1
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Kurosawa M, Kato F, Hishiki T, Ito S, Fujisawa H, Yamaguchi T, Moriguchi M, Hosokawa K, Watanabe T, Saito-Tarashima N, Minakawa N, Fujimuro M. Sofosbuvir Suppresses the Genome Replication of DENV1 in Human Hepatic Huh7 Cells. Int J Mol Sci 2024; 25:2022. [PMID: 38396699 PMCID: PMC10889370 DOI: 10.3390/ijms25042022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Dengue virus (DENV) causes dengue fever and dengue hemorrhagic fever, and DENV infection kills 20,000 people annually worldwide. Therefore, the development of anti-DENV drugs is urgently needed. Sofosbuvir (SOF) is an effective drug for HCV-related diseases, and its triphosphorylated metabolite inhibits viral RNA synthesis by the RNA-dependent RNA polymerase (RdRp) of HCV. (2'R)-2'-Deoxy-2'-fluoro-2'-methyluridine (FMeU) is the dephosphorylated metabolite produced from SOF. The effects of SOF and FMeU on DENV1 replication were analyzed using two DENV1 replicon-based methods that we previously established. First, a replicon-harboring cell assay showed that DENV1 replicon replication in human hepatic Huh7 cells was decreased by SOF but not by FMeU. Second, a transient replicon assay showed that DENV1 replicon replication in Huh7 cells was decreased by SOF; however, in hamster kidney BHK-21 cells, it was not suppressed by SOF. Additionally, the replicon replication in Huh7 and BHK-21 cells was not affected by FMeU. Moreover, we assessed the effects of SOF on infectious DENV1 production. SOF suppressed infectious DENV1 production in Huh7 cells but not in monkey kidney Vero cells. To examine the substrate recognition of the HCV and DENV1 RdRps, the complex conformation of SOF-containing DENV1 RdRp or HCV RdRp was predicted using AlphaFold 2. These results indicate that SOF may be used as a treatment for DENV1 infection.
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Affiliation(s)
- Madoka Kurosawa
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Fumihiro Kato
- Department of Virology III, National Institute of Infectious Diseases, Tokyo 208-0011, Japan;
| | - Takayuki Hishiki
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan;
| | - Saori Ito
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Hiroki Fujisawa
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Tatsuo Yamaguchi
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Misato Moriguchi
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Kohei Hosokawa
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Tadashi Watanabe
- Department of Virology, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan;
| | - Noriko Saito-Tarashima
- Graduate School of Pharmaceutical Science, Tokushima University, Tokushima 770-8505, Japan; (N.S.-T.); (N.M.)
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Tokushima 770-8505, Japan; (N.S.-T.); (N.M.)
| | - Masahiro Fujimuro
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
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2
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Uemura K, Nobori H, Sato A, Toba S, Kusakabe S, Sasaki M, Tabata K, Matsuno K, Maeda N, Ito S, Tanaka M, Anraku Y, Kita S, Ishii M, Kanamitsu K, Orba Y, Matsuura Y, Hall WW, Sawa H, Kida H, Matsuda A, Maenaka K. 2-thiouridine is a broad-spectrum antiviral nucleoside analogue against positive-strand RNA viruses. Proc Natl Acad Sci U S A 2023; 120:e2304139120. [PMID: 37831739 PMCID: PMC10589713 DOI: 10.1073/pnas.2304139120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/23/2023] [Indexed: 10/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are causing significant morbidity and mortality worldwide. Furthermore, over 1 million cases of newly emerging or re-emerging viral infections, specifically dengue virus (DENV), are known to occur annually. Because no virus-specific and fully effective treatments against these or many other viruses have been approved, there is an urgent need for novel, effective therapeutic agents. Here, we identified 2-thiouridine (s2U) as a broad-spectrum antiviral ribonucleoside analogue that exhibited antiviral activity against several positive-sense single-stranded RNA (ssRNA+) viruses, such as DENV, SARS-CoV-2, and its variants of concern, including the currently circulating Omicron subvariants. s2U inhibits RNA synthesis catalyzed by viral RNA-dependent RNA polymerase, thereby reducing viral RNA replication, which improved the survival rate of mice infected with DENV2 or SARS-CoV-2 in our animal models. Our findings demonstrate that s2U is a potential broad-spectrum antiviral agent not only against DENV and SARS-CoV-2 but other ssRNA+ viruses.
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Affiliation(s)
- Kentaro Uemura
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Osaka565-0871, Japan
| | - Haruaki Nobori
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
| | - Akihiko Sato
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo001-0021, Japan
| | - Shinsuke Toba
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Shinji Kusakabe
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Koshiro Tabata
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Keita Matsuno
- Unit of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- One Health Research Center, Hokkaido University, Sapporo001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Naoyoshi Maeda
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Shiori Ito
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Mayu Tanaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Yuki Anraku
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Mayumi Ishii
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo, Tokyo113-0033, Japan
| | - Kayoko Kanamitsu
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo, Tokyo113-0033, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Osaka565-0871, Japan
| | - William W. Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- National Virus Reference Laboratory, School of Medicine, University College of Dublin, DublinD04, Ireland
- Global Virus Network, Baltimore, MD21201
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo001-0021, Japan
- One Health Research Center, Hokkaido University, Sapporo001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- Global Virus Network, Baltimore, MD21201
| | - Hiroshi Kida
- Laboratory for Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Akira Matsuda
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo001-0021, Japan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo060-0812, Japan
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3
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Pagani I, Ottoboni L, Panina-Bordignon P, Martino G, Poli G, Taylor S, Turnbull JE, Yates E, Vicenzi E. Heparin Precursors with Reduced Anticoagulant Properties Retain Antiviral and Protective Effects That Potentiate the Efficacy of Sofosbuvir against Zika Virus Infection in Human Neural Progenitor Cells. Pharmaceuticals (Basel) 2023; 16:1385. [PMID: 37895856 PMCID: PMC10609960 DOI: 10.3390/ph16101385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 10/29/2023] Open
Abstract
Zika virus (ZIKV) infection during pregnancy can result in severe birth defects, such as microcephaly, as well as a range of other related health complications. Heparin, a clinical-grade anticoagulant, is shown to protect neural progenitor cells from death following ZIKV infection. Although heparin can be safely used during pregnancy, it retains off-target anticoagulant effects if directly employed against ZIKV infection. In this study, we investigated the effects of chemically modified heparin derivatives with reduced anticoagulant activities. These derivatives were used as experimental probes to explore the structure-activity relationships. Precursor fractions of porcine heparin, obtained during the manufacture of conventional pharmaceutical heparin with decreased anticoagulant activities, were also explored. Interestingly, these modified heparin derivatives and precursor fractions not only prevented cell death but also inhibited the ZIKV replication of infected neural progenitor cells grown as neurospheres. These effects were observed regardless of the specific sulfation position or overall charge. Furthermore, the combination of heparin with Sofosbuvir, an antiviral licensed for the treatment of hepatitis C (HCV) that also belongs to the same Flaviviridae family as ZIKV, showed a synergistic effect. This suggested that a combination therapy approach involving heparin precursors and Sofosbuvir could be a potential strategy for the prevention or treatment of ZIKV infections.
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Affiliation(s)
- Isabel Pagani
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Linda Ottoboni
- Neuroimmunology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Paola Panina-Bordignon
- Neuroimmunology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
| | - Gianvito Martino
- Neuroimmunology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
| | - Guido Poli
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
- Human Immuno-Virology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Sarah Taylor
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jeremy E Turnbull
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
- Department of Life Sciences, Keele University, Keele, Staffs ST5 5BG, UK
| | - Edwin Yates
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
- Department of Life Sciences, Keele University, Keele, Staffs ST5 5BG, UK
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
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4
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Martínez-González B, Gallego I, Gregori J, Soria ME, Somovilla P, de Ávila AI, García-Crespo C, Durán-Pastor A, Briones C, Gómez J, Quer J, Domingo E, Perales C. Fitness-Dependent, Mild Mutagenic Activity of Sofosbuvir for Hepatitis C Virus. Antimicrob Agents Chemother 2023; 67:e0039423. [PMID: 37367486 PMCID: PMC10353389 DOI: 10.1128/aac.00394-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/06/2023] [Indexed: 06/28/2023] Open
Abstract
The concept of a mild mutagen was coined to describe a minor mutagenic activity exhibited by some nucleoside analogues that potentiated their efficacy as antiretroviral agents. In the present study, we report the mild mutagen activity of sofosbuvir (SOF) for hepatitis C virus (HCV). Serial passages of HCV in human hepatoma cells, in the presence of SOF at a concentration well below its cytotoxic concentration 50 (CC50) led to pre-extinction populations whose mutant spectra exhibited a significant increase of C→U transitions, relative to populations passaged in the absence of SOF. This was reflected in an increase in several diversity indices that were used to characterize viral quasispecies. The mild mutagenic activity of SOF was largely absent when it was tested with isogenic HCV populations that displayed high replicative fitness. Thus, SOF can act as a mild mutagen for HCV, depending on HCV fitness. Possible mechanisms by which the SOF mutagenic activity may contribute to its antiviral efficacy are discussed.
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Affiliation(s)
- Brenda Martínez-González
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
| | - Isabel Gallego
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - María Eugenia Soria
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
| | - Pilar Somovilla
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Antoni Durán-Pastor
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | | | - Jordi Gómez
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
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5
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Shehzadi K, Saba A, Yu M, Liang J. Structure-Based Drug Design of RdRp Inhibitors against SARS-CoV-2. Top Curr Chem (Cham) 2023; 381:22. [PMID: 37318607 DOI: 10.1007/s41061-023-00432-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide pandemic since 2019, spreading rapidly and posing a significant threat to human health and life. With over 6 billion confirmed cases of the virus, the need for effective therapeutic drugs has become more urgent than ever before. RNA-dependent RNA polymerase (RdRp) is crucial in viral replication and transcription, catalysing viral RNA synthesis and serving as a promising therapeutic target for developing antiviral drugs. In this article, we explore the inhibition of RdRp as a potential treatment for viral diseases, analysing the structural information of RdRp in virus proliferation and summarizing the reported inhibitors' pharmacophore features and structure-activity relationship profiles. We hope that the information provided by this review will aid in structure-based drug design and aid in the global fight against SARS-CoV-2 infection.
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Affiliation(s)
- Kiran Shehzadi
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Afsheen Saba
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Mingjia Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
| | - Jianhua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing, 314019, China.
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6
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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: 0] [Impact Index Per Article: 0] [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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7
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Xu S, Del Pozo J, Romiti F, Fu Y, Mai BK, Morrison RJ, Lee K, Hu S, Koh MJ, Lee J, Li X, Liu P, Hoveyda AH. Diastereo- and enantioselective synthesis of compounds with a trifluoromethyl- and fluoro-substituted carbon centre. Nat Chem 2022; 14:1459-1469. [PMID: 36376387 PMCID: PMC9772297 DOI: 10.1038/s41557-022-01054-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
Molecules that contain one or more fluorine atoms are crucial to drug discovery. There are protocols available for the selective synthesis of different organofluorine compounds, including those with a fluoro-substituted or a trifluoromethyl-substituted stereogenic carbon centre. However, approaches for synthesizing compounds with a trifluoromethyl- and fluoro-substituent stereogenic carbon centre are far less common. This potentially impactful set of molecules thus remains severely underdeveloped. Here we introduce a catalytic regio-, diastereo- and enantioselective strategy for the preparation of homoallylic alcohols bearing a stereogenic carbon centre bound to a trifluoromethyl group and a fluorine atom. The process, which involves a polyfluoroallyl boronate and is catalysed by an in situ-formed organozinc complex, can be used for diastereodivergent preparation of tetrafluoro-monosaccharides, including ribose core analogues of the antiviral drug sofosbuvir (Sovaldi). Unexpected reactivity/selectivity profiles, probably originating from the trifluoromethyl- and fluoro-substituted carbon site, are discovered, foreshadowing other unique chemistries that remain unknown.
