1
|
Goyal N, Do C, Sridhar J, Shaik S, Thompson A, Perry T, Carter L, Foroozesh M. Design, Synthesis, and Biological Studies of Flavone-Based Esters and Acids as Potential P450 2A6 Inhibitors. Chem Res Toxicol 2023; 36:1973-1979. [PMID: 37963190 PMCID: PMC10731637 DOI: 10.1021/acs.chemrestox.3c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
As a potential means for smoking cessation and consequently prevention of smoking-related diseases and mortality, in this study, our goal was to investigate the inhibition of nicotine metabolism by P450 2A6. Smoking is the main cause of many diseases and disabilities and harms nearly every organ of the body. As reported by the Centers for Disease Control and Prevention (CDC), more than 16 million Americans are living with diseases caused by smoking. On average, the life expectancy of a smoker is about 10 years less than a nonsmoker. Smoking cessation can substantially reduce the incidence of smoking-related diseases, including cancer. At least, 70 of the more than 7000 cigarette smoke components, including polycyclic aromatic hydrocarbons, N-nitrosamines, and aromatic amines, are known carcinogens. Nicotine is the compound responsible for the addictive and psychopharmacological effects of tobacco. Cytochrome P450 enzymes are responsible for the phase I metabolism of many tobacco components, including nicotine. Nicotine is mainly metabolized by cytochrome P450s 2A6 and 2A13 to cotinine. This metabolism decreases the amount of available nicotine in the bloodstream, leading to increased smoking behavior and thus exposure to tobacco toxicants and carcinogens. Here, we report the syntheses and P450 2A6 inhibitory activities of a number of new flavone-based esters and acids. Three of the flavone derivatives studied were found to be potent competitive inhibitors of the enzyme. Docking studies were used to determine the possible mechanisms of the activity of these inhibitors.
Collapse
Affiliation(s)
- Navneet Goyal
- Department
of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
| | - Camilla Do
- Department
of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
| | - Jayalakshmi Sridhar
- Department
of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
| | - Shahensha Shaik
- Cell
and Molecular Biology and Bioinformatic Core, College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
| | - Anthony Thompson
- Department
of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
| | - Timothy Perry
- Department
of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
| | - Loren Carter
- Department
of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
| | - Maryam Foroozesh
- Department
of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
| |
Collapse
|
2
|
Yamaguchi Y, Nishizono N, Kobayashi D, Yoshimura T, Wada K, Kobayashi K, Oda K. Synthesis and biological evaluation of coumarin derivatives as selective CYP2A6 inhibitors. Bioorg Med Chem Lett 2023; 86:129206. [PMID: 36889653 DOI: 10.1016/j.bmcl.2023.129206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023]
Abstract
Cytochrome P450 2A6 (CYP2A6) inhibitors are expected to be suitable as smoking cessation aids and for cancer prevention. Because the typical coumarin-based CYP2A6 inhibitor methoxsalen also inhibits CYP3A4, unintended drug-drug interactions are still a concern. Therefore, the development of selective CYP2A6 inhibitors is desirable. In this study, we synthesized coumarin-based molecules, determined the IC50 values for CYP2A6 inhibition, verified the possibility of mechanism-based inhibition, and compared the selectivity for CYP2A6 versus CYP3A4. The results demonstrated that we developed CYP2A6 inhibitors that were more potent and selective than methoxsalen.
Collapse
Affiliation(s)
- Yuki Yamaguchi
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan.
| | - Naozumi Nishizono
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan
| | - Daisuke Kobayashi
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan
| | - Teruki Yoshimura
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan
| | - Keiji Wada
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan
| | - Kenichi Kobayashi
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan
| | - Kazuaki Oda
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan
| |
Collapse
|
3
|
Roberts AG, Stevens JC, Szklarz GD, Scott EE, Kumar S, Shah MB, Halpert JR. Four Decades of Cytochrome P450 2B Research: From Protein Adducts to Protein Structures and Beyond. Drug Metab Dispos 2023; 51:111-122. [PMID: 36310033 PMCID: PMC11022898 DOI: 10.1124/dmd.122.001109] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 01/03/2023] Open
Abstract
This article features selected findings from the senior author and colleagues dating back to 1978 and covering approximately three-fourths of the 60 years since the discovery of cytochrome P450. Considering the vast number of P450 enzymes in this amazing superfamily and their importance for so many fields of science and medicine, including drug design and development, drug therapy, environmental health, and biotechnology, a comprehensive review of even a single topic is daunting. To make a meaningful contribution to the 50th anniversary of Drug Metabolism and Disposition, we trace the development of the research in a single P450 laboratory through the eyes of seven individuals with different backgrounds, perspectives, and subsequent career trajectories. All co-authors are united in their fascination for the structural basis of mammalian P450 substrate and inhibitor selectivity and using such information to improve drug design and therapy. An underlying theme is how technological advances enable scientific discoveries that were impossible and even inconceivable to prior generations. The work performed spans the continuum from: 1) purification of P450 enzymes from animal tissues to purification of expressed human P450 enzymes and their site-directed mutants from bacteria; 2) inhibition, metabolism, and spectral studies to isothermal titration calorimetry, deuterium exchange mass spectrometry, and NMR; 3) homology models based on bacterial P450 X-ray crystal structures to rabbit and human P450 structures in complex with a wide variety of ligands. Our hope is that humanizing the scientific endeavor will encourage new generations of scientists to make fundamental new discoveries in the P450 field. SIGNIFICANCE STATEMENT: The manuscript summarizes four decades of work from Dr. James Halpert's laboratory, whose investigations have shaped the cytochrome P450 field, and provides insightful perspectives of the co-authors. This work will also inspire future drug metabolism scientists to make critical new discoveries in the cytochrome P450 field.
Collapse
Affiliation(s)
- Arthur G Roberts
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.).
| | - Jeffrey C Stevens
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.)
| | - Grazyna D Szklarz
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.)
| | - Emily E Scott
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.)
| | - Santosh Kumar
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.)
| | - Manish B Shah
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.)
| | - James R Halpert
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, 240 W. Green St., Athens, Georgia (A.G.R.); Unaffiliated (J.C.S.); Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia (G.D.S.); Departments of Medicinal Chemistry, Pharmacology, and Biological Chemistry and the Program in Biophysics, University of Michigan, Ann Arbor, Michigan (E.E.S.); Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, Tennessee (S.K.); Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York (M.B.S.); Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona (J.R.H.)
| |
Collapse
|
4
|
Feng L, Ning J, Tian X, Wang C, Yu Z, Huo X, Xie T, Zhang B, James TD, Ma X. Fluorescent probes for the detection and imaging of Cytochrome P450. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213740] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
5
|
Juvonen RO, Jokinen EM, Huuskonen J, Kärkkäinen O, Raunio H, Pentikäinen OT. Molecular docking and oxidation kinetics of 3-phenyl coumarin derivatives by human CYP2A13. Xenobiotica 2021; 51:1207-1216. [PMID: 33703988 DOI: 10.1080/00498254.2021.1898700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CYP2A13 enzyme is expressed in human extrahepatic tissues, while CYP2A6 is a hepatic enzyme. Reactions catalyzed by CYP2A13 activate tobacco-specific nitrosamines and some other toxic xenobiotics in lungs.To compare oxidation characteristics and substrate-enzyme active site interactions in CYP2A13 vs CYP2A6, we evaluated CYP2A13 mediated oxidation characteristics of 23 coumarin derivatives and modelled their interactions at the enzyme active site.CYP2A13 did not oxidize six coumarin derivatives to corresponding fluorescent 7-hydroxycoumarins. The Km-values of the other coumarins varied 0.85-97 µM, Vmax-values of the oxidation reaction varied 0.25-60 min-1, and intrinsic clearance varied 26-6190 kL/min*mol CYP2A13). Km of 6-chloro-3-(3-hydroxyphenyl)-coumarin was 0.85 (0.55-1.15 95% confidence limit) µM and Vmax 0.25 (0.23-0.26) min-1, whereas Km of 6-hydroxy-3-(3-hydroxyphenyl)-coumarin was 10.9 (9.9-11.8) µM and Vmax 60 (58-63) min-1. Docking analyses demonstrated that 6-chloro or 6-methoxy and 3-(3-hydroxyphenyl) or 3-(4-trifluoromethylphenyl) substituents of coumarin increased affinity to CYP2A13, whereas 3-triazole or 3-(3-acetate phenyl) or 3-(4-acetate phenyl) substituents decreased it.The active site of CYP2A13 accepts more diversified types of coumarin substrates than the hepatic CYP2A6 enzyme. New sensitive and convenient profluorescent CYP2A13 substrates were identified, such as 6-chloro-3-(3-hydroxyphenyl)-coumarin having high affinity and 6-hydroxy-3-(3-hydroxyphenyl)-coumarin with high intrinsic clearance.
Collapse
Affiliation(s)
- Risto O Juvonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Box 1627, 70211 Kuopio, Finland
| | - Elmeri M Jokinen
- Institute of Biomedicine, Faculty of Medicine, Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Juhani Huuskonen
- University of Jyvaskyla, Department of Chemistry, P.O. Box 35, FI-40014, Finland
| | - Olli Kärkkäinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Box 1627, 70211 Kuopio, Finland
| | - Hannu Raunio
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Box 1627, 70211 Kuopio, Finland
| | - Olli T Pentikäinen
- Institute of Biomedicine, Faculty of Medicine, Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland.,University of Jyvaskyla, Department of Chemistry, P.O. Box 35, FI-40014, Finland
| |
Collapse
|
6
|
Raunio H, Pentikäinen O, Juvonen RO. Coumarin-Based Profluorescent and Fluorescent Substrates for Determining Xenobiotic-Metabolizing Enzyme Activities In Vitro. Int J Mol Sci 2020; 21:ijms21134708. [PMID: 32630278 PMCID: PMC7369699 DOI: 10.3390/ijms21134708] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/03/2023] Open
Abstract
Activities of xenobiotic-metabolizing enzymes have been measured with various in vitro and in vivo methods, such as spectrophotometric, fluorometric, mass spectrometric, and radioactivity-based techniques. In fluorescence-based assays, the reaction produces a fluorescent product from a nonfluorescent substrate or vice versa. Fluorescence-based enzyme assays are usually highly sensitive and specific, allowing measurements on small specimens of tissues with low enzyme activities. Fluorescence assays are also amenable to miniaturization of the reaction mixtures and can thus be done in high throughput. 7-Hydroxycoumarin and its derivatives are widely used as fluorophores due to their desirable photophysical properties. They possess a large π-π conjugated system with electron-rich and charge transfer properties. This conjugated structure leads to applications of 7-hydroxycoumarins as fluorescent sensors for biological activities. We describe in this review historical highlights and current use of coumarins and their derivatives in evaluating activities of the major types of xenobiotic-metabolizing enzyme systems. Traditionally, coumarin substrates have been used to measure oxidative activities of cytochrome P450 (CYP) enzymes. For this purpose, profluorescent coumarins are very sensitive, but generally lack selectivity for individual CYP forms. With the aid of molecular modeling, we have recently described several new coumarin-based substrates for measuring activities of CYP and conjugating enzymes with improved selectivity.
Collapse
Affiliation(s)
- Hannu Raunio
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70600 Kuopio, Finland;
- Correspondence:
| | - Olli Pentikäinen
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20520 Turku, Finland;
| | - Risto O. Juvonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70600 Kuopio, Finland;
| |
Collapse
|
7
|
Guengerich FP. Cytochrome P450 2E1 and its roles in disease. Chem Biol Interact 2020; 322:109056. [PMID: 32198084 PMCID: PMC7217708 DOI: 10.1016/j.cbi.2020.109056] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/12/2019] [Accepted: 03/10/2020] [Indexed: 12/27/2022]
Abstract
Cytochrome P450 (P450) 2E1 is the major P450 enzyme involved in ethanol metabolism. That role is shared with two other enzymes that oxidize ethanol, alcohol dehydrogenase and catalase. P450 2E1 is also involved in the bioactivation of a number of low molecular weight cancer suspects, as validated in vivo in mouse models where cancers could be attenuated by deletion of Cyp2e1. P450 2E1 does not have a role in global production of reactive oxygen species but localized roles are possible, e.g. in mitochondria. The structures, conformations, and catalytic mechanisms of P450 2E1 have some unusual features among P450s. The concentration of hepatic P450 varies ≥10-fold among humans, possibly in part due to single nucleotide variants. The level of P450 2E1 may have relevance in the rates of oxidation of drugs, particularly acetaminophen and anesthetics.
