1
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Hirte S, Burk O, Tahir A, Schwab M, Windshügel B, Kirchmair J. Development and Experimental Validation of Regularized Machine Learning Models Detecting New, Structurally Distinct Activators of PXR. Cells 2022; 11:cells11081253. [PMID: 35455933 PMCID: PMC9029776 DOI: 10.3390/cells11081253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023] Open
Abstract
The pregnane X receptor (PXR) regulates the metabolism of many xenobiotic and endobiotic substances. In consequence, PXR decreases the efficacy of many small-molecule drugs and induces drug-drug interactions. The prediction of PXR activators with theoretical approaches such as machine learning (ML) proves challenging due to the ligand promiscuity of PXR, which is related to its large and flexible binding pocket. In this work we demonstrate, by the example of random forest models and support vector machines, that classifiers generated following classical training procedures often fail to predict PXR activity for compounds that are dissimilar from those in the training set. We present a novel regularization technique that penalizes the gap between a model’s training and validation performance. On a challenging test set, this technique led to improvements in Matthew correlation coefficients (MCCs) by up to 0.21. Using these regularized ML models, we selected 31 compounds that are structurally distinct from known PXR ligands for experimental validation. Twelve of them were confirmed as active in the cellular PXR ligand-binding domain assembly assay and more hits were identified during follow-up studies. Comprehensive analysis of key features of PXR biology conducted for three representative hits confirmed their ability to activate the PXR.
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Affiliation(s)
- Steffen Hirte
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria;
| | - Oliver Burk
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, University of Tübingen, 70376 Stuttgart, Germany; (O.B.); (M.S.)
| | - Ammar Tahir
- Division of Pharmacognosy, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria;
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, University of Tübingen, 70376 Stuttgart, Germany; (O.B.); (M.S.)
- Departments of Clinical Pharmacology and Biochemistry and Pharmacy, University of Tuebingen, 72074 Tübingen, Germany
- Cluster of Excellence IFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72074 Tübingen, Germany
| | - Björn Windshügel
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research Screening Port, 22525 Hamburg, Germany;
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | - Johannes Kirchmair
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria;
- Correspondence: ; Tel.: +43-1-4277-55104
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2
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Honkakoski P. Searching for CAR modulators. Drug Metab Dispos 2022; 50:1002-1009. [DOI: 10.1124/dmd.121.000482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 02/01/2022] [Indexed: 11/22/2022] Open
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3
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Touloupi K, Küblbeck J, Magklara A, Molnár F, Reinisalo M, Konstandi M, Honkakoski P, Pappas P. The Basis for Strain-Dependent Rat Aldehyde Dehydrogenase 1A7 ( ALDH1A7) Gene Expression. Mol Pharmacol 2019; 96:655-663. [PMID: 31575620 DOI: 10.1124/mol.119.117424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/06/2019] [Indexed: 11/22/2022] Open
Abstract
Aldehyde hydrogenases (ALDHs) belong to a large gene family involved in oxidation of both endogenous and exogenous compounds in mammalian tissues. Among ALDHs, the rat ALDH1A7 gene displays a curious strain dependence in phenobarbital (PB)-induced hepatic expression: the responsive RR strains exhibit induction of both ALDH1A7 and CYP2B mRNAs and activities, whereas the nonresponsive rr strains show induction of CYP2B only. Here, we investigated the responsiveness of ALDH1A1, ALDH1A7, CYP2B1, and CYP3A23 genes to prototypical P450 inducers, expression of nuclear receptors CAR and pregnane X receptor, and structure of the ALDH1A7 promoter in both rat strains. ALDH1A7 mRNA, associated protein and activity were strongly induced by PB and modestly induced by pregnenolone 16α-carbonitrile in the RR strain but negligibly in the rr strain, whereas induction of ALDH1A1 and P450 mRNAs was similar between the strains. Reporter gene and chromatin immunoprecipitation assays indicated that the loss of ALDH1A7 inducibility in the rr strain is profoundly linked with a 16-base pair deletion in the proximal promoter and inability of the upstream DNA sequences to recruit constitutive androstane receptor-retinoid X receptor heterodimers. SIGNIFICANCE STATEMENT: Genetic variation in rat ALDH1A7 promoter sequences underlie the large strain-dependent differences in expression and inducibility by phenobarbital of the aldehyde dehydrogenase activity. This finding has implications for the design and interpretation of pharmacological and toxicological studies on the effects and disposition of aldehydes.
