Structural basis for development of cathepsin B-specific noncovalent-type inhibitor: crystal structure of cathepsin B–E64c complex

In order to elucidate the substrate specificity of the Sn subsites (n=1–3) of cathepsin B, its crystal structure inhibited by E64c [(+)-(2S,3S)-3-(1-[N-(3-methylbutyl)amino]-leucylcarbonyl)oxirane-2-carboxylic acid] was analyzed by the X-ray diffraction method. Iterative manual rebuilding and convenient conjugate refinement of structure decreased R- and free R-factors to 19.7% and to 23.9%, respectively, where 130 water molecules were included for the refinement using 14,759 independent reflections from 10 to 2.3 Å resolution. The epoxy carbonyl carbon of E64c was covalently bonded to the Cys²⁹ S^γ atom and the remaining parts were located at Sn subsites (n=1–3). The substrate specificity of these subsites was characterized based on their interactions with the inhibitor. Base on these structural data, we developed a novel cathepsin B-specific noncovalent-type inhibitor, which may bind to S2′–S3. The molecular design of possessing structural elements of both CA074 and E64c, assisted by energy minimization and molecular dynamics (MD) simulation, may lead to a new lead noncovalent-type inhibitor.