Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives

Nat Commun. 2021 May 24;12(1):3061. doi: 10.1038/s41467-021-23313-7.


The SARS-CoV-2 pandemic has triggered global efforts to develop therapeutics. The main protease of SARS-CoV-2 (Mpro), critical for viral replication, is a key target for therapeutic development. An organoselenium drug called ebselen has been demonstrated to have potent Mpro inhibition and antiviral activity. We have examined the binding modes of ebselen and its derivative in Mpro via high resolution co-crystallography and investigated their chemical reactivity via mass spectrometry. Stronger Mpro inhibition than ebselen and potent ability to rescue infected cells were observed for a number of derivatives. A free selenium atom bound with cysteine of catalytic dyad has been revealed in crystallographic structures of Mpro with ebselen and MR6-31-2 suggesting hydrolysis of the enzyme bound organoselenium covalent adduct and formation of a phenolic by-product, confirmed by mass spectrometry. The target engagement with selenation mechanism of inhibition suggests wider therapeutic applications of these compounds against SARS-CoV-2 and other zoonotic beta-corona viruses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antiviral Agents / pharmacology
  • Azoles / chemistry
  • Azoles / pharmacology*
  • Catalytic Domain
  • Coronavirus 3C Proteases / antagonists & inhibitors*
  • Coronavirus 3C Proteases / metabolism
  • Crystallography, X-Ray
  • Cysteine / chemistry
  • Hydrolysis
  • Isoindoles
  • Models, Molecular
  • Organoselenium Compounds / chemistry
  • Organoselenium Compounds / pharmacology*
  • Protease Inhibitors / chemistry
  • Protease Inhibitors / pharmacology
  • Reference Standards
  • SARS-CoV-2 / drug effects
  • SARS-CoV-2 / enzymology*
  • Salicylanilides / chemistry
  • Salicylanilides / pharmacology
  • Selenium / metabolism


  • Antiviral Agents
  • Azoles
  • Isoindoles
  • Organoselenium Compounds
  • Protease Inhibitors
  • Salicylanilides
  • ebselen
  • 3C-like proteinase, SARS-CoV-2
  • Coronavirus 3C Proteases
  • Selenium
  • Cysteine