1
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Gao Q, Liu S, Zhou Y, Fan J, Ke S, Zhou Y, Fan K, Wang Y, Zhou Y, Xia Z, Deng X. Discovery of meisoindigo derivatives as noncovalent and orally available M pro inhibitors: their therapeutic implications in the treatment of COVID-19. Eur J Med Chem 2024; 273:116498. [PMID: 38762916 DOI: 10.1016/j.ejmech.2024.116498] [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: 02/16/2024] [Revised: 05/08/2024] [Accepted: 05/11/2024] [Indexed: 05/21/2024]
Abstract
The progressive emergence of SARS-CoV-2 variants has necessitated the urgent exploration of novel therapeutic strategies to combat the COVID-19 pandemic. The SARS-CoV-2 main protease (Mpro) represents an evolutionarily conserved therapeutic target for drug discovery. This study highlights the discovery of meisoindigo (Mei), derived from the traditional Chinese medicine (TCM) Indigo naturalis, as a novel non-covalent and nonpeptidic Mpro inhibitor. Substantial optimizations and structure-activity relationship (SAR) studies, guided by a structure-based drug design approach, led to the identification of several Mei derivatives, including S5-27 and S5-28, exhibiting low micromolar inhibition against SARS-CoV-2 Mpro with high binding affinity. Notably, S5-28 provided significant protection against wild-type SARS-CoV-2 in HeLa-hACE2 cells, with EC50 up to 2.66 μM. Furthermore, it displayed favorable physiochemical properties and remarkable gastrointestinal and metabolic stability, demonstrating its potential as an orally bioavailable drug for anti-COVID-19 therapy. This research presents a promising avenue for the development of new antiviral agents, offering hope in the ongoing battle against COVID-19.
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Affiliation(s)
- Qingtian Gao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Sixu Liu
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Yuzheng Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Jinbao Fan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Shufen Ke
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Yuqing Zhou
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Kaiqiang Fan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Yuxuan Wang
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Yingjun Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, 410013, Hunan, China
| | - Zanxian Xia
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China.
| | - Xu Deng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, 410013, Hunan, China.
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2
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Bairagya HR, Tasneem A, Sarmadhikari D. Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory. Proteins 2024; 92:735-749. [PMID: 38213131 DOI: 10.1002/prot.26665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/28/2023] [Accepted: 01/01/2024] [Indexed: 01/13/2024]
Abstract
The new viral strains of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are continuously rising, becoming more virulent, and transmissible. Therefore, the development of new antiviral drugs is essential. Due to its significant role in the viral life cycle of SARS-CoV-2, the main protease (Mpro) enzyme is a leading target for antiviral drug design. The Mpro monomer consists of domain DI, DII, and DI-DII interface. Twenty-one conserved water molecules (W4-W24) are occupied at these domains according to multiple crystal structure analyses. The crystal and MD structures reveal the presence of eight conserved water sites in domain DI, DII and remaining in the DI-DII interface. Grid-based inhomogeneous fluid solvation theory (GIST) was employed on MD structures of Mpro native to predict structural and thermodynamic properties of each conserved water site for focusing to identify the specific conserved water molecules that can easily be displaced by proposed ligands. Finally, MD water W13 is emerged as a promising candidate for water mimic drug design due to its low mean interaction energy, loose binding character with the protein, and its involvement in a water-mediated H-bond with catalytic His41 via the interaction Thr25(OG)---W13---W---His41(NE2). In this context, water occupancy, relative interaction energy, entropy, and topologies of W13 are thermodynamically acceptable for the water displacement method. Therefore, the strategic use of W13's geometrical position in the DI domain may be implemented for drug discovery against COVID disease by designing new ligands with appropriately oriented chemical groups to mimic its structural, electronic, and thermodynamic properties.
