Multiple Pharmacophores for the Investigation of Human UDP- Glucuronosyltransferase Isoform Substrate Selectivity Michael J. Sorich, John O. Miners, Ross A. McKinnon, and Paul A. Smith School of Pharmaceutical, Molecular and Biomedical Sciences, University of South Australia, Adelaide, South Australia, Australia (M.J.S., R.A.M.); and Department of Clinical Pharmacology, Flinders University and Flinders Medical Centre, Bedford Park, South Australia, Australia (J.O.M., P.A.S.) Received August 14, 2003; accepted November 3, 2003 This article is available online at http://molpharm.aspetjournals.org ABSTRACT The UDP-glucuronosyltransferase (UGT) enzyme ‘superfamily’ contributes to the metabolism of a myriad of drugs, nondrug xenobiotic agents, and endogenous compounds. Although the individual UGT isoforms exhibit distinct but overlapping sub- strate selectivities, structural features of substrates that confer selectivity remain largely unknown. Using methods developed for pharmacophore fingerprinting combined with optimization and pattern recognition techniques, subsets of pharmacoph- ores associated with the substrates and nonsubstrates of 12 human UGT isoforms were selected to generate predictive models of substrate selectivity and to elucidate the chemical and structural features associated with substrates and nonsub- strates. For all 12 UGT isoforms, the pharmacophore model generated showed predictive ability, as determined by a test set comprising 30% of the available data for each isoform. Models for UGT1A6, -1A7, -1A9, and -2B4 displayed the best predictive ability (75% of test set predicted correctly) and were further analyzed to interpret the pharmacophores se- lected as important. The individual pharmacophores differed among isoforms but generally represented relatively simple structural and chemical features. For example, an aromatic ring attached to the nucleophilic group was found to increase the likelihood of glucuronidation by UGT1A6, UGT1A7 and UGT1A9. A large hydrophobic region close to the nucleophile and a hydrogen bond acceptor 10 Å from the nucleophile were found to be common to most UGT2B4 substrates. The phar- macophores further suggest that the environment immediately adjacent to the nucleophilic site of conjugation is an important determinant of metabolism by a particular UGT. UDP-Glucuronosyltransferase (UGT) catalyzes the cova- lent linkage or ‘conjugation’ of glucuronic acid, derived from cofactor UDP-glucuronic acid, to a typically lipophilic sub- strate containing a suitable acceptor functional group (most commonly hydroxyl, carboxyl, or amine) according to a sec- ond-order nucleophilic mechanism (Radominska-Pandya et al., 1999). UGT has the capacity to metabolize a myriad of structurally diverse compounds, including drugs from all therapeutic classes, dietary chemicals, environmental pollut- ants, endogenous compounds (e.g., bile acids, bilirubin, and hydroxysteroids), and the products of phase I metabolism (Miners and Mackenzie, 1991; Radominska-Pandya et al., 1999; Tukey and Strassburg, 2000). Like other drug metabolizing enzymes that exhibit broad substrate selectivity (particularly cytochrome P450), UGT exists as an enzyme superfamily (Mackenzie et al., 1997; Tukey and Strassburg, 2000). The various UGT gene prod- ucts (‘isoforms’) have been classified into two families, UGT1 and UGT2, based on amino acid sequence identity. cDNAs encoding 16 UGT proteins have been isolated to date: UGT 1A1, 1A3, 1A4, 1A6, 1A7, 1A8, 1A9, 1A10, 2B4, 2B7, 2B10, 2B11, 2B15, 2B17, and 2B28. Available evidence suggests that the individual UGT isoforms exhibit distinct substrate selectivities but often have significant overlap (Radominska- Pandya et al., 1999; Tukey and Strassburg, 2000; Sorich et al., 2003). Numerous factors, including genetic polymor- phism and metabolic drug interactions, are known to influ- ence UGT activity in vivo; hence, the metabolic clearances of glucuronidated compounds may vary considerably (Miners and Mackenzie, 1991; Tukey and Strassburg, 2000). Undesirable pharmacokinetic properties are a significant cause of failure in new drug development, and drug interac- tions and impaired clearance caused by genetic polymor- phism are important in this regard (Ekins et al., 2000; In- gelman-Sundberg, 2001). Moreover, knowledge of drug interactions, genetic polymorphism and other factors alter- ing metabolic clearance is important for rationalising and This work was supported by a grant from the National Health and Medical Research Council of Australia. M.J.S. is a recipient of an Australian Postgrad- uate Award. ABBREVIATIONS: UGT, UDP-glucuronosyltransferase; PLSDA, partial least squares discriminant analysis; 2D, two-dimensional; 3D, three- dimensional. 0026-895X/04/6502-301–308$20.00 MOLECULAR PHARMACOLOGY Vol. 65, No. 2 Copyright © 2004 The American Society for Pharmacology and Experimental Therapeutics 2901/1126492 Mol Pharmacol 65:301–308, 2004 Printed in U.S.A. 301 at ASPET Journals on July 5, 2017 molpharm.aspetjournals.org Downloaded from