A noncovalent class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication

Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16119-24. doi: 10.1073/pnas.0805240105. Epub 2008 Oct 13.


We report the discovery and optimization of a potent inhibitor against the papain-like protease (PLpro) from the coronavirus that causes severe acute respiratory syndrome (SARS-CoV). This unique protease is not only responsible for processing the viral polyprotein into its functional units but is also capable of cleaving ubiquitin and ISG15 conjugates and plays a significant role in helping SARS-CoV evade the human immune system. We screened a structurally diverse library of 50,080 compounds for inhibitors of PLpro and discovered a noncovalent lead inhibitor with an IC(50) value of 20 microM, which was improved to 600 nM via synthetic optimization. The resulting compound, GRL0617, inhibited SARS-CoV viral replication in Vero E6 cells with an EC(50) of 15 microM and had no associated cytotoxicity. The X-ray structure of PLpro in complex with GRL0617 indicates that the compound has a unique mode of inhibition whereby it binds within the S4-S3 subsites of the enzyme and induces a loop closure that shuts down catalysis at the active site. These findings provide proof-of-principle that PLpro is a viable target for development of antivirals directed against SARS-CoV, and that potent noncovalent cysteine protease inhibitors can be developed with specificity directed toward pathogenic deubiquitinating enzymes without inhibiting host DUBs.

Publication types

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

MeSH terms

  • Antiviral Agents / chemistry
  • Antiviral Agents / classification
  • Antiviral Agents / metabolism
  • Antiviral Agents / pharmacology
  • Coronavirus 3C Proteases
  • Crystallography, X-Ray
  • Cysteine Endopeptidases / chemistry
  • Cysteine Endopeptidases / metabolism
  • Endopeptidases* / chemistry
  • Endopeptidases* / metabolism
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / classification
  • Enzyme Inhibitors / metabolism
  • Enzyme Inhibitors / pharmacology*
  • Models, Molecular
  • Protein Binding
  • Severe acute respiratory syndrome-related coronavirus / drug effects*
  • Severe acute respiratory syndrome-related coronavirus / physiology*
  • Substrate Specificity
  • Viral Proteins / antagonists & inhibitors*
  • Viral Proteins / chemistry
  • Viral Proteins / metabolism
  • Virus Replication / drug effects*


  • Antiviral Agents
  • Enzyme Inhibitors
  • Viral Proteins
  • Endopeptidases
  • Cysteine Endopeptidases
  • Coronavirus 3C Proteases
  • ubiquitin isopeptidase

Associated data

  • PDB/3E9S
  • PDB/RCSB049054