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Ackad EM, Biggers L, Meister M, Kontoyianni M. Equilibrium landscape of ingress/egress channels and gating residues of the Cytochrome P450 3A4. PLoS One 2024; 19:e0298424. [PMID: 38498575 PMCID: PMC10947690 DOI: 10.1371/journal.pone.0298424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 01/24/2024] [Indexed: 03/20/2024] Open
Abstract
The Cytochrome P450 (CYP) enzymes metabolize a variety of drugs, which may potentially lead to toxicity or reduced efficacy when drugs are co-administered. These drug-drug interactions are often manifested by CYP3A4, the most prevalent of all CYP isozymes. We carried out multiple MD simulations employing CAVER to quantify the channels, and Hidden Markov Models (HMM) to characterize the behavior of the gating residues. We discuss channel properties, bottleneck residues with respect to their likelihood to deem the respective channel ingress or egress, gating residues regarding their open or closed states, and channel location relative to the membrane. Channels do not display coordinated motion and randomly transition between different conformations. Gateway residues also behave in a random fashion. Our findings shed light on the equilibrium behavior of the gating residues and channels in the apo state.
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Affiliation(s)
- Edward Michael Ackad
- Department of Physics, Southern Illinois University Edwardsville, Edwardsville, IL, United States of America
| | - Laurence Biggers
- Department of Internal Medicine at UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Mary Meister
- University of Illinois College of Medicine, Chicago, IL, United States of America
| | - Maria Kontoyianni
- Department of Pharmaceutical Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, United States of America
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Connick JP, Reed JR, Cawley GF, Saha A, Backes WL. Functional characterization of CYP1 enzymes: Complex formation, membrane localization and function. J Inorg Biochem 2023; 247:112325. [PMID: 37479567 PMCID: PMC10529082 DOI: 10.1016/j.jinorgbio.2023.112325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/19/2023] [Accepted: 07/09/2023] [Indexed: 07/23/2023]
Abstract
CYP1A1, CYP1A2, and CYP1B1 have a high degree of sequence similarity, similar substrate selectivities and induction characteristics. However, experiments suggest that there are significant differences in their quaternary structures and function. The goal of this study was to characterize the CYP1 proteins regarding their ability to form protein-protein complexes, lipid microdomain localization, and ultimately function. This was accomplished by examining (1) substrate metabolism of the CYP1s as a function of NADPH-cytochrome P450 reductase (POR) concentration, and (2) quaternary structure, using bioluminescence resonance energy transfer (BRET). Both CYP1As were able to form BRET-detectable homomeric complexes, which was not observed with CYP1B1. When activities were measured as a function of [POR], CYP1A1 and CYP1B1 showed a hyperbolic response, consistent with mass-action binding; however, CYP1A2 produced a sigmoidal response, suggesting that the homomeric complex affected its function. Differences were observed in their ability to form heteromeric complexes. Whereas CYP1B1 and CYP1A1 formed a complex, neither the CYP1A1/CYP1A2 nor the CYP1B1/CYP1A2 pair formed BRET-detectable complexes. These proteins also differed in their lipid microdomain localization, with CYP1A2 and CYP1B1 residing in ordered membranes, and CYP1A1 in the disordered lipid regions. Taken together, despite their sequence similarities, there are substantial differences in quaternary structures and microdomain localization that can influence enzymatic activities. As these proteins exist in the endoplasmic reticulum with other ER-resident proteins, the P450s need to be considered as part of multi-enzyme systems rather than simply monomeric proteins interacting with their redox partners.
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Affiliation(s)
- J Patrick Connick
- Department of Pharmacology and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center -, New Orleans, LA 70112, USA
| | - James R Reed
- Department of Pharmacology and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center -, New Orleans, LA 70112, USA
| | - George F Cawley
- Department of Pharmacology and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center -, New Orleans, LA 70112, USA
| | - Aratrika Saha
- Department of Pharmacology and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center -, New Orleans, LA 70112, USA
| | - Wayne L Backes
- Department of Pharmacology and the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center -, New Orleans, LA 70112, USA.
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Korzekwa K. Enzyme Kinetics of Oxidative Metabolism-Cytochromes P450. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2342:237-256. [PMID: 34272697 DOI: 10.1007/978-1-0716-1554-6_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The cytochrome P450 enzymes (CYPs) are the most important enzymes in the oxidative metabolism of hydrophobic drugs and other foreign compounds (xenobiotics). The versatility of these enzymes results in some unusual kinetic properties, stemming from the simultaneous interaction of multiple substrates with the CYP active site. Often, the CYPs display kinetics that deviate from standard hyperbolic saturation or inhibition kinetics. Non-Michaelis-Menten or "atypical" saturation kinetics include sigmoidal, biphasic, and substrate inhibition kinetics (see Chapter 2 ). Interactions between substrates include competitive inhibition, noncompetitive inhibition, mixed inhibition, partial inhibition, activation, and activation followed by inhibition (see Chapters 4 and 6 ). Models and equations that can result in these kinetic profiles will be presented and discussed.
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Affiliation(s)
- Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, PA, USA.
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Koroleva PI, Kuzikov AV, Masamrekh RA, Filimonov DA, Dmitriev AV, Zaviyalova MG, Rikova SM, Shich EV, Makhova AA, Bulko TV, Gilep AA, Shumyantseva VV. Modeling of Drug-Drug Interactions between Omeprazole and Erythromycin in the Cytochrome P450-Dependent System In vitro. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2021. [DOI: 10.1134/s1990750821010030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Yonemura K, Ariyasu S, Stanfield JK, Suzuki K, Onoda H, Kasai C, Sugimoto H, Aiba Y, Watanabe Y, Shoji O. Systematic Evolution of Decoy Molecules for the Highly Efficient Hydroxylation of Benzene and Small Alkanes Catalyzed by Wild-Type Cytochrome P450BM3. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01951] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kai Yonemura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shinya Ariyasu
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Joshua Kyle Stanfield
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazuto Suzuki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hiroki Onoda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Chie Kasai
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hiroshi Sugimoto
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yoshihito Watanabe
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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6
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Koroleva PI, Kuzikov AV, Masamrekh RA, Filimonov DA, Dmitriev AV, Zaviyalova MG, Rikova SM, Shich EV, Makhova AA, Bulko TV, Gilep AA, Shumyantseva VV. [Modeling of drug-drug interactions between omeprazole and erythromycin with cytochrome P450 3A4 in vitro assay]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2020; 66:241-249. [PMID: 32588830 DOI: 10.18097/pbmc20206603241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the present study the electrochemical system based on recombinant cytochrome P450 3A4 (CYP3A4) was used for the investigation of potential drug-drug interaction between medicinal preparations employed for Helicobacter pylori eradication therapy. Drug interactions were demonstrated in association of omeprazole as a proton pump inhibitor (PPI) and macrolide antibiotic erythromycin during cytochrome P450 3A4-mediated metabolism. It was shown that in the presence of omeprazole the rate of N-demethylase activity of CYP3A4 to erythromycin measured by means of product (formaldehyde) formation decreased. Mass-spectrometry analysis of omeprazole sulfone as a CYP3A4-mediated metabolite demonstrated the absence of erythromycin influence on CYP3A4-dependent omeprazole metabolism. This phenomenon may be explained by lower spectral dissociation constant of CYP3A4-omeprazole complex (Kd = 18±2 μM) than that of CYP3A4-erythromycin complex (Kd = 52 μM). Using the electrochemical model of electrochemically-driven drug metabolism it is possible to register CYP3A4-mediated catalytic conversion of certain drugs. In vitro experiments of potential CYP3A4-mediated drug-drug interactions are in accordance with in silico modeling with program PASS and PoSMNA descriptors in the case of omeprazole/erythromycin combinations.