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Affiliation(s)
- Shibo Xu
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Juan Del Pozo
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Filippo Romiti
- Supramolecular Science and Engineering Institute, University of Strasbourg, CNRS, Strasbourg, France
| | - Yue Fu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan J Morrison
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - KyungA Lee
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Shaowei Hu
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Ming Joo Koh
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Jaehee Lee
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Xinghan Li
- Supramolecular Science and Engineering Institute, University of Strasbourg, CNRS, Strasbourg, France
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Amir H Hoveyda
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA.
- Supramolecular Science and Engineering Institute, University of Strasbourg, CNRS, Strasbourg, France.
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8
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Inhibition of Viral RNA-Dependent RNA Polymerases by Nucleoside Inhibitors: An Illustration of the Unity and Diversity of Mechanisms. Int J Mol Sci 2022; 23:ijms232012649. [PMID: 36293509 PMCID: PMC9604226 DOI: 10.3390/ijms232012649] [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: 09/25/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
RNA-dependent RNA polymerase (RdRP) is essential for the replication and expression of RNA viral genomes. This class of viruses comprise a large number of highly pathogenic agents that infect essentially all species of plants and animals including humans. Infections often lead to epidemics and pandemics that have remained largely out of control due to the lack of specific and reliable preventive and therapeutic regimens. This unmet medical need has led to the exploration of new antiviral targets, of which RdRP is a major one, due to the fact of its obligatory need in virus growth. Recent studies have demonstrated the ability of several synthetic nucleoside analogs to serve as mimics of the corresponding natural nucleosides. These mimics cause stalling/termination of RdRP, or misincorporation, preventing virus replication or promoting large-scale lethal mutations. Several such analogs have received clinical approval and are being routinely used in therapy. In parallel, the molecular structural basis of their inhibitory interactions with RdRP is being elucidated, revealing both traditional and novel mechanisms including a delayed chain termination effect. This review offers a molecular commentary on these mechanisms along with their clinical implications based on analyses of recent results, which should facilitate the rational design of structure-based antiviral drugs.
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Boulard Y, Bressanelli S. Recapitulating Trafficking of Nucleosides Into the Active Site of Polymerases of RNA Viruses: The Challenge and the Prize. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 3:705875. [PMID: 35047945 PMCID: PMC8757734 DOI: 10.3389/fmedt.2021.705875] [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: 05/06/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022] Open
Abstract
Nucleoside analogs are very effective antiviral agents with currently over 25 compounds approved for the therapy of viral infections. Still, their successful use against RNA viruses is very recent, despite RNA viruses comprising some of the most damaging human pathogens (e.g., Coronaviruses, Influenza viruses, or Flaviviridae such as dengue, Zika and hepatitis C viruses). The breakthrough came in 2013–2014, when the nucleoside analog Sofosbuvir became one of the cornerstones of current curative treatments for hepatitis C virus (HCV). An analog designed on the same principles, Remdesivir, has been the first approved compound against SARS-CoV-2, the coronavirus that causes the current COVID-19 pandemic. Both of these nucleoside analogs target the RNA-dependent RNA polymerase (RdRp) (NS5B for HCV, nsp12 for SARS-CoV-2). RdRps of RNA viruses display a peculiar elaboration of the classical polymerase architecture that leads to their active site being caged. Thus, triphosphate nucleosides and their analogs must access this active site in several steps along a narrow and dynamic tunnel. This makes straightforward computational approaches such as docking unsuitable for getting atomic-level details of this process. Here we give an account of ribose-modified nucleoside analogs as inhibitors of viral RdRps and of why taking into account the dynamics of these polymerases is necessary to understand nucleotide selection by RdRps. As a case study we use a computational protocol we recently described to examine the approach of the NTP tunnel of HCV NS5B by cellular metabolites of Sofosbuvir. We find major differences with natural nucleotides even at this early stage of nucleotide entry.
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Affiliation(s)
- Yves Boulard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Zenchenko AA, Drenichev MS, Il’icheva IA, Mikhailov SN. Antiviral and Antimicrobial Nucleoside Derivatives: Structural Features and Mechanisms of Action. Mol Biol 2021; 55:786-812. [PMID: 34955556 PMCID: PMC8682041 DOI: 10.1134/s0026893321040105] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/03/2021] [Accepted: 04/09/2021] [Indexed: 11/23/2022]
Abstract
The emergence of new viruses and resistant strains of pathogenic microorganisms has become a powerful stimulus in the search for new drugs. Nucleosides are a promising class of natural compounds, and more than a hundred drugs have already been created based on them, including antiviral, antibacterial and antitumor agents. The review considers the structural and functional features and mechanisms of action of known nucleoside analogs with antiviral, antibacterial or antiprotozoal activity. Particular attention is paid to the mechanisms that determine the antiviral effect of nucleoside analogs containing hydrophobic fragments. Depending on the structure and position of the hydrophobic substituent, such nucleosides can either block the process of penetration of viruses into cells or inhibit the stage of genome replication. The mechanisms of inhibition of viral enzymes by compounds of nucleoside and non-nucleoside nature have been compared. The stages of creation of antiparasitic drugs, which are based on the peculiarities of metabolic transformations of nucleosides in humans body and parasites, have been considered. A new approach to the creation of drugs is described, based on the use of prodrugs of modified nucleosides, which, as a result of metabolic processes, are converted into an effective drug directly in the target organ or tissue. This strategy makes it possible to reduce the general toxicity of the drug to humans and to increase the effectiveness of its action on cells infected by the virus.
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Affiliation(s)
- A. A. Zenchenko
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - M. S. Drenichev
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - I. A. Il’icheva
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - S. N. Mikhailov
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
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11
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Balatow P, Sandlin A, Cory TJ. An evaluation of ledipasvir + sofosbuvir for the treatment of chronic hepatitis C infection. Expert Opin Pharmacother 2021; 22:1839-1846. [PMID: 34157923 PMCID: PMC8478781 DOI: 10.1080/14656566.2021.1943359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
Introduction: Hepatitis C (HCV) is viral disease with a global impact. Over the last 10 years, the treatment of this disease has evolved. Treatment guidelines have evolved to adopt new medications for HCV. These drugs have shown efficacy over 90% throughout the class as well as a better safety profile than the previous recommended pharmacotherapy. Dual-therapy DAAs emerged with FDA approval of Ledipasvir/Sofosbuvir (LDV/SOF) in 2014.Areas Covered: LDV/SOF is a dual-therapy option for chronic HCV patients (>6 months of infection) in select genotypes. This article reviews the studies relevant to the pharmacokinetic/pharmacodynamic properties of these drugs as well as its trials leading to approval.Expert opinion: LDV/SOF is included in the AASLD/IDSA guidelines for the treatment of HCV genotypes 1a and 1b with or without cirrhosis and genotype 4 without cirrhosis with an evidence and recommendation rating of IA. Genotype 4 with cirrhosis and genotypes 5 and 6 carry a Class IIa level B recommendation. The combination is not FDA approved for genotypes 2 and 3. Single-pill regimens, like LDV/SOF, are important to maintain the quality of life of children and other special populations infected with HCV by shortening treatment regimens, avoiding complex pill regimens, and eliminating injection therapies.
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Affiliation(s)
- Pearson Balatow
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center College of Pharmacy, Memphis, USA
| | - Amber Sandlin
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center College of Pharmacy, Memphis, USA
| | - Theodore James Cory
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center College of Pharmacy, Memphis, USA
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12
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Yuan C, Goonetilleke EC, Unarta IC, Huang X. Incorporation efficiency and inhibition mechanism of 2'-substituted nucleotide analogs against SARS-CoV-2 RNA-dependent RNA polymerase. Phys Chem Chem Phys 2021; 23:20117-20128. [PMID: 34514487 DOI: 10.1039/d1cp03049c] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The ongoing pandemic caused by SARS-CoV-2 emphasizes the need for effective therapeutics. Inhibition of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) by nucleotide analogs provides a promising antiviral strategy. One common group of RdRp inhibitors, 2'-modified nucleotides, are reported to exhibit different behaviors in the SARS-CoV-2 RdRp transcription assay. Three of these analogs, 2'-O-methyl UTP, Sofosbuvir, and 2'-methyl CTP, act as effective inhibitors in previous biochemical experiments, while Gemcitabine and ara-UTP show no inhibitory activity. To understand the impact of the 2'-modification on their inhibitory effects, we conducted extensive molecular dynamics simulations and relative binding free energy calculations using the free energy perturbation method on SARS-CoV-2 replication-transcription complex (RTC) with these five nucleotide analogs. Our results reveal that the five nucleotide analogs display comparable binding affinities to SARS-CoV-2 RdRp and they can all be added to the nascent RNA chain. Moreover, we examine how the incorporation of these nucleotide triphosphate (NTP) analogs will impact the addition of the next nucleotide. Our results indicate that 2'-O-methyl UTP can weaken the binding of the subsequent NTP and consequently lead to partial chain termination. Additionally, Sofosbuvir and 2'-methyl CTP can cause immediate termination due to the strong steric hindrance introduced by their bulky 2'-methyl groups. In contrast, nucleotide analogs with smaller substitutions, such as the fluorine atoms and the ara-hydroxyl group in Gemcitabine and ara-UTP, have a marginal impact on the polymerization process. Our findings are consistent with experimental observations, and more importantly, shed light on the detailed molecular mechanism of SARS-CoV-2 RdRp inhibition by 2'-substituted nucleotide analogs, and may facilitate the rational design of antiviral agents to inhibit SARS-CoV-2 RdRp.
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Affiliation(s)
- Congmin Yuan
- Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong. .,Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong
| | - Eshani C Goonetilleke
- Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong. .,Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong
| | - Ilona Christy Unarta
- Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong. .,Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong
| | - Xuhui Huang
- Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong. .,Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong
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13
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Abdel-Tawab MAH, Abd El-Moghny MG, El Nashar RM. Recent advances in the chromatographic determination of the most commonly used anti-hepatitis C drug sofosbuvir and its co-administered drugs in human plasma. Biomed Chromatogr 2021; 36:e5238. [PMID: 34469609 DOI: 10.1002/bmc.5238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 08/08/2021] [Accepted: 08/26/2021] [Indexed: 11/10/2022]
Abstract
Sofosbuvir is a direct-acting antiviral drug that inhibits hepatitis C virus (HCV) NS5B polymerase, which in turn affects the virus replication inside biological systems. The clinical importance of sofosbuvir is based not only on its effect on HCV but also on other lethal viruses such as Zika and severe acute respiratory syndrome coronavirus disease 2019 (SARS-COVID-19). Accordingly, there is a continuous shedding of light on the development and validation of accurate and fast analytical methods for the determination of sofosbuvir in different environments. This work critically reviews the recent advances in chromatographic methods for the analysis of sofosbuvir and/or its metabolites in pure samples, pharmaceutical dosage forms, and in the presence of other co-administered drugs to highlight the current status and future perspectives to enhance its determination in different matrixes.
