1
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Yamamoto C, Taniguchi M, Furukawa K, Inaba T, Niiyama Y, Ide D, Mizutani S, Kuroda J, Tanino Y, Nishioka K, Watanabe Y, Takayama K, Nakaya T, Nukui Y. Nirmatrelvir Resistance in an Immunocompromised Patient with Persistent Coronavirus Disease 2019. Viruses 2024; 16:718. [PMID: 38793600 PMCID: PMC11125932 DOI: 10.3390/v16050718] [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: 04/03/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Although the coronavirus disease 2019 (COVID-19) pandemic is coming to an end, it still poses a threat to the immunocompromised and others with underlying diseases. Especially in cases of persistent COVID-19, new mutations conferring resistance to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) therapies have considerable clinical implications. We present a patient who independently acquired a T21I mutation in the 3CL protease after nirmatrelvir exposure. The T21I mutation in the 3CL protease is one of the most frequent mutations responsible for nirmatrelvir resistance. However, limited reports exist on actual cases of SARS-CoV-2 with T21I and other mutations in the 3CL protease. The patient, a 55 year-old male, had COVID-19 during chemotherapy for multiple myeloma. He was treated with nirmatrelvir early in the course of the disease but relapsed, and SARS-CoV-2 with a T21I mutation in the 3CL protease was detected in nasopharyngeal swab fluid. The patient had temporary respiratory failure but later recovered well. During treatment with remdesivir and dexamethasone, viruses with the T21I mutation in the 3CL protease showed a decreasing trend during disease progression while increasing during improvement. The impact of drug-resistant SARS-CoV-2 on the clinical course, including its severity, remains unknown. Our study is important for examining the clinical impact of nirmatrelvir resistance in COVID-19.
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Affiliation(s)
- Chie Yamamoto
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (K.F.); (T.I.); (Y.N.)
| | - Masashi Taniguchi
- Department of Infectious Disease, Kyoto City Hospital, Kyoto 604-8845, Japan;
| | - Keitaro Furukawa
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (K.F.); (T.I.); (Y.N.)
| | - Toru Inaba
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (K.F.); (T.I.); (Y.N.)
| | - Yui Niiyama
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.N.); (D.I.); (S.M.); (J.K.)
| | - Daisuke Ide
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.N.); (D.I.); (S.M.); (J.K.)
| | - Shinsuke Mizutani
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.N.); (D.I.); (S.M.); (J.K.)
| | - Junya Kuroda
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.N.); (D.I.); (S.M.); (J.K.)
| | - Yoko Tanino
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.T.); (K.N.); (Y.W.); (T.N.)
| | - Keisuke Nishioka
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.T.); (K.N.); (Y.W.); (T.N.)
| | - Yohei Watanabe
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.T.); (K.N.); (Y.W.); (T.N.)
| | - Koichi Takayama
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan;
| | - Takaaki Nakaya
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.T.); (K.N.); (Y.W.); (T.N.)
| | - Yoko Nukui
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (K.F.); (T.I.); (Y.N.)
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2
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El-Hddad SSA, Sobhy MH, El-Morsy A, Shoman NA, El-Adl K. Quinazolines and thiazolidine-2,4-dions as SARS-CoV-2 inhibitors: repurposing, in silico molecular docking and dynamics simulation. RSC Adv 2024; 14:13237-13250. [PMID: 38655479 PMCID: PMC11037030 DOI: 10.1039/d4ra02029d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 04/18/2024] [Indexed: 04/26/2024] Open
Abstract
This paper presents an extensive analysis of COVID-19 with a specific focus on VEGFR-2 inhibitors as potential treatments. The investigation includes an overview of computational methodologies employed in drug repurposing and highlights in silico research aimed at developing treatments for SARS-CoV-2. The study explores the possible effects of twenty-eight established VEGFR-2 inhibitors, which include amide and urea linkers, against SARS-CoV-2. Among these, nine inhibitors exhibit highly promising in silico outcomes (designated as 3-6, 11, 24, 26, 27, and sorafenib) and are subjected to extensive molecular dynamics (MD) simulations to evaluate the binding modes and affinities of these inhibitors to the SARS-CoV-2 Mpro across a 100 ns timeframe. Additionally, MD simulations are conducted to ascertain the binding free energy of the most compelling ligand-pocket complexes identified through docking studies. The findings provide valuable understanding regarding the dynamic and thermodynamic properties of the interactions between ligands and pockets, reinforcing the outcomes of the docking studies and presenting promising prospects for the creation of therapeutic treatments targeting COVID-19.