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Affiliation(s)
- P I Koroleva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A V Kuzikov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | - R A Masamrekh
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | | | - A V Dmitriev
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - S M Rikova
- Sechenov First Moscow Medical State University (Sechenov University), Moscow, Russia
| | - E V Shich
- Sechenov First Moscow Medical State University (Sechenov University), Moscow, Russia
| | - A A Makhova
- Sechenov First Moscow Medical State University (Sechenov University), Moscow, Russia
| | - T V Bulko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A A Gilep
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - V V Shumyantseva
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
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7
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Ramsden D, Fung C, Hariparsad N, Kenny JR, Mohutsky M, Parrott NJ, Robertson S, Tweedie DJ. Perspectives from the Innovation and Quality Consortium Induction Working Group on Factors Impacting Clinical Drug-Drug Interactions Resulting from Induction: Focus on Cytochrome 3A Substrates. Drug Metab Dispos 2019; 47:1206-1221. [PMID: 31439574 DOI: 10.1124/dmd.119.087270] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022] Open
Abstract
A recent publication from the Innovation and Quality Consortium Induction Working Group collated a large clinical data set with the goal of evaluating the accuracy of drug-drug interaction (DDI) prediction from in vitro data. Somewhat surprisingly, comparison across studies of the mean- or median-reported area under the curve ratio showed appreciable variability in the magnitude of outcome. This commentary explores the possible drivers of this range of outcomes observed in clinical induction studies. While recommendations on clinical study design are not being proposed, some key observations were informative during the aggregate analysis of clinical data. Although DDI data are often presented using median data, individual data would enable evaluation of how differences in study design, baseline expression, and the number of subjects contribute. Since variability in perpetrator pharmacokinetics (PK) could impact the overall DDI interpretation, should this be routinely captured? Maximal induction was typically observed after 5-7 days of dosing. Thus, when the half-life of the inducer is less than 30 hours, are there benefits to a more standardized study design? A large proportion of CYP3A4 inducers were also CYP3A4 inhibitors and/or inactivators based on in vitro data. In these cases, using CYP3A selective substrates has limitations. More intensive monitoring of changes in area under the curve over time is warranted. With selective CYP3A substrates, the net effect was often inhibition, whereas less selective substrates could discern induction through mechanisms not susceptible to inhibition. The latter included oral contraceptives, which raise concerns of reduced efficacy following induction. Alternative approaches for modeling induction, such as applying biomarkers and physiologically based pharmacokinetic modeling (PBPK), are also considered. SIGNIFICANCE STATEMENT: The goal of this commentary is to stimulate discussion on whether there are opportunities to optimize clinical drug-drug interaction study design. The overall aim is to reduce, understand and contextualize the variability observed in the magnitude of induction across reported clinical studies. A large clinical CYP3A induction dataset was collected and further analyzed to identify trends and gaps. Reporting individual victim PK data, characterizing perpetrator PK and including additional PK assessments for mixed-mechanism perpetrators may provide insights into how these factors impact differences observed in clinical outcomes. The potential utility of biomarkers and PBPK modeling are discussed in considering future directions.
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Affiliation(s)
- Diane Ramsden
- Alnylam Pharmaceuticals, Cambridge, Massachusetts (D.R.); Vertex Pharmaceuticals, Boston, Massachusetts (C.F., N.H., S.R.); Genentech, South San Francisco, California (J.R.K.); Eli Lilly and Company, Indianapolis, Indiana (M.M.); Roche Innovation Center, Basel, Switzerland (N.J.P.); and Merck & Co., Inc., Kenilworth, New Jersey (D.T.)
| | - Conrad Fung
- Alnylam Pharmaceuticals, Cambridge, Massachusetts (D.R.); Vertex Pharmaceuticals, Boston, Massachusetts (C.F., N.H., S.R.); Genentech, South San Francisco, California (J.R.K.); Eli Lilly and Company, Indianapolis, Indiana (M.M.); Roche Innovation Center, Basel, Switzerland (N.J.P.); and Merck & Co., Inc., Kenilworth, New Jersey (D.T.)
| | - Niresh Hariparsad
- Alnylam Pharmaceuticals, Cambridge, Massachusetts (D.R.); Vertex Pharmaceuticals, Boston, Massachusetts (C.F., N.H., S.R.); Genentech, South San Francisco, California (J.R.K.); Eli Lilly and Company, Indianapolis, Indiana (M.M.); Roche Innovation Center, Basel, Switzerland (N.J.P.); and Merck & Co., Inc., Kenilworth, New Jersey (D.T.)
| | - Jane R Kenny
- Alnylam Pharmaceuticals, Cambridge, Massachusetts (D.R.); Vertex Pharmaceuticals, Boston, Massachusetts (C.F., N.H., S.R.); Genentech, South San Francisco, California (J.R.K.); Eli Lilly and Company, Indianapolis, Indiana (M.M.); Roche Innovation Center, Basel, Switzerland (N.J.P.); and Merck & Co., Inc., Kenilworth, New Jersey (D.T.)
| | - Michael Mohutsky
- Alnylam Pharmaceuticals, Cambridge, Massachusetts (D.R.); Vertex Pharmaceuticals, Boston, Massachusetts (C.F., N.H., S.R.); Genentech, South San Francisco, California (J.R.K.); Eli Lilly and Company, Indianapolis, Indiana (M.M.); Roche Innovation Center, Basel, Switzerland (N.J.P.); and Merck & Co., Inc., Kenilworth, New Jersey (D.T.)
| | - Neil J Parrott
- Alnylam Pharmaceuticals, Cambridge, Massachusetts (D.R.); Vertex Pharmaceuticals, Boston, Massachusetts (C.F., N.H., S.R.); Genentech, South San Francisco, California (J.R.K.); Eli Lilly and Company, Indianapolis, Indiana (M.M.); Roche Innovation Center, Basel, Switzerland (N.J.P.); and Merck & Co., Inc., Kenilworth, New Jersey (D.T.)
| | - Sarah Robertson
- Alnylam Pharmaceuticals, Cambridge, Massachusetts (D.R.); Vertex Pharmaceuticals, Boston, Massachusetts (C.F., N.H., S.R.); Genentech, South San Francisco, California (J.R.K.); Eli Lilly and Company, Indianapolis, Indiana (M.M.); Roche Innovation Center, Basel, Switzerland (N.J.P.); and Merck & Co., Inc., Kenilworth, New Jersey (D.T.)
| | - Donald J Tweedie
- Alnylam Pharmaceuticals, Cambridge, Massachusetts (D.R.); Vertex Pharmaceuticals, Boston, Massachusetts (C.F., N.H., S.R.); Genentech, South San Francisco, California (J.R.K.); Eli Lilly and Company, Indianapolis, Indiana (M.M.); Roche Innovation Center, Basel, Switzerland (N.J.P.); and Merck & Co., Inc., Kenilworth, New Jersey (D.T.)
