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Visser SP. Second‐Coordination Sphere Effects on Selectivity and Specificity of Heme and Nonheme Iron Enzymes. Chemistry 2020; 26:5308-5327. [DOI: 10.1002/chem.201905119] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/04/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Sam P. Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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Shumaker R, Ren M, Aluri J, Dutcus CE, Rance C, He C. An Open-Label Phase 1 Study to Determine the Effect of Lenvatinib on the Pharmacokinetics of Midazolam, a CYP3A4 Substrate, in Patients with Advanced Solid Tumors. Eur J Drug Metab Pharmacokinet 2020; 45:373-383. [PMID: 32067158 PMCID: PMC7211203 DOI: 10.1007/s13318-020-00607-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND AND OBJECTIVE Lenvatinib is a multikinase inhibitor that inhibits enzyme activity but induces gene expression of cytochrome P450 3A4 (CYP3A4), an important enzyme for drug metabolism. We evaluated the impact of lenvatinib on CYP3A4 using midazolam as a probe substrate in patients with advanced solid tumors. The primary objective was to determine the pharmacokinetic effects of lenvatinib on midazolam, and the secondary objective was to assess the safety of lenvatinib. METHODS This multicenter, open-label, nonrandomized, phase 1 study involved patients with advanced cancer that progressed after treatment with approved therapies or for which no standard therapies were available. RESULTS Compared with baseline, coadministration of lenvatinib decreased the geometric mean ratio of the area under the concentration-time curve for midazolam on day 1 to 0.914 (90% confidence interval [CI] 0.850-0.983) but increased it on day 14 to 1.148 (90% CI 0.938-1.404). Coadministration of lenvatinib also decreased the geometric mean ratio of the maximum observed concentration for midazolam on day 1 to 0.862 (90% CI 0.753-0.988) but increased it on day 14 to 1.027 (90% CI 0.852-1.238). There was little change in the terminal elimination phase half-life of midazolam when administered with lenvatinib. The most common treatment-related adverse events were hypertension (20.0%), fatigue (16.7%), and diarrhea (10.0%). CONCLUSIONS Coadministration of lenvatinib had no clinically relevant effect on the pharmacokinetics of midazolam, a CYP3A4 substrate. The adverse events were consistent with the known safety profile of lenvatinib, and no new safety concerns were identified. CLINICALTRIALS. GOV IDENTIFIER NCT02686164.
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Affiliation(s)
- Robert Shumaker
- Formerly of Eisai Inc, 155 Tice Blvd, Woodcliff Lake, NJ, 07677, USA.
| | - Min Ren
- Biostatistics, Oncology Business Group, Eisai Inc, Woodcliff Lake, NJ, USA
| | - Jagadeesh Aluri
- Clinical Pharmacology Science, Medicine Development Center, Eisai Inc, Woodcliff Lake, NJ, USA
| | - Corina E Dutcus
- Clinical Research, Oncology Business Group, Eisai Inc, Woodcliff Lake, NJ, USA
| | - Christian Rance
- Clinical Operations, Oncology Business Group, Eisai Inc, Woodcliff Lake, NJ, USA
| | - Cixin He
- Biostatistics, Oncology Business Group, Eisai Inc, Woodcliff Lake, NJ, USA
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Wright WC, Chenge J, Wang J, Girvan HM, Yang L, Chai SC, Huber AD, Wu J, Oladimeji PO, Munro AW, Chen T. Clobetasol Propionate Is a Heme-Mediated Selective Inhibitor of Human Cytochrome P450 3A5. J Med Chem 2020; 63:1415-1433. [PMID: 31965799 PMCID: PMC7087482 DOI: 10.1021/acs.jmedchem.9b02067] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The human cytochrome P450 (CYP) enzymes CYP3A4 and CYP3A5 metabolize most drugs and have high similarities in their structure and substrate preference. Whereas CYP3A4 is predominantly expressed in the liver, CYP3A5 is upregulated in cancer, contributing to drug resistance. Selective inhibitors of CYP3A5 are, therefore, critical to validating it as a therapeutic target. Here we report clobetasol propionate (clobetasol) as a potent and selective CYP3A5 inhibitor identified by high-throughput screening using enzymatic and cell-based assays. Molecular dynamics simulations suggest a close proximity of clobetasol to the heme in CYP3A5 but not in CYP3A4. UV-visible spectroscopy and electron paramagnetic resonance analyses confirmed the formation of an inhibitory type I heme-clobetasol complex in CYP3A5 but not in CYP3A4, thus explaining the CYP3A5 selectivity of clobetasol. Our results provide a structural basis for selective CYP3A5 inhibition, along with mechanistic insights, and highlight clobetasol as an important chemical tool for target validation.
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Affiliation(s)
- William C. Wright
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
- Integrated Biomedical Sciences Program, University of
Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Jude Chenge
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Jingheng Wang
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Hazel M. Girvan
- Manchester Institute of Biotechnology, School of Natural
Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN,
UK
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Sergio C. Chai
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Andrew D. Huber
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Peter O. Oladimeji
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of Natural
Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN,
UK
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
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Feltrin C, Oliveira Simões CM. Reviewing the mechanisms of natural product-drug interactions involving efflux transporters and metabolic enzymes. Chem Biol Interact 2019; 314:108825. [PMID: 31553897 DOI: 10.1016/j.cbi.2019.108825] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/28/2019] [Accepted: 09/19/2019] [Indexed: 12/20/2022]
Abstract
The World Health Organization (WHO) and other worldwide health agencies have recently taken initiatives to encourage the use of traditional medicine and/or complementary/alternative medicine in order to promote well-being and public health. In this way, one of the WHO's concerns is the safe use of these therapies. Phytotherapy is a strategy consisting of the use of medicinal plants (MP) and/or herbal medicinal products (HMP) for medicinal purposes. The use of phytotherapy concomitantly with drugs may cause interactions compromising the expected pharmacological action or generating toxic effects. These interactions are complex processes that may occur with multiple medications targeting different metabolic pathways, and involving different compounds present in MP and HMP. Thus, the aim of this review was to summarize the main MP- and HMP-drug interactions that involve specific transporters (P-glycoprotein and BCRP) and CYP450 enzymes (CYP3A4 and CYP2D6), which play relevant roles in the mechanisms of interactions. Firstly, multiple databases were used to search studies describing in vitro or in vivo MP and HMP-drug interactions and, after that, a systematic note-taking and appraisal of the literature was conducted. It was observed that several MP and HMP, metabolic pathways and transcription factors are involved in the transporters and enzymes expression or in the modulation of their activity having the potential to provide such interactions. Thus, the knowledge of MP- and HMP-drug interaction mechanisms could contribute to prevent harmful interactions and can ensure the safe use of these products to help the establishment of the therapeutic planning in order to certify the best treatment strategy to be used.
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Affiliation(s)
- Clarissa Feltrin
- Programa de Pós-Graduação em Farmácia, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Cláudia Maria Oliveira Simões
- Programa de Pós-Graduação em Farmácia, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.
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Kiani YS, Ranaghan KE, Jabeen I, Mulholland AJ. Molecular Dynamics Simulation Framework to Probe the Binding Hypothesis of CYP3A4 Inhibitors. Int J Mol Sci 2019; 20:E4468. [PMID: 31510073 PMCID: PMC6769491 DOI: 10.3390/ijms20184468] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/22/2019] [Accepted: 09/01/2019] [Indexed: 12/20/2022] Open
Abstract
The Cytochrome P450 family of heme-containing proteins plays a major role in catalyzing phase I metabolic reactions, and the CYP3A4 subtype is responsible for the metabolism of many currently marketed drugs. Additionally, CYP3A4 has an inherent affinity for a broad spectrum of structurally diverse chemical entities, often leading to drug-drug interactions mediated by the inhibition or induction of the metabolic enzyme. The current study explores the binding of selected highly efficient CYP3A4 inhibitors by docking and molecular dynamics (MD) simulation protocols and their binding free energy calculated using the WaterSwap method. The results indicate the importance of binding pocket residues including Phe57, Arg105, Arg106, Ser119, Arg212, Phe213, Thr309, Ser312, Ala370, Arg372, Glu374, Gly481 and Leu483 for interaction with CYP3A4 inhibitors. The residue-wise decomposition of the binding free energy from the WaterSwap method revealed the importance of binding site residues Arg106 and Arg372 in the stabilization of all the selected CYP3A4-inhibitor complexes. The WaterSwap binding energies were further complemented with the MM(GB/PB)SA results and it was observed that the binding energies calculated by both methods do not differ significantly. Overall, our results could guide towards the use of multiple computational approaches to achieve a better understanding of CYP3A4 inhibition, subsequently leading to the design of highly specific and efficient new chemical entities with suitable ADMETox properties and reduced side effects.