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Affiliation(s)
- Katerina Touloupi
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Jenni Küblbeck
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Angeliki Magklara
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Ferdinand Molnár
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Mika Reinisalo
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Maria Konstandi
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Paavo Honkakoski
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Periklis Pappas
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
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Liang D, Li L, Lynch C, Mackowiak B, Hedrich WD, Ai Y, Yin Y, Heyward S, Xia M, Wang H, Xue F. Human constitutive androstane receptor agonist DL5016: A novel sensitizer for cyclophosphamide-based chemotherapies. Eur J Med Chem 2019; 179:84-99. [PMID: 31247375 DOI: 10.1016/j.ejmech.2019.06.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/29/2022]
Abstract
The DNA alkylating prodrug cyclophosphamide (CPA), alone or in combination with other agents, is one of the most commonly used anti-cancer agents. As a prodrug, CPA is activated by cytochrome P450 2B6 (CYP2B6), which is transcriptionally regulated by the human constitutive androstane receptor (hCAR). Therefore, hCAR agonists represent novel sensitizers for CPA-based therapies. Among known hCAR agonists, compound 6-(4-chlorophenyl)imidazo-[2,1-b]thiazole-5-carbaldehyde-O-(3,4-dichlorobenzyl)oxime (CITCO) is the most potent and broadly utilized in biological studies. Through structural modification of CITCO, we have developed a novel compound DL5016 (32), which has an EC50 value of 0.66 μM and EMAX value of 4.9 when activating hCAR. DL5016 robustly induced the expression of hCAR target gene CYP2B6, at both the mRNA and protein levels, and caused translocation of hCAR from the cytoplasm to the nucleus in human primary hepatocytes. The effects of DL5016 were highlighted by dramatically enhancing the efficacy of CPA-based cytotoxicity to non-Hodgkin lymphoma cells.
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Affiliation(s)
- Dongdong Liang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, United States
| | - Linhao Li
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, United States
| | - Caitlin Lynch
- 9800 Medical Center Drive, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Bryan Mackowiak
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, United States
| | - William D Hedrich
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, United States
| | - Yong Ai
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, United States
| | - Yue Yin
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, United States
| | - Scott Heyward
- BioIVT, 1450 S Rolling Rd, Halethorpe, MD, 21227, United States
| | - Menghang Xia
- 9800 Medical Center Drive, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Hongbing Wang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, United States.
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, United States.
