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Isoherranen N, Zhong G. Biochemical and physiological importance of the CYP26 retinoic acid hydroxylases. Pharmacol Ther 2019; 204:107400. [PMID: 31419517 PMCID: PMC6881548 DOI: 10.1016/j.pharmthera.2019.107400] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/06/2019] [Indexed: 12/19/2022]
Abstract
The Cytochrome P450 (CYP) family 26 enzymes contribute to retinoic acid (RA) metabolism and homeostasis in humans, mammals and other chordates. The three CYP26 family enzymes, CYP26A1, CYP26B1 and CYP26C1 have all been shown to metabolize all-trans-retinoic acid (atRA) it's 9-cisRA and 13-cisRA isomers and primary metabolites 4-OH-RA and 4-oxo-RA with high efficiency. While no crystal structures of CYP26 enzymes are available, the binding of various ligands has been extensively explored via homology modeling. All three CYP26 enzymes are inducible by treatment with atRA in various prenatal and postnatal tissues and cell types. However, current literature shows that in addition to regulation by atRA, CYP26 enzyme expression is also regulated by other endogenous processes and inflammatory cytokines. In humans and in animal models the expression patterns of CYP26 enzymes have been shown to be tissue and cell type specific, and the expression of the CYP26 enzymes is believed to regulate the formation of critical atRA concentration gradients in various tissue types. Yet, very little data exists on direct disease associations of altered CYP26 expression or activity. Nevertheless, data is emerging describing a variety of human genetic variations in the CYP26 enzymes that are associated with different pathologies. Interestingly, some of these genetic variants result in increased activity of the CYP26 enzymes potentially leading to complex gene-environment interactions due to variability in dietary intake of retinoids. This review highlights the current knowledge of structure-function of CYP26 enzymes and focuses on their role in human retinoid metabolism in different tissues.
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Affiliation(s)
- Nina Isoherranen
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA.
| | - Guo Zhong
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA, USA
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Zhong G, Ortiz D, Zelter A, Nath A, Isoherranen N. CYP26C1 Is a Hydroxylase of Multiple Active Retinoids and Interacts with Cellular Retinoic Acid Binding Proteins. Mol Pharmacol 2018; 93:489-503. [PMID: 29476041 DOI: 10.1124/mol.117.111039] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/22/2018] [Indexed: 01/10/2023] Open
Abstract
The clearance of retinoic acid (RA) and its metabolites is believed to be regulated by the CYP26 enzymes, but the specific roles of CYP26A1, CYP26B1, and CYP26C1 in clearing active vitamin A metabolites have not been defined. The goal of this study was to establish the substrate specificity of CYP26C1, and determine whether CYP26C1 interacts with cellular retinoic acid binding proteins (CRABPs). CYP26C1 was found to effectively metabolize all-trans retinoic acid (atRA), 9-cis-retinoic acid (9-cis-RA), 13-cis-retinoic acid, and 4-oxo-atRA with the highest intrinsic clearance toward 9-cis-RA. In comparison with CYP26A1 and CYP26B1, CYP26C1 resulted in a different metabolite profile for retinoids, suggesting differences in the active-site structure of CYP26C1 compared with other CYP26s. Homology modeling of CYP26C1 suggested that this is attributable to the distinct binding orientation of retinoids within the CYP26C1 active site. In comparison with other CYP26 family members, CYP26C1 was up to 10-fold more efficient in clearing 4-oxo-atRA (intrinsic clearance 153 μl/min/pmol) than CYP26A1 and CYP26B1, suggesting that CYP26C1 may be important in clearing this active retinoid. In support of this, CRABPs delivered 4-oxo-atRA and atRA for metabolism by CYP26C1. Despite the tight binding of 4-oxo-atRA and atRA with CRABPs, the apparent Michaelis-Menten constant in biological matrix (Km) value of these substrates with CYP26C1 was not increased when the substrates were bound with CRABPs, in contrast to what is predicted by free drug hypothesis. Together these findings suggest that CYP26C1 is a 4-oxo-atRA hydroxylase and may be important in regulating the concentrations of this active retinoid in human tissues.