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Affiliation(s)
- Hridoy R Bairagya
- Computational Drug Design and Bio-molecular Simulation Lab, Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Alvea Tasneem
- Mathematical and Computational Biology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Debapriyo Sarmadhikari
- Computational Drug Design and Bio-molecular Simulation Lab, Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
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3
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Lis K, Plewka J, Menezes F, Bielecka E, Chykunova Y, Pustelny K, Niebling S, Garcia AS, Garcia-Alai M, Popowicz GM, Czarna A, Kantyka T, Pyrc K. SARS-CoV-2 M pro oligomerization as a potential target for therapy. Int J Biol Macromol 2024; 267:131392. [PMID: 38582483 DOI: 10.1016/j.ijbiomac.2024.131392] [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: 03/05/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
The main protease (Mpro) of SARS-CoV-2 is critical in the virus's replication cycle, facilitating the maturation of polyproteins into functional units. Due to its conservation across taxa, Mpro is a promising target for broad-spectrum antiviral drugs. Targeting Mpro with small molecule inhibitors, such as nirmatrelvir combined with ritonavir (Paxlovid™), which the FDA has approved for post-exposure treatment and prophylaxis, can effectively interrupt the replication process of the virus. A key aspect of Mpro's function is its ability to form a functional dimer. However, the mechanics of dimerization and its influence on proteolytic activity remain less understood. In this study, we utilized biochemical, structural, and molecular modelling approaches to explore Mpro dimerization. We evaluated critical residues, specifically Arg4 and Arg298, that are essential for dimerization. Our results show that changes in the oligomerization state of Mpro directly affect its enzymatic activity and dimerization propensity. We discovered a synergistic relationship influencing dimer formation, involving both intra- and intermolecular interactions. These findings highlight the potential for developing allosteric inhibitors targeting Mpro, offering promising new directions for therapeutic strategies.
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Affiliation(s)
- Kinga Lis
- Jagiellonian University, Malopolska Centre of Biotechnology, Virogenetics, Laboratory of Virology, Gronostajowa 7a, 30-387 Cracow, Poland; Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24,31-155 Cracow, Poland
| | - Jacek Plewka
- Jagiellonian University, Malopolska Centre of Biotechnology, Virogenetics, Laboratory of Virology, Gronostajowa 7a, 30-387 Cracow, Poland
| | - Filipe Menezes
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Ewa Bielecka
- Jagiellonian University, Malopolska Centre of Biotechnology, Laboratory of Proteolysis and Post-translational Modification of Proteins, Gronostajowa 7a, 30-387 Cracow, Poland
| | - Yuliya Chykunova
- Jagiellonian University, Malopolska Centre of Biotechnology, Virogenetics, Laboratory of Virology, Gronostajowa 7a, 30-387 Cracow, Poland; Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Microbiology Department, Gronostajowa 7, 30-387, Cracow, Poland
| | - Katarzyna Pustelny
- Jagiellonian University, Malopolska Centre of Biotechnology, Gronostajowa 7a, 30-387 Cracow, Poland
| | - Stephan Niebling
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, Hamburg, Germany; Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Angelica Struve Garcia
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, Hamburg, Germany; Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, Hamburg, Germany; Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Grzegorz M Popowicz
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Anna Czarna
- Jagiellonian University, Malopolska Centre of Biotechnology, Gronostajowa 7a, 30-387 Cracow, Poland.
| | - Tomasz Kantyka
- Jagiellonian University, Malopolska Centre of Biotechnology, Laboratory of Proteolysis and Post-translational Modification of Proteins, Gronostajowa 7a, 30-387 Cracow, Poland.
| | - Krzysztof Pyrc
- Jagiellonian University, Malopolska Centre of Biotechnology, Virogenetics, Laboratory of Virology, Gronostajowa 7a, 30-387 Cracow, Poland.
