title: pH Dependence of inhibitors targeting the occluding loop of cathepsin B.
abstract: Potent and selective cathepsin B inhibitors have previously been synthesized based upon the natural product cysteine protease inhibitor E-64. X-ray crystal data indicates that these compounds interact through their free carboxylate with the positively charged histidine residues located on the prime-side of the active site within the occluding loop of cathepsin B. Herein, we examine the pH dependence of two prime-side-binding compounds. In each case there is a dramatic decrease in k(inact)/K(I) as the pH is raised from 4 to 7.8 corresponding to a single ionization of pK(a) 4.4. These results suggest that targeting of the occluding loop of cathepsin B may be a poor inhibitor design strategy if the enzyme environment has a pH greater than 5.5. However, this type of inhibitor may be a useful tool to help elucidate the role and the environment of cathepsin B in invading tumors.
authors.affiliation: Axys Pharmaceuticals Inc, 180 Kimball Way, South San Francisco, CA 94080, USA. bcathers@newbiotics.com
authors.forename: Brian E
authors.initials: BE
authors.lastname: Cathers
authors.forename: Cynthia
authors.initials: C
authors.lastname: Barrett
authors.forename: James T
authors.initials: JT
authors.lastname: Palmer
authors.forename: Robert M
authors.initials: RM
authors.lastname: Rydzewski
mesh_terms: D000595:Amino Acid Sequence; D002401:Cathepsin B / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D015853:Cysteine Proteinase Inhibitors / Q000737:chemistry* / Q000494:pharmacology*; D004151:Dipeptides / Q000737:chemistry / Q000494:pharmacology; D015195:Drug Design; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D007930:Leucine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000494:pharmacology; D008099:Liver / Q000201:enzymology; D010649:Phenylalanine / Q000031:analogs & derivatives; D010879:Piperazines / Q000737:chemistry / Q000494:pharmacology; D011485:Protein Binding; D017433:Protein Structure, Secondary; D013379:Substrate Specificity; D013450:Sulfones / Q000737:chemistry / Q000494:pharmacology; D014105:Tosyl Compounds
chemical_list: C473898:APC-5840; D015853:Cysteine Proteinase Inhibitors; D004151:Dipeptides; C473899:N-(chloroacetyl)-leucylprolin-tert-butyl ester; D010879:Piperazines; D013450:Sulfones; D014105:Tosyl Compounds; C487484:N-pip-phenylalanine-homophenylalanine-vinyl sulfone phenyl; D010649:Phenylalanine; D002401:Cathepsin B; D007930:Leucine; C024974:E 64