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Chazot A, Zimberger C, Feracci M, Moussa A, Good S, Sommadossi JP, Alvarez K, Ferron F, Canard B. The activation cascade of the broad-spectrum antiviral bemnifosbuvir characterized at atomic resolution. PLoS Biol 2024; 22:e3002743. [PMID: 39190717 DOI: 10.1371/journal.pbio.3002743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/09/2024] [Indexed: 08/29/2024] Open
Abstract
Bemnifosbuvir (AT-527) and AT-752 are guanosine analogues currently in clinical trials against several RNA viruses. Here, we show that these drugs require a minimal set of 5 cellular enzymes for activation to their common 5'-triphosphate AT-9010, with an obligate order of reactions. AT-9010 selectively inhibits essential viral enzymes, accounting for antiviral potency. Functional and structural data at atomic resolution decipher N6-purine deamination compatible with its metabolic activation. Crystal structures of human histidine triad nucleotide binding protein 1, adenosine deaminase-like protein 1, guanylate kinase 1, and nucleoside diphosphate kinase at 2.09, 2.44, 1.76, and 1.9 Å resolution, respectively, with cognate precursors of AT-9010 illuminate the activation pathway from the orally available bemnifosbuvir to AT-9010, pointing to key drug-protein contacts along the activation pathway. Our work provides a framework to integrate the design of antiviral nucleotide analogues, confronting requirements and constraints associated with activation enzymes along the 5'-triphosphate assembly line.
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Affiliation(s)
- Aurélie Chazot
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
| | - Claire Zimberger
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
| | - Mikael Feracci
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
| | - Adel Moussa
- ATEA Pharmaceuticals, Inc., Boston, Massachusetts, United States of America
| | - Steven Good
- ATEA Pharmaceuticals, Inc., Boston, Massachusetts, United States of America
| | | | - Karine Alvarez
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
| | - François Ferron
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
- European Virus Bioinformatics Center, Jena, Germany
| | - Bruno Canard
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
- European Virus Bioinformatics Center, Jena, Germany
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2
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Yengoyan A, Gomktsyan T, Pivazyan V, Ghazaryan E, Shainova R, Karapetyan A, Avetyan D, Aslanyan L, Baroyan K, Tuzikov A, Sargsyan M, Baghdasaryan B, Bayramyan N, Hakobyan S, Poghosyan A, Avetisyan A, Avagyan H, Hakobyan L, Zaven K. Study of different heterocycles showing significant anti-severe acute respiratory syndrome 2 activity in vitro and in vivo. Vet World 2024; 17:1281-1290. [PMID: 39077461 PMCID: PMC11283614 DOI: 10.14202/vetworld.2024.1281-1290] [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: 02/22/2024] [Accepted: 05/13/2024] [Indexed: 07/31/2024] Open
Abstract
Background and Aim With the emergence of severe acute respiratory syndrome-related coronavirus (SARS-CoV-2), antiviral drug development has gained increased significance due to the high incidence and potentially severe complications of the resulting coronavirus infection. Heterocycle compounds, acting as antimetabolites of DNA and RNA monomers, rank among the most effective antiviral drugs. These compounds' antiviral effects on various SARS-CoV-2 isolates, as found in existing data collections, form the basis for further research. The aim of this study was to examine the possible antiviral effect of some originally synthesized heterocyclic compounds. Materials and Methods The main methods were cell culturing, cytotoxicity assay, qRT-PCR assay, tissue and blood cells analysis, and micro-computed tomography (micro-CT) imaging. Results In both in vitro and in vivo conditions, the elimination of SARS-Cov-2 occurred significantly earlier after administration of the compounds compared to the control group. In hamsters, the primary symptoms of coronavirus disease disappeared following administration of heterocycle compounds. Conclusion Using delta and omicron strains of the SARS-CoV-2 virus, newly created heterocycle compound analogs dramatically reduced SARS-CoV-2 multiplication, resulting in a drop in viral RNA load in the supernatant under in vitro conditions. Improvements in pathological manifestations in the blood, bone marrow, and internal organs of hamsters demonstrated that heterocycle compounds inhibited SARS-CoV-2 replication both in vitro and in vivo.
