-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (KD ∼ 7-300 μM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.
Collapse
Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eszter Kassa
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Hanna Aronsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
| |
Collapse
|
30
|
Tran N, Dasari S, Barwell SAE, McLeod MJ, Kalyaanamoorthy S, Holyoak T, Ganesan A. The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease. Nat Commun 2023; 14:5625. [PMID: 37699927 PMCID: PMC10497556 DOI: 10.1038/s41467-023-40023-4] [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: 08/24/2022] [Accepted: 07/04/2023] [Indexed: 09/14/2023] Open
Abstract
The main protease of SARS-CoV-2 (Mpro) is an important target for developing COVID-19 therapeutics. Recent work has highlighted Mpro's susceptibility to undergo redox-associated conformational changes in response to cellular and immune-system-induced oxidation. Despite structural evidence indicating large-scale rearrangements upon oxidation, the mechanisms of conformational change and its functional consequences are poorly understood. Here, we present the crystal structure of an Mpro point mutant (H163A) that shows an oxidized conformation with the catalytic cysteine in a disulfide bond. We hypothesize that Mpro adopts this conformation under oxidative stress to protect against over-oxidation. Our metadynamics simulations illustrate a potential mechanism by which H163 modulates this transition and suggest that this equilibrium exists in the wild type enzyme. We show that other point mutations also significantly shift the equilibrium towards this state by altering conformational free energies. Unique avenues of SARS-CoV-2 research can be explored by understanding how H163 modulates this equilibrium.
Collapse
Affiliation(s)
- Norman Tran
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Sathish Dasari
- Department of Chemistry, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Sarah A E Barwell
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | | | - Subha Kalyaanamoorthy
- Department of Chemistry, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Todd Holyoak
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
| | - Aravindhan Ganesan
- ArGan's Lab, School of Pharmacy, Faculty of Science, University of Waterloo, 10A Victoria Street South, Kitchener, ON, N2G 1C5, Canada.
| |
Collapse
|
31
|
D′Oliviera A, Dai X, Mottaghinia S, Geissler EP, Etienne L, Zhang Y, Mugridge JS. Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529306. [PMID: 36865253 PMCID: PMC9980103 DOI: 10.1101/2023.02.20.529306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) is critical for the production of functional viral proteins during infection and, like many viral proteases, can also target host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 can be recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes global protein synthesis and cellular redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain required for tRNA modification activity in cells. Evolutionary analysis shows that the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 may be resistant to cleavage. In primates, regions outside the cleavage site with rapid evolution could indicate adaptation to ancient viral pathogens. We determined the structure of a TRMT1 peptide in complex with Mpro, revealing a substrate binding conformation distinct from the majority of available Mpro-peptide complexes. Kinetic parameters for peptide cleavage showed that the TRMT1(526-536) sequence is cleaved with comparable efficiency to the Mpro-targeted nsp8/9 viral cleavage site. Mutagenesis studies and molecular dynamics simulations together indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis that follows substrate binding. Our results provide new information about the structural basis for Mpro substrate recognition and cleavage that could help inform future therapeutic design and raise the possibility that proteolysis of human TRMT1 during SARS-CoV-2 infection suppresses protein translation and oxidative stress response to impact viral pathogenesis.
Collapse
Affiliation(s)
- Angel D′Oliviera
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
| | - Xuhang Dai
- Department of Chemistry, New York University, New York, NY 10003
| | - Saba Mottaghinia
- CIRI (Centre International de Recherche en Infectiologie), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Evan P. Geissler
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
| | - Lucie Etienne
- CIRI (Centre International de Recherche en Infectiologie), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY 10003
- Simons Center for Computational Physical Chemistry at New York University, New York, NY 10003
| | - Jeffrey S. Mugridge
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
| |
Collapse
|
32
|
Li J, Wang Y, Rajpoot S, Lavrijsen M, Pan Q, Li P, Baig MS. Investigating theobromine as a potential anti-human coronaviral agent. Microbiol Immunol 2023; 67:404-412. [PMID: 37415325 DOI: 10.1111/1348-0421.13086] [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: 12/22/2022] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/08/2023]
Abstract
Coronaviruses (CoVs) have long been known to infect humans, mainly alpha-CoV and beta-CoV. The vaccines developed for SARS-CoV-2 are likely not effective against other coronavirus species, whereas the risk of the emergence of new strains that may cause the next epidemic/pandemic is high. The development of antiviral drugs that are effective across different CoVs represents a viable strategy for improving pandemic preparedness. In this study, we aim to identify pan-coronaviral agents by targeting the conserved main protease (Mpro). For drug screening, the catalytic dyad of four human CoVs (HCoVs: SARS-CoV-2, and seasonal CoV NL63, OC43, and 229E) was targeted by molecular docking. The identified leading candidate theobromine, a xanthine derivative, was further tested in cell culture models of coronavirus infection. Theobromine binds strongly with the catalytic dyad (His41 and Cys144/145) of SARS-CoV-2 and HCoV-NL63 Mpro, mildly with HCoV-OC43, but not with HCoV-229E. However, theobromine only shows dose-dependent inhibition in Calu3 cells inoculated with SARS-CoV-2, but not in cells inoculated with seasonal CoVs. Theobromine exerts antiviral activity against coronavirus infections potentially through targeting Mpro. However, the antiviral potency is distinct among different CoVs.
