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Decombe A, Peersen O, Sutto-Ortiz P, Chamontin C, Piorkowski G, Canard B, Nisole S, Decroly E. Internal RNA 2'-O-methylation on the HIV-1 genome impairs reverse transcription. Nucleic Acids Res 2024; 52:1359-1373. [PMID: 38015463 PMCID: PMC10853786 DOI: 10.1093/nar/gkad1134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Viral RNA genomes are modified by epitranscriptomic marks, including 2'-O-methylation that is added by cellular or viral methyltransferases. 2'-O-Methylation modulates RNA structure, function and discrimination between self- and non-self-RNA by innate immune sensors such as RIG-I-like receptors. This is illustrated by human immunodeficiency virus type-1 (HIV-1) that decorates its RNA genome through hijacking the cellular FTSJ3 2'-O-methyltransferase, thereby limiting immune sensing and interferon production. However, the impact of such an RNA modification during viral genome replication is poorly understood. Here we show by performing endogenous reverse transcription on methylated or hypomethylated HIV-1 particles, that 2'-O-methylation negatively affects HIV-1 reverse transcriptase activity. Biochemical assays confirm that RNA 2'-O-methylation impedes reverse transcriptase activity, especially at low dNTP concentrations reflecting those in quiescent cells, by reducing nucleotide incorporation efficiency and impairing translocation. Mutagenesis highlights K70 as a critical amino acid for the reverse transcriptase to bypass 2'-O-methylation. Hence, the observed antiviral effect due to viral RNA 2'-O-methylation antagonizes the FTSJ3-mediated proviral effects, suggesting the fine-tuning of RNA methylation during viral replication.
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Affiliation(s)
- Alice Decombe
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille 13288, France
| | - Olve Peersen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Priscila Sutto-Ortiz
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille 13288, France
| | - Célia Chamontin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier 34090, France
| | - Géraldine Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), 13005 Marseille, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille 13288, France
| | - Sébastien Nisole
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier 34090, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille 13288, France
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2
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Campagnola G, Peersen O. Co-folding and RNA activation of poliovirus 3C pro polyprotein precursors. J Biol Chem 2023; 299:105258. [PMID: 37717698 PMCID: PMC10590986 DOI: 10.1016/j.jbc.2023.105258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023] Open
Abstract
Positive-strand RNA viruses use long open reading frames to express large polyproteins that are processed into individual proteins by viral proteases. Polyprotein processing is highly regulated and yields intermediate species with different functions than the fully processed proteins, increasing the biochemical diversity of the compact viral genome while also presenting challenges in that proteins must remain stably folded in multiple contexts. We have used circular dichroism spectroscopy and single molecule microscopy to examine the solution structure and self-association of the poliovirus P3 region protein composed of membrane binding 3A, RNA priming 3B (VPg), 3Cpro protease, and 3Dpol RNA-dependent RNA polymerase proteins. Our data indicate that co-folding interactions within the 3ABC segment stabilize the conformational state of the 3C protease region, and this stabilization requires the full-length 3A and 3B proteins. Enzymatic activity assays show that 3ABC is also an active protease, and it cleaves peptide substrates at rates comparable to 3Cpro. The cleavage of a larger polyprotein substrate is stimulated by the addition of RNA, and 3ABCpro becomes 20-fold more active than 3Cpro in the presence of stoichiometric amounts of viral cre RNA. The data suggest that co-folding within the 3ABC region results in a protease that can be highly activated toward certain cleavage sites by localization to specific RNA elements within the viral replication center, providing a mechanism for regulating viral polyprotein processing.
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Affiliation(s)
- Grace Campagnola
- Department of Biochemistry & Molecular Birology, Colorado State University, Fort Collins, Colorado, USA
| | - Olve Peersen
- Department of Biochemistry & Molecular Birology, Colorado State University, Fort Collins, Colorado, USA.
