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Insight into Interaction Mechanism of the Inhibitor pDI6W with MDM2 Based on Molecular Dynamics

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