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5
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Prantner V, Cinnamon Y, Küblbeck J, Molnár F, Honkakoski P. Functional Characterization of a Novel Variant of the Constitutive Androstane Receptor (CAR, NR1I3). NUCLEAR RECEPTOR RESEARCH 2018. [DOI: 10.32527/2018/101386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Viktoria Prantner
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.Box 1627, FI-70211 Kuopio, Finland. Present address: Neosmart Health Ltd., Aleksanterinkatu 13, FI-00100 Helsinki,
Finland
| | - Yuval Cinnamon
- The Monique and Jacques Roboh Department of Genetic Research, Hadassah - Hebrew University Medical Center, Jerusalem 91120, Israel. Present address: Department of Poultry and Aquaculture Sciences, Institute of Animal Science, Agricultural Research Organization, The Volcani Center, P.O.Box 6, Bet Dagan 50250, Israel
| | - Jenni Küblbeck
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.Box 1627, FI-70211 Kuopio, Finland
| | - Ferdinand Molnár
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.Box 1627, FI-70211 Kuopio, Finland. Present address: Department of Biology, School of Sciences and Technology, Nazarbayev University, Astana 010000, Kazakhstan
| | - Paavo Honkakoski
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.Box 1627, FI-70211 Kuopio, Finland
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6
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Jain S, Grandits M, Richter L, Ecker GF. Structure based classification for bile salt export pump (BSEP) inhibitors using comparative structural modeling of human BSEP. J Comput Aided Mol Des 2017; 31:507-521. [PMID: 28527154 PMCID: PMC5487762 DOI: 10.1007/s10822-017-0021-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 04/30/2017] [Indexed: 01/13/2023]
Abstract
The bile salt export pump (BSEP) actively transports conjugated monovalent bile acids from the hepatocytes into the bile. This facilitates the formation of micelles and promotes digestion and absorption of dietary fat. Inhibition of BSEP leads to decreased bile flow and accumulation of cytotoxic bile salts in the liver. A number of compounds have been identified to interact with BSEP, which results in drug-induced cholestasis or liver injury. Therefore, in silico approaches for flagging compounds as potential BSEP inhibitors would be of high value in the early stage of the drug discovery pipeline. Up to now, due to the lack of a high-resolution X-ray structure of BSEP, in silico based identification of BSEP inhibitors focused on ligand-based approaches. In this study, we provide a homology model for BSEP, developed using the corrected mouse P-glycoprotein structure (PDB ID: 4M1M). Subsequently, the model was used for docking-based classification of a set of 1212 compounds (405 BSEP inhibitors, 807 non-inhibitors). Using the scoring function ChemScore, a prediction accuracy of 81% on the training set and 73% on two external test sets could be obtained. In addition, the applicability domain of the models was assessed based on Euclidean distance. Further, analysis of the protein-ligand interaction fingerprints revealed certain functional group-amino acid residue interactions that could play a key role for ligand binding. Though ligand-based models, due to their high speed and accuracy, remain the method of choice for classification of BSEP inhibitors, structure-assisted docking models demonstrate reasonably good prediction accuracies while additionally providing information about putative protein-ligand interactions.
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Affiliation(s)
- Sankalp Jain
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Melanie Grandits
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Lars Richter
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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7
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Kato H, Yamaotsu N, Iwazaki N, Okamura S, Kume T, Hirono S. Precise prediction of activators for the human constitutive androstane receptor using structure-based three-dimensional quantitative structure–activity relationship methods. Drug Metab Pharmacokinet 2017; 32:179-188. [DOI: 10.1016/j.dmpk.2017.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 01/24/2017] [Accepted: 02/01/2017] [Indexed: 02/07/2023]
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8
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Lee K, You H, Choi J, No KT. Development of pharmacophore-based classification model for activators of constitutive androstane receptor. Drug Metab Pharmacokinet 2016; 32:172-178. [PMID: 28366619 DOI: 10.1016/j.dmpk.2016.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/21/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
Abstract
Constitutive androstane receptor (CAR) is predominantly expressed in the liver and is important for regulating drug metabolism and transport. Despite its biological importance, there have been few attempts to develop in silico models to predict the activity of CAR modulated by chemical compounds. The number of in silico studies of CAR may be limited because of CAR's constitutive activity under normal conditions, which makes it difficult to elucidate the key structural features of the interaction between CAR and its ligands. In this study, to address these limitations, we introduced 3D pharmacophore-based descriptors with an integrated ligand and structure-based pharmacophore features, which represent the receptor-ligand interaction. Machine learning methods (support vector machine and artificial neural network) were applied to develop an in silico model with the descriptors containing significant information regarding the ligand binding positions. The best classification model built with a solvent accessibility volume-based filter and the support vector machine showed good predictabilities of 87%, and 85.4% for the training set and validation set, respectively. This demonstrates that our model can be used to accurately predict CAR activators and offers structural information regarding ligand/protein interactions.
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Affiliation(s)
- Kyungro Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Hwan You
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Jiwon Choi
- Bioinformatics & Molecular Design Research Center, Yonsei University, Seoul 03722, South Korea
| | - Kyoung Tai No
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea; Bioinformatics & Molecular Design Research Center, Yonsei University, Seoul 03722, South Korea.