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Affiliation(s)
- Sanadelaslam S A El-Hddad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Omar Almukhtar University Al Bayda 991 Libya
| | - Mohamed H Sobhy
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development Cairo Egypt
| | - Ahmed El-Morsy
- Pharmaceutical Chemistry Department, College of Pharmacy, The Islamic University Najaf Iraq
| | - Nabil A Shoman
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Ahram Canadian University Giza Egypt
| | - Khaled El-Adl
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development Cairo Egypt
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University Cairo11884 Egypt
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3
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Hakim MS, Gunadi, Rahayu A, Wibawa H, Eryvinka LS, Supriyati E, Vujira KA, Iskandar K, Afiahayati, Daniwijaya EW, Oktoviani FN, Annisa L, Utami FDT, Amadeus VC, Nurhidayah SS, Leksono TP, Halim FV, Arguni E, Nuryastuti T, Wibawa T. Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia. Virus Genes 2024:10.1007/s11262-023-02048-1. [PMID: 38244104 DOI: 10.1007/s11262-023-02048-1] [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: 06/25/2023] [Accepted: 12/22/2023] [Indexed: 01/22/2024]
Abstract
During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022. Various bioinformatics tools were employed to investigate the evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study period, 213 and 139 isolates of Omicron and Delta variants were identified, respectively. Particularly in the Spike gene, mutations were significantly more abundant in Omicron than in Delta variants. Consistently, in all of four genes studied, the substitution rates of Omicron were higher than that of Delta variants, especially in the Spike and nsp12 genes. In addition, selective pressure analysis revealed several sites that were positively selected in particular genes, implying that these sites were functionally essential for virus evolution. In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.
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Affiliation(s)
- Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Gunadi
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ayu Rahayu
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates, Directorate General of Livestok Services, Ministry of Agriculture, Yogyakarta, Indonesia
| | - Laudria Stella Eryvinka
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Khanza Adzkia Vujira
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health and Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Farida Nur Oktoviani
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Luthvia Annisa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fadila Dyah Trie Utami
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Verrell Christopher Amadeus
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Setiani Silvy Nurhidayah
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tiara Putri Leksono
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fiqih Vidiantoro Halim
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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4
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Tian L, Qiang T, Yang X, Gao Y, Zhai X, Kang K, Du C, Lu Q, Gao H, Zhang D, Xie X, Liang C. Development of de-novo coronavirus 3-chymotrypsin-like protease (3CL pro) inhibitors since COVID-19 outbreak: A strategy to tackle challenges of persistent virus infection. Eur J Med Chem 2024; 264:115979. [PMID: 38048696 DOI: 10.1016/j.ejmech.2023.115979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/30/2023] [Accepted: 11/18/2023] [Indexed: 12/06/2023]
Abstract
Although no longer a public health emergency of international concern, COVID-19 remains a persistent and critical health concern. The development of effective antiviral drugs could serve as the ultimate piece of the puzzle to curbing this global crisis. 3-chymotrypsin-like protease (3CLpro), with its substrate specificity mirroring that of the main picornavirus 3C protease and conserved across various coronaviruses, emerges as an ideal candidate for broad-spectrum antiviral drug development. Moreover, it holds the potential as a reliable contingency option to combat emerging SARS-CoV-2 variants. In this light, the approved drugs, promising candidates, and de-novo small molecule therapeutics targeting 3CLpro since the COVID-19 outbreak in 2020 are discussed. Emphasizing the significance of diverse structural characteristics in inhibitors, be they peptidomimetic or nonpeptidic, with a shared mission to minimize the risk of cross-resistance. Moreover, the authors propose an innovative optimization strategy for 3CLpro reversible covalent PROTACs, optimizing pharmacodynamics and pharmacokinetics to better prepare for potential future viral outbreaks.
