Molecular characterization of CYP2B6 substrates

Abstract

CYP2B6 has not been as fully characterized at the molecular level as other members of the human cytochrome P450 family. As more widely used in vitro probes for characterizing the involvement of this enzyme in the metabolism of xenobiotics have become available, the number of molecules identified as CYP2B6 substrates has increased. In this study we have analyzed the available kinetic data generated by multiple laboratories with human recombinant expressed CYP2B6 and along with calculated molecular properties derived from the ChemSpider database, we have determined the molecular features that appear to be important for CYP2B6 substrates. In addition we have applied 2D and 3D QSAR methods to generate predictive pharmacophore and 2D models. For 28 molecules with K(m) data, the molecular weight (mean +/- SD) is 253.78+/-74.03, ACD/logP is 2.68+/-1.51, LogD(pH 5.5) is 1.51+/-1.43, LogD(pH 7.4) is 2.02+/-1.25, hydrogen bond donor (HBD) count is 0.57 +/-0.57, hydrogen bond acceptor (HBA) count is 2.57+/-1.37, rotatable bonds is 3.50+/-2.71 and total polar surface area (TPSA) is 27.63+/-19.42. A second set of 15 molecules without K(m) data possessed similar mean molecular property values. These properties are comparable to those of a set of 21 molecules used in a previous pharmacophore modeling study (Ekins et al., J Pharmacol Exp Ther 288 (1), 21-29, 1999). Only the LogD and HBD values were statistically significantly different between these different datasets. We have shown that CYP2B6 substrates are generally small hydrophobic molecules that are frequently central nervous system active, which may be important for drug discovery research.

Fig. 1

Sequence alignment of CYP2B6 and CYP2B4 (assession numbers P20813 and P00178, respectively) using ClustalW (EMBL-EBI) [84] * = identical in all sequences in the alignment; : = conserved substitutions; . = semi-conserved substitutions.

Fig. 2

Histograms of the molecular descriptor distributions of all 64 CYP2B6 substrates used in this study. A. Molecular weight (MWT), B. ACD/logP, C. LogD pH5.5, D. LogD pH 7.4, E.hydrogen bond donors (HBD), F. hydrogen bond acceptors (HBA), G. rotatable bond number (RB), H. polar surface area (PSA).

Fig. 2

Histograms of the molecular descriptor distributions of all 64 CYP2B6 substrates used in this study. A. Molecular weight (MWT), B. ACD/logP, C. LogD pH5.5, D. LogD pH 7.4, E.hydrogen bond donors (HBD), F. hydrogen bond acceptors (HBA), G. rotatable bond number (RB), H. polar surface area (PSA).

Fig. 2

Histograms of the molecular descriptor distributions of all 64 CYP2B6 substrates used in this study. A. Molecular weight (MWT), B. ACD/logP, C. LogD pH5.5, D. LogD pH 7.4, E.hydrogen bond donors (HBD), F. hydrogen bond acceptors (HBA), G. rotatable bond number (RB), H. polar surface area (PSA).

Fig. 2

Histograms of the molecular descriptor distributions of all 64 CYP2B6 substrates used in this study. A. Molecular weight (MWT), B. ACD/logP, C. LogD pH5.5, D. LogD pH 7.4, E.hydrogen bond donors (HBD), F. hydrogen bond acceptors (HBA), G. rotatable bond number (RB), H. polar surface area (PSA).

Fig. 3

A. NNK mapped to the original CYP2B6 pharmacophore, showing shape volume from 7-EFC. Note N-methyl group on left side is site of α-hydroxylation. H = hydrophobe, NBA = hydrogen bond acceptor B. Mapping of 16 of 28 substrates that conform to the 7-EFC shape. Pharmacophore shows 3 hydrophobic features (H) and one hydrogen bond acceptor (HBA) with vector. C. Phase pharmacophore with benzyloxyresorufin, A = hydrogen bond acceptor (with arrows), H = hydrophobe (sphere), R = ring aromatic (circle).