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Küblbeck J, Anttila T, Pulkkinen JT, Honkakoski P. Improved assays for xenosensor activation based on reverse transfection. Toxicol In Vitro 2015; 29:1759-65. [PMID: 26187274 DOI: 10.1016/j.tiv.2015.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 06/04/2015] [Accepted: 07/13/2015] [Indexed: 12/15/2022]
Abstract
Discovery of receptor-dependent mechanisms for regulation of drug metabolism has provided a new way to evaluate the propensity of drug candidates to cause induction of cytochrome P450 enzymes. Therefore, receptor-based reporter assays have become common in early stages of drug development projects and in mechanistic studies. Here, we report a reverse transfection system to conduct activation assays for human xenosensors AhR, CAR and PXR. The assay format is based on long-term stability and uniformity of DNA/carrier complexes on culture plates, avoiding multiple stages and variation inherent in conventional transfection methods. Consequently, these improved assays are streamlined, reproducible and formally validated with Z' factors exceeding 0.5. This novel reverse transfection system is expected to find use in diverse areas of early drug development such prediction of CYP induction, evaluation of species differences and in mechanistic studies.
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Affiliation(s)
- Jenni Küblbeck
- School of Pharmacy and Biocenter Kuopio, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
| | - Teemu Anttila
- School of Pharmacy and Biocenter Kuopio, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Juha T Pulkkinen
- School of Pharmacy and Biocenter Kuopio, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Paavo Honkakoski
- School of Pharmacy and Biocenter Kuopio, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
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Küblbeck J, Zancanella V, Prantner V, Molnár F, Squires EJ, Dacasto M, Honkakoski P, Giantin M. Characterization of ligand-dependent activation of bovine and pig constitutive androstane (CAR) and pregnane X receptors (PXR) with interspecies comparisons. Xenobiotica 2015; 46:200-10. [DOI: 10.3109/00498254.2015.1060374] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Cherian MT, Chai SC, Chen T. Small-molecule modulators of the constitutive androstane receptor. Expert Opin Drug Metab Toxicol 2015; 11:1099-114. [PMID: 25979168 DOI: 10.1517/17425255.2015.1043887] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
INTRODUCTION The constitutive androstane receptor (CAR) induces drug-metabolizing enzymes for xenobiotic metabolism. AREAS COVERED This review covers recent advances in elucidating the biological functions of CAR and its modulation by a growing number of agonists and inhibitors. EXPERT OPINION Extrapolation of animal CAR function to that of humans should be carefully scrutinized, particularly when rodents are used in evaluating the metabolic profile and carcinogenic properties of clinical drugs and environmental chemicals. Continuous efforts are needed to discover novel CAR inhibitors, with extensive understanding of their inhibitory mechanism, species selectivity, and discriminating power against other xenobiotic sensors.
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Affiliation(s)
- Milu T Cherian
- Postdoctoral fellow, St. Jude Children's Research Hospital, Department of Chemical Biology and Therapeutics , 262 Danny Thomas Place, Memphis, TN 38105 , USA
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12
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Pimkaew P, Küblbeck J, Petsalo A, Jukka J, Suksamrarn A, Juvonen R, Auriola S, Piyachaturawat P, Honkakoski P. Interactions of sesquiterpenes zederone and germacrone with the human cytochrome P450 system. Toxicol In Vitro 2013; 27:2005-12. [DOI: 10.1016/j.tiv.2013.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/02/2013] [Accepted: 07/03/2013] [Indexed: 11/16/2022]
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13
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An update on the constitutive androstane receptor (CAR). ACTA ACUST UNITED AC 2013; 28:79-93. [DOI: 10.1515/dmdi-2013-0009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/17/2013] [Indexed: 12/14/2022]
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14
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Avoiding PXR and CAR Activation and CYP3A4 Enzyme Induction. TOPICS IN MEDICINAL CHEMISTRY 2013. [DOI: 10.1007/7355_2013_24] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Windshügel B, Poso A. Constitutive activity and ligand-dependent activation of the nuclear receptor CAR-insights from molecular dynamics simulations. J Mol Recognit 2012; 24:875-82. [PMID: 21812062 DOI: 10.1002/jmr.1132] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The constitutive androstane receptor (CAR) possesses, unlike most other nuclear receptors, a pronounced basal activity in vitro whose structural basis is still not fully understood. Using comparative molecular dynamics simulations of CAR X-ray crystal structures, we evaluated the molecular basis for constitutive activity and ligand-dependent receptor activation. Our results suggest that a combination of van der Waals interactions and hydrogen bonds is required to maintain the activation helix in the active conformation also in absence of a ligand. Furthermore, we identified conformational rearrangements within the ligand-binding pocket upon agonist binding and an influence of CAR inducers pregnanedione and CITCO on the helical conformation of the activation helix. Based on the results a model for ligand-dependent CAR activation is suggested.
