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Open AccessArticle

A Combined Molecular Docking/Dynamics Approach to Probe the Binding Mode of Cancer Drugs with Cytochrome P450 3A4

Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
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Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Didier Astruc
Molecules 2015, 20(8), 14915-14935; https://doi.org/10.3390/molecules200814915
Received: 8 July 2015 / Revised: 11 August 2015 / Accepted: 12 August 2015 / Published: 14 August 2015
(This article belongs to the Collection Nanomedicine)
Cytarabine, daunorubicin, doxorubicin and vincristine are clinically used for combinatorial therapies of cancers in different combinations. However, the knowledge about the interaction of these drugs with the metabolizing enzyme cytochrome P450 is limited. Therefore, we utilized computational methods to predict and assess the drug-binding modes. In this study, we performed docking, MD simulations and free energy landscape analysis to understand the drug-enzyme interactions, protein domain motions and the most populated free energy minimum conformations of the docked protein-drug complexes, respectively. The outcome of docking and MD simulations predicted the productive, as well as the non-productive binding modes of the selected drugs. Based on these interaction studies, we observed that S119, R212 and R372 are the major drug-binding residues in CYP3A4. The molecular mechanics Poisson–Boltzmann surface area analysis revealed the dominance of hydrophobic forces in the CYP3A4-drug association. Further analyses predicted the residues that may contain favorable drug-specific interactions. The probable binding modes of the cancer drugs from this study may extend the knowledge of the protein-drug interaction and pave the way to design analogs with reduced toxicity. In addition, they also provide valuable insights into the metabolism of the cancer drugs. View Full-Text
Keywords: CYP450; drug metabolism; docking; molecular dynamics simulation CYP450; drug metabolism; docking; molecular dynamics simulation
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Panneerselvam, S.; Yesudhas, D.; Durai, P.; Anwar, M.A.; Gosu, V.; Choi, S. A Combined Molecular Docking/Dynamics Approach to Probe the Binding Mode of Cancer Drugs with Cytochrome P450 3A4. Molecules 2015, 20, 14915-14935.

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