Structural determinants of cytochrome P450 substrate specificity, binding affinity and catalytic rate

Biological Responses of Pacific Herring Embryos to Crude Oil Are Quantifiable at Exposure Levels Below Conventional Limits of Quantitation for PAHs in Water and Tissues

Pacific herring (Clupea pallasii), a cornerstone of marine food webs, generally spawn on marine macroalgae in shallow nearshore areas that are disproportionately at risk from oil spills. Herring embryos are also highly susceptible to toxicity from chemicals leaching from oil stranded in intertidal and subtidal zones. The water-soluble components of crude oil trigger an adverse outcome pathway that involves disruption of the physiological functions of cardiomyocytes in the embryonic herring heart. In previous studies, impaired ionoregulation (calcium and potassium cycling) in response to specific polycyclic aromatic hydrocarbons (PAHs) corresponds to lethal embryolarval heart failure or subtle chamber malformations at the high and low ends of the PAH exposure range, respectively. Sublethal cardiotoxicity, which involves an abnormal outgrowth (ballooning) of the cardiac ventricular chamber soon after hatching, subsequently compromises juvenile heart structure and function, leading to pathological hypertrophy of the ventricle and reduced individual fitness, measured as cardiorespiratory performance. Previous studies have not established a threshold for these sublethal and delayed-in-time effects, even with total (∑)PAH exposures as low as 29 ng/g of wet weight (tissue dose). Here, we extend these earlier findings showing that (1) cyp1a gene expression provides an oil exposure metric that is more sensitive than typical quantitation of PAHs via GC-MS and (2) heart morphometrics in herring embryos provide a similarly sensitive measure of toxic response. Early life stage injury to herring (impaired heart development) thus occurs below the quantitation limits for PAHs in both water and embryonic tissues as a conventional basis for assessing oil-induced losses to coastal marine ecosystems.

Extracellular Vesicles as Surrogates for Drug Metabolism and Clearance: Promise vs. Reality

Drug-metabolizing enzymes (DMEs) and transporters play a major role in drug efficacy and safety. They are regulated at multiple levels and by multiple factors. Estimating their expression and activity could contribute to predicting drug pharmacokinetics and their regulation by drugs or pathophysiological situations. Determining the expression of these proteins in the liver, intestine, and kidney requires the collection of biopsy specimens. Instead, the isolation of extracellular vesicles (EVs), which are nanovesicles released by most cells and present in biological fluids, could deliver this information in a less invasive way. In this article, we review the use of EVs as surrogates for the expression and activity of DMEs, uptake, and efflux transporters. Preliminary evidence has been provided for a correlation between the expression of some enzymes and transporters in EVs and the tissue of origin. In some cases, data obtained in EVs reflect the induction of phase I-DMEs in the tissues. Further studies are required to elucidate to what extent the regulation of other DMEs and transporters in the tissues reflects in the EV cargo. If an association between tissues and their EVs is firmly established, EVs may represent a significant advancement toward precision therapy based on the biotransformation and excretion capacity of each individual.

Establishment of killer whale (Orcinus orca) primary fibroblast cell cultures and their transcriptomic responses to pollutant exposure

Populations of killer whale (Orcinus orca) contain some of the most polluted animals on Earth. Yet, the knowledge on effects of chemical pollutants is limited in this species. Cell cultures and in vitro exposure experiments are pertinent tools to study effects of pollutants in free-ranging marine mammals. To investigate transcriptional responses to pollutants in killer whale cells, we collected skin biopsies of killer whales from the Northern Norwegian fjords and successfully established primary fibroblast cell cultures from the dermis of 4 out of 5 of them. Cells from the individual with the highest cell yield were exposed to three different concentrations of a mixture of persistent organic pollutants (POPs) that reflects the composition of the 10 most abundant POPs found in Norwegian killer whales (p,p'-DDE, trans-nonachlor, PCB52, 99, 101, 118, 138, 153, 180, 187). Transcriptional responses of 13 selected target genes were studied using digital droplet PCR, and whole transcriptome responses were investigated utilizing RNA sequencing. Among the target genes analysed, CYP1A1 was significantly downregulated in the cells exposed to medium (11.6 µM) and high (116 µM) concentrations of the pollutant mixture, while seven genes involved in endocrine functions showed a non-significant tendency to be upregulated at the highest exposure concentration. Bioinformatic analyses of RNA-seq data indicated that 13 and 43 genes were differentially expressed in the cells exposed to low and high concentrations of the mixture, respectively, in comparison to solvent control. Subsequent pathway and functional analyses of the differentially expressed genes indicated that the enriched pathways were mainly related to lipid metabolism, myogenesis and glucocorticoid receptor regulation. The current study results support previous correlative studies and provide cause-effect relationships, which is highly relevant for chemical and environmental management.

Toxicological responses of BEAS-2B cells to repeated exposures to benzene, toluene, m-xylene, and mesitylene using air-liquid interface method

In order to reduce exposure to toxic chemicals, the European REACH regulation (1907/2006) recommends substituting toxic molecules with compounds that are less harmful to human health and the environment. Toluene is one of the most frequently used solvents in industries despite its toxicity. The objective of this study is to better understand and compare the toxicity of toluene and its homologues in a bronchial cell model. Thus, human bronchial BEAS-2B cells were exposed to steams of toluene, m-xylene, mesitylene (1,3,5-trimethylbenzene), and benzene (20 and 100 ppm). Exposure was carried out using an air-liquid interface (ALI) system (Vitrocell) during 1 h/day for 1, 3, or 5 days. Cytotoxicity, xenobiotic metabolism enzyme gene expression, and inflammatory response were evaluated following cell exposures. BEAS-2B cell exposure to toluene and its homologues revealed the involvement of major (CYP2E1) and minor metabolic pathways (CYP1A1). A late induction of genes (EPHX1, DHDH, ALDH2, and ALDH3B1) was measured from Day 3 and can be linked to the formation of metabolites. An increase in the secretion level of inflammatory markers (TNF-α, IL-6, IL-8, MCP-1, and GM-CSF) was also observed. In parallel, regulation between inflammatory mediators and the expression of transmembrane glycoprotein mucin MUC1 was also studied. This in vitro approach with ALI system points out the relevance of conducting repeated exposures to detect potential late effects. The difference recorded after cell exposure to toluene and its homologues highlights the importance of substitution principle.

