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Publication Record


Development and Uses of Offline and Web-Searchable Metabolism Databases - The Case of Benzo[a]pyrene.
Rendic SP, Guengerich FP
(2018) Curr Drug Metab 19: 3-46
MeSH Terms: Animals, Benzo(a)pyrene, Cytochrome P-450 CYP1A1, Cytochrome P-450 CYP1B1, Databases, Factual, Humans
Show Abstract · Added March 14, 2018
BACKGROUND - The present work describes development of offline and web-searchable metabolism databases for drugs, other chemicals, and physiological compounds using human and model species, prompted by the large amount of data published after year 1990. The intent was to provide a rapid and accurate approach to published data to be applied both in science and to assist therapy.
METHODS - Searches for the data were done using the Pub Med database, accessing the Medline database of references and abstracts. In addition, data presented at scientific conferences (e.g., ISSX conferences) are included covering the publishing period beginning with the year 1976.
RESULTS - Application of the data is illustrated by the properties of benzo[a]pyrene (B[a]P) and its metabolites. Analysis show higher activity of P450 1A1 for activation of the (-)- isomer of trans-B[a]P-7,8-diol, while P4501B1 exerts higher activity for the (+)- isomer. P450 1A2 showed equally low activity in the metabolic activation of both isomers.
CONCLUSION - The information collected in the databases is applicable in prediction of metabolic drug-drug and/or drug-chemical interactions in clinical and environmental studies. The data on the metabolism of searched compound (exemplified by benzo[a]pyrene and its metabolites) also indicate toxicological properties of the products of specific reactions. The offline and web-searchable databases had wide range of applications (e.g. computer assisted drug design and development, optimization of clinical therapy, toxicological applications) and adjustment in everyday life styles.
Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
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6 MeSH Terms
Oxidation of pyrene, 1-hydroxypyrene, 1-nitropyrene and 1-acetylpyrene by human cytochrome P450 2A13.
Shimada T, Takenaka S, Murayama N, Kramlinger VM, Kim JH, Kim D, Liu J, Foroozesh MK, Yamazaki H, Guengerich FP, Komori M
(2016) Xenobiotica 46: 211-24
MeSH Terms: Animals, Aryl Hydrocarbon Hydroxylases, Cytochrome P-450 CYP1A1, Cytochrome P-450 CYP2A6, Humans, Lepidoptera, Models, Biological, Molecular Docking Simulation, Oxidation-Reduction, Polycyclic Compounds, Pyrenes
Show Abstract · Added March 14, 2018
1. The polycyclic hydrocarbons (PAHs), pyrene, 1-hydroxypyrene, 1-nitropyrene and 1-acetylpyrene, were found to induce Type I binding spectra with human cytochrome P450 (P450) 2A13 and were converted to various mono- and di-oxygenated products by this enzyme. 2. Pyrene was first oxidized by P450 2A13 to 1-hydroxypyrene which was further oxidized to di-oxygenated products, i.e. 1,8- and 1,6-dihydroxypyrene. Of five other human P450s examined, P450 1B1 catalyzed pyrene oxidation to 1-hydroxypyrene at a similar rate to P450 2A13 but was less efficient in forming dihydroxypyrenes. P450 2A6, a related human P450 enzyme, which did not show any spectral changes with these four PAHs, showed lower activities in oxidation of these compounds than P450 2A13. 3. 1-Nitropyrene and 1-acetylpyrene were also found to be efficiently oxidized by P450 2A13 to several oxygenated products, based on mass spectrometry analysis. 4. Molecular docking analysis supported preferred orientations of pyrene and its derivatives in the active site of P450 2A13, with lower interaction energies (U values) than observed for P450 2A6 and that several amino acid residues (including Ala-301, Asn-297 and Ala-117) play important roles in directing the orientation of these PAHs in the P450 2A13 active site. In addition, Phe-231 and Gly-329 were found to interact with pyrene to orient this compound in the active site of P450 1B1. 5. These results suggest that P450 2A13 is one of the important enzymes that oxidizes these PAH compounds and may determine how these chemicals are detoxicated and bioactivated in humans.
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11 MeSH Terms
Functional variants in CYP1A1 and GSTM1 are associated with clearance of cervical HPV infection.
