Received for publication February 24, 2006.
Revised May 5, 2006.
Accepted for publication May 9, 2006.

In Silico Prediction of Drug Binding to Cytochrome P450 2D6: Identification of a new Metabolite of Metoclopramide

Abstract

Patients with cancer are often taking many different classes of drugs to treat the effects of their malignancy and the side effects of treatment, as well as their co-morbidities. The potential for drug-drug interactions which may affect the efficacy of anti-cancer treatment is high and a major source of such interactions is competition for the drug-metabolising enzymes cytochromes P450. We have examined a series of 20 drugs commonly prescribed for cancer patients looking for potential interactions via cytochrome P450 2D6. We used a homology model of cytochrome P450 2D6 together with molecular docking techniques to perform an in silico screen for binding to CYP2D6. Experimental IC₅₀ values were determined for these compounds and compared with the model predictions to reveal a correlation with a regression coefficient of r² = 0.61. Importantly, the docked conformation of the commonly prescribed anti-emetic metoclopramide predicted a new site of metabolism that was further investigated through in vitro analysis with recombinant CYP2D6. An aromatic N-hydroxy metabolite of metoclopramide - consistent with predictions from our modelling studies - was identified by high performance liquid chromatography mass spectrometry. This metabolite was found to represent a major product of metabolism in human liver microsomes and CYP2D6 was identified as the main P450 isoform responsible for catalyzing its formation. In view of the prevalence of inter-individual variation in the CYP2D6 genotype and phenotype, we suggest that those experiencing adverse reactions with metoclopramide, e.g. extra-pyramidal syndrome, are likely to have a particular CYP2D6 genotype/phenotype. This warrants further investigation.

Key words: CYP inhibition, CYP2D, cytochrome P450 function, drug interactions, drug-drug interactions, human CYP enzymes, in vitro-in vivo prediction, ligand docking, recombinant proteins