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Affiliation(s)
- Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
| | - Xiuding Yang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Yue Gao
- College of Pharmacy, Jinan University, Guangzhou, 511436, PR China
| | - Xiaopei Zhai
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Xi'an, 710032, PR China
| | - Kairui Kang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Cong Du
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Qi Lu
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Hong Gao
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Shaanxi Pioneer Biotech Co., Ltd., Xi'an, 710021, PR China
| | - Dezhu Zhang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Xiaolin Xie
- Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Chengyuan Liang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
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5
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Arya R, Tripathi P, Nayak K, Ganesh J, Bihani SC, Ghosh B, Prashar V, Kumar M. Insights into the evolution of mutations in SARS-CoV-2 non-spike proteins. Microb Pathog 2023; 185:106460. [PMID: 37995880 DOI: 10.1016/j.micpath.2023.106460] [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: 06/12/2023] [Revised: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
The COVID-19 pandemic has been driven by the emergence of SARS-CoV-2 variants with mutations across all the viral proteins. Although mutations in the spike protein have received significant attention, understanding the prevalence and potential impact of mutations in other viral proteins is essential for comprehending the evolution of SARS-CoV-2. Here, we conducted a comprehensive analysis of approximately 14 million sequences of SARS-CoV-2 deposited in the GISAID database until December 2022 to identify prevalent mutations in the non-spike proteins at the global and country levels. Additionally, we evaluated the energetics of each mutation to better understand their impact on protein stability. While the consequences of many mutations remain unclear, we discuss potential structural and functional significance of some mutations. Our study highlights the ongoing evolutionary process of SARS-CoV-2 and underscores the importance of understanding changes in non-spike proteins.
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Affiliation(s)
- Rimanshee Arya
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Preeti Tripathi
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Karthik Nayak
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; School of Chemical Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari, Mumbai, 400098, India
| | - Janani Ganesh
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Subhash C Bihani
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Biplab Ghosh
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India; Beamline Development & Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Vishal Prashar
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
| | - Mukesh Kumar
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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6
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Hu Y, Lewandowski EM, Tan H, Zhang X, Morgan RT, Zhang X, Jacobs LMC, Butler SG, Gongora MV, Choy J, Deng X, Chen Y, Wang J. Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir. ACS CENTRAL SCIENCE 2023; 9:1658-1669. [PMID: 37637734 PMCID: PMC10451032 DOI: 10.1021/acscentsci.3c00538] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Indexed: 08/29/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) is the drug target of Pfizer's oral drug nirmatrelvir. The emergence of SARS-CoV-2 variants with mutations in Mpro raised the alarm of potential drug resistance. To identify potential clinically relevant drug-resistant mutants, we systematically characterized 102 naturally occurring Mpro mutants located at 12 residues at the nirmatrelvir-binding site, among which 22 mutations in 5 residues, including S144M/F/A/G/Y, M165T, E166 V/G/A, H172Q/F, and Q192T/S/L/A/I/P/H/V/W/C/F, showed comparable enzymatic activity to the wild-type (kcat/Km < 10-fold change) while being resistant to nirmatrelvir (Ki > 10-fold increase). X-ray crystal structures were determined for six representative mutants with and/or without GC-376/nirmatrelvir. Using recombinant SARS-CoV-2 viruses generated from reverse genetics, we confirmed the drug resistance in the antiviral assay and showed that Mpro mutants with reduced enzymatic activity had attenuated viral replication. Overall, our study identified several drug-resistant hotspots in Mpro that warrant close monitoring for possible clinical evidence of nirmatrelvir resistance, some of which have already emerged in independent viral passage assays conducted by others.