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Affiliation(s)
- Björn Windshügel
- Faculty of Health Sciences/School of Pharmacy, University of Eastern Finland, P.O. Box 1627, Kuopio 70211, Finland.
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16
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Jyrkkärinne J, Küblbeck J, Pulkkinen J, Honkakoski P, Laatikainen R, Poso A, Laitinen T. Molecular Dynamics Simulations for Human CAR Inverse Agonists. J Chem Inf Model 2012; 52:457-64. [DOI: 10.1021/ci200432k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Johanna Jyrkkärinne
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Jenni Küblbeck
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Juha Pulkkinen
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Paavo Honkakoski
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Reino Laatikainen
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Antti Poso
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Tuomo Laitinen
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
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17
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Furdas SD, Shekfeh S, Kannan S, Sippl W, Jung M. Rhodaninecarboxylic acids as novel inhibitors of histoneacetyltransferases. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md00211f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Virtual screening has identified rhodanine containing carboxylic acids as new inhibitors of histone acetyltransferases.
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Affiliation(s)
- Silviya D. Furdas
- Institute of Pharmaceutical Sciences
- Albert-Ludwigs-Unversity of Freiburg
- Freiburg
- Germany
| | - Suhaib Shekfeh
- Department of Pharmaceutical Chemistry
- Martin-Luther University of Halle-Wittenberg
- Germany
| | | | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry
- Martin-Luther University of Halle-Wittenberg
- Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences
- Albert-Ludwigs-Unversity of Freiburg
- Freiburg
- Germany
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18
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Küblbeck J, Laitinen T, Jyrkkärinne J, Rousu T, Tolonen A, Abel T, Kortelainen T, Uusitalo J, Korjamo T, Honkakoski P, Molnár F. Use of comprehensive screening methods to detect selective human CAR activators. Biochem Pharmacol 2011; 82:1994-2007. [DOI: 10.1016/j.bcp.2011.08.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 08/30/2011] [Accepted: 08/31/2011] [Indexed: 01/20/2023]
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19
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Küblbeck J, Jyrkkärinne J, Molnár F, Kuningas T, Patel J, Windshügel B, Nevalainen T, Laitinen T, Sippl W, Poso A, Honkakoski P. New in vitro tools to study human constitutive androstane receptor (CAR) biology: discovery and comparison of human CAR inverse agonists. Mol Pharm 2011; 8:2424-33. [PMID: 22044162 DOI: 10.1021/mp2003658] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The human constitutive androstane receptor (CAR, NR1I3) is one of the key regulators of xenobiotic and endobiotic metabolism. The unique properties of human CAR, such as the high constitutive activity and the complexity of signaling, as well as the lack of functional and predictive cell-based assays to study the properties of the receptor, have hindered the discovery of selective human CAR ligands. Here we report a novel human CAR inverse agonist, 1-[(2-methylbenzofuran-3-yl)methyl]-3-(thiophen-2-ylmethyl) urea (S07662), which suppresses human CAR activity, recruits the corepressor NCoR in cell-based assays, and attenuates the phenytoin- and 6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime (CITCO)-induced expression of CYP2B6 mRNA in human primary hepatocytes. The properties of S07662 are also compared with those of known human CAR inverse agonists by using an array of different in vitro and in silico assays. The identified compound S07662 can be used as a chemical tool to study the biological functions of human CAR and also as a starting point for the development of new drugs for various conditions involving the receptor.