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Affiliation(s)
- Yusra Sajid Kiani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
| | - Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
| | - Ishrat Jabeen
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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Ferrario V, Fischer M, Zhu Y, Pleiss J. Modelling of substrate access and substrate binding to cephalosporin acylases. Sci Rep 2019; 9:12402. [PMID: 31455800 PMCID: PMC6712217 DOI: 10.1038/s41598-019-48849-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/14/2019] [Indexed: 01/16/2023] Open
Abstract
Semisynthetic cephalosporins are widely used antibiotics currently produced by different chemical steps under harsh conditions, which results in a considerable amount of toxic waste. Biocatalytic synthesis by the cephalosporin acylase from Pseudomonas sp. strain N176 is a promising alternative. Despite intensive engineering of the enzyme, the catalytic activity is still too low for a commercially viable process. To identify the bottlenecks which limit the success of protein engineering efforts, a series of MD simulations was performed to study for two acylase variants (WT, M6) the access of the substrate cephalosporin C from the bulk to the active site and the stability of the enzyme-substrate complex. In both variants, cephalosporin C was binding to a non-productive substrate binding site (E86α, S369β, S460β) at the entrance to the binding pocket, preventing substrate access. A second non-productive binding site (G372β, W376β, L457β) was identified within the binding pocket, which competes with the active site for substrate binding. Noteworthy, substrate binding to the protein surface followed a Langmuir model resulting in binding constants K = 7.4 and 9.2 mM for WT and M6, respectively, which were similar to the experimentally determined Michaelis constants KM = 11.0 and 8.1 mM, respectively.
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Affiliation(s)
- Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Mona Fischer
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Yushan Zhu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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Masamrekh RA, Kuzikov AV, Haurychenka YI, Shcherbakov KA, Veselovsky AV, Filimonov DA, Dmitriev AV, Zavialova MG, Gilep AA, Shkel TV, Strushkevich NV, Usanov SA, Archakov AI, Shumyantseva VV. In vitro
interactions of abiraterone, erythromycin, and CYP3A4: implications for drug–drug interactions. Fundam Clin Pharmacol 2019; 34:120-130. [DOI: 10.1111/fcp.12497] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/12/2019] [Accepted: 07/04/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Rami A. Masamrekh
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
- Pirogov Russian National Research Medical University Ostrovityanova Street, 1 Moscow 117997 Russia
| | - Alexey V. Kuzikov
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
- Pirogov Russian National Research Medical University Ostrovityanova Street, 1 Moscow 117997 Russia
| | - Yaraslau I. Haurychenka
- Pirogov Russian National Research Medical University Ostrovityanova Street, 1 Moscow 117997 Russia
| | - Kirill A. Shcherbakov
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
| | | | - Dmitrii A. Filimonov
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
| | - Alexander V. Dmitriev
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
| | - Maria G. Zavialova
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
| | - Andrei A. Gilep
- Institute of Bioorganic Chemistry NASB 5 Academician V.F. Kuprevich Street, Build 2 Minsk BY‐220141 Belarus
| | - Tatsiana V. Shkel
- Institute of Bioorganic Chemistry NASB 5 Academician V.F. Kuprevich Street, Build 2 Minsk BY‐220141 Belarus
| | - Natallia V. Strushkevich
- Institute of Bioorganic Chemistry NASB 5 Academician V.F. Kuprevich Street, Build 2 Minsk BY‐220141 Belarus
| | - Sergey A. Usanov
- Institute of Bioorganic Chemistry NASB 5 Academician V.F. Kuprevich Street, Build 2 Minsk BY‐220141 Belarus
| | - Alexander I. Archakov
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
- Pirogov Russian National Research Medical University Ostrovityanova Street, 1 Moscow 117997 Russia
| | - Victoria V. Shumyantseva
- Institute of Biomedical Chemistry Pogodinskaya Street, 10, Build 8 Moscow 119121 Russia
- Pirogov Russian National Research Medical University Ostrovityanova Street, 1 Moscow 117997 Russia
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Carter AC, King JB, Mattes AO, Cai S, Singh N, Cichewicz RH. Natural-Product-Inspired Compounds as Countermeasures against the Liver Carcinogen Aflatoxin B 1. JOURNAL OF NATURAL PRODUCTS 2019; 82:1694-1703. [PMID: 31136174 DOI: 10.1021/acs.jnatprod.9b00290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Aflatoxin B1 (AfB1) ranks among the most potent liver carcinogens known, and the accidental or intentional exposure of humans and livestock to this toxin remains a serious global threat. One protective measure that had been proposed is employing small-molecule therapeutics capable of mitigating the toxicity of AfB1; however, to date, these efforts have had little clinical success. To identify molecular scaffolds that reduce the toxicity of AfB1, we developed a cell-based high-throughput high-content imaging assay that enabled our team to test natural products (pure compounds, fractions, and extracts) for protection of monolayers and spheroids composed of HepG2 liver cells against AfB1. The spheroid assay showed notable potential for further development, as it afforded greater sensitivity of HepG2 cells to AfB1, which is believed to better mimic the in vivo response of hepatocytes to the toxin. One of the most bioactive compounds to arise from this investigation was alternariol-9-methyl ether (1, purified from an Alternaria sp. isolate), which inspired the synthesis and testing of several structurally related molecules. Based on these findings, it is proposed that several types of natural and synthetic polyarene molecules that have undergone oxidative functionalization (e.g., compounds containing 3-methoxyphenol moieties) are promising starting points for the development of new agents that protect against AfB1 toxicity.
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Affiliation(s)
- Adam C Carter
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry & Biochemistry, Stephenson Life Science Research Center , University of Oklahoma , 101 Stephenson Parkway , Norman , Oklahoma 73019 , United States
| | - Jarrod B King
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry & Biochemistry, Stephenson Life Science Research Center , University of Oklahoma , 101 Stephenson Parkway , Norman , Oklahoma 73019 , United States
| | - Allison O Mattes
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry & Biochemistry, Stephenson Life Science Research Center , University of Oklahoma , 101 Stephenson Parkway , Norman , Oklahoma 73019 , United States
| | - Shengxin Cai
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry & Biochemistry, Stephenson Life Science Research Center , University of Oklahoma , 101 Stephenson Parkway , Norman , Oklahoma 73019 , United States
| | - Narender Singh
- CFD Research Corporation , 701 McMillian Way, Suite D , Huntsville , Alabama 35806 , United States
| | - Robert H Cichewicz
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry & Biochemistry, Stephenson Life Science Research Center , University of Oklahoma , 101 Stephenson Parkway , Norman , Oklahoma 73019 , United States
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Analysis of the Molecular Interactions between Cytochromes P450 3A4 and 1A2 and Aflatoxins: A Docking Study. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9122467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Mycotoxins known as aflatoxins (AF) are produced as a secondary metabolite by some species of Aspergillus fungi. They are considered carcinogenic, hepatotoxic, teratogenic, and mutagenic. In this study, the molecular structure, chemical reactivity, and charge transfer values of AFB1, B2, G1, and G2 were analyzed using density functional theory. Different methodologies—B3LYP/6-311G(d,p) and M06-2X/6-311G(d,p)—were applied for geometrical calculations. Chemical reactivity parameters were used in the calculation of charge transfer values during the interaction between protein and ligand. The binding energy, the electrostatic interactions, and the amino acids of the active site were determined by molecular docking analysis between AF and cytochromes P450 (3A4 and 1A2), employing different PDB files (CYP3A4:1TQN, 2V0M, 4NY4 and 1W0E, and CYP1A2:2HI4). Molecular docking analysis indicated that the central rings of the AF are involved in the interaction with the HEM group of the active site. The differences in the molecular structure of the AF affect their position regarding the HEM group. The resulting configurations presented considerable variation in the amino acids and the position of the coupling. The charge transfer values showed that there is oxidative damage inside the active site and that the HEM group is responsible for the main charge transferences.
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61
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Exploring the Chemical Space of Cytochrome P450 Inhibitors Using Integrated Physicochemical Parameters, Drug Efficiency Metrics and Decision Tree Models. COMPUTATION 2019. [DOI: 10.3390/computation7020026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The cytochrome P450s (CYPs) play a central role in the metabolism of various endogenous and exogenous compounds including drugs. CYPs are vulnerable to inhibition and induction which can lead to adverse drug reactions. Therefore, insights into the underlying mechanism of CYP450 inhibition and the estimation of overall CYP inhibitor properties might serve as valuable tools during the early phases of drug discovery. Herein, we present a large data set of inhibitors against five major metabolic CYPs (CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4) for the evaluation of important physicochemical properties and ligand efficiency metrics to define property trends across various activity levels (active, efficient and inactive). Decision tree models for CYP inhibition were developed with an accuracy >90% for both the training set and 10-folds cross validation. Overall, molecular weight (MW), hydrogen bond acceptors/donors (HBA/HBD) and lipophilicity (clogP/logPo/w) represent important physicochemical descriptors for CYP450 inhibitors. However, highly efficient CYP inhibitors show mean MW, HBA, HBD and logP values between 294.18–482.40,5.0–8.2,1–7.29 and 1.68–2.57, respectively. Our results might help in optimization of toxicological profiles associated with new chemical entities (NCEs), through a better understanding of inhibitor properties leading to CYP-mediated interactions.