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Affiliation(s)
- Yanmei Hu
- Department
of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Eric M. Lewandowski
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Haozhou Tan
- Department
of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Xiaoming Zhang
- Department
Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, United States
- Oklahoma
Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Ryan T. Morgan
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Xiujun Zhang
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Lian M. C. Jacobs
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Shane G. Butler
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Maura V. Gongora
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - John Choy
- Department
Biology, School of Arts and Sciences, the
Catholic University of America, Washington, DC 20064, United States
| | - Xufang Deng
- Department
Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, United States
- Oklahoma
Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Yu Chen
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Jun Wang
- Department
of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08854, United States
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7
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Beia ZC, Yu H, Wang H, Li Q, Wang B, Zhang D, Xu L, Zhao L, Dong S, Song Y. Orthogonal dual reporter-based gain-of-signal assay for probing SARS-CoV-2 3CL protease activity in living cells: inhibitor identification and mutation investigation. Emerg Microbes Infect 2023; 12:2211688. [PMID: 37144395 DOI: 10.1080/22221751.2023.2211688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The main protease (3-chymotrypsin-like protease, 3CLpro) of SARS-CoV-2 has become a focus of anti-coronavirus research. Despite efforts, drug development targeting 3CLpro has been hampered by limitations in the currently available activity assays. Additionally, the emergence of 3CLpro mutations in circulating SARS-CoV-2 variants has raised concerns about potential resistance. Both emphasize the need for a more reliable, sensitive, and facile 3CLpro assay. Here, we report an orthogonal dual reporter-based gain-of-signal assay for measuring 3CLpro activity in living cells. It builds on the finding that 3CLpro induces cytotoxicity and reporter expression suppression, which can be rescued by its inhibitor or mutation. This assay circumvents most limitations in previously reported assays, especially false positives caused by nonspecific compounds and signal interference from test compounds. It is also convenient and robust for high throughput screening of compounds and comparing the drug susceptibilities of mutants. Using this assay, we screened 1789 compounds, including natural products and protease inhibitors, with 45 compounds that have been reported to inhibit SARS-CoV-2 3CLpro among them. Except for the approved drug PF-07321332, only five of these inhibit 3CLpro in our assays: GC376; PF-00835231; S-217622; Boceprevir; and Z-FA-FMK. The susceptibilities of seven 3CLpro mutants prevalent in circulating variants to PF-07321332, S-217622, and GC376 were also assessed. Three mutants were identified as being less susceptible to PF-07321322 (P132H) and S-217622 (G15S, T21I). This assay should greatly facilitate the development of novel 3CLpro-targeted drugs and the monitoring of the susceptibility of emerging SARS-CoV-2 variants to 3CLpro inhibitors.
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Affiliation(s)
- Zhu-Chun Beia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Huanhuan Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
- The Affiliated AnNing First Hospital, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Hong Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
- Clinical laboratory, No.985 hospital, Joint Support Unit, Chinese People's Liberation Army, Taiyuan, 030001, China
| | - Baogang Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Dongna Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Likun Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Liangliang Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Shuwei Dong
- The Affiliated AnNing First Hospital, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Yabin Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
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8
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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.
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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
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9
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Gasparini P, Philot EA, Pantaleão SQ, Torres-Bonfim NESM, Kliousoff A, Quiroz RCN, Perahia D, Simões RP, Magro AJ, Scott AL. Unveiling mutation effects on the structural dynamics of the main protease from SARS-CoV-2 with hybrid simulation methods. J Mol Graph Model 2023; 121:108443. [PMID: 36870228 PMCID: PMC9945984 DOI: 10.1016/j.jmgm.2023.108443] [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: 10/10/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023]
Abstract
The main protease of SARS-CoV-2 (called Mpro or 3CLpro) is essential for processing polyproteins encoded by viral RNA. Several Mpro mutations were found in SARS-CoV-2 variants, which are related to higher transmissibility, pathogenicity, and resistance to neutralization antibodies. Macromolecules adopt several favored conformations in solution depending on their structure and shape, determining their dynamics and function. In this study, we used a hybrid simulation method to generate intermediate structures along the six lowest frequency normal modes and sample the conformational space and characterize the structural dynamics and global motions of WT SARS-CoV-2 Mpro and 48 mutations, including mutations found in P.1, B.1.1.7, B.1.351, B.1.525 and B.1.429+B.1.427 variants. We tried to contribute to the elucidation of the effects of mutation in the structural dynamics of SARS-CoV-2 Mpro. A machine learning analysis was performed following the investigation regarding the influence of the K90R, P99L, P108S, and N151D mutations on the dimeric interface assembling of the SARS-CoV-2 Mpro. The parameters allowed the selection of potential structurally stable dimers, which demonstrated that some single surface aa substitutions not located at the dimeric interface (K90R, P99L, P108S, and N151D) are able to induce significant quaternary changes. Furthermore, our results demonstrated, by a Quantum Mechanics method, the influence of SARS-CoV-2 Mpro mutations on the catalytic mechanism, confirming that only one of the chains of the WT and mutant SARS-CoV-2 Mpros are prone to cleave substrates. Finally, it was also possible to identify the aa residue F140 as an important factor related to the increasing enzymatic reactivity of a significant number of SARS-CoV-2 Mpro conformations generated by the normal modes-based simulations.