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Affiliation(s)
- Jenni Küblbeck
- Faculty of Health Sciences, School of Pharmacy, University of Eastern Finland & Biocenter Kuopio, P.O. Box 1627, FI-70211 Kuopio, Finland.
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20
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Moroy G, Martiny VY, Vayer P, Villoutreix BO, Miteva MA. Toward in silico structure-based ADMET prediction in drug discovery. Drug Discov Today 2011; 17:44-55. [PMID: 22056716 DOI: 10.1016/j.drudis.2011.10.023] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 10/07/2011] [Accepted: 10/21/2011] [Indexed: 12/12/2022]
Abstract
Quantitative structure-activity relationship (QSAR) methods and related approaches have been used to investigate the molecular features that influence the absorption, distribution, metabolism, excretion and toxicity (ADMET) of drugs. As the three-dimensional structures of several major ADMET proteins become available, structure-based (docking-scoring) computations can be carried out to complement or to go beyond QSAR studies. Applying docking-scoring methods to ADMET proteins is a challenging process because they usually have a large and flexible binding cavity; however, promising results relating to metabolizing enzymes have been reported. After reviewing current trends in the field we applied structure-based methods in the context of receptor flexibility in a case study involving the phase II metabolizing sulfotransferases. Overall, the explored concepts and results suggested that structure-based ADMET profiling will probably join the mainstream during the coming years.
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Affiliation(s)
- Gautier Moroy
- Inserm UMR-S 973, Molécules Thérapeutiques In Silico, Université Paris Diderot, Sorbonne Paris Cité, 35 Rue Helene Brion, 75013 Paris, France
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21
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Furdas SD, Shekfeh S, Bissinger EM, Wagner JM, Schlimme S, Valkov V, Hendzel M, Jung M, Sippl W. Synthesis and biological testing of novel pyridoisothiazolones as histone acetyltransferase inhibitors. Bioorg Med Chem 2011; 19:3678-89. [PMID: 21353783 DOI: 10.1016/j.bmc.2011.01.063] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 01/27/2011] [Accepted: 01/27/2011] [Indexed: 11/30/2022]
Abstract
We present a combination of database screening, synthesis and in vitro testing to identify novel histone acetyltransferase (HAT) inhibitors. The National Cancer Institute compound collection (NCI) and several commercial databases were filtered by similarity-based virtual screening to find new HAT inhibitors. Employing the recombinant HAT p300/CBP-associated factor (PCAF) and two different histone substrates for screening, pyridoisothiazolones were identified as inhibitors of human PCAF. Due to the limited solubility of the initial hits, we synthesized and tested them on PCAF. The compounds inhibit the proliferation of cancer cells. In summary, valuable chemical tools and potential lead candidates for new anticancer agents directed against HATs as new targets have been identified.