Collapse
Affiliation(s)
- Jiajing Li
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Yining Wang
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Sajjan Rajpoot
- Department of Biosciences & Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Marla Lavrijsen
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Pengfei Li
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Mirza S Baig
- Department of Biosciences & Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Jukič M, Kralj S, Kolarič A, Bren U. Design of Tetra-Peptide Ligands of Antibody Fc Regions Using In Silico Combinatorial Library Screening. Pharmaceuticals (Basel) 2023; 16:1170. [PMID: 37631085 PMCID: PMC10459493 DOI: 10.3390/ph16081170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Peptides, or short chains of amino-acid residues, are becoming increasingly important as active ingredients of drugs and as crucial probes and/or tools in medical, biotechnological, and pharmaceutical research. Situated at the interface between small molecules and larger macromolecular systems, they pose a difficult challenge for computational methods. We report an in silico peptide library generation and prioritization workflow using CmDock for identifying tetrapeptide ligands that bind to Fc regions of antibodies that is analogous to known in vitro recombinant peptide libraries' display and expression systems. The results of our in silico study are in accordance with existing scientific literature on in vitro peptides that bind to antibody Fc regions. In addition, we postulate an evolving in silico library design workflow that will help circumvent the combinatorial problem of in vitro comprehensive peptide libraries by focusing on peptide subunits that exhibit favorable interaction profiles in initial in silico peptide generation and testing.
Collapse
Affiliation(s)
- Marko Jukič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, SI-6000 Koper, Slovenia
- Institute of Environmental Protection and Sensors, Beloruska ulica 7, SI-2000 Maribor, Slovenia
| | - Sebastjan Kralj
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
| | - Anja Kolarič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Institute of Environmental Protection and Sensors, Beloruska ulica 7, SI-2000 Maribor, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, SI-6000 Koper, Slovenia
- Institute of Environmental Protection and Sensors, Beloruska ulica 7, SI-2000 Maribor, Slovenia
| |
Collapse
|
35
|
Jimmidi R, Chamakuri S, Lu S, Ucisik MN, Chen PJ, Bohren KM, Moghadasi SA, Versteeg L, Nnabuife C, Li JY, Qin X, Chen YC, Faver JC, Nyshadham P, Sharma KL, Sankaran B, Judge A, Yu Z, Li F, Pollet J, Harris RS, Matzuk MM, Palzkill T, Young DW. DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors. Commun Chem 2023; 6:164. [PMID: 37542196 PMCID: PMC10403511 DOI: 10.1038/s42004-023-00961-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/19/2023] [Indexed: 08/06/2023] Open
Abstract
The development of SARS-CoV-2 main protease (Mpro) inhibitors for the treatment of COVID-19 has mostly benefitted from X-ray structures and preexisting knowledge of inhibitors; however, an efficient method to generate Mpro inhibitors, which circumvents such information would be advantageous. As an alternative approach, we show here that DNA-encoded chemistry technology (DEC-Tec) can be used to discover inhibitors of Mpro. An affinity selection of a 4-billion-membered DNA-encoded chemical library (DECL) using Mpro as bait produces novel non-covalent and non-peptide-based small molecule inhibitors of Mpro with low nanomolar Ki values. Furthermore, these compounds demonstrate efficacy against mutant forms of Mpro that have shown resistance to the standard-of-care drug nirmatrelvir. Overall, this work demonstrates that DEC-Tec can efficiently generate novel and potent inhibitors without preliminary chemical or structural information.
Collapse
Affiliation(s)
- Ravikumar Jimmidi
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA.
| | - Shuo Lu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Melek Nihan Ucisik
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Peng-Jen Chen
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Kurt M Bohren
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455, USA
| | - Leroy Versteeg
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, 77030, USA
- Center for Vaccine Development, Texas Children's Hospital, 1102 Bates Street, Houston, Texas, 77030, USA
| | - Christina Nnabuife
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jian-Yuan Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Ying-Chu Chen
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - John C Faver
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Pranavanand Nyshadham
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Kiran L Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Zhifeng Yu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jeroen Pollet
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, 77030, USA
- Center for Vaccine Development, Texas Children's Hospital, 1102 Bates Street, Houston, Texas, 77030, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, 78229, USA
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA.
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA.