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Affiliation(s)
- Aleksandr Yengoyan
- Department of Pesticides Synthesis and Expertise National Agrarian University of Armenia, Teryan 74, Yerevan, 0009, Armenia
- Department of Chemistry Laboratory of Structural Bioinformatics, Russian-Armenian University, H. Emin, 123, Yerevan, 0051, Armenia
| | - Tiruhi Gomktsyan
- Department of Pesticides Synthesis and Expertise National Agrarian University of Armenia, Teryan 74, Yerevan, 0009, Armenia
| | - Vergush Pivazyan
- Department of Pesticides Synthesis and Expertise National Agrarian University of Armenia, Teryan 74, Yerevan, 0009, Armenia
| | - Emma Ghazaryan
- Department of Pesticides Synthesis and Expertise National Agrarian University of Armenia, Teryan 74, Yerevan, 0009, Armenia
| | - Roza Shainova
- Department of Pesticides Synthesis and Expertise National Agrarian University of Armenia, Teryan 74, Yerevan, 0009, Armenia
| | - Armen Karapetyan
- Department of Pesticides Synthesis and Expertise National Agrarian University of Armenia, Teryan 74, Yerevan, 0009, Armenia
| | - Diana Avetyan
- Laboratory of Human Genomics and Immunomics, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
| | - Levon Aslanyan
- Department of Mathematics, Institute for Informatics and Automation Problems of NAS RA, Yerevan, Armenia
| | - Karine Baroyan
- Department of Anatomy, Yerevan State Medical University after M. Heratsi, Armenia Yerevan, Armenia
| | - Alexander Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Belarus
| | - Mariam Sargsyan
- Department of Epidemiology and Parasitology, Armenian National Agrarian University, Yerevan, Armenia
| | - Bagrat Baghdasaryan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
| | - Nane Bayramyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
| | - Sona Hakobyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
| | - Arpine Poghosyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
| | - Aida Avetisyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
- Department of Human Anatomy, Yerevan State Medical University after M. Heratsi, Yerevan, Armenia
| | - Hranush Avagyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
- Department of Human Anatomy, Yerevan State Medical University after M. Heratsi, Yerevan, Armenia
| | - Lina Hakobyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
| | - Karalyan Zaven
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
- Department of Human Anatomy, Yerevan State Medical University after M. Heratsi, Yerevan, Armenia
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Shannon A, Chazot A, Feracci M, Falcou C, Fattorini V, Selisko B, Good S, Moussa A, Sommadossi JP, Ferron F, Alvarez K, Canard B. An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex. Nucleic Acids Res 2024; 52:1325-1340. [PMID: 38096103 PMCID: PMC10853775 DOI: 10.1093/nar/gkad1194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 02/10/2024] Open
Abstract
Nucleotide analogues (NA) are currently employed for treatment of several viral diseases, including COVID-19. NA prodrugs are intracellularly activated to the 5'-triphosphate form. They are incorporated into the viral RNA by the viral polymerase (SARS-CoV-2 nsp12), terminating or corrupting RNA synthesis. For Coronaviruses, natural resistance to NAs is provided by a viral 3'-to-5' exonuclease heterodimer nsp14/nsp10, which can remove terminal analogues. Here, we show that the replacement of the α-phosphate of Bemnifosbuvir 5'-triphosphate form (AT-9010) by an α-thiophosphate renders it resistant to excision. The resulting α-thiotriphosphate, AT-9052, exists as two epimers (RP/SP). Through co-crystallization and activity assays, we show that the Sp isomer is preferentially used as a substrate by nucleotide diphosphate kinase (NDPK), and by SARS-CoV-2 nsp12, where its incorporation causes immediate chain-termination. The same -Sp isomer, once incorporated by nsp12, is also totally resistant to the excision by nsp10/nsp14 complex. However, unlike AT-9010, AT-9052-RP/SP no longer inhibits the N-terminal nucleotidylation domain of nsp12. We conclude that AT-9052-Sp exhibits a unique mechanism of action against SARS-CoV-2. Moreover, the thio modification provides a general approach to rescue existing NAs whose activity is hampered by coronavirus proofreading capacity.
