Substrate specificity profiling and identification of a new class of inhibitor for the major protease of the SARS coronavirus

Biochemistry. 2007 Jul 31;46(30):8744-52. doi: 10.1021/bi0621415. Epub 2007 Jul 3.


Severe acute respiratory syndrome (SARS) is an emerging infectious disease associated with a high rate of mortality. The SARS-associated coronavirus (SARS-CoV) has been identified as the etiological agent of the disease. Although public health procedures have been effective in combating the spread of SARS, concern remains about the possibility of a recurrence. Various approaches are being pursued for the development of efficacious therapeutics. One promising approach is to develop small molecule inhibitors of the essential major polyprotein processing protease 3Clpro. Here we report a complete description of the tetrapeptide substrate specificity of 3Clpro using fully degenerate peptide libraries consisting of all 160,000 possible naturally occurring tetrapeptides. The substrate specificity data show the expected P1-Gln P2-Leu specificity and elucidate a novel preference for P1-His containing substrates equal to the expected preference for P1-Gln. These data were then used to develop optimal substrates for a high-throughput screen of a 2000 compound small-molecule inhibitor library consisting of known cysteine protease inhibitor scaffolds. We also report the 1.8 A X-ray crystal structure of 3Clpro bound to an irreversible inhibitor. This inhibitor, an alpha,beta-epoxyketone, inhibits 3Clpro with a k3/Ki of 0.002 microM(-1) s(-1) in a mode consistent with the substrate specificity data. Finally, we report the successful rational improvement of this scaffold with second generation inhibitors. These data provide the foundation for a rational small-molecule inhibitor design effort based upon the inhibitor scaffold identified, the crystal structure of the complex, and a more complete understanding of P1-P4 substrate specificity.

Publication types

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

MeSH terms

  • Amino Acid Substitution
  • Animals
  • Antiviral Agents / chemistry
  • Antiviral Agents / isolation & purification*
  • Antiviral Agents / metabolism
  • Antiviral Agents / pharmacology*
  • Catalytic Domain / drug effects
  • Chlorocebus aethiops
  • Coronavirus 3C Proteases
  • Crystallography, X-Ray
  • Cysteine Endopeptidases / chemistry
  • Cysteine Proteinase Inhibitors / chemistry
  • Cysteine Proteinase Inhibitors / classification
  • Cysteine Proteinase Inhibitors / pharmacology*
  • Dipeptides / chemistry
  • Dipeptides / isolation & purification
  • Dipeptides / metabolism
  • Dipeptides / pharmacology*
  • Epoxy Compounds / chemistry
  • Epoxy Compounds / isolation & purification
  • Epoxy Compounds / metabolism
  • Epoxy Compounds / pharmacology*
  • Models, Molecular
  • Oligopeptides / chemistry
  • Oligopeptides / isolation & purification
  • Oligopeptides / metabolism
  • Oligopeptides / pharmacology*
  • Peptide Library
  • Protein Structure, Tertiary
  • Severe acute respiratory syndrome-related coronavirus / drug effects
  • Severe acute respiratory syndrome-related coronavirus / enzymology*
  • Structure-Activity Relationship
  • Substrate Specificity
  • Vero Cells
  • Viral Proteins / antagonists & inhibitors*
  • Viral Proteins / chemistry
  • Virus Replication / drug effects


  • Antiviral Agents
  • Cysteine Proteinase Inhibitors
  • Dipeptides
  • Epoxy Compounds
  • Oligopeptides
  • Peptide Library
  • Viral Proteins
  • WRR 182
  • WRR 183
  • WRR 495
  • Cysteine Endopeptidases
  • Coronavirus 3C Proteases

Associated data

  • PDB/2OP9