Molecular characterization of ebselen binding activity to SARS-CoV-2 main protease

Sci Adv. 2020 Sep 11;6(37):eabd0345. doi: 10.1126/sciadv.abd0345. Print 2020 Sep.


There is an urgent need to repurpose drugs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent computational-experimental screenings have identified several existing drugs that could serve as effective inhibitors of the virus' main protease, Mpro, which is involved in gene expression and replication. Among these, ebselen (2-phenyl-1,2-benzoselenazol-3-one) appears to be particularly promising. Here, we examine, at a molecular level, the potential of ebselen to decrease Mpro activity. We find that it exhibits a distinct affinity for the catalytic region. Our results reveal a higher-affinity, previously unknown binding site localized between the II and III domains of the protein. A detailed strain analysis indicates that, on such a site, ebselen exerts a pronounced allosteric effect that regulates catalytic site access through surface-loop interactions, thereby inducing a reconfiguration of water hotspots. Together, these findings highlight the promise of ebselen as a repurposed drug against SARS-CoV-2.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Antiviral Agents / metabolism
  • Antiviral Agents / pharmacology*
  • Azoles / metabolism*
  • Azoles / pharmacology*
  • Betacoronavirus / drug effects*
  • Betacoronavirus / metabolism
  • Binding Sites
  • COVID-19
  • Catalytic Domain / drug effects
  • Coronavirus 3C Proteases
  • Coronavirus Infections / drug therapy*
  • Cysteine Endopeptidases / metabolism*
  • Drug Repositioning
  • Humans
  • Isoindoles
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Organoselenium Compounds / metabolism*
  • Organoselenium Compounds / pharmacology*
  • Pandemics
  • Pneumonia, Viral / drug therapy*
  • Protein Conformation / drug effects
  • SARS-CoV-2
  • Viral Nonstructural Proteins / metabolism*


  • Antiviral Agents
  • Azoles
  • Isoindoles
  • Organoselenium Compounds
  • Viral Nonstructural Proteins
  • ebselen
  • Cysteine Endopeptidases
  • Coronavirus 3C Proteases