Collapse
Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, 638 Robinson Research Building, 2200 Pierce Avenue, Nashville, TN, 37232-0146, USA.
| |
Collapse
|
8
|
Cerrone J, Lee CM, Mi T, Morgan ET. Nitric Oxide Mediated Degradation of CYP2A6 via the Ubiquitin-Proteasome Pathway in Human Hepatoma Cells. Drug Metab Dispos 2020; 48:544-552. [PMID: 32350062 DOI: 10.1124/dmd.119.089961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/06/2020] [Indexed: 12/14/2022] Open
Abstract
Several cytochrome P450 enzymes are known to be down-regulated by nitric oxide (NO). CYP2A6 is responsible for the metabolism of nicotine and several other xenobiotics, but its susceptibility to down-regulation by NO has not been reported. To address this question, we used Huh7 human hepatoma cell lines to express CYP2A6 with a C-terminal V5 tag (CYP2A6V5). NO donor treatment [dipropylenetriamine NONOate (DPTA)] down-regulated CYP2A6 protein to approximately 40% of control levels in 4 hours. An NO scavenging agent protected CYP2A6 from down-regulation by DPTA in a concentration-dependent manner, demonstrating that the down-regulation is NO-dependent. Experiments with the protein synthesis inhibitor cycloheximide showed that CYP2A6 protein down-regulation occurs posttranslationally. In the presence of proteasome inhibitors MG132 or bortezomib, NO-treated cells showed an accumulation of a high molecular mass signal, whereas autophagy inhibitors chloroquine and 3-methyladenine and the lysosomal and calpain inhibitor E64d had no effect. Immunoprecipitation of CYP2A6 followed by Western blotting with an antiubiquitin antibody showed that the high molecular mass species contain polyubiquitinated CYP2A6 protein. This suggests that NO led to the degradation of protein via the ubiquitin-proteasome pathway. The down-regulation by NO was blocked by the reversible CYP2A6 inhibitor pilocarpine but not by the suicide inhibitor methoxsalen, demonstrating that down-regulation requires NO access to the active site but does not require catalytic activity of the enzyme. These findings provide novel insights toward the regulation of CYP2A6 in a human cell line and can influence our understanding of CYP2A6-related drug metabolism. SIGNIFICANCE STATEMENT: This study demonstrates that the nicotine metabolizing enzyme CYP2A6 is down-regulated by nitric oxide, a molecule produced in large amounts in the context of inflammation and that is also inhaled from cigarette smoke. This occurs via ubiquitination and proteasomal degradation, and does not require catalytic activity of the enzyme. This work adds to the growing knowledge of the selective effect and mechanism of action of nitric oxide (NO) on cytochrome P450 enzymes and suggests a possible novel mode of interaction between nicotine and NO in cigarette smokers.
Collapse
Affiliation(s)
- John Cerrone
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, Georgia
| | - Choon-Myung Lee
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, Georgia
| | - Tian Mi
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, Georgia
| | - Edward T Morgan
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, Georgia
| |
Collapse
|
9
|
Strohmaier SJ, Huang W, Baek JM, Hunter DJB, Gillam EMJ. Rational evolution of the cofactor-binding site of cytochrome P450 reductase yields variants with increased activity towards specific cytochrome P450 enzymes. FEBS J 2019; 286:4473-4493. [PMID: 31276316 DOI: 10.1111/febs.14982] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 04/30/2019] [Accepted: 07/02/2019] [Indexed: 12/22/2022]
Abstract
NADPH-cytochrome P450 reductase (CPR) is the natural redox partner of microsomal cytochrome P450 enzymes. CPR shows a stringent preference for NADPH over the less expensive cofactor, NADH, economically limiting its use as a biocatalyst. The complexity of cofactor-linked CPR protein dynamics and the incomplete understanding of the interaction of CPR with both cofactors and electron acceptors present challenges for the successful rational engineering of a CPR with enhanced activity with NADH. Here, we report a rational evolution approach to enhance the activity of CPR with NADH, in which mutations were introduced into the NADPH-binding flavin adenine dinucleotide (FAD) domain. Multiple CPR mutants that used NADH more effectively than the wild-type CPR in the reduction of the surrogate electron acceptor, cytochrome c were found. However, most were inactive in supporting P450 activity, arguing against the use of cytochrome c as a surrogate electron acceptor. Unexpectedly, several mutants showed significantly improved activity towards CYP2C9 (mutant 1-014) and/or CYP2A6 (mutants 1-014, 1-015, 1-053 and 1-077) using NADPH, even though the mutations were introduced at locations remote from the putative CPR-P450 interaction face. Therefore, mutations at sites in the FAD domain of CPR may be promising future engineering targets to enhance P450-mediated substrate turnover. ENZYMES: NADPH-cytochrome P450 reductase - EC 1.6.2.4; cytochrome P450 - EC 1.14.14.1.
Collapse
Affiliation(s)
- Silja J Strohmaier
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Weiliang Huang
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Jong-Min Baek
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Dominic J B Hunter
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| |
Collapse
|
10
|
Lu Q, Song J, Wu P, Li C, Thiel W. Mechanistic Insights into the Directing Effect of Thr303 in Ethanol Oxidation by Cytochrome P450 2E1. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00907] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Qianqian Lu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, China
| | - Jinshuai Song
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, China
| | - Peng Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunsen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, China
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
11
|
Nagayoshi H, Murayama N, Kakimoto K, Tsujino M, Takenaka S, Katahira J, Lim YR, Kim D, Yamazaki H, Komori M, Guengerich FP, Shimada T. Oxidation of Flavone, 5-Hydroxyflavone, and 5,7-Dihydroxyflavone to Mono-, Di-, and Tri-Hydroxyflavones by Human Cytochrome P450 Enzymes. Chem Res Toxicol 2019; 32:1268-1280. [PMID: 30964977 DOI: 10.1021/acs.chemrestox.9b00078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biologically active plant flavonoids, including 5,7-dihydroxyflavone (57diOHF, chrysin), 4',5,7-trihydroxyflavone (4'57triOHF, apigenin), and 5,6,7-trihydroxyflavone (567triOHF, baicalein), have important pharmacological and toxicological significance, e.g., antiallergic, anti-inflammatory, antioxidative, antimicrobial, and antitumorgenic properties. In order to better understand the metabolism of these flavonoids in humans, we examined the oxidation of flavone, 5-hydroxyflavone (5OHF), and 57diOHF to various products by human cytochrome P450 (P450 or CYP) and liver microsomal enzymes. Individual human P450s and liver microsomes oxidized flavone to 6-hydroxyflavone, small amounts of 5OHF, and 11 other monohydroxylated products at different rates and also produced several dihydroxylated products (including 57diOHF and 7,8-dihydroxyflavone) from flavone. We also found that 5OHF was oxidized by several P450 enzymes and human liver microsomes to 57diOHF and further to 567triOHF, but the turnover rates in these reactions were low. Interestingly, both CYP1B1.1 and 1B1.3 converted 57diOHF to 567triOHF at turnover rates (on the basis of P450 contents) of >3.0 min-1, and CYP1A1 and 1A2 produced 567triOHF at rates of 0.51 and 0.72 min-1, respectively. CYP2A13 and 2A6 catalyzed the oxidation of 57diOHF to 4'57triOHF at rates of 0.7 and 0.1 min-1, respectively. Our present results show that different P450s have individual roles in oxidizing these phytochemical flavonoids and that these reactions may cause changes in their biological and toxicological properties in mammals.
Collapse
Affiliation(s)
- Haruna Nagayoshi
- Osaka Institute of Public Health , 1-3-69 Nakamichi , Higashinari-ku , Osaka 537-0025 , Japan
| | - Norie Murayama
- Laboratory of Drug Metabolism and Pharmacokinetics , Showa Pharmaceutical University , Machida , Tokyo 194-8543 , Japan
| | - Kensaku Kakimoto
- Osaka Institute of Public Health , 1-3-69 Nakamichi , Higashinari-ku , Osaka 537-0025 , Japan
| | - Masaki Tsujino
- Osaka Institute of Public Health , 1-3-69 Nakamichi , Higashinari-ku , Osaka 537-0025 , Japan
| | - Shigeo Takenaka
- Graduate School of Comprehensive Rehabilitation , Osaka Prefecture University , 3-7-30 , Habikino , Osaka 583-8555 , Japan
| | - Jun Katahira
- Laboratory of Cellular and Molecular Biology, Veterinary Sciences , Osaka Prefecture University , 1-58 Rinku-Orai-Kita , Izumisano , Osaka 598-8531 , Japan
| | - Young-Ran Lim
- Department of Biological Sciences , Konkuk University , Seoul 05029 , Korea
| | - Donghak Kim
- Department of Biological Sciences , Konkuk University , Seoul 05029 , Korea
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics , Showa Pharmaceutical University , Machida , Tokyo 194-8543 , Japan
| | - Masayuki Komori
- Laboratory of Cellular and Molecular Biology, Veterinary Sciences , Osaka Prefecture University , 1-58 Rinku-Orai-Kita , Izumisano , Osaka 598-8531 , Japan
| | - F Peter Guengerich
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States
| | - Tsutomu Shimada
- Laboratory of Cellular and Molecular Biology, Veterinary Sciences , Osaka Prefecture University , 1-58 Rinku-Orai-Kita , Izumisano , Osaka 598-8531 , Japan
| |
Collapse
|
12
|
Adekenov S. Study of antiopisthorchiasis activity of sesquiterpene lactones and their derivatives. Fitoterapia 2019; 133:200-211. [DOI: 10.1016/j.fitote.2018.12.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 10/27/2022]
|
13
|
Ahinko M, Niinivehmas S, Jokinen E, Pentikäinen OT. Suitability ofMMGBSAfor the selection of correct ligand binding modes from docking results. Chem Biol Drug Des 2018; 93:522-538. [DOI: 10.1111/cbdd.13446] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/01/2018] [Accepted: 11/11/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Mira Ahinko
- Department of Biological and Environmental Science & Nanoscience CenterUniversity of Jyvaskyla, MedChem.fi Jyvaskyla Finland
| | - Sanna Niinivehmas
- Department of Biological and Environmental Science & Nanoscience CenterUniversity of Jyvaskyla, MedChem.fi Jyvaskyla Finland
- Institute of Biomedicine, Integrative Physiology and PharmacologyUniversity of Turku, MedChem.fi Turku Finland
| | - Elmeri Jokinen
- Institute of Biomedicine, Integrative Physiology and PharmacologyUniversity of Turku, MedChem.fi Turku Finland
| | - Olli T. Pentikäinen
- Department of Biological and Environmental Science & Nanoscience CenterUniversity of Jyvaskyla, MedChem.fi Jyvaskyla Finland
- Institute of Biomedicine, Integrative Physiology and PharmacologyUniversity of Turku, MedChem.fi Turku Finland
| |
Collapse
|
14
|
Nagayoshi H, Murayama N, Kakimoto K, Takenaka S, Katahira J, Lim YR, Kim V, Kim D, Yamazaki H, Komori M, Guengerich FP, Shimada T. Site-specific oxidation of flavanone and flavone by cytochrome P450 2A6 in human liver microsomes. Xenobiotica 2018; 49:791-802. [PMID: 30048196 DOI: 10.1080/00498254.2018.1505064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The roles of human cytochrome P450 (P450 or CYP) 2A6 in the oxidation of flavanone [(2R)- and (2S)-enantiomers] and flavone were studied in human liver microsomes and recombinant human P450 enzymes. CYP2A6 was highly active in oxidizing flavanone to form flavone, 2'-hydroxy-, 4'-, and 6-hydroxyflavanones and in oxidizing flavone to form mono- and di-hydroxylated products, such as mono-hydroxy flavones M6, M7, and M11 and di-hydroxy flavones M3, M4, and M5. Liver microsomes prepared from human sample HH2, defective in coumarin 7-hydroxylation activity, were very inefficient in forming 2'-hydroxyflavanone from flavanone and a mono-hydroxylated product, M6, from flavone. Coumarin and anti-CYP2A6 antibodies strongly inhibited the formation of these metabolites in microsomes prepared from liver samples HH47 and 54, which were active in coumarin oxidation activities. Molecular docking analysis showed that the C2'-position of (2R)-flavanone (3.8 Å) was closer to the iron center of CYP2A6 than the C6-position (10 Å), while distances from C2' and C6 of (2S)-flavanone to the CYP2A6 were 6.91 Å and 5.42 Å, respectively. These results suggest that CYP2A6 catalyzes site-specific oxidation of (racemic) flavanone and also flavone in human liver microsomes. CYP1A2 and CYP2B6 were also found to play significant roles in some of the oxidations of these flavonoids by human liver microsomes.
