Origin of the stereospecificity in binding hydroxamates of α- and β-phenylalanine methylamide to thermolysin revealed by the X-ray crystallographic study

• Published in: Bioorganic & medicinal chemistry 2003-05, Vol.11 (11), p.2421-2426
• Main Authors: Kim, Seung-Jun, Kim, Dong H, Park, Jung Dae, Woo, Joo-Rang, Jin, Yonghao, Ryu, Seong Eon
• Format: Article
• Language: English
• Subjects: Amides - chemistry; Amides - metabolism; Binding Sites; Biological and medical sciences; Crystallography, X-Ray; Fundamental and applied biological sciences. Psychology; Hydroxamic Acids - chemistry; Hydroxamic Acids - metabolism; Interactions. Associations; Intermolecular phenomena; Medical sciences; Miscellaneous; Models, Molecular; Molecular biophysics; Pharmacology. Drug treatments; Phenylalanine - chemistry; Phenylalanine - metabolism; Stereoisomerism; Thermolysin - chemistry; Thermolysin - metabolism
• ISSN: 0968-0896; 1464-3391
• DOI: 10.1016/S0968-0896(03)00140-8

Optically active N-formyl- N-hydroxy-α-phenylalanine methylamide ( 1) and N-formyl- N-hydroxy-β-phenylalanine methylamide ( 2) were evaluated as inhibitors for thermolysin (TLN) to find that while the d-form is more potent than its enantiomer in the case of the hydroxamate of α-Phe-NHMe, in the inhibition with hydroxamate of β-Phe-NHMe, the l-isomer ( K i=1.66±0.05 μM) is more effective than its enantiomer. In order to shed light on the stereochemical preference observed in the inhibitions, X-ray crystallographic analyses of the crystalline TLN· d- 1 and TLN· l- 2 complexes were performed to the resolution of 2.1 Å. While l- 2 binds TLN like substrate does with its benzyl aromatic ring occupying the S 1′ pocket, the electron density in the S 1′ pocket in the complex of TLN· d- 1 is weak and could best be accounted for by the methylcarbamoyl moiety. For both inhibitors, the hydroxamate moiety coordinates the active site zinc ion in a bidentate fashion. Graphic