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Affiliation(s)
- Guo Zhong
- Departments of Pharmaceutics (G.Z., N.I.) and Medicinal Chemistry (D.O., A.N.), School of Pharmacy, and Department of Biochemistry, School of Medicine (A.Z.), University of Washington, Seattle, Washington
| | - David Ortiz
- Departments of Pharmaceutics (G.Z., N.I.) and Medicinal Chemistry (D.O., A.N.), School of Pharmacy, and Department of Biochemistry, School of Medicine (A.Z.), University of Washington, Seattle, Washington
| | - Alex Zelter
- Departments of Pharmaceutics (G.Z., N.I.) and Medicinal Chemistry (D.O., A.N.), School of Pharmacy, and Department of Biochemistry, School of Medicine (A.Z.), University of Washington, Seattle, Washington
| | - Abhinav Nath
- Departments of Pharmaceutics (G.Z., N.I.) and Medicinal Chemistry (D.O., A.N.), School of Pharmacy, and Department of Biochemistry, School of Medicine (A.Z.), University of Washington, Seattle, Washington
| | - Nina Isoherranen
- Departments of Pharmaceutics (G.Z., N.I.) and Medicinal Chemistry (D.O., A.N.), School of Pharmacy, and Department of Biochemistry, School of Medicine (A.Z.), University of Washington, Seattle, Washington
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Foti RS, Diaz P, Douguet D. Comparison of the ligand binding site of CYP2C8 with CYP26A1 and CYP26B1: a structural basis for the identification of new inhibitors of the retinoic acid hydroxylases. J Enzyme Inhib Med Chem 2016; 31:148-161. [PMID: 27424662 DOI: 10.1080/14756366.2016.1193734] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The CYP26s are responsible for metabolizing retinoic acid and play an important role in maintaining homeostatic levels of retinoic acid. Given the ability of CYP2C8 to metabolize retinoic acid, we evaluated the potential for CYP2C8 inhibitors to also inhibit CYP26. In vitro assays were used to evaluate the inhibition potencies of CYP2C8 inhibitors against CYP26A1 and CYP26B1. Using tazarotenic acid as a substrate for CYP26, IC50 values for 17 inhibitors of CYP2C8 were determined for CYP26A1 and CYP26B1, ranging from ∼20 nM to 100 μM, with a positive correlation observed between IC50s for CYP2C8 and CYP26A1. An evaluation of IC50's versus in vivo Cmax values suggests that inhibitors such as clotrimazole or fluconazole may interact with CYP26 at clinically relevant concentrations and may alter levels of retinoic acid. These findings provide insight into drug interactions resulting in elevated retinoic acid concentrations and expand upon the pharmacophore of CYP26 inhibition.
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Affiliation(s)
- Robert S Foti
- a Amgen Pharmacokinetics and Drug Metabolism , Cambridge , MA , USA
| | - Philippe Diaz
- b Department of Biomedical and Pharmaceutical Sciences , Core Laboratory for Neuromolecular Production, University of Montana , Missoula , MT , USA.,c Dermaxon , Missoula , MT , USA , and
| | - Dominique Douguet
- d CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Université Nice Sophia Antipolis , Valbonne , France
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Improved Homology Model of the Human all-trans Retinoic Acid Metabolizing Enzyme CYP26A1. Molecules 2016; 21:351. [PMID: 26999080 PMCID: PMC6274249 DOI: 10.3390/molecules21030351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/07/2016] [Accepted: 03/09/2016] [Indexed: 11/17/2022] Open
Abstract
A new CYP26A1 homology model was built based on the crystal structure of cyanobacterial CYP120A1. The model quality was examined for stereochemical accuracy, folding reliability, and absolute quality using a variety of different bioinformatics tools. Furthermore, the docking capabilities of the model were assessed by docking of the natural substrate all-trans-retinoic acid (atRA), and a group of known azole- and tetralone-based CYP26A1 inhibitors. The preferred binding pose of atRA suggests the (4S)-OH-atRA metabolite production, in agreement with recently available experimental data. The distances between the ligands and the heme group iron of the enzyme are in agreement with corresponding distances obtained for substrates and azole inhibitors for other cytochrome systems. The calculated theoretical binding energies agree with recently reported experimental data and show that the model is capable of discriminating between natural substrate, strong inhibitors (R116010 and R115866), and weak inhibitors (liarozole, fluconazole, tetralone derivatives).