Polymorphism in Cytochrome P450 3A4 Is Ethnicity Related

Can mutations in Cytochrome P450 3A4 (CYP3A4), the major food- and drug-metabolizing enzyme, serve as biomarkers for personalized precise medicine? Classical genetic studies provide only limited data regarding the frequencies of CYP3A4 mutations and their role in food–drug interactions. Here, in an analysis of one large database of 141,456 individuals, we found 856 SNPs (single nucleotide polymorphism), of which 312 are missense mutations, far more than the previously reported dozens. Analyzing the data further, it is demonstrated that the frequency of mutations differs among ethnic groups. Hierarchical clustering divided the mutations to seven groups, each corresponding to a specific ethnicity. To the best of our knowledge this is the first comprehensive analysis of CYP3A4 allele frequencies in distinct ethnic groups. We suggest ethnicity based classification of CYP3A4 SNPs as the first step toward precise diet and medicine. Understanding which and when polymorphism might have clinical significance is a tremendously complex task. Using modeling approach, we could predict changes in the binding poses of ligands in the active site of single variants. These changes might imply clinical effects of the overlooked protein-altering CYP3A4 mutations, by modifying drug metabolism and FDI. It may be concluded that dietary habits, and hence FDI, are matters of ethnicity. Consequently, ethnic-related polymorphism in CYP3A4 and diet may be one underlying mechanism of response to medical regimes. The approaches presented here have the power to highlight mutations of clinical relevance in any gene of interest, thus to complement the arsenal of classic genetic screening tools.

Halogen Substitution Influences Ketamine Metabolism by Cytochrome P450 2B6: In Vitro and Computational Approaches

Ketamine is analgesic at anesthetic and subanesthetic doses, and it has been used recently to treat depression. Biotransformation mediates ketamine effects, influencing both systemic elimination and bioactivation. CYP2B6 is the major catalyst of hepatic ketamine N-demethylation and metabolism at clinically relevant concentrations. Numerous CYP2B6 substrates contain halogens. CYP2B6 readily forms halogen-protein (particularly Cl-π) bonds, which influence substrate selectivity and active site orientation. Ketamine is chlorinated, but little is known about the metabolism of halogenated analogs. This investigation evaluated halogen substitution effects on CYP2B6-catalyzed ketamine analogs N-demethylation in vitro and modeled interactions with CYP2B6 using various computational approaches. Ortho phenyl ring halogen substituent changes caused substantial (18-fold) differences in K_m, on the order of Br (bromoketamine, 10 μM) < Cl < F < H (deschloroketamine, 184 μM). In contrast, V_max varied minimally (83-103 pmol/min/pmol CYP). Thus, apparent substrate binding affinity was the major consequence of halogen substitution and the major determinant of N-demethylation. Docking poses of ketamine and analogs were similar, sharing a π-stack with F297. Libdock scores were deschloroketamine < bromoketamine < ketamine < fluoroketamine. A Bayesian log K_m model generated with Assay Central had a ROC of 0.86. The probability of activity at 15 μM for ketamine and analogs was predicted with this model. Deschloroketamine scores corresponded to the experimental K_m, but the model was unable to predict activity with fluoroketamine. The binding pocket of CYP2B6 also suggested a hydrophobic component to substrate docking, on the basis of a strong linear correlation ( R² = 0.92) between lipophilicity ( Alog P) and metabolism (log K_m) of ketamine and analogs. This property may be the simplest design criteria to use when considering similar compounds and CYP2B6 affinity.

Multiple-endpoints gene alteration-based (MEGA) assay: A toxicogenomics approach for water quality assessment of wastewater effluents

Wastewater effluents contain a significant number of toxic contaminants, which, even at low concentrations, display a wide variety of toxic actions. In this study, we developed a multiple-endpoints gene alteration-based (MEGA) assay, a real-time PCR-based transcriptomic analysis, to assess the water quality of wastewater effluents for human health risk assessment and management. Twenty-one genes from the human hepatoblastoma cell line (HepG2), covering the basic health-relevant stress responses such as response to xenobiotics, genotoxicity, and cytotoxicity, were selected and incorporated into the MEGA assay. The genes related to the p53-mediated DNA damage response and cytochrome P450 were selected as markers for genotoxicity and response to xenobiotics, respectively. Additionally, the genes that were dose-dependently regulated by exposure to the wastewater effluents were chosen as markers for cytotoxicity. The alterations in the expression of an individual gene, induced by exposure to the wastewater effluents, were evaluated by real-time PCR and the results were validated by genotoxicity (e.g., comet assay) and cell-based cytotoxicity tests. In summary, the MEGA assay is a real-time PCR-based assay that targets cellular responses to contaminants present in wastewater effluents at the transcriptional level; it is rapid, cost-effective, and high-throughput and can thus complement any chemical analysis for water quality assessment and management.

Molecular Mechanisms of Crude Oil Developmental Toxicity in Fish

With major oil spills in Korea, the United States, and China in the past decade, there has been a dramatic increase in the number of studies characterizing the developmental toxicity of crude oil and its associated polycyclic aromatic compounds (PACs). The use of model fish species with associated tools for genetic manipulation, combined with high throughput genomics techniques in nonmodel fish species, has led to significant advances in understanding the cellular and molecular bases of functional and morphological defects arising from embryonic exposure to crude oil. Following from the identification of the developing heart as the primary target of crude oil developmental toxicity, studies on individual PACs have revealed a diversity of cardiotoxic mechanisms. For some PACs that are strong agonists of the aryl hydrocarbon receptor (AHR), defects in heart development arise in an AHR-dependent manner, which has been shown for potent organochlorine agonists, such as dioxins. However, crude oil contains a much larger fraction of compounds that have been found to interfere directly with cardiomyocyte physiology in an AHR-independent manner. By comparing the cellular and molecular responses to AHR-independent and AHR-dependent toxicity, this review focuses on new insights into heart-specific pathways underlying both acute and secondary adverse outcomes to crude oil exposure during fish development.

Simultaneous evaluation of substrate-dependent CYP3A inhibition using a CYP3A probe substrates cocktail

Cytochrome P450 (P450) 3A (CYP3A) is an enzyme responsible for the metabolism of therapeutic drugs such as midazolam, nifedipine, testosterone and triazolam. It is involved in 40% of all cases of P450-mediated metabolism of marketed drugs. Therefore, it is important to evaluate the CYP3A-mediated drug interaction potential of new chemical entities (NCEs). In the past, one P450 isoform-specific probe substrate has been used at a time to evaluate the degree of inhibition of P450 isoforms by using liquid chromatography-tandem mass spectrometry (LC-MS/MS). However, CYP3A enzymes have been shown to have a multi-substrate binding site. Therefore, multiple CYP3A substrates should be used to evaluate precisely the drug interaction potential of NCEs with the enzyme CYP3A. In this study, a method of screening NCEs for their potential to inhibit by CYP3A enzyme activity was developed. It involves the employment of a CYP3A substrate cocktail (including midazolam, testosterone and nifedipine). The concentration of each CYP3A probe substrate in vitro was optimized (0.1 μm for midazolam, 2 μm for testosterone and 2 μm for nifedipine) to minimize mutual drug interactions among probe substrates. The method was validated by comparing inhibition data obtained from the incubation of CYP3A with each individual substrate with data from incubation with a cocktail of all three substrates. The CYP3A inhibition profiles from the substrate cocktail approach were similar to those from the individual substrates approach. This new method could be an effective tool for the robust and accurate screening of the CYP3A inhibition potential of NCEs in drug discovery. Copyright © 2016 John Wiley & Sons, Ltd.