Collapse
Affiliation(s)
| | - Norie Murayama
- b Laboratory of Drug Metabolism and Pharmacokinetics , Showa Pharmaceutical University , Machida , Tokyo , Japan
| | | | - Shigeo Takenaka
- c Graduate School of Comprehensive Rehabilitation , Osaka Prefecture University , Habikino Osaka , Japan
| | - Jun Katahira
- d Laboratory of Cellular and Molecular Biology , Veterinary Sciences, Osaka Prefecture University , Izumisano , Osaka , Japan
| | - Young-Ran Lim
- e Department of Biological Sciences , Konkuk University , Seoul , Korea
| | - Vitchan Kim
- e Department of Biological Sciences , Konkuk University , Seoul , Korea
| | - Donghak Kim
- e Department of Biological Sciences , Konkuk University , Seoul , Korea
| | - Hiroshi Yamazaki
- b Laboratory of Drug Metabolism and Pharmacokinetics , Showa Pharmaceutical University , Machida , Tokyo , Japan
| | - Masayuki Komori
- d Laboratory of Cellular and Molecular Biology , Veterinary Sciences, Osaka Prefecture University , Izumisano , Osaka , Japan
| | - F Peter Guengerich
- f Department of Biochemistry Vanderbilt University School of Medicine , Nashville , Tennessee , USA
| | - Tsutomu Shimada
- d Laboratory of Cellular and Molecular Biology , Veterinary Sciences, Osaka Prefecture University , Izumisano , Osaka , Japan
| |
Collapse
|
15
|
Wang Y, Lin W, Wu N, He X, Wang J, Feng Z, Xie XQ. An insight into paracetamol and its metabolites using molecular docking and molecular dynamics simulation. J Mol Model 2018; 24:243. [PMID: 30121710 PMCID: PMC6733030 DOI: 10.1007/s00894-018-3790-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/09/2018] [Indexed: 10/28/2022]
Abstract
Paracetamol is a relatively safe analgesia/antipyretic drug without the risks of addiction, dependence, tolerance, and withdrawal when used alone. However, when administrated in an opioid/paracetamol combination product, which often contains a large quantity of paracetamol, it can be potentially dangerous due to the risk of hepatotoxicity. Paracetamol is known to be metabolized into N-(4-hydroxyphenyl)-arachidonamide (AM404) via fatty acid amide hydrolase (FAAH) and into N-acetyl-p-benzoquinone imine (NAPQI) via cytochrome P450 (CYP) enzymes. However, the underlying mechanism of paracetamol is still unclear. In addition, paracetamol has the potential to interact with other drugs that are also involved with CYP family enzymes (inducer/inhibitor/substrate), an example being illicit drugs. In our present work, we looked into the relationship between paracetamol and its metabolites (AM404 and NAPQI) using molecular docking and molecular dynamics (MD) simulations. We first carried out a series of molecular docking studies between paracetamol/AM404/NAQPI and their reported targets, including CYP 2E1, FAAH, TRPA1, CB1, and TRPV1. Subsequently, we performed MD simulations and energy decomposition for CB1-AM404, TRPV1-AM404, and TRPV1-NAPQI for further investigation of the dynamics interactions. Finally, we summarized and discussed the reported drug-drug interactions between paracetamol and central nervous system drugs, especially illicit drugs. Overall, we are able to provide new insights into the structural and functional roles of paracetamol and its metabolites that can inform the potential prevention and treatment of paracetamol overdose. Graphical abstract Paracetamol and its metabolites.
Collapse
Affiliation(s)
- Yuanqiang Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing, 400054, China
- Chongqing Key Laboratory of Target Based Drug Screening and Effect Evaluation, Chongqing, 400054, China
| | - Weiwei Lin
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Nan Wu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| |
Collapse
|
16
|
Fan JR, Li H, Zhang HX, Zheng QC. Exploring the structure characteristics and major channels of cytochrome P450 2A6, 2A13, and 2E1 with pilocarpine. Biopolymers 2018; 109:e23108. [PMID: 29484634 DOI: 10.1002/bip.23108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 12/25/2022]
Abstract
The majority of cytochromes P450 play a critical role in metabolism of endogenous and exogenous substrates, some of its products are carcinogens. Therefore, inhibition of P450 enzymes activity can promote the detoxification and elimination of chemical carcinogens. In this study, molecular dynamics (MD) simulations and adaptive steered molecular dynamics (ASMD) simulations were performed to explore the structure features and channel dynamics of three P450 isoforms 2A6, 2A13, and 2E1 bound with the common inhibitor pilocarpine. The binding free energy results combined with the PMF calculations give a reasonable ranking of binding affinity, which are consistent with the experimental data. Our results uncover how a sequence divergence of different CYP2 enzymes causes individual variations in major channel selections. On the basis of channel bottleneck and energy decomposition analysis, we propose a gating mechanism of their respective major channels in three enzymes, which may be attributed to a reversal of Phe209 in CYP2A6/2A13, as well as the rotation of Phe116 and Phe298 in CYP2E1. The hydrophobic residues not only make strong hydrophobic interactions with inhibitor, but also act as gatekeeper to regulate the opening of channel. The present study provides important insights into the structure-function relationships of three cytochrome P450s and the molecular basis for development of potent inhibitors.
Collapse
Affiliation(s)
- Jing-Rong Fan
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, People's Republic of China
| | - Heng Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, 130012, People's Republic of China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, People's Republic of China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, People's Republic of China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, 130012, People's Republic of China
| |
Collapse
|
17
|
Kakimoto K, Murayama N, Takenaka S, Nagayoshi H, Lim YR, Kim V, Kim D, Yamazaki H, Komori M, Guengerich FP, Shimada T. Cytochrome P450 2A6 and other human P450 enzymes in the oxidation of flavone and flavanone. Xenobiotica 2018; 49:131-142. [PMID: 29310511 DOI: 10.1080/00498254.2018.1426133] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
1. We previously reported that flavone and flavanone interact spectrally with cytochrome P450 (P450 or CYP) 2A6 and 2A13 and other human P450s and inhibit catalytic activities of these P450 enzymes. In this study, we studied abilities of CYP1A1, 1A2, 1B1, 2A6, 2A13, 2C9 and 3A4 to oxidize flavone and flavanone. 2. Human P450s oxidized flavone to 6- and 5-hydroxylated flavones, seven uncharacterized mono-hydroxylated flavones, and five di-hydroxylated flavones. CYP2A6 was most active in forming 6-hydroxy- and 5-hydroxyflavones and several mono- and di-hydroxylated products. 3. CYP2A6 was also very active in catalyzing flavanone to form 2'- and 6-hydroxyflavanones, the major products, at turnover rates of 4.8 min-1 and 1.3 min-1, respectively. Other flavanone metabolites were 4'-, 3'- and 7-hydroxyflavanone, three uncharacterized mono-hydroxylated flavanones and five mono-hydroxylated flavones, including 6-hydroxyflavone. CYP2A6 catalyzed flavanone to produce flavone at a turnover rate of 0.72 min-1 that was ∼3-fold higher than that catalyzed by CYP2A13 (0.29 min-1). 4. These results indicate that CYP2A6 and other human P450s have important roles in metabolizing flavone and flavanone, two unsubstituted flavonoids, present in dietary foods. Chemical mechanisms of P450-catalyzed desaturation of flavanone to form flavone are discussed.
Collapse
Affiliation(s)
- Kensaku Kakimoto
- a Osaka Institute of Public Health , Higashinari-ku , Osaka , Japan
| | - Norie Murayama
- b Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University , Machida , Tokyo , Japan
| | - Shigeo Takenaka
- c Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University , Habikino , Osaka , Japan
| | - Haruna Nagayoshi
- a Osaka Institute of Public Health , Higashinari-ku , Osaka , Japan
| | - Young-Ran Lim
- d Department of Biological Sciences , Konkuk University , Seoul , Korea
| | - Vitchan Kim
- d Department of Biological Sciences , Konkuk University , Seoul , Korea
| | - Donghak Kim
- d Department of Biological Sciences , Konkuk University , Seoul , Korea
| | - Hiroshi Yamazaki
- b Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University , Machida , Tokyo , Japan
| | - Masayuki Komori
- e Laboratory of Cellular and Molecular Biology, Veterinary Sciences, Osaka Prefecture University , Izumisano , Osaka , Japan , and
| | - F Peter Guengerich
- f Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , TN , USA
| | - Tsutomu Shimada
- e Laboratory of Cellular and Molecular Biology, Veterinary Sciences, Osaka Prefecture University , Izumisano , Osaka , Japan , and
| |
Collapse
|
18
|
Kumondai M, Hosono H, Maekawa M, Yamaguchi H, Mano N, Oda A, Hirasawa N, Hiratsuka M. Functional characterization of 9 CYP2A13 allelic variants by assessment of nicotine C-oxidation and coumarin 7-hydroxylation. Drug Metab Pharmacokinet 2017; 33:82-89. [PMID: 29342418 DOI: 10.1016/j.dmpk.2017.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 11/01/2017] [Accepted: 11/13/2017] [Indexed: 10/18/2022]
Abstract
Cytochrome P450 2A13 (CYP2A13) is responsible for the metabolism of chemical compounds such as nicotine, coumarin, and tobacco-specific nitrosamine. Several of these compounds have been recognized as procarcinogens activated by CYP2A13. We recently showed that CYP2A13*2 contributes to inter-individual variations observed in bladder cancer susceptibility because CYP2A13*2 might cause a decrease in enzymatic activity. Other CYP2A13 allelic variants may also affect cancer susceptibility. In this study, we performed an in vitro analysis of the wild-type enzyme (CYP2A13.1) and 8 CYP2A13 allelic variants, using nicotine and coumarin as representative CYP2A13 substrates. These CYP2A13 variant proteins were heterologously expressed in 293FT cells, and the kinetic parameters of nicotine C-oxidation and coumarin 7-hydroxylation were estimated. The quantities of CYP2A13 holoenzymes in microsomal fractions extracted from 293FT cells were determined by measuring reduced carbon monoxide-difference spectra. The kinetic parameters for CYP2A13.3, CYP2A13.4, and CYP2A13.10 could not be determined because of low metabolite concentrations. Five other CYP2A13 variants (CYP2A13.2, CYP2A13.5, CYP2A13.6, CYP2A13.8, and CYP2A13.9) showed markedly reduced enzymatic activity toward both substrates. These findings provide insights into the mechanism underlying inter-individual differences observed in genotoxicity and cancer susceptibility.