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Foti RS, Isoherranen N, Zelter A, Dickmann LJ, Buttrick BR, Diaz P, Douguet D. Identification of Tazarotenic Acid as the First Xenobiotic Substrate of Human Retinoic Acid Hydroxylase CYP26A1 and CYP26B1. J Pharmacol Exp Ther 2016; 357:281-92. [PMID: 26937021 DOI: 10.1124/jpet.116.232637] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/26/2016] [Indexed: 11/22/2022] Open
Abstract
Cytochrome P450 (CYP) 26A1 and 26B1 are heme-containing enzymes responsible for metabolizing all-trans retinoic acid (at-RA). No crystal structures have been solved, and therefore homology models that provide structural information are extremely valuable for the development of inhibitors of cytochrome P450 family 26 (CYP26). The objectives of this study were to use homology models of CYP26A1 and CYP26B1 to characterize substrate binding characteristics, to compare structural aspects of their active sites, and to support the role of CYP26 in the metabolism of xenobiotics. Each model was verified by dockingat-RA in the active site and comparing the results to known metabolic profiles ofat-RA. The models were then used to predict the metabolic sites of tazarotenic acid with results verified by in vitro metabolite identification experiments. The CYP26A1 and CYP26B1 homology models predicted that the benzothiopyranyl moiety of tazarotenic acid would be oriented toward the heme of each enzyme and suggested that tazarotenic acid would be a substrate of CYP26A1 and CYP26B1. Metabolite identification experiments indicated that CYP26A1 and CYP26B1 oxidatively metabolized tazarotenic acid on the predicted moiety, with in vitro rates of metabolite formation by CYP26A1 and CYP26B1 being the highest across a panel of enzymes. Molecular analysis of the active sites estimated the active-site volumes of CYP26A1 and CYP26B1 to be 918 Å(3)and 977 Å(3), respectively. Overall, the homology models presented herein describe the enzyme characteristics leading to the metabolism of tazarotenic acid by CYP26A1 and CYP26B1 and support a potential role for the CYP26 enzymes in the metabolism of xenobiotics.
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Affiliation(s)
- Robert S Foti
- Amgen Pharmacokinetics and Drug Metabolism, Seattle, Washington (R.S.F.); Department of Pharmaceutics, University of Washington, Seattle, Washington (N.I., A.Z., L.J.D., B.R.B.); Core Laboratory for Neuromolecular Production, Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana (P.D.); CNRS, Université Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, Valbonne, France (D.D.)
| | - Nina Isoherranen
- Amgen Pharmacokinetics and Drug Metabolism, Seattle, Washington (R.S.F.); Department of Pharmaceutics, University of Washington, Seattle, Washington (N.I., A.Z., L.J.D., B.R.B.); Core Laboratory for Neuromolecular Production, Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana (P.D.); CNRS, Université Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, Valbonne, France (D.D.)
| | - Alex Zelter
- Amgen Pharmacokinetics and Drug Metabolism, Seattle, Washington (R.S.F.); Department of Pharmaceutics, University of Washington, Seattle, Washington (N.I., A.Z., L.J.D., B.R.B.); Core Laboratory for Neuromolecular Production, Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana (P.D.); CNRS, Université Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, Valbonne, France (D.D.)
| | - Leslie J Dickmann
- Amgen Pharmacokinetics and Drug Metabolism, Seattle, Washington (R.S.F.); Department of Pharmaceutics, University of Washington, Seattle, Washington (N.I., A.Z., L.J.D., B.R.B.); Core Laboratory for Neuromolecular Production, Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana (P.D.); CNRS, Université Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, Valbonne, France (D.D.)
