The Binding Mode Prediction and Similar Ligand Potency in the Active Site of Vitamin D Receptor with QM / MM Interaction, MESP , and MD Simulation
作者: Nagamani SelvaramanSaravana Kumar SelvamKarthikeyan Muthusamy
作者单位: 1Pharmacogenomics and CADD Lab Department of Bioinformatics Alagappa University Karaikudi Tamil Nadu 630 004 India
刊名: Chemical Biology & Drug Design, 2016, Vol.88 (2), pp.272-280
来源数据库: Wiley Journal
DOI: 10.1111/cbdd.12754
关键词: distinct ligand potencynon‐secosteroidal ligandsQM / MM studiesvitamin D receptor
原始语种摘要: Non‐secosteroidal ligands are well‐known vitamin D receptor (VDR) agonists. In this study, we described a combined QM / MM to define the protein–ligand interaction energy a strong positive correlation in both QM – MM interaction energy and binding free energy against the biological activity. The molecular dynamics simulation study was performed, and specific interactions were extensively studied. The molecular docking results and surface analysis shed light on steric and electrostatic complementarities of these non‐secosteroidal ligands to VDR . Finally, the drug likeness properties were also calculated and found within the acceptable range. The results show that bulky group substitutions in side chain decrease the VDR activity, whereas a small substitution increased it. Functional...
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