Prediction of drug metabolism: the case of cytochrome P450 2D6

Cytochromes P450 (Cyt P450s) constitute the most important biotransformation enzymes involved in the biotransformation of drugs and other xenobiotics. Because drug metabolism by Cyt P450s plays such an important role in the disposition and in the pharmacological and toxicological effects of drugs, early consideration of ADME-properties is increasingly seen as essential for the discovery and the development of new drugs and drug candidates. The primary aim of this paper is to present various computational approaches used to rationalize and predict the activity and substrate selectivity of Cyt P450s, as well as the possibilities and limitations of these approaches, now and in the future. Attention is also paid to the experimental validation of these approaches by using high-throughput screening (HTS) of affinities to drug-drug interactions at the level of Cyt P450-isoenzymes. Since human Cyt P450 2D6 is one of the most important drug metabolizing enzymes and since in this regard much pioneering work has been done with this Cyt P450, Cyt P450 2D6 is chosen as a model for this discussion. Apart from early mechanism-based ab initio calculations on substrates of Cyt P450 2D6, pharmacophore modeling of ligands (i.e. both substrates and inhibitors) of Cyt P450 2D6 and protein homology modeling have been used successfully for the rationalisation and prediction of metabolite formation by this Cyt P450 isoenzyme. Significant protein structure-related species differences have been reported recently. It is concluded that not one computational approach is capable of rationalizing and reliably predicting metabolite formation by Cyt P450 2D6, but that it is rather the combination of the various complimentary approaches. It is moreover concluded, that experimental validation of the computational models and predictions is often still lacking. With the advent of novel, easily and well applicable in vitro based high throughput assays for ligand binding and turnover this limitation could be overcome soon, however. When effective links with other new and recent developments, such as bioinformatics, neural network computing, genomics and proteomics can be created, in silico rationalisation and prediction of drug metabolism by Cyt P450s is likely to become one of the key technologies in early drug discovery and development processes.     

Cytochrome P450 in vitro reaction phenotyping: a re-evaluation of approaches used for P450 isoform identification.

Marker substrates, chemical inhibitors, and inhibitory antibodies are important tools for the identification of cytochrome P450 (P450) isoform responsible for the metabolism of therapeutic agents in vitro. In view of the versatile and nonspecific nature of P450 enzymes, many of the marker substrates and chemical inhibitors used for P450 in vitro reaction phenotyping are isoform selective but not specific. Recently, the use of marker substrate and chemical inhibitors in CYP2D6 in vitro reaction phenotyping was questioned by Granvil et al. (2002). In comparison of a panel of 15 recombinant P450 enzymes, they found that in addition to CYP2D6, CYP1A1 is also capable of catalyzing the formation of 4-hydroxylated metabolite of debrisoquine and that the intrinsic clearance of debrisoquine by CYP2D6-mediated 4-hydroxylation is only about twice that by CYP1A1. In their study, they have also demonstrated that quinidine inhibits both CYP2D6- and CYP1A1-mediated debrisoquine 4-hydroxylation. In view of these important findings, we have reevaluated various approaches used to identify P450 isoform(s) responsible for the metabolism of therapeutic agents. While acknowledging the value of inhibitory antibodies in P450-phenotyping studies, it is our opinion that in well conducted in vitro experiments, isoform-selective chemical inhibitors can also provide valuable and reliable information. Hopefully, future efforts may produce even better P450 isoform-selective marker substrates and inhibitors.     