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA.
| |
Collapse
|
36
|
Moradi S, Wu Y, Walden P, Cui Z, Johnston WA, Petrov D, Alexandrov K. In Vitro Reconstitution and Analysis of SARS-CoV-2/Host Protein-Protein Interactions. ACS OMEGA 2023; 8:25009-25019. [PMID: 37483225 PMCID: PMC10357528 DOI: 10.1021/acsomega.3c01625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023]
Abstract
The emergence of viral threats such as Ebola, ZIKA, and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) requires a rapid and efficient approach for elucidating mechanisms of pathogenesis and development of therapeutics. In this context, cell-free protein synthesis (CFPS) holds a promise to resolve the bottlenecks of multiplexed protein production and interaction analysis among host and pathogen proteins. Here, we applied a eukaryotic CFPS system based on Leishmania tarentolae extract (LTE) protein expression in combination with AlphaLISA proximity-based protein interaction technology to identify intraviral and viral-human protein interactions of SARS-CoV-2 virus that can potentially be targeted by the existing or novel antiviral therapeutics. We produced and tested 54 putative human-viral protein pairs in vitro and identified 45 direct binary protein interactions. As a casing example of the assay's suitability for drug development applications, we analyzed the effect of a putative biologic on the human angiotensin-converting enzyme 2/receptor-binding domain (hACE2/RBD) interaction. This suggests that the presented pathogen characterization platform can facilitate the development of new therapeutic agents.
Collapse
Affiliation(s)
- Shayli
Varasteh Moradi
- CSIRO-QUT
Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic
Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics
and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Yue Wu
- CSIRO-QUT
Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic
Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics
and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Patricia Walden
- CSIRO-QUT
Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic
Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics
and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Zhenling Cui
- CSIRO-QUT
Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic
Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics
and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Wayne A. Johnston
- CSIRO-QUT
Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic
Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics
and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Dmitri Petrov
- Department
of Biology, Stanford University, Stanford, California 94305-5020, United
States
| | - Kirill Alexandrov
- CSIRO-QUT
Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic
Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics
and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| |
Collapse
|
37
|
Zabo S, Lobb KA. In Silico Substrate-Binding Profiling for SARS-CoV-2 Main Protease (M pro) Using Hexapeptide Substrates. Viruses 2023; 15:1480. [PMID: 37515167 PMCID: PMC10385622 DOI: 10.3390/v15071480] [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: 05/30/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
The SARS-CoV-2 main protease (Mpro) is essential for the life cycle of the COVID-19 virus. It cleaves the two polyproteins at 11 positions to generate mature proteins for virion formation. The cleavage site on these polyproteins is known to be Leu-Gln↓(Ser/Ala/Gly). A range of hexapeptides that follow the known sequence for recognition and cleavage was constructed using RDKit libraries and complexed with the crystal structure of Mpro (PDB ID 6XHM) through extensive molecular docking calculations. A subset of 131 of these complexes underwent 20 ns molecular dynamics simulations. The analyses of the trajectories from molecular dynamics included principal component analysis (PCA), and a method to compare PCA plots from separate trajectories was developed in terms of encoding PCA progression during the simulations. The hexapeptides formed stable complexes as expected, with reproducible molecular docking of the substrates given the extensiveness of the procedure. Only Lys-Leu-Gln*** (KLQ***) sequence complexes were studied for molecular dynamics. In this subset of complexes, the PCA analysis identified four classifications of protein motions across these sequences. KLQ*** complexes illustrated the effect of changes in substrate on the active site, with implications for understanding the substrate recognition of Mpro and informing the development of small molecule inhibitors.
Collapse
Affiliation(s)
- Sophakama Zabo
- Department of Chemistry, Rhodes University, Makhanda 6139, South Africa
| | - Kevin Alan Lobb
- Department of Chemistry, Rhodes University, Makhanda 6139, South Africa
| |
Collapse
|
38
|
Chan HT, Oliveira ASF, Schofield CJ, Mulholland AJ, Duarte F. Dynamical Nonequilibrium Molecular Dynamics Simulations Identify Allosteric Sites and Positions Associated with Drug Resistance in the SARS-CoV-2 Main Protease. JACS AU 2023; 3:1767-1774. [PMID: 37384148 PMCID: PMC10262681 DOI: 10.1021/jacsau.3c00185] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/30/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) plays an essential role in the coronavirus lifecycle by catalyzing hydrolysis of the viral polyproteins at specific sites. Mpro is the target of drugs, such as nirmatrelvir, though resistant mutants have emerged that threaten drug efficacy. Despite its importance, questions remain on the mechanism of how Mpro binds its substrates. Here, we apply dynamical nonequilibrium molecular dynamics (D-NEMD) simulations to evaluate structural and dynamical responses of Mpro to the presence and absence of a substrate. The results highlight communication between the Mpro dimer subunits and identify networks, including some far from the active site, that link the active site with a known allosteric inhibition site, or which are associated with nirmatrelvir resistance. They imply that some mutations enable resistance by altering the allosteric behavior of Mpro. More generally, the results show the utility of the D-NEMD technique for identifying functionally relevant allosteric sites and networks including those relevant to resistance.
