IDSite: An accurate approach to predict P450-mediated drug metabolism

Abstract

Accurate prediction of drug metabolism is crucial for drug design. Since a large majority of drugs metabolism involves P450 enzymes, we herein describe a computational approach, IDSite, to predict P450-mediated drug metabolism. To model induced-fit effects, IDSite samples the conformational space with flexible docking in Glide followed by two refinement stages using the Protein Local Optimization Program (PLOP). Sites of metabolism (SOMs) are predicted according to a physical-based score that evaluates the potential of atoms to react with the catalytic iron center. As a preliminary test, we present in this paper the prediction of hydroxylation and O-dealkylation sites mediated by CYP2D6 using two different models: a physical-based simulation model, and a modification of this model in which a small number of parameters are fit to a training set. Without fitting any parameters to experimental data, the Physical IDSite scoring recovers 83% of the experimental observations for 56 compounds with a very low false positive rate. With only 4 fitted parameters, the Fitted IDSite was trained with the subset of 36 compounds and successfully applied to the other 20 compounds, recovering 94% of the experimental observations with high sensitivity and specificity for both sets.

Figure 1

IDSite workflow

Figure 2

Definition of the binding box (yellow cube) and the positional constraint (yellow dotted sphere) in IDSite for CYP2D6.

Figure 3

Constraints applied to the heme region in the first refinement stage. The ferryl oxygen is a “dummy” atom (1.6 Å above the heme iron), only used to define the constraints in the IDSite calculations. (a) Constraints for sp³ carbons. (b) Constraints for sp² carbons.

Figure 4

Constraints applied to the heme region in the second refinement stage. The ferryl oxygen is a “dummy” atom (1.6 Å above the heme iron), only used to define the constraints in the IDSite calculations. (a) Constraints for sp³ carbons. (b) Constraints for sp² carbons.

Figure 5

Constraints applied to the salt bridge region of CYP2D6 in the first refinement stage.

Figure 6

Constraints applied to the salt bridge region of CYP2D6 in the second refinement stage.

Figure 7

Correlation between the intrinsic reactivities calculated with the methoxy radical model and the heme model (17 sites from selected 9 fragment compounds, details are shown in the supporting information).

Figure 8

IDSite predicted results for the training set.

Figure 8

IDSite predicted results for the training set.

Figure 8

IDSite predicted results for the training set.

Figure 9

IDSite predicted results for the test set.

Figure 9

IDSite predicted results for the test set.

Figure 10

(A) ROC curves comparing the full IDSite method to the reduced methods. (B) ROC curves superimposed on the results of Sheridan et al.

Figure 11

The energy and distance (constrained atom to the ferryl oxygen) changes during the MCM simulation during the first (A) and the second (B) refinement stages for 4-methoxyaphetamine.

Figure 12

The energy and distance (constrained atom to the ferryl oxygen) changes during the MCM simulation during the first (A) and the second (B) refinement stages for dextromethorphan.

Figure 13

The energy and distance (constrained atom to the ferryl oxygen) changes during the MCM simulation during the first (A) and the second (B) refinement stages for fluperlapine.

Figure 14

Illustration of the induced-fit effects modeled by IDSite. Cyan-white-red scheme is used to show the side chains from the least changed to the most changed, defined as the maximum mean absolute dihedral angle change for each residue.

Figure 15

(A) The lowest energy pose in the second refinement stage for 4-methoxyaphetamine. Orange sphere = “dummy” ferryl oxygen, green sphere = experimental and predicted SOM. (B) Comparison of side chains important for induced-fit effects. Crystal structure (green, PDBID: 2F9Q) minimized with the VSGB 2.0 model and superimposed onto the lowest energy pose with 4-methoxyamphetamine (salmon). Large dihedral changes are seen for Asp301 (Δchi2, 121°), Met374 (Δchi3, 114°), and Phe483 (Δchi1, 60°).

Figure 16

(A) The lowest energy pose in the second refinement stage for fluperlapine. Orange sphere = “dummy” ferryl oxygen, green sphere = experimental and predicted SOM. (B) Comparison of side chains important for induced fit effects. Crystal structure (green, PDBID: 2F9Q) minimized with the VSGB 2.0 model and superimposed onto the lowest energy pose with Fluperlapine (salmon). Large dihedral changes are seen for Phe120 (Δchi2, 73°), Glu216 (Δchi1, 60°), Asp301 (Δchi2, 64°), Met374 (Δchi3, 105°), and Phe483 (Δchi2, 94°).

Figure 17

(A) The lowest energy poses in the second refinement stage for metoprolol benzylic hydroxylation. (B) Comparison of side chains important for induced fit effects for metoprolol benzylic hydroxylation. (C) The lowest energy poses in the second refinement stage for metoprolol O-dealkylation. (D) Comparison of side chains important for induced fit effects for metoprolol O-dealkylation. For (A), (C) orange spheres = “dummy” ferryl oxygen, green spheres = experimental and predicted SOMs. For (B), (D) crystal structure (green, PDBID: 2F9Q) minimized with the VSGB 2.0 model and superimposed onto the lowest energy poses with metoprolol (salmon). For benzylic hydroxylation, large dihedral changes are seen for Glu216 (Δchi1, 60°), Asp301 (Δchi2, 66°), Met374 (Δchi3, 112°), and Phe483 (Δchi1, 40°); for O-dealkylation, large dihedral changes are seen for Phe120 (Δchi2, 67°), Glu216 (Δchi2, 50°), and Phe483 (Δchi2, 194°)

Figure 18

(A) The lowest energy pose in the second refinement stage for brofaromine. Orange sphere = “dummy” ferryl oxygen, green sphere = experimental and predicted SOM. (B) Intrinsic reactivities (red) for each site and the relative energy (blue) of the poses with the corresponding site constrained to the ferryl oxygen. The SOM observed experimentally is marked with a green circle.

Figure 19

(A) The lowest energy pose in the second refinement stage for nortriptyline. Orange sphere = “dummy” ferryl oxygen, green sphere = experimental and predicted SOM. (B) Intrinsic reactivities (red) for each site and the relative energy (blue) of the poses with the corresponding site constrained to the ferryl oxygen. The SOM observed experimentally is marked with a green circle.

Figure 20

The lowest energy pose in the second refinement stage for methoxyphenamine. Orange sphere = “dummy” ferryl oxygen, green sphere = experimental and predicted SOM. (A) Aromatic hydroxylation. (B) O-demethylation. (C) Intrinsic reactivities (red) for each site and the relative energy (blue) of the poses with the corresponding site constrained to the ferryl oxygen. The SOM observed experimentally is marked with a green circle.