Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for Severe Acute Respiratory Syndrome Coronavirus 2 3CL Protease

J Med Chem. 2022 Oct 27;65(20):13852-13865. doi: 10.1021/acs.jmedchem.2c01081. Epub 2022 Oct 13.


The coronavirus disease 2019 (COVID-19) pandemic has necessitated the development of antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 3C-like protease (3CLpro) is a promising target for COVID-19 treatment. Here, we report a new class of covalent inhibitors of 3CLpro that possess chlorofluoroacetamide (CFA) as a cysteine-reactive warhead. Based on an aza-peptide scaffold, we synthesized a series of CFA derivatives in enantiopure form and evaluated their biochemical efficiency. The data revealed that 8a (YH-6) with the R configuration at the CFA unit strongly blocks SARS-CoV-2 replication in infected cells, and its potency is comparable to that of nirmatrelvir. X-ray structural analysis showed that YH-6 formed a covalent bond with Cys145 at the catalytic center of 3CLpro. The strong antiviral activity and favorable pharmacokinetic properties of YH-6 suggest its potential as a lead compound for the treatment of COVID-19.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antiviral Agents / chemistry
  • Antiviral Agents / pharmacology
  • Antiviral Agents / therapeutic use
  • COVID-19 Drug Treatment*
  • Coronavirus 3C Proteases
  • Cysteine
  • Cysteine Endopeptidases / chemistry
  • Humans
  • Peptide Hydrolases
  • Peptides / chemistry
  • Protease Inhibitors / chemistry
  • Protease Inhibitors / pharmacology
  • Protease Inhibitors / therapeutic use
  • SARS-CoV-2*


  • Coronavirus 3C Proteases
  • Peptide Hydrolases
  • Protease Inhibitors
  • Cysteine
  • Cysteine Endopeptidases
  • Antiviral Agents
  • Peptides