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4
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Zhang Y, Guo J, Liu Y, Qu Y, Li YQ, Mu Y, Li W. An allosteric mechanism for potent inhibition of SARS-CoV-2 main proteinase. Int J Biol Macromol 2024; 265:130644. [PMID: 38462102 DOI: 10.1016/j.ijbiomac.2024.130644] [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] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
The main proteinase (Mpro) of SARS-CoV-2 plays a critical role in cleaving viral polyproteins into functional proteins required for viral replication and assembly, making it a prime drug target for COVID-19. It is well known that noncompetitive inhibition offers potential therapeutic options for treating COVID-19, which can effectively reduce the likelihood of cross-reactivity with other proteins and increase the selectivity of the drug. Therefore, the discovery of allosteric sites of Mpro has both scientific and practical significance. In this study, we explored the binding characteristics and inhibiting process of Mpro activity by two recently reported allosteric inhibitors, pelitinib and AT7519 which were obtained by the X-ray screening experiments, to probe the allosteric mechanism via molecular dynamic (MD) simulations. We found that pelitinib and AT7519 can stably bind to Mpro far from the active site. The binding affinity is estimated to be -24.37 ± 4.14 and - 26.96 ± 4.05 kcal/mol for pelitinib and AT7519, respectively, which is considerably stable compared with orthosteric drugs. Furthermore, the strong binding caused clear changes in the catalytic site of Mpro, thus decreasing the substrate accessibility. The community network analysis also validated that pelitinib and AT7519 strengthened intra- and inter-domain communication of Mpro dimer, resulting in a rigid Mpro, which could negatively impact substrate binding. In summary, our findings provide the detailed working mechanism for the two experimentally observed allosteric sites of Mpro. These allosteric sites greatly enhance the 'druggability' of Mpro and represent attractive targets for the development of new Mpro inhibitors.
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Affiliation(s)
- Yunju Zhang
- School of Physics, Shandong University, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao
| | - Yang Liu
- School of Physics, Shandong University, China
| | - Yuanyuan Qu
- School of Physics, Shandong University, China
| | | | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Weifeng Li
- School of Physics, Shandong University, China.
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5
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Mahgoub RE, Mohamed FE, Ali BR, Ferreira J, Rabeh WM, Atatreh N, Ghattas MA. Discovery of pyrimidoindol and benzylpyrrolyl inhibitors targeting SARS-CoV-2 main protease (M pro) through pharmacophore modelling, covalent docking, and biological evaluation. J Mol Graph Model 2024; 127:108672. [PMID: 37992552 DOI: 10.1016/j.jmgm.2023.108672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
The main protease (Mpro) enzyme has an imperative function in disease progression and the life cycle of the SARS-CoV-2 virus. Although the orally active drug nirmatrelvir (co-administered with ritonavir as paxlovid) has been approved for emergency use as the frontline antiviral agent, there are a number of limitations that necessitate the discovery of new drug scaffolds, such as poor pharmacokinetics and susceptibility to proteolytic degradation due to its peptidomimetic nature. This study utilized a novel virtual screening workflow that combines pharmacophore modelling, multiple-receptor covalent docking, and biological evaluation in order to find new Mpro inhibitors. After filtering and analysing ∼66,000 ligands from three different electrophilic libraries, 29 compounds were shortlisted for experimental testing, and two of them exhibited ≥20% inhibition at 100 μM. Our top candidate, GF04, is a benzylpyrrolyl compound that exhibited the highest inhibition activity of 38.3%, with a relatively small size (<350 Da) and leadlike character. Interestingly, our approach also identified another hit, DR07, a pyrimidoindol with a non-peptide character, and a molecular weight of 438.9 Da, reporting an inhibition of 26.3%. The established approach detailed in this study, in conjunction with the discovered inhibitors, has the capacity to yield novel perspectives for devising covalent inhibitors targeting the COVID-19 Mpro enzyme and other comparable targets.
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Affiliation(s)
- Radwa E Mahgoub
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, 15551, United Arab Emirates; Zayed Centre for Health Sciences, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Juliana Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates.