Concentrations and patterns of hydroxylated polybrominated diphenyl ethers and polychlorinated biphenyls in arctic foxes (Vulpes lagopus) from Svalbard

Concentrations and patterns of hydroxylated (OH) polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) were investigated in liver from arctic foxes (Vulpes lagopus) sampled from Svalbard 1997-2011 (n = 100). The most important OH-PBDE in the arctic foxes was 6-OH-BDE47 detected in 24% of the samples. Relationships between 6-OH-BDE47, δ(13)C and BDE47 suggest that 6-OH-BDE47 residues in arctic foxes are related to marine dietary input, while the relative importance of the metabolic/natural origin of this compound remains unclear. 4-OH-CB187 and 4-OH-CB146 were the main OH-PCBs among the analyzed compounds. The OH-PCB pattern in the present arctic foxes indicates that arctic foxes have a capacity to biotransform a wide range of PCBs of different structures. Formation and retention of OH-PCBs was tightly related to PCB exposure. Furthermore, ΣOH-PCB concentrations were four times higher in the leanest compared to the fattest foxes. Concentrations of 4-OH-CB187 and 4-OH-CB146 among the highest contaminated arctic foxes were similar to the previously reported concentrations for polar bears. Given the high endocrine disruptive potential of OH-PCBs, we suggest that endocrine system may be affected by the relatively high OH-PCB residues in the Svalbard arctic fox population.

Rational Development of Novel Activity Probes for the Analysis of Human Cytochromes P450

The identification and quantification of functional cytochromes P450 (CYPs) in biological samples is proving important for robust analyses of drug efficacy and metabolic disposition. In this study, a novel CYP activity-based probe was rationally designed and synthesised, demonstrating selective binding of CYP isoforms. The dependence of probe binding upon the presence of NADPH permits the selective detection of functionally active CYP. This allows the detection and analysis of these enzymes using biochemical and proteomic methodologies and approaches.

Predicting Mouse Liver Microsomal Stability with "Pruned" Machine Learning Models and Public Data

PURPOSE

Mouse efficacy studies are a critical hurdle to advance translational research of potential therapeutic compounds for many diseases. Although mouse liver microsomal (MLM) stability studies are not a perfect surrogate for in vivo studies of metabolic clearance, they are the initial model system used to assess metabolic stability. Consequently, we explored the development of machine learning models that can enhance the probability of identifying compounds possessing MLM stability.

METHODS

Published assays on MLM half-life values were identified in PubChem, reformatted, and curated to create a training set with 894 unique small molecules. These data were used to construct machine learning models assessed with internal cross-validation, external tests with a published set of antitubercular compounds, and independent validation with an additional diverse set of 571 compounds (PubChem data on percent metabolism).

RESULTS

"Pruning" out the moderately unstable / moderately stable compounds from the training set produced models with superior predictive power. Bayesian models displayed the best predictive power for identifying compounds with a half-life ≥1 h.

CONCLUSIONS

Our results suggest the pruning strategy may be of general benefit to improve test set enrichment and provide machine learning models with enhanced predictive value for the MLM stability of small organic molecules. This study represents the most exhaustive study to date of using machine learning approaches with MLM data from public sources.

Characterization of the active site properties of CYP4F12

Cytochrome P450 4F12 is a drug-metabolizing enzyme that is primarily expressed in the liver, kidney, colon, small intestine, and heart. The properties of CYP4F12 that may impart an increased catalytic selectivity (decreased promiscuity) were explored through in vitro metabolite elucidation, kinetic isotope effect experiments, and computational modeling of the CYP4F12 active site. By using astemizole as a probe substrate for CYP4F12 and CYP3A4, it was observed that although CYP4F12 favored astemizole O-demethylation as the primary route of metabolism, CYP3A4 was capable of metabolizing astemizole at multiple sites on the molecule. Deuteration of astemizole at the site of O-demethylation resulted in an isotope effect of 7.1 as well as an 8.3-fold decrease in the rate of clearance for astemizole by CYP4F12. Conversely, although an isotope effect of 3.8 was observed for the formation of the O-desmethyl metabolite when deuterated astemizole was metabolized by CYP3A4, there was no decrease in the clearance of astemizole. Development of a homology model of CYP4F12 based on the crystal structure of cytochrome P450 BM3 predicted an active site volume for CYP4F12 that was approximately 76% of the active site volume of CYP3A4. As predicted, multiple favorable binding orientations were available for astemizole docked into the active site of CYP3A4, but only a single binding orientation with the site of O-demethylation oriented toward the heme was identified for CYP4F12. Overall, it appears that although CYP4F12 may be capable of binding similar ligands to other cytochrome P450 enzymes such as CYP3A4, the ability to achieve catalytically favorable orientations may be inherently more difficult because of the increased steric constraints of the CYP4F12 active site.

Impact of biomarkers on clinical trial risk

The last decade has witnessed the cost of drug development rise dramatically; concurrently, the number of new drug approvals has declined. Clinical trial failure rates have contributed significantly to this 'innovation' crisis and are directly related to clinical trial risk. One strategy that is often touted to resolve this challenge depends on embracing a personalized medicine approach where treatment is tailored to a patient's unique genetic background. We highlight a new risk-based paradigm of clinical trial risk that evaluates the utility of biomarkers in drug development and their risk mitigation benefits. Furthermore, examples elucidating the current state of biomarker integration during clinical trials and the potential risks posed by doing so will be discussed.

Understanding a substrate's product regioselectivity in a family of enzymes: a case study of acetaminophen binding in cytochrome P450s

Product regioselectivity as influenced by molecular recognition is a key aspect of enzyme catalysis. We applied large-scale two-dimensional (2D) umbrella sampling (USP) simulations to characterize acetaminophen (APAP) binding in the active sites of the family of Cytochrome P450 (CYP) enzymes as a case study to show the different regioselectivity exhibited by a single substrate in comparative enzymes. Our results successfully explain the experimentally observed product regioselectivity for all five human CYPs included in this study, demonstrating that binding events play an important role in determining regioselectivity. In CYP2C9 and CYP3A4, weak interactions in an overall large active site cavity result in a fairly small binding free energy difference between APAP reactive binding states, consistent with experimental results that show little preference for resulting metabolites. In contrast, in CYP1A2 and CYP2E1, APAP is strongly restrained by a compact binding pocket, leading to a preferred binding conformation. The calculated binding equilibrium of APAP within the compact active site of CYP2A6 is able to predict the experimentally documented product ratios and is also applied to explain APAP regioselectivity in CYP1A2 and CYP2C9. APAP regioselectivity seems to be related to the selectivity for one binding conformation over another binding conformation as dictated by the size and shape of the active site. Additionally, unlike docking and molecular dynamics (MD), our free energy calculations successfully reproduced a unique APAP pose in CYP3A4 that had been reported experimentally, suggesting this approach is well suited to find the realistic binding pose and the lowest-energy starting structure for studying the chemical reaction step in the future.