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3
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Laajala M, Zwaagstra M, Martikainen M, Nekoua MP, Benkahla M, Sane F, Gervais E, Campagnola G, Honkimaa A, Sioofy-Khojine AB, Hyöty H, Ojha R, Bailliot M, Balistreri G, Peersen O, Hober D, Van Kuppeveld F, Marjomäki V. Vemurafenib Inhibits Acute and Chronic Enterovirus Infection by Affecting Cellular Kinase Phosphatidylinositol 4-Kinase Type IIIβ. Microbiol Spectr 2023; 11:e0055223. [PMID: 37436162 PMCID: PMC10433971 DOI: 10.1128/spectrum.00552-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/14/2023] [Indexed: 07/13/2023] Open
Abstract
Enteroviruses are one of the most abundant viruses causing mild to serious acute infections in humans and also contributing to chronic diseases like type 1 diabetes. Presently, there are no approved antiviral drugs against enteroviruses. Here, we studied the potency of vemurafenib, an FDA-approved RAF kinase inhibitor for treating BRAFV600E mutant-related melanoma, as an antiviral against enteroviruses. We showed that vemurafenib prevented enterovirus translation and replication at low micromolar dosage in an RAF/MEK/ERK-independent manner. Vemurafenib was effective against group A, B, and C enteroviruses, as well as rhinovirus, but not parechovirus or more remote viruses such as Semliki Forest virus, adenovirus, and respiratory syncytial virus. The inhibitory effect was related to a cellular phosphatidylinositol 4-kinase type IIIβ (PI4KB), which has been shown to be important in the formation of enteroviral replication organelles. Vemurafenib prevented infection efficiently in acute cell models, eradicated infection in a chronic cell model, and lowered virus amounts in pancreas and heart in an acute mouse model. Altogether, instead of acting through the RAF/MEK/ERK pathway, vemurafenib affects the cellular PI4KB and, hence, enterovirus replication, opening new possibilities to evaluate further the potential of vemurafenib as a repurposed drug in clinical care. IMPORTANCE Despite the prevalence and medical threat of enteroviruses, presently, there are no antivirals against them. Here, we show that vemurafenib, an FDA-approved RAF kinase inhibitor for treating BRAFV600E mutant-related melanoma, prevents enterovirus translation and replication. Vemurafenib shows efficacy against group A, B, and C enteroviruses, as well as rhinovirus, but not parechovirus or more remote viruses such as Semliki Forest virus, adenovirus, and respiratory syncytial virus. The inhibitory effect acts through cellular phosphatidylinositol 4-kinase type IIIβ (PI4KB), which has been shown to be important in the formation of enteroviral replication organelles. Vemurafenib prevents infection efficiently in acute cell models, eradicates infection in a chronic cell model, and lowers virus amounts in pancreas and heart in an acute mouse model. Our findings open new possibilities to develop drugs against enteroviruses and give hope for repurposing vemurafenib as an antiviral drug against enteroviruses.
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Affiliation(s)
- Mira Laajala
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Marleen Zwaagstra
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Mari Martikainen
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | | | - Mehdi Benkahla
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, Lille, France
| | - Famara Sane
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, Lille, France
| | - Emily Gervais
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Grace Campagnola
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Anni Honkimaa
- Department of Virology, Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Amir-Babak Sioofy-Khojine
- Department of Virology, Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Heikki Hyöty
- Department of Virology, Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
| | - Ravi Ojha
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Marie Bailliot
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Giuseppe Balistreri
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Olve Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Didier Hober
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, Lille, France
| | - Frank Van Kuppeveld
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Varpu Marjomäki
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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Fagre A, Lewis J, Eckley M, Zhan S, Rocha SM, Sexton NR, Burke B, Geiss B, Peersen O, Bass T, Kading R, Rovnak J, Ebel GD, Tjalkens RB, Aboellail T, Schountz T. SARS-CoV-2 infection, neuropathogenesis and transmission among deer mice: Implications for spillback to New World rodents. PLoS Pathog 2021; 17:e1009585. [PMID: 34010360 PMCID: PMC8168874 DOI: 10.1371/journal.ppat.1009585] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 06/01/2021] [Accepted: 04/24/2021] [Indexed: 12/21/2022] Open
Abstract