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Yahya G, Hashem Mohamed N, Pijuan J, Seleem NM, Mosbah R, Hess S, Abdelmoaty AA, Almeer R, Abdel‐Daim MM, Shulaywih Alshaman H, Juraiby I, Metwally K, Storchova Z. Profiling the physiological pitfalls of anti-hepatitis C direct-acting agents in budding yeast. Microb Biotechnol 2021; 14:2199-2213. [PMID: 34378349 PMCID: PMC8449668 DOI: 10.1111/1751-7915.13904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 02/05/2023] Open
Abstract
Sofosbuvir and Daclatasvir are among the direct-acting antiviral (DAA) medications prescribed for the treatment of chronic hepatitis C (CHC) virus infection as combination therapy with other antiviral medications. DAA-based therapy achieves high cure rates, reaching up to 97% depending on the genotype of the causative hepatitis C virus (HCV). While DAAs have been approved as an efficient and well-tolerated therapy for CHC, emerging concerns about adverse cardiac side effects, higher risk of recurrence and occurrence of hepatocellular carcinoma (HCC) and doubts of genotoxicity have been reported. In our study, we investigated in detail physiological off-targets of DAAs and dissected the effects of these drugs on cellular organelles using budding yeast, a unicellular eukaryotic organism. DAAs were found to disturb the architecture of the endoplasmic reticulum (ER) and the mitochondria, while showing no apparent genotoxicity or DNA damaging effect. Our study provides evidence that DAAs are not associated with genotoxicity and highlights the necessity for adjunctive antioxidant therapy to mitigate the adverse effects of DAAs on ER and mitochondria.
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Affiliation(s)
- Galal Yahya
- Department of Microbiology and ImmunologyFaculty of PharmacyZagazig UniversityAl Sharqia44519Egypt
- Department of Molecular GeneticsFaculty of BiologyTechnical University of KaiserslauternPaul‐Ehrlich Str. 24Kaiserslautern67663Germany
| | | | - Jordi Pijuan
- Laboratory of Neurogenetics and Molecular Medicine ‐ IPERInstitut de Recerca Sant Joan de DéuBarcelona08950Spain
| | - Noura M. Seleem
- Department of Microbiology and ImmunologyFaculty of PharmacyZagazig UniversityAl Sharqia44519Egypt
| | - Rasha Mosbah
- Infection Control UnitHospitals of Zagazig UniversityAl SharqiaEgypt
| | - Steffen Hess
- Department of Cell BiologyFaculty of BiologyTechnical University of KaiserslauternKaiserslauternGermany
| | - Ahmed A. Abdelmoaty
- Department of Tropical MedicineFaculty of MedicineZagazig UniversityZagazig44519Egypt
| | - Rafa Almeer
- Department of ZoologyCollege of ScienceKing Saud UniversityP.O. Box 2455Riyadh11451Saudi Arabia
| | - Mohamed M. Abdel‐Daim
- Department of ZoologyCollege of ScienceKing Saud UniversityP.O. Box 2455Riyadh11451Saudi Arabia
- Pharmacology DepartmentCollege of Veterinary MedicineSuez Canal UniversityIsmailiaEgypt
| | | | - Ibrahim Juraiby
- General Directorate of Health AffairsMinistry of HealthJazan82723Saudi Arabia
| | - Kamel Metwally
- Department of Pharmaceutical ChemistryFaculty of PharmacyTabuk UniversityTabuk47713Saudi Arabia
- Department of Medicinal ChemistryFaculty of PharmacyZagazig UniversityZagazig44519Egypt
| | - Zuzana Storchova
- Department of Molecular GeneticsFaculty of BiologyTechnical University of KaiserslauternPaul‐Ehrlich Str. 24Kaiserslautern67663Germany
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15
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Srivastava M, Mittal L, Kumari A, Asthana S. Molecular Dynamics Simulations Reveal the Interaction Fingerprint of Remdesivir Triphosphate Pivotal in Allosteric Regulation of SARS-CoV-2 RdRp. Front Mol Biosci 2021; 8:639614. [PMID: 34490343 PMCID: PMC8417884 DOI: 10.3389/fmolb.2021.639614] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/24/2021] [Indexed: 01/18/2023] Open
Abstract
The COVID-19 pandemic has now strengthened its hold on human health and coronavirus' lethal existence does not seem to be going away soon. In this regard, the optimization of reported information for understanding the mechanistic insights that facilitate the discovery towards new therapeutics is an unmet need. Remdesivir (RDV) is established to inhibit RNA-dependent RNA polymerase (RdRp) in distinct viral families including Ebola and SARS-CoV-2. Therefore, its derivatives have the potential to become a broad-spectrum antiviral agent effective against many other RNA viruses. In this study, we performed comparative analysis of RDV, RMP (RDV monophosphate), and RTP (RDV triphosphate) to undermine the inhibition mechanism caused by RTP as it is a metabolically active form of RDV. The MD results indicated that RTP rearranges itself from its initial RMP-pose at the catalytic site towards NTP entry site, however, RMP stays at the catalytic site. The thermodynamic profiling and free-energy analysis revealed that a stable pose of RTP at NTP entrance site seems critical to modulate the inhibition as its binding strength improved more than its initial RMP-pose obtained from docking at the catalytic site. We found that RTP not only occupies the residues K545, R553, and R555, essential to escorting NTP towards the catalytic site, but also interacts with other residues D618, P620, K621, R624, K798, and R836 that contribute significantly to its stability. From the interaction fingerprinting it is revealed that the RTP interact with basic and conserved residues that are detrimental for the RdRp activity, therefore it possibly perturbed the catalytic site and blocked the NTP entrance site considerably. Overall, we are highlighting the RTP binding pose and key residues that render the SARS-CoV-2 RdRp inactive, paving crucial insights towards the discovery of potent inhibitors.
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Affiliation(s)
| | | | | | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
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16
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Bhatia S, Narayanan N, Nagpal S, Nair DT. Antiviral therapeutics directed against RNA dependent RNA polymerases from positive-sense viruses. Mol Aspects Med 2021; 81:101005. [PMID: 34311994 DOI: 10.1016/j.mam.2021.101005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 01/18/2023]
Abstract
Viruses with positive-sense single stranded RNA (+ssRNA) genomes are responsible for different diseases and represent a global health problem. In addition to developing new vaccines that protect against severe illness on infection, it is imperative to identify new antiviral molecules to treat infected patients. The genome of these RNA viruses generally codes for an enzyme with RNA dependent RNA polymerase (RdRP) activity. This molecule is centrally involved in the duplication of the RNA genome. Inhibition of this enzyme by small molecules will prevent duplication of the RNA genome and thus reduce the viral titer. An overview of the different therapeutic strategies used to inhibit RdRPs from +ssRNA viruses is provided, along with an analysis of these enzymes to highlight new binding sites for inhibitors.
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Affiliation(s)
- Sonam Bhatia
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India
| | - Naveen Narayanan
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India
| | - Shilpi Nagpal
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Deepak T Nair
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India.
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17
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Gordon CJ, Tchesnokov EP, Schinazi RF, Götte M. Molnupiravir promotes SARS-CoV-2 mutagenesis via the RNA template. J Biol Chem 2021; 297:100770. [PMID: 33989635 PMCID: PMC8110631 DOI: 10.1016/j.jbc.2021.100770] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 04/29/2021] [Accepted: 05/09/2021] [Indexed: 01/01/2023] Open
Abstract
The RNA-dependent RNA polymerase of the severe acute respiratory syndrome coronavirus 2 is an important target in current drug development efforts for the treatment of coronavirus disease 2019. Molnupiravir is a broad-spectrum antiviral that is an orally bioavailable prodrug of the nucleoside analogue β-D-N4-hydroxycytidine (NHC). Molnupiravir or NHC can increase G to A and C to U transition mutations in replicating coronaviruses. These increases in mutation frequencies can be linked to increases in antiviral effects; however, biochemical data of molnupiravir-induced mutagenesis have not been reported. Here we studied the effects of the active compound NHC 5’-triphosphate (NHC-TP) against the purified severe acute respiratory syndrome coronavirus 2 RNA-dependent RNA polymerase complex. The efficiency of incorporation of natural nucleotides over the efficiency of incorporation of NHC-TP into model RNA substrates followed the order GTP (12,841) > ATP (424) > UTP (171) > CTP (30), indicating that NHC-TP competes predominantly with CTP for incorporation. No significant inhibition of RNA synthesis was noted as a result of the incorporated monophosphate in the RNA primer strand. When embedded in the template strand, NHC-monophosphate supported the formation of both NHC:G and NHC:A base pairs with similar efficiencies. The extension of the NHC:G product was modestly inhibited, but higher nucleotide concentrations could overcome this blockage. In contrast, the NHC:A base pair led to the observed G to A (G:NHC:A) or C to U (C:G:NHC:A:U) mutations. Together, these biochemical data support a mechanism of action of molnupiravir that is primarily based on RNA mutagenesis mediated via the template strand.
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Affiliation(s)
- Calvin J Gordon
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Raymond F Schinazi
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Center for AIDS Research, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada; Li Ka Shing Institute of Virology at University of Alberta, Edmonton, Alberta, Canada.
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Resistance to a Nucleoside Analog Antiviral Drug from More Rapid Extension of Drug-Containing Primers. mBio 2021; 12:mBio.03492-20. [PMID: 33563814 PMCID: PMC7885103 DOI: 10.1128/mbio.03492-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Nucleoside analogs are mainstays of antiviral therapy. Although resistance to these drugs hinders their use, understanding resistance can illuminate mechanisms of the drugs and their targets. Certain nucleoside analogs, such as ganciclovir (GCV), a leading therapy for human cytomegalovirus (HCMV), contain the equivalent of a 3'-hydoxyl moiety, yet their triphosphates can terminate genome synthesis (nonobligate chain termination). For ganciclovir, chain termination is delayed until incorporation of the subsequent nucleotide, after which viral polymerase idling (repeated addition and removal of incorporated nucleotides) prevents extension. Here, we investigated how an alanine-to-glycine substitution at residue 987 (A987G), in conserved motif V in the thumb subdomain of the catalytic subunit (Pol) of HCMV DNA polymerase, affects polymerase function to overcome delayed chain termination and confer ganciclovir resistance. Steady-state enzyme kinetic studies revealed no effects of this substitution on incorporation of ganciclovir-triphosphate into DNA that could explain resistance. We also found no effects of the substitution on Pol's exonuclease activity, and the mutant enzyme still exhibited idling after incorporation of GCV and the subsequent nucleotide. However, despite extending normal DNA primers similarly to wild-type enzyme, A987G Pol more rapidly extended ganciclovir-containing DNA primers, thereby overcoming chain termination. The mutant Pol also more rapidly extended RNA primers, a previously unreported activity for HCMV Pol. Structural analysis of related Pols bound to primer-templates provides a rationale for these results. These studies uncover a new drug resistance mechanism, potentially applicable to other nonobligate chain-terminating nucleoside analogs, and shed light on polymerase functions.IMPORTANCE While resistance to antiviral drugs can hinder their clinical use, understanding resistance mechanisms can illuminate how these drugs and their targets act. We studied a substitution in the human cytomegalovirus (HCMV) DNA polymerase that confers resistance to a leading anti-HCMV drug, ganciclovir. Ganciclovir is a nucleoside analog that terminates DNA replication after its triphosphate and the subsequent nucleotide are incorporated. We found that the substitution studied here results in an increased rate of extension of drug-containing DNA primers, thereby overcoming termination, which is a new mechanism of drug resistance. The substitution also induces more rapid extension of RNA primers, a function that had not previously been reported for HCMV polymerase. Thus, these results provide a novel resistance mechanism with potential implications for related nucleoside analogs that act against established and emerging viruses, and shed light on DNA polymerase functions.