The Effect of CYP2B6, CYP2D6, and CYP3A4 Alleles on Methadone Binding: A Molecular Docking Study

Current methadone maintenance therapy (MMT) is yet to ensure 100% successful treatment as the optimum dosage has yet to be determined. Overdose leads to death while lower dose causes the opioid withdrawal effect. Single-nucleotide polymorphisms (SNP) in cytochrome P450s (CYPs), the methadone metabolizers, have been showen to be the main factor for the interindividual variability of methadone clinical effects. In this study, we investigated the effect of SNPs in three major methadone metabolizers (CYP2B6, CYP2D6, and CYP3A4) on methadone binding affinity. Results showed thatCYP2B6*11,CYP2B6*12,CYP2B6*18, andCYP3A4*12have significantly higher binding affinity toR-methadone compared to wild type.S-methadone has higher binding affinity inCYP3A4*3,CYP3A4*11, andCYP3A4*12compared to wild type.R-methadone was shown to be the active form of methadone; thus individuals with CYP alleles that binds better toR-methadone will have higher methadone metabolism rate. Therefore, a higher dosage of methadone is necessary to obtain the opiate effect compared to a normal individual and vice versa. These results provide an initial prediction on methadone metabolism rate for individuals with mutant type CYP which enables prescription of optimum methadone dosage for individuals with CYP alleles.

Effect of reduced food intake on toxicokinetics of halogenated organic contaminants in herring gull (Larus argentatus) chicks

The aim of the present study was to investigate how contaminant exposure and reduced food intake affect tissue distribution and biotransformation of halogenated organic contaminants (HOCs) in Arctic seabirds using herring gull (Larus argentatus) as a model species. Herring gull chicks were exposed for 44 d to cod liver oil containing a typical mixture of contaminants. Following exposure, food intake was reduced for a one-week period in a subgroup of the chicks. Polyclorinated biphenyls, organochlorine pesticides, and brominated flame retardants, as well as a wide range of hydroxy, methyl sulfone, and methoxy compounds were measured in liver, brain, and plasma samples. Additionally, phase I biotransformation enzyme activities and phase I and II messenger ribonucleic acid (mRNA) expression were investigated in the liver, brain, or both. Both contaminant exposure and reduced food intake had an increasing effect on the concentrations of HOCs and their metabolites. The HOC exposure and reduced food intake also led to increased 7-ethoxyresorufin-O-deethylation (EROD) activity, whereas mRNA expression of the biotransformation enzymes increased only following the reduced food intake. Tissue distribution of HOCs and their metabolites was not affected by either contaminant exposure or reduced food intake. In conclusion, the results indicate that biotransformation capacity and formation of HOC metabolites increase during reduced food intake. This finding supports the hypothesis that reduced food intake increases the susceptibility of Arctic animals to the effects of lipophilic HOCs.

Strategies for the generation, validation and application of in silico ADMET models in lead generation and optimization

INTRODUCTION

The most desirable chemical starting point in drug discovery is a hit or lead with a good overall profile, and where there may be issues; a clear SAR strategy should be identifiable to minimize the issue. Filtering based on drug-likeness concepts are a first step, but more accurate theoretical methods are needed to i) estimate the biological profile of molecule in question and ii) based on the underlying structure-activity relationships used by the model, estimate whether it is likely that the molecule in question can be altered to remove these liabilities.

AREAS COVERED

In this paper, the authors discuss the generation of ADMET models and their practical use in decision making. They discuss the issues surrounding data collation, experimental errors, the model assessment and validation steps, as well as the different types of descriptors and statistical models that can be used. This is followed by a discussion on how the model accuracy will dictate when and where it can be used in the drug discovery process. The authors also discuss how models can be developed to more effectively enable multiple parameter optimization.

EXPERT OPINION

Models can be applied in lead generation and lead optimization steps to i) rank order a collection of hits, ii) prioritize the experimental assays needed for different hit series, iii) assess the likelihood of resolving a problem that might be present in a particular series in lead optimization and iv) screen a virtual library based on a hit or lead series to assess the impact of diverse structural changes on the predicted properties.

Docking and QSAR comparative studies of polycyclic aromatic hydrocarbons and other procarcinogen interactions with cytochromes P450 1A1 and 1B1

To obtain chemical clues on the process of bioactivation by cytochromes P450 1A1 and 1B1, some QSAR studies were carried out based on cellular experiments of the metabolic activation of polycyclic aromatic hydrocarbons and heterocyclic aromatic compounds by those enzymes. Firstly, the 3D structures of cytochromes 1A1 and 1B1 were built using homology modelling with a cytochrome 1A2 template. Using these structures, 32 ligands including heterocyclic aromatic compounds, polycyclic aromatic hydrocarbons and corresponding diols, were docked with LigandFit and CDOCKER algorithms. Binding mode analysis highlighted the importance of hydrophobic interactions and the hydrogen bonding network between cytochrome amino acids and docked molecules. Finally, for each enzyme, multilinear regression and artificial neural network QSAR models were developed and compared. These statistical models highlighted the importance of electronic, structural and energetic descriptors in metabolic activation process, and could be used for virtual screening of ligand databases. In the case of P450 1A1, the best model was obtained with artificial neural network analysis and gave an r (2) of 0.66 and an external prediction [Formula: see text] of 0.73. Concerning P450 1B1, artificial neural network analysis gave a much more robust model, associated with an r (2) value of 0.73 and an external prediction [Formula: see text] of 0.59.

Factors affecting phase I stereoselective biotransformation of chiral polychlorinated biphenyls by rat cytochrome P-450 2B1 isozyme

In vitro incubations of rat cytochrome P-450 (CYP) 2B1 isozyme with three chiral polychlorinated biphenyl (PCB) congeners (PCBs 45, 95, and 132) were performed to investigate factors affecting phase I stereoselective biotransformation. Rat CYP2B1 preferentially biotransformed the second-eluting atropisomers of PCBs 45 and 95 at low substrate concentration ranges (≤15 μM). Biotransformation competition by different congeners was also observed, with increasing competition at higher chlorination. Competition decreased the biotransformation rates of each congener stereoselectively, affecting atropisomeric composition. No atropisomeric enrichment was observed for PCB 132 upon incubation of the racemate. However, under the same conditions, significant differences in biotransformation kinetics were observed in individual atropisomer incubations, indicating that (+)-PCB 132 and (-)-PCB 132 were competitively biotransformed. Homology modeling and docking studies suggested that each atropisomer had different interactions with rat CYP2B1 and could dock with the isozyme at different locations. This is one possible explanation for stereoselective biotransformation and competition of chiral PCBs at the molecular level. Our results suggest that the lack of predictive capability for stereoselectivity of PCBs and other chiral pollutants in biota may be due to competitive and/or inhibitory activities of different substrates, including individual enantiomers of the same compound.

Role of the cytochrome P450 enzyme system in veterinary pharmacokinetics: where are we now? Where are we going?

