Inhibition of SARS-CoV-2 polymerase by nucleotide analogs from a single-molecule perspective

eLife

Bruno Canard¹  Ashleigh Shannon¹  Thi-Tuyet-Nhung Le¹  Robert N Kirchdoerfer²  Hongjie Xia³  Pei-Yong Shi⁴  Steven Almo⁵  Tyler L Grove⁵  Martin Depken⁶  Craig E Cameron⁷  Jamie J Arnold⁷  Yan Xiang⁸  Xiangzhi Meng⁸  Flavia S Papini⁹  Mona Seifert⁹  Pauline van Nies⁹  Subhas C Bera⁹  David Dulin^1,10  Lawrence D Harris^1,11  James M Wood^1,11 

[1] Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, Marseille, France;Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, United States;Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, United States;Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Institute for Human Infections and Immunity, University of Texas Medical Branch, Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, United States;Department of Biochemistry, Albert Einstein College of Medicine, Bronx, Institute for Protein Innovation, Boston, United States;Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands;Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, United States;Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, United States;Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany;Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany;Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, Netherlands;The Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand;

关键词: SARS-CoV-2;    antiviral drugs;    mechanism of action;    Remdesivir;    high throughput magnetic tweezers;    single molecule biophysics;    Virus;   

DOI  :  10.7554/eLife.70968

来源: eLife Sciences Publications, Ltd

【 摘 要 】

The absence of ‘shovel-ready’ anti-coronavirus drugs during vaccine development has exceedingly worsened the SARS-CoV-2 pandemic. Furthermore, new vaccine-resistant variants and coronavirus outbreaks may occur in the near future, and we must be ready to face this possibility. However, efficient antiviral drugs are still lacking to this day, due to our poor understanding of the mode of incorporation and mechanism of action of nucleotides analogs that target the coronavirus polymerase to impair its essential activity. Here, we characterize the impact of remdesivir (RDV, the only FDA-approved anti-coronavirus drug) and other nucleotide analogs (NAs) on RNA synthesis by the coronavirus polymerase using a high-throughput, single-molecule, magnetic-tweezers platform. We reveal that the location of the modification in the ribose or in the base dictates the catalytic pathway(s) used for its incorporation. We show that RDV incorporation does not terminate viral RNA synthesis, but leads the polymerase into backtrack as far as 30 nt, which may appear as termination in traditional ensemble assays. SARS-CoV-2 is able to evade the endogenously synthesized product of the viperin antiviral protein, ddhCTP, though the polymerase incorporates this NA well. This experimental paradigm is essential to the discovery and development of therapeutics targeting viral polymerases.

【 授权许可】

CC BY