Collapse
Affiliation(s)
- H. T.
Henry Chan
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - A. Sofia F. Oliveira
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Fernanda Duarte
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| |
Collapse
|
39
|
Ambrosio FA, Costa G, Romeo I, Esposito F, Alkhatib M, Salpini R, Svicher V, Corona A, Malune P, Tramontano E, Ceccherini-Silberstein F, Alcaro S, Artese A. Targeting SARS-CoV-2 Main Protease: A Successful Story Guided by an In Silico Drug Repurposing Approach. J Chem Inf Model 2023; 63:3601-3613. [PMID: 37227780 DOI: 10.1021/acs.jcim.3c00282] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) is a crucial enzyme for viral replication and has been considered an attractive drug target for the treatment of COVID-19. In this study, virtual screening techniques and in vitro assays were combined to identify novel Mpro inhibitors starting from around 8000 FDA-approved drugs. The docking analysis highlighted 17 promising best hits, biologically characterized in terms of their Mpro inhibitory activity. Among them, 7 cephalosporins and the oral anticoagulant betrixaban were able to block the enzyme activity in the micromolar range with no cytotoxic effect at the highest concentration tested. After the evaluation of the degree of conservation of Mpro residues involved in the binding with the studied ligands, the ligands' activity on SARS-CoV-2 replication was assessed. The ability of betrixaban to affect SARS-CoV-2 replication associated to its antithrombotic effect could pave the way for its possible use in the treatment of hospitalized COVID-19 patients.
Collapse
Affiliation(s)
- Francesca Alessandra Ambrosio
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Isabella Romeo
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | - Mohammad Alkhatib
- Dipartimento di Medicina Sperimentale, Università degli Studi di Roma "Tor Vergata", Via Montpellier, 1, 00133 Roma, Italy
| | - Romina Salpini
- Dipartimento di Medicina Sperimentale, Università degli Studi di Roma "Tor Vergata", Via Montpellier, 1, 00133 Roma, Italy
| | - Valentina Svicher
- Dipartimento di Medicina Sperimentale, Università degli Studi di Roma "Tor Vergata", Via Montpellier, 1, 00133 Roma, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | - Paolo Malune
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | | | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| |
Collapse
|
40
|
Schake P, Dishnica K, Kaiser F, Leberecht C, Haupt VJ, Schroeder M. An interaction-based drug discovery screen explains known SARS-CoV-2 inhibitors and predicts new compound scaffolds. Sci Rep 2023; 13:9204. [PMID: 37280244 DOI: 10.1038/s41598-023-35671-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/19/2023] [Indexed: 06/08/2023] Open
Abstract
The recent outbreak of the COVID-19 pandemic caused by severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) has shown the necessity for fast and broad drug discovery methods to enable us to react quickly to novel and highly infectious diseases. A well-known SARS-CoV-2 target is the viral main 3-chymotrypsin-like cysteine protease (Mpro), known to control coronavirus replication, which is essential for the viral life cycle. Here, we applied an interaction-based drug repositioning algorithm on all protein-compound complexes available in the protein database (PDB) to identify Mpro inhibitors and potential novel compound scaffolds against SARS-CoV-2. The screen revealed a heterogeneous set of 692 potential Mpro inhibitors containing known ones such as Dasatinib, Amodiaquine, and Flavin mononucleotide, as well as so far untested chemical scaffolds. In a follow-up evaluation, we used publicly available data published almost two years after the screen to validate our results. In total, we are able to validate 17% of the top 100 predictions with publicly available data and can furthermore show that predicted compounds do cover scaffolds that are yet not associated with Mpro. Finally, we detected a potentially important binding pattern consisting of 3 hydrogen bonds with hydrogen donors of an oxyanion hole within the active side of Mpro. Overall, these results give hope that we will be better prepared for future pandemics and that drug development will become more efficient in the upcoming years.