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Affiliation(s)
- Silviya D Furdas
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Germany
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22
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Lau AJ, Yang G, Rajaraman G, Baucom CC, Chang TKH. Differential effect of meclizine on the activity of human pregnane X receptor and constitutive androstane receptor. J Pharmacol Exp Ther 2010; 336:816-26. [PMID: 21131266 DOI: 10.1124/jpet.110.175927] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Conflicting data exist as to whether meclizine is an activator of human pregnane X receptor (hPXR). Therefore, we conducted a detailed, systematic investigation to determine whether meclizine affects hPXR activity by performing a cell-based reporter gene assay, a time-resolved fluorescence resonance energy transfer competitive ligand-binding assay, a mammalian two-hybrid assay to assess coactivator recruitment, and a hPXR target gene expression assay. In pregnane X receptor (PXR)-transfected HepG2 cells, meclizine activated hPXR to a greater extent than rat PXR. It bound to hPXR ligand-binding domain and recruited steroid receptor coactivator-1 to the receptor. Consistent with its hPXR agonism, meclizine increased hPXR target gene expression (CYP3A4) in human hepatocytes. However, it did not increase but decreased testosterone 6β-hydroxylation, suggesting inhibition of CYP3A catalytic activity. Meclizine has also been reported to be an inverse agonist and antagonist of human constitutive androstane receptor (hCAR). Therefore, given that certain tissues (e.g., liver) express both hPXR and hCAR and that various genes are cross-regulated by them, we quantified the expression of a hCAR- and hPXR-regulated gene (CYP2B6) in cultured human hepatocytes treated with meclizine. This drug did not decrease constitutive CYP2B6 mRNA expression or attenuate hCAR agonist-mediated increase in CYP2B6 mRNA and CYP2B6-catalyzed bupropion hydroxylation levels. These observations reflect hPXR agonism and the lack of hCAR inverse agonism and antagonism by meclizine, which were assessed by a hCAR reporter gene assay and mammalian two-hybrid assay. In conclusion, meclizine is a hPXR agonist, and it does not act as a hCAR inverse agonist or antagonist in cultured human hepatocytes.
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Affiliation(s)
- Aik Jiang Lau
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
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23
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Li H, Wang H. Activation of xenobiotic receptors: driving into the nucleus. Expert Opin Drug Metab Toxicol 2010; 6:409-26. [PMID: 20113149 DOI: 10.1517/17425251003598886] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
IMPORTANCE OF THE FIELD Xenobiotic receptors (XRs) play pivotal roles in regulating the expression of genes that determine the clearance and detoxification of xenobiotics, such as drugs and environmental chemicals. Recently, it has become increasingly evident that most XRs shuttle between the cytoplasm and nucleus, and activation of such receptors is directly associated with xenobiotic-induced nuclear import. AREAS COVERED IN THIS REVIEW The scope of this review covers research literature that discusses nuclear translocation and activation of XRs, as well as unpublished data generated from this laboratory. Specific emphasis is given to the constitutive androstane receptor (CAR), the pregnane X receptor and the aryl hydrocarbon receptor. WHAT THE READERS WILL GAIN A number of molecular chaperons presumably associated with cellular localization of XRs have been identified. Primary hepatocyte cultures have been established as a unique model retaining inactive CAR in the cytoplasm. Moreover, several splicing variants of human CAR exhibit altered cellular localization and chemical activation. TAKE HOME MESSAGE Nuclear accumulation is an essential step in the activation of XRs. Although great strides have been made, much remains to be understood concerning the mechanisms underlying intracellular localization and trafficking of XRs, which involve both direct ligand-binding and indirect pathways.
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Affiliation(s)
- Haishan Li
- University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences, 20 Penn Street, Baltimore, MD 21201, USA
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24
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Mota LC, Hernandez JP, Baldwin WS. Constitutive androstane receptor -null mice are sensitive to the toxic effects of parathion: association with reduced cytochrome p450-mediated parathion metabolism [corrected]. Drug Metab Dispos 2010; 38:1582-8. [PMID: 20573718 DOI: 10.1124/dmd.110.032961] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Constitutive androstane receptor [corrected](CAR) is activated by several chemicals and in turn regulates multiple detoxification genes. Our research demonstrates that parathion is one of the most potent, environmentally relevant CAR activators with an EC(50) of 1.43 microM. Therefore, animal studies were conducted to determine whether CAR was activated by parathion in vivo. Surprisingly, CAR-null mice, but not wild-type (WT) mice, showed significant parathion-induced toxicity. However, parathion did not induce Cyp2b expression, suggesting that parathion is not a CAR activator in vivo, presumably because of its short half-life. CAR expression is also associated with the expression of several drug-metabolizing cytochromes P450 (P450). CAR-null mice demonstrate lower expression of Cyp2b9, Cyp2b10, Cyp2c29, and Cyp3a11 primarily, but not exclusively in males. Therefore, we incubated microsomes from untreated WT and CAR-null mice with parathion in the presence of esterase inhibitors to determine whether CAR-null mice show perturbed P450-mediated parathion metabolism compared with that in WT mice. The metabolism of parathion to paraoxon and p-nitrophenol (PNP) was reduced in CAR-null mice with male CAR-null mice showing reduced production of both paraoxon and PNP, and female CAR-null mice showing reduced production of only PNP. Overall, the data indicate that CAR-null mice metabolize parathion slower than WT mice. These results provide a potential mechanism for increased sensitivity of individuals with lower CAR activity such as newborns to parathion and potentially other chemicals due to decreased metabolic capacity.