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Yousefi H, Mashouri L, Okpechi SC, Alahari N, Alahari SK. Repurposing existing drugs for the treatment of COVID-19/SARS-CoV-2 infection: A review describing drug mechanisms of action. Biochem Pharmacol 2021; 183:114296. [PMID: 33191206 PMCID: PMC7581400 DOI: 10.1016/j.bcp.2020.114296] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023]
Abstract
The outbreak of a novel coronavirus (SARS-CoV-2) has caused a major public health concern across the globe. SARS-CoV-2 is the seventh coronavirus that is known to cause human disease. As of September 2020, SARS-CoV-2 has been reported in 213 countries and more than 31 million cases have been confirmed, with an estimated mortality rate of ∼3%. Unfortunately, a drug or vaccine is yet to be discovered to treat COVID-19. Thus, repurposing of existing cancer drugs will be a novel approach in treating COVID-19 patients. These drugs target viral replication cycle, viral entry and translocation to the nucleus. Some can enhance innate antiviral immune response as well. Hence this review focuses on comprehensive list of 22 drugs that work against COVID-19 infection. These drugs include fingolimod, colchicine, N4-hydroxycytidine, remdesivir, methylprednisone, oseltamivir, icatibant, perphanizine, viracept, emetine, homoharringtonine, aloxistatin, ribavirin, valrubicin, famotidine, almitrine, amprenavir, hesperidin, biorobin, cromolyn sodium, and antibodies- tocilzumab and sarilumab. Also, we provide a list of 31 drugs that are predicted to function against SARS-CoV-2 infection. In summary, we provide succinct overview of various therapeutic modalities. Among these 53 drugs, based on various clinical trials and literature, remdesivir, nelfinavir, methylpredinosolone, colchicine, famotidine and emetine may be used for COVID-19. SIGNIFICANCE: It is of utmost important priority to develop novel therapies for COVID-19. Since the effect of SARS-CoV-2 is so severe, slowing the spread of diseases will help the health care system, especially the number of visits to Intensive Care Unit (ICU) of any country. Several clinical trials are in works around the globe. Moreover, NCI developed a recent and robust response to COVID-19 pandemic. One of the NCI's goals is to screen cancer related drugs for identification of new therapies for COVID-19. https://www.cancer.gov/news-events/cancer-currents-blog/2020/covid-19-cancer-nci-response?cid=eb_govdel.
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Affiliation(s)
- Hassan Yousefi
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center School of Medicine, New Orleans, LA, USA
| | - Ladan Mashouri
- Department of Medical Sciences, University of Arkansas, Little Rock, AK, USA
| | - Samuel C Okpechi
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center School of Medicine, New Orleans, LA, USA
| | - Nikhilesh Alahari
- Department of Biological Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Suresh K Alahari
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center School of Medicine, New Orleans, LA, USA; Stanley Scott Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA.
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20
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Maheden K, Todd B, Gordon CJ, Tchesnokov EP, Götte M. Inhibition of viral RNA-dependent RNA polymerases with clinically relevant nucleotide analogs. Enzymes 2021; 49:315-354. [PMID: 34696837 PMCID: PMC8517576 DOI: 10.1016/bs.enz.2021.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The treatment of viral infections remains challenging, in particular in the face of emerging pathogens. Broad-spectrum antiviral drugs could potentially be used as a first line of defense. The RNA-dependent RNA polymerase (RdRp) of RNA viruses serves as a logical target for drug discovery and development efforts. Herein we discuss compounds that target RdRp of poliovirus, hepatitis C virus, influenza viruses, respiratory syncytial virus, and the growing data on coronaviruses. We focus on nucleotide analogs and mechanisms of action and resistance.
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Affiliation(s)
- Kieran Maheden
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Brendan Todd
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Calvin J Gordon
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada; Li Ka Shing Institute of Virology at University of Alberta, Edmonton, AB, Canada.
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21
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Lu G, Zhang X, Zheng W, Sun J, Hua L, Xu L, Chu XJ, Ding S, Xiong W. Development of a Simple In Vitro Assay To Identify and Evaluate Nucleotide Analogs against SARS-CoV-2 RNA-Dependent RNA Polymerase. Antimicrob Agents Chemother 2020; 65:e01508-20. [PMID: 33122171 PMCID: PMC7927875 DOI: 10.1128/aac.01508-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Nucleotide analogs targeting viral RNA polymerase have been proved to be an effective strategy for antiviral treatment and are promising antiviral drugs to combat the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. In this study, we developed a robust in vitro nonradioactive primer extension assay to quantitatively evaluate the efficiency of incorporation of nucleotide analogs by SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). Our results show that many nucleotide analogs can be incorporated into RNA by SARS-CoV-2 RdRp and that the incorporation of some of them leads to chain termination. The discrimination values of nucleotide analogs over those of natural nucleotides were measured to evaluate the incorporation efficiency of nucleotide analog by SARS-CoV-2 RdRp. In agreement with the data published in the literature, we found that the incorporation efficiency of remdesivir-TP is higher than that of ATP and incorporation of remdesivir-TP caused delayed chain termination, which can be overcome by higher concentrations of the next nucleotide to be incorporated. Our data also showed that the delayed chain termination pattern caused by remdesivir-TP incorporation is different for different template sequences. Multiple incorporations of remdesivir-TP caused chain termination under our assay conditions. Incorporation of sofosbuvir-TP is very low, suggesting that sofosbuvir may not be very effective in treating SARS-CoV-2 infection. As a comparison, 2'-C-methyl-GTP can be incorporated into RNA efficiently, and the derivative of 2'-C-methyl-GTP may have therapeutic application in treating SARS-CoV-2 infection. This report provides a simple screening method that should be useful for evaluating nucleotide-based drugs targeting SARS-CoV-2 RdRp and for studying the mechanism of action of selected nucleotide analogs.
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Affiliation(s)
- Gaofei Lu
- Global Health Drug Discovery Institute, Beijing, China
| | - Xi Zhang
- Global Health Drug Discovery Institute, Beijing, China
| | - Weinan Zheng
- Global Health Drug Discovery Institute, Beijing, China
| | - Jialei Sun
- Global Health Drug Discovery Institute, Beijing, China
| | - Lan Hua
- Global Health Drug Discovery Institute, Beijing, China
| | - Lan Xu
- Global Health Drug Discovery Institute, Beijing, China
| | - Xin-Jie Chu
- Global Health Drug Discovery Institute, Beijing, China
| | - Sheng Ding
- Global Health Drug Discovery Institute, Beijing, China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Wen Xiong
- Global Health Drug Discovery Institute, Beijing, China
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22
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Yu H, Yang H, Shi E, Tang W. Development and Clinical Application of Phosphorus-Containing Drugs. MEDICINE IN DRUG DISCOVERY 2020; 8:100063. [PMID: 32864606 PMCID: PMC7445155 DOI: 10.1016/j.medidd.2020.100063] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 12/20/2022] Open
Abstract
Phosphorus-containing drugs belong to an important class of therapeutic agents and are widely applied in daily clinical practices. Structurally, the phosphorus-containing drugs can be classified into phosphotriesters, phosphonates, phosphinates, phosphine oxides, phosphoric amides, bisphosphonates, phosphoric anhydrides, and others; functionally, they are often designed as prodrugs with improved selectivity and bioavailability, reduced side effects and toxicity, or biomolecule analogues with endogenous materials and antagonistic endoenzyme supplements. This review summarized the phosphorus-containing drugs currently on the market as well as a few promising molecules at clinical studies, with particular emphasis on their structural features, biological mechanism, and indications.
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Affiliation(s)
- Hanxiao Yu
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Ling Ling Road, Shanghai 200032, China
| | - He Yang
- Shenzhen Grubbs Institute, Southern University of Science and Technology, Shenzhen, 518055, China,Corresponding authors
| | - Enxue Shi
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China,Corresponding authors
| | - Wenjun Tang
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Ling Ling Road, Shanghai 200032, China,School of Chemistry and Material Sciences, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China,Correspondence to: W. Tang, State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Ling Ling Road, Shanghai 200032, China
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23
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Ju J, Li X, Kumar S, Jockusch S, Chien M, Tao C, Morozova I, Kalachikov S, Kirchdoerfer RN, Russo JJ. Nucleotide analogues as inhibitors of SARS-CoV Polymerase. Pharmacol Res Perspect 2020; 8:e00674. [PMID: 33124786 PMCID: PMC7596664 DOI: 10.1002/prp2.674] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 01/18/2023] Open
Abstract
SARS-CoV-2, a member of the coronavirus family, has caused a global public health emergency. Based on our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously reasoned that the FDA-approved hepatitis C drug EPCLUSA (Sofosbuvir/Velpatasvir) should inhibit coronaviruses, including SARS-CoV-2. Here, using model polymerase extension experiments, we demonstrate that the active triphosphate form of Sofosbuvir is incorporated by low-fidelity polymerases and SARS-CoV RNA-dependent RNA polymerase (RdRp), and blocks further incorporation by these polymerases; the active triphosphate form of Sofosbuvir is not incorporated by a host-like high-fidelity DNA polymerase. Using the same molecular insight, we selected 3'-fluoro-3'-deoxythymidine triphosphate and 3'-azido-3'-deoxythymidine triphosphate, which are the active forms of two other anti-viral agents, Alovudine and AZT (an FDA-approved HIV/AIDS drug) for evaluation as inhibitors of SARS-CoV RdRp. We demonstrate the ability of two of these HIV reverse transcriptase inhibitors to be incorporated by SARS-CoV RdRp where they also terminate further polymerase extension. Given the 98% amino acid similarity of the SARS-CoV and SARS-CoV-2 RdRps, we expect these nucleotide analogues would also inhibit the SARS-CoV-2 polymerase. These results offer guidance to further modify these nucleotide analogues to generate more potent broad-spectrum anti-coronavirus agents.
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Affiliation(s)
- Jingyue Ju
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
- Department of Molecular Pharmacology and TherapeuticsColumbia UniversityNew YorkNYUSA
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
| | - Steffen Jockusch
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of ChemistryColumbia UniversityNew YorkNYUSA
| | - Minchen Chien
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
| | - Irina Morozova
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
| | - Sergey Kalachikov
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
| | - Robert N. Kirchdoerfer
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- Institute of Molecular VirologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - James J. Russo
- Center for Genome Technology and Biomolecular EngineeringColumbia UniversityNew YorkNew YorkUSA
- Department of Chemical EngineeringColumbia UniversityNew YorkNYUSA
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24
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de Almeida SMV, Santos Soares JC, Dos Santos KL, Alves JEF, Ribeiro AG, Jacob ÍTT, da Silva Ferreira CJ, Dos Santos JC, de Oliveira JF, de Carvalho Junior LB, de Lima MDCA. COVID-19 therapy: What weapons do we bring into battle? Bioorg Med Chem 2020; 28:115757. [PMID: 32992245 PMCID: PMC7481143 DOI: 10.1016/j.bmc.2020.115757] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/29/2020] [Accepted: 09/03/2020] [Indexed: 01/18/2023]
Abstract
Urgent treatments, in any modality, to fight SARS-CoV-2 infections are desired by society in general, by health professionals, by Estate-leaders and, mainly, by the scientific community, because one thing is certain amidst the numerous uncertainties regarding COVID-19: knowledge is the means to discover or to produce an effective treatment against this global disease. Scientists from several areas in the world are still committed to this mission, as shown by the accelerated scientific production in the first half of 2020 with over 25,000 published articles related to the new coronavirus. Three great lines of publications related to COVID-19 were identified for building this article: The first refers to knowledge production concerning the virus and pathophysiology of COVID-19; the second regards efforts to produce vaccines against SARS-CoV-2 at a speed without precedent in the history of science; the third comprehends the attempts to find a marketed drug that can be used to treat COVID-19 by drug repurposing. In this review, the drugs that have been repurposed so far are grouped according to their chemical class. Their structures will be presented to provide better understanding of their structural similarities and possible correlations with mechanisms of actions. This can help identifying anti-SARS-CoV-2 promising therapeutic agents.
