Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19

J Med Chem. 2020 Nov 12;63(21):12725-12747. doi: 10.1021/acs.jmedchem.0c01063. Epub 2020 Oct 15.

Abstract

The novel coronavirus disease COVID-19 that emerged in 2019 is caused by the virus SARS CoV-2 and named for its close genetic similarity to SARS CoV-1 that caused severe acute respiratory syndrome (SARS) in 2002. Both SARS coronavirus genomes encode two overlapping large polyproteins, which are cleaved at specific sites by a 3C-like cysteine protease (3CLpro) in a post-translational processing step that is critical for coronavirus replication. The 3CLpro sequences for CoV-1 and CoV-2 viruses are 100% identical in the catalytic domain that carries out protein cleavage. A research effort that focused on the discovery of reversible and irreversible ketone-based inhibitors of SARS CoV-1 3CLpro employing ligand-protease structures solved by X-ray crystallography led to the identification of 3 and 4. Preclinical experiments reveal 4 (PF-00835231) as a potent inhibitor of CoV-2 3CLpro with suitable pharmaceutical properties to warrant further development as an intravenous treatment for COVID-19.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Antiviral Agents / chemical synthesis
  • Antiviral Agents / metabolism
  • Antiviral Agents / pharmacology*
  • COVID-19 Drug Treatment
  • Catalytic Domain
  • Chlorocebus aethiops
  • Coronavirus 3C Proteases / antagonists & inhibitors*
  • Coronavirus 3C Proteases / chemistry
  • Coronavirus 3C Proteases / metabolism
  • Crystallography, X-Ray
  • Humans
  • Ketones / chemical synthesis
  • Ketones / metabolism
  • Ketones / pharmacology*
  • Protease Inhibitors / chemical synthesis
  • Protease Inhibitors / metabolism
  • Protease Inhibitors / pharmacology*
  • Protein Binding
  • SARS-CoV-2 / drug effects*
  • Vero Cells

Substances

  • Antiviral Agents
  • Ketones
  • Protease Inhibitors
  • Coronavirus 3C Proteases