Collapse
Affiliation(s)
- Masaki Kumondai
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Hiroki Hosono
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Masamitsu Maekawa
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, 980-8574, Japan
| | - Hiroaki Yamaguchi
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, 980-8574, Japan
| | - Nariyasu Mano
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, 980-8574, Japan
| | - Akifumi Oda
- Faculty of Pharmacy, Meijo University, Nagoya, 468-8503, Japan
| | - Noriyasu Hirasawa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Masahiro Hiratsuka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, 980-8574, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8575, Japan.
| |
Collapse
|
19
|
Shukla R, Chetri PB, Sonkar A, Pakharukova MY, Mordvinov VA, Tripathi T. Identification of novel natural inhibitors of Opisthorchis felineus cytochrome P450 using structure-based screening and molecular dynamic simulation. J Biomol Struct Dyn 2017; 36:3541-3556. [PMID: 29029597 DOI: 10.1080/07391102.2017.1392897] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Opisthorchis felineus is the etiological agent of opisthorchiasis in humans. O. felineus cytochrome P450 (OfCYP450) is an important enzyme in the parasite xenobiotic metabolism. To identify the potential anti-opisthorchid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,65,869) against the OfCYP450. The ligands were screened against OfCYP450 in four sequential docking modes that resulted in 361 ligands having better docking score. These compounds were evaluated for Lipinski and ADMET prediction, and 10 compounds were found to fit well with re-docking studies. After refinement by docking and drug-likeness analyses, four potential inhibitors (ZINC2358298, ZINC8790946, ZINC70707116, and ZINC85878789) were identified. These ligands with reference compounds (itraconazole and fluconazole) were further subjected to molecular dynamics simulation (MDS) and binding energy analyses to compare the dynamic structure of protein after ligand binding and the stability of the OfCYP450 and bound complexes. The binding energy analyses were also calculated. The results suggested that the compounds had a negative binding energy with -259.41, -110.09, -188.25, -163.30, -202.10, and -158.79 kJ mol-1 for itraconazole, fluconazole, and compounds with IDs ZINC2358298, ZINC8790946, ZINC70707116, and ZINC85878789, respectively. These lead compounds displayed significant pharmacological and structural properties to be drug candidates. On the basis of MDS results and binding energy analyses, we concluded that ZINC8790946, ZINC70707116, and ZINC85878789 have excellent potential to inhibit OfCYP450.
Collapse
Affiliation(s)
- Rohit Shukla
- a Molecular and Structural Biophysics Laboratory, Department of Biochemistry , North-Eastern Hill University , Shillong 793022 , India
| | - Purna B Chetri
- a Molecular and Structural Biophysics Laboratory, Department of Biochemistry , North-Eastern Hill University , Shillong 793022 , India
| | - Amit Sonkar
- a Molecular and Structural Biophysics Laboratory, Department of Biochemistry , North-Eastern Hill University , Shillong 793022 , India
| | - Maria Y Pakharukova
- b Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics , Siberian Branch of the Russian Academy of Sciences , 10 Lavrentiev ave., Novosibirsk 630090 , Russia
| | - Viatcheslav A Mordvinov
- b Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics , Siberian Branch of the Russian Academy of Sciences , 10 Lavrentiev ave., Novosibirsk 630090 , Russia
| | - Timir Tripathi
- a Molecular and Structural Biophysics Laboratory, Department of Biochemistry , North-Eastern Hill University , Shillong 793022 , India
| |
Collapse
|
20
|
Shimada T, Murayama N, Kakimoto K, Takenaka S, Lim YR, Yeom S, Kim D, Yamazaki H, Guengerich FP, Komori M. Oxidation of 1-chloropyrene by human CYP1 family and CYP2A subfamily cytochrome P450 enzymes: catalytic roles of two CYP1B1 and five CYP2A13 allelic variants. Xenobiotica 2017. [PMID: 28648140 DOI: 10.1080/00498254.2017.1347306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
1. 1-Chloropyrene, one of the major chlorinated polycyclic aromatic hydrocarbon contaminants, was incubated with human cytochrome P450 (P450 or CYP) enzymes including CYP1A1, 1A2, 1B1, 2A6, 2A13, 2B6, 2C9, 2D6, 2E1, 3A4 and 3A5. Catalytic differences in 1-chloropyrene oxidation by polymorphic two CYP1B1 and five CYP2A13 allelic variants were also examined. 2. CYP1A1 oxidized 1-chloropyrene at the 6- and 8-positions more actively than at the 3-position, while both CYP1B1.1 and 1B1.3 preferentially catalyzed 6-hydroxylation. 3. Five CYP2A13 allelic variants oxidized 8-hydroxylation much more than 6- and 3-hydroxylation, and the variant CYP2A13.3 was found to slowly catalyze these reactions with a lower kcat value than other CYP2A13.1 variants. 4. CYP2A6 catalyzed 1-chloropyrene 6-hydroxylation at a higher rate than the CYP2A13 enzymes, but the rate was lower than the CYP1A1 and 1B1 variants. Other human P450 enzymes had low activities towards 1-chloropyrene. 5. Molecular docking analysis suggested differences in the interaction of 1-chloropyrene with active sites of CYP1 and 2 A enzymes. In addition, a naturally occurring Thr134 insertion in CYP2A13.3 was found to affect the orientation of Asn297 in the I-helix in interacting with 1-chloropyrene (and also 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, NNK) and caused changes in the active site of CYP2A13.3 as compared with CYP2A13.1.
Collapse
Affiliation(s)
- Tsutomu Shimada
- a Laboratory of Cellular and Molecular Biology, Osaka Prefecture University , Osaka , Japan
| | - Norie Murayama
- b Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University , Machida , Tokyo
| | | | - Shigeo Takenaka
- d Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University , Osaka , Japan
| | - Young-Ran Lim
- e Department of Biological Sciences , Konkuk University , Seoul , Korea , and
| | - Sora Yeom
- e Department of Biological Sciences , Konkuk University , Seoul , Korea , and
| | - Donghak Kim
- e Department of Biological Sciences , Konkuk University , Seoul , Korea , and
| | - Hiroshi Yamazaki
- b Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University , Machida , Tokyo
| | - F Peter Guengerich
- f Department of Biochemistry , Vanderbilt University School of Medicine , Nashville, TN , USA
| | - Masayuki Komori
- a Laboratory of Cellular and Molecular Biology, Osaka Prefecture University , Osaka , Japan
| |
Collapse
|
21
|
Uehara S, Uno Y, Tomioka E, Inoue T, Sasaki E, Yamazaki H. Functional characterization and tissue expression of marmoset cytochrome P450 2E1. Biopharm Drug Dispos 2017; 38:394-397. [DOI: 10.1002/bdd.2080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/22/2017] [Accepted: 04/30/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Shotaro Uehara
- Laboratory of Drug Metabolism and Pharmacokinetics; Showa Pharmaceutical University; Machida Tokyo 194-8543 Japan
| | - Yasuhiro Uno
- Pharmacokinetics and Bioanalysis Center; Shin Nippon Biomedical Laboratories, Ltd.; Kainan Wakayama Japan
| | - Etsuko Tomioka
- Laboratory of Drug Metabolism and Pharmacokinetics; Showa Pharmaceutical University; Machida Tokyo 194-8543 Japan
| | - Takashi Inoue
- Department of marmoset research; Central Institute for Experimental Animals; Kawasaki Japan
| | - Erika Sasaki
- Department of marmoset research; Central Institute for Experimental Animals; Kawasaki Japan
- Keio Advanced Research Center; Keio University; Minato-ku Tokyo Japan
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics; Showa Pharmaceutical University; Machida Tokyo 194-8543 Japan
| |
Collapse
|
22
|
Ratha P, Chitra L, Ancy I, Kumaradhas P, Palvannan T. New amino acid-Schiff base derived from s-allyl cysteine and methionine alleviates carbon tetrachloride-induced liver dysfunction. Biochimie 2017; 138:70-81. [PMID: 28454919 DOI: 10.1016/j.biochi.2017.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 04/09/2017] [Accepted: 04/22/2017] [Indexed: 12/22/2022]
Abstract
In spite of the tremendous stride in modern medicine, conventional drugs used in the hepatotoxic management are mostly inadequate. The present study aims in the synthesis of novel Schiff base compound derived using s-allyl cystiene and methionine. The newly synthesized compound, 2-((2-((2-(allylthio)-1-carboxyethyl)imino)ethylidene)amino)-4-(methylthio)butanoic acid (ACEMB) was characterized using UV-visible spectrophotometer, FTIR, 1HNMR, and GC-MS. ACEMB showed potent in vitro antioxidant property. Chronic administration of ACEMB prior to CCl4 intoxication: i) attenuated the leakage of liver injury markers, such as, enzymes (AST, ALT, GGT, ALP and LDH) and biomolecules (bilirubin) into the blood circulation; ii) normalized the concentration of total proteins, albumin and globulin to control level; and iii) protected the liver against dyslipidemia. These effects of ACEMB show the preservation of endoplasmic reticulum function against CCl4 toxicity in the liver. The protective effect of ACEMB was due to its antioxidant property, which was revealed by reduced oxidative stress (TBARS and HP) and enhanced functions of the endogenous antioxidative system (SOD, catalase, GPx, GST, GSH, vitamin E and C) against CCl4 intoxication. Also, ACEMB protected the functional activities of the various mitochondrial tricarboxylic acid cycle and oxidative phosphorylation enzymes. The biochemical alterations are in concurrence with the histological observations, wherein ACEMB pretreatment prevented the vacuolation, degeneration of nuclei and necrosis of hepatocytes. In addition, in silico analysis reveals the interaction of ACEMB in the active site of cytochrome P450. ACEMB mediates hepatoprotective effect by substituting itself as an antioxidant and decreasing oxidative stress, thereby diminishing the intracellular organelle dysfunction against CCl4 toxicity in the liver.
Collapse
Affiliation(s)
- Periyasamy Ratha
- Department of Biochemistry, Periyar University, Salem, Tamil Nadu 636011, India
| | - Loganathan Chitra
- Department of Biochemistry, Periyar University, Salem, Tamil Nadu 636011, India
| | - Iruthayaraj Ancy
- Department of Physics, Periyar University, Salem, Tamil Nadu 636011, India
| | - Poomani Kumaradhas
- Department of Physics, Periyar University, Salem, Tamil Nadu 636011, India
| | | |
Collapse
|
23
|
Shimada T. Inhibition of Carcinogen-Activating Cytochrome P450 Enzymes by Xenobiotic Chemicals in Relation to Antimutagenicity and Anticarcinogenicity. Toxicol Res 2017; 33:79-96. [PMID: 28443179 PMCID: PMC5402866 DOI: 10.5487/tr.2017.33.2.079] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 02/16/2017] [Indexed: 12/27/2022] Open
Abstract
A variety of xenobiotic chemicals, such as polycyclic aromatic hydrocarbons (PAHs), aryl- and heterocyclic amines and tobacco related nitrosamines, are ubiquitous environmental carcinogens and are required to be activated to chemically reactive metabolites by xenobiotic-metabolizing enzymes, including cytochrome P450 (P450 or CYP), in order to initiate cell transformation. Of various human P450 enzymes determined to date, CYP1A1, 1A2, 1B1, 2A13, 2A6, 2E1, and 3A4 are reported to play critical roles in the bioactivation of these carcinogenic chemicals. In vivo studies have shown that disruption of Cyp1b1 and Cyp2a5 genes in mice resulted in suppression of tumor formation caused by 7,12-dimethylbenz[a]anthracene and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, respectively. In addition, specific inhibitors for CYP1 and 2A enzymes are able to suppress tumor formation caused by several carcinogens in experimental animals in vivo, when these inhibitors are applied before or just after the administration of carcinogens. In this review, we describe recent progress, including our own studies done during past decade, on the nature of inhibitors of human CYP1 and CYP2A enzymes that have been shown to activate carcinogenic PAHs and tobacco-related nitrosamines, respectively, in humans. The inhibitors considered here include a variety of carcinogenic and/or non-carcinogenic PAHs and acethylenic PAHs, many flavonoid derivatives, derivatives of naphthalene, phenanthrene, biphenyl, and pyrene and chemopreventive organoselenium compounds, such as benzyl selenocyanate and benzyl selenocyanate; o-XSC, 1,2-, 1,3-, and 1,4-phenylenebis( methylene)selenocyanate.