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8
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Hackett JC. Membrane-embedded substrate recognition by cytochrome P450 3A4. J Biol Chem 2018; 293:4037-4046. [PMID: 29382727 DOI: 10.1074/jbc.ra117.000961] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/26/2018] [Indexed: 12/15/2022] Open
Abstract
Cytochrome P450 3A4 (CYP3A4) is the dominant xenobiotic-metabolizing enzyme in the liver and intestine and is involved in the disposition of more than 50% of drugs. Because of its ability to bind multiple substrates, its reaction kinetics are complex, and its association with the microsomal membrane confounds our understanding of how this enzyme recognizes and recruits diverse substrates. Testosterone (TST) hydroxylation is the prototypical CYP3A4 reaction, displaying positive homotropic cooperativity with three binding sites. Here, exploiting the capability of accelerated molecular dynamics (aMD) to sample events in the millisecond regime, I performed >25-μs aMD simulations in the presence of three TST molecules. These simulations identified high-occupancy surface-binding sites as well as a pathway for TST ingress into the CYP3A4 active site originating in the membrane. Adaptive biasing force analysis of the latter pathway revealed a metastable intermediate that could constitute a third binding site at high TST concentrations. Prompted by the observation that interactions between TST and the G'-helix mobilize the ligand into the active site, a free-energy analysis of TST distribution in the membrane was conducted and revealed that the depth of the G'-helix is optimal for extracting TST. In summary, these simulations confirm separate, but adjacent substrate-binding sites within the enzyme and the existence of an auxiliary TST-binding site. The broader impact of these simulations is that they support a mechanism in which cytochromes P450 directly recruit membrane-solubilized substrates.
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Affiliation(s)
- John C Hackett
- From the Department of Physiology and Biophysics and the Massey Cancer Center, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298-0035
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9
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Rowland A, van Dyk M, Warncken D, Mangoni AA, Sorich MJ, Rowland A. Evaluation of modafinil as a perpetrator of metabolic drug-drug interactions using a model informed cocktail reaction phenotyping trial protocol. Br J Clin Pharmacol 2018; 84:501-509. [PMID: 29178272 DOI: 10.1111/bcp.13478] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/19/2017] [Accepted: 11/13/2017] [Indexed: 01/01/2023] Open
Abstract
AIM To evaluate the capacity for modafinil to be a perpetrator of metabolic drug-drug interactions by altering cytochrome P450 activity following a single dose and dosing to steady state. METHODS A single centre, open label, single sequence cocktail drug interaction trial. On days 0, 2 and 8 participants were administered an oral drug cocktail comprising 100 mg caffeine, 30 mg dextromethorphan, 25 mg losartan, 1 mg midazolam and 20 mg enteric-coated omeprazole. Timed blood samples were collected prior to and for up to 6 h post cocktail dosing. Between days 2 and 8 participants orally self-administered 200 mg modafinil each morning. RESULTS Following a single 200 mg dose of modafinil mean (± 95% CI) AUC ratios for caffeine, dextromethorphan, losartan, midazolam and omeprazole were 0.95 (± 0.08), 1.01 (± 0.35), 0.97 (± 0.10), 0.98 (± 0.10) and 1.36 (± 0.06), respectively. Following dosing of modafinil to steady state (200 mg for 7 days), AUC ratios for caffeine, dextromethorphan, losartan, midazolam and omeprazole were 0.90 (± 0.16), 0.79 (± 0.09), 0.98 (± 0.11), 0.66 (± 0.12) and 1.90 (± 0.53), respectively. CONCLUSIONS These data support consideration of the risk of clinically relevant metabolic drug-drug interactions perpetrated by modafinil when this drug is co-administered with drugs that are primarily cleared by CYP2C19 (single modafinil dose or steady state modafinil dosing) or CYP3A4 (steady state modafinil dosing only) catalysed metabolic pathways.
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Affiliation(s)
- Angela Rowland
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Madelé van Dyk
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - David Warncken
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Arduino A Mangoni
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Michael J Sorich
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Andrew Rowland
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, Australia
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10
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Denisov IG, Baylon JL, Grinkova YV, Tajkhorshid E, Sligar SG. Drug-Drug Interactions between Atorvastatin and Dronedarone Mediated by Monomeric CYP3A4. Biochemistry 2017; 57:805-816. [PMID: 29200287 DOI: 10.1021/acs.biochem.7b01012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Heterotropic interactions between atorvastatin (ARVS) and dronedarone (DND) have been deciphered using global analysis of the results of binding and turnover experiments for pure drugs and their mixtures. The in vivo presence of atorvastatin lactone (ARVL) was explicitly taken into account by using pure ARVL in analogous experiments. Both ARVL and ARVS inhibit DND binding and metabolism, while a significantly higher affinity of CYP3A4 for ARVL makes the latter the main modulator of activity (effector) in this system. Molecular dynamics simulations reveal significantly different modes of interactions of DND and ARVL with the substrate binding pocket and with a peripheral allosteric site. Interactions of both substrates with residues F213 and F219 at the allosteric site play a critical role in the communication of conformational changes induced by effector binding to productive binding of the substrate at the catalytic site.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, ‡Center for Biophysics and Quantitative Biology, and §Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Javier L Baylon
- Department of Biochemistry, ‡Center for Biophysics and Quantitative Biology, and §Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Yelena V Grinkova
- Department of Biochemistry, ‡Center for Biophysics and Quantitative Biology, and §Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, ‡Center for Biophysics and Quantitative Biology, and §Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry, ‡Center for Biophysics and Quantitative Biology, and §Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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11
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Bondarenko LB, Shayakhmetova GM, Voronina AK, Kovalenko VM. Age-dependent features of CYP3A, CYP2C, and CYP2E1 functioning at metabolic syndrome. J Basic Clin Physiol Pharmacol 2017; 27:603-610. [PMID: 27371822 DOI: 10.1515/jbcpp-2016-0012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/04/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Complex investigations of cytochrome P450 (CYP) isoforms with metabolic syndrome (MS) development are limited, and specific features of adolescent's metabolisms are generally disregarded. The aim of present study was a comparative estimation of MS-mediated changes in CYP3A, CYP2C, and CYP2E1 mRNA expression and enzymatic activities, as well as antioxidant system parameters of adult and pubertal rats. METHODS Wistar albino male rats of two age categories [young animals of 21 days age (50-70 g) and adults (160-180 g)] were divided into four groups (eight animals in each group): (1) control 1 (intact young rats), (2) control 2 (intact adult rats), (3) MS3 (young rats with MS), and (4) MS4 (adult rats with MS). The MS was induced by full replacement of drinking water by 20% fructose solution (200 g/L). After 60 days of MS modeling, the investigation of rat liver CYP3A, CYP2C, and CYP2E1 mRNA expressions, their enzyme-marker activities, as well as the antioxidant system parameters was conducted. RESULTS Levels of liver CYP2E1 mRNA expression increased with MS: 40% (adults) and 80% (pubertal rats). Pubertal rats had also increased CYP3A2 mRNA expression (30%) and decreased CYP2C mRNA expression (30%). Changes in CYP2E1 and CYP2C enzymatic activities were consistent with the changes of corresponding gene expressions at both age-groups with MS. Simultaneously, liver reduced glutathione contents, and glutathione transferase and reductase activities were decreased in pubertal animals. CONCLUSIONS CYP isoform expression rates and glutathione system were greatly violated with MS. The greater changes were observed in pubertal rats with MS.
