A cell-based assay to discover inhibitors of SARS-CoV-2 RNA dependent RNA polymerase

Antiviral Res. 2021 Jun:190:105078. doi: 10.1016/j.antiviral.2021.105078. Epub 2021 Apr 21.

Abstract

Antiviral therapeutics is one effective avenue to control and end this devastating COVID-19 pandemic. The viral RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 has been recognized as a valuable target of antivirals. However, the cell-free SARS-CoV-2 RdRp biochemical assay requires the conversion of nucleotide prodrugs into the active triphosphate forms, which regularly occurs in cells yet is a complicated multiple-step chemical process in vitro, and thus hinders the utility of this cell-free assay in the rapid discovery of RdRp inhibitors. In addition, SARS-CoV-2 exoribonuclease provides the proof-reading capacity to viral RdRp, thus creates relatively high resistance threshold of viral RdRp to nucleotide analog inhibitors, which must be examined and evaluated in the development of this class of antivirals. Here, we report a cell-based assay to evaluate the efficacy of nucleotide analog compounds against SARS-CoV-2 RdRp and assess their tolerance to viral exoribonuclease-mediated proof-reading. By testing seven commonly used nucleotide analog viral polymerase inhibitors, Remdesivir, Molnupiravir, Ribavirin, Favipiravir, Penciclovir, Entecavir and Tenofovir, we found that both Molnupiravir and Remdesivir showed the strong inhibition of SARS-CoV-2 RdRp, with EC50 value of 0.22 μM and 0.67 μM, respectively. Moreover, our results suggested that exoribonuclease nsp14 increases resistance of SARS-CoV-2 RdRp to nucleotide analog inhibitors. We also determined that Remdesivir presented the highest resistance to viral exoribonuclease activity in cells. Therefore, we have developed a cell-based SARS-CoV-2 RdRp assay which can be deployed to discover SARS-CoV-2 RdRp inhibitors that are urgently needed to treat COVID-19 patients.

Keywords: Antiviral; COVID-19; High-throughput; Nucleotide analog inhibitor; RdRp; Remdesivir; SARS-CoV-2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • A549 Cells
  • Adenosine Monophosphate / analogs & derivatives
  • Adenosine Monophosphate / pharmacology
  • Alanine / analogs & derivatives
  • Alanine / pharmacology
  • Antiviral Agents / pharmacology*
  • COVID-19 / virology
  • COVID-19 Drug Treatment*
  • Cell Survival / drug effects
  • Drug Discovery*
  • Exoribonucleases / antagonists & inhibitors
  • HEK293 Cells
  • High-Throughput Screening Assays
  • Humans
  • RNA, Viral / genetics
  • RNA-Dependent RNA Polymerase / antagonists & inhibitors*
  • SARS-CoV-2 / drug effects*
  • SARS-CoV-2 / enzymology*
  • SARS-CoV-2 / genetics
  • Viral Nonstructural Proteins / antagonists & inhibitors

Substances

  • Antiviral Agents
  • RNA, Viral
  • Viral Nonstructural Proteins
  • remdesivir
  • Adenosine Monophosphate
  • RNA-Dependent RNA Polymerase
  • Exoribonucleases
  • NSP14 protein, SARS-CoV-2
  • Alanine