Collapse
Affiliation(s)
- Philipp Schake
- Bioinformatics, Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Saxony, Germany.
| | | | | | | | | | - Michael Schroeder
- Bioinformatics, Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Saxony, Germany
| |
Collapse
|
41
|
Kovalevsky A, Aniana A, Coates L, Bonnesen PV, Nashed NT, Louis JM. Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors. J Biol Chem 2023:104886. [PMID: 37271339 PMCID: PMC10238122 DOI: 10.1016/j.jbc.2023.104886] [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: 03/21/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/06/2023] Open
Abstract
The effect of mutations of the catalytic dyad residues of SARS-CoV-2 main protease (MProWT) on the thermodynamics of binding of covalent inhibitors comprising nitrile [nirmatrelvir (NMV), NBH2], aldehyde (GC373) and ketone (BBH1) warheads to MPro is examined together with room temperature X-ray crystallography. When lacking the nucleophilic C145, NMV binding is ∼400-fold weaker corresponding to 3.5 kcal/mol and 13.3 °C decreases in free energy (ΔG) and thermal stability (Tm), respectively, relative to MProWT. The H41A mutation results in a 20-fold increase in the dissociation constant (Kd), and 1.7 kcal/mol and 1.4 °C decreases in ΔG and Tm, respectively. Increasing the pH from 7.2 to 8.2 enhances NMV binding to MProH41A, whereas no significant change is observed in binding to MProWT. Structures of the four inhibitor complexes with MPro1-304/C145A show that the active site geometries of the complexes are nearly identical to that of MProWT with the nucleophilic sulfur of C145 positioned to react with the nitrile or the carbonyl carbon. These results support a two-step mechanism for the formation of the covalent complex involving an initial non-covalent binding followed by a nucleophilic attack by the thiolate anion of C145 on the warhead carbon. Noncovalent inhibitor ensitrelvir (ESV) exhibits a binding affinity to MProWT that is similar to NMV but differs in its thermodynamic signature from NMV. The binding of ESV to MProC145A also results in a significant, but smaller, increase in Kd and decrease in ΔG and Tm, relative to NMV.
Collapse
Affiliation(s)
- Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA.
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Peter V Bonnesen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nashaat T Nashed
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, 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.
| |
Collapse
|
42
|
Farkaš B, Minneci M, Misevicius M, Rozas I. A Tale of Two Proteases: M Pro and TMPRSS2 as Targets for COVID-19 Therapies. Pharmaceuticals (Basel) 2023; 16:834. [PMID: 37375781 DOI: 10.3390/ph16060834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Considering the importance of the 2019 outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulting in the coronavirus disease 2019 (COVID-19) pandemic, an overview of two proteases that play an important role in the infection by SARS-CoV-2, the main protease of SARS-CoV-2 (MPro) and the host transmembrane protease serine 2 (TMPRSS2), is presented in this review. After summarising the viral replication cycle to identify the relevance of these proteases, the therapeutic agents already approved are presented. Then, this review discusses some of the most recently reported inhibitors first for the viral MPro and next for the host TMPRSS2 explaining the mechanism of action of each protease. Afterward, some computational approaches to design novel MPro and TMPRSS2 inhibitors are presented, also describing the corresponding crystallographic structures reported so far. Finally, a brief discussion on a few reports found some dual-action inhibitors for both proteases is given. This review provides an overview of two proteases of different origins (viral and human host) that have become important targets for the development of antiviral agents to treat COVID-19.
Collapse
Affiliation(s)
- Barbara Farkaš
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Marco Minneci
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Matas Misevicius
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| |
Collapse
|
43
|
Shao Q, Xiong M, Li J, Hu H, Su H, Xu Y. Unraveling the catalytic mechanism of SARS-CoV-2 papain-like protease with allosteric modulation of C270 mutation using multiscale computational approaches. Chem Sci 2023; 14:4681-4696. [PMID: 37181765 PMCID: PMC10171076 DOI: 10.1039/d3sc00166k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Papain-like protease (PLpro) is a promising therapeutic target against SARS-CoV-2, but its restricted S1/S2 subsites pose an obstacle in developing active site-directed inhibitors. We have recently identified C270 as a novel covalent allosteric site for SARS-CoV-2 PLpro inhibitors. Here we present a theoretical investigation of the proteolysis reaction catalyzed by the wild-type SARS-CoV-2 PLpro as well as the C270R mutant. Enhanced sampling MD simulations were first performed to explore the influence of C270R mutation on the protease dynamics, and sampled thermodynamically favorable conformations were then submitted to MM/PBSA and QM/MM MD simulations for thorough characterization of the protease-substrate binding and covalent reactions. The disclosed proteolysis mechanism of PLpro, as characterized by the occurrence of proton transfer from the catalytic C111 to H272 prior to the substrate binding and with deacylation being the rate-determining step of the whole proteolysis process, is not completely identical to that of the 3C-like protease, another key cysteine protease of coronaviruses. The C270R mutation alters the structural dynamics of the BL2 loop that indirectly impairs the catalytic function of H272 and reduces the binding of the substrate with the protease, ultimately showing an inhibitory effect on PLpro. Together, these results provide a comprehensive understanding at the atomic level of the key aspects of SARS-CoV-2 PLpro proteolysis, including the catalytic activity allosterically regulated by C270 modification, which is crucial to the follow-up inhibitor design and development.
