Exploration Of The Chlorpyirfosmethyl Oxon Escape Pathway From Acylpeptide Hydrolases Using Steered Molecular Dynamics Simulations

Acylpeptide hydrolases (APH) catalyze the removal of N-acylated amino acidsfrom blocked peptides.APH is significantly more sensitive thanacetylcholinesterase， a target of Alzheimer’s disease, to inhibition byorganophosphorus (OP) compounds. To date, the binding pose of OP compounds ofAPH, as well as the different OP compounds binding and inducing conformationalchanges in two domains, namely, α/β hydrolase and β-propeller, the mainunbindingpathway and the residues around the pathways,remain poorly understood.Here, we report a computational study of APH bound to chlorpyrifosmethyl oxonand dichlorvos. Structural interaction fingerprintanalysis was used to predict thebinding pose of the OP compounds of APH. Results indicated that Phe485may be animportant residue for the binding of OP compounds. Molecular dynamics（MD）simulations were also performed to explore the conformational changes between thechlorpyrifosmethyl oxon and dichlorvos bound to APH, which indicated that thestructural feature of chlorpyrifosmethyl oxon binding in APH permittedpartialopening of theβ-propeller fold and α/β hydrolase then allowedchlorpyrifosmethyl oxon to easily enter the catalytic site.With the two APH pathways previously proposed by experimental data and usingCAVER3.0to analyse the trajectory from the Molecular dynamics simulation ofAPH,finally, we identified P1and P2are the two potential pathways for substrate tothe active site of APH.With an estimated relative importance of P1> P2for its sizeand the bottleneck residues obtained by the analysis of the MDtrajectory usingCAVER3.0. In addition, we make an exploration of the chlorpyrifosmethyl oxonescape pathway using steered molecular dynamics(SMD) simulations to identify theoptimal route for substrate. We apply SMD simulations to identify potential escaperoutes of chlorpyrifos from hydrolase hydrophobic cavities in the APH-inhibitorcomplex. We identify the major pathway, P2, using SMD simulations, and Arg526,Glu88, Gly86, and Asn65are identified as important residues for the ligand leavingvia P2. Our results provide a reliable theoretical clues for the design of more effectivedrugs to APH-targeting, as well as a better understanding of the selective of inhibitorsfor APH from POP family.