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 A resolution. The epoxy carbonyl carbon of E64c was covalently bonded to the Cys(29) S(gamma) 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.
Yamamoto
Atsushi
A
Department of Physical Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
Tomoo
Koji
K
Matsugi
Ken-ichi
K
Hara
Tadaoki
T
In
Yasuko
Y
Murata
Mitsuo
M
Kitamura
Kunihiro
K
Ishida
Toshimasa
T
D000818:Animals; D002401:Cathepsin B / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism; D002417:Cattle; D018360:Crystallography, X-Ray; D015853:Cysteine Proteinase Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D004151:Dipeptides / Q000737:chemistry / Q000494:pharmacology; D015195:Drug Design; D066298:In Vitro Techniques; D007930:Leucine / Q000031:analogs & derivatives* / Q000737:chemistry* / Q000494:pharmacology; D046911:Macromolecular Substances; D008958:Models, Molecular; D011487:Protein Conformation; D055672:Static Electricity; D013379:Substrate Specificity; D013816:Thermodynamics
D015853:Cysteine Proteinase Inhibitors; D004151:Dipeptides; D046911:Macromolecular Substances; C068250:N-(3-propylcarbamoyloxirane-2-carbonyl)-isoleucyl-proline; C032425:N-(N-(3-carboxyoxirane-2-carbonyl)leucyl)isoamylamine; D002401:Cathepsin B; D007930:Leucine