title: Insight into binding mechanisms of inhibitors MKP56, MKP73, MKP86, and MKP97 to HIV-1 protease by using molecular dynamics simulation.
abstract: HIV-1 protease (PR) has been a significant target for design of potent inhibitors curing acquired immunodeficiency syndrome. Molecular dynamics simulations coupled with molecular mechanics Poisson-Boltzmann surface area method were performed to study interaction modes of four inhibitors MKP56, MKP73, MKP86, and MKP97 with PR. The results suggest that the main force controlling interactions of inhibitors with PR should be contributed by van der Waals interactions between inhibitors and PR. The cross-correlation analyses based on MD trajectories show that inhibitor binding produces significant effect on the flap dynamics of PR. Hydrogen bond analyses indicate that inhibitors can form stable hydrogen bonding interactions with the residues from the catalytic strands of PR. The contributions of separate residues to inhibitor bindings are evaluated by using residue-based free energy decomposition method and the results demonstrate that the CH-π and CH-CH interactions between the hydrophobic groups of inhibitors with residues drive the associations of inhibitors with PR. We expect that this study can provide a significant theoretical aid for design of potent inhibitors targeting PR.
authors.affiliation: a School of Science , Shandong Jianzhu University , Jinan 250101 , China.
authors.forename: Shuhua
authors.initials: S
authors.lastname: Shi
authors.affiliation: b College of Physics and Electronics , Shandong Normal University , Jinan 250014 , China.
authors.forename: Shaolong
authors.initials: S
authors.lastname: Zhang
authors.affiliation: b College of Physics and Electronics , Shandong Normal University , Jinan 250014 , China.
authors.forename: Qinggang
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D001665:Binding Sites / Q000187:drug effects; D002384:Catalysis; D024882:Drug Resistance, Viral / Q000235:genetics*; D019277:Entropy; D015658:HIV Infections / Q000188:drug therapy* / Q000235:genetics / Q000821:virology; D017320:HIV Protease Inhibitors / Q000737:chemistry* / Q000627:therapeutic use; D015497:HIV-1 / Q000737:chemistry / Q000187:drug effects* / Q000235:genetics / Q000472:pathogenicity; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D011485:Protein Binding
chemical_list: D017320:HIV Protease Inhibitors
keywords: CH–π interaction; HIV-1 protease; MM-PBSA; binding free energy; molecular dynamics simulations