Modelling species selectivity in rat and human cytochrome P450 2D enzymes.

Updated models of the Rat Cytochrome P450 2D enzymes are produced based on the recent x-ray structures of the Human P450 2D6 enzyme both with and without a ligand bound. The differences in species selectivity between the epimers quinine and quinidine are rationalised using these models and the results are discussed with regard to previous studies. A close approach to the heme is not observed in this study. The x-ray structure of the enzyme with a ligand bound is shown to be a better model for explaining the observed experimental binding of quinine and quinidine. Hence models with larger closed binding sites are recommended for comparative docking studies. This is consistent with molecular recognition in Cytochrome P450 enzymes being the result of a number of non-specific interactions in a large binding site.

Classification Models for Predicting Cytochrome P450 Enzyme-Substrate Selectivity.

Cytochrome P450 (CYP) is an important drug-metabolizing enzyme family. Different CYPs often have different substrate preferences. In addition, one drug molecule may be preferentially metabolized by one or more CYP enzymes. Therefore, the classification and prediction of substrate specificity of CYP enzymes are of importance to the understanding of drug metabolisms and may help guide the development of new drugs. In this study, we used three different machine learning methods to classify CYP substrates for predicting CYP-substrate specificity based solely on structural and physicochemical properties of the substrates. We first built a simple decision tree model to classify substrates of four CYP enzymes, 1A2, 2C9, 2D6 and 3A4 with more than 78 % classification accuracy. We then built a single-label eight-class model and a multilabel five-class model to classify substrates of eight CYP enzymes and to classify substrates that can be metabolized by more than one CYP enzymes, respectively. Above 90 % and >80 % prediction accuracy was achieved for the single-label and multilabel models, respectively. The main improvement of our models over existing ones is the automated and unbiased selection of descriptors by genetic algorithms, which makes our methods applicable for larger data sets and increased number of CYP enzymes.

Long-range effects of a peripheral mutation on the enzymatic activity of cytochrome P450 1A2.

The human cytochrome P450 1A2 is an important drug metabolizing and procarcinogen activating enzyme. An experimental study found that a peripheral mutation, F186L, at ∼26 Šaway from the enzyme's active site, caused a significant reduction in the enzymatic activity of 1A2 deethylation reactions. In this paper, we explored the effects of this mutation by carrying out molecular dynamics simulations and structural analyses. We found that the long-range effects of the F186L mutation were through a change in protein flexibility and a collective protein motion that caused the main substrate access channel to be mostly closed in the mutant. Our work is the first that combined both access channel analysis and protein motion analysis to elucidate mechanisms of mutation-induced allostery in a CYP protein. Such structural modeling and analysis approaches may be applied to other CYP proteins and other enzymes with buried active sites and may help guide protein engineering and drug design.

Human CYPs involved in drug metabolism: structures, substrates and binding affinities.

IMPORTANCE OF THE FIELD: There is current interest in the CYPs primarily due to their important role in the Phase I metabolism of foreign compounds, including pharmaceuticals, agrochemicals and environmental pollutants, to which mankind is exposed. AREAS COVERED IN THIS REVIEW: The roles of the human CYPs are introduced in the context of using structural modelling and quantitative structure-activity relationships for rationalizing substrate binding, selectivity and rates of metabolism, particularly for drugs in current clinical use. The importance of compound lipophilicity in both substrate binding and metabolic rate is emphasised, together with the employment of an automated docking method (AutoDock) for estimating binding energy and likely route of metabolism for drug substrates. WHAT THE READER WILL GAIN: The location of key interacting groups on both substrate and enzyme tends to define the preferred outcome of CYP-mediated drug metabolism in the majority of cases investigated thus far. This enables one to draw up a simple model of the important features present in the binding sites of CYPs which relate to substrate selectivity and likely positions of metabolism. TAKE HOME MESSAGE: For the major CYPs involved in human drug metabolism, it would appear that there is a relatively well-defined key distance, in terms of number of intervening atoms, between the main sites of binding and CYP-mediated metabolism.

An evaluation of ondansetron binding interactions with human cytochrome P450 enzymes CYP3A4 and CYP2D6.

The results of an evaluation study of ondansetron binding to human cytochromes P450 CYP3A4 and CYP2D6 is reported. The methodology includes NMR spectroscopic measurements of substrate to heme iron distances together with molecular modelling of the enzyme-substrate interactions. It is shown that there is a generally good agreement between the experimental and calculated binding affinities for ondansetron towards CYP2D6 and CYP3A4 enzymes, based on interactive docking studies. Moreover, the modelled binding orientations for ondansetron in CYP2D6 and CYP3A4 are largely consistent with the NMR data and with the known routes for P450-mediated metabolism of this compound.

Quantitative structure-activity relationships (QSARs) for inhibitors and substrates of CYP2B enzymes: importance of compound lipophilicity in explanation of potency differences.

The results of quantitative structure-activity relationship (QSAR) studies on inhibitors and substrates of cytochrome P450 2B (CYP2B) subfamily enzymes are reported. It was found that lipophilicity (in the form of log P) is the most important property for explaining the variations in inhibitory activity, and there are similarities between QSARs for both substrates and inhibitors for CYP2B6 (human), and also between those of other CYP2B enzymes, such as CYP2B1 (rat) and CYP2B4 (rabbit). Both linear and quadratic lipophilicity relationships are evidenced in human and other mammalian species, and the particular type of expression found is probably due to the nature of the compounds under investigation, as it is usually the homologous series which tend to show quadratic relationships in log P. The findings from QSAR studies can be rationalized by molecular modelling of the active site interactions with both P450 crystal structures and homology models of CYP2B subfamily enzymes.

Electronic and structural aspects of p450-mediated drug metabolism.

From a consideration of first principles for enzymes kinetics, we have employed theoretical methods which enable one to analyse the kinetics of cytochrome P450-mediated reactions which have been based on the known physicochemical principles underlying the majority of chemical or enzymatic reactions. A comparison is made between the correlation equations produced from the QSAR analysis of experimental P450 reaction rate data and those obtained from first principles, where there appears to be a generally satisfactory concordance between the two procedures. In this respect, we have developed expressions based on standard reaction kinetics theory which incorporate the Eyring and Marcus relationships. The analysis of P450-catalyzed reaction rates is elaborated to encompass a treatment of metabolic clearance, and satisfactory correlations are obtained with literature values for both intrinsic clearance and whole body clearance in terms of compound lipophilicity derived from log P data, where P is the octanol/water partition coefficient. The importance of ionization potential as a factor in the overall catalytic turnover of P450-mediated reactions is noted, especially in combination with the lipophilicity parameter, log P.

Molecular modelling of CYP2F substrates: comparison of naphthalene metabolism by human, rat and mouse CYP2F subfamily enzymes.

We have constructed three-dimensional molecular models of some cytochrome P450 (CYP) CYP2F subfamily forms via homology with CYP2C5 where sequence identities are in the region of 55%, thus representing high degrees of confidence in the accuracy of the models produced. The three-dimensional structures of these CYP2F enzymes have been compared by molecular overlay, especially with regard to the active site regions, and it would appear that the substitution of a lysine (Lys-301) in human CYP2F1 for the usual glutamate (Glu-301) in mouse CYP2F2, goat CYPF3 and rat CYP2F4 prior to the conserved distal threonine residue may well constitute a significant factor in any species differences between these CYP2F enzymes. Both substrate binding to CYP2F2 and metabolic clearance by CYP2F enzymes correlate with the lipophilicity, parameter, log P (where P is the octanol/water partition coefficient of the substrate). Other features of CYP2F substrate binding are likely to include pi-pi stacking interactions between aromatic rings and hydrogen bonding in some cases. The metabolism of the respiratory toxicant naphthalene is compared and contrasted between three mammalian species, namely mouse, rat and human. The CYPs involved in the metabolic activation and detoxification of naphthalene are discussed in the light of current evidence from both experimental and theoretical studies. It is noted that the CYP2F subfamily enzymes are associated with the activation of naphthalene in all three mammalian species, although there are marked differences between man and the two rodent species in the toxicity of this compound.

Analysis of CYP2D6 substrate interactions by computational methods.

Cytochrome P450 CYP2D6 is involved in the oxidation of well over 150 drugs and, in general, those which contain a basic nitrogen atom in the molecule. To clarify how the residues of CYP2D6 are utilized for orientating a wide range of its specific substrates and distinguishing them from a variety of other organic compounds, docking studies by AutoDock and molecular dynamics (MD) simulations were conducted. Specific ligands were docked to both the homology model and crystal structures optimally to estimate the site of reaction on the ligand molecule and the binding energy for the complex, which were generally in good agreement with the experimental data. MD simulation for the CYP2D6-propranolol complex was then carried out to reveal the amino acid residues interacting with the substrate at the active site. Phe-120, Glu-216, Asp-301, and Phe-483 are identified as the substrate-binding residues in agreement with previously reported site-directed mutagenesis data and the crystal structure reported recently (PDB code: 2F9Q). As well as these residues, our theoretical prediction suggests that Phe-219 and Glu-222 are also important residues for mediating oxidation of substrates, especially propranolol.

Up-regulation of CYP1A/B in rat lung and liver, and human liver precision-cut slices by a series of polycyclic aromatic hydrocarbons; association with the Ah locus and importance of molecular size.

Exposure of precision-cut rat liver slices to six structurally diverse polycyclic aromatic hydrocarbons, namely benzo[a]pyrene, benzo[b]fluoranthene, dibenzo[a,h]anthracene, dibenzo[a,l]pyrene, fluoranthene and 1-methylphenanthrene, led to induction of ethoxyresorufin O-deethylase, CYP1A apoprotein and CYP1A1 mRNA levels, but to a markedly different extent. In liver slices, constitutive CYP1A1 mRNA levels were higher, as well as being markedly more inducible by PAHs, compared with CYP1B1, a similar profile to that observed in human liver slices following exposure to the PAHs. Increase in ethoxyresorufin O-deethylase and in CYP1A1 apoprotein levels was also observed when precision-cut rat lung slices were incubated with the same PAHs, the order of induction potency being similar to that observed in liver slices. Under the same conditions of exposure, CYP1B1 apoprotein levels were elevated in the lung. Up-regulation of CYP1A1 by the six PAHs correlated with their affinity for the Ah receptor, determined using the chemical-activated luciferase expression (CALUX) assay. It may be concluded that (a) precision-cut liver and lung slices may be used to assess the CYP1 induction potential of chemicals at the activity, apoprotein and mRNA levels; (b) rat is a promising surrogate animal for human in studies to evaluate CYP1 induction potential; (c) CYP1A1 is far more inducible than CYP1B1 in both rat liver and lung; (d) CYP1 up-regulation by PAHs is related to their affinity for the Ah receptor, and finally (e) computer analysis revealed that the ratio of molecular length/width is an important determinant of CYP1 induction potency among equiplanar PAHs.

Quantitative structure-activity relationships (QSARs) in inhibitors of various cytochromes P450: the importance of compound lipophilicity.

The results of extensive quantitative structure-activity relationship (QSAR) analyses on 15 series of cytochrome P450 inhibitors, covering a total of 7 enzymes and 199 compounds, are reported. In general, it is found that lipophilicity represents the most important single factor in describing differences in inhibitory potency towards P450 enzymes. In two instances, this relationship is parabolic in nature but, by and large, the logarithm of inhibitory activity relates linearly with log P, where P is the octanol-water partition coefficient. On occasions, other parameters are involved in the QSAR expressions but there are many examples where either log P or its ionization-corrected equivalent, log D7.4, are the sole structural descriptors of inhibition. The correlations presented exhibit a range in R value from 0.85 to 0.99, where R is the correlation coefficient, and it is found that R is greater than 0.9 in 80% of the QSARs presented. It is apparent from these findings, therefore, that compound lipophilicity plays a major role in the ability of xenobiotics to inhibit enzymes of the cytochrome P450 superfamily, presumably due to the essentially hydrophobic nature of the active site region.

Lipophilicity relationships in inhibitors of CYP2C9 and CYP2C19 enzymes.

Quantitative structure-activity relationships (QSARs) within a series of cytochrome P450 2C9 (CYP2C9) and cytochrome P450 2C19 (CYP2C19) inhibitors are reported. In particular, it is noted that compound lipophilicity, in the form of log P values (where P is the octanol/water partition coefficient), is an important factor in explaining the variation in inhibitory potency within these series of compounds, many of which also act as substrates for the respective enzymes. In addition, there is a role for hydrogen bonding and pi-pi stacking interactions within the P450 active site which represent secondary factors in the binding processes of these compounds.

Structural modelling of the human drug-metabolizing cytochromes P450.

The structural and functional aspects of cytochrome P450 (CYP) enzymes are reviewed in the light of current developments in X-ray crystallography and other physical evidence, together with recent findings on the regulation of, and polymorphisms in, the human drug-metabolizing CYPs. It is emphasized that the crystal structures of eukaryotic CYPs are particuarly useful for constructing homology models of the human enzymes associated with drug metabolism, and that these models can aid in the high-throughput screening of novel compounds destined for human exposure.

Investigating human P450s involved in drug metabolism via homology with high-resolution P450 crystal structures of the CYP2C subfamily.

The important role of high-resolution crystal structures of cytochrome P450 (CYP) enzymes for the generation of P450 models by homology is discussed. The main focus is on human P450 enzymes involved in drug metabolism, where the role of homology modelling has been emphasized in the recent literature. Report of the first human P450 crystal structure has provided an opportunity for comparison between those modelled from other crystallographic templates, and the recent substrate-bound rabbit CYP2C5 structure exemplifies the relevance of high-resolution template structures to generating 3-D models of P450s where the homology is relatively high. In particular, the homology models of human CYP1 and CYP2 family enzymes are presented, where good agreement with experiment findings are apparent.

Quantitative structure-activity relationships (QSARs) within cytochromes P450 2B (CYP2B) subfamily enzymes: the importance of lipophilicity for binding and metabolism.

The results of qualitative structure-activity relationship (QSAR) analysis are reported for several series of compounds which act as substrates for mammalian CYP2B subfamily enzymes, together with a homologous series of aliphatic primary amines which are known to inhibit CYP2B enzymes. It is found that the compound lipophilicity in the form of the log P value (where P is the octanol/water partition coefficient) is related, either linearly or quadratically, to equilibrium constants of inhibition (Ki), binding (Ks) or metabolism (Km) depending on the series of compounds in question. In some instances, the difference between frontier orbital energy levels (deltaE) also features in several of the log P expressions with biological activity. Also present in a small number of correlations are parameters which are likely to be related to logP: namely, Rm, which is the partitioning factor derived from thin layer chromatography (TLC) retention times, and also the compound molecular weight (Mr). All of these three parameters ((log P, Rm and Mr) are thought to be related to the compound's ability to desolvate the P450 active site when they bind to the enzyme. Although the linear relationships between lipophilicity and CYP2B-related activity point to a major role for desolvation of the enzyme binding site in the overall interaction, it is noted that there may be an optimal log P value displayed by preferred substrates as shown by parabolic relationships with this lipophilic parameter. In addition, there is a remarkable similarity in the coefficients for the log P term of any QSAR expression, which suggests that the hydrophobicity of CYP2B active sites may be broadly equivalent between the various mammalian species.

The astronomical pulse of global extinction events.

The linkage between astronomical cycles and the periodicity of mass extinctions is reviewed and discussed. In particular, the apparent 26 million year cycle of global extinctions may be related to the motion of the solar system around the galaxy, especially perpendicular to the galactic plane. The potential relevance of Milankovitch cycles is also explored in the light of current evidence for the possible causes of extinction events over a geological timescale.

Quantitative structure-activity relationships (QSars) in CYP3A4 inhibitors: the importance of lipophilic character and hydrogen bonding.

The results of Quantitative Structure-Activity Relationship (QSAR) analyses on three series of CYP3A4 inhibitors are reported for enzyme inhibition expressed as Ki values. These include a small series of structurally related statins and two larger groupings of structurally diverse compounds, some of which display competitive inhibition of CYP3A4 whereas others act via heme iron ligation. In all cases, however, it is apparent that there are lipophilicity relationships associated with CYP3A4 inhibitory activity in the total of 46 compounds investigated. This is evidenced by linear correlations between inhibition of CYP3A4 and the octanol-water partition coefficient (P value) when expressed logarithmically (ie., log P). In the case of the statins, however, the distribution coefficient (D) at pH 7 is used due to the effect of compound ionization. Conversion of equilibrium constants (ie. Ki and P) to the corresponding free energy changes (deltaG values) facilitates exploration of the likely intermolecular forces of interaction between the inhibitors and the active site region of CYP3A4. In this respect, there appears to be good agreement between QSAR analyses and molecular modelling of the CYP3A4 enzyme itself, and both are consistent with the known mechanisms of inhibition displayed.

