Unimolecular and Bimolecular Binding System for the Prediction of CYP2D6-Mediated Metabolism

Abstract

ABSTRACT:We have developed a template system for the prediction of CYP2D6-mediated metabolism of compounds. The system is composed of two types of two-dimensional templates (templates A and B), which were generated from mutually occupied areas of typical CYP2D6 substrates. The areas of templates are expressed as hexagonal blocks for application to the two-dimensional structures of chemicals. Experiments with 93 reactions with 69 typical substrates indicated the necessity for two similar but distinct shapes for template A (A1 and A2) for optimal placement. A frequently occupied area for substrates in template A1 was defined as a trigger area in which to capture a substrate for initiation of metabolism. Another frequently occupied area was found near the site of metabolism in template B. Both frequently occupied areas are linked to a pinching area. Occupancy of substrates on two template areas is suggested to be essential for the metabolism of CYPD6 substrates. In cases of CYP2D6 substrates without simultaneous occupancy of both areas, bimolecular placement, in which two molecules are placed coordinately, is proposed. Metabolism of small molecules, including naphthalene and quinoline, became explainable with the use of this idea. Validation of this template system with the use of both good and poor CYP2D6 substrates indicated clear advantages of the present system as a tool for drug modification, in addition to enabling highly accurate estimation of the site of metabolism.

A Computational Understanding of Inter-Individual Variability in CYP2D6 Activity to Investigate the Impact of Missense Mutations on Ochratoxin A Metabolism

“…Interestingly, the atom, undergoing of the two probe substrates dextromethorphan and bufuralol, showed lower inter-atomic distances to the Fe-heme compared to OTA ( Figure 2 ). These results are consistent with previous evidence describing OTA as a minor and non optimal substrate of CYP2D6 [ 22 ]. This evidence suggests that the inter-atomic distance between the atom undergoing the metabolic reaction and the Fe-heme provides a potential discriminant to distinguish CYP2D6 major probe substrates from CYP2D6 minor substrates that are poorly or not metabolised.…”

“…In contrast, CYP2D6*14A has no metabolic activity towards either probe substrates, while CYP2D6*51 had very low metabolic activity towards bufuralol and no activity reported for dextromethorphan [ 27 ]. OTA has been previously described as a minor substrate of CYP2D6 [ 22 ], but no data have been produced yet to investigate this hypothesis, particularly for different CYP2D6 variants.…”

“…However, non-microbial carboxypeptidases have also been described to hydrolyse OTA to OTalpha, including the bovine carboxypeptidase A and the porcine ortholog carboxypeptidase B [ 15 , 19 , 20 ]. Hydroxylation on the isocoumarin portion of OTA leading to 4-(R/S)-hydroxy-OTA -and 10-OH-OTA has been described from in vitro and in vivo studies as a minor metabolic route, and CYP2D6 together with CYP2B6 have been shown to be involved in the formation of these hydroxy metabolites [ 15 , 21 , 22 , 23 , 24 ]. In addition, 4-OH-OTA has been shown to be less toxic compared to OTA [ 25 , 26 ], and different kinetic properties are also expected for 4-OH-OTA inkling different affinities transporters involved in its renal excretion/re-uptake or enterohepatic circulation.…”

Deciphering Key Interactions of Ligands with CYP3A4-Template* system

“…The resultant data of their catalyses have been accumulated for more than twentyyears. With uses of the advantages, we reconstituted the active sites of the CYP enzymes through assemblies of ligands as fused-grid Templates [3][4][5][6][7] . These Template systems have been refined with introductions of ideas of region-specific interactions and step-wise movements in the active site such as Right-side movement.…”

Prediction and Characterization of CYP3A4-mediated Metabolisms of Azole Fungicides: an Application of the Fused-grid Template* system

“…We developed prediction systems for ligand interactions of seven human CYP-forms using grid-based Templates [9][10][11][12][13][14][15][16] . These Templates are constructed with assemblies of ligand interactions and constituted as flat fused-hexagonal grids.…”