Collapse
Affiliation(s)
- Tsutomu Shimada
- Laboratory of Cellular and Molecular Biology, Graduate School of Life and Environmental Sciences, Veterinary Sciences, Osaka Prefecture University, Osaka, Japan
| |
Collapse
|
24
|
Shimada T, Kakimoto K, Takenaka S, Koga N, Uehara S, Murayama N, Yamazaki H, Kim D, Guengerich FP, Komori M. Roles of Human CYP2A6 and Monkey CYP2A24 and 2A26 Cytochrome P450 Enzymes in the Oxidation of 2,5,2',5'-Tetrachlorobiphenyl. Drug Metab Dispos 2016; 44:1899-1909. [PMID: 27625140 PMCID: PMC6047209 DOI: 10.1124/dmd.116.072991] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/12/2016] [Indexed: 11/22/2022] Open
Abstract
2,5,2',5'-Tetrachlorobiphenyl (TCB) induced type I binding spectra with cytochrome P450 (P450) 2A6 and 2A13, with Ks values of 9.4 and 0.51 µM, respectively. However, CYP2A6 oxidized 2,5,2',5'-TCB to form 4-hydroxylated products at a much higher rate (∼1.0 minute-1) than CYP2A13 (∼0.02 minute-1) based on analysis by liquid chromatography-tandem mass spectrometry. Formation of 4-hydroxy-2,5,2',5'-TCB by CYP2A6 was greater than that of 3-hydroxy-2,5,2',5'-TCB and three other hydroxylated products. Several human P450 enzymes, including CYP1A1, 1A2, 1B1, 2B6, 2D6, 2E1, 2C9, and 3A4, did not show any detectable activities in oxidizing 2,5,2',5'-TCB. Cynomolgus monkey CYP2A24, which shows 95% amino acid identity to human CYP2A6, catalyzed 4-hydroxylation of 2,5,2',5'-TCB at a higher rate (∼0.3 minute-1) than CYP2A26 (93% identity to CYP2A6, ∼0.13 minute-1) and CYP2A23 (94% identity to CYP2A13, ∼0.008 minute-1). None of these human and monkey CYP2A enzymes were catalytically active in oxidizing other TCB congeners, such as 2,4,3',4'-, 3,4,3',4'-, and 3,5,3',5'-TCB. Molecular docking analysis suggested that there are different orientations of interaction of 2,5,2',5'-TCB with the active sites (over the heme) of human and monkey CYP2A enzymes, and that ligand interaction energies (U values) of bound protein-ligand complexes show structural relationships of interaction of TCBs and other ligands with active sites of CYP2A enzymes. Catalytic differences in human and monkey CYP2A enzymes in the oxidation of 2,5,2',5'-TCB are suggested to be due to amino acid changes at substrate recognition sites, i.e., V110L, I209S, I300F, V365M, S369G, and R372H, based on the comparison of primary sequences.
Collapse
Affiliation(s)
- Tsutomu Shimada
- Laboratory of Cellular and Molecular Biology, Osaka Prefecture University, Izumisano, Osaka, Japan (T.S., S.T., M.K.); Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan (K.K.); Faculty of Nutritional Sciences, Nakamura Gakuen University, Johnan-ku, Fukuoka, Japan (N.K.); Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan (S.U., N.M., H.Y.); Department of Biological Sciences, Konkuk University, Seoul, South Korea (D.K.); and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee (F.P.G.)
| | - Kensaku Kakimoto
- Laboratory of Cellular and Molecular Biology, Osaka Prefecture University, Izumisano, Osaka, Japan (T.S., S.T., M.K.); Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan (K.K.); Faculty of Nutritional Sciences, Nakamura Gakuen University, Johnan-ku, Fukuoka, Japan (N.K.); Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan (S.U., N.M., H.Y.); Department of Biological Sciences, Konkuk University, Seoul, South Korea (D.K.); and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee (F.P.G.)
| | - Shigeo Takenaka
- Laboratory of Cellular and Molecular Biology, Osaka Prefecture University, Izumisano, Osaka, Japan (T.S., S.T., M.K.); Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan (K.K.); Faculty of Nutritional Sciences, Nakamura Gakuen University, Johnan-ku, Fukuoka, Japan (N.K.); Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan (S.U., N.M., H.Y.); Department of Biological Sciences, Konkuk University, Seoul, South Korea (D.K.); and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee (F.P.G.)
| | - Nobuyuki Koga
- Laboratory of Cellular and Molecular Biology, Osaka Prefecture University, Izumisano, Osaka, Japan (T.S., S.T., M.K.); Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan (K.K.); Faculty of Nutritional Sciences, Nakamura Gakuen University, Johnan-ku, Fukuoka, Japan (N.K.); Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan (S.U., N.M., H.Y.); Department of Biological Sciences, Konkuk University, Seoul, South Korea (D.K.); and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee (F.P.G.)
| | - Shotaro Uehara
- Laboratory of Cellular and Molecular Biology, Osaka Prefecture University, Izumisano, Osaka, Japan (T.S., S.T., M.K.); Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan (K.K.); Faculty of Nutritional Sciences, Nakamura Gakuen University, Johnan-ku, Fukuoka, Japan (N.K.); Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan (S.U., N.M., H.Y.); Department of Biological Sciences, Konkuk University, Seoul, South Korea (D.K.); and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee (F.P.G.)
| | - Norie Murayama
- Laboratory of Cellular and Molecular Biology, Osaka Prefecture University, Izumisano, Osaka, Japan (T.S., S.T., M.K.); Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan (K.K.); Faculty of Nutritional Sciences, Nakamura Gakuen University, Johnan-ku, Fukuoka, Japan (N.K.); Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan (S.U., N.M., H.Y.); Department of Biological Sciences, Konkuk University, Seoul, South Korea (D.K.); and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee (F.P.G.)
| | - Hiroshi Yamazaki
- Laboratory of Cellular and Molecular Biology, Osaka Prefecture University, Izumisano, Osaka, Japan (T.S., S.T., M.K.); Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan (K.K.); Faculty of Nutritional Sciences, Nakamura Gakuen University, Johnan-ku, Fukuoka, Japan (N.K.); Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan (S.U., N.M., H.Y.); Department of Biological Sciences, Konkuk University, Seoul, South Korea (D.K.); and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee (F.P.G.)
| | - Donghak Kim
- Laboratory of Cellular and Molecular Biology, Osaka Prefecture University, Izumisano, Osaka, Japan (T.S., S.T., M.K.); Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan (K.K.); Faculty of Nutritional Sciences, Nakamura Gakuen University, Johnan-ku, Fukuoka, Japan (N.K.); Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan (S.U., N.M., H.Y.); Department of Biological Sciences, Konkuk University, Seoul, South Korea (D.K.); and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee (F.P.G.)
| | - F Peter Guengerich
- Laboratory of Cellular and Molecular Biology, Osaka Prefecture University, Izumisano, Osaka, Japan (T.S., S.T., M.K.); Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan (K.K.); Faculty of Nutritional Sciences, Nakamura Gakuen University, Johnan-ku, Fukuoka, Japan (N.K.); Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan (S.U., N.M., H.Y.); Department of Biological Sciences, Konkuk University, Seoul, South Korea (D.K.); and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee (F.P.G.)
| | - Masayuki Komori
- Laboratory of Cellular and Molecular Biology, Osaka Prefecture University, Izumisano, Osaka, Japan (T.S., S.T., M.K.); Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan (K.K.); Faculty of Nutritional Sciences, Nakamura Gakuen University, Johnan-ku, Fukuoka, Japan (N.K.); Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, Japan (S.U., N.M., H.Y.); Department of Biological Sciences, Konkuk University, Seoul, South Korea (D.K.); and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee (F.P.G.)
| |
Collapse
|
25
|
Ledford C, McMahon M, Whitesell A, Khan G, Kandagatla SK, Hurst DP, Reggio PH, Raner GM. A dual substrate kinetic model for cytochrome P450 BM3-F87G catalysis: simultaneous binding of long chain aldehydes and 4-fluorophenol. Biotechnol Lett 2016; 39:311-321. [PMID: 27864654 DOI: 10.1007/s10529-016-2252-7] [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: 08/25/2016] [Accepted: 11/03/2016] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To develop a model for binding and catalysis associated with the stimulation of 4-fluorophenol (4-FP) oxidation in the presence of long chain aldehydes by the enzymatic catalyst, cytochrome P450BM3-F87G. RESULTS A variation of the Michaeli-Menten kinetic model was employed to describe interactions at the active site of the enzyme, along with computer aided modeling approaches. In addition to the hydroquinone product arising from de-fluorination of 4-FP, a second product (p-fluorocatechol) was also observed and, like the hydroquinone, its rate of formation increased in the presence of the aldehyde. When only aldehyde was present with the enzyme, BM3-F87G catalyzed its oxidation to the corresponding carboxylic acid; however, this activity was inhibited when 4-FP was added to the reaction. A 3D computer model of the active site containing both aldehyde and 4-FP was generated, guided by these kinetic observations. Finally, partitioning between the two phenolic products was examined with an emphasis on the conditions directing the initial epoxidation at either the 2,3- or 3,4-positions on the substrate. Temperature, reaction time, substrate concentration, and the structure of the aldehyde had no substantial effect on the overall product ratios, however the NADPH coupling efficiency decreased when unsaturated aldehydes were included, or when the temperature of the reaction was reduced. CONCLUSIONS The unsaturated aldehyde, trans-2-decenal, stimulates BM3-F87G catalyzed oxidation of 4-fluorophenol through a cooperative active site binding mode that doesn't influence product distributions or coupling efficiencies, while 4-fluorophenol acts as a competitive inhibitor of aldehyde oxidation.
Collapse
Affiliation(s)
- Chelsea Ledford
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Monica McMahon
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Ashley Whitesell
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Ghalib Khan
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Suneel K Kandagatla
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Dow P Hurst
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Patricia H Reggio
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Gregory M Raner
- Department of Biology and Chemistry, Liberty University, Lynchburg, VA, USA.
| |
Collapse
|
26
|
Scheler U, Brandt W, Porzel A, Rothe K, Manzano D, Božić D, Papaefthimiou D, Balcke GU, Henning A, Lohse S, Marillonnet S, Kanellis AK, Ferrer A, Tissier A. Elucidation of the biosynthesis of carnosic acid and its reconstitution in yeast. Nat Commun 2016; 7:12942. [PMID: 27703160 PMCID: PMC5059481 DOI: 10.1038/ncomms12942] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 08/11/2016] [Indexed: 12/03/2022] Open
Abstract
Rosemary extracts containing the phenolic diterpenes carnosic acid and its derivative carnosol are approved food additives used in an increasingly wide range of products to enhance shelf-life, thanks to their high anti-oxidant activity. We describe here the elucidation of the complete biosynthetic pathway of carnosic acid and its reconstitution in yeast cells. Cytochrome P450 oxygenases (CYP76AH22-24) from Rosmarinus officinalis and Salvia fruticosa already characterized as ferruginol synthases are also able to produce 11-hydroxyferruginol. Modelling-based mutagenesis of three amino acids in the related ferruginol synthase (CYP76AH1) from S. miltiorrhiza is sufficient to convert it to a 11-hydroxyferruginol synthase (HFS). The three sequential C20 oxidations for the conversion of 11-hydroxyferruginol to carnosic acid are catalysed by the related CYP76AK6-8. The availability of the genes for the biosynthesis of carnosic acid opens opportunities for the metabolic engineering of phenolic diterpenes, a class of compounds with potent anti-oxidant, anti-inflammatory and anti-tumour activities. Diterpenes are plant products with high antioxidant properties and potential application as food additives and therapeutics. Here, the authors describe the complete biosynthetic pathway of carnosic acid and reconstruct it in yeast, opening the way to metabolic engineering of phenolic diterpenes.
Collapse
Affiliation(s)
- Ulschan Scheler
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - Wolfgang Brandt
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - Andrea Porzel
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - Kathleen Rothe
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - David Manzano
- Program of Plant Metabolism and Metabolic Engineering, Centre for Research in Agricultural Genomics, Campus UAB, 08193 Bellaterra, Spain.,Faculty of Pharmacy, Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Dragana Božić
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dimitra Papaefthimiou
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Gerd Ulrich Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - Anja Henning
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - Swanhild Lohse
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - Angelos K Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Albert Ferrer
- Program of Plant Metabolism and Metabolic Engineering, Centre for Research in Agricultural Genomics, Campus UAB, 08193 Bellaterra, Spain.,Faculty of Pharmacy, Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| |
Collapse
|
27
|
Shimada T, Takenaka S, Kakimoto K, Murayama N, Lim YR, Kim D, Foroozesh MK, Yamazaki H, Guengerich FP, Komori M. Structure-Function Studies of Naphthalene, Phenanthrene, Biphenyl, and Their Derivatives in Interaction with and Oxidation by Cytochromes P450 2A13 and 2A6. Chem Res Toxicol 2016; 29:1029-40. [PMID: 27137136 PMCID: PMC5293596 DOI: 10.1021/acs.chemrestox.6b00083] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Naphthalene, phenanthrene, biphenyl, and their derivatives having different ethynyl, propynyl, butynyl, and propargyl ether substitutions were examined for their interaction with and oxidation by cytochromes P450 (P450) 2A13 and 2A6. Spectral interaction studies suggested that most of these chemicals interacted with P450 2A13 to induce Type I binding spectra more readily than with P450 2A6. Among the various substituted derivatives examined, 2-ethynylnaphthalene, 2-naphthalene propargyl ether, 3-ethynylphenanthrene, and 4-biphenyl propargyl ether had larger ΔAmax/Ks values in inducing Type I binding spectra with P450 2A13 than their parent compounds. P450 2A13 was found to oxidize naphthalene, phenanthrene, and biphenyl to 1-naphthol, 9-hydroxyphenanthrene, and 2- and/or 4-hydroxybiphenyl, respectively, at much higher rates than P450 2A6. Other human P450 enzymes including P450s 1A1, 1A2, 1B1, 2C9, and 3A4 had lower rates of oxidation of naphthalene, phenanthrene, and biphenyl than P450s 2A13 and 2A6. Those alkynylated derivatives that strongly induced Type I binding spectra with P450s 2A13 and 2A6 were extensively oxidized by these enzymes upon analysis with HPLC. Molecular docking studies supported the hypothesis that ligand-interaction energies (U values) obtained with reported crystal structures of P450 2A13 and 2A6 bound to 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, indole, pilocarpine, nicotine, and coumarin are of use in understanding the basis of possible molecular interactions of these xenobiotic chemicals with the active sites of P450 2A13 and 2A6 enzymes. In fact, the ligand-interaction energies with P450 2A13 4EJG bound to these chemicals were found to relate to their induction of Type I binding spectra.
Collapse
Affiliation(s)
- Tsutomu Shimada
- Laboratory of Cellular and Molecular Biology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-Orai-Kita, Izumisano, Osaka 598-8531, Japan
| | - Shigeo Takenaka
- Laboratory of Cellular and Molecular Biology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-Orai-Kita, Izumisano, Osaka 598-8531, Japan
| | - Kensaku Kakimoto
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Norie Murayama
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Young-Ran Lim
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Donghak Kim
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Maryam K. Foroozesh
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - F. Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Masayuki Komori
- Laboratory of Cellular and Molecular Biology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-Orai-Kita, Izumisano, Osaka 598-8531, Japan
| |
Collapse
|
28
|
Spicakova A, Anzenbacher P, Liskova B, Kuca K, Fusek J, Anzenbacherova E. Evaluation of possible inhibition of human liver drug metabolizing cytochromes P450 by two new acetylcholinesterase oxime-type reactivators. Food Chem Toxicol 2015; 88:100-4. [PMID: 26747974 DOI: 10.1016/j.fct.2015.11.024] [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: 09/06/2015] [Revised: 11/20/2015] [Accepted: 11/28/2015] [Indexed: 02/06/2023]
Abstract
Two non-symmetric bispyridine oxime - based reactivators of acetylcholinesterase enzyme (AChE), labeled as K027 (1-(4-carbamoylpyridinium)-3-(4-hydroxyiminomethylpyridinium)-propane dibromide) and K203 ((E)-1-(4- carbamoylpyridinium)-4-(4-hydroxyiminomethylpyridinium)-but-2-ene dibromide) were tested for their potential to inhibit activities of human liver microsomal cytochromes P450 (CYP). Both oximes are very potent reactivators of organophosphate-inhibited AChE. An interaction of both compounds with CYP in human liver microsomal preparation was detected using difference spectroscopy. The compounds were shown to bind to CYP enzymes with spectral binding constants of 5.04 ± 1.79 nM (K027) and 5.2 ± 2.6 nM (K203). Enzymology studies were subsequently performed aimed at determining which of the nine most important CYP involved in drug is affected by this interaction. The results have shown no prominent inhibition of individual CYP activities with either compounds except in the case of CYP2E1 and K203. Diagnostic Dixon plot revealed that K203 acted as an uncompetitive inhibitor of CYP2E1. Inhibition of this activity however is not as prominent as to make a potent drug interaction likely. Hence, the interaction of K027 and K203 oxime-type AChE reactivators with human liver microsomal CYP enzymes does not seem to be of prominent clinical importance and both compounds could be safely used in this respect as antidotes with low risk of drug interactions.
Collapse
Affiliation(s)
- Alena Spicakova
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15 Olomouc, Czech Republic
| | - Pavel Anzenbacher
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15 Olomouc, Czech Republic
| | - Barbora Liskova
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15 Olomouc, Czech Republic
| | - Kamil Kuca
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defense, 500 01 Hradec Kralove, Czech Republic; Biomedical Research Center, University Hospital Hradec Kralove, 500 01 Hradec Kralove, Czech Republic.
| | - Josef Fusek
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defense, 500 01 Hradec Kralove, Czech Republic
| | - Eva Anzenbacherova
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15 Olomouc, Czech Republic.
| |
Collapse
|
29
|
How mutations affecting the ligand-receptor interactions: a combined MD and QM/MM calculation on CYP2E1 and its two mutants. Chem Res Chin Univ 2015. [DOI: 10.1007/s40242-015-5071-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
30
|
Shimada T, Takenaka S, Murayama N, Kramlinger VM, Kim JH, Kim D, Liu J, Foroozesh MK, Yamazaki H, Guengerich FP, Komori M. Oxidation of pyrene, 1-hydroxypyrene, 1-nitropyrene and 1-acetylpyrene by human cytochrome P450 2A13. Xenobiotica 2015; 46:211-24. [PMID: 26247835 PMCID: PMC5270756 DOI: 10.3109/00498254.2015.1069419] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
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.
Collapse
Affiliation(s)
- Tsutomu Shimada
- Laboratory of Cellular and Molecular Biology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-Orai-Kita, Izumisano, Osaka 598-8531, Japan
| | - Shigeo Takenaka
- Laboratory of Cellular and Molecular Biology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-Orai-Kita, Izumisano, Osaka 598-8531, Japan
| | - Norie Murayama
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Valerie M. Kramlinger
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Joo-Hwan Kim
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Donghak Kim
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Jiawang Liu
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
| | - Maryam K. Foroozesh
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - F. Peter Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Masayuki Komori
- Laboratory of Cellular and Molecular Biology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-Orai-Kita, Izumisano, Osaka 598-8531, Japan
| |
Collapse
|
31
|
Shah MB, Wilderman PR, Liu J, Jang HH, Zhang Q, Stout CD, Halpert JR. Structural and biophysical characterization of human cytochromes P450 2B6 and 2A6 bound to volatile hydrocarbons: analysis and comparison. Mol Pharmacol 2015; 87:649-59. [PMID: 25585967 PMCID: PMC4366795 DOI: 10.1124/mol.114.097014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/12/2015] [Indexed: 11/22/2022] Open
Abstract
X-ray crystal structures of complexes of cytochromes CYP2B6 and CYP2A6 with the monoterpene sabinene revealed two distinct binding modes in the active sites. In CYP2B6, sabinene positioned itself with the putative oxidation site located closer to the heme iron. In contrast, sabinene was found in an alternate conformation in the more compact CYP2A6, where the larger hydrophobic side chains resulted in a significantly reduced active-site cavity. Furthermore, results from isothermal titration calorimetry indicated a much more substantial contribution of favorable enthalpy to sabinene binding to CYP2B6 as opposed to CYP2A6, consistent with the previous observations with (+)-α-pinene. Structural analysis of CYP2B6 complexes with sabinene and the structurally similar (3)-carene and comparison with previously solved structures revealed how the movement of the F206 side chain influences the volume of the binding pocket. In addition, retrospective analysis of prior structures revealed that ligands containing -Cl and -NH functional groups adopted a distinct orientation in the CYP2B active site compared with other ligands. This binding mode may reflect the formation of Cl-π or NH-π bonds with aromatic rings in the active site, which serve as important contributors to protein-ligand binding affinity and specificity. Overall, the findings from multiple techniques illustrate how drugs metabolizing CYP2B6 and CYP2A6 handle a common hydrocarbon found in the environment. The study also provides insight into the role of specific functional groups of the ligand that may influence the binding to CYP2B6.
Collapse
Affiliation(s)
- Manish B Shah
- Department of Pharmaceutical Sciences, The University of Connecticut, Storrs, Connecticut (M.B.S., P.R.W., J.L., J.R.H.); School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea (H.-H.J.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.)
| | - P Ross Wilderman
- Department of Pharmaceutical Sciences, The University of Connecticut, Storrs, Connecticut (M.B.S., P.R.W., J.L., J.R.H.); School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea (H.-H.J.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.)
| | - Jingbao Liu
- Department of Pharmaceutical Sciences, The University of Connecticut, Storrs, Connecticut (M.B.S., P.R.W., J.L., J.R.H.); School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea (H.-H.J.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.)
| | - Hyun-Hee Jang
- Department of Pharmaceutical Sciences, The University of Connecticut, Storrs, Connecticut (M.B.S., P.R.W., J.L., J.R.H.); School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea (H.-H.J.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.)
| | - Qinghai Zhang
- Department of Pharmaceutical Sciences, The University of Connecticut, Storrs, Connecticut (M.B.S., P.R.W., J.L., J.R.H.); School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea (H.-H.J.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.)
| | - C David Stout
- Department of Pharmaceutical Sciences, The University of Connecticut, Storrs, Connecticut (M.B.S., P.R.W., J.L., J.R.H.); School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea (H.-H.J.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.)
| | - James R Halpert
- Department of Pharmaceutical Sciences, The University of Connecticut, Storrs, Connecticut (M.B.S., P.R.W., J.L., J.R.H.); School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea (H.-H.J.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.)
| |
Collapse
|
32
|
Structural basis for cooperative binding of azoles to CYP2E1 as interpreted through guided molecular dynamics simulations. J Mol Graph Model 2014; 56:43-52. [PMID: 25544389 DOI: 10.1016/j.jmgm.2014.11.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/21/2014] [Accepted: 11/30/2014] [Indexed: 01/20/2023]
Abstract
CYP2E1 metabolizes a wide array of small, hydrophobic molecules, resulting in their detoxification or activation into carcinogens through Michaelis-Menten as well as cooperative mechanisms. Nevertheless, the molecular determinants for CYP2E1 specificity and metabolic efficiency toward these compounds are still unknown. Herein, we employed computational docking studies coupled to molecular dynamics simulations to provide a critical perspective for understanding a structural basis for cooperativity observed for an array of azoles from our previous binding and catalytic studies (Hartman et al., 2014). The resulting 28 CYP2E1 complexes in this study revealed a common passageway for azoles that included a hydrophobic steric barrier causing a pause in movement toward the active site. The entrance to the active site acted like a second sieve to restrict access to the inner chamber. Collectively, these interactions impacted the final orientation of azoles reaching the active site and hence could explain differences in their biochemical properties observed in our previous studies, such as the consequences of methylation at position 5 of the azole ring. The association of a second azole demonstrated significant differences in interactions stabilizing the bound complex than observed for the first binding event. Intermolecular interactions occurred between the two azoles as well as CYP2E1 residue side chains and backbone and involved both hydrophobic contacts and hydrogen bonds. The relative importance of these interactions depended on the structure of the respective azoles indicating the absence of specific defining criteria for binding unlike the well-characterized dominant role of hydrophobicity in active site binding. Consequently, the structure activity relationships described here and elsewhere are necessary to more accurately identify factors impacting the observation and significance of cooperativity in CYP2E1 binding and catalysis toward drugs, dietary compounds, and pollutants.
Collapse
|
33
|
Sheng Y, Chen Y, Wang L, Liu G, Li W, Tang Y. Effects of protein flexibility on the site of metabolism prediction for CYP2A6 substrates. J Mol Graph Model 2014; 54:90-9. [DOI: 10.1016/j.jmgm.2014.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/25/2014] [Accepted: 09/30/2014] [Indexed: 12/01/2022]
|
34
|
Cui YL, Zheng QC, Zhang JL, Zhang HX. Molecular basis of the recognition of arachidonic acid by cytochrome P450 2E1 along major access tunnel. Biopolymers 2014; 103:53-66. [DOI: 10.1002/bip.22567] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 09/23/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Ying-Lu Cui
- State Key Laboratory of Theoretical and Computational Chemistry; Institute of Theoretical Chemistry, Jilin University; Changchun People's Republic of China
| | - Qing-Chuan Zheng
- State Key Laboratory of Theoretical and Computational Chemistry; Institute of Theoretical Chemistry, Jilin University; Changchun People's Republic of China
| | - Ji-Long Zhang
- State Key Laboratory of Theoretical and Computational Chemistry; Institute of Theoretical Chemistry, Jilin University; Changchun People's Republic of China
| | - Hong-Xing Zhang
- State Key Laboratory of Theoretical and Computational Chemistry; Institute of Theoretical Chemistry, Jilin University; Changchun People's Republic of China
| |
Collapse
|
35
|
Kandagatla SK, Mack T, Simpson S, Sollenberger J, Helton E, Raner GM. Inhibition of human cytochrome P450 2E1 and 2A6 by aldehydes: structure and activity relationships. Chem Biol Interact 2014; 219:195-202. [PMID: 24924949 DOI: 10.1016/j.cbi.2014.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/05/2014] [Accepted: 05/21/2014] [Indexed: 11/29/2022]
Abstract
The purpose of this study was to probe active site structure and dynamics of human cytochrome P4502E1 and P4502A6 using a series of related short chain fatty aldehydes. Binding efficiency of the aldehydes was monitored via their ability to inhibit the binding and activation of the probe substrates p-nitrophenol (2E1) and coumarin (2A6). Oxidation of the aldehydes was observed in reactions with individually expressed 2E1, but not 2A6, suggesting alternate binding modes. For saturated aldehydes the optimum chain length for inhibition of 2E1 was 9 carbons (KI=7.8 ± 0.3 μM), whereas for 2A6 heptanal was most potent (KI=15.8 ± 1.1 μM). A double bond in the 2-position of the aldehyde significantly decreased the observed KI relative to the corresponding saturated compound in most cases. A clear difference in the effect of the double bond was observed between the two isoforms. With 2E1, the double bond appeared to remove steric constraints on aldehyde binding with KI values for the 5-12 carbon compounds ranging between 2.6 ± 0.1 μM and 12.8 ± 0.5 μM, whereas steric effects remained the dominant factor in the binding of the unsaturated aldehydes to 2A6 (observed KI values between 7.0 ± 0.5 μM and >1000 μM). The aldehyde function was essential for effective inhibition, as the corresponding carboxylic acids had very little effect on enzyme activity over the same range of concentrations, and branching at the 3-position of the aldehydes increased the corresponding KI value in all cases examined. The results suggest that a conjugated π-system may be a key structural determinant in the binding of these compounds to both enzymes, and may also be an important feature for the expansion of the active site volume in 2E1.
Collapse
Affiliation(s)
- Suneel K Kandagatla
- The University of North Carolina at Greensboro, Department of Chemistry and Biochemistry, Greensboro, NC, United States
| | - Todd Mack
- The University of North Carolina at Greensboro, Department of Chemistry and Biochemistry, Greensboro, NC, United States
| | - Sean Simpson
- The University of North Carolina at Greensboro, Department of Chemistry and Biochemistry, Greensboro, NC, United States
| | - Jill Sollenberger
- The University of North Carolina at Greensboro, Department of Chemistry and Biochemistry, Greensboro, NC, United States
| | - Eric Helton
- The University of North Carolina at Greensboro, Department of Chemistry and Biochemistry, Greensboro, NC, United States
| | - Gregory M Raner
- The University of North Carolina at Greensboro, Department of Chemistry and Biochemistry, Greensboro, NC, United States.
| |
Collapse
|
36
|
Pouyfung P, Prasopthum A, Sarapusit S, Srisook E, Rongnoparut P. Mechanism-based Inactivation of Cytochrome P450 2A6 and 2A13 by Rhinacanthus nasutus Constituents. Drug Metab Pharmacokinet 2014; 29:75-82. [DOI: 10.2133/dmpk.dmpk-13-rg-048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
37
|
Blake LC, Roy A, Neul D, Schoenen FJ, Aubé J, Scott EE. Benzylmorpholine analogs as selective inhibitors of lung cytochrome P450 2A13 for the chemoprevention of lung cancer in tobacco users. Pharm Res 2013; 30:2290-302. [PMID: 23756756 PMCID: PMC3781598 DOI: 10.1007/s11095-013-1054-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 04/02/2013] [Indexed: 10/26/2022]
Abstract
PURPOSE 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), one of the most prevalent and procarcinogenic compounds in tobacco, is bioactivated by respiratory cytochrome P450 (CYP) 2A13, forming DNA adducts and initiating lung cancer. CYP2A13 inhibition offers a novel strategy for chemoprevention of tobacco-associated lung cancer. METHODS Twenty-four analogs of a 4-benzylmorpholine scaffold identified by high throughput screening were evaluated for binding and inhibition of both functional human CYP2A enzymes, CYP2A13 and the 94%-identical hepatic CYP2A6, whose inhibition is undesirable. Thus, selectivity is a major challenge in compound design. RESULTS A key feature resulting in CYP2A13-selective binding and inhibition was substitution at the benzyl ortho position, with three analogs being >25-fold selective for CYP2A13 over CYP2A6. CONCLUSIONS Two such analogs were negative for genetic and hERG toxicities and metabolically stable in human lung microsomes, but displayed rapid metabolism in human liver and in mouse and rat lung and liver microsomes, likely due to CYP2B-mediated degradation. A specialized knockout mouse mimicking the human lung demonstrates compound persistence in lung and provides an appropriate test model. Compound delivered by inhalation may be effective in the lung but rapidly cleared otherwise, limiting systemic exposure.
Collapse
Affiliation(s)
- Linda C. Blake
- Department of Medicinal Chemistry, 1251 Wescoe Hall Dr., University of Kansas, Lawrence, KS 66045, United States
| | - Anuradha Roy
- High Throughput Screening Laboratory, 2034 Becker Drive, University of Kansas, Lawrence, KS 66047, United States
| | - David Neul
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., La Jolla, CA 92121
| | - Frank J. Schoenen
- University of Kansas Specialized Chemistry Center, University of Kansas, 2034 Becker Drive, Lawrence, KS 66047
| | - Jeffrey Aubé
- Department of Medicinal Chemistry, 1251 Wescoe Hall Dr., University of Kansas, Lawrence, KS 66045, United States
- University of Kansas Specialized Chemistry Center, University of Kansas, 2034 Becker Drive, Lawrence, KS 66047
| | - Emily E. Scott
- Department of Medicinal Chemistry, 1251 Wescoe Hall Dr., University of Kansas, Lawrence, KS 66045, United States
| |
Collapse
|
38
|
Wilderman PR, Shah MB, Jang HH, Stout CD, Halpert JR. Structural and thermodynamic basis of (+)-α-pinene binding to human cytochrome P450 2B6. J Am Chem Soc 2013; 135:10433-40. [PMID: 23786449 PMCID: PMC3754432 DOI: 10.1021/ja403042k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite recent advances in atomic-level understanding of drug and inhibitor interactions with human cytochromes P450, the decades-old questions of chemical and structural determinants of hydrocarbon binding are still unanswered. (+)-α-Pinene is a monoterpene hydrocarbon that is widely distributed in the environment and a potent P450 2B inhibitor. Therefore, a combined biophysical and structural analysis of human P450 2B6 interactions with (+)-α-pinene was undertaken to elucidate the basis of the very high affinity binding. Binding of (+)-α-pinene to the P450 active site was demonstrated by a Type I spectral shift. Thermodynamics of ligand binding were explored using isothermal titration calorimetry and compared to those of P450 2A6, which is much less flexible than 2B6 based on comparison of multiple X-ray crystal structures. Consistent with expectation, entropy is the major driving force for hydrocarbon binding to P450 2A6, as evidenced by the calorimetric results. However, formation of the 2B6-(+)-α-pinene complex has a significant enthalpic component. A 2.0 Å resolution crystal structure of this enzyme-ligand complex reveals that the highly plastic 2B6 utilizes previously unrecognized rearrangements of protein motifs. The results indicate that the specific components of enthalpic contribution to ligand binding are closely tied to the degree of enzyme flexibility.
Collapse
Affiliation(s)
- P Ross Wilderman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States.
| | | | | | | | | |
Collapse
|
39
|
Abstract
X-ray crystal structures are available for 29 eukaryotic microsomal, chloroplast, or mitochondrial cytochrome P450s, including two non-monooxygenase P450s. These structures provide a basis for understanding structure-function relations that underlie their distinct catalytic activities. Moreover, structural plasticity has been characterized for individual P450s that aids in understanding substrate binding in P450s that mediate drug clearance.
Collapse
Affiliation(s)
- Eric F Johnson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA.
| | | |
Collapse
|
40
|
Shimada T, Kim D, Murayama N, Tanaka K, Takenaka S, Nagy LD, Folkman LM, Foroozesh MK, Komori M, Yamazaki H, Guengerich FP. Binding of diverse environmental chemicals with human cytochromes P450 2A13, 2A6, and 1B1 and enzyme inhibition. Chem Res Toxicol 2013; 26:517-28. [PMID: 23432429 DOI: 10.1021/tx300492j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A total of 68 chemicals including derivatives of naphthalene, phenanthrene, fluoranthene, pyrene, biphenyl, and flavone were examined for their abilities to interact with human P450s 2A13 and 2A6. Fifty-one of these 68 chemicals induced stronger Type I binding spectra (iron low- to high-spin state shift) with P450 2A13 than those seen with P450 2A6, i.e., the spectral binding intensities (ΔAmax/Ks ratio) determined with these chemicals were always higher for P450 2A13. In addition, benzo[c]phenanthrene, fluoranthene, 2,3-dihydroxy-2,3-dihydrofluoranthene, pyrene, 1-hydroxypyrene, 1-nitropyrene, 1-acetylpyrene, 2-acetylpyrene, 2,5,2',5'-tetrachlorobiphenyl, 7-hydroxyflavone, chrysin, and galangin were found to induce a Type I spectral change only with P450 2A13. Coumarin 7-hydroxylation, catalyzed by P450 2A13, was strongly inhibited by 2'-methoxy-5,7-dihydroxyflavone, 2-ethynylnaphthalene, 2'-methoxyflavone, 2-naphththalene propargyl ether, acenaphthene, acenaphthylene, naphthalene, 1-acetylpyrene, flavanone, chrysin, 3-ethynylphenanthrene, flavone, and 7-hydroxyflavone; these chemicals induced Type I spectral changes with low Ks values. On the basis of the intensities of the spectral changes and inhibition of P450 2A13, we classified the 68 chemicals into eight groups based on the order of affinities for these chemicals and inhibition of P450 2A13. The metabolism of chemicals by P450 2A13 during the assays explained why some of the chemicals that bound well were poor inhibitors of P450 2A13. Finally, we compared the 68 chemicals for their abilities to induce Type I spectral changes of P450 2A13 with the Reverse Type I binding spectra observed with P450 1B1: 45 chemicals interacted with both P450s 2A13 and 1B1, indicating that the two enzymes have some similarty of structural features regarding these chemicals. Molecular docking analyses suggest similarities at the active sites of these P450 enzymes. These results indicate that P450 2A13, as well as Family 1 P450 enzymes, is able to catalyze many detoxication and activation reactions with chemicals of environmental interest.