Sudenga SL, Shrestha S, Macaluso M, Partridge EE, Johanning GL, Piyathilake CJ
(2014) Gynecol Oncol 135: 560-4
MeSH Terms: Adult, Cohort Studies, Cytochrome P-450 CYP1A1, DNA, Viral, Female, Genotype, Glutathione Transferase, Humans, Papillomaviridae, Papillomavirus Infections, Uterine Cervical Diseases, Uterine Cervical Neoplasms
Show Abstract · Added August 15, 2017
OBJECTIVE - We evaluated time to clearance of high risk (HR) HPV infection in relation to functional variants in three genes (CYP1A1, GSTT1, and GSTM1).
METHODS - The study group consisted of 450 HR-HPV infected women from the Atypical squamous cells of undetermined significance-low-grade squamous intraepithelial Lesion Triage Study (ALTS) cohort followed up at the clinical center at Birmingham, Alabama. The Cox proportional hazard model with the Wei-Lin-Weisfeld (WLW) approach was used, controlling for relevant covariates.
RESULTS - Women who were polymorphic for CYP1A1 experienced an HR-HPV clearance rate that was 20% (HR=0.80, p=0.04) lower than women without the polymorphism for CYP1A1, adjusting for all other cofactors. The GSTM1 null genotype was associated with higher HR-HPV clearance rate (HR=1.39, p=0.006). The polymorphism in GSTT1 was not significantly associated with time to clearance of HR-HPV.
CONCLUSIONS - Xenobiotic metabolism genes may influence the natural history of HR-HPV infection and its progression to cervical cancer.
Copyright © 2014 Elsevier Inc. All rights reserved.
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12 MeSH Terms
Targeted multiplex imaging mass spectrometry with single chain fragment variable (scfv) recombinant antibodies.
Thiery G, Mernaugh RL, Yan H, Spraggins JM, Yang J, Parl FF, Caprioli RM
(2012) J Am Soc Mass Spectrom 23: 1689-96
MeSH Terms: Animals, Antibodies, Monoclonal, Aryl Hydrocarbon Hydroxylases, Avidin, Biotin, Breast, Breast Neoplasms, Cytochrome P-450 CYP1A1, Cytochrome P-450 CYP1B1, Enzyme-Linked Immunosorbent Assay, Female, Histocytochemistry, Humans, Mass Spectrometry, Mice, Molecular Imaging, Rats, Recombinant Proteins, Sensitivity and Specificity, Single-Chain Antibodies
Show Abstract · Added March 7, 2014
Recombinant scfv antibodies specific for CYP1A1 and CYP1B1 P450 enzymes were combined with targeted imaging mass spectrometry to simultaneously detect the P450 enzymes present in archived, paraffin-embedded, human breast cancer tissue sections. By using CYP1A1 and CYP1B1 specific scfv, each coupled to a unique reporter molecule (i.e., a mass tag) it was possible to simultaneously detect multiple antigens within a single tissue sample with high sensitivity and specificity using mass spectrometry. The capability of imaging multiple antigens at the same time is a significant advance that overcomes technical barriers encountered when using present day approaches to develop assays that can simultaneously detect more than a single antigen in the same tissue sample.
1 Communities
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20 MeSH Terms
Bioactivation of fluorinated 2-aryl-benzothiazole antitumor molecules by human cytochrome P450s 1A1 and 2W1 and deactivation by cytochrome P450 2S1.
Wang K, Guengerich FP
(2012) Chem Res Toxicol 25: 1740-51
MeSH Terms: Antineoplastic Agents, Benzothiazoles, Biocatalysis, Chromatography, High Pressure Liquid, Cytochrome P-450 CYP1A1, Cytochrome P-450 Enzyme System, Cytochrome P450 Family 2, DNA Adducts, Humans, Kinetics, Microsomes, Liver, Oxidation-Reduction, Spectrometry, Mass, Electrospray Ionization, Thiazoles
Show Abstract · Added March 7, 2014
Both 2-(4-amino-3-methylphenyl)-5-fluorobenzothiazole (5F 203) and 5-fluoro-2-(3,4-dimethoxyphenyl)-benzothiazole (GW 610) contain the benzothiazole pharmacophore and possess potent and selective in vitro antitumor properties. Prior studies suggested the involvement of cytochrome P450 (P450) 1A1 and 2W1-mediated bioactivation in the antitumor activities and P450 2S1-mediated deactivation of 5F 203 and GW 610. In the present study, the biotransformation pathways of 5F 203 and GW 610 by P450s 1A1, 2W1, and 2S1 were investigated, and the catalytic parameters of P450 1A1- and 2W1-catalyzed oxidation were determined in steady-state kinetic studies. The oxidations of 5F 203 catalyzed by P450s 1A1 and 2W1 yielded different products, and the formation of a hydroxylamine was observed for the first time in the latter process. Liquid chromatography-mass spectrometry (LC-MS) analysis with the synthetic hydroxylamine and also a P450 2W1/5F 203 incubation mixture indicated the formation of dGuo adduct via a putative nitrenium intermediate. P450 2W1-catalyzed oxidation of GW 610 was 5-fold more efficient than the P450 1A1-catalyzed reaction. GW 610 underwent a two-step oxidation process catalyzed by P450 1A1 or 2W1: a regiospecific O-demethylation and a further hydroxylation. Glutathione (GSH) conjugates of 5F 203 and GW 610, presumably through a quninoneimine and a 1,2-quinone intermediate, respectively, were detected. These results demonstrate that human P450s 1A1 and 2W1 mediate 5F 203 and GW 610 bioactivation to reactive intermediates and lead to GSH conjugates and a dGuo adduct, which may account for the antitumor activities of 5F 203 and GW 610 and also be involved in cell toxicity. P450 2S1 can catalyze the reduction of the hydroxylamine to the amine 5F 203 under anaerobic conditions and, to a lesser extent, under aerobic conditions, thus attenuating the anticancer activity.
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14 MeSH Terms
Spectral modification and catalytic inhibition of human cytochromes P450 1A1, 1A2, 1B1, 2A6, and 2A13 by four chemopreventive organoselenium compounds.
Shimada T, Murayama N, Tanaka K, Takenaka S, Guengerich FP, Yamazaki H, Komori M
(2011) Chem Res Toxicol 24: 1327-37
MeSH Terms: Animals, Antineoplastic Agents, Aryl Hydrocarbon Hydroxylases, Binding Sites, Biocatalysis, Catalytic Domain, Computer Simulation, Cyanates, Cytochrome P-450 CYP1A1, Cytochrome P-450 CYP1A2, Cytochrome P-450 CYP1A2 Inhibitors, Cytochrome P-450 CYP1B1, Cytochrome P-450 CYP2A6, Cytochrome P-450 Enzyme Inhibitors, Cytochrome P-450 Enzyme System, Humans, Neoplasms, Organoselenium Compounds, Protein Binding, Rats
Show Abstract · Added March 26, 2014
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.
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20 MeSH Terms
Estrogen metabolism and exposure in a genotypic-phenotypic model for breast cancer risk prediction.
Crooke PS, Justenhoven C, Brauch H, GENICA Consortium, Dawling S, Roodi N, Higginbotham KS, Plummer WD, Schuyler PA, Sanders ME, Page DL, Smith JR, Dupont WD, Parl FF
(2011) Cancer Epidemiol Biomarkers Prev 20: 1502-15
MeSH Terms: Adult, Algorithms, Area Under Curve, Aryl Hydrocarbon Hydroxylases, Breast Neoplasms, Cytochrome P-450 CYP1A1, Cytochrome P-450 CYP1B1, Estradiol, Estrogens, Estrogens, Catechol, Female, Genetic Predisposition to Disease, Genotype, Humans, Middle Aged, Models, Theoretical, Phenotype, Risk Factors
Show Abstract · Added March 20, 2014
BACKGROUND - Current models of breast cancer risk prediction do not directly reflect mammary estrogen metabolism or genetic variability in exposure to carcinogenic estrogen metabolites.
METHODS - We developed a model that simulates the kinetic effect of genetic variants of the enzymes CYP1A1, CYP1B1, and COMT on the production of the main carcinogenic estrogen metabolite, 4-hydroxyestradiol (4-OHE(2)), expressed as area under the curve metric (4-OHE(2)-AUC). The model also incorporates phenotypic factors (age, body mass index, hormone replacement therapy, oral contraceptives, and family history), which plausibly influence estrogen metabolism and the production of 4-OHE(2). We applied the model to two independent, population-based breast cancer case-control groups, the German GENICA study (967 cases, 971 controls) and the Nashville Breast Cohort (NBC; 465 cases, 885 controls).
