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Snyder LR, Kilde I, Nemudryi A, Wiedenheft B, Koutmos M, Koutmou KS. Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription. RNA (NEW YORK, N.Y.) 2024; 30:1141-1150. [PMID: 38942480 PMCID: PMC11331411 DOI: 10.1261/rna.079991.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/20/2024] [Indexed: 06/30/2024]
Abstract
SARS-CoV-2, the causative virus of the COVID-19 pandemic, follows SARS and MERS as recent zoonotic coronaviruses causing severe respiratory illness and death in humans. The recurrent impact of zoonotic coronaviruses demands a better understanding of their fundamental molecular biochemistry. Nucleoside modifications, which modulate many steps of the RNA life cycle, have been found in SARS-CoV-2 RNA, although whether they confer a pro- or antiviral effect is unknown. Regardless, the viral RNA-dependent RNA polymerase will encounter these modifications as it transcribes through the viral genomic RNA. We investigated the functional consequences of nucleoside modification on the pre-steady state kinetics of SARS-CoV-2 RNA-dependent RNA transcription using an in vitro reconstituted transcription system with modified RNA templates. Our findings show that N 6-methyladenosine and 2'-O-methyladenosine modifications slow the rate of viral transcription at magnitudes specific to each modification, which has the potential to impact SARS-CoV-2 genome maintenance.
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Affiliation(s)
- Laura R Snyder
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ingrid Kilde
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Artem Nemudryi
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717, USA
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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2
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Anderson TK, Hoferle PJ, Chojnacki KJ, Lee K, Coon J, Kirchdoerfer R. An alphacoronavirus polymerase structure reveals conserved replication factor functions. Nucleic Acids Res 2024; 52:5975-5986. [PMID: 38442273 PMCID: PMC11162792 DOI: 10.1093/nar/gkae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/18/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
Coronaviruses are a diverse subfamily of viruses containing pathogens of humans and animals. This subfamily of viruses replicates their RNA genomes using a core polymerase complex composed of viral non-structural proteins: nsp7, nsp8 and nsp12. Most of our understanding of coronavirus molecular biology comes from betacoronaviruses like SARS-CoV and SARS-CoV-2, the latter of which is the causative agent of COVID-19. In contrast, members of the alphacoronavirus genus are relatively understudied despite their importance in human and animal health. Here we have used cryo-electron microscopy to determine structures of the alphacoronavirus porcine epidemic diarrhea virus (PEDV) core polymerase complex bound to RNA. One structure shows an unexpected nsp8 stoichiometry despite remaining bound to RNA. Biochemical analysis shows that the N-terminal extension of one nsp8 is not required for in vitro RNA synthesis for alpha- and betacoronaviruses. Our work demonstrates the importance of studying diverse coronaviruses in revealing aspects of coronavirus replication and identifying areas of conservation to be targeted by antiviral drugs.
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Affiliation(s)
- Thomas K Anderson
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peter J Hoferle
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kennan J Chojnacki
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kenneth W Lee
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Robert N Kirchdoerfer
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
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Zhang R, Li H, Xie H, Hou X, Zhou L, Cao A, Zeshan B, Zhou Y, Wang X. Comparing the molecular evolution and recombination patterns of predominant PRRSV-2 lineages co-circulating in China. Front Microbiol 2024; 15:1398470. [PMID: 38737413 PMCID: PMC11088243 DOI: 10.3389/fmicb.2024.1398470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) poses widespread epidemics in swine herds, yet the drivers underlying lineage replacements/fitness dynamics remain unclear. To delineate the evolutionary trajectories of PRRSV-2 lineages prevalent in China, we performed a comprehensive longitudinal phylodynamic analysis of 822 viral sequences spanning 1991-2022. The objectives encompassed evaluating lineage dynamics, genetic diversity, recombination patterns and glycosylation profiles. A significant shift in the dominance of PRRSV-2 sub-lineages has been observed over the past 3 decades, transitioning from sub-lineage 8.7 to sub-lineage 1.8, followed by extensive diversification. The analysis revealed discordant recombination patterns between the two dominant viral sub-lineages 1.8 and 8.7, underscoring that modular genetic exchanges contribute significantly to their evolutionary shaping. Additionally, a strong association was found between recombination breakpoint locations and transcriptional regulatory sequences (TRSs). Glycosylation patterns also demonstrated considerable variability across sub-lineages and temporally, providing evidence for immune-driven viral evolution. Furthermore, we quantified different evolutionary rates across sub-lineages, with sub-lineage 1.8 uniquely displaying the highest nucleotide substitution rates. Taken together, these findings provide refined insight into the evolutionary mechanisms underpinning cyclic shifts in dominance among regionally circulating PRRSV sub-lineages.
