Peptide length and leaving-group sterics influence potency of peptide phosphonate protease inhibitors

Chem Biol. 2011 Jan 28;18(1):48-57. doi: 10.1016/j.chembiol.2010.11.007.


The ability to follow enzyme activity in a cellular context represents a challenging technological frontier that impacts fields ranging from disease pathogenesis to epigenetics. Activity-based probes (ABPs) label the active form of an enzyme via covalent modification of catalytic residues. Here we present an analysis of parameters influencing potency of peptide phosphonate ABPs for trypsin-fold S1A proteases, an abundant and important class of enzymes with similar substrate specificities. We find that peptide length and stability influence potency more than sequence composition and present structural evidence that steric interactions at the prime-side of the substrate-binding cleft affect potency in a protease-dependent manner. We introduce guidelines for the design of peptide phosphonate ABPs and demonstrate their utility in a live-cell labeling application that specifically targets active S1A proteases at the cell surface of cancer cells.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Catalytic Domain
  • Cell Line, Tumor
  • Drug Design
  • Humans
  • Models, Molecular
  • Organophosphonates / chemistry*
  • Peptide Hydrolases / metabolism*
  • Peptides / chemical synthesis
  • Peptides / chemistry*
  • Peptides / metabolism
  • Peptides / pharmacology*
  • Protease Inhibitors / chemical synthesis
  • Protease Inhibitors / chemistry*
  • Protease Inhibitors / metabolism
  • Protease Inhibitors / pharmacology*
  • Serine Endopeptidases / chemistry
  • Serine Endopeptidases / metabolism
  • Serine Proteases / chemistry
  • Serine Proteases / metabolism
  • Staining and Labeling
  • Structure-Activity Relationship


  • Organophosphonates
  • Peptides
  • Protease Inhibitors
  • Peptide Hydrolases
  • Serine Proteases
  • Serine Endopeptidases