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62
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Erdogan H. One small step for cytochrome P450 in its catalytic cycle, one giant leap for enzymology. J PORPHYR PHTHALOCYA 2019. [DOI: 10.1142/s1088424619300040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The intermediates operating in the cytochrome P450 catalytic cycle have been investigated for more than half a century, fascinating many enzymologists. Each intermediate has its unique role to carry out diverse oxidations. Natural time course of the catalytic cycle is quite fast, hence, not all of the reactive intermediates could be isolated during physiological catalysis. Different high-valent iron intermediates have been proposed as primary oxidants: the candidates are compound 0 (Cpd 0, [FeOOH][Formula: see text]P450) and compound I (Cpd I, Fe(IV)[Formula: see text]O por[Formula: see text]P450). Among them, the role of Cpd I in hydroxylation is fairly well understood due the discovery of the peroxide shunt. This review endeavors to put the outstanding research efforts conducted to isolate and characterize the intermediates together. In addition to spectral features of each intermediate in the catalytic cycle, the oxidizing powers of Cpd 0 and Cpd I will be discussed along with most recent scientific findings.
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Affiliation(s)
- Huriye Erdogan
- Department of Chemistry, Gebze Technical University, Gebze, 41400, Kocaeli, Turkey
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63
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Nair PC, McKinnon RA, Miners JO. Computational Prediction of the Site(s) of Metabolism and Binding Modes of Protein Kinase Inhibitors Metabolized by CYP3A4. Drug Metab Dispos 2019; 47:616-631. [DOI: 10.1124/dmd.118.085167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/18/2019] [Indexed: 01/13/2023] Open
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Four Major Channels Detected in the Cytochrome P450 3A4: A Step toward Understanding Its Multispecificity. Int J Mol Sci 2019; 20:ijms20040987. [PMID: 30823507 PMCID: PMC6412807 DOI: 10.3390/ijms20040987] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/12/2019] [Accepted: 02/20/2019] [Indexed: 12/27/2022] Open
Abstract
We computed the network of channels of the 3A4 isoform of the cytochrome P450 (CYP) on the basis of 16 crystal structures extracted from the Protein Data Bank (PDB). The calculations were performed with version 2 of the CCCPP software that we developed for this research project. We identified the minimal cost paths (MCPs) output by CCCPP as probable ways to access to the buried active site. The algorithm of calculation of the MCPs is presented in this paper, with its original method of visualization of the channels. We found that these MCPs constitute four major channels in CYP3A4. Among the many channels proposed by Cojocaru et al. in 2007, we found that only four of them open in 3A4. We provide a refined description of these channels together with associated quantitative data.
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de Vries R, Jacobs F, Mannens G, Snoeys J, Cuyckens F, Chien C, Ward P. Apalutamide Absorption, Metabolism, and Excretion in Healthy Men, and Enzyme Reaction in Human Hepatocytes. Drug Metab Dispos 2019; 47:453-464. [PMID: 30787101 DOI: 10.1124/dmd.118.084517] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/04/2019] [Indexed: 12/18/2022] Open
Abstract
In this phase 1 study, the absolute bioavailability and absorption, metabolism, and excretion (AME) of apalutamide, a competitive inhibitor of the androgen receptor, were evaluated in 12 healthy men. Subjects received 240 mg of apalutamide orally plus a 15-minute intravenous infusion of 100 µg of apalutamide containing 9.25 kBq (250 nCi) of 14C-apalutamide (2 hours postdose) for absolute bioavailability assessment or plus one 400-µg capsule containing 37 kBq (1000 nCi) of 14C-apalutamide for AME assessment. Content of 14C and metabolite profiling for whole blood, plasma, urine, feces, and expired air samples were analyzed using accelerator mass spectrometry. Apalutamide absolute oral bioavailability was ≈100%. After oral administration, apalutamide, its N-desmethyl metabolite (M3), and an inactive carboxylic acid metabolite (M4) accounted for most 14C in plasma (45%, 44%, and 3%, respectively). Apalutamide elimination was slow, with a mean plasma half-life of 151-178 hours. The mean cumulative recovery of total 14C over 70 days postdose was 64.6% in urine and 24.3% in feces. The urinary excretion of apalutamide, M3, and M4 was 1.2%, 2.7%, and 31.1% of dose, respectively. Fecal excretion of apalutamide, M3, and M4 was 1.5%, 2.0%, and 2.4% of dose, respectively. Seventeen apalutamide metabolites and six main metabolic clearance pathways were identified. In vitro studies confirmed CYP2C8 and CYP3A4 roles in apalutamide metabolism.
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Affiliation(s)
- Ronald de Vries
- Janssen Research & Development, Beerse, Belgium (R.d.V., F.J., G.M., J.S., F.C.); Janssen Research & Development, Spring House, Pennsylvania (C.C.); and Janssen Research & Development, San Diego, California (P.W.)
| | - Frank Jacobs
- Janssen Research & Development, Beerse, Belgium (R.d.V., F.J., G.M., J.S., F.C.); Janssen Research & Development, Spring House, Pennsylvania (C.C.); and Janssen Research & Development, San Diego, California (P.W.)
| | - Geert Mannens
- Janssen Research & Development, Beerse, Belgium (R.d.V., F.J., G.M., J.S., F.C.); Janssen Research & Development, Spring House, Pennsylvania (C.C.); and Janssen Research & Development, San Diego, California (P.W.)
| | - Jan Snoeys
- Janssen Research & Development, Beerse, Belgium (R.d.V., F.J., G.M., J.S., F.C.); Janssen Research & Development, Spring House, Pennsylvania (C.C.); and Janssen Research & Development, San Diego, California (P.W.)
| | - Filip Cuyckens
- Janssen Research & Development, Beerse, Belgium (R.d.V., F.J., G.M., J.S., F.C.); Janssen Research & Development, Spring House, Pennsylvania (C.C.); and Janssen Research & Development, San Diego, California (P.W.)
| | - Caly Chien
- Janssen Research & Development, Beerse, Belgium (R.d.V., F.J., G.M., J.S., F.C.); Janssen Research & Development, Spring House, Pennsylvania (C.C.); and Janssen Research & Development, San Diego, California (P.W.)
| | - Peter Ward
- Janssen Research & Development, Beerse, Belgium (R.d.V., F.J., G.M., J.S., F.C.); Janssen Research & Development, Spring House, Pennsylvania (C.C.); and Janssen Research & Development, San Diego, California (P.W.)
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66
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Xue Y, Li J, Wu Z, Liu G, Tang Y, Li W. Computational insights into the different catalytic activities of CYP3A4 and CYP3A5 toward schisantherin E. Chem Biol Drug Des 2019; 93:854-864. [PMID: 30637977 DOI: 10.1111/cbdd.13475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/24/2018] [Accepted: 12/30/2018] [Indexed: 12/11/2022]
Abstract
The cytochromes CYP3A4 and CYP3A5 share 84% sequence identity, but they exhibit different catalytic activities toward some substrates. Schisantherin E (SE) was recently identified as a selective substrate of CYP3A5, which exhibited catalytic efficiency that was more than 23 times higher than CYP3A4. At present, however, the structural determinants responsible for the different catalytic activities of the two enzymes toward SE have not been fully understood. In this study, a combination of molecular docking, molecular dynamic simulations, and binding free energy calculation was performed on the CYP3A4/CYP3A5-SE systems to investigate the issue. The results demonstrate that Ser119 in CYP3A4 and Glu374 in CYP3A5 formed direct hydrogen bonding with SE, respectively. Additionally, one water molecule located between the B-C loop and the I helix mediated different hydrogen-bonding networks between CYP3A4/3A5 and SE. The residue differences (Phe/Leu108 and Leu/Phe210) triggered the distinct conformational changes of the Phe-cluster residues, especially Phe213 and Phe215, which formed stronger hydrophobic interactions with SE in CYP3A5. The calculated binding free energies were consistent with the experimental results.
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Affiliation(s)
- Yuhan Xue
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Junhao Li
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
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67
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Xiao K, Gao J, Weng SJ, Fang Y, Gao N, Wen Q, Jin H, Qiao HL. CYP3A4/5 Activity Probed with Testosterone and Midazolam: Correlation between Two Substrates at the Microsomal and Enzyme Levels. Mol Pharm 2018; 16:382-392. [PMID: 30517006 DOI: 10.1021/acs.molpharmaceut.8b01043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Testosterone (TST) and midazolam (MDZ) are widely used as probes to detect CYP3A4/5 activity, but the data acquired with these two substrates do not correlate well at the microsomal level (per milligram of microsomal protein), and the reason is unclear. In this study, CYP3A4/5 activity was probed with TST and MDZ at the microsomal and enzyme levels (per picomole of CYP3A4/5) in 72 human liver samples. Correlation coefficients were lower in Vmax and CLint at the microsomal level, as compared with those at the enzyme level ( Vmax 0.658 vs 0.883; CLint no correlation vs 0.796). Compared with TST, MDZ was found to correlate better with the content of CYP3A4/5 (no correlation vs 0.431) and CYP3A5 (no correlation vs 0.447), and huge variations in enzyme content existed among different genotypes, which explained the lower degree of correlation at the microsomal level. In addition, different genotypes had varying effects on activity at the enzyme level, whereas the difference between activity at the enzyme level probed with TST and that probed with MDZ was not obvious ( P > 0.05), indicating that the effect of gene polymorphisms on correlation between activity probed with these two substrates was limited at the enzyme level. In conclusion, our study demonstrates a high degree of correlation between CYP3A4/5 activity probed with TST and MDZ at the enzyme level but not at the microsomal level and allows us to correctly understand the influence of gene polymorphisms on the correlations.