RESULTS - In the GENICA study, premenopausal women at the 90th percentile of 4-OHE(2)-AUC among control subjects had a risk of breast cancer that was 2.30 times that of women at the 10th control 4-OHE(2)-AUC percentile (95% CI: 1.7-3.2, P = 2.9 × 10(-7)). This relative risk was 1.89 (95% CI: 1.5-2.4, P = 2.2 × 10(-8)) in postmenopausal women. In the NBC, this relative risk in postmenopausal women was 1.81 (95% CI: 1.3-2.6, P = 7.6 × 10(-4)), which increased to 1.83 (95% CI: 1.4-2.3, P = 9.5 × 10(-7)) when a history of proliferative breast disease was included in the model.
CONCLUSIONS - The model combines genotypic and phenotypic factors involved in carcinogenic estrogen metabolite production and cumulative estrogen exposure to predict breast cancer risk.
IMPACT - The estrogen carcinogenesis-based model has the potential to provide personalized risk estimates.
©2011 AACR
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18 MeSH Terms
Structure-function relationships of inhibition of human cytochromes P450 1A1, 1A2, 1B1, 2C9, and 3A4 by 33 flavonoid derivatives.
Shimada T, Tanaka K, Takenaka S, Murayama N, Martin MV, Foroozesh MK, Yamazaki H, Guengerich FP, Komori M
(2010) Chem Res Toxicol 23: 1921-35
MeSH Terms: Aryl Hydrocarbon Hydroxylases, Binding Sites, Computer Simulation, Cytochrome P-450 CYP1A1, Cytochrome P-450 CYP1A2, Cytochrome P-450 CYP1A2 Inhibitors, Cytochrome P-450 CYP1B1, Cytochrome P-450 CYP2C9, Cytochrome P-450 CYP3A, Cytochrome P-450 CYP3A Inhibitors, Cytochrome P-450 Enzyme Inhibitors, Cytochrome P-450 Enzyme System, Flavonoids, Humans, Kinetics, Structure-Activity Relationship
Show Abstract · Added March 7, 2014
Structure-function relationships for the inhibition of human cytochrome P450s (P450s) 1A1, 1A2, 1B1, 2C9, and 3A4 by 33 flavonoid derivatives were studied. Thirty-two of the 33 flavonoids tested produced reverse type I binding spectra with P450 1B1, and the potencies of binding were correlated with the abilities to inhibit 7-ethoxyresorufin O-deethylation activity. The presence of a hydroxyl group in flavones, for example, 3-, 5-, and 7-monohydroxy- and 5,7-dihydroxyflavone, decreased the 50% inhibition concentration (IC50) of P450 1B1 from 0.6 μM to 0.09, 0.21, 0.25, and 0.27 μM, respectively, and 3,5,7-trihydroxyflavone (galangin) was the most potent, with an IC50 of 0.003 μM. The introduction of a 4'-methoxy- or 3',4'-dimethoxy group into 5,7-dihydroxyflavone yielded other active inhibitors of P450 1B1 with IC50 values of 0.014 and 0.019 μM, respectively. The above hydroxyl and/or methoxy groups in flavone molecules also increased the inhibition activity with P450 1A1 but not always toward P450 1A2, where 3-, 5-, or 7-hydroxyflavone and 4'-methoxy-5,7-dihydroxyflavone were less inhibitory than flavone itself. P450 2C9 was more inhibited by 7-hydroxy-, 5,7-dihydroxy-, and 3,5,7-trihydroxyflavones than by flavone but was weakly inhibited by 3- and 5-hydroxyflavone. Flavone and several other flavonoids produced type I binding spectra with P450 3A4, but such binding was not always related to the inhibitiory activities toward P450 3A4. These results indicate that there are different mechanisms of inhibition for P450s 1A1, 1A2, 1B1, 2C9, and 3A4 by various flavonoid derivatives and that the number and position of hydroxyl and/or methoxy groups highly influence the inhibitory actions of flavonoids toward these enzymes. Molecular docking studies suggest that there are different mechanisms involved in the interaction of various flavonoids with the active site of P450s, thus causing differences in inhibition of these P450 catalytic activities by flavonoids.
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16 MeSH Terms
Surfing a genetic association interaction network to identify modulators of antibody response to smallpox vaccine.