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Affiliation(s)
- P Gasparini
- Computational Biology and Biophysics Laboratory, Federal University of ABC - UFABC, Santo André, São Paulo, Brazil
| | - E A Philot
- Computational Biology and Biophysics Laboratory, Federal University of ABC - UFABC, Santo André, São Paulo, Brazil
| | - S Q Pantaleão
- Computational Biology and Biophysics Laboratory, Federal University of ABC - UFABC, Santo André, São Paulo, Brazil
| | - N E S M Torres-Bonfim
- Computational Biology and Biophysics Laboratory, Federal University of ABC - UFABC, Santo André, São Paulo, Brazil
| | - A Kliousoff
- Computational Biology and Biophysics Laboratory, Federal University of ABC - UFABC, Santo André, São Paulo, Brazil
| | - R C N Quiroz
- Computational Biology and Biophysics Laboratory, Federal University of ABC - UFABC, Santo André, São Paulo, Brazil
| | - D Perahia
- École Normale Supérieure Paris-Saclay, LBPA, Scaly, France
| | - R P Simões
- Department of Bioprocesses and Biotechnology, School of Agriculture (FCA), Unesp, Botucatu, São Paulo, Brazil
| | - A J Magro
- Department of Bioprocesses and Biotechnology, School of Agriculture (FCA), Unesp, Botucatu, São Paulo, Brazil; Institute of Biotechnology (IBTEC), Unesp, Botucatu, São Paulo, Brazil
| | - A L Scott
- Computational Biology and Biophysics Laboratory, Federal University of ABC - UFABC, Santo André, São Paulo, Brazil.
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10
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Focosi D, McConnell S, Shoham S, Casadevall A, Maggi F, Antonelli G. Nirmatrelvir and COVID-19: development, pharmacokinetics, clinical efficacy, resistance, relapse, and pharmacoeconomics. Int J Antimicrob Agents 2023; 61:106708. [PMID: 36603694 DOI: 10.1016/j.ijantimicag.2022.106708] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
Nirmatrelvir/ritonavir (N/R) is one of the most effective antiviral drugs against SARS-CoV-2. The preclinical development, pharmacodynamics and pharmacokinetics of N/R are reviewed herein. Randomized clinical trials have been conducted exclusively with pre-Omicron variants of concern, but in vitro studies show that efficacy against all Omicron sublineages is preserved, as confirmed by post-marketing observational studies. Nevertheless, investigations of large viral genome repositories have shown that mutation in the main protease causing resistance to N/R are increasingly frequent. In addition, virological and clinical rebounds after N/R discontinuation have been reported in immunocompetent patients. This finding is of concern when translated to immunocompromised patients, in whom N/R efficacy has not been formally investigated in clinical trials. Economical sustainability and perspectives for this therapeutic arena are discussed.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy.