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6
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Gerhart J, Cox DS, Singh RSP, Chan PLS, Rao R, Allen R, Shi H, Masters JC, Damle B. A Comprehensive Review of the Clinical Pharmacokinetics, Pharmacodynamics, and Drug Interactions of Nirmatrelvir/Ritonavir. Clin Pharmacokinet 2024; 63:27-42. [PMID: 38177893 PMCID: PMC10786959 DOI: 10.1007/s40262-023-01339-y] [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] [Accepted: 12/11/2023] [Indexed: 01/06/2024]
Abstract
Nirmatrelvir is a potent and selective inhibitor of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease that is used as an oral antiviral coronavirus disease 2019 (COVID-19) treatment. To sustain unbound systemic trough concentrations above the antiviral in vitro 90% effective concentration value (EC90), nirmatrelvir is coadministered with 100 mg of ritonavir, a pharmacokinetic enhancer. Ritonavir inhibits nirmatrelvir's cytochrome P450 (CYP) 3A4-mediated metabolism which results in renal elimination becoming the primary route of nirmatrelvir elimination when dosed concomitantly. Nirmatrelvir exhibits absorption-limited nonlinear pharmacokinetics. When coadministered with ritonavir in patients with mild-to-moderate COVID-19, nirmatrelvir reaches a maximum concentration of 3.43 µg/mL (11.7× EC90) in approximately 3 h on day 5 of dosing, with a geometric mean day 5 trough concentration of 1.57 µg/mL (5.4× EC90). Drug interactions with nirmatrelvir/ritonavir (PAXLOVIDTM) are primarily attributed to ritonavir-mediated CYP3A4 inhibition, and to a lesser extent CYP2D6 and P-glycoprotein inhibition. Population pharmacokinetics and quantitative systems pharmacology modeling support twice daily dosing of 300 mg/100 mg nirmatrelvir/ritonavir for 5 days, with a reduced 150 mg/100 mg dose for patients with moderate renal impairment. Rapid clinical development of nirmatrelvir/ritonavir in response to the emerging COVID-19 pandemic was enabled by innovations in clinical pharmacology research, including an adaptive phase 1 trial design allowing direct to pivotal phase 3 development, fluorine nuclear magnetic resonance spectroscopy to delineate absorption, distribution, metabolism, and excretion profiles, and innovative applications of model-informed drug development to accelerate development.
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Affiliation(s)
- Jacqueline Gerhart
- Pfizer Inc, Research and Development, 500 Arcola Road, Collegeville, PA, 19424, USA.
| | - Donna S Cox
- Pfizer Inc, Research and Development, 500 Arcola Road, Collegeville, PA, 19424, USA
| | | | | | - Rohit Rao
- Pfizer Inc, Research and Development, Cambridge, MA, USA
| | - Richard Allen
- Pfizer Inc, Research and Development, Cambridge, MA, USA
| | - Haihong Shi
- Pfizer Inc, Research and Development, Groton, CT, USA
| | | | - Bharat Damle
- Pfizer Inc, Research and Development, New York, NY, USA
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7
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Song L, Gao S, Ye B, Yang M, Cheng Y, Kang D, Yi F, Sun JP, Menéndez-Arias L, Neyts J, Liu X, Zhan P. Medicinal chemistry strategies towards the development of non-covalent SARS-CoV-2 M pro inhibitors. Acta Pharm Sin B 2024; 14:87-109. [PMID: 38239241 PMCID: PMC10792984 DOI: 10.1016/j.apsb.2023.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 01/22/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life cycle. The covalent Mpro inhibitor nirmatrelvir (in combination with ritonavir, a pharmacokinetic enhancer) and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic use. Effective antiviral drugs are needed to fight the pandemic, while non-covalent Mpro inhibitors could be promising alternatives due to their high selectivity and favorable druggability. Numerous non-covalent Mpro inhibitors with desirable properties have been developed based on available crystal structures of Mpro. In this article, we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent Mpro inhibitors, followed by a general overview and critical analysis of the available information. Prospective viewpoints and insights into current strategies for the development of non-covalent Mpro inhibitors are also discussed.
