Insight into Interaction Mechanism of the Inhibitor pDI6W with MDM2 Based on Molecular Dynamics
Year: 2013
Author: Jianzhong Chen, Zhi-Qiang Liang, Qing-Gang Zhang, Xiao-Yang Liu, Wei Wang, Jin-Qing Liu
Journal of Atomic and Molecular Sciences, Vol. 4 (2013), Iss. 3 : pp. 225–234
Abstract
The p53-MDM2 interaction has been an important target of drug design curing cancers. In this work, Molecular dynamics (MD) simulation coupled with molecular mechanics/Poisson Boltzmann surface area method (MM-PBSA) is performed to calculate binding free energy of peptide inhibitor pDI6W to MDM2. The results show that van der Waals energy is the dominant factor of the pDI6W-MDM2 interaction. Cross-correlation matrix calculated suggests that the main motion of the residues in MMDM2 induced by the inhibitor binding is anti-correlation motion. The calculations of residue-residue interactions between pDI6W and MDM2 not only prove that five residues Phe19’, Trp22’, Trp23’, Leu26’ and Thr27’ from pDI6W can produce strong interactions with MDM2, but also show that $CH$-$π,$ $CH$-$CH$ and $π$−$π$ interactions drive the binding of pDI6W in the hydrophobic cleft of MDM2. This study can provide theoretical helps for anti-cancer drug designs.
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Journal Article Details
Publisher Name: Global Science Press
Language: English
DOI: https://doi.org/10.4208/jmas.063012.072912a
Journal of Atomic and Molecular Sciences, Vol. 4 (2013), Iss. 3 : pp. 225–234
Published online: 2013-01
AMS Subject Headings: Global Science Press
Copyright: COPYRIGHT: © Global Science Press
Pages: 10
Keywords: molecular dynamics simulation cross-correlation matrix p53-MDM2 interaction binding free energy MM-PBSA.
Author Details
Jianzhong Chen Email
Zhi-Qiang Liang Email
Qing-Gang Zhang Email
Xiao-Yang Liu Email
Wei Wang Email
Jin-Qing Liu Email