| | - Scott McConnell
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
| | - Shmuel Shoham
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
| | - Arturo Casadevall
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases "Spallanzani", Rome, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, Sapienza University of Rome, and Sapienza University Hospital "Policlinico Umberto I", Rome, Italy
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11
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Yang F, Jiang XL, Tariq A, Sadia S, Ahmed Z, Sardans J, Aleem M, Ullah R, Bussmann RW. Potential medicinal plants involved in inhibiting 3CL pro activity: A practical alternate approach to combating COVID-19. JOURNAL OF INTEGRATIVE MEDICINE 2022; 20:488-496. [PMID: 35985974 PMCID: PMC9359926 DOI: 10.1016/j.joim.2022.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/29/2022] [Indexed: 01/25/2023]
Abstract
At present, a variety of vaccines have been approved, and existing antiviral drugs are being tested to find an effective treatment for coronavirus disease 2019 (COVID-19). However, no standardized treatment has yet been approved by the World Health Organization. The virally encoded chymotrypsin-like protease (3CLpro) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which facilitates the replication of SARS-CoV in the host cells, is one potential pharmacological target for the development of anti-SARS drugs. Online search engines, such as Web of Science, Google Scholar, Scopus and PubMed, were used to retrieve data on the traditional uses of medicinal plants and their inhibitory effects against the SARS-CoV 3CLpro. Various pure compounds, including polyphenols, terpenoids, chalcones, alkaloids, biflavonoids, flavanones, anthraquinones and glycosides, have shown potent inhibition of SARS-CoV-2 3CLpro activity with 50% inhibitory concentration (IC50) values ranging from 2-44 µg/mL. Interestingly, most of these active compounds, including xanthoangelol E (isolated from Angelica keiskei), dieckol 1 (isolated from Ecklonia cava), amentoflavone (isolated from Torreya nucifera), celastrol, pristimerin, tingenone and iguesterin (isolated from Tripterygium regelii), tannic acid (isolated from Camellia sinensis), and theaflavin-3,3'-digallate, 3-isotheaflav1in-3 gallate and dihydrotanshinone I (isolated from Salvia miltiorrhiza), had IC50 values of less than 15 µg/mL. Kinetic mechanistic studies of several active compounds revealed that their mode of inhibition was dose-dependent and competitive, with Ki values ranging from 2.4-43.8 μmol/L. Given the significance of plant-based compounds and the many promising results obtained, there is still need to explore the phytochemical and mechanistic potentials of plants and their products. These medicinal plants could serve as an effective inexpensive nutraceutical for the general public to help manage COVID-19.
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Affiliation(s)
- Fan Yang
- The Medical Center of General Practice, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu 610041, Sichuan Province, China
| | - Xiao-Lan Jiang
- The Medical Center of General Practice, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu 610041, Sichuan Province, China.
| | - Akash Tariq
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830041, Xinjiang Uygur Autonomous Region, China.
| | - Sehrish Sadia
- Department of Biological Sciences, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki 55300, Pakistan
| | - Zeeshan Ahmed
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830041, Xinjiang Uygur Autonomous Region, China
| | - Jordi Sardans
- Consejo Superior de Investigaciones Científicas, Global Ecology Unit, Centre for Ecological Research and Forestry Applications-Consejo Superior de Investigaciones Científicas-Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Catalonia, Spain; Centre for Ecological Research and Forestry Applications, Cerdanyola del Vallès 08193, Catalonia, Spain
| | - Muhammad Aleem
- Department of Biological Sciences, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki 55300, Pakistan
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Rainer W Bussmann
- Department of Ethnobotany, Institute of Botany, llia State University, Tbilisi 0105, Georgia
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12
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Hu X, Lin C, Xu Q, Zhou X, Zeng P, McCormick PJ, Jiang H, Li J, Zhang J. Structural Basis for the Inhibition of Coronaviral Main Proteases by a Benzothiazole-Based Inhibitor. Viruses 2022; 14:v14092075. [PMID: 36146880 PMCID: PMC9505605 DOI: 10.3390/v14092075] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/10/2022] [Accepted: 09/15/2022] [Indexed: 11/25/2022] Open
Abstract
The ongoing spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused hundreds of millions of cases and millions of victims worldwide with serious consequences to global health and economies. Although many vaccines protecting against SARS-CoV-2 are currently available, constantly emerging new variants necessitate the development of alternative strategies for prevention and treatment of COVID-19. Inhibitors that target the main protease (Mpro) of SARS-CoV-2, an essential enzyme that promotes viral maturation, represent a key class of antivirals. Here, we showed that a peptidomimetic compound with benzothiazolyl ketone as warhead, YH-53, is an effective inhibitor of SARS-CoV-2, SARS-CoV, and MERS-CoV Mpros. Crystal structures of Mpros from SARS-CoV-2, SARS-CoV, and MERS-CoV bound to the inhibitor YH-53 revealed a unique ligand-binding site, which provides new insights into the mechanism of inhibition of viral replication. A detailed analysis of these crystal structures defined the key molecular determinants required for inhibition and illustrate the binding mode of Mpros from other coronaviruses. In consideration of the important role of Mpro in developing antivirals against coronaviruses, insights derived from this study should add to the design of pan-coronaviral Mpro inhibitors that are safer and more effective.