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12
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Lee E, Shon JC, Liu KH. Simultaneous evaluation of substrate-dependent CYP3A inhibition using a CYP3A probe substrates cocktail. Biopharm Drug Dispos 2017; 37:366-72. [PMID: 27323294 DOI: 10.1002/bdd.2019] [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] [Received: 05/03/2016] [Revised: 06/13/2016] [Accepted: 06/15/2016] [Indexed: 02/03/2023]
Abstract
Cytochrome P450 (P450) 3A (CYP3A) is an enzyme responsible for the metabolism of therapeutic drugs such as midazolam, nifedipine, testosterone and triazolam. It is involved in 40% of all cases of P450-mediated metabolism of marketed drugs. Therefore, it is important to evaluate the CYP3A-mediated drug interaction potential of new chemical entities (NCEs). In the past, one P450 isoform-specific probe substrate has been used at a time to evaluate the degree of inhibition of P450 isoforms by using liquid chromatography-tandem mass spectrometry (LC-MS/MS). However, CYP3A enzymes have been shown to have a multi-substrate binding site. Therefore, multiple CYP3A substrates should be used to evaluate precisely the drug interaction potential of NCEs with the enzyme CYP3A. In this study, a method of screening NCEs for their potential to inhibit by CYP3A enzyme activity was developed. It involves the employment of a CYP3A substrate cocktail (including midazolam, testosterone and nifedipine). The concentration of each CYP3A probe substrate in vitro was optimized (0.1 μm for midazolam, 2 μm for testosterone and 2 μm for nifedipine) to minimize mutual drug interactions among probe substrates. The method was validated by comparing inhibition data obtained from the incubation of CYP3A with each individual substrate with data from incubation with a cocktail of all three substrates. The CYP3A inhibition profiles from the substrate cocktail approach were similar to those from the individual substrates approach. This new method could be an effective tool for the robust and accurate screening of the CYP3A inhibition potential of NCEs in drug discovery. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Eunyoung Lee
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Jong Cheol Shon
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Kwang-Hyeon Liu
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 41566, South Korea.
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Reed JR, Backes WL. Physical Studies of P450-P450 Interactions: Predicting Quaternary Structures of P450 Complexes in Membranes from Their X-ray Crystal Structures. Front Pharmacol 2017; 8:28. [PMID: 28194112 PMCID: PMC5276844 DOI: 10.3389/fphar.2017.00028] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/16/2017] [Indexed: 01/15/2023] Open
Abstract
Cytochrome P450 enzymes, which catalyze oxygenation reactions of both exogenous and endogenous chemicals, are membrane bound proteins that require interaction with their redox partners in order to function. Those responsible for drug and foreign compound metabolism are localized primarily in the endoplasmic reticulum of liver, lung, intestine, and other tissues. More recently, the potential for P450 enzymes to exist as supramolecular complexes has been shown by the demonstration of both homomeric and heteromeric complexes. The P450 units in these complexes are heterogeneous with respect to their distribution and function, and the interaction of different P450s can influence P450-specific metabolism. The goal of this review is to examine the evidence supporting the existence of physical complexes among P450 enzymes. Additionally, the review examines the crystal lattices of different P450 enzymes derived from X-ray diffraction data to make assumptions regarding possible quaternary structures in membranes and in turn, to predict how the quaternary structures could influence metabolism and explain the functional effects of specific P450-P450 interactions.
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Affiliation(s)
- James R Reed
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans LA, USA
| | - Wayne L Backes
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans LA, USA
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Allosteric activation of midazolam CYP3A5 hydroxylase activity by icotinib – Enhancement by ketoconazole. Biochem Pharmacol 2016; 121:67-77. [DOI: 10.1016/j.bcp.2016.09.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 09/15/2016] [Indexed: 11/20/2022]
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Banerjee S, Goyal S, Mazumdar S. Role of substituents on the reactivity and product selectivity in reactions of naphthalene derivatives catalyzed by the orphan thermostable cytochrome P450, CYP175A1. Bioorg Chem 2015; 62:94-105. [DOI: 10.1016/j.bioorg.2015.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 08/13/2015] [Accepted: 08/17/2015] [Indexed: 11/28/2022]
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Denisov IG, Grinkova YV, Baylon JL, Tajkhorshid E, Sligar SG. Mechanism of drug-drug interactions mediated by human cytochrome P450 CYP3A4 monomer. Biochemistry 2015; 54:2227-39. [PMID: 25777547 DOI: 10.1021/acs.biochem.5b00079] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Using Nanodiscs, we quantitate the heterotropic interaction between two different drugs mediated by monomeric CYP3A4 incorporated into a nativelike membrane environment. The mechanism of this interaction is deciphered by global analysis of multiple-turnover experiments performed under identical conditions using the pure substrates progesterone (PGS) and carbamazepine (CBZ) and their mixtures. Activation of CBZ epoxidation and simultaneous inhibition of PGS hydroxylation are measured and quantitated through differences in their respective affinities for both a remote allosteric site and the productive catalytic site near the heme iron. Preferred binding of PGS at the allosteric site and a stronger preference for CBZ binding at the productive site give rise to a nontrivial drug-drug interaction. Molecular dynamics simulations indicate functionally important conformational changes caused by PGS binding at the allosteric site and by two CBZ molecules positioned inside the substrate binding pocket. Structural changes involving Phe-213, Phe-219, and Phe-241 are thought to be responsible for the observed synergetic effects and positive allosteric interactions between these two substrates. Such a mechanism is likely of general relevance to the mutual heterotropic effects caused by biologically active compounds that exhibit different patterns of interaction with the distinct allosteric and productive sites of CYP3A4, as well as other xenobiotic metabolizing cytochromes P450 that are also involved in drug-drug interactions. Importantly, this work demonstrates that a monomeric CYP3A4 can display the full spectrum of activation and cooperative effects that are observed in hepatic membranes.