Collapse
Affiliation(s)
- Qiang Shao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jiameng Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Hangchen Hu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
| |
Collapse
|
44
|
Ahmad S, Mirza MU, Trant JF. Dock-able linear and homodetic di, tri, tetra and pentapeptide library from canonical amino acids: SARS-CoV-2 Mpro as a case study. J Pharm Anal 2023; 13:523-534. [PMID: 37275125 PMCID: PMC10104786 DOI: 10.1016/j.jpha.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/07/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Peptide-based therapeutics are increasingly pushing to the forefront of biomedicine with their promise of high specificity and low toxicity. Although noncanonical residues can always be used, employing only the natural 20 residues restricts the chemical space to a finite dimension allowing for comprehensive in silico screening. Towards this goal, the dataset comprising all possible di-, tri-, and tetra-peptide combinations of the canonical residues has been previously reported. However, with increasing computational power, the comprehensive set of pentapeptides is now also feasible for screening as the comprehensive set of cyclic peptides comprising four or five residues. Here, we provide both the complete and prefiltered libraries of all di-, tri-, tetra-, and penta-peptide sequences from 20 canonical amino acids and their homodetic (N-to-C-terminal) cyclic homologues. The FASTA, simplified molecular-input line-entry system (SMILES), and structure-data file (SDF)-three dimension (3D) libraries can be readily used for screening against protein targets. We also provide a simple method and tool for conducting identity-based filtering. Access to this dataset will accelerate small peptide screening workflows and encourage their use in drug discovery campaigns. As a case study, the developed library was screened against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease to identify potential small peptide inhibitors.
Collapse
Affiliation(s)
- Sarfraz Ahmad
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, Ontario, Canada
- Binary Star Research Services, LaSalle N9J 3X8, Ontario, Canada
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, Ontario, Canada
- Binary Star Research Services, LaSalle N9J 3X8, Ontario, Canada
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, Ontario, Canada
- Binary Star Research Services, LaSalle N9J 3X8, Ontario, Canada
| |
Collapse
|
45
|
Chen S, Arutyunova E, Lu J, Khan MB, Rut W, Zmudzinski M, Shahbaz S, Iyyathurai J, Moussa EW, Turner Z, Bai B, Lamer T, Nieman JA, Vederas JC, Julien O, Drag M, Elahi S, Young HS, Lemieux MJ. SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals. ACS CENTRAL SCIENCE 2023; 9:696-708. [PMID: 37122453 PMCID: PMC10042146 DOI: 10.1021/acscentsci.3c00054] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Indexed: 05/03/2023]
Abstract
The main protease of SARS-CoV-2 (Mpro) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in Mpro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 Mpro mutants provided structural insight into their altered functionality. Additionally, we show Mpro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting Mpro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.
Collapse
Affiliation(s)
- Sizhu
Amelia Chen
- 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
| | - 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
| | - Jimmy Lu
- 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
| | - Wioletta Rut
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Mikolaj Zmudzinski
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shima Shahbaz
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jegan Iyyathurai
- 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
| | - Eman W. Moussa
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Zoe Turner
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - 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
| | - Tess Lamer
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, 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
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Marcin Drag
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shokrollah Elahi
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Howard S. Young
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, 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
| |
Collapse
|
46
|
Narwal M, Armache JP, Edwards TJ, Murakami KS. SARS-CoV-2 polyprotein substrate regulates the stepwise M pro cleavage reaction. J Biol Chem 2023; 299:104697. [PMID: 37044215 PMCID: PMC10084705 DOI: 10.1016/j.jbc.2023.104697] [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: 02/15/2023] [Revised: 03/22/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
The processing of the Coronavirus polyproteins pp1a and pp1ab by the main protease Mpro to produce mature proteins is a crucial event in virus replication and a promising target for antiviral drug development. Mpro cleaves polyproteins in a defined order, but how Mpro and/or the polyproteins determine the order of cleavage remains enigmatic due to a lack of structural information about polyprotein-bound Mpro. Here, we present the cryo-EM structures of SARS-CoV-2 Mpro in an apo form and in complex with the nsp7-10 region of the pp1a polyprotein. The complex structure shows that Mpro interacts with only the recognition site residues between nsp9 and nsp10, without any association with the rest of the polyprotein. Comparison between the apo form and polyprotein-bound structures of Mpro highlights the flexible nature of the active site region of Mpro, which allows it to accommodate 10 recognition sites found in the polyprotein. These observations suggest that the role of Mpro in selecting a preferred cleavage site is limited and underscore the roles of the structure, conformation and/or dynamics of the polyproteins in determining the sequence of polyprotein cleavage by Mpro.
