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Int. J. Mol. Sci. 2013, 14(12), 24514-24530; doi:10.3390/ijms141224514
Article

CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations

1
, 1,†
, 2
 and 1,*
Received: 1 November 2013; in revised form: 28 November 2013 / Accepted: 4 December 2013 / Published: 17 December 2013
(This article belongs to the Special Issue Xenobiotic Metabolism)
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Abstract: Because of the large flexibility and malleability of Cytochrome P450 enzymes (CYPs), in silico prediction of CYP binding affinities to drugs and other xenobiotic compounds is a true challenge. In the current work, we use an iterative linear interaction energy (LIE) approach to compute CYP binding affinities from molecular dynamics (MD) simulation. In order to improve sampling of conformational space, we combine results from simulations starting with different relevant protein-ligand geometries. For calculated binding free energies of a set of thiourea compounds binding to the flexible CYP 2D6 isoform, improved correlation with experiment was obtained by combining results of MD runs starting from distinct protein conformations and ligand-binding orientations. This accuracy was obtained from relatively short MD simulations, which makes our approach computationally attractive for automated calculations of ligand-binding affinities to flexible proteins such as CYPs.
Keywords: binding free energies; LIE method; CYP 2D6; thiourea ligands binding free energies; LIE method; CYP 2D6; thiourea ligands
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Perić-Hassler, L.; Stjernschantz, E.; Oostenbrink, C.; Geerke, D.P. CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations. Int. J. Mol. Sci. 2013, 14, 24514-24530.

AMA Style

Perić-Hassler L, Stjernschantz E, Oostenbrink C, Geerke DP. CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations. International Journal of Molecular Sciences. 2013; 14(12):24514-24530.

Chicago/Turabian Style

Perić-Hassler, Lovorka; Stjernschantz, Eva; Oostenbrink, Chris; Geerke, Daan P. 2013. "CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations." Int. J. Mol. Sci. 14, no. 12: 24514-24530.


Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert