Comprehensive characterization of cytochrome P450 isozyme selectivity across chemical libraries

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The cytochrome P450 (CYP) gene family catalyzes drug metabolism and bioactivation and is therefore relevant to drug development. We determined potency values for 17,143 compounds against five recombinant CYP isozymes (1A2, 2C9, 2C19, 2D6 and 3A4) using an in vitro bioluminescent assay. The compounds included libraries of US Food and Drug Administration (FDA)-approved drugs and screening libraries. We observed cross-library isozyme inhibition (30–78%) with important differences between libraries. Whereas only 7% of the typical screening library was inactive against all five isozymes, 33% of FDA-approved drugs were inactive, reflecting the optimized pharmacological properties of the latter. Our results suggest that low CYP 2C isozyme activity is a common property of drugs, whereas other isozymes, such as CYP 2D6, show little discrimination between drugs and unoptimized compounds found in screening libraries. We also identified chemical substructures that differentiated between the five isozymes. The pharmacological compendium described here should further the understanding of CYP isozymes.

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Figure 1: qHTS of five cytochrome P450 isozymes (CYP 1A2, 2C9, 2C19, 2D6 and 3A4).
Figure 2: Distribution and differences in CYP activity between MLSMR versus FDA sets and comparison to published descriptions.
Figure 3: Clustering of CYP isozyme activity across the 17,000-compound collection.
Figure 4: Fragment analysis of CYP activity.
Figure 5: Fragment analysis of CYP activity for more complex heterocycles.

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This research was supported by the Molecular Libraries Initiative of the National Institutes of Health Roadmap for Medical Research and the Intramural Research Program of the National Human Genome Research Institute. Work in Trinity College Dublin was supported by Enterprise Ireland, the Chemical Computing Group, OpenEye Scientific and Accelrys. We thank S. Jefferies and G. Carta for helpful discussions, S. Michael and C. Klumpp for help with robotic automation of the assays and P. Shinn for preparation of compound dilutions and library plates.

Author information

H.V. collected experimental data; H.V., N.S., R.H., T.J., D.F., N.A., M.S., D.G.L. and D.S.A. performed analysis; H.V., N.S., T.J., D.F., R.H., D.G.L., J.I., C.P.A. and D.S.A wrote the paper.

Correspondence to Douglas S Auld.

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Supplementary Text and Figures

Supplementary Figs. 1–8 and Supplementary Table 2 (PDF 524 kb)

Supplementary Table 1

CYP activity of substructures (XLS 870 kb)

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Veith, H., Southall, N., Huang, R. et al. Comprehensive characterization of cytochrome P450 isozyme selectivity across chemical libraries. Nat Biotechnol 27, 1050–1055 (2009) doi:10.1038/nbt.1581

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