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Affiliation(s)
- Sinara Mônica Vitalino de Almeida
- Laboratório de Biologia Molecular, Universidade de Pernambuco, Garanhuns, PE, Brazil; Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil; Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Recife, PE, Brazil.
| | - José Cleberson Santos Soares
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Keriolaine Lima Dos Santos
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - Amélia Galdino Ribeiro
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Íris Trindade Tenório Jacob
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | | | - Jamerson Ferreira de Oliveira
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - Maria do Carmo Alves de Lima
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil
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25
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Robson F, Khan KS, Le TK, Paris C, Demirbag S, Barfuss P, Rocchi P, Ng WL. Coronavirus RNA Proofreading: Molecular Basis and Therapeutic Targeting. Mol Cell 2020; 79:710-727. [PMID: 32853546 PMCID: PMC7402271 DOI: 10.1016/j.molcel.2020.07.027] [Citation(s) in RCA: 249] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/24/2020] [Accepted: 07/29/2020] [Indexed: 01/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) that is wreaking havoc on worldwide public health and economies has heightened awareness about the lack of effective antiviral treatments for human coronaviruses (CoVs). Many current antivirals, notably nucleoside analogs (NAs), exert their effect by incorporation into viral genomes and subsequent disruption of viral replication and fidelity. The development of anti-CoV drugs has long been hindered by the capacity of CoVs to proofread and remove mismatched nucleotides during genome replication and transcription. Here, we review the molecular basis of the CoV proofreading complex and evaluate its potential as a drug target. We also consider existing nucleoside analogs and novel genomic techniques as potential anti-CoV therapeutics that could be used individually or in combination to target the proofreading mechanism.
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Affiliation(s)
- Fran Robson
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Khadija Shahed Khan
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Thi Khanh Le
- Life Science Department, University of Science and Technology of Hanoi (USTH), Hanoi, Vietnam; Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University U105, Institut Paoli-Calmettes, Marseille, France
| | - Clément Paris
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University U105, Institut Paoli-Calmettes, Marseille, France
| | - Sinem Demirbag
- Faculty of Engineering and Natural Sciences, Sabanci University, İstanbul, Turkey
| | - Peter Barfuss
- Université Paris-Est, Cermics (ENPC), INRIA, 77455 Marne-la-Vallée, France
| | - Palma Rocchi
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University U105, Institut Paoli-Calmettes, Marseille, France
| | - Wai-Lung Ng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong.
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26
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Wang G, Dyatkina N, Prhavc M, Williams C, Serebryany V, Hu Y, Huang Y, Wu X, Chen T, Huang W, Rajwanshi VK, Deval J, Fung A, Jin Z, Stoycheva A, Shaw K, Gupta K, Tam Y, Jekle A, Smith DB, Beigelman L. Synthesis and Anti-HCV Activity of Sugar-Modified Guanosine Analogues: Discovery of AL-611 as an HCV NS5B Polymerase Inhibitor for the Treatment of Chronic Hepatitis C. J Med Chem 2020; 63:10380-10395. [PMID: 32816483 DOI: 10.1021/acs.jmedchem.0c00935] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chronic hepatitis C (CHC) is a major liver disease caused by the hepatitis C virus. The current standard of care for CHC can achieve cure rates above 95%; however, the drugs in current use are administered for a period of 8-16 weeks. A combination of safe and effective drugs with a shorter treatment period is highly desirable. We report synthesis and biological evaluation of a series of 2',3'- and 2',4'-substituted guanosine nucleotide analogues. Their triphosphates exhibited potent inhibition of the HCV NS5B polymerase with IC50 as low as 0.13 μM. In the HCV replicon assay, the phosphoramidate prodrugs of these analogues demonstrated excellent activity with EC50 values as low as 5 nM. A lead compound AL-611 showed high levels of the nucleoside 5'-triphosphate in vitro in primary human hepatocytes and in vivo in dog liver following oral administration.
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Affiliation(s)
- Guangyi Wang
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Natalia Dyatkina
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Marija Prhavc
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Caroline Williams
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Vladimir Serebryany
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Yujian Hu
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, P. R. China
| | - Yongfei Huang
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, P. R. China
| | - Xiangyang Wu
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, P. R. China
| | - Tongqian Chen
- Pharmaron Beijing, Co. Ltd., No. 6, TaiHe Road, BDA, Beijing 100176, P. R. China
| | - Wensheng Huang
- Pharmaron Beijing, Co. Ltd., No. 6, TaiHe Road, BDA, Beijing 100176, P. R. China
| | - Vivek K Rajwanshi
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Jerome Deval
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Amy Fung
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Zhinan Jin
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Antitsa Stoycheva
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Kenneth Shaw
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Kusum Gupta
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Yuen Tam
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Andreas Jekle
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - David B Smith
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Leonid Beigelman
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
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27
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Pooladanda V, Thatikonda S, Godugu C. The current understanding and potential therapeutic options to combat COVID-19. Life Sci 2020; 254:117765. [PMID: 32437797 PMCID: PMC7207108 DOI: 10.1016/j.lfs.2020.117765] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023]
Abstract
The ongoing wreaking global outbreak of the novel human beta coronavirus (CoV) pathogen was presumed to be from a seafood wholesale market in Wuhan, China, belongs to the Coronaviridae family in the Nidovirales order. The virus is highly contagious with potential human-human transmission which was named as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has spread across six continents and emerged as a global pandemic in short span with alarming levels of spread and severity. This virus associated symptoms and infectious respiratory illness is designated as coronavirus disease 19 (COVID-19). The SARS-CoV-2 possesses enveloped club-like spike protein projections with positive-sense large RNA genome and has a unique replication strategy. This virus was believed to have zoonotic origin with genetical identity to bat and pangolin CoV. In the current review, we introduce a general overview about the human CoVs and the associated diseases, the origin, structure, replication and key clinical events that occur in the COVID-19 pathogenicity. Furthermore, we focused on possible therapeutic options such as repurposing drugs including antimalarials, antivirals, antiparasitic drugs, and anti-HIV drugs, as well as monoclonal antibodies, vaccines as potential treatment options. Also we have summarized the latest research progress on the usage of stem cell therapy, human convalescent serum, interferon's, in the treatment of COVID-19.
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Affiliation(s)
- Venkatesh Pooladanda
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500037, India
| | - Sowjanya Thatikonda
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500037, India
| | - Chandraiah Godugu
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500037, India.
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28
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Min JS, Kim GW, Kwon S, Jin YH. A Cell-Based Reporter Assay for Screening Inhibitors of MERS Coronavirus RNA-Dependent RNA Polymerase Activity. J Clin Med 2020; 9:E2399. [PMID: 32727069 PMCID: PMC7465106 DOI: 10.3390/jcm9082399] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022] Open
Abstract
Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and coronavirus disease 2019 (COVID-19) are emerging zoonotic diseases caused by coronavirus (CoV) infections. The viral RNA-dependent RNA polymerase (RdRp) has been suggested as a valuable target for antiviral therapeutics because the sequence homology of CoV RdRp is highly conserved. We established a cell-based reporter assay for MERS-CoV RdRp activity to test viral polymerase inhibitors. The cell-based reporter system was composed of the bicistronic reporter construct and the MERS-CoV nsp12 plasmid construct. Among the tested nine viral polymerase inhibitors, ribavirin, sofosbuvir, favipiravir, lamivudine, zidovudine, valacyclovir, vidarabine, dasabuvir, and remdesivir, only remdesivir exhibited a dose-dependent inhibition. Meanwhile, the Z-factor and Z'-factor of this assay for screening inhibitors of MERS-CoV RdRp activity were 0.778 and 0.782, respectively. Ribavirin and favipiravir did not inhibit the MERS-CoV RdRp activity, and non-nucleoside HCV RdRp inhibitor, dasabuvir, partially inhibited MERS-CoV RdRp activity. Taken together, the cell-based reporter assay for MERS-CoV RdRp activity confirmed remdesivir as a direct inhibitor of MERS-CoV RdRp in cells. A cell-based MERS-CoV RdRp activity reporter assay is reliable and accurate for screening MERS-CoV RdRp-specific inhibitors. It may provide a valuable platform for developing antiviral drugs for emerging CoV infections.
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Affiliation(s)
- Jung Sun Min
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, Korea; (J.S.M.); (G.-W.K.)
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
| | - Geon-Woo Kim
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, Korea; (J.S.M.); (G.-W.K.)
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
| | - Sunoh Kwon
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, Korea; (J.S.M.); (G.-W.K.)
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
| | - Young-Hee Jin
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
- KM Application Center, Korea Institute of Oriental Medicine, Daegu 41062, Korea
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29
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Shannon A, Le NTT, Selisko B, Eydoux C, Alvarez K, Guillemot JC, Decroly E, Peersen O, Ferron F, Canard B. Remdesivir and SARS-CoV-2: Structural requirements at both nsp12 RdRp and nsp14 Exonuclease active-sites. Antiviral Res 2020; 178:104793. [PMID: 32283108 PMCID: PMC7151495 DOI: 10.1016/j.antiviral.2020.104793] [Citation(s) in RCA: 227] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 12/20/2022]
Abstract
The rapid global emergence of SARS-CoV-2 has been the cause of significant health concern, highlighting the immediate need for antivirals. Viral RNA-dependent RNA polymerases (RdRp) play essential roles in viral RNA synthesis, and thus remains the target of choice for the prophylactic or curative treatment of several viral diseases, due to high sequence and structural conservation. To date, the most promising broad-spectrum class of viral RdRp inhibitors are nucleoside analogues (NAs), with over 25 approved for the treatment of several medically important viral diseases. However, Coronaviruses stand out as a particularly challenging case for NA drug design due to the presence of an exonuclease (ExoN) domain capable of excising incorporated NAs and thus providing resistance to many of these available antivirals. Here we use the available structures of the SARS-CoV RdRp and ExoN proteins, as well as Lassa virus N exonuclease to derive models of catalytically competent SARS-CoV-2 enzymes. We then map a promising NA candidate, GS-441524 (the active metabolite of Remdesivir) to the nucleoside active site of both proteins, identifying the residues important for nucleotide recognition, discrimination, and excision. Interestingly, GS-441524 addresses both enzyme active sites in a manner consistent with significant incorporation, delayed chain termination, and altered excision due to the ribose 1'-CN group, which may account for the increased antiviral effect compared to other available analogues. Additionally, we propose structural and function implications of two previously identified RdRp resistance mutations in relation to resistance against Remdesivir. This study highlights the importance of considering the balance between incorporation and excision properties of NAs between the RdRp and ExoN.
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Affiliation(s)
- Ashleigh Shannon
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288, Marseille, France
| | - Nhung Thi-Tuyet Le
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288, Marseille, France
| | - Barbara Selisko
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288, Marseille, France
| | - Cecilia Eydoux
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288, Marseille, France
| | - Karine Alvarez
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288, Marseille, France
| | - Jean-Claude Guillemot
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288, Marseille, France
| | - Etienne Decroly
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288, Marseille, France
| | - Olve Peersen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA; Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288, Marseille, France
| | - Francois Ferron
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288, Marseille, France.
| | - Bruno Canard
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288, Marseille, France.
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Villalba B, Li J, Johnson KA. Resistance to excision determines efficiency of hepatitis C virus RNA-dependent RNA polymerase inhibition by nucleotide analogs. J Biol Chem 2020; 295:10112-10124. [PMID: 32457046 DOI: 10.1074/jbc.ra120.013422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/11/2020] [Indexed: 12/26/2022] Open
Abstract
NS5B is the RNA-dependent RNA polymerase that catalyzes the replication of the hepatitis C virus genome. It is a major target for antiviral drugs including nucleoside analogs, such as the prodrugs mericitabine and sofosbuvir, which get metabolized to 2'-fluoro-2'C-methylcytidine-5'-triphosphate and 2'-fluoro-2'C-methyluridine-5'-triphosphate, respectively. These analogs act as chain terminators after they are incorporated during RNA synthesis. Recently, it has been shown that NS5B can efficiently remove chain terminators by a nucleotide-mediated excision reaction that rescues RNA synthesis. In this study, we use transient-state kinetics to understand the efficiency of inhibition for five nucleoside analogs. We show that CTP analogs are readily incorporated into a growing primer by NS5B but are also efficiently excised. In contrast, although UMP analogs are more slowly incorporated, the excision of UMP is slow and inefficient, and modifications to the 2'-carbon of the UTP ribose ring further decreased rates of excision to an undetectable level. Taken together, these data suggest that the clinical effectiveness of sofosbuvir is largely a function of being intractable to nucleotide-mediated excision compared with similar nucleoside analogs.