Drug metabolism is a core determinant of the dose-effectiveness-toxicity relationship of many compounds. It is also critical to the human food safety assessment of drug residues in the edible tissues of food-producing animals. This article describes the current state of knowledge regarding the role of the cytochrome P450 superfamily of enzymes in determining the metabolic profile of compounds administered to companion animals (e.g., dog and cat) and to food-producing animal species (e.g., cattle, swine, chickens). In turn, this knowledge reflects the collection of insights derived from the recognized population variability observed in human drug metabolism, our general understanding of the kinetics of various drug-metabolism pathways, emerging tools that enable the role of pharmacogenetics to be studied and the characterization of drug metabolism in individual veterinary species. Ultimately, by increasing our insights with regard to factors that can influence drug metabolism, our knowledge of metabolic pathways, sources of within- and between-species variability in pharmacokinetics and the development of in silico models that can be used to predict pharmacokinetic profiles from these diverse sources of information. We will improve our ability to generate the population inferences needed to insure the target animal safety, product effectiveness and the human food safety of veterinary pharmaceuticals.

Insights into molecular basis of cytochrome p450 inhibitory promiscuity of compounds

Cytochrome P450 inhibitory promiscuity of a drug has potential effects on the occurrence of clinical drug-drug interactions. Understanding how a molecular property is related to the P450 inhibitory promiscuity could help to avoid such adverse effects. In this study, an entropy-based index was defined to quantify the P450 inhibitory promiscuity of a compound based on a comprehensive data set, containing more than 11,500 drug-like compounds with inhibition against five major P450 isoforms, 1A2, 2C9, 2C19, 2D6, and 3A4. The results indicated that the P450 inhibitory promiscuity of a compound would have a moderate correlation with molecular aromaticity, a minor correlation with molecular lipophilicity, and no relations with molecular complexity, hydrogen bonding ability, and TopoPSA. We also applied an index to quantify the susceptibilities of different P450 isoforms to inhibition based on the same data set. The results showed that there was a surprising level of P450 inhibitory promiscuity even for substrate specific P450, susceptibility to inhibition follows the rank-order: 1A2 > 2C19 > 3A4 > 2C9 > 2D6. There was essentially no correlation between P450 inhibitory potency and specificity and minor negative trade-offs between P450 inhibitory promiscuity and catalytic promiscuity. In addition, classification models were built to predict the P450 inhibitory promiscuity of new chemicals using support vector machine algorithm with different fingerprints. The area under the receiver operating characteristic curve of the best model was about 0.9, evaluated by 5-fold cross-validation. These findings would be helpful for understanding the mechanism of P450 inhibitory promiscuity and improving the P450 inhibitory selectivity of new chemicals in drug discovery.

A single active-site mutation of P450BM-3 dramatically enhances substrate binding and rate of product formation

Identifying key structural features of cytochromes P450 is critical in understanding the catalytic mechanism of these important drug-metabolizing enzymes. Cytochrome P450BM-3 (BM-3), a structural and mechanistic P450 model, catalyzes the regio- and stereoselective hydroxylation of fatty acids. Recent work has demonstrated the importance of water in the mechanism of BM-3, and site-specific mutagenesis has helped to elucidate mechanisms of substrate recognition, binding, and product formation. One of the amino acids identified as playing a key role in the active site of BM-3 is alanine 328, which is located in the loop between the K helix and β 1-4. In the A328V BM-3 mutant, substrate affinity increases 5-10-fold and the turnover number increases 2-8-fold compared to wild-type enzyme. Unlike wild-type enzyme, this mutant is purified from E. coli with endogenous substrate bound due to the higher binding affinity. Close examination of the crystal structures of the substrate-bound native and A328V mutant BMPs indicates that the positioning of the substrate is essentially identical in the two forms of the enzyme, with the two valine methyl groups occupying voids present in the active site of the wild-type substrate-bound structure.

Enabling clearance predictions to emerge from in silico actions of quasi-autonomous hepatocyte components

We demonstrate the feasibility of using in silico hepatocyte cultures (ISHCs) to provide predictions of the intrinsic clearance (CL) of compounds in hepatocyte cultures. We compare results with predictions obtained using a multiple linear regression method. Our expectation is that the method can be extended to predict in vivo clearance of new compounds in humans. Within ISHCs, mobile "compounds" carry information describing referent compound properties. We used an iterative refinement protocol for ISHC refinement and development of parameterization methods. Quasi-autonomous "hepatocytes" and their components (including "transporters" and "enzymes") use a small, event-specific subset of compound properties to decide how to interact with encountered compounds each simulation cycle. The probability of occurrence for each event is specified by a rule that uses a subset of compound properties known to influence that event in vitro. ISHC experiments mimic in vitro counterparts. In silico clearance is measured the same as in vitro clearance and is used to predict a corresponding CL value. For 39 of 73 compounds having calculated CL S.D.s, 79% of ISHC predictions and 23% of regression predictions were within CL ± 2 S.D. For all 73 compounds, 38% of ISHC predictions and 32% of regression predictions were within a factor of 2 of the referent CL values. ISHC details during simulations stand as a mechanistic hypothesis of how clearance phenomena emerge during in vitro experiments.

Cytochrome P450 isozyme protein verified in the skin of southern hemisphere humpback whales (Megaptera novaeangliae): implications for biochemical biomarker assessment

Large mysticete whales represent a unique challenge for chemical risk assessment. Few epidemiological investigations are possible due to the low incidence of adult stranding events. Similarly their often extreme life-history adaptations of prolonged migration and fasting challenge exposure assumptions. Molecular biomarkers offer the potential to complement information yielded through tissue chemical analysis, as well as providing evidence of a molecular response to chemical exposure. In this study we confirm the presence of cytochrome P450 reductase (CPR) and cytochrome P450 isoenzyme 1A1 (CYP1A1) in epidermal tissue of southern hemisphere humpback whales (Megaptera novaeangliae). The detection of CYP1A1 in the integument of the humpback whale affords the opportunity for further quantitative non-destructive investigations of enzyme activity as a function of chemical stress.

Health effects from long-range transported contaminants in Arctic top predators: An integrated review based on studies of polar bears and relevant model species