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Affiliation(s)
- Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Aurélie Chazot
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Mikael Feracci
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Camille Falcou
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Véronique Fattorini
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Barbara Selisko
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Steven Good
- ATEA Pharmaceuticals, Inc., 225 Franklin St., Suite 2100, Boston, MA 02110, USA
| | - Adel Moussa
- ATEA Pharmaceuticals, Inc., 225 Franklin St., Suite 2100, Boston, MA 02110, USA
| | | | - François Ferron
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Karine Alvarez
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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Lu J, Xing H, Wang C, Tang M, Wu C, Ye F, Yin L, Yang Y, Tan W, Shen L. Mpox (formerly monkeypox): pathogenesis, prevention, and treatment. Signal Transduct Target Ther 2023; 8:458. [PMID: 38148355 PMCID: PMC10751291 DOI: 10.1038/s41392-023-01675-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 12/28/2023] Open
Abstract
In 2022, a global outbreak of Mpox (formerly monkeypox) occurred in various countries across Europe and America and rapidly spread to more than 100 countries and regions. The World Health Organization declared the outbreak to be a public health emergency of international concern due to the rapid spread of the Mpox virus. Consequently, nations intensified their efforts to explore treatment strategies aimed at combating the infection and its dissemination. Nevertheless, the available therapeutic options for Mpox virus infection remain limited. So far, only a few numbers of antiviral compounds have been approved by regulatory authorities. Given the high mutability of the Mpox virus, certain mutant strains have shown resistance to existing pharmaceutical interventions. This highlights the urgent need to develop novel antiviral drugs that can combat both drug resistance and the potential threat of bioterrorism. Currently, there is a lack of comprehensive literature on the pathophysiology and treatment of Mpox. To address this issue, we conducted a review covering the physiological and pathological processes of Mpox infection, summarizing the latest progress of anti-Mpox drugs. Our analysis encompasses approved drugs currently employed in clinical settings, as well as newly identified small-molecule compounds and antibody drugs displaying potential antiviral efficacy against Mpox. Furthermore, we have gained valuable insights from the process of Mpox drug development, including strategies for repurposing drugs, the discovery of drug targets driven by artificial intelligence, and preclinical drug development. The purpose of this review is to provide readers with a comprehensive overview of the current knowledge on Mpox.
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Affiliation(s)
- Junjie Lu
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Hubei Province, Xiangyang, 441021, China
| | - Hui Xing
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Hubei Province, Xiangyang, 441021, China
| | - Chunhua Wang
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Hubei Province, Xiangyang, 441021, China
| | - Mengjun Tang
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Hubei Province, Xiangyang, 441021, China
| | - Changcheng Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Fan Ye
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Hubei Province, Xiangyang, 441021, China
| | - Lijuan Yin
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for infectious disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, 518112, China.
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Liang Shen
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Hubei Province, Xiangyang, 441021, China.
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5
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Xu T, Zhang L. Current understanding of nucleoside analogs inhibiting the SARS-CoV-2 RNA-dependent RNA polymerase. Comput Struct Biotechnol J 2023; 21:4385-4394. [PMID: 37711189 PMCID: PMC10498173 DOI: 10.1016/j.csbj.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Since the outbreak of the COVID-19 pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) has become a main target for antiviral therapeutics due to its essential role in viral replication and transcription. Thus, nucleoside analogs structurally resemble the natural RdRp substrate and hold great potential as inhibitors. Until now, extensive experimental investigations have been performed to explore nucleoside analogs to inhibit the RdRp, and concerted efforts have been made to elucidate the underlying molecular mechanisms further. This review begins by discussing the nucleoside analogs that have demonstrated inhibition in the experiments. Second, we examine the current understanding of the molecular mechanisms underlying the action of nucleoside analogs on the SARS-CoV-2 RdRp. Recent findings in structural biology and computational research are presented through the classification of inhibitory mechanisms. This review summarizes previous experimental findings and mechanistic investigations of nucleoside analogs inhibiting SARS-CoV-2 RdRp. It would guide the rational design of antiviral medications and research into viral transcriptional mechanisms.
