title: In silico identification and crystal structure validation of caspase-3 inhibitors without a P1 aspartic acid moiety.
abstract: Using a fragment-based docking procedure, several small-molecule inhibitors of caspase-3 were identified and tested and the crystal structures of three inhibitor complexes were determined. The crystal structures revealed that one inhibitor (NSC 18508) occupies only the S1 subsite, while two other inhibitors (NSC 89167 and NSC 251810) bind only to the prime part of the substrate-binding site. One of the major conformational changes observed in all three caspase-3-inhibitor complexes is a rotation of the Tyr204 side chain, which blocks the S2 subsite. In addition, the structural variability of the residues shaping the S1-S4 as well as the S1' subsites supports an induced-fit mechanism for the binding of the inhibitors in the active site. The high-resolution crystal structures reported here provide novel insights into the architecture of the substrate-binding site, which might be useful for the design of more potent caspase inhibitors.
authors.affiliation: Department of Biochemistry, University of Zürich, Zürich, Switzerland.
authors.forename: Rajkumar
authors.initials: R
authors.lastname: Ganesan
authors.forename: Stjepan
authors.initials: S
authors.lastname: Jelakovic
authors.forename: Peer R E
authors.initials: PR
authors.lastname: Mittl
authors.forename: Amedeo
authors.initials: A
authors.lastname: Caflisch
authors.forename: Markus G
authors.initials: MG
authors.lastname: Grütter
mesh_terms: D001224:Aspartic Acid / Q000737:chemistry; D053148:Caspase 3 / Q000737:chemistry*; D061945:Caspase Inhibitors; D019295:Computational Biology; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry*; D006801:Humans; D008958:Models, Molecular; D017434:Protein Structure, Tertiary
chemical_list: D061945:Caspase Inhibitors; D004791:Enzyme Inhibitors; D001224:Aspartic Acid; C505407:CASP3 protein, human; D053148:Caspase 3