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Binding free energies of inhibitors to iron porphyrin complex as a model for Cytochrome P450
Author(s) -
Lee Joo Yun,
Kang Nam Sook,
Kang Young Kee
Publication year - 2012
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.22009
Subject(s) - chemistry , solvation , heme , density functional theory , cytochrome p450 , stereochemistry , porphyrin , binding energy , cytochrome , hemeprotein , hydantoin , computational chemistry , enzyme , organic chemistry , molecule , physics , nuclear physics
The binding free energies of the inhibitor‐heme model complexes are calculated using the density functional methods and the implicit solvation models in water, where the 16 structurally diverse compounds with a spectrum of IC 50 values from 0.05 (clotrimazole) to 1000 (piroxicam) μ M are chosen as inhibitors for Cytochrome P450 3A4 (CYP3A4). CYP3A4 is the most predominant constituent of the human hepatic CYP enzymes that play a role in metabolizing structurally diverse xenobiotics. The observed free energy change for each inhibitory binding, Δ G inh 0 , is obtained from its IC 50 value. The total binding free energy (Δ G b 0 ) of each inhibitor‐heme model complex is calculated by the sum of its relative free energy (Δ G 0 ) in the gas phase and solvation free energy to the water–heme model complex. The UB3LYP/LanL2DZ level of theory provides the correct relative stabilities of the high‐ and low‐spin states for the penta‐ and hexa‐coordinated ferric complexes, respectively. The optimized distances of the inhibitor nitrogen (or water oxygen) and the methyl mercaptide S to the ferric iron of the inhibitor‐heme model complexes at the same level of theory are consistent with the values of the corresponding X‐ray structures, except for the econazole complex. The correlation coefficient r 2 values of 0.91 and 0.75 are obtained from the Δ G b 0 −Δ G inh 0and Δ G 0 −Δ G inh 0plots, respectively, at the UM06/LanL2DZ:CPCM_UB3LYP/LanL2DZ//UB3LYP/LanL2DZ level of theory in water. This indicates that the total binding free energies calculated for the inhibitor‐heme model complexes can be a good descriptor in interpreting the inhibitor binding to CYP3A4 and the relative free energies in the gas phase are mainly responsible for the total binding free energies in water, although the desolvation can be a factor to affect the binding affinity of the inhibitors to CYP3A4. From the theozyme analysis of the X‐ray structures for ketoconazole‐ and metyrapone‐CYP3A4 complexes, the interaction free energy of the neighboring residues with each inhibitor in the active site is calculated to be about −3 kcal mol −1 in water, whose the interaction energy and the desolvation free energy change are about −5 and 2 kcal mol −1 , respectively. © 2011 Wiley Periodicals, Inc. Biopolymers 97: 219–228, 2012.