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Affiliation(s)
- Brian Villalba
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
| | - Jiawen Li
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
| | - Kenneth A Johnson
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
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31
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Shaw TA, Ablenas CJ, Desrochers GF, Powdrill MH, Bilodeau DA, Vincent-Rocan JF, Niu M, Monette A, Mouland AJ, Beauchemin AM, Pezacki JP. A Bifunctional Nucleoside Probe for the Inhibition of the Human Immunodeficiency Virus-Type 1 Reverse Transcriptase. Bioconjug Chem 2020; 31:1537-1544. [DOI: 10.1021/acs.bioconjchem.0c00191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Tyler A. Shaw
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Christopher J. Ablenas
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Geneviève F. Desrochers
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Megan H. Powdrill
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Jean-François Vincent-Rocan
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Meijuan Niu
- Lady Davis Institute at the Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, Québec H3T 1E2, Canada
| | - Anne Monette
- Lady Davis Institute at the Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, Québec H3T 1E2, Canada
| | - Andrew J. Mouland
- Lady Davis Institute at the Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, Québec H3T 1E2, Canada
- Department of Medicine, McGill University, 3999 Côte-Ste-Catherine Road, Montréal, Québec H3T 1E2, Canada
| | - André M. Beauchemin
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
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Abstract
Viral population numbers are extremely large compared with those of their host species. Population bottlenecks are frequent during the life cycle of viruses and can reduce viral populations transiently to very few individuals. Viruses have to confront several types of constraints that can be divided into basal, cell-dependent, and organism-dependent constraints. Viruses overcome them exploiting a number of molecular mechanisms, with an important contribution of population numbers and genome variation. The adaptive potential of viruses is reflected in modifications of cell tropism and host range, escape to components of the host immune response, and capacity to alternate among different host species, among other phenotypic changes. Despite a fitness cost of most mutations required to overcome a selective constraint, viruses can find evolutionary pathways that ensure their survival in equilibrium with their hosts.
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33
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Boehr AK, Arnold JJ, Oh HS, Cameron CE, Boehr DD. 2'-C-methylated nucleotides terminate virus RNA synthesis by preventing active site closure of the viral RNA-dependent RNA polymerase. J Biol Chem 2019; 294:16897-16907. [PMID: 31575662 PMCID: PMC6851289 DOI: 10.1074/jbc.ra119.010214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/28/2019] [Indexed: 01/25/2023] Open
Abstract
The 2'-C-methyl ribonucleosides are nucleoside analogs representing an important class of antiviral agents, especially against positive-strand RNA viruses. Their value is highlighted by the highly successful anti-hepatitis C drug sofosbuvir. When appropriately phosphorylated, these nucleotides are successfully incorporated into RNA by the virally encoded RNA-dependent RNA polymerase (RdRp). This activity prevents further RNA extension, but the mechanism is poorly characterized. Previously, we had identified NMR signatures characteristic of formation of RdRp-RNA binary and RdRp-RNA-NTP ternary complexes for the poliovirus RdRp, including an open-to-closed conformational change necessary to prepare the active site for catalysis of phosphoryl transfer. Here we used these observations as a framework for interpreting the effects of 2'-C-methyl adenosine analogs on RNA chain extension in solution-state NMR spectroscopy experiments, enabling us to gain additional mechanistic insights into 2'-C-methyl ribonucleoside-mediated RNA chain termination. Contrary to what has been proposed previously, poliovirus RdRp that was bound to RNA with an incorporated 2'-C-methyl nucleotide could still bind to the next incoming NTP. Our results also indicated that incorporation of the 2'-C-methyl nucleotide does not disrupt RdRp-RNA interactions and does not prevent translocation. Instead, incorporation of the 2'-C-methyl nucleotide blocked closure of the RdRp active site upon binding of the next correct incoming NTP, which prevented further nucleotide addition. We propose that other nucleotide analogs that act as nonobligate chain terminators may operate through a similar mechanism.
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Affiliation(s)
- Alyson K Boehr
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Hyung S Oh
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - David D Boehr
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
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Espy N, Nagle E, Pfeffer B, Garcia K, Chitty AJ, Wiley M, Sanchez-Lockhart M, Bavari S, Warren T, Palacios G. T-705 induces lethal mutagenesis in Ebola and Marburg populations in macaques. Antiviral Res 2019; 170:104529. [PMID: 31195019 DOI: 10.1016/j.antiviral.2019.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 06/02/2019] [Indexed: 10/26/2022]
Abstract
Nucleoside analogues (NA) disrupt RNA viral RNA-dependent RNA polymerase (RdRP) function and fidelity for multiple viral families. The mechanism of action (MOA) of T-705 has been attributed alternatively or concurrently to chain termination and lethal mutagenesis depending on the viral species during in vitro studies. In this study, we evaluated the effect of T-705 on the viral population in non-human primates (NHPs) after challenge with Ebola virus (EBOV) or Marburg virus (MARV) to identify the predominant in vivo MOA. We used common virological assays in conjunction with deep sequencing to characterize T-705 effects. T-705 exhibited antiviral activity that was associated with a reduction in specific infectivity and an accumulation of low frequency nucleotide variants in plasma samples collected day 7 post infection. Stranded analysis of deep sequencing data to identify chain termination demonstrated no change in the transcriptional gradient in negative stranded viral reads and minimal changes in positive stranded viral reads in T-705 treated animals, questioning as a MOA in vivo. These findings indicate that lethal mutagenesis is a MOA of T-705 that may serve as an indication of therapeutic activity of NAs for evaluation in clinical settings. This study expands our understanding of MOAs of these compounds for the Filovirus family and provides further evidence that lethal mutagenesis could be a preponderant MOA for this class of therapeutic compounds.
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Affiliation(s)
- Nicole Espy
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Elyse Nagle
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Brad Pfeffer
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Karla Garcia
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Alex J Chitty
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Michael Wiley
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Mariano Sanchez-Lockhart
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Travis Warren
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA.
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Wang G, Dyatkina N, Prhavc M, Williams C, Serebryany V, Hu Y, Huang Y, Wan J, Wu X, Deval J, Fung A, Jin Z, Tan H, Shaw K, Kang H, Zhang Q, Tam Y, Stoycheva A, Jekle A, Smith DB, Beigelman L. Synthesis and Anti-HCV Activities of 4'-Fluoro-2'-Substituted Uridine Triphosphates and Nucleotide Prodrugs: Discovery of 4'-Fluoro-2'- C-methyluridine 5'-Phosphoramidate Prodrug (AL-335) for the Treatment of Hepatitis C Infection. J Med Chem 2019; 62:4555-4570. [PMID: 30951311 DOI: 10.1021/acs.jmedchem.9b00143] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We report the synthesis and biological evaluation of a series of 4'-fluoro-2'- C-substituted uridines. Triphosphates of the uridine analogues exhibited a potent inhibition of hepatitis C virus (HCV) NS5B polymerase with IC50 values as low as 27 nM. In an HCV subgenomic replicon assay, the phosphoramidate prodrugs of these uridine analogues demonstrated a very potent activity with EC50 values as low as 20 nM. A lead compound AL-335 (53) demonstrated high levels of the nucleoside triphosphate in vitro in primary human hepatocytes and Huh-7 cells as well as in dog liver following a single oral dose. Compound 53 was selected for the clinical development where it showed promising results in phase 1 and 2 trials.
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Affiliation(s)
- Guangyi Wang
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Natalia Dyatkina
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Marija Prhavc
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Caroline Williams
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Vladimir Serebryany
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Yujian Hu
- Department of Medicinal Chemistry , WuXi AppTec , Shanghai 200131 , P. R. China
| | - Yongfei Huang
- Department of Medicinal Chemistry , WuXi AppTec , Shanghai 200131 , P. R. China
| | - Jinqiao Wan
- Department of Medicinal Chemistry , WuXi AppTec , Shanghai 200131 , P. R. China
| | - Xiangyang Wu
- Department of Medicinal Chemistry , WuXi AppTec , Shanghai 200131 , P. R. China
| | - Jerome Deval
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Amy Fung
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Zhinan Jin
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Hua Tan
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Kenneth Shaw
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Hyunsoon Kang
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Qingling Zhang
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Yuen Tam
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Antitsa Stoycheva
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Andreas Jekle
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - David B Smith
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
| | - Leonid Beigelman
- Janssen BioPharma, Inc. , South San Francisco , California 94080 , United States
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36
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Mechanism of Inhibition of Ebola Virus RNA-Dependent RNA Polymerase by Remdesivir. Viruses 2019; 11:v11040326. [PMID: 30987343 PMCID: PMC6520719 DOI: 10.3390/v11040326] [Citation(s) in RCA: 396] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/27/2019] [Accepted: 03/29/2019] [Indexed: 11/17/2022] Open
Abstract
Remdesivir (GS-5734) is a 1'-cyano-substituted adenosine nucleotide analogue prodrug that shows broad-spectrum antiviral activity against several RNA viruses. This compound is currently under clinical development for the treatment of Ebola virus disease (EVD). While antiviral effects have been demonstrated in cell culture and in non-human primates, the mechanism of action of Ebola virus (EBOV) inhibition for remdesivir remains to be fully elucidated. The EBOV RNA-dependent RNA polymerase (RdRp) complex was recently expressed and purified, enabling biochemical studies with the relevant triphosphate (TP) form of remdesivir and its presumptive target. In this study, we confirmed that remdesivir-TP is able to compete for incorporation with adenosine triphosphate (ATP). Enzyme kinetics revealed that EBOV RdRp and respiratory syncytial virus (RSV) RdRp incorporate ATP and remdesivir-TP with similar efficiencies. The selectivity of ATP against remdesivir-TP is ~4 for EBOV RdRp and ~3 for RSV RdRp. In contrast, purified human mitochondrial RNA polymerase (h-mtRNAP) effectively discriminates against remdesivir-TP with a selectivity value of ~500-fold. For EBOV RdRp, the incorporated inhibitor at position i does not affect the ensuing nucleotide incorporation event at position i+1. For RSV RdRp, we measured a ~6-fold inhibition at position i+1 although RNA synthesis was not terminated. Chain termination was in both cases delayed and was seen predominantly at position i+5. This pattern is specific to remdesivir-TP and its 1'-cyano modification. Compounds with modifications at the 2'-position show different patterns of inhibition. While 2'-C-methyl-ATP is not incorporated, ara-ATP acts as a non-obligate chain terminator and prevents nucleotide incorporation at position i+1. Taken together, our biochemical data indicate that the major contribution to EBOV RNA synthesis inhibition by remdesivir can be ascribed to delayed chain termination. The long distance of five residues between the incorporated nucleotide analogue and its inhibitory effect warrant further investigation.