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Affiliation(s)
- Kang Xiao
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , Henan 450052 , People's Republic of China
| | - Jie Gao
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , Henan 450052 , People's Republic of China
| | - Shi-Jia Weng
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , Henan 450052 , People's Republic of China
| | - Yan Fang
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , Henan 450052 , People's Republic of China
| | - Na Gao
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , Henan 450052 , People's Republic of China
| | - Qiang Wen
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , Henan 450052 , People's Republic of China
| | - Han Jin
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , Henan 450052 , People's Republic of China
| | - Hai-Ling Qiao
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , Henan 450052 , People's Republic of China
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68
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Castrignanò S, Di Nardo G, Sadeghi SJ, Gilardi G. Influence of inter-domain dynamics and surrounding environment flexibility on the direct electrochemistry and electrocatalysis of self-sufficient cytochrome P450 3A4-BMR chimeras. J Inorg Biochem 2018; 188:9-17. [DOI: 10.1016/j.jinorgbio.2018.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/21/2018] [Accepted: 08/02/2018] [Indexed: 12/18/2022]
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69
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Fuhr U, Hsin CH, Li X, Jabrane W, Sörgel F. Assessment of Pharmacokinetic Drug-Drug Interactions in Humans: In Vivo Probe Substrates for Drug Metabolism and Drug Transport Revisited. Annu Rev Pharmacol Toxicol 2018; 59:507-536. [PMID: 30156973 DOI: 10.1146/annurev-pharmtox-010818-021909] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Pharmacokinetic parameters of selective probe substrates are used to quantify the activity of an individual pharmacokinetic process (PKP) and the effect of perpetrator drugs thereon in clinical drug-drug interaction (DDI) studies. For instance, oral caffeine is used to quantify hepatic CYP1A2 activity, and oral dagibatran etexilate for intestinal P-glycoprotein (P-gp) activity. However, no probe substrate depends exclusively on the PKP it is meant to quantify. Lack of selectivity for a given enzyme/transporter and expression of the respective enzyme/transporter at several sites in the human body are the main challenges. Thus, a detailed understanding of the role of individual PKPs for the pharmacokinetics of any probe substrate is essential to allocate the effect of a perpetrator drug to a specific PKP; this is a prerequisite for reliably informed pharmacokinetic models that will allow for the quantitative prediction of perpetrator effects on therapeutic drugs, also in respective patient populations not included in DDI studies.
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Affiliation(s)
- Uwe Fuhr
- Department I of Pharmacology, University Hospital Cologne, 50931 Cologne, Germany;
| | - Chih-Hsuan Hsin
- Department I of Pharmacology, University Hospital Cologne, 50931 Cologne, Germany;
| | - Xia Li
- Department I of Pharmacology, University Hospital Cologne, 50931 Cologne, Germany;
| | - Wafaâ Jabrane
- Department I of Pharmacology, University Hospital Cologne, 50931 Cologne, Germany;
| | - Fritz Sörgel
- Institute for Biomedical and Pharmaceutical Research, 90562 Nürnberg-Heroldsberg, Germany
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70
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71
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Arendse LB, Blackburn JM. Effects of polymorphic variation on the thermostability of heterogenous populations of CYP3A4 and CYP2C9 enzymes in solution. Sci Rep 2018; 8:11876. [PMID: 30089838 PMCID: PMC6082832 DOI: 10.1038/s41598-018-30195-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/23/2018] [Indexed: 12/11/2022] Open
Abstract
The effect of non-synonymous single nucleotide polymorphisms (SNPs) on cytochrome P450 (CYP450) drug metabolism is currently poorly understood due to the large number of polymorphisms, the diversity of potential substrates and the complexity of CYP450 function. Previously we carried out in silico studies to explore the effect of SNPs on CYP450 function, using in silico calculations to predict the effect of mutations on protein stability. Here we have determined the effect of eight CYP3A4 and seven CYP2C9 SNPs on the thermostability of proteins in solution to test these predictions. Thermostability assays revealed distinct CYP450 sub-populations with only 65–70% of wild-type CYP3A4 and CYP2C9 susceptible to rapid heat-induced P450 to P420 conversion. CYP3A4 mutations G56D, P218R, S222P, I223R, L373F and M445T and CYP2C9 mutations V76M, I359L and I359T were destabilising, increasing the proportion of protein sensitive to the rapid heat-induced P450 to P420 conversion and/or reducing the half-life of this conversion. CYP2C9 Q214L was the only stabilising mutation. These results corresponded well with the in silico protein stability calculations, confirming the value of these predictions and together suggest that the changes in thermostability result from destabilisation/stabilisation of the protein fold, changes in the haem-binding environment or effects on oligomer formation/conformation.
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Affiliation(s)
- Lauren B Arendse
- Institute for Infectious Disease & Molecular Medicine, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, South Africa
| | - Jonathan M Blackburn
- Institute for Infectious Disease & Molecular Medicine, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, South Africa.
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72
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Ferrario V, Hansen N, Pleiss J. Interpretation of cytochrome P450 monooxygenase kinetics by modeling of thermodynamic activity. J Inorg Biochem 2018. [DOI: 10.1016/j.jinorgbio.2018.02.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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73
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Šrejber M, Navrátilová V, Paloncýová M, Bazgier V, Berka K, Anzenbacher P, Otyepka M. Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners. J Inorg Biochem 2018; 183:117-136. [DOI: 10.1016/j.jinorgbio.2018.03.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/16/2018] [Accepted: 03/01/2018] [Indexed: 01/08/2023]
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74
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Thayumanavan P, Loganathan C, Iruthayaraj A, Poomani K, Nallaiyan S. S-allyl-glutathione, a synthetic analogue of glutathione protected liver against carbon tetrachloride toxicity: Focus towards anti-oxidative efficiency. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2018; 58:21-28. [PMID: 29278860 DOI: 10.1016/j.etap.2017.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/30/2017] [Accepted: 12/13/2017] [Indexed: 06/07/2023]
Abstract
A simple analogue of well known natural antioxidant glutathione (GSH) called S-allyl-glutathione (SAG) was evaluated against carbon tetrachloride (CCl4)-induced oxidative stress liver injury in rat. Pretreatment of SAG attenuated the CCl4-toxicity induced elevation of liver injury markers such as enzymes (AST, ALT, GGT, ALP and LDH) and bilirubin in the blood circulation. Such protective effect of SAG resulted in preservation of liver function observed as normal level of total protein and albumin in plasma as well as inhibition of dyslipidemia in liver. In addition, in silico analysis has proved that SAG has strong affinity with the amino acids present in active site of the human cytochrome P450 2E1 and 3A4. Three important mechanisms provided by SAG such as scavenging of reactive oxidants, replenishing of endogenous antioxidants (SOD, catalase, GPx, GSH and vitamin C) and protection of mitochondrial function (oxidative phosphorylation complex activities) are involved in the optimal function of liver against CCl4-toxicity.
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Affiliation(s)
| | - Chitra Loganathan
- Department of Biochemistry, Periyar University, Salem, Tamil Nadu 636011, India
| | - Ancy Iruthayaraj
- Department of Physics, Periyar University, Salem, Tamil Nadu 636011, India
| | - Kumaradhas Poomani
- Department of Physics, Periyar University, Salem, Tamil Nadu 636011, India
| | - Selvan Nallaiyan
- Department of Biochemistry, Government Arts College, Kumbakonam, Tamil Nadu 612002, India.
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75
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Mak PJ, Denisov IG. Spectroscopic studies of the cytochrome P450 reaction mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:178-204. [PMID: 28668640 PMCID: PMC5709052 DOI: 10.1016/j.bbapap.2017.06.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties. For a long time, the focus of cytochrome P450 research was to understand the underlying reaction mechanism of each enzymatic step, with the biggest challenge being identification and characterization of the powerful oxidizing intermediates. Spectroscopic methods, such as electronic absorption (UV-Vis), electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electron nuclear double resonance (ENDOR), Mössbauer, X-ray absorption (XAS), and resonance Raman (rR), have been useful tools in providing multifaceted and detailed mechanistic insights into the biophysics and biochemistry of these fascinating enzymes. The combination of spectroscopic techniques with novel approaches, such as cryoreduction and Nanodisc technology, allowed for generation, trapping and characterizing long sought transient intermediates, a task that has been difficult to achieve using other methods. Results obtained from the UV-Vis, rR and EPR spectroscopies are the main focus of this review, while the remaining spectroscopic techniques are briefly summarized. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Saint Louis University, St. Louis, MO, United States.
| | - Ilia G Denisov
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States.