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Affiliation(s)
- Tiantian Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Fujian 361005, China
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6
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De Castro F, Stefàno E, De Luca E, Benedetti M, Fanizzi FP. Platinum-Nucleos(t)ide Compounds as Possible Antimetabolites for Antitumor/Antiviral Therapy: Properties and Perspectives. Pharmaceutics 2023; 15:941. [PMID: 36986802 PMCID: PMC10058173 DOI: 10.3390/pharmaceutics15030941] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/06/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023] Open
Abstract
Nucleoside analogues (NAs) are a family of compounds which include a variety of purine and pyrimidine derivatives, widely used as anticancer and antiviral agents. For their ability to compete with physiological nucleosides, NAs act as antimetabolites exerting their activity by interfering with the synthesis of nucleic acids. Much progress in the comprehension of their molecular mechanisms has been made, including providing new strategies for potentiating anticancer/antiviral activity. Among these strategies, new platinum-NAs showing a good potential to improve the therapeutic indices of NAs have been synthesized and studied. This short review aims to describe the properties and future perspectives of platinum-NAs, proposing these complexes as a new class of antimetabolites.
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Affiliation(s)
| | | | | | - Michele Benedetti
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, Centro Ecotekne, 73100 Lecce, Italy
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7
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Chinthapatla R, Sotoudegan M, Srivastava P, Anderson TK, Moustafa I, Passow K, Kennelly S, Moorthy R, Dulin D, Feng J, Harki D, Kirchdoerfer R, Cameron C, Arnold J. Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease. Nucleic Acids Res 2023; 51:315-336. [PMID: 36546762 PMCID: PMC9841423 DOI: 10.1093/nar/gkac1177] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/11/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022] Open
Abstract
Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.
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Affiliation(s)
- Rukesh Chinthapatla
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Mohamad Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Pankaj Srivastava
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Thomas K Anderson
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kellan T Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samantha A Kennelly
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Dulin
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Joy Y Feng
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig E Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jamie J Arnold
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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Pagliano P, Sellitto C, Ascione T, Scarpati G, Folliero V, Piazza O, Franci G, Filippelli A, Conti V. The preclinical discovery and development of molnupiravir for the treatment of SARS-CoV-2 (COVID-19). Expert Opin Drug Discov 2022; 17:1299-1311. [PMID: 36508255 DOI: 10.1080/17460441.2022.2153828] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Molnupiravir (MOV) is a broad-spectrum oral antiviral agent approved for the treatment of COVID-19. The results from in vitro and in vivo studies suggested MOV activity against many RNA viruses such as influenza virus and some alphaviruses agents of epidemic encephalitis. MOV is a prodrug metabolized into the ribonucleoside analog β-D-N4-hydroxycytidine. It is incorporated into the viral RNA chain causing mutations impairing coding activity of the virus, thereby inhibiting viral replication. AREAS COVERED This review analyzes the in vitro and in vivo studies that have highlighted the efficacy of MOV and the main pre-authorization randomized controlled trials evaluating its safety, tolerability, and pharmacokinetics, as well as its antiviral efficacy against SARS-COV-2 infection. EXPERT OPINION MOV is an antiviral agent with an excellent tolerability profile with few drug-drug interactions. Treatment of mild-to-moderate COVID-19 can benefit from MOV administration in the precocious phases of the disease, prior to the trigger of an aberrant immune response responsible for the parenchymal damage to pulmonary and extrapulmonary tissues. However, its suspected mutagenic effect can be a factor limiting its use at least in selected populations and studies on its teratogen effects should be planned before it is authorized for use in the pediatric population or in pregnant women.