Coronavirus disease-19 (COVID-19) emerged in late 2019 in China and rapidly became pandemic. As with other coronaviruses, a preponderance of evidence suggests the virus originated in horseshoe bats (Rhinolophus spp.) and may have infected an intermediate host prior to spillover into humans. A significant concern is that SARS-CoV-2 could become established in secondary reservoir hosts outside of Asia. To assess this potential, we challenged deer mice (Peromyscus maniculatus) with SARS-CoV-2 and found robust virus replication in the upper respiratory tract, lungs and intestines, with detectable viral RNA for up to 21 days in oral swabs and 6 days in lungs. Virus entry into the brain also occurred, likely via gustatory-olfactory-trigeminal pathway with eventual compromise to the blood-brain barrier. Despite this, no conspicuous signs of disease were observed, and no deer mice succumbed to infection. Expression of several innate immune response genes were elevated in the lungs, including IFNα, IFNβ, Cxcl10, Oas2, Tbk1 and Pycard. Elevated CD4 and CD8β expression in the lungs was concomitant with Tbx21, IFNγ and IL-21 expression, suggesting a type I inflammatory immune response. Contact transmission occurred from infected to naive deer mice through two passages, showing sustained natural transmission and localization into the olfactory bulb, recapitulating human neuropathology. In the second deer mouse passage, an insertion of 4 amino acids occurred to fixation in the N-terminal domain of the spike protein that is predicted to form a solvent-accessible loop. Subsequent examination of the source virus from BEI Resources determined the mutation was present at very low levels, demonstrating potent purifying selection for the insert during in vivo passage. Collectively, this work has determined that deer mice are a suitable animal model for the study of SARS-CoV-2 respiratory disease and neuropathogenesis, and that they have the potential to serve as secondary reservoir hosts in North America.
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Affiliation(s)
- Anna Fagre
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Juliette Lewis
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Miles Eckley
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Shijun Zhan
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Savannah M. Rocha
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Nicole R. Sexton
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Bradly Burke
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Brian Geiss
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Olve Peersen
- Department of Biochemistry and Molecular Biology, College of Natural Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Todd Bass
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Rebekah Kading
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Joel Rovnak
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gregory D. Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Ronald B. Tjalkens
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Tawfik Aboellail
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Tony Schountz
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
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5
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Shannon A, Selisko B, Le NTT, Huchting J, Touret F, Piorkowski G, Fattorini V, Ferron F, Decroly E, Meier C, Coutard B, Peersen O, Canard B. Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis. Nat Commun 2020; 11:4682. [PMID: 32943628 PMCID: PMC7499305 DOI: 10.1038/s41467-020-18463-z] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
The ongoing Corona Virus Disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has emphasized the urgent need for antiviral therapeutics. The viral RNA-dependent-RNA-polymerase (RdRp) is a promising target with polymerase inhibitors successfully used for the treatment of several viral diseases. We demonstrate here that Favipiravir predominantly exerts an antiviral effect through lethal mutagenesis. The SARS-CoV RdRp complex is at least 10-fold more active than any other viral RdRp known. It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. The coronavirus RdRp complex represents an Achilles heel for SARS-CoV, supporting nucleoside analogues as promising candidates for the treatment of COVID-19.
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Affiliation(s)
- Ashleigh Shannon
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Barbara Selisko
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Nhung-Thi-Tuyet Le
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Johanna Huchting
- Faculty of Sciences, Department of Chemistry, Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, D-20146, Hamburg, Germany
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Géraldine Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Véronique Fattorini
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - François Ferron
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Chris Meier
- Faculty of Sciences, Department of Chemistry, Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, D-20146, Hamburg, Germany
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Olve Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA.
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France.
