Inhibition of sars-cov-2 polymerase by nucleotide analogs from a single-molecule perspective

Mona Seifert, Subhas C. Bera, Pauline Van Nies, Robert N. Kirchdoerfer, Ashleigh Shannon, Thi Tuyet Nhung Le, Xiangzhi Meng, Hongjie Xia, James M. Wood, Lawrence D. Harris, Flavia S. Papini, Jamie J. Arnold, Steven Almo, Tyler L. Grove, Pei Yong Shi, Yan Xiang, Bruno Canard, Martin Depken, Craig E. Cameron, David Dulin

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article numbere70968
JournaleLife
Volume10
DOIs
StatePublished - Oct 2021

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

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