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Affiliation(s)
- Xiaohui Hu
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China
| | - Cheng Lin
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Qin Xu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Xuelan Zhou
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen 518118, China
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Pei Zeng
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen 518118, China
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Peter J. McCormick
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London, London E1 4NS, UK
| | - Haihai Jiang
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China
- Correspondence: (H.J.); (J.L.); (J.Z.)
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
- Correspondence: (H.J.); (J.L.); (J.Z.)
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China
- Correspondence: (H.J.); (J.L.); (J.Z.)
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13
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Hu Y, Lewandowski EM, Tan H, Zhang X, Morgan RT, Zhang X, Jacobs LMC, Butler SG, Gongora MV, Choy J, Deng X, Chen Y, Wang J. Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.28.497978. [PMID: 36119652 PMCID: PMC9479041 DOI: 10.1101/2022.06.28.497978] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The SARS-CoV-2 main protease (M pro ) is the drug target of Pfizer’s oral drug Paxlovid. The emergence of SARS-CoV-2 variants with mutations in M pro raised the alarm of potential drug resistance. In this study, we identified 100 naturally occurring M pro mutations located at the nirmatrelvir binding site, among which 20 mutants, including S144M/F/A/G/Y, M165T, E166G, H172Q/F, and Q192T/S/L/A/I/P/H/V/W/C/F, showed comparable enzymatic activity to the wild-type (k cat /K m <10-fold change) and resistance to nirmatrelvir (K i >10-fold increase). X-ray crystal structures were determined for seven representative mutants with and/or without GC-376/nirmatrelvir. Viral growth assay showed that M pro mutants with reduced enzymatic activity led to attenuated viral replication. Overall, our study identified several drug resistant hot spots that warrant close monitoring for possible clinical evidence of Paxlovid resistance. One Sentence Summary Paxlovid resistant SARS-CoV-2 viruses with mutations in the main protease have been identified from clinical isolates.
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Affiliation(s)
- Yanmei Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, NJ, 08854, United States
| | - Eric M. Lewandowski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, NJ, 08854, United States
| | - Xiaoming Zhang
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, United States
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, 74078, United States
| | - Ryan T. Morgan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Lian M. C. Jacobs
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Shane G. Butler
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Maura V. Gongora
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - John Choy
- Department Biology, School of Arts and Sciences, the Catholic University of America, Washington DC, 20064, United States
| | - Xufang Deng
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, United States
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, 74078, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, NJ, 08854, United States
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14
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Hu Q, Xiong Y, Zhu GH, Zhang YN, Zhang YW, Huang P, Ge GB. The SARS-CoV-2 main protease (M pro): Structure, function, and emerging therapies for COVID-19. MedComm (Beijing) 2022; 3:e151. [PMID: 35845352 PMCID: PMC9283855 DOI: 10.1002/mco2.151] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 12/21/2022] Open
Abstract
The main proteases (Mpro), also termed 3‐chymotrypsin‐like proteases (3CLpro), are a class of highly conserved cysteine hydrolases in β‐coronaviruses. Increasing evidence has demonstrated that 3CLpros play an indispensable role in viral replication and have been recognized as key targets for preventing and treating coronavirus‐caused infectious diseases, including COVID‐19. This review is focused on the structural features and biological function of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) main protease Mpro (also known as 3CLpro), as well as recent advances in discovering and developing SARS‐CoV‐2 3CLpro inhibitors. To better understand the characteristics of SARS‐CoV‐2 3CLpro inhibitors, the inhibition activities, inhibitory mechanisms, and key structural features of various 3CLpro inhibitors (including marketed drugs, peptidomimetic, and non‐peptidomimetic synthetic compounds, as well as natural compounds and their derivatives) are summarized comprehensively. Meanwhile, the challenges in this field are highlighted, while future directions for designing and developing efficacious 3CLpro inhibitors as novel anti‐coronavirus therapies are also proposed. Collectively, all information and knowledge presented here are very helpful for understanding the structural features and inhibitory mechanisms of SARS‐CoV‐2 3CLpro inhibitors, which offers new insights or inspiration to medicinal chemists for designing and developing more efficacious 3CLpro inhibitors as novel anti‐coronavirus agents.
