Binding free energies of inhibitors to iron porphyrin complex as a model for Cytochrome P450

Abstract

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) μM 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, ΔG inh0, is obtained from its IC(50) value. The total binding free energy (ΔG b0) of each inhibitor-heme model complex is calculated by the sum of its relative free energy (ΔG(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 ΔG b0-ΔG inh0 and ΔG(0) -ΔG inh0 plots, 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.

Current Approaches for Investigating and Predicting Cytochrome P450 3A4-Ligand Interactions

“…The binding free energies of 16 structurally diverse CYP3A4 inhibitors to the iron porphyrin model, calculated using DFT and the implicit solvation methods in water, were shown to be a good descriptor in interpreting the CYP3A4-inhibitor interaction [102]. The relative free energies in the gas phase were mainly responsible for the total binding free energies in water, although desolvation could affect the inhibitor affinity.…”

Understanding the mechanism of cytochrome P450 3A4: recent advances and remaining problems

“…Finally, it was reported recently that the inhibitor binding to CYP3A4 can be predicted fairly well based on the total binding free energies calculated for the inhibitor-heme model complexes. 67 …”

“…Determination of the CYP3A4 X-ray structures triggered a number of theoretical studies that provided deeper insights into the catalytic mechanism and substrate/inhibitor binding, and made possible a more accurate prediction of small-molecule association to CYP3A4. [59][60][61][62][63][64][65][66][67][68] The first MD simulations were conducted by Park et al 59 to clarify the roles of solvent dynamics and the active site loops in the ligand binding process and heme iron coordination. They showed that the malleability of the F-F′ loop (residues 211-218) defines the broad substrate specificity of CYP3A4, and that its complex with the inhibitor metyrapone is stabilized not only via direct coordination to the heme iron but also through a hydrogen bond between the metyrapone carbonyl oxygen and the Ser119 hydroxyl.…”

Reply to “comment on ‘binding free energies of inhibitors to iron porphyrin complex as a model for cytochrome P450’”

“…W ith regard to our article, referenced in the title above, 1 Rydberg has raised two important issues. 2 The first issue is that why only the water-assisted binding of fluconazole to ferric iron was considered in the analysis, although there are two binding modes of fluconazole with the heme iron, that is, the direct and water-assisted bindings, in the Xray structure of CYP121-fluconazole complex.…”

“…3 As described in the Introduction section of our article, 1 these two binding modes were used as the initial structures for optimization, and only the results for the water-assisted binding were included in the analysis. 1 This is why only the water-assisted binding of fluconazole to heme was considered in the analysis, although this is not explicitly described in our article. However, the former value for the direct binding is much larger compared with the observed value of 26.28 kcal/mol obtained from its IC 50 value.…”