Metabolism of coumarin by human P450s: a molecular modelling study.

The oxidative metabolism of coumarin via several human cytochrome P450 (CYP) enzymes from families CYP1, CYP2 and CYP3 is rationalized in terms of molecular modelling studies carried out on the key interactions with various amino acid residues in the relevant active sites. The findings from modelling by homology with the CYP2C5 crystallographic template are in agreement with the known metabolism of coumarin in human P450s from the CYP1, CYP2 and CYP3 families, which has been published recently, and with independently reported information from site-directed mutagenesis studies.

Inhibition of human CYP1A2 oxidation of 5,6-dimethyl-xanthenone-4-acetic acid by acridines: a molecular modelling study.

1. The aim of the present study was to investigate the structural requirements for the inhibition of 6-methyl-hydroxylation of the antitumour agent 5,6-dimethyl-xanthenone-4-acetic acid (DMXAA) by acridine analogues and use a CYP1A2 homology model to provide some insight into this interaction. 2. Concentrations causing 50% inhibition (IC50) of the 6-methylhydroxylation of DMXAA were determined in human liver microsomes in the presence of various acridines. Some of the acridines were also tested for their ability to inhibit the CYP1A2-mediated 7-ethoxyresorufin O-de-ethylation. The molecular modelling studies of human CYP1A2 used the crystal structure of rabbit CYP2C5 as a template based on protein sequence homology and an interactive docking procedure using a dynamic hydrogen bond feature. 3. The in vitro IC50 studies for the inhibition of 6-methylhydroxylation of DMXAA indicated: (i) the importance of the position of the carboxamide side-chain on the acridine nucleus (and, to a lesser extent, its composition); (ii) the addition of hydroxyl groups to the 5-, 6- and 7-position of the acridine nucleus diminished the inhibitory potency; and (iii) amsacrine (acridine nucleus with methansulphonanilide side-chain at the 9-position) had no significant inhibitory effect. Similar structural trends were observed for the inhibition of O-de-ethylation of 7-ethoxyresorufin by acridines, supporting the involvement of CYP1A2 in DMXAA 6-methyl hydroxylation. 4. The molecular modelling studies indicated: (i) both DMXAA and N-[2-(dimethylamino)-ethyl]acridine-4-carboxamide (DACA) form two hydrogen bonds plus putative pi-pi stacking interactions with the CYP1A2-binding domain, typical of CYP1A2 substrates and inhibitors; (ii) the DMXAA 6-methyl group is 4.0 A from the central iron atom of the heme moiety and ideal for oxidation; (iii) the known oxidation sites for DACA are orientated away from the heme iron, supporting the non-involvement of CYP1A2; and (iv) amsacrine did not fit the putative CYP1A2 site owing to the steric hindrance of the bulky methanesulphonanilide side-chain. 5. These results suggest that docking studies with this homology model may be useful in the design of further acridine anticancer agents, in particular to identify agents that do not interact either as substrates or inhibitors with the CYP1A2-binding domain.

Molecular modelling of human microsomal epoxide hydrolase (EH) by homology with a fungal (Aspergillus niger) EH crystal structure of 1.8 A resolution: structure-activity relationships in epoxides inhibiting EH activity.

Homology modelling of the human microsomal epoxide hydrolase (EH) enzyme based on the fungal (Aspergillus niger) EH crystallographic template is reported. The active site lies in a well-defined, essentially hydrophobic, pocket within the overall enzyme structure. Two tyrosine residues, that are conserved in all known mammalian EH sequences, are able to form hydrogen bonds (one per tyrosine residue) with the epoxide oxygen atom on the known EH substrate, styrene oxide. There is also a small hydrophobic cleft, within the active site region, where the phenyl group of styrene oxide can bind, but this appears to be restricted such that the presence of bulky side-chains will render poor substrate status to the incoming epoxide molecule. Quantitative structure-activity relationship (QSAR) studies on a series of low molecular weight epoxides provide useful results which appear to be generally consistent with the human microsomal EH model, and thus may be used predictively for assessing the EH substrate and/or inhibitor status of untested compounds.