Abstract
Aminopeptidases remove the N-terminal amino acids from proteins by hydrolysis. Previously we synthesized an aminopeptidase mimic [Zn2(bomp)(OCOCH3)2]BPh4 [bomp− = 2,6-bis[bis(2-methoxyethyl)aminomethyl]-4-methylphenolate] and reported that the aminopeptidase mimic hydrolyzed L-leucine-p-nitroanilide as a substrate. Although the structure of the aminopeptidase mimic was determined by single-crystal X-ray diffraction method, the structure of the substrate incorporation mode (how the substrate was incorporated) was not clarified. Therefore, in this study, we investigate the substrate incorporation mode using the technique of conformational analysis based on the Density Functional Theory (DFT). We have found an efficient incorporation mode for the aminopeptidase-like reaction. In the structure the substrate is incorporated in its best conformation, and the Zn-OH nucleophile is very close to the substrate. Moreover, one of the chelating arms of the ligand (bomp−) is hydrogen-bonded to the Zn-OH nucleophile, so the arm is expected to work as a general base catalyst capable of enhancing the Zn-OH nucleophile. Furthermore, the other zinc(II)ion is expected to work as a general acid catalyst capable of enhancing the electrophilicity of the carbonyl carbon on the substrate. We have concluded that the aminopeptidase activity is expected to be increased if the ratio of the efficient substrate incorporation mode is increased.