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Affiliation(s)
- Pasquale Pagliano
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," Unit of Infectious Diseases, University of Salerno, Baronissi, Italy
| | - Carmine Sellitto
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," Unit of Pharmacology, University of Salerno, Baronissi, Italy
| | - Tiziana Ascione
- Department of Medicine, Service of Infectious Diseases, Cardarelli Hospital, Naples, Italy
| | - Giuliana Scarpati
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," Unit of Anesthesiology, University of Salerno, Baronissi, Italy
| | - Veronica Folliero
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Ornella Piazza
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," Unit of Anesthesiology, University of Salerno, Baronissi, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," Unit of Microbiology, University of Salerno, Baronissi, Italy
| | - Amelia Filippelli
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," Unit of Pharmacology, University of Salerno, Baronissi, Italy
| | - Valeria Conti
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," Unit of Pharmacology, University of Salerno, Baronissi, Italy
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9
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Campollo O, Amaya G, McCormick PA. Milestones in the discovery of hepatitis C. World J Gastroenterol 2022; 28:5395-5402. [PMID: 36312838 PMCID: PMC9611700 DOI: 10.3748/wjg.v28.i37.5395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/11/2022] [Accepted: 08/16/2022] [Indexed: 02/06/2023] Open
Abstract
The discovery of hepatitis C has been a landmark in public health as it brought the opportunity to save millions of lives through the diagnosis, prevention and cure of the disease. The combined work of three researchers, Alter H, Houghton M and Rice C, which set the basis for the diagnosis, treatment and prevention of hepatitis C apart from laying the ground work for a new approach to study infections in general and developing new antiviral agents. This is a story of a transfusion-associated infection. A series of clinical studies demonstrated the existence of an infectious agent associated with hepatitis. That was followed by the identification of what was later known to be the hepatitis C virus (HCV) and the development of diagnostic tests. It all preceded the full molecular identification and demonstration of a causal effect. Finally it ended up with the development and discovery of a new class of therapeutic drugs, the direct acting antivirals, which are now used not only to cure the disease but most probably, to eliminate the problem. This work started with Dr Alter H who demonstrated that a new virus was responsible for the majority of post-transfusion hepatitis followed by Houghton M who cloned the virus and developed the blood test to identify those cases that carried the virus. Finally, the work of Rice C demonstrated that a cloned HCV produced after applying molecular biology techniques could cause long-standing infection and cause the same disease as the one observed in humans.
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Affiliation(s)
- Octavio Campollo
- Center of Studies on Alcohol and Addictions, Antiguo Hospital Civil de Guadalajara, Department of Medical Clinics, Universidad de Guadalajara, Guadalajara 44280, Jalisco, Mexico
| | - Gerardo Amaya
- Medical Clinics, CUCS, Universidad de Guadalajara, Guadalajara 44280, Jalisco, Mexico
| | - P Aiden McCormick
- Department of Hepatology, Saint Vincent’s University Hospital, National Liver Transplant Unit, Dublin D04, Ireland
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Chinthapatla R, Sotoudegan M, Anderson T, Moustafa IM, Passow KT, Kennelly SA, Moorthy R, Dulin D, Feng JY, Harki DA, Kirchdoerfer R, Cameron CE, Arnold JJ. Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.11.503614. [PMID: 35982684 PMCID: PMC9387131 DOI: 10.1101/2022.08.11.503614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.
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Affiliation(s)
- Rukesh Chinthapatla
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Mohamad Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Thomas Anderson
- Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ibrahim M. Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kellan T. Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samantha A. Kennelly
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Dulin
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Joy Y. Feng
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert Kirchdoerfer
- Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig E. Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jamie J. Arnold
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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11
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Luo X, Wang X, Yao Y, Gao X, Zhang L. Unveiling the "Template-Dependent" Inhibition on the Viral Transcription of SARS-CoV-2. J Phys Chem Lett 2022; 13:7197-7205. [PMID: 35912566 PMCID: PMC9363016 DOI: 10.1021/acs.jpclett.2c01314] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Remdesivir is one nucleotide analogue prodrug capable to terminate RNA synthesis in SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) by two distinct mechanisms. Although the "delayed chain termination" mechanism has been extensively investigated, the "template-dependent" inhibitory mechanism remains elusive. In this study, we have demonstrated that remdesivir embedded in the template strand seldom directly disrupted the complementary NTP incorporation at the active site. Instead, the translocation of remdesivir from the +2 to the +1 site was hindered due to the steric clash with V557. Moreover, we have elucidated the molecular mechanism characterizing the drug resistance upon V557L mutation. Overall, our studies have provided valuable insight into the "template-dependent" inhibitory mechanism exerted by remdesivir on SARS-CoV-2 RdRp and paved venues for an alternative antiviral strategy for the COVID-19 pandemic. As the "template-dependent" inhibition occurs across diverse viral RdRps, our findings may also shed light on a common acting mechanism of inhibitors.