| | - Brian R Buttrick
- Amgen Pharmacokinetics and Drug Metabolism, Seattle, Washington (R.S.F.); Department of Pharmaceutics, University of Washington, Seattle, Washington (N.I., A.Z., L.J.D., B.R.B.); Core Laboratory for Neuromolecular Production, Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana (P.D.); CNRS, Université Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, Valbonne, France (D.D.)
| | - Philippe Diaz
- Amgen Pharmacokinetics and Drug Metabolism, Seattle, Washington (R.S.F.); Department of Pharmaceutics, University of Washington, Seattle, Washington (N.I., A.Z., L.J.D., B.R.B.); Core Laboratory for Neuromolecular Production, Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana (P.D.); CNRS, Université Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, Valbonne, France (D.D.)
| | - Dominique Douguet
- Amgen Pharmacokinetics and Drug Metabolism, Seattle, Washington (R.S.F.); Department of Pharmaceutics, University of Washington, Seattle, Washington (N.I., A.Z., L.J.D., B.R.B.); Core Laboratory for Neuromolecular Production, Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana (P.D.); CNRS, Université Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, Valbonne, France (D.D.)
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Blais SP, Kornblatt JA, Barbeau X, Bonnaure G, Lagüe P, Chênevert R, Lapointe J. tRNAGlu increases the affinity of glutamyl-tRNA synthetase for its inhibitor glutamyl-sulfamoyl-adenosine, an analogue of the aminoacylation reaction intermediate glutamyl-AMP: mechanistic and evolutionary implications. PLoS One 2015; 10:e0121043. [PMID: 25860020 PMCID: PMC4393105 DOI: 10.1371/journal.pone.0121043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/11/2015] [Indexed: 12/05/2022] Open
Abstract
For tRNA-dependent protein biosynthesis, amino acids are first activated by aminoacyl-tRNA synthetases (aaRSs) yielding the reaction intermediates aminoacyl-AMP (aa-AMP). Stable analogues of aa-AMP, such as aminoacyl-sulfamoyl-adenosines, inhibit their cognate aaRSs. Glutamyl-sulfamoyl-adenosine (Glu-AMS) is the best known inhibitor of Escherichia coli glutamyl-tRNA synthetase (GluRS). Thermodynamic parameters of the interactions between Glu-AMS and E. coli GluRS were measured in the presence and in the absence of tRNA by isothermal titration microcalorimetry. A significant entropic contribution for the interactions between Glu-AMS and GluRS in the absence of tRNA or in the presence of the cognate tRNAGlu or of the non-cognate tRNAPhe is indicated by the negative values of –TΔSb, and by the negative value of ΔCp. On the other hand, the large negative enthalpy is the dominant contribution to ΔGb in the absence of tRNA. The affinity of GluRS for Glu-AMS is not altered in the presence of the non-cognate tRNAPhe, but the dissociation constant Kd is decreased 50-fold in the presence of tRNAGlu; this result is consistent with molecular dynamics results indicating the presence of an H-bond between Glu-AMS and the 3’-OH oxygen of the 3’-terminal ribose of tRNAGlu in the Glu-AMS•GluRS•tRNAGlu complex. Glu-AMS being a very close structural analogue of Glu-AMP, its weak binding to free GluRS suggests that the unstable Glu-AMP reaction intermediate binds weakly to GluRS; these results could explain why all the known GluRSs evolved to activate glutamate only in the presence of tRNAGlu, the coupling of glutamate activation to its transfer to tRNA preventing unproductive cleavage of ATP.
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Affiliation(s)
- Sébastien P. Blais
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- The Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Québec, Canada
- * E-mail: (SPB); (JL)
| | - Jack A. Kornblatt
- Department of Biology, Centre for Structural and Functional Genomics, Faculty of Arts and Science, Concordia University, Montréal, Canada
| | - Xavier Barbeau
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Département de Chimie, Université Laval, Québec, Canada
- The Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Québec, Canada
| | - Guillaume Bonnaure
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- The Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Québec, Canada
| | - Patrick Lagüe
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- The Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Québec, Canada
| | - Robert Chênevert
- Département de Chimie, Université Laval, Québec, Canada
- The Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Québec, Canada
| | - Jacques Lapointe
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- The Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Québec, Canada
- * E-mail: (SPB); (JL)
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7
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Nelson CH, Buttrick BR, Isoherranen N. Therapeutic potential of the inhibition of the retinoic acid hydroxylases CYP26A1 and CYP26B1 by xenobiotics. Curr Top Med Chem 2014; 13:1402-28. [PMID: 23688132 DOI: 10.2174/1568026611313120004] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 02/21/2013] [Indexed: 12/27/2022]
Abstract
Retinoic acid (RA), the active metabolite of vitamin A, is an important endogenous signaling molecule regulating cell cycle and maintenance of epithelia. RA isomers are also used as drugs to treat various cancers and dermatological diseases. However, the therapeutic uses of RA isomers are limited due to side effects such as teratogenicity and resistance to treatment emerging mainly from autoinduction of RA metabolism. To improve the therapeutic usefulness of retinoids, RA metabolism blocking agents (RAMBAs) have been developed. These inhibitors generally target the cytochrome P450 (CYP) enzymes because RA clearance is predominantly mediated by P450s. Since the initial identification of inhibitors of RA metabolism, CYP26 enzymes have been characterized as the main enzymes responsible for RA clearance. This makes CYP26 enzymes an attractive target for the development of novel therapeutics for cancer and dermatological conditions. The basic principle of development of CYP26 inhibitors is that endogenous RA concentrations will be increased in the presence of a CYP26 inhibitor, thus, potentiating the activity of endogenous RA in a cell-type specific manner. This will reduce side effects compared to administration of RA and allow for more targeted therapy. In clinical trials, inhibitors of RA metabolism have been effective in treatment of psoriasis and other dermatological conditions as well as in some cancers. However, no CYP26 inhibitor has yet been approved for clinical use. This review summarizes the history of development of RAMBAs, the clinical and preclinical studies with the various structural series and the available knowledge of structure activity relationships of CYP26 inhibitors.
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Affiliation(s)
- Cara H Nelson
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA 98195, USA
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Dallaire-Dufresne S, Barbeau X, Sarty D, Tanaka KH, Denoncourt AM, Lagüe P, Reith ME, Charette SJ. Aeromonas salmonicida Ati2 is an effector protein of the type three secretion system. Microbiology (Reading) 2013; 159:1937-1945. [DOI: 10.1099/mic.0.067959-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Stéphanie Dallaire-Dufresne
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec G1V 4G5, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada
- Institut de biologie intégrative et des systèmes, Faculté des sciences et de génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada
| | - Xavier Barbeau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada
- Institut de biologie intégrative et des systèmes, Faculté des sciences et de génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada
| | - Darren Sarty
- Aquatic and Crop Resource Development, National Research Council Canada, Halifax, Nova Scotia B3H 3Z1, Canada
| | - Katherine H. Tanaka
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec G1V 4G5, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada
- Institut de biologie intégrative et des systèmes, Faculté des sciences et de génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada
| | - Alix M. Denoncourt
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec G1V 4G5, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada
- Institut de biologie intégrative et des systèmes, Faculté des sciences et de génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada
| | - Patrick Lagüe
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada
- Institut de biologie intégrative et des systèmes, Faculté des sciences et de génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada
| | - Michael E. Reith
- Aquatic and Crop Resource Development, National Research Council Canada, Halifax, Nova Scotia B3H 3Z1, Canada
| | - Steve J. Charette
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec G1V 4G5, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada
- Institut de biologie intégrative et des systèmes, Faculté des sciences et de génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada
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9
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Shimshoni JA, Roberts AG, Scian M, Topletz AR, Blankert SA, Halpert JR, Nelson WL, Isoherranen N. Stereoselective formation and metabolism of 4-hydroxy-retinoic Acid enantiomers by cytochrome p450 enzymes. J Biol Chem 2012; 287:42223-32. [PMID: 23071109 DOI: 10.1074/jbc.m112.404475] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All-trans-retinoic acid (atRA), the major active metabolite of vitamin A, plays a role in many biological processes, including maintenance of epithelia, immunity, and fertility and regulation of apoptosis and cell differentiation. atRA is metabolized mainly by CYP26A1, but other P450 enzymes such as CYP2C8 and CYP3As also contribute to atRA 4-hydroxylation. Although the primary metabolite of atRA, 4-OH-RA, possesses a chiral center, the stereochemical course of atRA 4-hydroxylation has not been studied previously. (4S)- and (4R)-OH-RA enantiomers were synthesized and separated by chiral column HPLC. CYP26A1 was found to form predominantly (4S)-OH-RA. This stereoselectivity was rationalized via docking of atRA in the active site of a CYP26A1 homology model. The docked structure showed a well defined niche for atRA within the active site and a specific orientation of the β-ionone ring above the plane of the heme consistent with stereoselective abstraction of the hydrogen atom from the pro-(S)-position. In contrast to CYP26A1, CYP3A4 formed the 4-OH-RA enantiomers in a 1:1 ratio and CYP3A5 preferentially formed (4R)-OH-RA. Interestingly, CYP3A7 and CYP2C8 preferentially formed (4S)-OH-RA from atRA. Both (4S)- and (4R)-OH-RA were substrates of CYP26A1 but (4S)-OH-RA was cleared 3-fold faster than (4R)-OH-RA. In addition, 4-oxo-RA was formed from (4R)-OH-RA but not from (4S)-OH-RA by CYP26A1. Overall, these findings show that (4S)-OH-RA is preferred over (4R)-OH-RA by the enzymes regulating atRA homeostasis. The stereoselectivity observed in CYP26A1 function will aid in better understanding of the active site features of the enzyme and the disposition of biologically active retinoids.
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Affiliation(s)
- Jakob A Shimshoni
- Department of Pharmaceutics, University of Washington, Seattle, Washington 98195, USA
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10
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Saenz-Méndez P, Elmabsout AA, Sävenstrand H, Awadalla MKA, Strid Å, Sirsjö A, Eriksson LA. Homology Models of Human All-Trans Retinoic Acid Metabolizing Enzymes CYP26B1 and CYP26B1 Spliced Variant. J Chem Inf Model 2012; 52:2631-7. [DOI: 10.1021/ci300264u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Patricia Saenz-Méndez
- Computational Chemistry and Biology
Group, Facultad de Química, UdelaR, 11800 Montevideo, Uruguay
| | - Ali Ateia Elmabsout
- Department of Clinical Medicine, School of Health Sciences, Örebro University, SE-701 82, Örebro,
Sweden
| | - Helena Sävenstrand
- Department of Science
and Technology, Örebro Life Science Center, Örebro University, SE-701 82, Örebro, Sweden
| | | | - Åke Strid
- Department of Science
and Technology, Örebro Life Science Center, Örebro University, SE-701 82, Örebro, Sweden
| | - Allan Sirsjö
- Department of Clinical Medicine, School of Health Sciences, Örebro University, SE-701 82, Örebro,
Sweden
| | - Leif A. Eriksson
- Department of Chemistry and Molecular
Biology, University of Gothenburg, 412
96 Göteborg, Sweden
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Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC. Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. J Chem Inf Model 2012; 52:617-48. [PMID: 22339582 PMCID: PMC3317594 DOI: 10.1021/ci200542m] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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Metabolism of xenobiotics remains a central challenge