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Affiliation(s)
- Ilia G Denisov
- †Department of Biochemistry, ‡Center for Biophysics and Computational Biology, and §Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yelena V Grinkova
- †Department of Biochemistry, ‡Center for Biophysics and Computational Biology, and §Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Javier L Baylon
- †Department of Biochemistry, ‡Center for Biophysics and Computational Biology, and §Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- †Department of Biochemistry, ‡Center for Biophysics and Computational Biology, and §Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- †Department of Biochemistry, ‡Center for Biophysics and Computational Biology, and §Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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He F, Zhang W, Zeng C, Xia C, Xiong Y, Zhang H, Huang S, Liu M. Mechanism of Action of Panaxytriol on Midazolam 1′-Hydroxylation and 4-Hydroxylation Mediated by CYP3A in Liver Microsomes and Rat Primary Hepatocytes. Biol Pharm Bull 2015; 38:1470-7. [DOI: 10.1248/bpb.b15-00143] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Fang He
- Clinical Pharmacology Institute, Nanchang University/Jiangxi Province Key Lab of Clinical Pharmacokinetics
- Jiangxi Province Cancer Hospital
| | - Wen Zhang
- Clinical Pharmacology Institute, Nanchang University/Jiangxi Province Key Lab of Clinical Pharmacokinetics
| | - Caiwen Zeng
- Clinical Pharmacology Institute, Nanchang University/Jiangxi Province Key Lab of Clinical Pharmacokinetics
- Jiangxi Province Cancer Hospital
| | - Chunhua Xia
- Clinical Pharmacology Institute, Nanchang University/Jiangxi Province Key Lab of Clinical Pharmacokinetics
| | - Yuqing Xiong
- Clinical Pharmacology Institute, Nanchang University/Jiangxi Province Key Lab of Clinical Pharmacokinetics
| | - Hong Zhang
- Clinical Pharmacology Institute, Nanchang University/Jiangxi Province Key Lab of Clinical Pharmacokinetics
| | - Shibo Huang
- Clinical Pharmacology Institute, Nanchang University/Jiangxi Province Key Lab of Clinical Pharmacokinetics
| | - Mingyi Liu
- Clinical Pharmacology Institute, Nanchang University/Jiangxi Province Key Lab of Clinical Pharmacokinetics
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Abstract
The cytochrome P450 enzymes (CYPs) are the most important enzymes in the oxidative metabolism of hydrophobic drugs and other foreign compounds (xenobiotics). The versatility of these enzymes results in some unusual kinetic properties, stemming from the simultaneous interaction of multiple substrates with the CYP active site. Often, the CYPs display kinetics that deviate from standard hyperbolic saturation or inhibition kinetics. Non-Michaelis-Menten or "atypical" saturation kinetics include sigmoidal, biphasic, and substrate inhibition kinetics (see Chapter 3 ). Interactions between substrates include competitive inhibition, noncompetitive inhibition, mixed inhibition, partial inhibition, activation, and activation followed by inhibition (see Chapter 4 ). Models and equations that can result in these kinetic profiles will be presented and discussed.
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Zeng C, He F, Xia C, Zhang H, Xiong Y. Identification of the Active Components in Shenmai Injection that Differentially Affect Cyp3a4-Mediated 1′-Hydroxylation and 4-Hydroxylation of Midazolam. Drug Metab Dispos 2013; 41:785-90. [DOI: 10.1124/dmd.112.048025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Kuze J, Mutoh T, Takenaka T, Oda N, Hanioka N, Narimatsu S. Evaluation of animal models for intestinal first-pass metabolism of drug candidates to be metabolized by CYP3A enzymes via in vivo and in vitro oxidation of midazolam and triazolam. Xenobiotica 2013; 43:598-606. [PMID: 23282066 DOI: 10.3109/00498254.2012.751517] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
1. To search an appropriate evaluation methodology for the intestinal first-pass metabolism of new drug candidates, grapefruit juice (GFJ)- and vehicle (tap water)-pretreated mice or rats were orally administered midazolam (MDZ) or triazolam (TRZ), and blood levels of the parent compounds and their metabolites were measured by liquid chromatography/MS/MS. A significant effect of GFJ to elevate the blood levels was observed only for TRZ in mice. 2. In vitro experiments using mouse, rat and human intestinal and hepatic microsomal fractions demonstrated that GFJ suppressed the intestinal microsomal oxidation of MDZ and especially TRZ. Substrate inhibition by MDZ caused reduction in 1'-hydroxylation but not 4-hydroxylation in both intestinal and hepatic microsomal fractions. The kinetic profiles of MDZ oxidation and the substrate inhibition in mouse intestinal and hepatic microsomal fractions were very similar to those in human microsomes but were different from those in rat microsomes. Furthermore, MDZ caused mechanism-based inactivation of cytochrome P450 3A-dependent TRZ 1'-hydroxylation in mouse, rat and human intestinal microsomes with similar potencies. 3. These results are useful information in the analysis of data obtained in mouse and rat for the evaluation of first-pass effects of drug candidates to be metabolized by CYP3A enzymes.
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Affiliation(s)
- J Kuze
- Tsukuba Research Center, Taiho Pharmaceutical Company, Ibaraki, Japan
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Xue Q, Kato D, Kamata T, Guo Q, You T, Niwa O. Human cytochrome P450 3A4 and a carbon nanofiber modified film electrode as a platform for the simple evaluation of drug metabolism and inhibition reactions. Analyst 2013; 138:6463-8. [DOI: 10.1039/c3an01313h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kamel A, Harriman S. Inhibition of cytochrome P450 enzymes and biochemical aspects of mechanism-based inactivation (MBI). DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 10:e177-89. [PMID: 24050247 DOI: 10.1016/j.ddtec.2012.09.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Mechanism-based inactivation (MBI) often involves metabolic bioactivation of the xenobiotic by cytochrome P450s (CYPs) to an electrophilic reactive intermediate and results in quasi-irreversible or irreversible inactivation. Such reactive intermediate can cause quasi-irreversible inhibition through coordination to the ferrous state, Fe(II), of the P450 enzyme forming a tight noncovalent bond leading to the formation of metabolic-intermediate complex (MIC). By contrast, irreversible inactivation is one of the most common causes for the observed drug–drug interaction (DDI) and usually implies the formation of a covalent bond between the metabolite and the enzyme via alkylation of either the heme or the P450 apoprotein. Here we illustrate the important points of the current literature understanding of the mechanisms of inhibition of CYP enzymes with emphasis on general mechanistic aspects of MBI for some drugs/moieties associated with the phenomenon. Additionally, the utility of computational and in silico approaches to address bioactivation issues will be briefly discussed.