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Rivero-Juarez A, Brieva T, Frias M, Rivero A. Pharmacodynamic and pharmacokinetic evaluation of the combination of daclatasvir/sofosbuvir/ribavirin in the treatment of chronic hepatitis C. Expert Opin Drug Metab Toxicol 2018; 14:901-910. [PMID: 30058394 DOI: 10.1080/17425255.2018.1506765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The combination of daclatasvir (DCV), sofosbuvir (SOF), and ribavirin (RBV) is a direct-acting antiviral (DAA) regimen for the treatment of hepatitis C virus (HCV) infection. The inclusion of newer effective DAAs such as SOF and DCV with high efficacy and excellent tolerance introduced a new scenario in HCV infection therapy: high rates of sustained virological response (SVR), shorter therapies, less toxicity, and interferon-free treatments. This combination was approved for the treatment of HCV in treatment-naive or treatment-experienced patients with chronic HCV genotype 1 or 3 infection. Areas covered: This review summarizes the pharmacokinetics, pharmacodynamics, efficacy, and safety of DCV plus SOF and RBV therapy in the treatment of HCV infection. The topics include data regarding drug absorption, distribution, metabolism, excretion, and antiviral activity strategies, such as clinical dose selection and treatment duration. Expert opinion: This combination, taken orally with or without food, has an excellent pharmacokinetic and pharmacodynamic profile. DAC/SOF/RBV achieves very high rates of SVR in treatment-naive and treatment-experienced patients with chronic HCV infection, including difficult-to-treat patients such as those with compensated cirrhosis, post-transplant recurrence, or HIV-1 co-infection.
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Affiliation(s)
- Antonio Rivero-Juarez
- a Unidad de Enfermedades Infecciosas, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC) , Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba , Cordoba , Spain
| | - Teresa Brieva
- a Unidad de Enfermedades Infecciosas, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC) , Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba , Cordoba , Spain
| | - Mario Frias
- a Unidad de Enfermedades Infecciosas, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC) , Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba , Cordoba , Spain
| | - Antonio Rivero
- a Unidad de Enfermedades Infecciosas, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC) , Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba , Cordoba , Spain
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Cory TJ, Mu Y, Gong Y, Kodidela S, Kumar S. Sofosbuvir + velpatasvir + voxilaprevir for the treatment of hepatitis C infection. Expert Opin Pharmacother 2018; 19:749-757. [PMID: 29634360 DOI: 10.1080/14656566.2018.1459567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Hepatitis C is a disease with a significant global impact. Over the last several years, the treatment of the disease has been revolutionized. Therapy has transformed over the last several years with the approval of second generation direct acting antivirals, and currently utilized medications for the treatment of hepatitis C are significantly more efficacious with better safety profiles than previously approved treatments. Treatment for individuals who have failed therapy on direct acting antivirals has, until recently, been complex and difficult to treat, but the approval of sofosbuvir/velpatasvir/voxilaprevir represents a new therapeutic option for these individuals. Areas covered: Sofosbuvir/velpatasvir/voxilaprevir is a recently approved therapeutic combination for the treatment of hepatitis C. This article reviews the studies leading to the approval of the combination, and its efficacy and safety profile. Expert opinion: Sofosbuvir/velpatasvir/voxilaprevir fills one of the previously unfilled niches for the treatment of hepatitis C, that of the treatment of individuals who have failed therapy with resistant virus. With the filling of this niche, there appears to be a general slowing of the development of new therapeutics. Although understandable, in the long term, there are considerable risks associated with the decreased development of new drugs to treat hepatitis C.
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Affiliation(s)
- Theodore J Cory
- a Department of Clinical Pharmacy and Translational Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , TN , USA
| | - Ying Mu
- a Department of Clinical Pharmacy and Translational Science , University of Tennessee Health Science Center College of Pharmacy , Memphis , TN , USA
| | - Yuqing Gong
- b Department of Pharmaceutical Sciences , University of Tennessee Health Science Center College of Pharmacy , Memphis , TN , USA
| | - Sunitha Kodidela
- b Department of Pharmaceutical Sciences , University of Tennessee Health Science Center College of Pharmacy , Memphis , TN , USA
| | - Santosh Kumar
- b Department of Pharmaceutical Sciences , University of Tennessee Health Science Center College of Pharmacy , Memphis , TN , USA
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Simple In Vitro Assay To Evaluate the Incorporation Efficiency of Ribonucleotide Analog 5'-Triphosphates into RNA by Human Mitochondrial DNA-Dependent RNA Polymerase. Antimicrob Agents Chemother 2018; 62:AAC.01830-17. [PMID: 29180528 PMCID: PMC5786792 DOI: 10.1128/aac.01830-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/21/2017] [Indexed: 01/27/2023] Open
Abstract
There is a growing body of evidence suggesting that some ribonucleoside/ribonucleotide analogs may be incorporated into mitochondrial RNA by human mitochondrial DNA-dependent RNA polymerase (POLRMT) and disrupt mitochondrial RNA synthesis. An assessment of the incorporation efficiency of a ribonucleotide analog 5′-triphosphate by POLRMT may be used to evaluate the potential mitochondrial toxicity of the analog early in the development process. In this report, we provide a simple method to prepare active recombinant POLRMT. A robust in vitro nonradioactive primer extension assay was developed to assay the incorporation efficiency of ribonucleotide analog 5′-triphosphates. Our results show that many ribonucleotide analogs, including some antiviral compounds currently in various preclinical or clinical development stages, can be incorporated into newly synthesized RNA by POLRMT and that the incorporation of some of them can lead to chain termination. The discrimination (D) values of ribonucleotide analog 5′-triphosphates over those of natural ribonucleotide triphosphates (rNTPs) were measured to evaluate the incorporation efficiency of the ribonucleotide analog 5′-triphosphates by POLRMT. The discrimination values of natural rNTPs under the condition of misincorporation by POLRMT were used as a reference to evaluate the potential mitochondrial toxicity of ribonucleotide analogs. We propose the following criteria for the potential mitochondrial toxicity of ribonucleotide analogs based on D values: a safe compound has a D value of >105; a potentially toxic compound has a D value of >104 but <105; and a toxic compound has a D value of <104. This report provides a simple screening method that should assist investigators in designing ribonucleoside-based drugs having lower mitochondrial toxicity.
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40
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Jordan PC, Stevens SK, Deval J. Nucleosides for the treatment of respiratory RNA virus infections. Antivir Chem Chemother 2018; 26:2040206618764483. [PMID: 29562753 PMCID: PMC5890544 DOI: 10.1177/2040206618764483] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/07/2018] [Indexed: 12/20/2022] Open
Abstract
Influenza virus, respiratory syncytial virus, human metapneumovirus, parainfluenza virus, coronaviruses, and rhinoviruses are among the most common viruses causing mild seasonal colds. These RNA viruses can also cause lower respiratory tract infections leading to bronchiolitis and pneumonia. Young children, the elderly, and patients with compromised cardiac, pulmonary, or immune systems are at greatest risk for serious disease associated with these RNA virus respiratory infections. In addition, swine and avian influenza viruses, together with severe acute respiratory syndrome-associated and Middle Eastern respiratory syndrome coronaviruses, represent significant pandemic threats to the general population. In this review, we describe the current medical need resulting from respiratory infections caused by RNA viruses, which justifies drug discovery efforts to identify new therapeutic agents. The RNA polymerase of respiratory viruses represents an attractive target for nucleoside and nucleotide analogs acting as inhibitors of RNA chain synthesis. Here, we present the molecular, biochemical, and structural fundamentals of the polymerase of the four major families of RNA respiratory viruses: Orthomyxoviridae, Pneumoviridae/Paramyxoviridae, Coronaviridae, and Picornaviridae. We summarize past and current efforts to develop nucleoside and nucleotide analogs as antiviral agents against respiratory virus infections. This includes molecules with very broad antiviral spectrum such as ribavirin and T-705 (favipiravir), and others targeting more specifically one or a few virus families. Recent advances in our understanding of the structure(s) and function(s) of respiratory virus polymerases will likely support the discovery and development of novel nucleoside analogs.
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Affiliation(s)
- Paul C Jordan
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, USA
| | - Sarah K Stevens
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, USA
| | - Jerome Deval
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, USA
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41
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Xu HT, Colby-Germinario SP, Hassounah SA, Fogarty C, Osman N, Palanisamy N, Han Y, Oliveira M, Quan Y, Wainberg MA. Evaluation of Sofosbuvir (β-D-2'-deoxy-2'-α-fluoro-2'-β-C-methyluridine) as an inhibitor of Dengue virus replication<sup/>. Sci Rep 2017; 7:6345. [PMID: 28740124 PMCID: PMC5524696 DOI: 10.1038/s41598-017-06612-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/31/2017] [Indexed: 12/26/2022] Open
Abstract
We evaluated Sofosbuvir (SOF), the anti-hepatitis C virus prodrug of β-d-2'-deoxy-2'-α-fluoro-2'-β-C-methyluridine-5'-monophosphate, for potential inhibitory activity against DENV replication. Both cell-based and biochemical assays, based on use of purified DENV full-length NS5 enzyme, were studied. Cytopathic effect protection and virus yield reduction assays confirmed that SOF possessed anti-DENV activity in cell culture with a 50% effective concentration (EC50) of 4.9 µM and 1.4 µM respectively. Real-time RT-PCR verified that SOF inhibits generation of viral RNA with an EC50 of 9.9 µM. Purified DENV NS5 incorporated the active triphosphate form (SOF-TP) into nascent RNA, causing chain-termination. Relative to the natural UTP, the incorporation efficiency of SOF-TP was low (discrimination value = 327.5). In a primer extension assay, SOF-TP was active against DENV NS5 wild-type polymerase activity with an IC50 of 14.7 ± 2.5 µM. The S600T substitution in the B Motif of DENV polymerase conferred 4.3-fold resistance to SOF-TP; this was due to decreased incorporation efficiency rather than enhanced excision of the incorporated SOF nucleotide. SOF has antiviral activity against DENV replication. The high discrimination value in favor of UTP in enzyme assays may not necessarily preclude antiviral activity in cells. SOF may be worthy of evaluation against severe DENV infections in humans.
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Affiliation(s)
- Hong-Tao Xu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.
| | - Susan P Colby-Germinario
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Said A Hassounah
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Clare Fogarty
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Nathan Osman
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Navaneethan Palanisamy
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.,HBIGS, University of Heidelberg, Heidelberg, Germany
| | - Yingshan Han
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Yudong Quan
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
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42
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Analysis of Ribonucleotide 5'-Triphosphate Analogs as Potential Inhibitors of Zika Virus RNA-Dependent RNA Polymerase by Using Nonradioactive Polymerase Assays. Antimicrob Agents Chemother 2017; 61:AAC.01967-16. [PMID: 27993851 DOI: 10.1128/aac.01967-16] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/13/2016] [Indexed: 01/20/2023] Open
Abstract
Zika virus (ZIKV) is an emerging human pathogen that is spreading rapidly through the Americas and has been linked to the development of microcephaly and to a dramatically increased number of Guillain-Barré syndrome cases. Currently, no vaccine or therapeutic options for the prevention or treatment of ZIKV infections exist. In the study described in this report, we expressed, purified, and characterized full-length nonstructural protein 5 (NS5) and the NS5 polymerase domain (NS5pol) of ZIKV RNA-dependent RNA polymerase. Using purified NS5, we developed an in vitro nonradioactive primer extension assay employing a fluorescently labeled primer-template pair. Both purified NS5 and NS5pol can carry out in vitro RNA-dependent RNA synthesis in this assay. Our results show that Mn2+ is required for enzymatic activity, while Mg2+ is not. We found that ZIKV NS5 can utilize single-stranded DNA but not double-stranded DNA as a template or a primer to synthesize RNA. The assay was used to compare the efficiency of incorporation of analog 5'-triphosphates by the ZIKV polymerase and to calculate their discrimination versus that of natural ribonucleotide triphosphates (rNTPs). The 50% inhibitory concentrations for analog rNTPs were determined in an alternative nonradioactive coupled-enzyme assay. We determined that, in general, 2'-C-methyl- and 2'-C-ethynyl-substituted analog 5'-triphosphates were efficiently incorporated by the ZIKV polymerase and were also efficient chain terminators. Derivatives of these molecules may serve as potential antiviral compounds to be developed to combat ZIKV infection. This report provides the first characterization of ZIKV polymerase and demonstrates the utility of in vitro polymerase assays in the identification of potential ZIKV inhibitors.
