Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis

Nat Struct Mol Biol. 2021 Sep;28(9):740-746. doi: 10.1038/s41594-021-00651-0. Epub 2021 Aug 11.

Abstract

Molnupiravir is an orally available antiviral drug candidate currently in phase III trials for the treatment of patients with COVID-19. Molnupiravir increases the frequency of viral RNA mutations and impairs SARS-CoV-2 replication in animal models and in humans. Here, we establish the molecular mechanisms underlying molnupiravir-induced RNA mutagenesis by the viral RNA-dependent RNA polymerase (RdRp). Biochemical assays show that the RdRp uses the active form of molnupiravir, β-D-N4-hydroxycytidine (NHC) triphosphate, as a substrate instead of cytidine triphosphate or uridine triphosphate. When the RdRp uses the resulting RNA as a template, NHC directs incorporation of either G or A, leading to mutated RNA products. Structural analysis of RdRp-RNA complexes that contain mutagenesis products shows that NHC can form stable base pairs with either G or A in the RdRp active center, explaining how the polymerase escapes proofreading and synthesizes mutated RNA. This two-step mutagenesis mechanism probably applies to various viral polymerases and can explain the broad-spectrum antiviral activity of molnupiravir.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antiviral Agents / chemistry
  • Antiviral Agents / metabolism
  • Antiviral Agents / pharmacology
  • Base Sequence
  • COVID-19 / drug therapy
  • COVID-19 / prevention & control*
  • COVID-19 / virology
  • Cytidine / analogs & derivatives*
  • Cytidine / chemistry
  • Cytidine / metabolism
  • Cytidine / pharmacology
  • Humans
  • Hydroxylamines / chemistry
  • Hydroxylamines / metabolism*
  • Hydroxylamines / pharmacology
  • Models, Molecular
  • Molecular Structure
  • Mutagenesis / drug effects
  • Mutagenesis / genetics*
  • Mutation / drug effects
  • Mutation / genetics
  • Nucleic Acid Conformation
  • Protein Binding / drug effects
  • Protein Conformation
  • RNA, Viral / chemistry
  • RNA, Viral / genetics*
  • RNA, Viral / metabolism
  • RNA-Dependent RNA Polymerase / chemistry
  • RNA-Dependent RNA Polymerase / genetics
  • RNA-Dependent RNA Polymerase / metabolism
  • SARS-CoV-2 / drug effects
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / physiology
  • Virus Replication / drug effects
  • Virus Replication / genetics

Substances

  • Antiviral Agents
  • Hydroxylamines
  • RNA, Viral
  • Cytidine
  • RNA-Dependent RNA Polymerase
  • molnupiravir