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Affiliation(s)
- Riteng Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Hui Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Honglin Xie
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaolan Hou
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Lixuan Zhou
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Aiqiao Cao
- Shenzhen Institute of Quality and Safety Inspection and Research, Shenzhen, Guangdong, China
| | - Basit Zeshan
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, Sandakan, Sabah, Malaysia
| | - Yefei Zhou
- Department of Life Science, Nanjing Xiaozhuang University, Nanjing, Jiangsu, China
| | - Xinglong Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
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4
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Shannon A, Chazot A, Feracci M, Falcou C, Fattorini V, Selisko B, Good S, Moussa A, Sommadossi JP, Ferron F, Alvarez K, Canard B. An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex. Nucleic Acids Res 2024; 52:1325-1340. [PMID: 38096103 PMCID: PMC10853775 DOI: 10.1093/nar/gkad1194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 02/10/2024] Open
Abstract
Nucleotide analogues (NA) are currently employed for treatment of several viral diseases, including COVID-19. NA prodrugs are intracellularly activated to the 5'-triphosphate form. They are incorporated into the viral RNA by the viral polymerase (SARS-CoV-2 nsp12), terminating or corrupting RNA synthesis. For Coronaviruses, natural resistance to NAs is provided by a viral 3'-to-5' exonuclease heterodimer nsp14/nsp10, which can remove terminal analogues. Here, we show that the replacement of the α-phosphate of Bemnifosbuvir 5'-triphosphate form (AT-9010) by an α-thiophosphate renders it resistant to excision. The resulting α-thiotriphosphate, AT-9052, exists as two epimers (RP/SP). Through co-crystallization and activity assays, we show that the Sp isomer is preferentially used as a substrate by nucleotide diphosphate kinase (NDPK), and by SARS-CoV-2 nsp12, where its incorporation causes immediate chain-termination. The same -Sp isomer, once incorporated by nsp12, is also totally resistant to the excision by nsp10/nsp14 complex. However, unlike AT-9010, AT-9052-RP/SP no longer inhibits the N-terminal nucleotidylation domain of nsp12. We conclude that AT-9052-Sp exhibits a unique mechanism of action against SARS-CoV-2. Moreover, the thio modification provides a general approach to rescue existing NAs whose activity is hampered by coronavirus proofreading capacity.
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Affiliation(s)
- Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Aurélie Chazot
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Mikael Feracci
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Camille Falcou
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Véronique Fattorini
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Barbara Selisko
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Steven Good
- ATEA Pharmaceuticals, Inc., 225 Franklin St., Suite 2100, Boston, MA 02110, USA
| | - Adel Moussa
- ATEA Pharmaceuticals, Inc., 225 Franklin St., Suite 2100, Boston, MA 02110, USA
| | | | - François Ferron
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Karine Alvarez
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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5
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Palyanov AY, Palyanova NV. On the space of SARS-CoV-2 genetic sequence variants. Vavilovskii Zhurnal Genet Selektsii 2023; 27:839-850. [PMID: 38213712 PMCID: PMC10777302 DOI: 10.18699/vjgb-23-97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 01/13/2024] Open
Abstract
The coronavirus pandemic caused by the SARS-CoV-2 virus, which humanity resisted using the latest advances in science, left behind, among other things, extensive genetic data. Every day since the end of 2019, samples of the virus genomes have been collected around the world, which makes it possible to trace its evolution in detail from its emergence to the present. The accumulated statistics of testing results showed that the number of confirmed cases of SARS-CoV-2 infection was at least 767.5 million (9.5 % of the current world population, excluding asymptomatic people), and the number of sequenced virus genomes is more than 15.7 million (which is over 2 % of the total number of infected people). These new data potentially contain information about the mechanisms of the variability and spread of the virus, its interaction with the human immune system, the main parameters characterizing the mechanisms of the development of a pandemic, and much more. In this article, we analyze the space of possible variants of SARS-CoV-2 genetic sequences both from a mathematical point of view and taking into account the biological limitations inherent in this system, known both from general biological knowledge and from the consideration of the characteristics of this particular virus. We have developed software capable of loading and analyzing SARS-CoV-2 nucleotide sequences in FASTA format, determining the 5' and 3' UTR positions, the number and location of unidentified nucleotides ("N"), performing alignment with the reference sequence by calling the program designed for this, determining mutations, deletions and insertions, as well as calculating various characteristics of virus genomes with a given time step (days, weeks, months, etc.). The data obtained indicate that, despite the apparent mathematical diversity of possible options for changing the virus over time, the corridor of the evolutionary trajectory that the coronavirus has passed through seems to be quite narrow. Thus it can be assumed that it is determined to some extent, which allows us to hope for a possibility of modeling the evolution of the coronavirus.