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43
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Brieva T, Rivero A, Rivero-Juarez A. Pharmacokinetic drug evaluation of velpatasvir plus sofosbuvir for the treatment of hepatitis C virus infection. Expert Opin Drug Metab Toxicol 2017; 13:483-490. [PMID: 28165830 DOI: 10.1080/17425255.2017.1292253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
INTRODUCTION The fixed-dose combination therapy of sofosbuvir (SOF) plus velpatasvir (VEL) is the first pangenotypic, direct-acting antiviral (DAA), single-treatment regimen (STR) for the treatment of hepatitis C virus (HCV) infection to be commercialized. It is approved for the treatment of HCV genotypes 1, 2, 3, 4, 5, and 6. Following approval in 2016, new pharmacokinetic and pharmacodynamic data were reported, which led to important clinical applications. Areas covered: This review provides a summary of the pharmacokinetics, pharmacodynamics, efficacy and safety of SOF/VEL therapy for treatment of HCV infection. The topics covered include data regarding the drug's absorption, distribution, metabolism, excretion and antiviral activity strategies, such as clinical dose selection and treatment duration. Expert opinion: This novel combination therapy containing 400 mg of SOF plus 100 mg of VEL, taken orally, once daily, with or without food, has an excellent pharmacokinetic and pharmacodynamic profile. SOF/VEL achieved very high rates of sustained virological response in treatment-naive and treatment-experienced patients with chronic HCV genotype 1-6 infection, including those with compensated cirrhosis or HIV-1 co-infection.
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Affiliation(s)
- Teresa Brieva
- a Unidad de Enfermedades Infecciosas , Hospital Universitario Reina Sofía de Córdoba, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba , Cordoba , Spain
| | - Antonio Rivero
- a Unidad de Enfermedades Infecciosas , Hospital Universitario Reina Sofía de Córdoba, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba , Cordoba , Spain
| | - Antonio Rivero-Juarez
- a Unidad de Enfermedades Infecciosas , Hospital Universitario Reina Sofía de Córdoba, Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba , Cordoba , Spain
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44
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Potisopon S, Ferron F, Fattorini V, Selisko B, Canard B. Substrate selectivity of Dengue and Zika virus NS5 polymerase towards 2'-modified nucleotide analogues. Antiviral Res 2016; 140:25-36. [PMID: 28041959 DOI: 10.1016/j.antiviral.2016.12.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 12/28/2016] [Accepted: 12/29/2016] [Indexed: 12/11/2022]
Abstract
In targeting the essential viral RNA-dependent RNA-polymerase (RdRp), nucleotide analogues play a major role in antiviral therapies. In the Flaviviridae family, the hepatitis C virus (HCV) can be eradicated from chronically infected patients using a combination of drugs which generally include the 2'-modified uridine analogue Sofosbuvir, delivered as nucleotide prodrug. Dengue and Zika viruses are emerging flaviviruses whose RdRp is closely related to that of HCV, yet no nucleoside drug has been clinically approved for these acute infections. We have purified dengue and Zika virus full-length NS5, the viral RdRps, and used them to assemble a stable binary complex made of NS5 and virus-specific RNA primer/templates. The complex was used to assess the selectivity of NS5 towards nucleotide analogues bearing modifications at the 2'-position. We show that dengue and Zika virus RdRps exhibit the same discrimination pattern: 2'-O-Me > 2'-C-Me-2'-F > 2'-C-Me nucleoside analogues, unlike HCV RdRp for which the presence of the 2'-F is beneficial rendering the discrimination pattern 2'-O-Me > 2'-C-Me ≥ 2'-C-Me-2'-F. Both 2'-C-Me and 2'-C-Me-2'-F analogues act as non-obligate RNA chain terminators. The dengue and Zika NS5 nucleotide selectivity towards 2'-modified NTPs mirrors potency of the corresponding analogues in infected cell cultures.
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Affiliation(s)
- Supanee Potisopon
- Aix-Marseille Université, AFMB (Laboratoire d'Architecture et Fonction de Macromolécules Biologiques) UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France
| | - François Ferron
- Aix-Marseille Université, AFMB (Laboratoire d'Architecture et Fonction de Macromolécules Biologiques) UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France
| | - Véronique Fattorini
- Aix-Marseille Université, AFMB (Laboratoire d'Architecture et Fonction de Macromolécules Biologiques) UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France
| | - Barbara Selisko
- Aix-Marseille Université, AFMB (Laboratoire d'Architecture et Fonction de Macromolécules Biologiques) UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France.
| | - Bruno Canard
- Aix-Marseille Université, AFMB (Laboratoire d'Architecture et Fonction de Macromolécules Biologiques) UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France.
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45
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Abet V, Filace F, Recio J, Alvarez-Builla J, Burgos C. Prodrug approach: An overview of recent cases. Eur J Med Chem 2016; 127:810-827. [PMID: 27823878 DOI: 10.1016/j.ejmech.2016.10.061] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 01/01/2023]
Abstract
In this review we highlight the most modern trends in the prodrug strategy. In drug research and development, the prodrug concept has found a number of useful applications. Selected examples of this approach are provided in this paper and they are classified according to the aim of their design.
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Affiliation(s)
- Valentina Abet
- Departamento de Química Orgánica, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Fabiana Filace
- Departamento de Química Orgánica, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Javier Recio
- Departamento de Química Orgánica, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Julio Alvarez-Builla
- Departamento de Química Orgánica, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain.
| | - Carolina Burgos
- Departamento de Química Orgánica, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain.
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46
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Stevaert A, Naesens L. The Influenza Virus Polymerase Complex: An Update on Its Structure, Functions, and Significance for Antiviral Drug Design. Med Res Rev 2016; 36:1127-1173. [PMID: 27569399 PMCID: PMC5108440 DOI: 10.1002/med.21401] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/18/2016] [Accepted: 06/24/2016] [Indexed: 12/11/2022]
Abstract
Influenza viruses cause seasonal epidemics and pandemic outbreaks associated with significant morbidity and mortality, and a huge cost. Since resistance to the existing anti‐influenza drugs is rising, innovative inhibitors with a different mode of action are urgently needed. The influenza polymerase complex is widely recognized as a key drug target, given its critical role in virus replication and high degree of conservation among influenza A (of human or zoonotic origin) and B viruses. We here review the major progress that has been made in recent years in unravelling the structure and functions of this protein complex, enabling structure‐aided drug design toward the core regions of the PA endonuclease, PB1 polymerase, or cap‐binding PB2 subunit. Alternatively, inhibitors may target a protein–protein interaction site, a cellular factor involved in viral RNA synthesis, the viral RNA itself, or the nucleoprotein component of the viral ribonucleoprotein. The latest advances made for these diverse pharmacological targets have yielded agents in advanced (i.e., favipiravir and VX‐787) or early clinical testing, besides several experimental inhibitors in various stages of development, which are all covered here.
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Affiliation(s)
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
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47
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Barrier-Independent, Fitness-Associated Differences in Sofosbuvir Efficacy against Hepatitis C Virus. Antimicrob Agents Chemother 2016; 60:3786-93. [PMID: 27067341 DOI: 10.1128/aac.00581-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/05/2016] [Indexed: 12/24/2022] Open
Abstract
Sofosbuvir displays a high phenotypic barrier to resistance, and it is a component of several combination therapies for hepatitis C virus (HCV) infections. HCV fitness can be a determinant of decreased sensitivity to direct-acting antiviral agents such as telaprevir or daclatasvir, but fitness-dependent decreased drug sensitivity has not been established for drugs with a high phenotypic barrier to resistance. Low- and high-fitness HCV populations and biological clones derived from them were used to infect Huh-7.5 hepatoma cells. Sofosbuvir efficacy was analyzed by measuring virus progeny production during several passages and by selection of possible sofosbuvir resistance mutations determined by sequencing the NS5B-coding region of the resulting populations. Sofosbuvir exhibited reduced efficacy against high-fitness HCV populations, without the acquisition of sofosbuvir-specific resistance mutations. A reduced sofosbuvir efficacy, similar to that observed with the parental populations, was seen for high-fitness individual biological clones. In independently derived high-fitness HCV populations or clones passaged in the presence of sofosbuvir, M289L was selected as the only substitution in the viral polymerase NS5B. In no case was the sofosbuvir-specific resistance substitution S282T observed. High HCV fitness can lead to decreased sensitivity to sofosbuvir, without the acquisition of specific sofosbuvir resistance mutations. Thus, fitness-dependent drug sensitivity can operate with HCV inhibitors that display a high barrier to resistance. This mechanism may underlie treatment failures not associated with selection of sofosbuvir-specific resistance mutations, linked to in vivo fitness of pretreatment viral populations.
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48
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Wang G, Wan J, Hu Y, Wu X, Prhavc M, Dyatkina N, Rajwanshi VK, Smith DB, Jekle A, Kinkade A, Symons JA, Jin Z, Deval J, Zhang Q, Tam Y, Chanda S, Blatt L, Beigelman L. Synthesis and Anti-Influenza Activity of Pyridine, Pyridazine, and Pyrimidine C-Nucleosides as Favipiravir (T-705) Analogues. J Med Chem 2016; 59:4611-24. [DOI: 10.1021/acs.jmedchem.5b01933] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guangyi Wang
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - Jinqiao Wan
- Department
of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, P.R. China
| | - Yujian Hu
- Department
of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, P.R. China
| | - Xiangyang Wu
- Department
of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, P.R. China
| | - Marija Prhavc
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - Natalia Dyatkina
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - Vivek K. Rajwanshi
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - David B. Smith
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - Andreas Jekle
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - April Kinkade
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - Julian A. Symons
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - Zhinan Jin
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - Jerome Deval
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - Qingling Zhang
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - Yuen Tam
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - Sushmita Chanda
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - Lawrence Blatt
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
| | - Leonid Beigelman
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical
Companies, South San Francisco, California 94080, United States
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49
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Domingo E. Interaction of Virus Populations with Their Hosts. VIRUS AS POPULATIONS 2016. [PMCID: PMC7150142 DOI: 10.1016/b978-0-12-800837-9.00004-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Viral population numbers are extremely large compared with those of their host species. Population bottlenecks are frequent during the life cycle of viruses and can reduce viral populations transiently to very few individuals. Viruses have to confront several types of constraints that can be divided in basal, cell-dependent, and organism-dependent constraints. Viruses overcome them exploiting a number of molecular mechanisms, with an important contribution of population numbers and genome variation. The adaptive potential of viruses is reflected in modifications of cell tropism and host range, escape to components of the host immune response, and capacity to alternate among different host species, among other phenotypic changes. Despite a fitness cost of most mutations required to overcome a selective constraint, viruses can find evolutionary pathways that ensure their survival in equilibrium with their hosts.
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50
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Demkowicz S, Rachon J, Daśko M, Kozak W. Selected organophosphorus compounds with biological activity. Applications in medicine. RSC Adv 2016. [DOI: 10.1039/c5ra25446a] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The purpose of this article is to provide an overview of the latest applications of organophosphorus compounds (OPs) that exhibit biological activity.
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Affiliation(s)
- Sebastian Demkowicz
- Department of Organic Chemistry
- Chemical Faculty
- Gdansk University of Technology
- 80-233 Gdansk
- Poland
| | - Janusz Rachon
- Department of Organic Chemistry
- Chemical Faculty
- Gdansk University of Technology
- 80-233 Gdansk
- Poland
| | - Mateusz Daśko
- Department of Organic Chemistry
- Chemical Faculty
- Gdansk University of Technology
- 80-233 Gdansk
- Poland
| | - Witold Kozak
- Department of Organic Chemistry
- Chemical Faculty
- Gdansk University of Technology
- 80-233 Gdansk
- Poland
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