A method for identifying active site inhibitors of scission enzyme that cleaves the backbones or side groups of peptides, and for using the resultant inactivators to inhibit the target scission enzyme. Kinetic assays are employed to identify peptide substrates that tightly bind to the active site of the target protease but that are not easily cleaved. These noncleavable but tightly binding substrates are optionally structurally modified to yield inhibitory compounds with optimized properties. Additionally these substrates exhibit apparent specificity for a transition state or ground state configuration of the protease.