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6
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Fagre A, Lewis J, Eckley M, Zhan S, Rocha SM, Sexton NR, Burke B, Geiss B, Peersen O, Kading R, Rovnak J, Ebel GD, Tjalkens RB, Aboellail T, Schountz T. SARS-CoV-2 infection, neuropathogenesis and transmission among deer mice: Implications for reverse zoonosis to New World rodents. bioRxiv 2020:2020.08.07.241810. [PMID: 32793912 PMCID: PMC7418741 DOI: 10.1101/2020.08.07.241810] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Coronavirus disease-19 (COVID-19) emerged in November, 2019 in China and rapidly became pandemic. As with other coronaviruses, a preponderance of evidence suggests the virus originated in horseshoe bats (Rhinolophus spp.) and likely underwent a recombination event in an intermediate host prior to entry into human populations. A significant concern is that SARS-CoV-2 could become established in secondary reservoir hosts outside of Asia. To assess this potential, we challenged deer mice (Peromyscus maniculatus) with SARS-CoV-2 and found robust virus replication in the upper respiratory tract, lungs and intestines, with detectable viral RNA for up to 21 days in oral swabs and 14 days in lungs. Virus entry into the brain also occurred, likely via gustatory-olfactory-trigeminal pathway with eventual compromise to the blood brain barrier. Despite this, no conspicuous signs of disease were observed and no deer mice succumbed to infection. Expression of several innate immune response genes were elevated in the lungs, notably IFNα, Cxcl10, Oas2, Tbk1 and Pycard. Elevated CD4 and CD8β expression in the lungs was concomitant with Tbx21, IFNγ and IL-21 expression, suggesting a type I inflammatory immune response. Contact transmission occurred from infected to naive deer mice through two passages, showing sustained natural transmission. In the second deer mouse passage, an insertion of 4 amino acids occurred to fixation in the N-terminal domain of the spike protein that is predicted to form a solvent-accessible loop. Subsequent examination of the source virus from BEI Resources indicated the mutation was present at very low levels, demonstrating potent purifying selection for the insert during in vivo passage. Collectively, this work has determined that deer mice are a suitable animal model for the study of SARS-CoV-2 pathogenesis, and that they have the potential to serve as secondary reservoir hosts that could lead to periodic outbreaks of COVID-19 in North America.
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Affiliation(s)
- Anna Fagre
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Juliette Lewis
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Miles Eckley
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Shijun Zhan
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Savannah M Rocha
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Nicole R Sexton
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Bradly Burke
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Brian Geiss
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Olve Peersen
- Department of Biochemistry and Molecular Biology, College of Natural Sciences, Colorado State University, Fort Collins, CO 80523
| | - Rebekah Kading
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Joel Rovnak
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Ronald B Tjalkens
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Tawfik Aboellail
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
| | - Tony Schountz
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523
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7
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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: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Shannon A, Selisko B, Le NTT, Huchting J, Touret F, Piorkowski G, Fattorini V, Ferron F, Decroly E, Meier C, Coutard B, Peersen O, Canard B. Favipiravir strikes the SARS-CoV-2 at its Achilles heel, the RNA polymerase. bioRxiv 2020:2020.05.15.098731. [PMID: 32511380 PMCID: PMC7263509 DOI: 10.1101/2020.05.15.098731] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ongoing Corona Virus Disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has emphasized the urgent need for antiviral therapeutics. The viral RNA-dependent-RNA-polymerase (RdRp) is a promising target with polymerase inhibitors successfully used for the treatment of several viral diseases. Here we show that Favipiravir exerts an antiviral effect as a nucleotide analogue through a combination of chain termination, slowed RNA synthesis and lethal mutagenesis. The SARS-CoV RdRp complex is at least 10-fold more active than any other viral RdRp known. It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. The coronavirus RdRp complex represents an Achilles heel for SARS-CoV, supporting nucleoside analogues as promising candidates for the treatment of COVID-19.
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Affiliation(s)
- A. Shannon
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - B. Selisko
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - NTT Le
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - J. Huchting
- University of Hamburg, Faculty of Sciences, Department of Chemistry, Organic Chemistry, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany
| | - F. Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - G. Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - V. Fattorini
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - F. Ferron
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - E. Decroly
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - C Meier
- University of Hamburg, Faculty of Sciences, Department of Chemistry, Organic Chemistry, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany
| | - B. Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - O. Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - B. Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
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Martínez-Sobrido L, Peersen O, Nogales A. Temperature Sensitive Mutations in Influenza A Viral Ribonucleoprotein Complex Responsible for the Attenuation of the Live Attenuated Influenza Vaccine. Viruses 2018; 10:E560. [PMID: 30326610 PMCID: PMC6213772 DOI: 10.3390/v10100560] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/03/2018] [Accepted: 10/12/2018] [Indexed: 01/29/2023] Open
Abstract
Live attenuated influenza vaccines (LAIV) have prevented morbidity and mortality associated with influenza viral infections for many years and represent the best therapeutic option to protect against influenza viral infections in humans. However, the development of LAIV has traditionally relied on empirical methods, such as the adaptation of viruses to replicate at low temperatures. These approaches require an extensive investment of time and resources before identifying potential vaccine candidates that can be safely implemented as LAIV to protect humans. In addition, the mechanism of attenuation of these vaccines is poorly understood in some cases. Importantly, LAIV are more efficacious than inactivated vaccines because their ability to mount efficient innate and adaptive humoral and cellular immune responses. Therefore, the design of potential LAIV based on known properties of viral proteins appears to be a highly appropriate option for the treatment of influenza viral infections. For that, the viral RNA synthesis machinery has been a research focus to identify key amino acid substitutions that can lead to viral attenuation and their use in safe, immunogenic, and protective LAIV. In this review, we discuss the potential to manipulate the influenza viral RNA-dependent RNA polymerase (RdRp) complex to generate attenuated forms of the virus that can be used as LAIV for the treatment of influenza viral infections, one of the current and most effective prophylactic options for the control of influenza in humans.