Heterotropic cooperativity in oxidation mediated by cytochrome p450

Cytochrome P450s (P450 or CYPs) comprise a superfamily of enzymes that catalyze the oxidation of a wide variety of xenobiotic chemicals. Although most of P450 inhibitors decrease the metabolic activities mediated by the corresponding P450 forms, unexpected phenomena, which are called as activation or heterotropic cooperativity, have been often observed. We summarize Michaelis-Menten constants (K(m)), maximal velocities (V(max)), V(max)/K(m) (intrinsic clearance) values, and/or metabolic activities for 22 activators and 24 substrates (30 reactions) mainly mediated by CYP3A4 among human P450 forms. Although an allosteric mechanism has been invoked to explain the cooperativity, the activation patterns or phenomena are dependent on substrates and selected enzyme sources in vitro. Interestingly, recent studies have been shown that human P450 forms other than CYP3A4, such as CYP1A2, CYP2C8, CYP2C9, CYP2D6, and CYP3A7, are also activated by some compounds, whereas there are few reports on CYP3A5. Several models describing interaction among substrates, effectors, and enzymes have been proposed, however, the detailed mechanism for the activation is still generally unknown even though some crystal structures have been shown. A few cases of the cooperativity of CYP3A in experimental animals have been presented, whereas the clinical significance of P450 cooperativity is still unclear. The collective findings provide fundamental and useful information for the activation of P450s by chemicals despite some contradictive kinetic parameters for the same reactions reported. To understand causal factor(s) and mechanism(s) for such different reports summarized here is still one of the hot research topics to be solved in current activation reactions.     

Role of gene knockout and transgenic mice in the study of xenobiotic metabolism

The role of P450s in xenobiotic metabolism, toxicity, and carcinogenicity has been studied for many years by using in vitro approaches and limited in vivo investigations. Genetic analysis to study the effects of xenobiotics in intact animals has only recently been carried out by use of gene knockout mice. Mice lacking expression of these enzymes have no or only modest phenotypes, indicating that their xenobiotic-metabolizing enzymes are not critical for mammalian development or physiological homeostasis. The null mice have been used to study the roll of xenobiotic-metabolizing enzymes in chemical toxicity and carcinogenicity. There are marked species differences in the expression and catalytic activities of P450s that metabolize xenobiotics, and this complicates the extrapolation of data obtained in rodents for use in drug development and human risk assessment. This is especially notable between mice and rats, commonly used experimental models, and humans. To begin to develop more predictive models, P450 humanized mice were produced and characterized by using genomic clones containing the complete coding and regulatory regions of genes, as transgenes. Humanized lines expressing CYP2D6 and CYP3A4 human P450 were characterized and found to accurately express human P450 proteins and catalytic activities at levels comparable to or higher than the corresponding activities found in human tissues. These novel mouse lines offer the opportunity to predict human drug and carcinogen metabolism and disposition and to search for endogenous substrates for human P450s.     

Engineering cytochrome p450 enzymes

The last 20 years have seen the widespread and routine application of methods in molecular biology such as molecular cloning, recombinant protein expression, and the polymerase chain reaction. This has had implications not only for the study of toxicological mechanisms but also for the exploitation of enzymes involved in xenobiotic clearance. The engineering of P450s has been performed with several purposes. The first and most fundamental has been to enable successful recombinant expression in host systems such as bacteria. This in turn has led to efforts to solubilize the proteins as a prerequisite to crystallization and structure determination. Lagging behind has been the engineering of enzyme activity, hampered in part by our still-meager comprehension of fundamental structure-function relationships in P450s. However, the emerging technique of directed evolution holds promise in delivering both engineered enzymes for use in biocatalysis and incidental improvements in our understanding of sequence-structure and sequence-function relationships, provided that data mining can extract the fundamental correlations underpinning the data. From the very first studies on recombinant P450s, efforts were directed toward constructing fusions between P450s and redox partners in the hope of generating more efficient enzymes. While this aim has been allowed to lie fallow for some time, this area merits further investigation as does the development of surface-displayed P450 systems for biocatalytic and biosensor applications. The final application of engineered P450s will require other aspects of their biology to be addressed, such as tolerance to heat, solvents, and high substrate and product concentrations. The most important application of these enzymes in toxicology in the near future is likely to be the biocatalytic generation of drug metabolites for the pharmaceutical industry. Further tailoring will be necessary for specific toxicological applications, such as in bioremediation.     

Comparative modelling of cytochromes P450

The superfamily of enzymes known as the cytochromes P450 (P450s) comprises a wide-ranging class of proteins with diverse functions. They are known, amongst other things, to be involved in the hormonal regulation of metabolism and reproduction, as well as having a major clinical significance through their association with diseases such as cancer, diabetes and hepatitis. Knowledge of the three-dimensional (3D) structure of a protein gives insight into its function. The 3D structures of P450s are therefore of considerable scientific interest. A number of high-resolution structures of P450s have been determined by X-ray crystallography and studies of these structures have provided valuable insights into the mechanism of these enzymes. Only one of these structures is mammalian and as yet there is no structural information on human P450s in the public domain. Until such a structure is solved it is necessary to employ alternative methods to gain structural insight into how human P450s perform their biological function. Here we report on the use of comparative modelling to predict the structure of human P450s based on knowledge of their amino acid sequences plus the 3D structures of other (not human) P450s. As an illustrative example of these techniques we have modelled the structure of P450 2C5 using five bacterial P450 structures as templates. We examine the importance of selecting suitable templates, obtaining a good amino acid sequence alignment, and evaluating the models generated. To improve the quality of the models an iterative cycle of sequence alignment, model building, and model evaluation is employed. The result is a model with excellent stereochemistry, good amino acid side chain environment properties, and a Calpha trace similar to the crystal structure.     

Spectral modification and catalytic inhibition of human cytochromes P450 1A1, 1A2, 1B1, 2A6, and 2A13 by four chemopreventive organoselenium compounds

Several organoselenium compounds including benzyl selenocyanate (BSC), 1,2-phenylenebis(methylene)selenocyanate (o-XSC), 1,3-phenylenebis(methylene)selenocyanate (m-XSC), and 1,4-phenylenebis(methylene)selenocyanate (p-XSC) have been shown to prevent cancers caused by polycyclic aromatic hydrocarbons (PAHs) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in experimental animals; these chemical carcinogens are activated by human P450 1 and 2A family enzymes, respectively, to carcinogenic metabolites. In this study, we examined whether these selenium compounds interact with and inhibit human P450 1 and 2A enzymes in vitro. Four organoselenium compounds induced reverse Type I binding spectra with P450 1A1, 1A2, and 1B1 and Type I binding spectra with P450 2A6 and 2A13. The spectral dissociation constants (K(s)) for the interaction of P450 1B1 with these chemicals were 3.6-5.7 μM; the values were lower than those with seen with P450 1A1 (19-30 μM) or 1A2 (6.3-13 μM). The K(s) values for Type I binding of P450 2A13 with m-XSC and BSC were both 0.20 μM; the values were very low compared to those for the interaction of P450 2A6 with m-XSC (5.7 μM) and BSC (2.0 μM). Four selenium compounds directly inhibited 7-ethoxyresorufin O-deethylation activities catalyzed by P450 1A1, 1A2, and 1B1 with IC(50) values <1.0 μM, except for the inhibition of P450 1A2 by BSC (1.3 μM). Coumarin 7-hydroxylation activities of P450 2A13 were more inhibited by four selenium compounds than those of P450 2A6, with IC(50) values of 0.22-1.4 μM for P450 2A13 and 2.4-6.2 μM for P450 2A6. Molecular docking studies of the interaction of four organoselenium compounds with human P450 enzymes suggest that these chemicals can be docked into the active sites of these human P450 enzymes and that the sites of the selenocyanate functional groups of these chemicals differ between the P450 1 and 2A family enzymes.     

Crystallization of cytochromes P450 and substrate-enzyme interactions

Our understanding of structure-function relationships have made considerable advances owing to the increasing number of new P450 crystal structures. This is especially true with mammalian P450s. As always, the main bottleneck in a structure determination project is crystallization. While the crystallization techniques used for P450 crystal growth are not much different from that utilized for other proteins, special protein engineering strategies have been developed in order to generate soluble, homogeneous membrane-bound P450 samples amendable for crystallization. Newly determined P450 structures also provide convincing evidence that P450 enzymes are highly dynamic and flexible. Common structural elements found in all P450s have been identified that undergo large conformational changes to allow substrate access and product release. In addition, flexible regions may enable the active site to adapt to the binding of substrates of different size, shape, and polarity. This review will focus on the successful membrane P450 crystallization techniques and the new structural insights based on the growing P450 structure database.     

Effect of 4-(4-chlorobenzyl)pyridine on rat hepatic microsomal cytochrome P450 and drug-metabolizing enzymes in vivo and in vitro

The effect of 4-(4-chlorobenzyl)pyridine (4-CBP) on rat hepatic microsomal cytochrome P450 (P450) and its molecular species (CYP2B1, 2E1, 3A2, 2C11, and 2C12), and on drug-metabolizing enzyme activities were examined in vivo and in vitro. Treatment of rats with 4-CBP resulted in the induction of P450 and drug-metabolizing enzymes in a dose-dependent manner, but it was markedly inhibitory at higher dose levels. Immunoblot analyses revealed that 4-CBP induces both CYP2B1 and 2E1; however, both were decreased by increasing the dose of 4-CBP. The in vitro inhibitory experiment revealed that 4-CBP strongly inhibited benzphetamine N-demethylase activity, but not dimethylnitrosamine N-demethylase activity. The present findings provide information on the induction and inhibition effect of chlorinated benzylpyridine on hepatic microsomal P450s and drug-metabolizing enzymes in vivo and in vitro.     

Functional expression of human cytochrome P450 enzymes in Escherichia coli

Knowledge regarding cytochrome P450 (P450) is crucial to the fields of drug therapy and drug development, as well as in our understanding of the mechanisms underlying the metabolic activation of potentially toxic and carcinogenic compounds. Escherichia coli is the most extensively utilized host in the production of recombinant human P450 enzymes. However, the recovery of substantial yields of functionally active P450 proteins remains problematic. Mammalian P450 protein was first expressed in 1991, via the modification of the N-terminal amino acid sequences in E. coli cells. Since that time, a variety of strategies have been established for the functional expression of recombinant P450s in E. coli, including N-terminal modification, the use of molecular chaperones, and culturing at lower temperatures. In all cases, human P450 expressed in E. coli cells has been shown to efficiently catalyze the oxidation of representative substrates at efficient rates. These recombinant P450s are applicable to studies which estimate the kinetic parameters of drug oxidation, and have also been used to determine the metabolic pathways of drugs and carcinogens exploited by human P450s. Despite the potential of P450s in various pharmaceutical and biotechnological fields, however, a host of substantial challenges must be overcome before these enzymes can be routinely utilized. Intrinsically, these enzymes are not very active, and exhibit poor stability. In this review, we have described current developments in the heterologous expression of human P450 enzymes.     

Photoaffinity ligands in the study of cytochrome p450 active site structure

While photoaffinity ligands have been widely used to probe the structures of many receptors and nucleic acid binding proteins, their effective use in the study of cytochrome p450 structure is less established. Nevertheless, significant advances in this field have been made since the technique was first applied to p450cam in 1979. In several cases, especially studies involving p450s of the 1A and 2B families, peptides covalently modified with photoaffinity ligands have been isolated and characterized. Some of these peptides were predicted by molecular modeling to line substrate binding regions of the enzymes. Other data obtained from such studies were more difficult to reconcile with theory. This review addresses the status of photoaffinity labeling as a tool for studying cytochrome p450 structure. In addition, potential future directions in this field are discussed, including the development of heme-directed agents and validation of their effectiveness as photoaffinity ligands using sperm whale myoglobin as a test protein. The potential for hydroxyaromatic compounds to serve as photoactivated probes of active site nucleophiles is also discussed. This class of compounds and its derivatives has long been known in the fields of photochemistry and photophysics to be precursors of reactive radicals and quinone methides that are likely to serve as effective active site probes of the p450s.     

Factors confounding the successful extrapolation of in vitro CYP3A inhibition information to the in vivo condition.