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Sadeghi SJ, Ferrero S, Di Nardo G, Gilardi G. Drug–drug interactions and cooperative effects detected in electrochemically driven human cytochrome P450 3A4. Bioelectrochemistry 2012; 86:87-91. [DOI: 10.1016/j.bioelechem.2012.02.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 02/26/2012] [Accepted: 02/28/2012] [Indexed: 10/28/2022]
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Denisov IG, Sligar SG. A novel type of allosteric regulation: functional cooperativity in monomeric proteins. Arch Biochem Biophys 2012; 519:91-102. [PMID: 22245335 PMCID: PMC3329180 DOI: 10.1016/j.abb.2011.12.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 10/14/2022]
Abstract
Cooperative functional properties and allosteric regulation in cytochromes P450 play an important role in xenobiotic metabolism and define one of the main mechanisms of drug-drug interactions. Recent experimental results suggest that ability to bind simultaneously two or more small organic molecules can be the essential feature of cytochrome P450 fold, and often results in rich and complex pattern of allosteric behavior. Manifestations of non-Michaelis kinetics include homotropic and heterotropic activation and inhibition effects depending on the stoichiometric ratios of substrate and effector, changes in the regio- and stereospecificity of catalytic transformations, and often give rise to the clinically important drug-drug interactions. In addition, functional response of P450 systems is modulated by the presence of specific and non-specific effector molecules, metal ions, membrane incorporation, formation of homo- and hetero-oligomers, and interactions with the protein redox partners. In this article we briefly overview the main factors contributing to the allosteric effects in cytochromes P450 with the main focus on the sources of cooperative behavior in xenobiotic metabolizing monomeric heme enzymes with their conformational flexibility and extremely broad substrate specificity. The novel mechanism of functional cooperativity in P450 enzymes does not require substantial binding cooperativity, rather it implies the presence of one or more binding sites with higher affinity than the single catalytically active site in the vicinity of the heme iron.
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Affiliation(s)
- Ilia G. Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801
| | - Stephen G. Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801
- Beckman Institute, University of Illinois, Urbana, IL, 61801
- School of Molecular and Cellular Biology, University of Illinois, Urbana, IL, 61801
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Pérez-Nueno VI, Ritchie DW. Identifying and characterizing promiscuous targets: implications for virtual screening. Expert Opin Drug Discov 2011; 7:1-17. [PMID: 22468890 DOI: 10.1517/17460441.2011.632406] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Ligand-based shape matching approaches have become established as important and popular virtual screening (VS) techniques. However, despite their relative success, the question of how to best choose the initial query compounds and their conformations remains largely unsolved. This issue gains importance when dealing with promiscuous targets, that is, proteins that bind multiple ligand scaffold families in one or more binding site. Conventional shape matching VS approaches assume that there is only one binding mode for a given protein target. This may be true for some targets, but it is certainly not true in all cases. Several recent studies have shown that some protein targets bind to different ligands in different ways. AREAS COVERED The authors discuss the concept of promiscuity in the context of virtual drug screening, and present and analyze several examples of promiscuous targets. The article also reports on the impact of the query conformation on the performance of shape-based VS and the potential to improve VS performance by using consensus shape clustering techniques. EXPERT OPINION The notion of polypharmacology is becoming highly relevant in drug discovery. Understanding and exploiting promiscuity present challenges and opportunities for drug discovery endeavors. The examples of promiscuity presented here suggest that promiscuous targets and ligands are much more common than previously assumed, and this should be taken into account in practical VS protocols. Although some progress has been made, there is a need to develop more sophisticated computational techniques and protocols that can identify and characterize promiscuous targets on a genomic scale.
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Woods CM, Fernandez C, Kunze KL, Atkins WM. Allosteric activation of cytochrome P450 3A4 by α-naphthoflavone: branch point regulation revealed by isotope dilution analysis. Biochemistry 2011; 50:10041-51. [PMID: 22004098 DOI: 10.1021/bi2013454] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450 3A4 (CYP3A4) is the dominant xenobiotic metabolizing CYP. Despite great interest in CYP enzymology, two in vitro aspects of CYP3A4 catalysis are still not well understood, namely, sequential metabolism and allosteric activation. We have therefore investigated such a system in which both phenomena are present. Here we report that the sequential metabolism of Nile Red (NR) is accelerated by the heterotropic allosteric effector α-naphthoflavone (ANF). ANF increases the rates of formation for NR metabolites M1 and M2 and also perturbs the metabolite ratio in favor of M2. Thus, ANF has as an allosteric effect on a kinetic branch point. Co-incubating deuterium-labeled NR and unlabeled M1, we show that ANF increases k(cat)/k(off) ~1.8-fold in favor of the k(cat) of M2 production. Steady-state metabolic experiments are analyzed using a kinetic model in which the enzyme and substrates are not in rapid equilibrium, and this distinction allows for the estimation of rates of catalysis for the formation of both the primary (M1) and secondary (M2) products, as well as the partitioning of enzyme between these states. These results are compared with those of earlier spectroscopic investigations of NR and ANF cooperativity, and a mechanism of ANF heteroactivation is presented that involves effects on substrate off rate and coupling efficiency.
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Affiliation(s)
- Caleb M Woods
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, Washington 98195-7610, USA
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Reddy VBG, Doss GA, Karanam BV, Samuel K, Lanza TJ, Lin LS, Yu NX, Zhang AS, Raab CE, Stearns RA, Kumar S. In vitro and in vivo metabolism of a novel cannabinoid-1 receptor inverse agonist, taranabant, in rats and monkeys. Xenobiotica 2011; 40:650-62. [PMID: 20608842 DOI: 10.3109/00498254.2010.501117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The metabolism and excretion of taranabant (MK-0364, N-[(1S,2S)-3-(4-chlorophenyl)-2-(3-cyanophenyl)-1-methylpropyl]-2-methyl-2{[5-(trifluoromethyl)pyridine-2-yl]oxy}propanamide), a potent cannabinoid-1 receptor inverse agonist, were evaluated in rats and rhesus monkeys. Following administration of [¹⁴C]taranabant, the majority of the radioactivity was excreted within 72 h. In both rats and rhesus monkeys, taranabant was eliminated primarily via oxidative metabolism, followed by excretion of metabolites into bile. Major pathways of metabolism that were common to rats and rhesus monkeys included hydroxylation at the benzylic carbon adjacent to the cyanophenyl ring to form a biologically active circulating metabolite M1, and oxidation of one of the two geminal methyl groups of taranabant or M1 to the corresponding diastereomeric carboxylic acids. Oxidation of the cyanophenyl ring, followed by conjugation with glutathione or glucuronic acid, was a major pathway of metabolism only in the rat and was not detected in the rhesus monkey. Metabolism profiles of taranabant in liver microsomes in vitro were qualitatively similar in rats, rhesus monkeys and humans and included formation of M1 and oxidation of taranabant or M1 to the corresponding carboxylic acids via oxidation of a geminal methyl group. In human liver microsomes, metabolism of taranabant was mediated primarily by CYP3A4.