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Affiliation(s)
- A Yu Palyanov
- A.P. Ershov Institute of Informatics Systems of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - N V Palyanova
- Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Feracci M, Eydoux C, Fattorini V, Lo Bello L, Gauffre P, Selisko B, Sutto-Ortiz P, Shannon A, Xia H, Shi PY, Noel M, Debart F, Vasseur JJ, Good S, Lin K, Moussa A, Sommadossi JP, Chazot A, Alvarez K, Guillemot JC, Decroly E, Ferron F, Canard B. AT-752 targets multiple sites and activities on the Dengue virus replication enzyme NS5. Antiviral Res 2023; 212:105574. [PMID: 36905944 DOI: 10.1016/j.antiviral.2023.105574] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/12/2023]
Abstract
AT-752 is a guanosine analogue prodrug active against dengue virus (DENV). In infected cells, it is metabolized into 2'-methyl-2'-fluoro guanosine 5'-triphosphate (AT-9010) which inhibits RNA synthesis in acting as a RNA chain terminator. Here we show that AT-9010 has several modes of action on DENV full-length NS5. AT-9010 does not inhibit the primer pppApG synthesis step significantly. However, AT-9010 targets two NS5-associated enzyme activities, the RNA 2'-O-MTase and the RNA-dependent RNA polymerase (RdRp) at its RNA elongation step. Crystal structure and RNA methyltransferase (MTase) activities of the DENV 2 MTase domain in complex with AT-9010 at 1.97 Å resolution shows the latter bound to the GTP/RNA-cap binding site, accounting for the observed inhibition of 2'-O but not N7-methylation activity. AT-9010 is discriminated ∼10 to 14-fold against GTP at the NS5 active site of all four DENV1-4 NS5 RdRps, arguing for significant inhibition through viral RNA synthesis termination. In Huh-7 cells, DENV1-4 are equally sensitive to AT-281, the free base of AT-752 (EC50 ≈ 0.50 μM), suggesting broad spectrum antiviral properties of AT-752 against flaviviruses.
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Affiliation(s)
- Mikael Feracci
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Cécilia Eydoux
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Véronique Fattorini
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Lea Lo Bello
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Pierre Gauffre
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Barbara Selisko
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Priscila Sutto-Ortiz
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, Sealy Institute for Drug Discovery, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, Sealy Institute for Drug Discovery, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
| | - Mathieu Noel
- IBMM, UMR 5247 CNRS-UM1-UM2, Department of Nucleic Acids, Montpellier University, Place E. Bataillon, 34095, Montpellier Cedex 05, France
| | - Françoise Debart
- IBMM, UMR 5247 CNRS-UM1-UM2, Department of Nucleic Acids, Montpellier University, Place E. Bataillon, 34095, Montpellier Cedex 05, France
| | - Jean-Jacques Vasseur
- IBMM, UMR 5247 CNRS-UM1-UM2, Department of Nucleic Acids, Montpellier University, Place E. Bataillon, 34095, Montpellier Cedex 05, France
| | - Steve Good
- Atea Pharmaceuticals, Inc., 225 Franklin St., Suite 2100, Boston, MA, 02110, USA
| | - Kai Lin
- Atea Pharmaceuticals, Inc., 225 Franklin St., Suite 2100, Boston, MA, 02110, USA
| | - Adel Moussa
- Atea Pharmaceuticals, Inc., 225 Franklin St., Suite 2100, Boston, MA, 02110, USA
| | | | - Aurélie Chazot
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Karine Alvarez
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Jean-Claude Guillemot
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Etienne Decroly
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - François Ferron
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France.