For the most part, the majority of adverse drug-drug interactions, which are pharmacokinetic in origin, can be understood in terms of alterations of cytochrome P450-catalyzed reactions. Much is known about the human P450 enzymes, and in many cases it is possible to apply this information to clinically related issues. Of the relatively small subset of the total number of human P450s, CYP3A4 appears to be responsible for the largest fraction of the drug oxidation reactions. As a consequence many important drug-drug interactions observed in the clinic are associated with drugs which are principally metabolized by CYP3A4. The two major reasons for drug-drug interactions involving CYP3A4 are induction and inhibition, with inhibition appearing to be the more important in terms of known clinical problems. Fortunately, with the available knowledge of human P450s and in vitro reagents, it is possible to do experiments with drugs to predict the in vivo condition. The goal of these studies is not only to improve predictions about which drugs might show serious P450 interaction problems, but also to decrease the number of in vivo interaction studies that must be performed in drug development. The focus of the current report is to describe some of the confounding factors associated with in vitro drug inhibition studies and the impact of these issues on in vitro/in vivo extrapolations.     

A passion for P450s (rememberances of the early history of research on cytochrome P450).

Many members of the superfamily of hemeproteins, known as cytochrome P450 (P450 or CYP), are currently described in the literature (over 2000 at the date of this writing) [see Nelson, 2003 (http://drnelson.utmem.edu/CytochromeP450.html)]. In mammalian tissues, the P450s play central roles in drug and xenobiotic metabolism as well as steroid hormone synthesis, fat-soluble vitamin metabolism, and the conversion of polyunsaturated fatty acids to biologically active molecules. P450s also play a major role in plants by catalyzing the synthesis of a large number of secondary metabolites. Today we appreciate the unique oxygen chemistry catalyzed by the P450 enzymes as well as the dramatic effect of protein structural changes resulting in modifications of substrate specificity. Recent scientific advances have shown the importance of genetic differences (polymorphisms) in altering the physiological response of an animal to endo- and exo-biotic chemicals. In many instances these changes can be directly attributed to small differences in the amino acid sequence of a P450. The present article describes some of the early events associated with the establishment of the biological function of P450s. The 1950s and 1960s showed the transition of P450 from an unknown spectroscopic curiosity to the major player it now occupies in maintaining cellular homeostasis. The P450s are now recognized to occupy a great variety of phylogenetically distributed isoform activities. Much has been learned about the P450s, but much more remains as poorly understood. It has been almost 50 years since this class of unique proteins were discovered and their catalytic functions characterized. The present article describes the background and early history of research leading to our present knowledge of the cytochromes P450. Hopefully we will learn lessons from this history as we venture forward down the path of future scientific discovery.     

Impact of nonspecific binding to microsomes and phospholipid on the inhibition of cytochrome P4502D6: implications for relating in vitro inhibition data to in vivo drug interactions.

The effects of microsomal concentration on the inhibitory potencies of four compounds--fluoxetine, quinidine, imipramine, and ezlopitant--on heterologously expressed recombinant CYP2D6-catalyzed bufuralol 1'-hydroxylase activity were determined. Increasing microsomal concentration from 0.0088 to 2.0 mg/ml, using additional microsomes not containing cytochrome P450, resulted in a marked increase in IC(50) and K(I) values for fluoxetine, ezlopitant, and imipramine, when inhibition constants were calculated using the nominal concentration of inhibitor added to the incubation mixture. The extent of nonspecific binding of these inhibitors to microsomes was determined using equilibrium dialysis. The extent of binding increased with increasing microsomal concentration. Binding was greatest for ezlopitant, followed by fluoxetine, imipramine, and quinidine. Correcting inhibition constants for the extent of nonspecific binding resulted in greater consistency of these values with differing microsomal protein concentrations. This effect was also studied with added phospholipid. Inhibition constants increased with increasing phospholipid, and nonspecific binding was also observed for these four drugs to phospholipid. This suggests that the phospholipid component of microsomes possesses some or all of the responsibility for nonspecific binding, and its effect on inhibitors of drug-metabolizing enzymes. These findings suggest that inhibition constants for drugs as inhibitors of microsomal drug-metabolizing enzymes, such as cytochrome P450, should be corrected for the extent of nonspecific binding to components of the in vitro matrix. The implications of this on the prediction of drug-drug interactions from in vitro data are discussed.     