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76
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In vitro metabolism study of a novel P38 kinase inhibitor: in silico predictions, structure elucidation using MS/MS-I. Future Med Chem 2018; 10:201-220. [DOI: 10.4155/fmc-2017-0126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Metabolism study of PH-797804, a promising newly developed drug for treatment of chronic inflammation which inhibits P38 mitogen-activated protein kinase. Materials & methods: Susceptibility of PH-797804 to metabolism was first investigated using SMARTCyp and Xenosite web servers. Molecular docking of the drug into CYP3A4 crystal structures evaluated binding interactions with active site. The predicted results were confirmed by in vitro incubation with rat S9 fraction. Metabolites of PH-797804 were identified by MS/MS. Results: A hydroxy metabolite and a cysteine/glutathione conjugate were detected. Computational prediction of reactive site of PH-797804 was conducted. Conclusion: The probable cysteine/glutathione adduct is indicative of potential drug chemical reactivity with potential to damage DNA and may provide guidance to the design of analogs with minimum toxicity.
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77
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Lee SH, Kim HY, Back SY, Han HK. Piperine-mediated drug interactions and formulation strategy for piperine: recent advances and future perspectives. Expert Opin Drug Metab Toxicol 2017; 14:43-57. [PMID: 29250980 DOI: 10.1080/17425255.2018.1418854] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Piperine has various pharmacological effects and can modulate the functional activity of metabolic enzymes and drug transporters. Consequently, there is a great interest in the application of piperine as an alternative medicine or bioavailability enhancer. Areas covered: This review deals with the effects of piperine on metabolizing enzymes and drug transporters. It provides the readers with an update on transporter-mediated and also metabolic enzyme-mediated piperine-drug interactions, with emphasis on its in vivo implications. This article also encompasses recent advances in the formulation approaches and technologies for optimizing the delivery of piperine. Expert opinion: Piperine can influence the pharmacokinetics of coadministered drugs, which may result in a therapeutically beneficial or adverse effect. Given that piperine inhibits or stimulates the activity of metabolic enzymes and transporters depending on the treatment conditions, the clinical significance of piperine-drug interactions should be assessed by varying the dose, dosing frequency, and the duration of treatment. In particular, better understanding the clinical relevance of piperine-drug interactions based on long-term assessments will provide a strong basis for the feasibility and applicability of piperine as a bioenhancer or a health-promoting agent. The development of effective formulations is also critical to facilitate the therapeutic applications of piperine.
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Affiliation(s)
- Sang Hoon Lee
- a College of Pharmacy , Dongguk University-Seoul , Goyang , Korea
| | - Hyeon Young Kim
- a College of Pharmacy , Dongguk University-Seoul , Goyang , Korea
| | - Seung Yun Back
- a College of Pharmacy , Dongguk University-Seoul , Goyang , Korea
| | - Hyo-Kyung Han
- a College of Pharmacy , Dongguk University-Seoul , Goyang , Korea
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78
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Jonsson-Schmunk K, Schafer SC, Croyle MA. Impact of nanomedicine on hepatic cytochrome P450 3A4 activity: things to consider during pre-clinical and clinical studies. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2017. [DOI: 10.1007/s40005-017-0376-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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79
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Lin XX, Lian GH, Xu Y, Zhao Q, Xiao J, Peng SF, Xiao MF, Ouyang DS, Tan ZR, Wang YC, Peng JB, Zhang W, Chen Y. The potent mechanism-based inactivation of CYP2D6 and CYP3A4 with fusidic acid in in vivo bioaccumulation. Xenobiotica 2017; 48:999-1005. [PMID: 29027845 DOI: 10.1080/00498254.2017.1390628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
1. The accumulation of fusidic acid (FA) after multiple doses of FA has been reported on in previous studies but the related mechanisms have not been clarified fully. In the present study, we explain the mechanisms related to the mechanism-based inactivation of CYP2D6 and CYP3A4. 2. The irreversible inhibitory effects of FA on CYP2D6 and CYP3A4 were examined via a series of experiments, including: (a) time-, concentration- and NADPH-dependent inactivation, (b) substrate protection in enzyme inactivation and (c) partition ratio with recombinant human CYP enzymes. Metoprolol α-hydroxylation and midazolam 1'-hydroxylation were used as marker reactions for CYP2D6 and CYP3A4 activities, and HPLC-MS/MS measurement was also utilised. 3. FA caused to the time- and concentration-dependent inactivation of CYP2D6 and CYP3A4. About 55.8% of the activity of CYP2D6 and 75.8% of the activity of CYP3A4 were suppressed after incubation with 10 μM FA for 15 min. KI and kinact were found to be 2.87 μM and 0.033 min-1, respectively, for CYP2D6, while they were 1.95 μM and 0.029 min-1, respectively, for CYP3A4. Inhibition of CYP2D6 and CYP3A4 activity was found to require the presence of NADPH. Substrates of CYP2D6 and CYP3A4 showed that the enzymes were protected against the inactivation induced by FA. The estimated partition ratio for the inactivation was 7 for CYP2D6 and 12 for CYP3A4. 4. FA is a potent mechanism-based inhibitor of CYP2D6 and CYP3A4, which may explain the accumulation of FA in vivo.
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Affiliation(s)
- Xiu-Xian Lin
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - Guang-Hui Lian
- c Department of gastroenterology , Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - Ying Xu
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - Qing Zhao
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - Jian Xiao
- d Department of Pharmacy , Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - Shi-Fang Peng
- e Department of Hepatology and Infectious Diseases , Xiangya Hospital, Central South University , Changsha , Hunan , China , and.,f Health Management Center, Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - Mei-Fang Xiao
- e Department of Hepatology and Infectious Diseases , Xiangya Hospital, Central South University , Changsha , Hunan , China , and.,f Health Management Center, Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - Dong-Sheng Ouyang
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - Zhi-Rong Tan
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - Yi-Cheng Wang
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - Jing-Bo Peng
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - Wei Zhang
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - Yao Chen
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
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80
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Castrignanò S, D'Avino S, Di Nardo G, Catucci G, Sadeghi SJ, Gilardi G. Modulation of the interaction between human P450 3A4 and B. megaterium reductase via engineered loops. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:116-125. [PMID: 28734977 DOI: 10.1016/j.bbapap.2017.07.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/09/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Chimerogenesis involving cytochromes P450 is a successful approach to generate catalytically self-sufficient enzymes. However, the connection between the different functional modules should allow a certain degree of flexibility in order to obtain functional and catalytically efficient proteins. We previously applied the molecular Lego approach to develop a chimeric P450 3A4 enzyme linked to the reductase domain of P450 BM3 (BMR). Three constructs were designed with the connecting loop containing no glycine, 3 glycine or 5 glycine residues and showed a different catalytic activity and coupling efficiency. Here we investigate how the linker affects the ability of P450 3A4 to bind substrates and inhibitors. We measure the electron transfer rates and the catalytic properties of the enzyme also in the presence of ketoconazole as inhibitor. The data show that the construct 3A4-5GLY-BMR with the longest loop better retains the binding ability and cooperativity for testosterone, compared to P450 3A4. In both 3A4-3GLY-BMR and 3A4-5GLY-BMR, the substrate induces an increase in the first electron transfer rate and a shorter lag phase related to a domain rearrangements, when compared to the construct without Gly. These data are consistent with docking results and secondary structure predictions showing a propensity to form helical structures in the loop of the 3A4-BMR and 3A4-3GLY-BMR. All three chimeras retain the ability to bind the inhibitor ketoconazole and show an IC50 comparable with those reported for the wild type protein. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Silvia Castrignanò
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino, Italy
| | - Serena D'Avino
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino, Italy
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino, Italy
| | - Gianluca Catucci
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino, Italy
| | - Sheila J Sadeghi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, Torino, Italy.
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81
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Basom EJ, Manifold BA, Thielges MC. Conformational Heterogeneity and the Affinity of Substrate Molecular Recognition by Cytochrome P450cam. Biochemistry 2017; 56:3248-3256. [PMID: 28581729 DOI: 10.1021/acs.biochem.7b00238] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The broad and variable substrate specificity of cytochrome P450 enzymes makes them a model system for studying the determinants of protein molecular recognition. The archetypal cytochrome P450cam (P450cam) is a relatively specific P450, a feature once attributed to the high rigidity of its active site. However, increasingly studies have provided evidence of the importance of conformational changes to P450cam activity. Here we used infrared (IR) spectroscopy to investigate the molecular recognition of P450cam. Toward this goal, and to assess the influence of a hydrogen bond (H-bond) between active site residue Y96 and substrates, two variants in which Y96 is replaced by a cyanophenyl (Y96CNF) or phenyl (Y96F) group were characterized in complexes with the substrates camphor, isoborneol, and camphane. These combinations allow for a comparison of complexes in which the moieties on both the protein and substrate can serve as a H-bond donor, acceptor, or neither. The IR spectra of heme-bound CO and the site-specifically incorporated CN of Y96CNF were analyzed to characterize the number and nature of environments in each protein, both in the free and bound states. Although the IR spectra do not support the idea that protein-substrate H-bonding is central to P450cam recognition, the data altogether suggest that the differing conformational heterogeneity in the active site of the P450cam variants and changes in heterogeneity upon binding of different substrates likely contribute to their variable affinities via a conformational selection mechanism. This study further extends our understanding of the molecular recognition of archetypal P450cam and demonstrates the application of IR spectroscopy combined with selective protein modification to delineate protein-ligand interactions.