for the discovery
and development of drugs, cosmetics, nutritional supplements, and
agrochemicals. Metabolic transformations are frequently related to
the incidence of toxic effects that may result from the emergence
of reactive species, the systemic accumulation of metabolites, or
by induction of metabolic pathways. Experimental investigation of
the metabolism of small organic molecules is particularly resource
demanding; hence, computational methods are of considerable interest
to complement experimental approaches. This review provides a broad
overview of structure- and ligand-based computational methods for
the prediction of xenobiotic metabolism. Current computational approaches
to address xenobiotic metabolism are discussed from three major perspectives:
(i) prediction of sites of metabolism (SOMs), (ii) elucidation of
potential metabolites and their chemical structures, and (iii) prediction
of direct and indirect effects of xenobiotics on metabolizing enzymes,
where the focus is on the cytochrome P450 (CYP) superfamily of enzymes,
the cardinal xenobiotics metabolizing enzymes. For each of these domains,
a variety of approaches and their applications are systematically
reviewed, including expert systems, data mining approaches, quantitative
structure–activity relationships (QSARs), and machine learning-based
methods, pharmacophore-based algorithms, shape-focused techniques,
molecular interaction fields (MIFs), reactivity-focused techniques,
protein–ligand docking, molecular dynamics (MD) simulations,
and combinations of methods. Predictive metabolism is a developing
area, and there is still enormous potential for improvement. However,
it is clear that the combination of rapidly increasing amounts of
available ligand- and structure-related experimental data (in particular,
quantitative data) with novel and diverse simulation and modeling
approaches is accelerating the development of effective tools for
prediction of in vivo metabolism, which is reflected by the diverse
and comprehensive data sources and methods for metabolism prediction
reviewed here. This review attempts to survey the range and scope
of computational methods applied to metabolism prediction and also
to compare and contrast their applicability and performance.
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Affiliation(s)
- Johannes Kirchmair
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
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Topletz AR, Thatcher JE, Zelter A, Lutz JD, Tay S, Nelson WL, Isoherranen N. Comparison of the function and expression of CYP26A1 and CYP26B1, the two retinoic acid hydroxylases. Biochem Pharmacol 2011; 83:149-63. [PMID: 22020119 DOI: 10.1016/j.bcp.2011.10.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 10/16/2022]
Abstract
All-trans-retinoic acid (atRA) is an important signaling molecule in all chordates. The cytochrome P450 enzymes CYP26 are believed to partially regulate cellular concentrations of atRA via oxidative metabolism and hence affect retinoid homeostasis and signaling. CYP26A1 and CYP26B1 are atRA hydroxylases that catalyze formation of similar metabolites in cell systems. However, they have only 40% sequence similarity suggesting differences between the two enzymes. The aim of this study was to determine whether CYP26A1 and CYP26B1 have similar catalytic activity, form different metabolites from atRA and are expressed in different tissues in adults. The mRNA expression of CYP26A1 and CYP26B1 correlated between human tissues except for human cerebellum in which CYP26B1 was the predominant CYP26 and liver in which CYP26A1 dominated. Quantification of CYP26A1 and CYP26B1 protein in human tissues was in agreement with the mRNA expression and showed correlation between the two isoforms. Qualitatively, recombinant CYP26A1 and CYP26B1 formed the same primary and sequential metabolites from atRA. Quantitatively, CYP26B1 had a lower K(m) (19nM) and V(max) (0.8 pmol/min/pmol) than CYP26A1 (K(m)=50 nM and V(max)=10 pmol/min/pmol) for formation of 4-OH-RA. The major atRA metabolites 4-OH-RA, 18-OH-RA and 4-oxo-RA were all substrates of CYP26A1 and CYP26B1, and CYP26A1 had a 2-10-fold higher catalytic activity towards all substrates tested. This study shows that CYP26A1 and CYP26B1 are qualitatively similar RA hydroxylases with overlapping expression profiles. CYP26A1 has higher catalytic activity than CYP26B1 and seems to be responsible for metabolism of atRA in tissues that function as a barrier for atRA exposure.