Davis NA, Crowe JE, Pajewski NM, McKinney BA
(2010) Genes Immun 11: 630-6
MeSH Terms: Algorithms, Antibody Formation, Cytochrome P-450 CYP1A1, Gene Regulatory Networks, Genes, Genome-Wide Association Study, Humans, Markov Chains, NADPH Oxidases, Phenotype, Polymorphism, Single Nucleotide, Retinoid X Receptor alpha, Smallpox Vaccine
Show Abstract · Added August 6, 2012
The variation in antibody response to vaccination likely involves small contributions of numerous genetic variants, such as single-nucleotide polymorphisms (SNPs), which interact in gene networks and pathways. To accumulate the bits of genetic information relevant to the phenotype that are distributed throughout the interaction network, we develop a network eigenvector centrality algorithm (SNPrank) that is sensitive to the weak main effects, gene-gene interactions and small higher-order interactions through hub effects. Analogous to Google PageRank, we interpret the algorithm as the simulation of a random SNP surfer (RSS) that accumulates bits of information in the network through a dynamic probabilistic Markov chain. The transition matrix for the RSS is based on a data-driven genetic association interaction network (GAIN), the nodes of which are SNPs weighted by the main-effect strength and edges weighted by the gene-gene interaction strength. We apply SNPrank to a GAIN analysis of a candidate-gene association study on human immune response to smallpox vaccine. SNPrank implicates a SNP in the retinoid X receptor α (RXRA) gene through a network interaction effect on antibody response. This vitamin A- and D-signaling mediator has been previously implicated in human immune responses, although it would be neglected in a standard analysis because its significance is unremarkable outside the context of its network centrality. This work suggests SNPrank to be a powerful method for identifying network effects in genetic association data and reveals a potential vitamin regulation network association with antibody response.
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13 MeSH Terms
Overexpression of Cu/Zn-superoxide dismutase and/or catalase accelerates benzo(a)pyrene detoxification by upregulation of the aryl hydrocarbon receptor in mouse endothelial cells.
Wang Z, Yang H, Ramesh A, Roberts LJ, Zhou L, Lin X, Zhao Y, Guo Z
(2009) Free Radic Biol Med 47: 1221-9
MeSH Terms: Animals, Aorta, Aryl Hydrocarbon Hydroxylases, Benzo(a)pyrene, Blotting, Western, Catalase, Cells, Cultured, Cytochrome P-450 CYP1A1, Cytochrome P-450 CYP1B1, Endothelium, Vascular, F2-Isoprostanes, Furans, Glutathione Transferase, Inactivation, Metabolic, Mice, RNA, Messenger, RNA, Small Interfering, Receptors, Aryl Hydrocarbon, Reverse Transcriptase Polymerase Chain Reaction, Superoxide Dismutase, Up-Regulation
Show Abstract · Added February 22, 2016
A reduction in endogenously generated reactive oxygen species in vivo delays benzo(a)pyrene (BaP)-accelerated atherosclerosis, as revealed in hypercholesterolemic mice overexpressing Cu/Zn-superoxide dismutase (SOD) and/or catalase. To understand the molecular events involved in this protective action, we studied the effects of Cu/Zn-SOD and/or catalase overexpression on BaP detoxification and on aryl hydrocarbon receptor (AhR) expression and its target gene expression in mouse aortic endothelial cells (MAECs). Our data demonstrate that overexpression of Cu/Zn-SOD and/or catalase leads to an 18- to 20-fold increase in the expression of AhR protein in MAECs. After BaP exposure, the amount of AhR binding to the cytochrome P450 (CYP) 1A1 promoter was significantly greater, and the concentrations of BaP reactive intermediates were significantly less in MAECs overexpressing Cu/Zn-SOD and/or catalase than in wild-type cells. In addition, the BaP-induced CYP1A1 and 1B1 protein levels and BaP-elevated glutathione S-transferase (GST) activity were significantly higher in these transgenic cells, in parallel with elevated GSTp1, CYP1A1, and CYP1B1 mRNA levels, compared to wild-type MAECs. Moreover, knockdown of AhR with RNA interference diminished the Cu/Zn-SOD and catalase enhancement of CYP1A1 expression, GST activity, and BaP detoxification. These data demonstrate that overexpression of Cu/Zn-SOD and/or catalase is associated with upregulation of AhR and its target genes, such as xenobiotic-metabolizing enzymes.
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21 MeSH Terms