DICP OpenIR
Subject Area物理化学
Identification of Novel Potential beta-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculations
Liu, Jianling2; Liu, Mengmeng1,2; Yao, Yao1; Wang, Jinan1; Li, Yan3; Li, Guohui4; Wang, Yonghua1,5,6; WangYonghua
KeywordBeta-n-acetyl-d-hexosaminidase Ofhex1 Inhibitor Virtual Screening Molecular Dynamics Mm/pbsa
Source PublicationINTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
2012-04-01
ISSN1661-6596
DOI10.3390/ijms13044545
Volume13Issue:4Pages:4545-4563
Indexed BySCI
SubtypeArticle
Department11
Funding Project1106
Contribution Rank4,6
WOS HeadingsScience & Technology ; Physical Sciences
WOS SubjectChemistry, Multidisciplinary
WOS Research AreaChemistry
WOS KeywordAMBER FORCE-FIELD ; CHITINASE INHIBITOR ; AUTOMATED DOCKING ; BINDING ; DEGRADATION ; DERIVATIVES ; AFFINITIES ; MECHANICS ; LIGANDS ; ARGIFIN
AbstractChitinolytic beta-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 beta-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 x 10(6) 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 pi-pi 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.
Language英语
WOS IDWOS:000303454700035
Citation statistics
Cited Times:11[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://cas-ir.dicp.ac.cn/handle/321008/118178
Collection中国科学院大连化学物理研究所
Corresponding AuthorWangYonghua
Affiliation1.NW A&F Univ, Ctr Bioinformat, Yangling 712100, Shaanxi, Peoples R China
2.NW Univ Xian, Coll Life Sci, Xian 710069, Shaanxi, Peoples R China
3.Dalian Univ Technol, Sch Chem Engn, Dalian 116012, Peoples R China
4.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Lab Mol Modeling & Design, Dalian 116023, Peoples R China
5.NW A&F Univ, Coll Plant Protect, Yangling 712100, Peoples R China
6.NW A&F Univ, State Key Lab Crop Stress Biol Arid Areas, Yangling 712100, Peoples R China
Recommended Citation
GB/T 7714
Liu, Jianling,Liu, Mengmeng,Yao, Yao,et al. Identification of Novel Potential beta-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculations[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2012,13(4):4545-4563.
APA Liu, Jianling.,Liu, Mengmeng.,Yao, Yao.,Wang, Jinan.,Li, Yan.,...&WangYonghua.(2012).Identification of Novel Potential beta-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculations.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,13(4),4545-4563.
MLA Liu, Jianling,et al."Identification of Novel Potential beta-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculations".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 13.4(2012):4545-4563.
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