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Affiliation(s)
- V B G Reddy
- Drug Metabolism and Pharmacokinetics, Merck Research Laboratories, Rahway, NJ 07065, USA.
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Abstracts. Drug Metab Rev 2011. [DOI: 10.3109/03602532.2011.567811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Shinkyo R, Guengerich FP. Inhibition of human cytochrome P450 3A4 by cholesterol. J Biol Chem 2011; 286:18426-33. [PMID: 21471209 DOI: 10.1074/jbc.m111.240457] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
If cholesterol is a substrate of P450 3A4, then it follows that it should also be an inhibitor, particularly in light of the high concentrations found in liver. Heme perturbation spectra indicated a K(d) value of 8 μM for the P450 3A4-cholesterol complex. Cholesterol inhibited the P450 3A4-catalyzed oxidations of nifedipine and quinidine, two prototypic substrates, in liver microsomes and a reconstituted enzyme system with K(i) ∼ 10 μM in an apparently non-competitive manner. The concentration of cholesterol could be elevated 4-6-fold in cultured human hepatocytes by incubation with cholesterol; the level of P450 3A4 and cell viability were not altered under the conditions used. Nifedipine oxidation was inhibited when the cholesterol level was increased. We conclude that cholesterol is both a substrate and an inhibitor of P450 3A4, and a model is presented to explain the kinetic behavior. We propose that the endogenous cholesterol in hepatocytes should be considered in models of prediction of metabolism of drugs and steroids, even in the absence of changes in the concentrations of free cholesterol.
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Affiliation(s)
- Raku Shinkyo
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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Frank DJ, Denisov IG, Sligar SG. Analysis of heterotropic cooperativity in cytochrome P450 3A4 using alpha-naphthoflavone and testosterone. J Biol Chem 2010; 286:5540-5. [PMID: 21177853 DOI: 10.1074/jbc.m110.182055] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 3A4 (CYP3A4) displays non-Michaelis-Menten kinetics for many of the substrates it metabolizes, including testosterone (TST) and α-naphthoflavone (ANF). Heterotropic effects between these two substrates can further complicate the metabolic profile of the enzyme. In this work, monomeric CYP3A4 solubilized in Nanodiscs has been studied for its ability to interact with varying molar ratios of ANF and TST. Comparison of the observed heme spin state, NADPH consumption, and product formation rates with a non-cooperative model calculated from a linear combination of the global analysis of each substrate reveals a detailed landscape of the heterotropic interactions and indicates negligible binding cooperativity between ANF and TST. The observed effect of ANF on the kinetics of TST metabolism is due to the additive action of the second substrate with no specific allosteric effects.
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Affiliation(s)
- Daniel J Frank
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois, Urbana, Illinois 61801, USA
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Abstract
The transcription factor NF-E2-related factor (NRF2) is a key regulator of several enzymatic pathways, including cytoprotective enzymes in highly metabolic organs. In this review, we summarize the ongoing research related to NRF2 activity in cancer development, focusing on in vivo studies using NRF2 knockout (KO) mice, which have helped in defining the crucial role of NRF2 in chemoprevention. The lower cancer protection observed in NRF2 KO mice under calorie restriction (CR) suggests that most of the beneficial effects of CR on the carcinogenesis process are likely mediated by NRF2. We propose that future interventions in cancer treatment would be carried out through the activation of NRF2 in somatic cells, which will lead to a delay or prevention of the onset of some forms of human cancers, and subsequently an extension of health- and lifespan.
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Pearson JT, Siu S, Meininger DP, Wienkers LC, Rock DA. In Vitro Modulation of Cytochrome P450 Reductase Supported Indoleamine 2,3-Dioxygenase Activity by Allosteric Effectors Cytochrome b5 and Methylene Blue. Biochemistry 2010; 49:2647-56. [DOI: 10.1021/bi100022c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Josh T. Pearson
- Biochemistry and Biophysics Group, Department of Pharmacokinetics and Drug Metabolism
| | | | | | - Larry C. Wienkers
- Biochemistry and Biophysics Group, Department of Pharmacokinetics and Drug Metabolism
| | - Dan A. Rock
- Biochemistry and Biophysics Group, Department of Pharmacokinetics and Drug Metabolism
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Ranaghan KE, Mulholland AJ. Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods. INT REV PHYS CHEM 2010. [DOI: 10.1080/01442350903495417] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Zhou J, Tracy TS, Remmel RP. Glucuronidation of dihydrotestosterone and trans-androsterone by recombinant UDP-glucuronosyltransferase (UGT) 1A4: evidence for multiple UGT1A4 aglycone binding sites. Drug Metab Dispos 2009; 38:431-40. [PMID: 20007295 DOI: 10.1124/dmd.109.028712] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
UDP-glucuronosyltransferase (UGT) 1A4-catalyzed glucuronidation is an important drug elimination pathway. Although atypical kinetic profiles (nonhyperbolic, non-Michaelis-Menten) of UGT1A4-catalyzed glucuronidation have been reported occasionally, systematic kinetic studies to explore the existence of multiple aglycone binding sites in UGT1A4 have not been conducted. To this end, two positional isomers, dihydrotestosterone (DHT) and trans-androsterone (t-AND), were used as probe substrates, and their glucuronidation kinetics with HEK293-expressed UGT1A4 were evaluated both alone and in the presence of a UGT1A4 substrate [tamoxifen (TAM) or lamotrigine (LTG)]. Coincubation with TAM, a high-affinity UGT1A4 substrate, resulted in a concentration-dependent activation/inhibition effect on DHT and t-AND glucuronidation, whereas LTG, a low-affinity UGT1A4 substrate, noncompetitively inhibited both processes. The glucuronidation kinetics of TAM were then evaluated both alone and in the presence of different concentrations of DHT or t-AND. TAM displayed substrate inhibition kinetics, suggesting that TAM may have two binding sites in UGT1A4. However, the substrate inhibition kinetic profile of TAM became more hyperbolic as the DHT or t-AND concentration was increased. Various two-site kinetic models adequately explained the interactions between TAM and DHT or TAM and t-AND. In addition, the effect of TAM on LTG glucuronidation was evaluated. In contrast to the mixed effect of TAM on DHT and t-AND glucuronidation, TAM inhibited LTG glucuronidation. Our results suggest that multiple aglycone binding sites exist within UGT1A4, which may result in atypical kinetics (both homotropic and heterotropic) in a substrate-dependent fashion.