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Affiliation(s)
- Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, New York, NY 14642, USA.
| | - Olve Peersen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, CO 80523, USA.
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, New York, NY 14642, USA.
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Rai DK, Diaz-San Segundo F, Campagnola G, Keith A, Schafer EA, Kloc A, de Los Santos T, Peersen O, Rieder E. Attenuation of Foot-and-Mouth Disease Virus by Engineered Viral Polymerase Fidelity. J Virol 2017; 91:e00081-17. [PMID: 28515297 PMCID: PMC5651715 DOI: 10.1128/jvi.00081-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 05/03/2017] [Indexed: 12/21/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) RNA-dependent RNA polymerase (RdRp) (3Dpol) catalyzes viral RNA synthesis. Its characteristic low fidelity and absence of proofreading activity allow FMDV to rapidly mutate and adapt to dynamic environments. In this study, we used the structure of FMDV 3Dpol in combination with previously reported results from similar picornaviral polymerases to design point mutations that would alter replication fidelity. In particular, we targeted Trp237 within conserved polymerase motif A because of the low reversion potential inherent in the single UGG codon. Using biochemical and genetic tools, we show that the replacement of tryptophan 237 with phenylalanine imparts higher fidelity, but replacements with isoleucine and leucine resulted in lower-fidelity phenotypes. Viruses containing these W237 substitutions show in vitro growth kinetics and plaque morphologies similar to those of the wild-type (WT) A24 Cruzeiro strain in BHK cells, and both high- and low-fidelity variants retained fitness during coinfection with the wild-type virus. The higher-fidelity W237F (W237FHF) mutant virus was more resistant to the mutagenic nucleoside analogs ribavirin and 5-fluorouracil than the WT virus, whereas the lower-fidelity W237I (W237ILF) and W237LLF mutant viruses exhibited lower ribavirin resistance. Interestingly, the variant viruses showed heterogeneous and slightly delayed growth kinetics in primary porcine kidney cells, and they were significantly attenuated in mouse infection experiments. These data demonstrate, for a single virus, that either increased or decreased RdRp fidelity attenuates virus growth in animals, which is a desirable feature for the development of safer and genetically more stable vaccine candidates.IMPORTANCE Foot-and-mouth disease (FMD) is the most devastating disease affecting livestock worldwide. Here, using structural and biochemical analyses, we have identified FMDV 3Dpol mutations that affect polymerase fidelity. Recombinant FMDVs containing substitutions at 3Dpol tryptophan residue 237 were genetically stable and displayed plaque phenotypes and growth kinetics similar to those of the wild-type virus in cell culture. We further demonstrate that viruses harboring either a W237FHF substitution or W237ILF and W237LLF mutations were highly attenuated in animals. Our study shows that obtaining 3Dpol fidelity variants by protein engineering based on polymerase structure and function could be exploited for the development of attenuated FMDV vaccine candidates that are safer and more stable than strains obtained by selective pressure via mutagenic nucleotides or adaptation approaches.