The aim of this review is to provide a thorough overview of the health effects from the complexed biomagnified mixture of long-range transported industrial organochlorines (OCs), polybrominated diphenyl ethers (PBDEs), perfluorinated compounds (PFCs) and mercury (Hg) on polar bear (Ursus maritimus) health. Multiple scientific studies of polar bears indicate negative relationships between exposure to these contaminants and health parameters; however, these are all of a correlative nature and do not represent true cause-and-effects. Therefore, information from controlled studies of farmed Norwegian Arctic foxes (Vulpes lagopus) and housed East and West Greenland sledge dogs (Canis familiaris) were included as supportive weight of evidence in the clarification of contaminant exposure and health effects in polar bears. The review showed that hormone and vitamin concentrations, liver, kidney and thyroid gland morphology as well as reproductive and immune systems of polar bears are likely to be influenced by contaminant exposure. Furthermore, exclusively based on polar bear contaminant studies, bone density reduction and neurochemical disruption and DNA hypomethylation of the brain stem seemed to occur. The range of tissue concentration, at which these alterations were observed in polar bears, were ca. 1-70,000 ng/g lw for OCs (blood plasma concentrations of some PCB metabolites even higher), ca. 1-1000 ng/g lw for PBDEs and for PFCs and Hg 114-3052 ng/g ww and 0.1-50 microg/g ww, respectively. Similar concentrations were found in farmed foxes and housed sledge dogs while the lack of dose response designs did not allow an estimation of threshold levels for oral exposure and accumulated tissue concentrations. Nor was it possible to pinpoint a specific group of contaminants being more important than others nor analyze their interactions. For East Greenland polar bears the corresponding daily SigmaOC and SigmaPBDE oral exposure was estimated to be 35 and 0.34 microg/kg body weight, respectively. Furthermore, PFC concentrations, at which population effect levels could occur, are likely to be reached around year 2012 for the East Greenland polar bear subpopulation if current increasing temporal trends continue. Such proposed reproductive population effects were supported by physiological based pharmacokinetic (PBPK) modelling of critical body residues (CBR) with risk quotients >or=1 for SigmaPCB, dieldrin, SigmaPFC and SigmaOHC (organohalogen contaminant). The estimated daily TEQ for East Greenland polar bears and East Greenland sledge dogs were 32-281-folds above WHO SigmaTEQ guidelines for humans. Compared to human tolerable daily intake (TDI), these were exceeded for PCBs, dieldrin, chlordanes and SigmaHCH in East Greenland polar bears. Comparisons like these should be done with caution, but together with the CBR modelling and T-score estimations, these were the only available tools for polar bear risk evaluation. In conclusion, polar bears seem to be susceptible to contaminant induced stress that may have an overall sub-clinical impact on their health and population status via impacts on their immune and reproductive systems.

Comprehensive characterization of cytochrome P450 isozyme selectivity across chemical libraries

The cytochrome P450 (CYP) gene family catalyzes drug metabolism and bioactivation and is therefore relevant to drug development. We determined potency values for 17,143 compounds against five recombinant CYP isozymes (1A2, 2C9, 2C19, 2D6 and 3A4) using an in vitro bioluminescent assay. The compounds included libraries of US Food and Drug Administration (FDA)-approved drugs and screening libraries. We observed cross-library isozyme inhibition (30-78%) with important differences between libraries. Whereas only 7% of the typical screening library was inactive against all five isozymes, 33% of FDA-approved drugs were inactive, reflecting the optimized pharmacological properties of the latter. Our results suggest that low CYP 2C isozyme activity is a common property of drugs, whereas other isozymes, such as CYP 2D6, show little discrimination between drugs and unoptimized compounds found in screening libraries. We also identified chemical substructures that differentiated between the five isozymes. The pharmacological compendium described here should further the understanding of CYP isozymes.

Concentrations, patterns and metabolites of organochlorine pesticides in relation to xenobiotic phase I and II enzyme activities in ringed seals (Phoca hispida) from Svalbard and the Baltic Sea

The present study investigates the concentrations and patterns of organochlorine pesticides (OCPs) and their metabolites in liver and plasma of two ringed seal populations (Phoca hispida): lower contaminated Svalbard population and more contaminated Baltic Sea population. Among OCPs, p,p'-DDE and sum-chlordanes were the highest in concentration. With increasing hepatic contaminant concentrations and activities of xenobiotic-metabolizing enzymes, the concentrations of 3-methylsulfonyl-p,p'-DDE and the concentration ratios of pentachlorophenol/hexachlorobenzene increased, and the toxaphene pattern shifted more towards persistent Parlar-26 and -50 and less towards more biodegradable Parlar-44. Relative concentrations of the chlordane metabolites, oxychlordane and -heptachlorepoxide, to sum-chlordanes were higher in the seals from Svalbard compared to the seals from the Baltic, while the trend was opposite for cis- and trans-nonachlor. The observed differences in the OCP patterns in the seals from the two populations are probably related to the catalytic activity of xenobiotic-metabolizing enzymes, and also to differences in dietary exposure.

Biotransformation of PCBs in relation to phase I and II xenobiotic-metabolizing enzyme activities in ringed seals (Phoca hispida) from Svalbard and the Baltic Sea

Polychlorinated biphenyls (PCBs) may induce activity of hepatic enzymes, mainly Phase I monooxygenases and conjugating Phase II enzymes, that catalyze the metabolism of PCBs leading to formation of metabolites and to potential adverse health effects. The present study investigates the concentration and pattern of PCBs, the induction of hepatic phase I and II enzymes, and the formation of hydroxy (OH) and methylsulfonyl (CH3SO2=MeSO2) PCB metabolites in two ringed seal (Phoca hispida) populations, which are contrasted by the degree of contamination exposure, that is, highly contaminated Baltic Sea (n=31) and less contaminated Svalbard (n=21). Phase I enzymes were measured as ethoxyresorufin-O-deethylation (EROD), benzyloxyresorufin-O-dealkylation (BROD), methoxyresorufin-O-demethylation (MROD), and pentoxyresorufin-O-dealkylation (PROD) activities, and phase II enzymes were measured as uridine diphosphophate glucuronosyl transferase (UDPGT) and glutathione-S-transferase (GST). Geographical comparison, multivariate, and correlation analysis indicated that sigma-PCB had a positive impact on Phase I enzyme and GST activities leading to biotransformation of group III (vicinal ortho-meta-H atoms and < or =1 ortho-chlorine (Cl)) and IV PCBs (vicinal meta-para-H atoms and < or =2 ortho-Cl). The potential precursors for the main OH-PCBs detected in plasma in the Baltic seals were group III PCBs. MeSO2-PCBs detected in liver were mainly products of group IV PCB metabolism. Both CYP1A- and CYP2B-like enzymes are suggested to be involved in the PCB biotransformation in ringed seals.

Structural requirements for inhibitors of cytochromes P450 2B: Assessment of the enzyme interaction with diamondoids

The series of diamondoids: adamantane, diamantane, triamantane, 2-isopropenyl-2-methyladamantane and 3-isopropenyl-3-methyldiamantane (3-IPMDIA), were employed to elucidate the molecular basis of their interaction with the active site of cytochromes P450 (CYP) of a 2B subfamily. These potent inhibitors of CYP2B enzymes were docked into the homology model of CYP2B4. Apparent dissociation constants calculated for the complexes of CYP2B4 with docked diamandoids agreed closely with the experimental data showing inhibition potency of the compounds and their binding affinity to CYP2B4. Superimposed structures of docked diamondoids mapped binding site residues. As they are mainly non-polar residues, the hydrophobicity plays the major role in the binding of diamondoids. Overlapping structure of diamondoids defined an elliptical binding cavity (5.9A inner diameter, 7.9A length) forming an angle of approximately 43 degrees with the heme plane. CYP2B specific diamondoids, namely 3-IPMDIA, showing the highest binding affinity, should be considered for a potential clinical use.

