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Identiﬁcation of Novel Potential β-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculations
College of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, China
Center of Bioinformatics, Northwest A&F University, Yangling, Shaanxi 712100, China
School of Chemical Engineering, Dalian University of Technology, Dalian, 116012, China
Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
* Author to whom correspondence should be addressed.
Received: 7 February 2012; in revised form: 13 March 2012 / Accepted: 26 March 2012 / Published: 10 April 2012
Abstract: Chitinolytic β-N-acetyl-D-hexosaminidases, as a class of chitin hydrolysis enzyme in insects, are a potential species-specific target for developing environmentally-friendly pesticides. Until now, pesticides targeting chitinolytic β-N-acetyl-D-hexosaminidase have not been developed. This study demonstrates a combination of different theoretical methods for investigating the key structural features of this enzyme responsible for pesticide inhibition, thus allowing for the discovery of novel small molecule inhibitors. Firstly, based on the currently reported crystal structure of this protein (OfHex1.pdb), we conducted a pre-screening of a drug-like compound database with 8 × 106 compounds by using the expanded pesticide-likeness criteria, followed by docking-based screening, obtaining 5 top-ranked compounds with favorable docking conformation into OfHex1. Secondly, molecular docking and molecular dynamics simulations are performed for the five complexes and demonstrate that one main hydrophobic pocket formed by residues Trp424, Trp448 and Trp524, which is significant for stabilization of the ligand–receptor complex, and key residues Asp477 and Trp490, are respectively responsible for forming hydrogen-bonding and π–π stacking interactions with the ligands. Finally, the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) analysis indicates that van der Waals interactions are the main driving force for the inhibitor binding that agrees with the fact that the binding pocket of OfHex1 is mainly composed of hydrophobic residues. These results suggest that screening the ZINC database can maximize the identification of potential OfHex1 inhibitors and the computational protocol will be valuable for screening potential inhibitors of the binding mode, which is useful for the future rational design of novel, potent OfHex1-specific pesticides.
Keywords: β-N-acetyl-D-hexosaminidase; OfHex1; inhibitor; virtual screening; molecular dynamics; MM/PBSA
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MDPI and ACS Style
Liu, J.; Liu, M.; Yao, Y.; Wang, J.; Li, Y.; Li, G.; Wang, Y. Identiﬁcation of Novel Potential β-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculations. Int. J. Mol. Sci. 2012, 13, 4545-4563.
Liu J, Liu M, Yao Y, Wang J, Li Y, Li G, Wang Y. Identiﬁcation of Novel Potential β-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculations. International Journal of Molecular Sciences. 2012; 13(4):4545-4563.
Liu, Jianling; Liu, Mengmeng; Yao, Yao; Wang, Jinan; Li, Yan; Li, Guohui; Wang, Yonghua. 2012. "Identiﬁcation of Novel Potential β-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculations." Int. J. Mol. Sci. 13, no. 4: 4545-4563.