Collapse
Affiliation(s)
- Manju Narwal
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Center for Structural Biology, Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
| | - Thomas J Edwards
- National Cryo-EM Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Center for Structural Biology, Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
47
|
Zhang H, Liang B, Sang X, An J, Huang Z. Discovery of Potential Inhibitors of SARS-CoV-2 Main Protease by a Transfer Learning Method. Viruses 2023; 15:v15040891. [PMID: 37112871 PMCID: PMC10143255 DOI: 10.3390/v15040891] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 remains a global public health threat and has prompted the development of antiviral therapies. Artificial intelligence may be one of the strategies to facilitate drug development for emerging and re-emerging diseases. The main protease (Mpro) of SARS-CoV-2 is an attractive drug target due to its essential role in the virus life cycle and high conservation among SARS-CoVs. In this study, we used a data augmentation method to boost transfer learning model performance in screening for potential inhibitors of SARS-CoV-2 Mpro. This method appeared to outperform graph convolution neural network, random forest and Chemprop on an external test set. The fine-tuned model was used to screen for a natural compound library and a de novo generated compound library. By combination with other in silico analysis methods, a total of 27 compounds were selected for experimental validation of anti-Mpro activities. Among all the selected hits, two compounds (gyssypol acetic acid and hyperoside) displayed inhibitory effects against Mpro with IC50 values of 67.6 μM and 235.8 μM, respectively. The results obtained in this study may suggest an effective strategy of discovering potential therapeutic leads for SARS-CoV-2 and other coronaviruses.
Collapse
|
48
|
Omage FB, Madabeni A, Tucci AR, Nogara PA, Bortoli M, Rosa ADS, Neuza Dos Santos Ferreira V, Teixeira Rocha JB, Miranda MD, Orian L. Diphenyl Diselenide and SARS-CoV-2: in silico Exploration of the Mechanisms of Inhibition of Main Protease (M pro) and Papain-like Protease (PL pro). J Chem Inf Model 2023; 63:2226-2239. [PMID: 36952618 PMCID: PMC10091420 DOI: 10.1021/acs.jcim.3c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The SARS-CoV-2 pandemic has prompted global efforts to develop therapeutics. The main protease of SARS-CoV-2 (Mpro) and the papain-like protease (PLpro) are essential for viral replication and are key targets for therapeutic development. In this work, we investigate the mechanisms of SARS-CoV-2 inhibition by diphenyl diselenide (PhSe)2 which is an archetypal model of diselenides and a renowned potential therapeutic agent. The in vitro inhibitory concentration of (PhSe)2 against SARS-CoV-2 in Vero E6 cells falls in the low micromolar range. Molecular dynamics (MD) simulations and density functional theory (DFT) calculations [level of theory: SMD-B3LYP-D3(BJ)/6-311G(d,p), cc-pVTZ] are used to inspect non-covalent inhibition modes of both proteases via π-stacking and the mechanism of covalent (PhSe)2 + Mpro product formation involving the catalytic residue C145, respectively. The in vitro CC50 (24.61 μM) and EC50 (2.39 μM) data indicate that (PhSe)2 is a good inhibitor of the SARS-CoV-2 virus replication in a cell culture model. The in silico findings indicate potential mechanisms of proteases' inhibition by (PhSe)2; in particular, the results of the covalent inhibition here discussed for Mpro, whose thermodynamics is approximatively isoergonic, prompt further investigation in the design of antiviral organodiselenides.
Collapse
Affiliation(s)
- Folorunsho Bright Omage
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul 97105-900, Brazil
| | - Andrea Madabeni
- Dipartimento di Scienze Chimiche, Università Degli Studi di Padova, Via Marzolo 1, Padova 35131, Italy
| | - Amanda Resende Tucci
- Laboratório de Vírus Respiratórios e Do Sarampo, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21041-210, Brazil
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21041-210, Brazil
| | - Pablo Andrei Nogara
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul 97105-900, Brazil
| | - Marco Bortoli
- Institute of Computational Chemistry and Catalysis (IQCC) and Department of Chemistry, Faculty of Sciences, University of Girona, C/M. A. Capmany 69, Girona 17003, Spain
| | - Alice Dos Santos Rosa
- Laboratório de Vírus Respiratórios e Do Sarampo, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21041-210, Brazil
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21041-210, Brazil
| | - Vivian Neuza Dos Santos Ferreira
- Laboratório de Vírus Respiratórios e Do Sarampo, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21041-210, Brazil
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21041-210, Brazil
| | - João Batista Teixeira Rocha
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul 97105-900, Brazil
| | - Milene Dias Miranda
- Laboratório de Vírus Respiratórios e Do Sarampo, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21041-210, Brazil
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21041-210, Brazil
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Università Degli Studi di Padova, Via Marzolo 1, Padova 35131, Italy
| |
Collapse
|
49
|
Noske GD, Song Y, Fernandes RS, Chalk R, Elmassoudi H, Koekemoer L, Owen CD, El-Baba TJ, Robinson CV, Oliva G, Godoy AS. An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition. Nat Commun 2023; 14:1545. [PMID: 36941262 PMCID: PMC10027274 DOI: 10.1038/s41467-023-37035-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
The main protease from SARS-CoV-2 (Mpro) is responsible for cleavage of the viral polyprotein. Mpro self-processing is called maturation, and it is crucial for enzyme dimerization and activity. Here we use C145S Mpro to study the structure and dynamics of N-terminal cleavage in solution. Native mass spectroscopy analysis shows that mixed oligomeric states are composed of cleaved and uncleaved particles, indicating that N-terminal processing is not critical for dimerization. A 3.5 Å cryo-EM structure provides details of Mpro N-terminal cleavage outside the constrains of crystal environment. We show that different classes of inhibitors shift the balance between oligomeric states. While non-covalent inhibitor MAT-POS-e194df51-1 prevents dimerization, the covalent inhibitor nirmatrelvir induces the conversion of monomers into dimers, even with intact N-termini. Our data indicates that the Mpro dimerization is triggered by induced fit due to covalent linkage during substrate processing rather than the N-terminal processing.