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Anderson TK, Hoferle PJ, Lee KW, Coon JJ, Kirchdoerfer RN. An alphacoronavirus polymerase structure reveals conserved co-factor functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532841. [PMID: 36993498 PMCID: PMC10055115 DOI: 10.1101/2023.03.15.532841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Coronaviruses are a diverse subfamily of viruses containing pathogens of humans and animals. This subfamily of viruses replicates their RNA genomes using a core polymerase complex composed of viral non-structural proteins: nsp7, nsp8 and nsp12. Most of our understanding of coronavirus molecular biology comes from the betacoronaviruses like SARS-CoV and SARS-CoV-2, the latter of which is the causative agent of COVID-19. In contrast, members of the alphacoronavirus genus are relatively understudied despite their importance in human and animal health. Here we have used cryo-electron microscopy to determine the structure of the alphacoronavirus porcine epidemic diarrhea virus (PEDV) core polymerase complex bound to RNA. Our structure shows an unexpected nsp8 stoichiometry in comparison to other published coronavirus polymerase structures. Biochemical analysis shows that the N-terminal extension of one nsp8 is not required for in vitro RNA synthesis for alpha and betacoronaviruses as previously hypothesized. Our work shows the importance of studying diverse coronaviruses to reveal aspects of coronavirus replication while also identifying areas of conservation to be targeted by antiviral drugs.
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Affiliation(s)
- Thomas K. Anderson
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706
| | - Peter J. Hoferle
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706
| | - Kenneth W. Lee
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - Joshua J. Coon
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Robert N. Kirchdoerfer
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706
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8
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Shannon A, Canard B. Kill or corrupt: Mechanisms of action and drug-resistance of nucleotide analogues against SARS-CoV-2. Antiviral Res 2023; 210:105501. [PMID: 36567022 PMCID: PMC9773703 DOI: 10.1016/j.antiviral.2022.105501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Nucleoside/tide analogues (NAs) have long been used in the fight against viral diseases, and now present a promising option for the treatment of COVID-19. Once activated to the 5'-triphosphate state, NAs act by targeting the viral RNA-dependent RNA-polymerase for incorporation into the viral RNA genome. Incorporated analogues can either 'kill' (terminate) synthesis, or 'corrupt' (genetically or chemically) the RNA. Against coronaviruses, the use of NAs has been further complicated by the presence of a virally encoded exonuclease domain (nsp14) with proofreading and repair capacities. Here, we describe the mechanism of action of four promising anti-COVID-19 NAs; remdesivir, molnupiravir, favipiravir and bemnifosbuvir. Their distinct mechanisms of action best exemplify the concept of 'killers' and 'corruptors'. We review available data regarding their ability to be incorporated and excised, and discuss the specific structural features that dictate their overall potency, toxicity, and mutagenic potential. This should guide the synthesis of novel analogues, lend insight into the potential for resistance mutations, and provide a rational basis for upcoming combinations therapies.
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Affiliation(s)
- Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France.
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9
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Progress on COVID-19 Chemotherapeutics Discovery and Novel Technology. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238257. [PMID: 36500347 PMCID: PMC9736643 DOI: 10.3390/molecules27238257] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 11/29/2022]
Abstract
COVID-19 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel highly contagious and pathogenic coronavirus that emerged in late 2019. SARS-CoV-2 spreads primarily through virus-containing droplets and small particles of air pollution, which greatly increases the risk of inhaling these virus particles when people are in close proximity. COVID-19 is spreading across the world, and the COVID-19 pandemic poses a threat to human health and public safety. To date, there are no specific vaccines or effective drugs against SARS-CoV-2. In this review, we focus on the enzyme targets of the virus and host that may be critical for the discovery of chemical compounds and natural products as antiviral drugs, and describe the development of potential antiviral drugs in the preclinical and clinical stages. At the same time, we summarize novel emerging technologies applied to the research on new drug development and the pathological mechanisms of COVID-19.
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