Quantifying and Predicting the Promiscuity and Isoform Specificity of Small-Molecule Cytochrome P450 Inhibitors

Abstract

ABSTRACT:Drug promiscuity (i.e., inhibition of multiple enzymes by a single compound) is increasingly recognized as an important pharmacological consideration in the drug development process. However, systematic studies of functional or physicochemical characteristics that correlate with drug promiscuity are handicapped by the lack of a good way of quantifying promiscuity. In this article, we present a new entropy-based index of drug promiscuity. We apply this index to two high-throughput data sets describing inhibition of cytochrome P450 isoforms by smallmolecule drugs and drug candidates, and we demonstrate how drug promiscuity or specificity can be quantified. For these drug-metabolizing enzymes, we find that there is essentially no correlation between a drug's potency and specificity. We also present an index to quantify the susceptibilities of different enzymes to inhibition by diverse substrates. Finally, we use partial least-squares regression to successfully predict isoform specificity and promiscuity of small molecules, using a set of fingerprint-based descriptors.

Comparison of the ligand binding site of CYP2C8 with CYP26A1 and CYP26B1: a structural basis for the identification of new inhibitors of the retinoic acid hydroxylases

“…In vitro inhibition assays CYP2C8 in vitro IC 50 values were obtained from previously reported literature sources 44,50,51 . An initial single point inhibition screen (n ¼ 3) was then used to estimate the inhibition potency of the set of known CYP2C8 inhibitors against CYP26A1 or CYP26B1.…”

“…Incubations conditions (n ¼ 3) were similar to those used in the screening assay except for the inhibition concentrations, which ranged from 0 to 100 mM. CYP26A1 and CYP26B1 IC 50 values were estimated using a three parameter inhibition model as shown in Equation (1), where Activity max represents the observed probe substrate activity with no inhibitor, Activity min is the probe substrate activity at the maximum inhibitor concentration and [I] is the concentration of inhibitor in the incubation. IC 50 incubations were performed in triplicate.…”

“…In order to determine the unbound fraction of clotrimazole in the IC 50 and spectral binding assays, equilibrium dialysis was conducted under relevant conditions. Experiments were performed in triplicate using the Rapid Equilibrium Dialysis Device (Thermo Fisher Scientific, Waltham, MA) which was prepared according to the manufacturer's recommendations.…”

“…CYP2C8 has also been shown to metabolize at-RA, 9-cis-retinoic acid and 13-cis-retinoic acid [45][46][47][48][49] . Potent in vitro inhibitors of CYP2C8-catalyzed metabolism include montelukast, candesartan cilexetil, zafirlukast, clotrimazole and fluconazole 44,50,51 . Clinically relevant drug interactions attributed to CYP2C8 inhibition have been noted for rosiglitazone, repaglinide and cerivastatin when co-administered with the CYP2C8 inhibitor gemfibrozil [52][53][54][55] .…”

“Drugs on oxygen”: an update and perspective on the role of cytochrome P450 testing in pharmacology

“…It should be noted also that most strategies are designed to identify inhibition of specific CYPs. The correct quantification and prediction of promiscuous CYP inhibitors is still an unsolved challenge [33].…”