An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 Mpro inhibitor

Cell Chem Biol. 2021 Dec 16;28(12):1795-1806.e5. doi: 10.1016/j.chembiol.2021.05.018. Epub 2021 Jun 25.


Designing covalent inhibitors is increasingly important, although it remains challenging. Here, we present covalentizer, a computational pipeline for identifying irreversible inhibitors based on structures of targets with non-covalent binders. Through covalent docking of tailored focused libraries, we identify candidates that can bind covalently to a nearby cysteine while preserving the interactions of the original molecule. We found ∼11,000 cysteines proximal to a ligand across 8,386 complexes in the PDB. Of these, the protocol identified 1,553 structures with covalent predictions. In a prospective evaluation, five out of nine predicted covalent kinase inhibitors showed half-maximal inhibitory concentration (IC50) values between 155 nM and 4.5 μM. Application against an existing SARS-CoV Mpro reversible inhibitor led to an acrylamide inhibitor series with low micromolar IC50 values against SARS-CoV-2 Mpro. The docking was validated by 12 co-crystal structures. Together these examples hint at the vast number of covalent inhibitors accessible through our protocol.

Keywords: COVID-19; DOCKovalent; M(pro); SARS-CoV-2; computer-aided drug discovery; covalent docking; covalent inhibitors; irreversible inhibitors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acrylamide / chemistry
  • Acrylamide / metabolism
  • Binding Sites
  • COVID-19 / pathology
  • COVID-19 / virology
  • Catalytic Domain
  • Computational Biology / methods
  • Databases, Protein
  • Drug Design*
  • Humans
  • Inhibitory Concentration 50
  • Molecular Docking Simulation
  • Protein Kinase Inhibitors / chemistry*
  • Protein Kinase Inhibitors / metabolism
  • SARS-CoV-2 / enzymology*
  • SARS-CoV-2 / isolation & purification
  • Viral Matrix Proteins / antagonists & inhibitors*
  • Viral Matrix Proteins / metabolism


  • Protein Kinase Inhibitors
  • Viral Matrix Proteins
  • membrane protein, SARS-CoV-2
  • Acrylamide