X-ray structural and biological evaluation of a series of potent and highly selective inhibitors of human coronavirus papain-like proteases

J Med Chem. 2014 Mar 27;57(6):2393-412. doi: 10.1021/jm401712t. Epub 2014 Mar 14.


Structure-guided design was used to generate a series of noncovalent inhibitors with nanomolar potency against the papain-like protease (PLpro) from the SARS coronavirus (CoV). A number of inhibitors exhibit antiviral activity against SARS-CoV infected Vero E6 cells and broadened specificity toward the homologous PLP2 enzyme from the human coronavirus NL63. Selectivity and cytotoxicity studies established a more than 100-fold preference for the coronaviral enzyme over homologous human deubiquitinating enzymes (DUBs), and no significant cytotoxicity in Vero E6 and HEK293 cell lines is observed. X-ray structural analyses of inhibitor-bound crystal structures revealed subtle differences between binding modes of the initial benzodioxolane lead (15g) and the most potent analogues 3k and 3j, featuring a monofluoro substitution at para and meta positions of the benzyl ring, respectively. Finally, the less lipophilic bis(amide) 3e and methoxypyridine 5c exhibit significantly improved metabolic stability and are viable candidates for advancing to in vivo studies.

Publication types

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

MeSH terms

  • Animals
  • Antiviral Agents / chemical synthesis*
  • Antiviral Agents / metabolism
  • Antiviral Agents / pharmacology*
  • Cell Survival / drug effects
  • Chlorocebus aethiops
  • Coronavirus / drug effects
  • Coronavirus / enzymology*
  • Cysteine Proteinase Inhibitors / chemical synthesis
  • Cysteine Proteinase Inhibitors / pharmacology
  • Humans
  • Indicators and Reagents
  • Molecular Conformation
  • Mutagenesis / drug effects
  • Papain / chemistry*
  • Peptide Hydrolases / chemistry*
  • Peptide Hydrolases / metabolism
  • Phospholipase A2 Inhibitors / chemical synthesis
  • Phospholipase A2 Inhibitors / pharmacology
  • Protein Binding
  • SARS Virus / drug effects
  • SARS Virus / enzymology
  • Structure-Activity Relationship
  • Vero Cells
  • X-Ray Diffraction


  • Antiviral Agents
  • Cysteine Proteinase Inhibitors
  • Indicators and Reagents
  • Phospholipase A2 Inhibitors
  • Peptide Hydrolases
  • Papain

Associated data

  • PDB/4OVZ
  • PDB/4OW0