Collapse
Affiliation(s)
- Gabriela Dias Noske
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Yun Song
- Electron Bio-imaging Centre, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Rafaela Sachetto Fernandes
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Rod Chalk
- Centre for Medicines Discovery, Oxford University, OX1 3QU, Oxford, UK
| | - Haitem Elmassoudi
- Centre for Medicines Discovery, Oxford University, OX1 3QU, Oxford, UK
| | - Lizbé Koekemoer
- Centre for Medicines Discovery, Oxford University, OX1 3QU, Oxford, UK
| | - C David Owen
- Electron Bio-imaging Centre, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Tarick J El-Baba
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OX1 3TA, Oxford, UK
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, OX1 3QU, Oxford, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OX1 3TA, Oxford, UK
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, OX1 3QU, Oxford, UK
| | - Glaucius Oliva
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Andre Schutzer Godoy
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil.
| |
Collapse
|
50
|
Garg A, Goel N, Abhinav N, Varma T, Achari A, Bhattacharjee P, Kamal IM, Chakrabarti S, Ravichandiran V, Reddy AM, Gupta S, Jaisankar P. Virtual screening of natural products inspired in-house library to discover potential lead molecules against the SARS-CoV-2 main protease. J Biomol Struct Dyn 2023; 41:2033-2045. [PMID: 35043750 DOI: 10.1080/07391102.2022.2027271] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
SARS-CoV-2, a new coronavirus emerged in 2019, causing a global healthcare epidemic. Although a variety of drug targets have been identified as potential antiviral therapies, and effective candidate against SARS-CoV-2 remains elusive. One of the most promising targets for combating COVID-19 is SARS-CoV-2 Main protease (Mpro, a protein responsible for viral replication. In this work, an in-house curated library was thoroughly evaluated for druggability against Mpro. We identified four ligands (FG, Q5, P5, and PJ4) as potential inhibitors based on docking scores, predicted binding energies (MMGBSA), in silico ADME, and RMSD trajectory analysis. Among the selected ligands, FG, a natural product from Andrographis nallamalayana, exhibited the highest binding energy of -10.31 kcal/mol close to the docking score of clinical candidates Boceprevir and GC376. Other ligands (P5, natural product from cardiospermum halicacabum and two synthetic molecules Q5 and PJ4) have shown comparable docking scores ranging -7.65 kcal/mol to -7.18 kcal/mol. Interestingly, we found all four top ligands had Pi bond interaction with the main amino acid residues HIS41 and CYS145 (catalytic dyad), H-bonding interactions with GLU166, ARG188, and GLN189, and hydrophobic interactions with MET49 and MET165 in the binding site of Mpro. According to the ADME analysis, Q5 and P5 are within the acceptable range of drug likeliness, compared to FG and PJ4. The interaction stability of the lead molecules with viral protease was verified using replicated MD simulations. Thus, the present study opens up the opportunity of developing drug candidates targeting SARS-CoV-2 main protease (Mpro) to mitigate the disease.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Aakriti Garg
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, Chunilal Bhawan, Kolkata, India.,Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Narender Goel
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, Chunilal Bhawan, Kolkata, India.,Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Nipun Abhinav
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, Chunilal Bhawan, Kolkata, India.,Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Tanmay Varma
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, Chunilal Bhawan, Kolkata, India
| | - Anushree Achari
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Pinaki Bhattacharjee
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Izaz Monir Kamal
- Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saikat Chakrabarti
- Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Velayutham Ravichandiran
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, Chunilal Bhawan, Kolkata, India
| | | | - Sreya Gupta
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, Chunilal Bhawan, Kolkata, India
| | - Parasuraman Jaisankar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| |
Collapse
|