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Affiliation(s)
- Linda C Mota
- Environmental Toxicology, Clemson University, Clemson, SC 29634, USA
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25
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Hernandez J, Mota L, Baldwin W. Activation of CAR and PXR by Dietary, Environmental and Occupational Chemicals Alters Drug Metabolism, Intermediary Metabolism, and Cell Proliferation. CURRENT PHARMACOGENOMICS AND PERSONALIZED MEDICINE 2009; 7:81-105. [PMID: 20871735 PMCID: PMC2944248 DOI: 10.2174/187569209788654005] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The constitutive androstane receptor (CAR) and the pregnane × receptor (PXR) are activated by a variety of endogenous and exogenous ligands, such as steroid hormones, bile acids, pharmaceuticals, and environmental, dietary, and occupational chemicals. In turn, they induce phase I-III detoxification enzymes and transporters that help eliminate these chemicals. Because many of the chemicals that activate CAR and PXR are environmentally-relevant (dietary and anthropogenic), studies need to address whether these chemicals or mixtures of these chemicals may increase the susceptibility to adverse drug interactions. In addition, CAR and PXR are involved in hepatic proliferation, intermediary metabolism, and protection from cholestasis. Therefore, activation of CAR and PXR may have a wide variety of implications for personalized medicine through physiological effects on metabolism and cell proliferation; some beneficial and others adverse. Identifying the chemicals that activate these promiscuous nuclear receptors and understanding how these chemicals may act in concert will help us predict adverse drug reactions (ADRs), predict cholestasis and steatosis, and regulate intermediary metabolism. This review summarizes the available data on CAR and PXR, including the environmental chemicals that activate these receptors, the genes they control, and the physiological processes that are perturbed or depend on CAR and PXR action. This knowledge contributes to a foundation that will be necessary to discern interindividual differences in the downstream biological pathways regulated by these key nuclear receptors.
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Affiliation(s)
- J.P. Hernandez
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - L.C. Mota
- Institute of Environmental Toxicology, Clemson University, Pendleton, SC, USA
| | - W.S. Baldwin
- Institute of Environmental Toxicology, Clemson University, Pendleton, SC, USA
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26
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Jyrkkärinne J, Windshügel B, Rönkkö T, Tervo AJ, Küblbeck J, Lahtela-Kakkonen M, Sippl W, Poso A, Honkakoski P. Insights into ligand-elicited activation of human constitutive androstane receptor based on novel agonists and three-dimensional quantitative structure-activity relationship. J Med Chem 2009; 51:7181-92. [PMID: 18983136 DOI: 10.1021/jm800731b] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The human constitutive androstane receptor (CAR, NR1I3) is an important regulator of xenobiotic metabolism and other physiological processes. So far, only few CAR agonists are known and no explicit mechanism has been proposed for their action. Thus, we aimed to generate a 3D QSAR model that could explain the molecular determinants of CAR agonist action. To obtain a sufficient number of agonists that cover a wide range of activity, we applied a virtual screening approach using both structure- and ligand-based methods. We identified 27 novel human CAR agonists on which a 3D QSAR model was generated. The model, complemented by coregulator recruitment and mutagenesis results, suggests a potential activation mechanism for human CAR and may serve to predict potential activation of CAR for compounds emerging from drug development projects or for chemicals undergoing toxicological risk assessment.
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Affiliation(s)
- Johanna Jyrkkärinne
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Kuopio, P.O. Box 1627, 70211 Kuopio, Finland
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