Development and validation of an in silico P450 profiler based on pharmacophore models

In today's drug discovery process, the very early consideration of ADME properties is aimed at a reduction of drug candidate drop out rate in later development stages. Apart from in vitro testing, in silico methods are evaluated as complementary screening tools for compounds with unfavorable ADME attributes. Especially members of the cytochrome P450 (P450) enzyme superfamily-- e.g. P450 1A2, P450 2C9, P450 2C19, P450 2D6, and P450 3A4-- contribute to xenobiotic metabolism, and compound interaction with one of these enzymes is therefore critically evaluated. Pharmacophore models are widely used to identify common features amongst ligands for any target. In this study, both structure-based and ligand-based models for prominent drug-metabolizing members of the P450 family were generated employing the software packages LigandScout and Catalyst. Essential chemical ligand features for substrate and inhibitor activity for all five P450 enzymes investigated were determined and analyzed. Finally, a collection of 11 pharmacophores for substrates and inhibitors was evaluated as an in silico P450 profiling tool that could be used for early ADME estimation of new chemical entities.     

Drug-induced changes in P450 enzyme expression at the gene expression level: a new dimension to the analysis of drug-drug interactions

Drug-drug interactions (DDIs) caused by direct chemical inhibition of key drug-metabolizing cytochrome P450 enzymes by a co-administered drug have been well documented and well understood. However, many other well-documented DDIs cannot be so readily explained. Recent investigations into drug and other xenobiotic-mediated expression changes of P450 genes have broadened our understanding of drug metabolism and DDI. In order to gain additional information on DDI, we have integrated existing information on drugs that are substrates, inhibitors, or inducers of important drug-metabolizing P450s with new data on drug-mediated expression changes of the same set of cytochrome P450s from a large-scale microarray gene expression database of drug-treated rat tissues. Existing information on substrates and inhibitors has been updated and reorganized into drug-cytochrome P450 matrices in order to facilitate comparative analysis of new information on inducers and suppressors. When examined at the gene expression level, a total of 119 currently marketed drugs from 265 examined were found to be cytochrome P450 inducers, and 83 were found to be suppressors. The value of this new information is illustrated with a more detailed examination of the DDI between PPARalpha agonists and HMG-CoA reductase inhibitors. This paper proposes that the well-documented, but poorly understood, increase in incidence of rhabdomyolysis when a PPARalpha agonist is co-administered with a HMG-CoA reductase inhibitor is at least in part the result of PPARalpha-induced general suppression of drug metabolism enzymes in liver. The authors believe this type of information will provide insights to other poorly understood DDI questions and stimulate further laboratory and clinical investigations on xenobiotic-mediated induction and suppression of drug metabolism.     

Cytochrome P450: Molecular Architecture,Mechanism, and Prospects for Rational Inhibitor Design

Cytochromes P450 catalyze the insertion of one O₂-derived oxygen atom into an aliphatic or aromatic molecule. P450s are best known for the metabolism of xenobiotic molecules, where hydroxylation renders insoluble hydrocarbons more soluble for easier elimination. In addition to this important catabolic function, P450s catalyze key steps in steroid and plant growth regulator metabolism. A variety of therapeutic, fungicidal, and agochemical agents that perturb these metabolic pathways very likely operate by binding in the lipophilic P450 active site and coordinating with the heme iron atom. Recent determination of a bacterial P450 crystal structure, P450cam from Pseudomonas putida, in addition to the crystal structure of four inhibited complexes, has provided some insight into the potential use of P450 as a model system for the rational design of therapeutic agents. The crystal structure has also shed light on the P450 catalytic mechanism. P450cam operates differently from peroxidase or catalase in cleaving the O–O bond, since unlike these other enzymes, P450 contains no acid–base catalytic groups near the oxygen binding site. Instead, the O₂ pocket is lined with aliphatic and aromatic residues. This strongly suggests that the catalytic push required to cleave the O–O bond resides with the ability of the Cys heme ligand to donate electron density to the heme–oxy system. A comparison of the substrate-free and -bound P450cam crystal structures has revealed some interesting aspects regarding the dynamics of substrate binding. The structures of both forms of P450cam are the same except that in the substrate-free enzyme, the active-site pocket fills with a network of water molecules, one of which coordinates with the iron atom. Despite this lack of any significant conformational rearrangement of protein groups, a careful analysis of crystallographic temperature factors shows dynamical differences. Segments of the protein that are separated in the sequence but that lie close to one another in the structure and that define a small entrance to the substrate pocket undergo significantly higher thermal motion in the substrate-free enzyme. This suggests that dynamical fluctuations at the molecular surface play an important role in controlling substrate binding.     