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Affiliation(s)
- Letian Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
| | - Bing Ye
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Mianling Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yusen Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Fan Yi
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas & Autonomous University of Madrid), Madrid 28049, Spain
| | - Johan Neyts
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven 3000, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
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8
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De SK. Discovery of Novel Cysteine Protease Inhibitors for the Treatment of Coronavirus (COVID-19). Curr Med Chem 2024; 31:1165-1169. [PMID: 37211851 DOI: 10.2174/0929867330666230519163305] [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: 02/11/2023] [Revised: 04/09/2023] [Accepted: 04/19/2023] [Indexed: 05/23/2023]
Abstract
The application describes compounds, such as compounds of general Formula, with warheads and their use in treating medical diseases or disorders, such as viral infections. Pharmaceutical compositions and synthetic methods of various compounds with warheads are included. The compounds are inhibitors of proteases, such as the 3C, CL- or 3CL-like protease.
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Affiliation(s)
- Surya K De
- Department of Chemistry, Conju-Probe, San Diego, California, USA
- Department of Chemistry, Bharath University, Chennai, Tamil Nadu, 600126, India
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9
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Alzyoud L, Mahgoub RE, Mohamed FE, Ali BR, Ferreira J, Rabeh WM, Atatreh N, Ghattas MA. The Discovery of Novel Small Oxindole-Based Inhibitors Targeting the SARS-CoV-2 Main Protease (M pro ). Chem Biodivers 2023; 20:e202301176. [PMID: 37861105 DOI: 10.1002/cbdv.202301176] [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: 08/07/2023] [Revised: 10/14/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Abstract
With the potential for coronaviruses to re-emerge and trigger future pandemics, the urgent development of antiviral inhibitors against SARS-CoV-2 is essential. The Mpro enzyme is crucial for disease progression and the virus's life cycle. It possesses allosteric sites that can hinder its catalytic activity, with some of these sites located at or near the dimerization interface. Among them, sites #2 and #5 possess druggable pockets and are predicted to bind drug-like molecules. Consequently, a commercially available ligand library containing ~7 million ligands was used to target site #2 via structure-based virtual screening. After extensive filtering, docking, and post-docking analyses, 53 compounds were chosen for biological testing. An oxindole derivative was identified as a Mpro non-competitive reversible inhibitor with a Ki of 115 μM and an IC50 of 101.9 μM. Throughout the 200 ns-long MD trajectories, our top hit has shown a very stable binding mode, forming several interactions with residues in sites #2 and #5. Moreover, derivatives of our top hit were acquired for biological testing to gain deeper insights into their structure-activity relationship. To sum up, drug-like allosteric inhibitors seem promising and can provide us with an additional weapon in our war against the recent pandemic, and possibly other coronaviruses-caused diseases.
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Affiliation(s)
- Lara Alzyoud
- College of Pharmacy, Al Ain University, Abu, Dhabi, 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, 64141, United Arab Emirates
| | - Radwa E Mahgoub
- College of Pharmacy, Al Ain University, Abu, Dhabi, 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, 64141, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
- Zayed Centre for Health Sciences, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Juliana Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu, Dhabi, 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, 64141, United Arab Emirates
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University, Abu, Dhabi, 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, 64141, United Arab Emirates
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10
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Kubra B, Badshah SL, Faisal S, Sharaf M, Emwas AH, Jaremko M, Abdalla M. Inhibition of the predicted allosteric site of the SARS-CoV-2 main protease through flavonoids. J Biomol Struct Dyn 2023; 41:9103-9120. [PMID: 36404610 DOI: 10.1080/07391102.2022.2140201] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/19/2022] [Indexed: 11/22/2022]
Abstract
Since its emergence in 2019, coronavirus infection (COVID-19) has become a global pandemic and killed several million people worldwide. Even though several types of vaccines are available against the COVID-19 virus, SARS-CoV-2, new strains are emerging that pose a constant danger to vaccine effectiveness. In this computational study, we identified and predicted potent allosteric inhibitors of the SARS-CoV-2 main protease (Mpro). Via molecular docking and simulations, more than 100 distinct flavonoids were docked with the allosteric site of Mpro. Docking experiments revealed four top hit compounds (Hesperidin, Schaftoside, Brickellin, and Marein) that bound strongly to the Mpro predicted allosteric site. Simulation analyses further revealed that these continually interacted with the enzyme's allosteric region throughout the simulation time. ADMET and Lipinski drug likenesses were calculated to indicate the therapeutic value of the top four hits: They were non-toxic and exhibited high human intestinal absorption concentrations. These novel allosteric site inhibitors provide a higher chance of drugging SARS-CoV2 Mpro due to the rapid mutation rate of the viral enzyme's active sites. Our findings provide a new avenue for developing novel allosteric inhibitors of SARS-CoV-2 Mpro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bibi Kubra
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Mohamed Sharaf
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, Shandong, China
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11
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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.
