In vitro and pharmacophore insights into CYP3A enzymes

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Abstract

The cytochrome P450 3A (CYP3A) enzymes have a major role in the metabolism of drugs in humans. Their wide substrate specificity and induction by a vast array of structurally diverse compounds presents the possibility of metabolic drug–drug interactions. Understanding the enzymes themselves is crucial. Over the past decade, this has occurred mostly with in vitro studies, although more recent approaches incorporate computational models to predict CYP inhibition and substrate potential. The three-dimensional displacement, or pharmacophore, of chemical features in space that are derived from inhibition data have produced pharmacophores for CYP3A4, CYP3A5 and CYP3A7, and provide new insights into ligand binding for each enzyme.

Section snippets

CYP3A4 complexity

Recently, it has become apparent that the kinetic interaction between CYP enzymes and their substrates in vitro is often atypical, as exemplified by CYP3A4 (Fig. 1). There are several reviews on this topic 9, 10, 11. Adding to this complexity, constituents of the incubation buffer appear to alter both the behavior of the enzyme [12] and the conformation of the active site [13]. Furthermore, chemical inhibition of catalysis by CYP3A4 is substrate dependent 5, 14, 15 and the inhibition response

Beyond in vitro

The pharmaceutical industry pays considerable attention to computational approaches that predict the absorption, distribution, metabolism, excretion and toxicology of test a molecule to eliminate failures well before precious resources are allocated for the development of the compound 25, 26, 27, 28, 29. Drug–drug interaction data can be turned into three-dimensional, visual, computational models (termed ‘pharmacophores’), that describe key features of molecules that are likely to be important

Caveats and context

It is important to note that some of the inhibitors used in this analysis (clotrimazole, erythromycin, ketoconazole and mibefradil) might not inhibit CYP3A by a strictly competitive mechanism and that we have used only a single substrate probe (BFC) in this analysis. Therefore, our pharmacophores might be limited in their representation compared to the CYP active site and it might be useful to use the present pharmacophore approach with competitive inhibitors of multiple substrate probes in

Similarities and differences

In many cases, the three CYP3A enzymes have similar catalytic characteristics in terms of substrate specificity, regiospecificity and kinetics [35]. However, for some molecules there are significant differences between the enzymes. For example, the CYP3A4 substrate cisapride is not an adequate substrate for CYP3A7 [41], whereas the 16-α hydroxylation of dehydroepiandrosterone sulfate is catalyzed preferentially by CYP3A7 [42]. Significant regiospecific differences in substrate metabolism also

Concluding remarks

Combining experimental and computational approaches to probe the molecular features necessary for substrates and inhibitors to interact with the binding domain in each CYP3A enzyme complements other studies. Future datasets of inhibitors of structurally diverse substrate probes for these enzymes might enable further definition of different regions of the active sites of CYP3A, in particular the molecular features that are required to interact with distinct binding domains of CYP3A. Ultimately,

Acknowledgements

We gratefully acknowledge Thuy Ho and Stephanie D. Turner for technical assistance, and Charles L. Crespi and Rajesh Sangar for comments and discussion.

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