Crystal structure of cathepsin B inhibited with CA030 at 2.0-A resolution: A basis for the design of specific epoxysuccinyl inhibitors

Biochemistry. 1995 Apr 11;34(14):4791-7. doi: 10.1021/bi00014a037.

Abstract

Crystals of cysteine protease human cathepsin B inhibited with CA030 (ethyl ester of epoxysuccinyl-Ile-Pro-OH) [Murata, M., et al. (1991) FEBS Lett. 280, 307-310; Towatari, T., et al. (1991) FEBS Lett. 280, 311-315] were isomorphous to a previous published structure of cathepsin B [Musil, D., et al. (1991) EMBO J. 10, 2321-2330]. The crystal structure of the complex was refined at 2.0-A resolution to an R-value of 0.194. CA030 is well-defined in the electron density. The Ile-Pro-OH part of CA030 mimics a substrate P1' and P2' residues. The structure thus reveals for the first time a substratelike interaction in the S1' and S2' sites of a papain-like cysteine protease. The CA030 ethyl ester group occupies the S2 site. The structure confirms the role of residues His 110 and His 111 as the receptors of a peptidic substrate C-terminal carboxylic group. The structure suggests that an epoxysuccinyl fragment can be used to extend binding into primed and nonprimed substrate binding sites of a papain-like cysteine protease.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Cathepsin B / antagonists & inhibitors
  • Cathepsin B / chemistry*
  • Crystallography, X-Ray
  • Dipeptides / metabolism
  • Dipeptides / pharmacology*
  • Drug Design
  • Leucine / analogs & derivatives
  • Leucine / chemistry
  • Molecular Sequence Data
  • Protein Conformation

Substances

  • Dipeptides
  • N-(3-ethoxycarbonyloxirane-2-carbonyl)-isoleucyl-proline
  • Cathepsin B
  • Leucine
  • E 64