Punicalagin as an allosteric NSP13 helicase inhibitor potently suppresses SARS-CoV-2 replication in vitro

Antiviral Res. 2022 Oct:206:105389. doi: 10.1016/j.antiviral.2022.105389. Epub 2022 Aug 17.

Abstract

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) helicase NSP13 plays a conserved role in the replication of coronaviruses and has been identified as an ideal target for the development of antiviral drugs against SARS-CoV-2. Here, we identify a novel NSP13 helicase inhibitor punicalagin (PUG) through high-throughput screening. Surface plasmon resonance (SPR)-based analysis and molecular docking calculation reveal that PUG directly binds NSP13 on the interface of domains 1A and 2A, with a KD value of 21.6 nM. Further biochemical and structural analyses suggest that PUG inhibits NSP13 on ATP hydrolysis and prevents it binding to DNA substrates. Finally, the antiviral studies show that PUG effectively suppresses the SARS-CoV-2 replication in A549-ACE2 and Vero cells, with EC50 values of 347 nM and 196 nM, respectively. Our work demonstrates the potential application of PUG in the treatment of coronavirus disease 2019 (COVID-19) and identifies an allosteric inhibition mechanism for future drug design targeting the viral helicases.

Keywords: Helicase; Inhibitor; NSP13; Punicalagin; SARS-CoV-2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antiviral Agents / chemistry
  • Antiviral Agents / pharmacology
  • COVID-19 Drug Treatment*
  • Chlorocebus aethiops
  • DNA Helicases / metabolism
  • Humans
  • Hydrolyzable Tannins
  • Molecular Docking Simulation
  • RNA Helicases / chemistry
  • SARS-CoV-2*
  • Vero Cells

Substances

  • Antiviral Agents
  • Hydrolyzable Tannins
  • punicalagin
  • DNA Helicases
  • RNA Helicases