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Affiliation(s)
- Ariel R Topletz
- Department of Pharmaceutics, University of Washington, Seattle, United States
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Wu B, Sun J, Cheng SP, Gu JD, Li AM, Zhang XX. Comparative analysis of binding affinities between styrene and mammalian CYP2E1 by bioinformatics approaches. ECOTOXICOLOGY (LONDON, ENGLAND) 2011; 20:1041-1046. [PMID: 21424721 DOI: 10.1007/s10646-011-0643-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/11/2011] [Indexed: 05/30/2023]
Abstract
Cytochrome P450 2E1 (CYP2E1) is a cytochrome P450 enzyme involved in styrene metabolism. This study compared the binding affinities between styrene and 11 mammalian CYP2E1 systems using bioinformatics methods. Firstly, amino acid sequences of CYP2E1s were obtained from the Swiss-Prot database. Then, taking the crystal structure of human CYP2E1 as a template, 3D models of the CYP2E1s of other mammals were constructed using the SWISS-MODEL program. Finally, the generated homology models were applied to calculate their docking capacities against styrene and polystyrene using the Surflex-Dock program, which could automatically dock ligands into a receptor's ligand binding site using a protomol based approach and assess the affinity by an empirically derived scoring function. Docking experiments showed that the studied mammalian CYP2E1s had high binding affinities with styrene. For polystyrene, the dimmer of styrene has high binding affinities with CYP2E1s, however, trimer and other high polymers were found hard to be docked into the CYP2E1s. The results of this study indicated that bioinformatics approaches might be useful tools to predict styrene and polystyrene affinities with mammalian CYP2E1s.
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Affiliation(s)
- Bing Wu
- State Key Laboratory of Pollutant Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210046, People's Republic of China
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Thatcher JE, Buttrick B, Shaffer SA, Shimshoni JA, Goodlett DR, Nelson WL, Isoherranen N. Substrate specificity and ligand interactions of CYP26A1, the human liver retinoic acid hydroxylase. Mol Pharmacol 2011; 80:228-39. [PMID: 21521770 DOI: 10.1124/mol.111.072413] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
All-trans-retinoic acid (atRA) is the active metabolite of vitamin A. atRA is also used as a drug, and synthetic atRA analogs and inhibitors of retinoic acid (RA) metabolism have been developed. The hepatic clearance of atRA is mediated primarily by CYP26A1, but design of CYP26A1 inhibitors is hindered by lack of information on CYP26A1 structure and structure-activity relationships of its ligands. The aim of this study was to identify the primary metabolites of atRA formed by CYP26A1 and to characterize the ligand selectivity and ligand interactions of CYP26A1. On the basis of high-resolution tandem mass spectrometry data, four metabolites formed from atRA by CYP26A1 were identified as 4-OH-RA, 4-oxo-RA, 16-OH-RA and 18-OH-RA. 9-cis-RA and 13-cis-RA were also substrates of CYP26A1. Forty-two compounds with diverse structural properties were tested for CYP26A1 inhibition using 9-cis-RA as a probe, and IC(50) values for 10 inhibitors were determined. The imidazole- and triazole-containing inhibitors [S-(R*,R*)]-N-[4-[2-(dimethylamino)-1-(1H-imidazole-1-yl)propyl]-phenyl]2-benzothiazolamine (R116010) and (R)-N-[4-[2-ethyl-1-(1H-1,2,4-triazol-1-yl)butyl]phenyl]-2-benzothiazolamine (R115866) were the most potent inhibitors of CYP26A1 with IC(50) values of 4.3 and 5.1 nM, respectively. Liarozole and ketoconazole were significantly less potent with IC(50) values of 2100 and 550 nM, respectively. The retinoic acid receptor (RAR) γ agonist CD1530 was as potent an inhibitor of CYP26A1 as ketoconazole with an IC(50) of 530 nM, whereas the RARα and RARβ agonists tested did not significantly inhibit CYP26A1. The pan-RAR agonist 4-[(E)-2-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)-1-propenyl]benzoic acid and the peroxisome proliferator-activated receptor ligands rosiglitazone and pioglitazone inhibited CYP26A1 with IC(50) values of 3.7, 4.2, and 8.6 μM, respectively. These data demonstrate that CYP26A1 has high ligand selectivity but accepts structurally related nuclear receptor agonists as inhibitors.
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Affiliation(s)
- Jayne E Thatcher
- Department of Pharmaceutics, Box 357610, University of Washington, Seattle, WA 98195, USA
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