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Affiliation(s)
- Qing Hu
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China.,Clinical Pharmacy Center Cancer Center Department of Pharmacy Zhejiang Provincial People's Hospital Affiliated People's Hospital Hangzhou Medical College, Hangzhou Zhejiang China
| | - Yuan Xiong
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China
| | - Guang-Hao Zhu
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China
| | - Ya-Ni Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China
| | - Yi-Wen Zhang
- Clinical Pharmacy Center Cancer Center Department of Pharmacy Zhejiang Provincial People's Hospital Affiliated People's Hospital Hangzhou Medical College, Hangzhou Zhejiang China
| | - Ping Huang
- Clinical Pharmacy Center Cancer Center Department of Pharmacy Zhejiang Provincial People's Hospital Affiliated People's Hospital Hangzhou Medical College, Hangzhou Zhejiang China
| | - Guang-Bo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China
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15
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Sia BZ, Boon WX, Yap YY, Kumar S, Ng CH. Prediction of the effects of the top 10 nonsynonymous variants from 30229 SARS-CoV-2 strains on their proteins. F1000Res 2022; 11:9. [PMID: 35707000 PMCID: PMC9184924 DOI: 10.12688/f1000research.72904.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/12/2022] [Indexed: 12/23/2022] Open
Abstract
Background: SARS-CoV-2 virus is a highly transmissible pathogen that causes COVID-19. The outbreak originated in Wuhan, China in December 2019. A number of nonsynonymous mutations located at different SARS-CoV-2 proteins have been reported by multiple studies. However, there are limited computational studies on the biological impacts of these mutations on the structure and function of the proteins. Methods: In our study nonsynonymous mutations of the SARS-CoV-2 genome and their frequencies were identified from 30,229 sequences. Subsequently, the effects of the top 10 highest frequency nonsynonymous mutations of different SARS-CoV-2 proteins were analyzed using bioinformatics tools including co-mutation analysis, prediction of the protein structure stability and flexibility analysis, and prediction of the protein functions. Results: A total of 231 nonsynonymous mutations were identified from 30,229 SARS-CoV-2 genome sequences. The top 10 nonsynonymous mutations affecting nine amino acid residues were ORF1a nsp5 P108S, ORF1b nsp12 P323L and A423V, S protein N501Y and D614G, ORF3a Q57H, N protein P151L, R203K and G204R. Many nonsynonymous mutations showed a high concurrence ratio, suggesting these mutations may evolve together and interact functionally. Our result showed that ORF1a nsp5 P108S, ORF3a Q57H and N protein P151L mutations may be deleterious to the function of SARS-CoV-2 proteins. In addition, ORF1a nsp5 P108S and S protein D614G may destabilize the protein structures while S protein D614G may have a more open conformation compared to the wild type. Conclusion: The biological consequences of these nonsynonymous mutations of SARS-CoV-2 proteins should be further validated by in vivo and in vitro experimental studies in the future.
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Affiliation(s)
- Boon Zhan Sia
- Faculty of Information Science and Technology, Multimedia University, Bukit Beruang, Melaka, 75450, Malaysia
| | - Wan Xin Boon
- Faculty of Information Science and Technology, Multimedia University, Bukit Beruang, Melaka, 75450, Malaysia
| | - Yoke Yee Yap
- Faculty of Information Science and Technology, Multimedia University, Bukit Beruang, Melaka, 75450, Malaysia
| | - Shalini Kumar
- Faculty of Information Science and Technology, Multimedia University, Bukit Beruang, Melaka, 75450, Malaysia
| | - Chong Han Ng
- Faculty of Information Science and Technology, Multimedia University, Bukit Beruang, Melaka, 75450, Malaysia
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