Methods for Predicting Human Drug Metabolism

Drug metabolism information is a necessary component of drug discovery and development. The key issues in drug metabolism include identifying: the enzyme(s) involved, the site(s) of metabolism, the resulting metabolite(s), and the rate of metabolism. Methods for predicting human drug metabolism from in vitro and computational methodologies and determining relationships between the structure and metabolic activity of molecules are also critically important for understanding potential drug interactions and toxicity. There are numerous experimental and computational approaches that have been developed in order to predict human metabolism which have their own limitations. It is apparent that few of the computational tools for metabolism prediction alone provide the major integrated functions needed to assist in drug discovery. Similarly the different in vitro methods for human drug metabolism themselves have implicit limitations. The utilization of these methods for pharmaceutical and other applications as well as their integration is discussed as it is likely that hybrid methods will provide the most success.

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.

Biotransformation of polybrominated diphenyl ethers and polychlorinated biphenyls in beluga whale (Delphinapterus leucas) and rat mammalian model using an in vitro hepatic microsomal assay

Although polychlorinated biphenyls (PCBs) and polybrominated diphenyl ether (PBDE) flame retardants are important organic contaminants in the tissues of marine mammals, including those species from the Arctic, there is exceedingly little direct evidence on congener-specific biotransformation. We determined and compared the in vitro metabolism of environmentally relevant PCB (4,4'-di-CB15, 2,3',5-tri-CB26, 2,4,5-tri-CB31, 2,2',5,5'-tetra-CB52, 3,3',4,4'-tetra-CB77, 2,2',4,5,5'-penta-CB101, 2,3,3',4,4'-penta-CB105 and 2,3',4,4',5-penta-CB118), and PBDE (4,4'-di-BDE15, 2,4,4'-tri-BDE28, 2,2',4,4'-tetra-BDE47, 2,2',4,5'-tetra-BDE49, 2,2',4,4',5-penta-BDE99, 2,2',4,4',6-penta-BDE100, 2,2',4,4',5,5'-hexa-BDE153, 2,2',4,4',5,6'-hexa-BDE154 and 2,2',3,4,4',5',6-hepta-BDE183) congeners using hepatic microsomes of a beluga whale (Delphinapterus leucas) from the Arviat (western Hudson Bay) area of the Canadian Arctic. Ortho-meta bromine-unsubstituted BDE15, BDE28 and BDE47 were significantly metabolized (100%, 11% and 5% depleted, respectively) by beluga, whereas control rat microsomes (from pooled male Wistar Han rats) metabolized BDE28, BDE49, BDE99 and BDE154 (13%, 44%, 11% and 17% depleted, respectively). CB15 and CB77 (putative CYP1A substrates) were more rapidly metabolized (100% and 93% depleted, respectively) by male beluga than CB26 and CB31 (CYP1A/CYP2B-like) (25% and 29% depleted, respectively), which were more rapidly metabolized than CB52 (CYP2B-like) (13% depleted). Higher chlorinated CB101 and CB105 showed no depletion. Rat control microsomes metabolized CB15 to a lesser extent (32% depleted) than beluga, but much more rapidly transformed CB52 (51% depleted, respectively). Within the 90 min in vitro assay time frame, the preference was towards metabolism of ortho-meta unsubstituted congeners (for both PCBs and PBDEs) in beluga whale, whereas for rat controls, meta-para unsubstituted congeners also substantially metabolized. For both beluga whale and rat, metabolic rates were inversely associated with the degree of halogenation. For the rapidly biotransformed CB15 and BDE15, water-soluble OH-metabolites were detected after incubation. These results indicate that CYP-mediated oxidative hepatic biotransformation is a metabolic pathway in the toxicokinetics of both PCB and PBDE congeners in beluga whales and in the rat model. This may suggest that the formation of potentially toxic oxidative PCB and PBDE products (metabolites), in addition to the parent pollutants, may be contributing to contaminant-related stress effects on the health of beluga whale.

Mechanistic Insight into the Activity of Tyrosinase from Variable-Temperature Studies in an Aqueous/Organic Solvent

The activity of mushroom tyrosinase towards a representative series of phenolic and diphenolic substrates structurally related to tyrosine has been investigated in a mixed solvent of 34.4% methanol-glycerol (7:1, v/v) and 65.6% (v/v) aqueous 50 mM Hepes buffer at pH 6.8 at various temperatures. The kinetic activation parameters controlling the enzymatic reactions and the thermodynamic parameters associated with the process of substrate binding to the enzyme active species have been deduced from the temperature variation of the kcat and KM parameters. The activation free energy is dominated by the enthalpic term, the value of which lies in the relatively narrow range of 61+/-9 kJ mol(-1) irrespective of substrate or reaction type (monophenolase or diphenolase). The activation entropies are small and generally negative and contribute no more than 10% to the activation free energy. The substrate binding parameters are characterized by large and negative enthalpy and entropy contributions, which are typically dictated by polar protein-substrate interactions. The substrate 4-hydroxyphenylpropionic acid exhibits a strikingly anomalous temperature dependence of the enzymatic oxidation rate, with deltaH(double dagger) approximately = 150 kJ mol(-1) and deltaS(double dagger) approximately = 280 J K(-1) mol(-1), due to the fact that it can competitively bind to the enzyme through the phenol group, like the other substrates, or the carboxylate group, like carboxylic acid inhibitors. A kinetic model that takes into account the dual substrate/inhibitor nature of this compound enables rationalization of this anomalous behavior.

An assessment of the toxicological significance of anthropogenic contaminants in Canadian arctic wildlife

Anthropogenic contaminants have been a concern in the Canadian arctic for over 30 years due to relatively high concentrations of bioaccumulating and biomagnifying organochlorine contaminants (OCs) and toxic metals found in some arctic biota and humans. However, few studies have addressed the potential effects of these contaminants in Canadian arctic wildlife. Prior to 1997, biological effects data were minimal and insufficient at any level of biological organization. The present review summarizes recent studies on biological effects related to contaminant exposure, and compares new tissue concentration data to threshold effects levels. Weak relationships between cadmium, mercury and selenium burdens and health biomarkers in common eider ducks (Somateria mollissima borealis) in Nunavut were found but it was concluded that metals were not influencing the health of these birds. Black guillemots (Cepphus grylle) examined near PCB-contaminated Saglek Bay, Labrador, had enlarged livers, elevated EROD and liver lipid levels and reduced retinol (vitamin A) and retinyl palmitate levels, which correlated to PCB levels in the birds. Circulating levels of thyroid hormones in polar bears (Ursus maritimus) were correlated to PCB and HO-PCB plasma concentrations, but the impact at the population level is unknown. High PCB and organochlorine pesticide concentrations were found to be strongly associated with impaired humoral and cell-mediated immune responses in polar bears, implying an increased infection risk that could impact the population. In beluga whale (Delphinapterus leucas), cytochromes P450 (phase I) and conjugating (phase II) enzymes have been extensively profiled (immunochemically and catalytically) in liver, demonstrating the importance of contaminants in relation to enzyme induction, metabolism and potential contaminant bioactivation and fate. Concentrations of OCs and metals in arctic terrestrial wildlife, fish and seabirds are generally below effects thresholds, with the possible exception of PCBs in burbot (Lota lota) in some Yukon lakes, Greenland shark (Somniosus microcephalus), glaucous and great black-backed gulls (Larus hyperboreus and L. marinus), and TEQs of dioxin-like chemicals in seabird eggs. PCB and DDT concentrations in several arctic marine mammal species exceed effects thresholds, although evidence of stress in these populations is lacking. There is little evidence that contaminants are having widespread effects on the health of Canadian arctic organisms, with the possible exception of polar bears. However, further research and better understanding of organohalogen exposure in arctic biota is needed considering factors such as tissue levels that exceed effects thresholds, exposure to "new" organohalogen contaminants of concern, contaminated regions, and climate change.