Collapse
Affiliation(s)
- Tsutomu Shimada
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Liu Y, Liu BY, Hao P, Li X, Li YX, Wang JF. π-π Stacking mediated drug-drug interactions in human CYP2E1. Proteins 2013; 81:945-54. [PMID: 23349037 DOI: 10.1002/prot.24260] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/11/2013] [Indexed: 11/07/2022]
Abstract
Because of having many low molecular mass substrates, CYP2E1 is of particular interests to the pharmaceutical industry. Many evidences showed that this enzyme can adopt multiple substrates to significantly reduce the oxidation rate of the substrates. The detailed mechanism for this observation is still unclear. In the current study, we employed GPU-accelerated molecular dynamics simulations to study the multiple-binding mode of human CYP2E1, with an aim of offering a mechanistic explanation for the unexplained multiple-substrate binding. Our results showed that Thr303 and Phe478 were key factors for the substrate recognition and multiple-substrate binding. The former can form a significant hydrogen bond to recognize and position the substrate in the productive binding orientation in the active site. The latter acted as a mediator for the substrate communications via π-π stacking interactions. In the multiple-binding mode, the aforementioned π-π stacking interactions formed by the aromatic rings of both substrates and Phe478 drove the first substrate far away from the catalytic center, orienting in an additional binding position and going against the substrate metabolism. All these findings could give atomic insights into the detailed mechanism for the multiple-substrate binding in human CYP2E1, providing useful information for the drug metabolism mechanism and personalized use of clinical drugs.
Collapse
Affiliation(s)
- Yue Liu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | | | | | | | | | | |
Collapse
|
42
|
Yu X, Cojocaru V, Wade RC. Conformational diversity and ligand tunnels of mammalian cytochrome P450s. Biotechnol Appl Biochem 2013; 60:134-45. [DOI: 10.1002/bab.1074] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 12/04/2012] [Indexed: 01/31/2023]
Affiliation(s)
- Xiaofeng Yu
- Molecular and Cellular Modeling Group; Heidelberg Institute for Theoretical Studies; Heidelberg; Germany
| | - Vlad Cojocaru
- Department of Cell and Developmental Biology; Max Planck Institute for Molecular Biomedicine; Münster; Germany
| | | |
Collapse
|
43
|
Shah MB, Jang HH, Zhang Q, David Stout C, Halpert JR. X-ray crystal structure of the cytochrome P450 2B4 active site mutant F297A in complex with clopidogrel: insights into compensatory rearrangements of the binding pocket. Arch Biochem Biophys 2013; 530:64-72. [PMID: 23296089 DOI: 10.1016/j.abb.2012.12.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 12/22/2012] [Accepted: 12/23/2012] [Indexed: 12/22/2022]
Abstract
Prior X-ray crystal structures of cytochrome P450 2B4 revealed the pivotal role of rearrangement of the side chains of residues F206 and F297 in the active site in accommodating various inhibitors or substrates. To explore the role of these residues, 2B4 F206A and F297A were created by site-directed mutagenesis and characterized functionally. The structure of F297A with clopidogrel demonstrated the reorientation of the ligand such that the methyl ester group is oriented toward the heme, whereas the thiophene moiety now extends to the additional void in the F297A mutant. Most interestingly, movement of the I helix and several amino acid side chains within the active site was observed in apparent response to the altered binding orientation. Results of flexible docking using the 2B4 wild type or the F297A-virtual mutant positioned either the thiophene or chlorophenyl group closer to heme. However, docking of clopidogrel using the real F297A mutant or a virtual mutant with the I-helix re-positioned oriented clopidogrel preferentially with either the methyl ester or the chlorophenyl group closest to heme. The study provides insight into how the altered active site adapts to accommodate and interact with the substrate in a distinct orientation while maintaining the overall closed protein conformation.
Collapse
Affiliation(s)
- Manish B Shah
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | | | | | | | | |
Collapse
|
44
|
Leach AG. Tactics to Avoid Inhibition of Cytochrome P450s. TOPICS IN MEDICINAL CHEMISTRY 2013. [DOI: 10.1007/7355_2013_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
|
45
|
Rydberg P, Jørgensen MS, Jacobsen TA, Jacobsen AM, Madsen KG, Olsen L. Nitrogen Inversion Barriers Affect the N-Oxidation of Tertiary Alkylamines by Cytochromes P450. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
46
|
Rydberg P, Jørgensen MS, Jacobsen TA, Jacobsen AM, Madsen KG, Olsen L. Nitrogen inversion barriers affect the N-oxidation of tertiary alkylamines by cytochromes P450. Angew Chem Int Ed Engl 2012. [PMID: 23192954 DOI: 10.1002/anie.201206207] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Patrik Rydberg
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | | | | | | | | | | |
Collapse
|
47
|
DeVore NM, Scott EE. Nicotine and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone binding and access channel in human cytochrome P450 2A6 and 2A13 enzymes. J Biol Chem 2012; 287:26576-85. [PMID: 22700965 DOI: 10.1074/jbc.m112.372813] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Cytochromes P450 (CYP) from the 2A subfamily are known for their roles in the metabolism of nicotine, the addictive agent in tobacco, and activation of the tobacco procarcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Although both the hepatic CYP2A6 and respiratory CYP2A13 enzymes metabolize these compounds, CYP2A13 does so with much higher catalytic efficiency, but the structural basis for this has been unclear. X-ray structures of nicotine complexes with CYP2A13 (2.5 Å) and CYP2A6 (2.3 Å) yield a structural rationale for the preferential binding of nicotine to CYP2A13. Additional structures of CYP2A13 with NNK reveal either a single NNK molecule in the active site with orientations corresponding to metabolites known to form DNA adducts and initiate lung cancer (2.35 Å) or with two molecules of NNK bound (2.1 Å): one in the active site and one in a more distal staging site. Finally, in contrast to prior CYP2A structures with enclosed active sites, CYP2A13 conformations were solved that adopt both open and intermediate conformations resulting from an ∼2.5 Å movement of the F to G helices. This channel occurs in the same region where the second, distal NNK molecule is bound, suggesting that the channel may be used for ligand entry and/or exit from the active site. Altogether these structures provide multiple new snapshots of CYP2A13 conformations that assist in understanding the binding and activation of an important human carcinogen, as well as critical comparisons in the binding of nicotine, one of the most widely used and highly addictive drugs in human use.
Collapse
Affiliation(s)
- Natasha M DeVore
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, USA
| | | |
Collapse
|
48
|
Stephens ES, Walsh AA, Scott EE. Evaluation of inhibition selectivity for human cytochrome P450 2A enzymes. Drug Metab Dispos 2012; 40:1797-802. [PMID: 22696418 DOI: 10.1124/dmd.112.045161] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cytochrome P450 (P450) enzymes are mixed-function oxidases that catalyze the metabolism of xenobiotics and endogenous biochemicals. Selective inhibitors are needed to accurately distinguish the contributions of individual P450 enzymes in the metabolism of drugs and the activation of procarcinogens in human tissues, but very frequently these enzymes have substantial overlapping selectivity. We evaluated a chemically diverse set of nine previously identified CYP2A6 inhibitors to determine which are able to discriminate between human CYP2A enzymes CYP2A6 and the 94%-identical CYP2A13 enzyme. Inhibitor binding to recombinant purified enzyme was evaluated, and affinities were determined. K(i) values were determined for inhibition of p-nitrophenol 2-hydroxylation, a reaction accomplished by CYP2A13 and CYP2A6 with more similar catalytic efficiencies (k(cat)/K(m) 0.19 and 0.12 μM⁻¹ · min⁻¹, respectively) than hydroxylation of the classic substrate coumarin (0.11 and 0.53 μM⁻¹ · min⁻¹, respectively). Of the nine compounds assayed, only tranylcypromine and (R)-(+)-menthofuran had a greater than 10-fold preference for CYP2A6 inhibition versus CYP2A13 inhibition. Most compounds evaluated [tryptamine, 4-dimethylaminobenzaldehyde, phenethyl isothiocyanate, β-nicotyrine, (S)-nicotine, and pilocarpine] demonstrated only moderate or no preference for inhibition of one CYP2A enzyme over the other. However, 8-methoxypsoralen has a 6-fold lower K(i) for CYP2A13 than for CYP2A6. This information is useful to inform reinterpretation of previous data with these inhibitors and to guide future studies seeking to determine which human CYP2A enzyme is responsible for the in vivo metabolism of compounds in human tissues expressing both enzymes.
Collapse
Affiliation(s)
- Eva S Stephens
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas, USA
| | | | | |
Collapse
|
49
|
Shahrokh K, Cheatham TE, Yost GS. Conformational dynamics of CYP3A4 demonstrate the important role of Arg212 coupled with the opening of ingress, egress and solvent channels to dehydrogenation of 4-hydroxy-tamoxifen. Biochim Biophys Acta Gen Subj 2012; 1820:1605-17. [PMID: 22677141 DOI: 10.1016/j.bbagen.2012.05.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/22/2012] [Accepted: 05/23/2012] [Indexed: 12/12/2022]
Abstract
BACKGROUND Structure-based methods for P450 substrates are commonly used during drug development to identify sites of metabolism. However, docking studies using available X-ray structures for the major drug-metabolizing P450, CYP3A4, do not always identify binding modes supportive of the production of high-energy toxic metabolites. Minor pathways such as P450-catalyzed dehydrogenation have been experimentally shown to produce reactive products capable of forming biomolecular adducts which can lead to increased risk toxicities. 4-Hydroxy-tamoxifen (4OHT) is metabolized by CYP3A4 via competing hydroxylation and dehydrogenation reactions. METHODS Ab initio gas-phase electronic structural characterization of 4OHT was used to develop a docking scoring scheme. Conformational sampling of CYP3A4 with molecular dynamics simulations along multiple trajectories were used to generate representative structures for docking studies using recently published heme parameters. A key predicted binding mode was tested experimentally using site-directed mutagenesis of CYP3A4 and liquid chromatography-mass spectroscopy analysis. RESULTS Docking with MD-refined CYP3A4 structures incorporating hexa-coordinate heme parameters identifies a unique binding mode involving ARG212 and channel 4, unobserved in the starting PDB ID: 1TQN X-ray structure. The models supporting dehydrogenation are consistent with results from in vitro incubations. GENERAL SIGNIFICANCE Our models indicate that coupled structural contributions of the ingress, egress and solvent channels to the CYP3A4 active site geometries play key roles in the observed 4OHT binding modes. Thus adequate sampling of the conformational space of these drug-metabolizing promiscuous enzymes is important for substrates that may bind in malleable regions of the enzyme active-site.
Collapse
Affiliation(s)
- Kiumars Shahrokh
- Department of Pharmacology and Toxicology, College of Pharmacy, Skaggs Hall 201, University of Utah, Salt Lake City, UT 84112, USA
| | | | | |
Collapse
|