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Affiliation(s)
- Edward J Basom
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Bryce A Manifold
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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82
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Bolzon LB, dos Santos JS, Silva DB, Crevelin EJ, Moraes LA, Lopes NP, Assis MD. Apigenin-7-O-glucoside oxidation catalyzed by P450-bioinspired systems. J Inorg Biochem 2017; 170:117-124. [PMID: 28236787 DOI: 10.1016/j.jinorgbio.2017.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 02/14/2017] [Accepted: 02/17/2017] [Indexed: 12/30/2022]
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83
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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.
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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
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84
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Allosteric cross-talk in chromatin can mediate drug-drug synergy. Nat Commun 2017; 8:14860. [PMID: 28358030 PMCID: PMC5379107 DOI: 10.1038/ncomms14860] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/07/2017] [Indexed: 12/15/2022] Open
Abstract
Exploitation of drug-drug synergism and allostery could yield superior therapies by capitalizing on the immensely diverse, but highly specific, potential associated with the biological macromolecular landscape. Here we describe a drug-drug synergy mediated by allosteric cross-talk in chromatin, whereby the binding of one drug alters the activity of the second. We found two unrelated drugs, RAPTA-T and auranofin, that yield a synergistic activity in killing cancer cells, which coincides with a substantially greater number of chromatin adducts formed by one of the compounds when adducts from the other agent are also present. We show that this occurs through an allosteric mechanism within the nucleosome, whereby defined histone adducts of one drug promote reaction of the other drug at a distant, specific histone site. This opens up possibilities for epigenetic targeting and suggests that allosteric modulation in nucleosomes may have biological relevance and potential for therapeutic interventions.
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85
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Polic V, Auclair K. Allosteric Activation of Cytochrome P450 3A4 via Progesterone Bioconjugation. Bioconjug Chem 2017; 28:885-889. [PMID: 28339191 DOI: 10.1021/acs.bioconjchem.6b00604] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human cytochrome P450 3A4 (CYP3A4) is responsible for the metabolism of the majority of drugs. As such, it is implicated in many adverse drug-drug and food-drug interactions, and is of significant interest to the pharmaceutical industry. This enzyme is known to simultaneously bind multiple ligands and display atypical enzyme kinetics, suggestive of allostery and cooperativity. As well, evidence of a postulated peripheral allosteric binding site has provoked debate around its significance and location. We report the use of bioconjugation to study the significance of substrate binding at the proposed allosteric site and its effect on CYP3A4 activity. CYP3A4 mutants were created and covalently modified with various small molecules including progesterone. The labeled mutants displayed enhanced kinetic stability and improved activity in testosterone and 7-benzyloxy-(4-trifluoromethyl)coumarin oxidation assays. Our work applies a new strategy to study cytochrome P450 allostery and supports the hypothesis that substrate binding at the postulated allosteric site of CYP3A4 may induce functional cooperativity.
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Affiliation(s)
- Vanja Polic
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Karine Auclair
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
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86
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Marsch GA, Carlson BT, Guengerich FP. 7,8-benzoflavone binding to human cytochrome P450 3A4 reveals complex fluorescence quenching, suggesting binding at multiple protein sites. J Biomol Struct Dyn 2017; 36:841-860. [PMID: 28278026 DOI: 10.1080/07391102.2017.1301270] [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: 01/04/2023]
Abstract
Human cytochrome P450 (P450) 3A4 is involved in the metabolism of one-half of marketed drugs and shows cooperative interactions with some substrates and other ligands. The interaction between P450 3A4 and the known allosteric effector 7,8-benzoflavone (α-naphthoflavone, αNF) was characterized using steady-state fluorescence spectroscopy. The binding interaction of P450 3A4 and αNF effectively quenched the fluorescence of both the enzyme and ligand. The Hill Equation and Stern-Volmer fluorescence quenching models were used to evaluate binding of ligand to enzyme. P450 3A4 fluorescence was quenched by titration with αNF; at the relatively higher [αNF]/[P450 3A4] ratios in this experiment, two weaker quenching interactions were revealed (Kd 1.8-2.5 and 6.5 μM). A range is given for the stronger interaction since αNF quenching of P450 3A4 fluorescence changed the protein spectral profile: quenching of 315 nm emission was slightly more efficient (Kd 1.8 μM) than the quenching of protein fluorescence at 335 and 355 nm (Kd 2.5 and 2.1 μM, respectively). In the reverse titration, αNF fluorescence was quenched by P450 3A4; at the lower [αNF]/[P450 3A4] ratios here, two strong quenching interactions were revealed (Kd 0.048 and 1.0 μM). Thus, four binding interactions of αNF to P450 3A4 are suggested by this study, one of which may be newly recognized and which could affect studies of drug oxidations by this important enzyme.
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Affiliation(s)
- Glenn A Marsch
- a Physics Department , Grove City College , Grove City , PA , 16127-2104 , USA
| | - Benjamin T Carlson
- a Physics Department , Grove City College , Grove City , PA , 16127-2104 , USA
| | - F Peter Guengerich
- b Department of Biochemistry , Vanderbilt University School of Medicine , 638B Robinson Research Building, 2200 Pierce Avenue, Nashville , TN , 37232-0146 , USA
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87
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Du H, Li J, Cai Y, Zhang H, Liu G, Tang Y, Li W. Computational Investigation of Ligand Binding to the Peripheral Site in CYP3A4: Conformational Dynamics and Inhibitor Discovery. J Chem Inf Model 2017; 57:616-626. [DOI: 10.1021/acs.jcim.7b00012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Hanwen Du
- Shanghai Key Laboratory of New Drug Design,
School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Junhao Li
- Shanghai Key Laboratory of New Drug Design,
School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yingchun Cai
- Shanghai Key Laboratory of New Drug Design,
School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Hongxiao Zhang
- Shanghai Key Laboratory of New Drug Design,
School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design,
School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design,
School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design,
School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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88
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Challenges in assignment of allosteric effects in cytochrome P450-catalyzed substrate oxidations to structural dynamics in the hemoprotein architecture. J Inorg Biochem 2017; 167:100-115. [DOI: 10.1016/j.jinorgbio.2016.11.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/17/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
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89
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Watanabe A, Takakusa H, Kimura T, Inoue SI, Kusuhara H, Ando O. Difference in Mechanism-Based Inhibition of Cytochrome P450 3A4 and 3A5 by a Series of Fluoroquinolone Antibacterial Agents. Drug Metab Dispos 2016; 45:336-341. [PMID: 27974381 DOI: 10.1124/dmd.116.073783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 12/13/2016] [Indexed: 11/22/2022] Open
Abstract
A series of fluoroquinolone antibacterial compounds were found to be irreversible (compounds 1-5) and quasi-irreversible (compounds 6-9) inhibitors of CYP3A4. The purpose of this study was to evaluate their mechanism-based inhibition (MBI) potency against CYP3A5. Compounds 1-5 were also irreversible inhibitors of CYP3A5, whereas compounds 6-9 showed neither irreversible nor quasi-irreversible inhibition of CYP3A5. Compounds 6 and 8 did not form a metabolite-intermediate complex with the heme of CYP3A5 during incubation. The structural analysis of the metabolites after incubation of compounds 1 and 6 with CYP3A5 revealed that their metabolites were identical to those produced by CYP3A4, including the precursors of which are speculated to account for the MBI of CYP3A4. The homology modeling of CYP3A5 suggests that four residues around the nitroso intermediate of compound 6 in the substrate-binding pocket of CYP3A4 correspond with the bulkier residues in CYP3A5-especially Phe210 in CYP3A5-which might contribute to the steric hindrance with the nitroso intermediate of compound 6. The substrate-binding pocket structure of CYP3A5 might prevent the nitroso intermediate from coordinate binding with the heme, thereby preventing quasi-irreversible inhibition. Our study may provide new insights into the observable differences between the inhibition of CYP3A4 and CYP3A5.
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Affiliation(s)
- Akiko Watanabe
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Company, Ltd., Tokyo, Japan (A.W., H.T., S.I., O.A.); Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Company, Ltd., Tokyo, Japan (T.K.); and Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan (H.K.)
| | - Hideo Takakusa
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Company, Ltd., Tokyo, Japan (A.W., H.T., S.I., O.A.); Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Company, Ltd., Tokyo, Japan (T.K.); and Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan (H.K.)
| | - Takako Kimura
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Company, Ltd., Tokyo, Japan (A.W., H.T., S.I., O.A.); Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Company, Ltd., Tokyo, Japan (T.K.); and Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan (H.K.)
| | - Shin-Ichi Inoue
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Company, Ltd., Tokyo, Japan (A.W., H.T., S.I., O.A.); Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Company, Ltd., Tokyo, Japan (T.K.); and Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan (H.K.)
| | - Hiroyuki Kusuhara
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Company, Ltd., Tokyo, Japan (A.W., H.T., S.I., O.A.); Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Company, Ltd., Tokyo, Japan (T.K.); and Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan (H.K.)
| | - Osamu Ando
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Company, Ltd., Tokyo, Japan (A.W., H.T., S.I., O.A.); Structural Biology Group, Biological Research Department, Daiichi Sankyo RD Novare Company, Ltd., Tokyo, Japan (T.K.); and Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan (H.K.)