Computational prediction of human drug metabolism

There is an urgent requirement within the pharmaceutical and biotechnology industries, regulatory authorities and academia to improve the success of molecules that are selected for clinical trials. Although absorption, distribution, metabolism, excretion and toxicity (ADME/Tox) properties are some of the many components that contribute to successful drug discovery and development, they represent factors for which we currently have in vitro and in vivo data that can be modelled computationally. Understanding the possible toxicity and the metabolic fate of xenobiotics in the human body is particularly important in early drug discovery. There is, therefore, a need for computational methodologies for uncovering the relationships between the structure and the biological activity of novel molecules. The convergence of numerous technologies, including high-throughput techniques, databases, ADME/Tox modelling and systems biology modelling, is leading to the foundation of systems-ADME/Tox. Results from experiments can be integrated with predictions to globally simulate and understand the likely complete effects of a molecule in humans. The development and early application of major components of MetaDrug (GeneGo, Inc.) software will be described, which includes rule-based metabolite prediction, quantitative structure-activity relationship models for major drug metabolising enzymes, and an extensive database of human protein-xenobiotic interactions. This represents a combined approach to predicting drug metabolism. MetaDrug can be readily used for visualising Phase I and II metabolic pathways, as well as interpreting high-throughput data derived from microarrays as networks of interacting objects. This will ultimately aid in hypothesis generation and the early triaging of molecules likely to have undesirable predicted properties or measured effects on key proteins and cellular functions.

Quantitative structure-activity relationships (QSARs) within the cytochrome P450 system: QSARs describing substrate binding, inhibition and induction of P450s

Quantitative structure-activity relationships (QSARs) within substrates, inducers and inhibitors of cytochromes P450 involved in xenobiotic metabolism are reported, together with QSARs associated with induction, inhibition and metabolic rate. The importance of frontier orbitals and shape descriptors, such as planarity (estimated by the area/depth(2) parameter) and rectangularity (estimated by the length/width parameter) is discussed, particularly in the context of the COMPACT system which discriminates between several P450 families associated with the activation and detoxication of xenobiotics. The use of parameters, particularly those derived from homology modelling of mammalian (especially human) P450s that are involved in exogenous metabolism, in generating QSARs for P450 substrates is discussed in the context of explaining differences in the binding affinities of human P450 substrates which are pharmacologically active.

Characterization and profiling of hepatic cytochromes P450 and phase II xenobiotic-metabolizing enzymes in beluga whales (Delphinapterus leucas) from the St. Lawrence River Estuary and the Canadian Arctic

Cytochromes P450 (CYP, phase I) and conjugating (phase II) enzymes can be induced by and influence the toxicokinetics (metabolism) and toxicity of xenobiotic contaminants in exposed organisms. Beluga whale (Delphinapterus leucas) from the endangered St. Lawrence (SL) River Estuary population exhibit deleterious health effects and various severe pathologies that have been associated with contaminant exposure. In contrast, such effects (e.g. reproductive and immunological impairment) are generally less frequent in less exposed populations in the Canadian Arctic (CA). In the present study, opportunistic sampling resulted in the collection immediately after death of liver tissue from a single female neonate SL beluga (SL6) and male and female CA beluga (n=10) from the Arviat region of western Hudson Bay, in addition to sampling of stranded carcasses of male and female SL beluga (n=5) at least 12 h postmortem. We immunologically characterized cross-reactive proteins of hepatic microsomal CYP1A, CYP2B, CYP3A, CYP2E, epoxide hydrolase (EH) and uridine diphosphoglucuronosyl transferase (UDPGT) isozymes. Cross-reactive proteins were found in all SL and CA beluga using anti-rat CYP1A1, anti-rainbow trout CYP3A, anti-human CYP2E1, anti-rabbit EH and anti-human UDPGT1A1 polyclonal antibodies (Abs), whereas faintly cross-reactive CYP2B proteins were only found in SL6 and the CA samples using an anti-rabbit CYP2B1 Ab. In corresponding catalytic activity assessments, only SL6 and all CA beluga microsomal samples exhibited CYP1A-mediated 7-ethoxyresorufin O-deethylase (EROD) activity (51-260 pmol/mg/min), CYP3A-mediated activity (113-899 pmol/mg/min) based on the formation of 6beta-hydroxytestosterone using a testosterone hydroxylase assay, and UDPGT activity (830-4956 pmol/mg/min) based on 1-naphthylglucuronide formation. The marginal cross-reactivity with the anti-CYP2B1 Ab and lack of catalytically measurable hydroxytestosterone isomers associated with CYP2B-type activity in all the SL and CA animals is suggestive of low CYP2B-type enzyme expression in beluga. The absence of measurable total P450 enzyme levels and catalytic activities in samples from the stranded SL belugas suggested catalytically inactive enzymes as a consequence of tissue degradation related due to the time delay of sample collection after death. However, all SL and CA animals demonstrated similar, immunologically cross-reactive phase I and II hepatic enzyme profiles, which is suggestive of the importance of metabolism in the toxicokinetics and fate of xenobiotics in animals from both populations

QUANTITATIVE STRUCTURE-METABOLISM RELATIONSHIP MODELING OF METABOLICN-DEALKYLATION REACTION RATES

It is widely recognized that preclinical drug discovery can be improved via the parallel assessment of bioactivity, absorption, distribution, metabolism, excretion, and toxicity properties of molecules. High-throughput computational methods may enable such assessment at the earliest, least expensive discovery stages, such as during screening compound libraries and the hit-to-lead process. As an attempt to predict drug metabolism and toxicity, we have developed an approach for evaluation of the rate of N-dealkylation mediated by two of the most important human cytochrome P450s (P450), namely CYP3A4 and CYP2D6. We have taken a novel approach by using descriptors generated for the whole molecule, the reaction centroid, and the leaving group, and then applying neural network computations and sensitivity analysis to generate quantitative structure-metabolism relationship models. The quality of these models was assessed by using the cross-validated correlation coefficients of 0.82 for CYP3A4 and 0.79 for CYP2D6 as well as external test molecules for each enzyme. The relative performance of different neural networks was also compared, and modular neural networks with two hidden layers provided the best predictive ability. Functional dependencies between the neural network input and output variables, generalization ability, and limitations of the described approach are also discussed. These models represent an initial approach to predicting the rate of P450-mediated metabolism and may be applied and integrated with other models for P450 binding to produce a systems-based approach for predicting drug metabolism.