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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.
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12
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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.
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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
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13
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Ksouri A, Klouz A, Bouhaouala-Zahar B, Moussa F, Bezzarga M. Docking-Based Evidence for the Potential of ImmunoDefender: A Novel Formulated Essential Oil Blend Incorporating Synergistic Antiviral Bioactive Compounds as Promising Mpro Inhibitors against SARS-CoV-2. Molecules 2023; 28:molecules28114296. [PMID: 37298772 DOI: 10.3390/molecules28114296] [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: 04/09/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023] Open
Abstract
Essential oils (Eos) have demonstrated antiviral activity, but their toxicity can hinder their use as therapeutic agents. Recently, some essential oil components have been used within safe levels of acceptable daily intake limits without causing toxicity. The "ImmunoDefender," a novel antiviral compound made from a well-known mixture of essential oils, is considered highly effective in treating SARS-CoV-2 infections. The components and doses were chosen based on existing information about their structure and toxicity. Blocking the main protease (Mpro) of SARS-CoV-2 with high affinity and capacity is critical for inhibiting the virus's pathogenesis and transmission. In silico studies were conducted to examine the molecular interactions between the main essential oil components in "ImmunoDefender" and SARS-CoV-2 Mpro. The screening results showed that six key components of ImmunoDefender formed stable complexes with Mpro via its active catalytic site with binding energies ranging from -8.75 to -10.30 kcal/mol, respectively for Cinnamtannin B1, Cinnamtannin B2, Pavetannin C1, Syzyginin B, Procyanidin C1, and Tenuifolin. Furthermore, three essential oil bioactive inhibitors, Cinnamtannin B1, Cinnamtannin B2, and Pavetannin C, had significant ability to bind to the allosteric site of the main protease with binding energies of -11.12, -10.74, and -10.79 kcal/mol; these results suggest that these essential oil bioactive compounds may play a role in preventing the attachment of the translated polyprotein to Mpro, inhibiting the virus's pathogenesis and transmission. These components also had drug-like characteristics similar to approved and effective drugs, suggesting that further pre-clinical and clinical studies are needed to confirm the generated in silico outcomes.
