Molecular dynamics simulations of acylpeptide hydrolase bound to chlorpyrifosmethyl oxon and dichlorvos

• Published in: International journal of molecular sciences 2015-03, Vol.16 (3), p.6217-6234
• Main Authors: Jin, Hanyong, Zhou, Zhenhuan, Wang, Dongmei, Guan, Shanshan, Han, Weiwei
• Format: Article
• Language: English
• Subjects: acylpeptide hydrolase; Chlorpyrifos - chemistry; Chlorpyrifos - metabolism; Dichlorvos - chemistry; Dichlorvos - metabolism; docking study; Drug therapy; Molecular biology; Molecular Dynamics Simulation; organophosphorus compound; Peptide Hydrolases - chemistry; Peptide Hydrolases - metabolism; Protein Binding; Simulation
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms16036217

Acylpeptide hydrolases (APHs) catalyze the removal of N-acylated amino acids from blocked peptides. Like other prolyloligopeptidase (POP) family members, APHs are believed to be important targets for drug design. To date, the binding pose of organophosphorus (OP) compounds of APH, as well as the different OP compounds binding and inducing conformational changes in two domains, namely, α/β hydrolase and β-propeller, remain poorly understood. We report a computational study of APH bound to chlorpyrifosmethyl oxon and dichlorvos. In our docking study, Val471 and Gly368 are important residues for chlorpyrifosmethyl oxon and dichlorvos binding. Molecular dynamics simulations were also performed to explore the conformational changes between the chlorpyrifosmethyl oxon and dichlorvos bound to APH, which indicated that the structural feature of chlorpyrifosmethyl oxon binding in APH permitted partial opening of the β-propeller fold and allowed the chlorpyrifosmethyl oxon to easily enter the catalytic site. These results may facilitate the design of APH-targeting drugs with improved efficacy.