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90
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Chen D, Lin XX, Zhao Q, Xiao J, Peng SF, Xiao MF, Ouyang DS, Tan ZR, Wang YC, Peng JB, Zhang W, Chen Y. Screening of drug metabolizing enzymes for fusidic acid and its interactions with isoform-selective substrates in vitro. Xenobiotica 2016; 47:778-784. [PMID: 27571049 DOI: 10.1080/00498254.2016.1230795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
1. Fusidic acid (FA) is widely used for the treatment of infections of sensitive osteomyelitis or skin and soft tissue caused by bacteria. However, the role of cytochrome P450s (CYPs) in the metabolism of FA is unclear. In the present study, we screened the main CYPs for the metabolism of FA and studied its interactions with isoform-selective substrates in vitro. 2. The main CYP450s were screened according to the inhibitory effect of specific inhibitors on the metabolism of FA in human liver microsomes (HLMs) or recombinant CYP isoforms. Enzyme kinetic parameters including Ki, Ki', Vmax, and IC50 were calculated to determine the potential of FA to affect CYP-mediated metabolism of isoform-selective substrates. 3. FA metabolism rate was inhibited by 49.8% and 83.1% under CYP2D6, CYP3A4 selective inhibitors in HLMs. In recombinant experiment, the inhibitory effects on FA metabolism were 83.3% for CYP2D6 and 58.9% for CYP3A4, respectively. FA showed inhibition on CYP2D6 and CYP3A4 with Kis of 13.9 and 38.6 μM, respectively. Other CYP isoforms including CYP1A2, CYP2A6, CYP2C9, CYP2E1, and CYP2C19 showed minimal or no effect on the metabolism of FA. 4. FA was primarily metabolized by CYP2D6 and CYP3A4 and showed a noncompetitive inhibition on CYP2D6 and a mixed competitive inhibition on CYP3A4. Drug-drug interactions between FA and other chemicals, especially with substrates of CYP2D6 and CYP3A4, are phenomena that clinicians need to be aware of and cautious about.
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Affiliation(s)
- D Chen
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - X-X Lin
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - Q Zhao
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - J Xiao
- c Department of Pharmacy , Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - S-F Peng
- d Department of Hepatology and Infectious Diseases , Xiangya Hospital, Central South University , Changsha , Hunan , China , and.,e Health Management Center, Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - M-F Xiao
- d Department of Hepatology and Infectious Diseases , Xiangya Hospital, Central South University , Changsha , Hunan , China , and.,e Health Management Center, Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - D-S Ouyang
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - Z-R Tan
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - Y-C Wang
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - J-B Peng
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - W Zhang
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
| | - Y Chen
- a Department of Clinical Pharmacology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b Institute of Clinical Pharmacology, Central South University , Changsha , Hunan , China
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91
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Haarhoff ZE, Kramer MA, Zvyaga TA, Zhang J, Bhutani P, Subramanian M, Rodrigues AD. Comprehensive evaluation of liver microsomal cytochrome P450 3A (CYP3A) inhibition: comparison of cynomolgus monkey and human. Xenobiotica 2016; 47:470-478. [DOI: 10.1080/00498254.2016.1203042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | | | | | - Jun Zhang
- Bristol-Myers Squibb, Wallingford, CT, USA,
| | - Priyadeep Bhutani
- Biocon Bristol-Myers Squibb Research and Development Center, Syngene International Limited, Bangalore, Karnataka, India
| | - Murali Subramanian
- Biocon Bristol-Myers Squibb Research and Development Center, Syngene International Limited, Bangalore, Karnataka, India
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92
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Watanabe A, Takakusa H, Kimura T, Inoue SI, Kusuhara H, Ando O. Analysis of Mechanism-Based Inhibition of CYP 3A4 by a Series of Fluoroquinolone Antibacterial Agents. Drug Metab Dispos 2016; 44:1608-16. [DOI: 10.1124/dmd.116.071654] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/27/2016] [Indexed: 11/22/2022] Open
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93
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Meng C, Wei Z, Zhang Y, Yan L, He H, Zhang L, Xing Q. Regulation of cytochrome P450 3A4 by small vault RNAb derived from the non-coding vault RNA1 of multidrug resistance-linked vault particle. Mol Med Rep 2016; 14:387-93. [PMID: 27177257 DOI: 10.3892/mmr.2016.5228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 01/25/2016] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 3A4 (CYP3A4) is the most abundant cytochrome P450 enzyme in human liver and intestine, contributing to the metabolism of >60% of all pharmaceuticals. The expression levels of hepatic CYP3A4 show great inter‑individual variation. However, the detailed regulatory mechanism of CYP3A4 expression has remained largely elusive. It has been reported that the non‑coding RNA small vault (sv)RNAb targets the 3' untranslated region (3'UTR) of CYP3A4 in MCF7 cells. However, to date, the role of svRNAb has not been examined in human liver tissue and hepatic cell lines such as HepG2, which was the aim of the present study. Polymerase chain reaction analysis indicated that the expression of CYP3A4 was significantly different within a study cohort (n=19). In addition, a significant negative correlation was observed between svRNAb and CYP3A4 expression in human liver tissue samples. Furthermore, a luciferase assay on HepG2 cells verified that svRNAb directly targets CYP3A4 and regulates the expression of CYP3A4 by interacting with the validated binding sites of the CYP3A4 3'UTR. The results provided insight into the variation of the expression of CYP3A4 among individuals and provided a novel method for the adjustment of personalized drug treatment. Furthermore, the present study provided a mechanism of the regulatory role of svRNAb in multidrug‑resistant cells.
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Affiliation(s)
- Chunjie Meng
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Zhiyun Wei
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Yiting Zhang
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Liang Yan
- Department of Pharmacology, School of Medicine, Zhengzhou University, Zhengzhou, Henan 450006, P.R. China
| | - Hang He
- Department of Pharmacology, School of Medicine, Zhengzhou University, Zhengzhou, Henan 450006, P.R. China
| | - Lirong Zhang
- Department of Pharmacology, School of Medicine, Zhengzhou University, Zhengzhou, Henan 450006, P.R. China
| | - Qinghe Xing
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
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94
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Ma ZC, Wang YG, Tan HL, Liang QD, Xiao CR, Tang XL, Gao Y. Interactions between drug metabolizing enzymes and traditional Chinese medicine. Shijie Huaren Xiaohua Zazhi 2016; 24:994-1001. [DOI: 10.11569/wcjd.v24.i7.994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Drug metabolizing enzymes are key in determining the fate of drugs, and their inhibitory or inducing effects are the primary mechanism of drug interactions. In this paper, we discuss the method for detecting the interactions between drug metabolizing enzymes and traditional Chinese medicine; identify the possible substrates of drug metabolizing enzymes at the level of active ingredients, effective group and decoction pieces; analyze the effect of traditional Chinese medicine on drug metabolizing enzymes at the levels of mRNA, protein and the enzyme activity, as well as the inhibitory or inducing effects of chemical components on metabolizing enzymes; identify the specific subtype; and clarify the metabolic processes, the basis of compatibility, and interactions between drug metabolizing enzyme and traditional Chinese medicine, with an aim to provide the basis for compatibility and rational administration in clinical practice.
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95
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Potęga A, Fedejko-Kap B, Mazerska Z. Mechanism-based inactivation of human cytochrome P450 1A2 and 3A4 isoenzymes by anti-tumor triazoloacridinone C-1305. Xenobiotica 2016; 46:1056-1065. [PMID: 26928326 DOI: 10.3109/00498254.2016.1147623] [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] [Indexed: 01/16/2023]
Abstract
1. 5-Dimethylaminopropylamino-8-hydroxytriazoloacridinone, C-1305, is a promising anti-tumor therapeutic agent with high activity against several experimental tumors. 2. It was determined to be a potent and selective inhibitor of liver microsomal and human recombinant cytochrome P450 (CYP) 1A2 and 3A4 isoenzymes. Therefore, C-1305 might modulate the effectiveness of other drugs used in multidrug therapy. 3. The objective of this study was to investigate the mechanism of the observed C-1305-mediated inactivation of CYP1A2 and CYP3A4. 4. Our findings indicated that C-1305 produced a time- and concentration-dependent decrease in 7-ethoxycoumarin O-deethylation (CYP1A2, KI = 10.8 ± 2.14 μM) and testosterone 6β-hydroxylation (CYP3A4, KI = 9.1 ± 2.82 μM). The inactivation required the presence of NADPH, was unaffected by a nucleophilic trapping agent (glutathione) and a reactive oxygen species scavenger (catalase), attenuated by a CYP-specific substrate (7-ethoxycoumarin or testosterone), and was not reversed by potassium ferricyanide. The estimated partition ratios of 1086 and 197 were calculated for the inactivation of CYP1A2 and CYP3A4, respectively. 5. In conclusion, C-1305 inhibited human recombinant CYP1A2 and CYP3A4 isoenzymes by mechanism-based inactivation. The obtained knowledge about specific interactions between C-1305 and/or its metabolites, and CYP isoforms would be useful for predicting the possible drug-drug interactions in potent multidrug therapy.