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Affiliation(s)
- Xueying Luo
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002 Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xiaowei Wang
- Department
of Chemical and Biological Engineering, Department of Mathematics, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yuan Yao
- Department
of Mathematics, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Xin Gao
- Computer
Science Program, Computer, Electrical and Mathematical Sciences and
Engineering (CEMSE) Division, King Abdullah
University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- KAUST
Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Lu Zhang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002 Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100049 Beijing, China
- Fujian Provincial
Key Laboratory of Theoretical and Computational Chemistry, 361005 Fujian, China
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12
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Ho WS, Zhang R, Tan YL, Chai CLL. COVID-19 and the promise of small molecule therapeutics: Are there lessons to be learnt? Pharmacol Res 2022; 179:106201. [PMID: 35367622 PMCID: PMC8970615 DOI: 10.1016/j.phrs.2022.106201] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/17/2022] [Accepted: 03/29/2022] [Indexed: 12/12/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic had grounded the world to a standstill. As the disease continues to rage two years on, it is apparent that effective therapeutics are critical for a successful endemic living with COVID-19. A dearth in suitable antivirals has prompted researchers and healthcare professionals to investigate existing and developmental drugs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although some of these drugs initially appeared to be promising for the treatment of COVID-19, they were ultimately found to be ineffective. In this review, we provide a retrospective analysis on the merits and limitations of some of these drugs that were tested against SARS-CoV-2 as well as those used for adjuvant therapy. While many of these drugs are no longer part of our arsenal for the treatment of COVID-19, important lessons can be learnt. The recent inclusion of molnupiravir and Paxlovid™ as treatment options for COVID-19 represent our best hope to date for endemic living with COVID-19. Our viewpoints on these two drugs and their prospects as current and future antiviral agents will also be provided.
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Affiliation(s)
- Wei Shen Ho
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
| | - Ruirui Zhang
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
| | - Yeong Lan Tan
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
| | - Christina Li Lin Chai
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore.
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13
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Gong P. Within and Beyond the Nucleotide Addition Cycle of Viral RNA-dependent RNA Polymerases. Front Mol Biosci 2022; 8:822218. [PMID: 35083282 PMCID: PMC8784604 DOI: 10.3389/fmolb.2021.822218] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Nucleotide addition cycle (NAC) is a fundamental process utilized by nucleic acid polymerases when carrying out nucleic acid biosynthesis. An induced-fit mechanism is usually taken by these polymerases upon NTP/dNTP substrate binding, leading to active site closure and formation of a phosphodiester bond. In viral RNA-dependent RNA polymerases, the post-chemistry translocation is stringently controlled by a structurally conserved motif, resulting in asymmetric movement of the template-product duplex. This perspective focuses on viral RdRP NAC and related mechanisms that have not been structurally clarified to date. Firstly, RdRP movement along the template strand in the absence of catalytic events may be relevant to catalytic complex dissociation or proofreading. Secondly, pyrophosphate or non-cognate NTP-mediated cleavage of the product strand 3′-nucleotide can also play a role in reactivating paused or arrested catalytic complexes. Furthermore, non-cognate NTP substrates, including NTP analog inhibitors, can not only alter NAC when being misincorporated, but also impact on subsequent NACs. Complications and challenges related to these topics are also discussed.
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Affiliation(s)
- Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, China
- *Correspondence: Peng Gong,
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