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Affiliation(s)
- Devendra K Rai
- Plum Island Animal Disease Center, North Atlantic Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, New York, USA
- University of Connecticut, Storrs, Connecticut, USA
| | - Fayna Diaz-San Segundo
- Plum Island Animal Disease Center, North Atlantic Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, New York, USA
- University of Connecticut, Storrs, Connecticut, USA
| | - Grace Campagnola
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Anna Keith
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Elizabeth A Schafer
- Plum Island Animal Disease Center, North Atlantic Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, New York, USA
| | - Anna Kloc
- Plum Island Animal Disease Center, North Atlantic Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, New York, USA
- Oak Ridge Institute for Science and Education, Plum Island Animal Disease Center Research Participation Program, Oak Ridge, Tennessee, USA
| | - Teresa de Los Santos
- Plum Island Animal Disease Center, North Atlantic Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, New York, USA
| | - Olve Peersen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Elizabeth Rieder
- Plum Island Animal Disease Center, North Atlantic Area, Agricultural Research Service, U.S. Department of Agriculture, Greenport, New York, USA
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Campagnola G, Weygandt M, Scoggin K, Peersen O. Crystal structure of coxsackievirus B3 3Dpol highlights the functional importance of residue 5 in picornavirus polymerases. J Virol 2008; 82:9458-64. [PMID: 18632862 PMCID: PMC2546958 DOI: 10.1128/jvi.00647-08] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2008] [Accepted: 07/10/2008] [Indexed: 11/20/2022] Open
Abstract
The crystal structure of the coxsackievirus B3 polymerase has been solved at 2.25-A resolution and is shown to be highly homologous to polymerases from poliovirus, rhinovirus, and foot-and-mouth disease viruses. Together, these structures highlight several conserved structural elements in picornaviral polymerases, including a proteolytic activation-dependent N-terminal structure that is essential for full activity. Interestingly, a comparison of all of the picornaviral polymerase structures shows an unusual conformation for residue 5, which is always located at a distortion in the beta-strand composed of residues 1 to 8. In our earlier structure of the poliovirus polymerase, we attributed this conformation to a crystal packing artifact, but the observation that this conformation is conserved among picornaviruses led us to examine the role of this residue in further detail. Here we use coxsackievirus polymerase to show that elongation activity correlates with the hydrophobicity of residue 5 and, surprisingly, more hydrophobic residues result in higher activity. Based on structural analysis, we propose that this residue becomes buried during the nucleotide repositioning step that occurs prior to phosphoryl transfer. We present a model in which the buried N terminus observed in all picornaviral polymerases is essential for stabilizing the structure during this conformational change.
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Affiliation(s)
- Grace Campagnola
- Department of Biochemistry and Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870, USA
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Abstract
The Neu receptor tyrosine kinase is constitutively activated by a single amino acid change in the transmembrane domain of the receptor. The mutation of Val664 to glutamate or glutamine induces receptor dimerization and autophosphorylation of the receptor's intracellular kinase domain. The ability of this single mutation to activate the receptor is sequence-dependent, suggesting that specific helix-helix interactions stabilize the transmembrane dimer. We have determined the local secondary structure and interhelical contacts in the region of position 664 in peptide models of the activated receptor using solid-state rotational resonance and rotational echo double-resonance (REDOR) NMR methods. Intrahelical (13)C rotational resonance distance measurements were made between 1-(13)C-Thr662 and 2-(13)C-Gly665 on peptides corresponding to the wild-type Neu and activated Neu transmembrane sequences containing valine and glutamate at position 664, respectively. We observed similar internuclear distances (4.5 +/- 0.2 A) in both Neu and Neu*, indicating that the region near residue 664 is helical and is not influenced by mutation. Interhelical (15)N...(13)C REDOR measurements between Gln664 side chains on opposing helices were not consistent with hydrogen bonding between the side chain functional groups. However, interhelical rotational resonance measurements between 1-(13)C-Glu664 and 2-(13)C-Gly665 and between 1-(13)C-Gly665 and 2-(13)C-Gly665 demonstrated close contacts (4.3-4.5 A) consistent with the packing of Gly665 in the Neu* dimer interface. These measurements provide structural constraints for modeling the transmembrane dimer and define the rotational orientation of the transmembrane helices in the activated receptor.
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Affiliation(s)
- Steven O Smith
- Department of Biochemistry and Cell Biology, Center for Structural Biology, SUNY Stony Brook, Stony Brook, New York 11794-5115, USA.
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Peersen O, Groesbeek M, Aimoto S, Smith SO. Analysis of Rotational Resonance Magnetization Exchange Curves from Crystalline Peptides. J Am Chem Soc 2002. [DOI: 10.1021/ja00132a023] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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