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Affiliation(s)
- Agnieszka Potęga
- a Department of Pharmaceutical Technology and Biochemistry , Chemical Faculty, Gdańsk University of Technology , Gdańsk , Poland
| | - Barbara Fedejko-Kap
- a Department of Pharmaceutical Technology and Biochemistry , Chemical Faculty, Gdańsk University of Technology , Gdańsk , Poland
| | - Zofia Mazerska
- a Department of Pharmaceutical Technology and Biochemistry , Chemical Faculty, Gdańsk University of Technology , Gdańsk , Poland
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Schmölz L, Birringer M, Lorkowski S, Wallert M. Complexity of vitamin E metabolism. World J Biol Chem 2016; 7:14-43. [PMID: 26981194 PMCID: PMC4768118 DOI: 10.4331/wjbc.v7.i1.14] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/25/2015] [Accepted: 01/19/2016] [Indexed: 02/05/2023] Open
Abstract
Bioavailability of vitamin E is influenced by several factors, most are highlighted in this review. While gender, age and genetic constitution influence vitamin E bioavailability but cannot be modified, life-style and intake of vitamin E can be. Numerous factors must be taken into account however, i.e., when vitamin E is orally administrated, the food matrix may contain competing nutrients. The complex metabolic processes comprise intestinal absorption, vascular transport, hepatic sorting by intracellular binding proteins, such as the significant α-tocopherol-transfer protein, and hepatic metabolism. The coordinated changes involved in the hepatic metabolism of vitamin E provide an effective physiological pathway to protect tissues against the excessive accumulation of, in particular, non-α-tocopherol forms. Metabolism of vitamin E begins with one cycle of CYP4F2/CYP3A4-dependent ω-hydroxylation followed by five cycles of subsequent β-oxidation, and forms the water-soluble end-product carboxyethylhydroxychroman. All known hepatic metabolites can be conjugated and are excreted, depending on the length of their side-chain, either via urine or feces. The physiological handling of vitamin E underlies kinetics which vary between the different vitamin E forms. Here, saturation of the side-chain and also substitution of the chromanol ring system are important. Most of the metabolic reactions and processes that are involved with vitamin E are also shared by other fat soluble vitamins. Influencing interactions with other nutrients such as vitamin K or pharmaceuticals are also covered by this review. All these processes modulate the formation of vitamin E metabolites and their concentrations in tissues and body fluids. Differences in metabolism might be responsible for the discrepancies that have been observed in studies performed in vivo and in vitro using vitamin E as a supplement or nutrient. To evaluate individual vitamin E status, the analytical procedures used for detecting and quantifying vitamin E and its metabolites are crucial. The latest methods in analytics are presented.
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98
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Maldonado A, Johnson A, Gochfeld D, Slattery M, Ostrander GK, Bingham JP, Schlenk D. Hard coral (Porites lobata) extracts and homarine on cytochrome P450 expression in Hawaiian butterflyfishes with different feeding strategies. Comp Biochem Physiol C Toxicol Pharmacol 2016; 179:57-63. [PMID: 26297807 DOI: 10.1016/j.cbpc.2015.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/07/2015] [Accepted: 08/10/2015] [Indexed: 12/27/2022]
Abstract
Dietary specialists tend to be less susceptible to the effects of chemical defenses produced by their prey compared to generalist predators that feed upon a broader range of prey species. While many researchers have investigated the ability of insects to detoxify dietary allelochemicals, little research has been conducted in marine ecosystems. We investigated metabolic detoxification pathways in three species of butterflyfishes: the hard coral specialist feeder, Chaetodon multicinctus, and two generalist feeders, Chaetodon auriga and Chaetodon kleinii. Each species was fed tissue homogenate of the hard coral Porites lobata or the feeding deterrent compound homarine (found in the coral extract), and the expression and catalytic activity of cytochrome P450 (CYP) 3A-like and CYP2-like enzymes were examined after one-week of treatment. The P. lobata homogenate significantly induced content and catalytic activity of CYP2-like and CYP3A-like forms, by 2-3 fold and by 3-9 fold, respectively, in C. multicinctus. Homarine caused a significant decrease of CYP2-like and CYP3A-like proteins at the high dose in C. kleinii and 60-80% mortality in that species. Homarine also induced CYP3A-like content by 3-fold and catalytic activity by 2-fold in C. auriga, while causing non-monotonic increases in CYP2-like and CYP3A-like catalytic activity in C. multicinctus. Our results indicate that dietary exposure to coral homogenates and the feeding deterrent constituent within these homogenates caused species-specific modulation of detoxification enzymes consistent with the prey selection strategies of generalist and specialist butterflyfishes.
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Affiliation(s)
- Aileen Maldonado
- Department of Environmental Science, University of California, Riverside, 2258 Geology, 900 University Ave., Riverside, CA 92521, USA.
| | - Amber Johnson
- Department of Environmental Science, University of California, Riverside, 2258 Geology, 900 University Ave., Riverside, CA 92521, USA
| | - Deborah Gochfeld
- National Center for Natural Products Research and Department of BioMolecular Science, University of Mississippi, P.O. Box 1848, University, MS 38677, USA
| | - Marc Slattery
- National Center for Natural Products Research and Department of BioMolecular Science, University of Mississippi, P.O. Box 1848, University, MS 38677, USA
| | - Gary K Ostrander
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306-1330, USA
| | - Jon-Paul Bingham
- Department of Molecular Bioscience and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Ag. Science 218, Honolulu, HI 96822, USA
| | - Daniel Schlenk
- Department of Environmental Science, University of California, Riverside, 2258 Geology, 900 University Ave., Riverside, CA 92521, USA
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99
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Denisov IG, Mak PJ, Grinkova YV, Bastien D, Bérubé G, Sligar SG, Kincaid JR. The use of isomeric testosterone dimers to explore allosteric effects in substrate binding to cytochrome P450 CYP3A4. J Inorg Biochem 2015; 158:77-85. [PMID: 26774838 DOI: 10.1016/j.jinorgbio.2015.12.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/07/2015] [Accepted: 12/28/2015] [Indexed: 02/06/2023]
Abstract
Cytochrome P450 CYP3A4 is the main drug-metabolizing enzyme in the human liver, being responsible for oxidation of 50% of all pharmaceuticals metabolized by human P450 enzymes. Possessing a large substrate binding pocket, it can simultaneously bind several substrate molecules and often exhibits a complex pattern of drug-drug interactions. In order to better understand structural and functional aspects of binding of multiple substrate molecules to CYP3A4 we used resonance Raman and UV-VIS spectroscopy to document the effects of binding of synthetic testosterone dimers of different configurations, cis-TST2 and trans-TST2. We directly demonstrate that the binding of two steroid molecules, which can assume multiple possible configurations inside the substrate binding pocket of monomeric CYP3A4, can lead to active site structural changes that affect functional properties. Using resonance Raman spectroscopy, we have documented perturbations in the ferric and Fe-CO states by these substrates, and compared these results with effects caused by binding of monomeric TST. While the binding of trans-TST2 yields results similar to those obtained with monomeric TST, the binding of cis-TST2 is much tighter and results in significantly more pronounced conformational changes of the porphyrin side chains and Fe-CO unit. In addition, binding of an additional monomeric TST molecule in the remote allosteric site significantly improves binding affinity and the overall spin shift for CYP3A4 with trans-TST2 dimer bound inside the substrate binding pocket. This result provides the first direct evidence for an allosteric effect of the peripheral binding site at the protein-membrane interface on the functional properties of CYP3A4.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States.
| | - Piotr J Mak
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, United States.
| | - Yelena V Grinkova
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States.
| | - Dominic Bastien
- Département de chimie, biochimie et physique, Université du Québec à Trois-Rivières, Trois-Rivières, Québec G9A 5H7, Canada.
| | - Gervais Bérubé
- Département de chimie, biochimie et physique, Université du Québec à Trois-Rivières, Trois-Rivières, Québec G9A 5H7, Canada.
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States; Department of Chemistry, University of Illinois, Urbana, IL 61801, United States.
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, United States.
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A Combined Molecular Docking/Dynamics Approach to Probe the Binding Mode of Cancer Drugs with Cytochrome P450 3A4. Molecules 2015; 20:14915-35. [PMID: 26287147 PMCID: PMC6332164 DOI: 10.3390/molecules200814915] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 12/23/2022] Open
Abstract
Cytarabine, daunorubicin, doxorubicin and vincristine are clinically used for combinatorial therapies of cancers in different combinations. However, the knowledge about the interaction of these drugs with the metabolizing enzyme cytochrome P450 is limited. Therefore, we utilized computational methods to predict and assess the drug-binding modes. In this study, we performed docking, MD simulations and free energy landscape analysis to understand the drug-enzyme interactions, protein domain motions and the most populated free energy minimum conformations of the docked protein-drug complexes, respectively. The outcome of docking and MD simulations predicted the productive, as well as the non-productive binding modes of the selected drugs. Based on these interaction studies, we observed that S119, R212 and R372 are the major drug-binding residues in CYP3A4. The molecular mechanics Poisson–Boltzmann surface area analysis revealed the dominance of hydrophobic forces in the CYP3A4-drug association. Further analyses predicted the residues that may contain favorable drug-specific interactions. The probable binding modes of the cancer drugs from this study may extend the knowledge of the protein-drug interaction and pave the way to design analogs with reduced toxicity. In addition, they also provide valuable insights into the metabolism of the cancer drugs.
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