Identification of binding sites of non-I-helix water molecules in mammalian cytochromes p450.

The cytochromes P450 (P450s) enzymes are integral in determining the disposition of many therapeutic compounds. At the molecular level, the details of P450 catalysis are still under investigation, but the importance of water-mediated proton shuttles seems evident in the catalytic cycle as it progresses through various heme iron-oxygen enzyme intermediates. The study of P450-bound waters has been largely restricted to bacterial enzymes that may or may not reflect the location or function of waters in human drug-metabolizing P450s. However, in recent years, 16 structures of mammalian P450s containing crystallographic waters have been deposited in the Protein Data Bank. Described herein is the identification of seven well defined water clusters in mammalian P450s identified by calculating the density of globally aligned waters as reported by Tanner and coworkers [Bottoms CA, White TA, and Tanner JJ (2006) Proteins 64:404-421 (DOI: 10.1002/prot.21014)]. All water binding sites were in or within the immediate vicinity of the active sites of the P450s, but most were not near the conserved I-helix threonine often implicated in P450 catalysis. Therefore, it is possible that some of the water binding sites identified here ultimately determine P450 catalytic efficiency either by working as an extension of the I-helix water network, or by acting in novel proton shuttles that modulate the nonproductive shunting of reactive oxygen species.     

Drug-induced changes in P450 enzyme expression at the gene expression level: A new dimension to the analysis of drug–drug interactions

Drug–drug interactions (DDIs) caused by direct chemical inhibition of key drug-metabolizing cytochrome P450 enzymes by a co-administered drug have been well documented and well understood. However, many other well-documented DDIs cannot be so readily explained. Recent investigations into drug and other xenobiotic-mediated expression changes of P450 genes have broadened our understanding of drug metabolism and DDI. In order to gain additional information on DDI, we have integrated existing information on drugs that are substrates, inhibitors, or inducers of important drug-metabolizing P450s with new data on drug-mediated expression changes of the same set of cytochrome P450s from a large-scale microarray gene expression database of drug-treated rat tissues. Existing information on substrates and inhibitors has been updated and reorganized into drug–cytochrome P450 matrices in order to facilitate comparative analysis of new information on inducers and suppressors. When examined at the gene expression level, a total of 119 currently marketed drugs from 265 examined were found to be cytochrome P450 inducers, and 83 were found to be suppressors. The value of this new information is illustrated with a more detailed examination of the DDI between PPARα agonists and HMG-CoA reductase inhibitors. This paper proposes that the well-documented, but poorly understood, increase in incidence of rhabdomyolysis when a PPARα agonist is co-administered with a HMG-CoA reductase inhibitor is at least in part the result of PPARα-induced general suppression of drug metabolism enzymes in liver. The authors believe this type of information will provide insights to other poorly understood DDI questions and stimulate further laboratory and clinical investigations on xenobiotic-mediated induction and suppression of drug metabolism.     

Utility of recombinant cytochrome p450 enzymes: a drug metabolism perspective

An important role of human cytochrome P450s (P450s) has been well recognized in the area of drug metabolism and pharmacokinetics. It has become possible in recent years to express catalytically active forms of these enzymes in various host systems. The resulting recombinant human P450s are either purified for studies of protein structure and the mechanism of catalysis or isolated in microsomal forms to serve the purposes of P450 phenotyping, metabolic stability screening and inhibitory potential evaluation. Intact mammalian cells expressing human enzymes may also be used to test the mutagenic and toxicity potential of drug candidates. The issue remains, however, that the data derived from recombinant P450s are not always consistent with those generated from human tissue preparations. The aim of this communication is to discuss applications of recombinant P450s in the drug discovery and development setting, with an emphasis on comparison of recombinant and human liver microsomal systems.