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Affiliation(s)
- Ayoub Ksouri
- Laboratoire des Biomolécules, Venins et Applications Théranostiques, Institut Pasteur de Tunis, Université Tunis El Manar, 13 Place Pasteur, BP74, Tunis 1002, Tunisia
| | - Anis Klouz
- Faculté de Médecine de Tunis, Université Tunis El Manar, 15 Rue Djebel Lakhdhar, La Rabta, Tunis 1007, Tunisia
| | - Balkiss Bouhaouala-Zahar
- Laboratoire des Biomolécules, Venins et Applications Théranostiques, Institut Pasteur de Tunis, Université Tunis El Manar, 13 Place Pasteur, BP74, Tunis 1002, Tunisia
- Faculté de Médecine de Tunis, Université Tunis El Manar, 15 Rue Djebel Lakhdhar, La Rabta, Tunis 1007, Tunisia
| | - Fathi Moussa
- Institute of Physical Chemistry, CNRS-UMR 8000, University Paris-Saclay, Rue Noetzlin, 91190 Gif-sur-Yvette, France
| | - Mounir Bezzarga
- Laboratoire de Modélisation Mathématique, Faculté des Sciences de Tunis, Université Tunis El Manar, Analyse Harmonique et Théorie du Potentiel, Campus Universitaire, Tunis 1068, Tunisia
- Institut Préparatoire aux Etudes d'Ingénieurs de Tunis, Université de Tunis, Tunis 1068, Tunisia
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14
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Spiegel M, Ciardullo G, Marino T, Russo N. Computational investigation on the antioxidant activities and on the M pro SARS-CoV-2 non-covalent inhibition of isorhamnetin. Front Chem 2023; 11:1122880. [PMID: 36762196 PMCID: PMC9902383 DOI: 10.3389/fchem.2023.1122880] [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: 12/13/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023] Open
Abstract
In the present work, we report a computational study on some important chemical properties of the flavonoid isorhamnetin, used in traditional medicine in many countries. In the course of the study we determined the acid-base equilibria in aqueous solution, the possible reaction pathways with the •OOH radical and the corresponding kinetic constants, the complexing capacity of copper ions, and the reduction of these complexes by reducing agents such as superoxide and ascorbic anion by using density functional level of theory Density Functional Theory. Finally, the non-covalent inhibition ability of the SARS-CoV-2 main protease enzyme by isorhamnetin was examined by molecular dynamics (MD) and docking investigation.
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Affiliation(s)
- Maciej Spiegel
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Cosenza, Italy,Department of Pharmacognosy and Herbal Medicines, Wroclaw Medical University, Wroclaw, Poland
| | - Giada Ciardullo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Cosenza, Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Cosenza, Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Cosenza, Italy,*Correspondence: Nino Russo,
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15
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Green and efficient one-pot three-component synthesis of novel drug-like furo[2,3–d]pyrimidines as potential active site inhibitors and putative allosteric hotspots modulators of both SARS-CoV-2 MPro and PLPro. Bioorg Chem 2023; 135:106390. [PMID: 37037129 PMCID: PMC9883075 DOI: 10.1016/j.bioorg.2023.106390] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/29/2023]
Abstract
In this paper, an environmentally benign, convenient, and efficient one-pot three-component reaction has been developed for the regioselective synthesis of novel 5-aroyl(or heteroaroyl)-6-(alkylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-diones (4a‒n) through the sequential condensation of aryl(or heteroaryl)glyoxal monohydrates (1a‒g), 1,3-dimethylbarbituric acid (2), and alkyl(viz. cyclohexyl or tert-butyl)isocyanides (3a or 3b) catalyzed by ultra-low loading ZrOCl2•8H2O (just 2 mol%) in water at 50 ˚C. After synthesis and characterization of the mentioned furo[2,3-d]pyrimidines (4a‒n), their multi-targeting inhibitory properties were investigated against the active site and putative allosteric hotspots of both SARS-CoV-2 main protease (MPro) and papain-like protease (PLPro) based on molecular docking studies and compare the attained results with various medicinal compounds which approximately in three past years were used, introduced, and or repurposed to fight against COVID-19. Furthermore, drug-likeness properties of the mentioned small heterocyclic frameworks (4a‒n) have been explored using in silico ADMET analyses. Interestingly, the molecular docking studies and ADMET-related data revealed that the novel series of furo[2,3-d]pyrimidines (4a‒n), especially 5-(3,4-methylendioxybenzoyl)-6-(cyclohexylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-dione (4g) as hit one is potential COVID-19 drug candidate, can subject to further in vitro and in vivo studies. It is worthwhile to note that the protein-ligand-type molecular docking studies on the human body temperature-dependent MPro protein that surprisingly contains zincII (ZnII) ion between His41/Cys145 catalytic dyad in the active site, which undoubtedly can make new plans for designing novel SARS-CoV-2 MPro inhibitors, is performed for the first time in this paper, to the best of our knowledge.
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