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Affiliation(s)
- Jin Zhou
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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35
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Differential effect of Shenmai injection, a herbal preparation, on the cytochrome P450 3A-mediated 1′-hydroxylation and 4-hydroxylation of midazolam. Chem Biol Interact 2009; 180:440-8. [DOI: 10.1016/j.cbi.2009.03.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Multiplicity ofn-heptane oxidation pathways catalyzed by cytochrome P450. J Biochem Mol Toxicol 2009; 23:287-94. [DOI: 10.1002/jbt.20291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Frank DJ, Denisov IG, Sligar SG. Mixing apples and oranges: Analysis of heterotropic cooperativity in cytochrome P450 3A4. Arch Biochem Biophys 2009; 488:146-52. [PMID: 19560436 DOI: 10.1016/j.abb.2009.06.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2009] [Revised: 05/28/2009] [Accepted: 06/19/2009] [Indexed: 11/29/2022]
Abstract
Heterotropic cooperative phenomena have been documented in studies with cytochrome P450 3A4, with few attempts to quantify this behavior other than to show the apparent stimulatory effect of certain CYP3A4 substrates on the enzyme's catalytic activity for others. Here CYP3A4 solubilized in Nanodiscs is studied for its ability to interact with two substrates, alpha-naphthoflavone and testosterone, which produce transitions in the heme spin state with apparent spectral affinities (corrected for membrane partitioning) of 7 and 38 microM, respectively. Simultaneous addition of both substrates at fixed molar ratios allows for the separation of specific heterotropic cooperative interactions from the simple additive affinities for the given substrate ratios. The absence of any changes in the normalized spectral dissociation constant due to changes in substrate ratio reveals that the observed stimulatory effect is largely due to differences in the relative substrate affinities and the presence of additional substrate in the system, rather than any specific positive heterotropic interactions between the two substrates.
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Affiliation(s)
- Daniel J Frank
- School of Molecular and Cellular Biology, University of Illinois, Urbana, IL 61801, USA
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38
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Denisov IG, Frank DJ, Sligar SG. Cooperative properties of cytochromes P450. Pharmacol Ther 2009; 124:151-67. [PMID: 19555717 DOI: 10.1016/j.pharmthera.2009.05.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 05/28/2009] [Indexed: 02/07/2023]
Abstract
Cytochromes P450 form a large and important class of heme monooxygenases with a broad spectrum of substrates and corresponding functions, from steroid hormone biosynthesis to the metabolism of xenobiotics. Despite decades of study, the molecular mechanisms responsible for the complex non-Michaelis behavior observed with many members of this superfamily during metabolism, often termed 'cooperativity', remain to be fully elucidated. Although there is evidence that oligomerization may play an important role in defining the observed cooperativity, some monomeric cytochromes P450, particularly those involved in xenobiotic metabolism, also display this behavior due to their ability to simultaneously bind several substrate molecules. As a result, formation of distinct enzyme-substrate complexes with different stoichiometry and functional properties can give rise to homotropic and heterotropic cooperative behavior. This review aims to summarize the current understanding of cooperativity in cytochromes P450, with a focus on the nature of cooperative effects in monomeric enzymes.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States of America
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39
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Davydov DR, Halpert JR. Allosteric P450 mechanisms: multiple binding sites, multiple conformers or both? Expert Opin Drug Metab Toxicol 2009; 4:1523-35. [PMID: 19040328 DOI: 10.1517/17425250802500028] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
According to the initial hypothesis on the mechanisms of cooperativity in drug-metabolizing cytochromes P450, a loose fit of a single substrate molecule in the P450 active site results in a requirement for the binding of multiple ligand molecules for efficient catalysis. Although simultaneous occupancy of the active site by multiple ligands is now well established, there is increasing evidence that the mechanistic basis of cooperativity also involves an important ligand-induced conformational transition. Moreover, recent studies demonstrate that the conformational heterogeneity of the enzyme is stabilized by ligand-dependent interactions of several P450 molecules. Application of the concept of an oligomeric allosteric enzyme to microsomal cytochromes P450 in combination with a general paradigm of multiple ligand occupancy of the active site provides an excellent explanation for complex manifestations of the atypical kinetic behavior of the enzyme.
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Affiliation(s)
- Dmitri R Davydov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, 9500 Gilman Drive, La Jolla, CA 9209, USA.
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40
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Atypical kinetic behavior of chloroperoxidase-mediated oxidative halogenation of polycyclic aromatic hydrocarbons. Arch Biochem Biophys 2008; 480:33-40. [DOI: 10.1016/j.abb.2008.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2008] [Revised: 09/09/2008] [Accepted: 09/09/2008] [Indexed: 11/24/2022]
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41
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He K, Qian M, Wong H, Bai SA, He B, Brogdon B, Grace JE, Xin B, Wu J, Ren SX, Zeng H, Deng Y, Graden DM, Olah TV, Unger SE, Luettgen JM, Knabb RM, Pinto DJ, Lam PYS, Duan J, Wexler RR, Decicco CP, Christ DD, Grossman SJ. N-in-1 dosing pharmacokinetics in drug discovery: experience, theoretical and practical considerations. J Pharm Sci 2008; 97:2568-80. [PMID: 17914718 DOI: 10.1002/jps.21196] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
N-in-1 (or cassette) dosing pharmacokinetics (PK) has been used in drug discovery for rapid assessment of PK properties of new chemical entities. However, because of potential for drug-drug interactions this procedure is still controversial. This study was to retrospectively evaluate the N-in-1 dosing approach in drug discovery with an emphasis on the potential for drug-drug interactions. The systemic clearance, volume of distribution, oral bioavailability, and renal excretion of the 31 lead compounds in rats, dogs or chimpanzees were significantly correlated between the N-in-1 dosing and discrete studies with r values of 0.69, 0.91, 0.53, and 0.83 (p < 0.005 for all), respectively. PK parameters for 11 quality control compounds which were involved in 194 N-in-1 studies for screening approximately 1000 compounds had coefficient of variations of less than 70%. The intrinsic microsomal clearances generated from the N-in-1 and discrete incubations were nearly identical (r = 0.97, p < 0.0001). The intrinsic clearances of quality control compound from the N-in-1 incubations were consistent with its discrete CL(int) estimate (cv: 5.4%). Therefore, N-in-1 dosing is a useful approach in drug discovery to quickly obtain initial PK estimates. Potential drug-drug interactions that result in confounding PK estimates do not occur as frequently as expected.
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Affiliation(s)
- Kan He
- Department of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Company, PO Box 4000, Princeton, New Jersey 08543-4000, USA
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42
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Uchaipichat V, Galetin A, Houston JB, Mackenzie PI, Williams JA, Miners JO. Kinetic Modeling of the Interactions between 4-Methylumbelliferone, 1-Naphthol, and Zidovudine Glucuronidation by UDP-Glucuronosyltransferase 2B7 (UGT2B7) Provides Evidence for Multiple Substrate Binding and Effector Sites. Mol Pharmacol 2008; 74:1152-62. [DOI: 10.1124/mol.108.048645] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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43
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Bell L, Bickford S, Nguyen PH, Wang J, He T, Zhang B, Friche Y, Zimmerlin A, Urban L, Bojanic D. Evaluation of fluorescence- and mass spectrometry-based CYP inhibition assays for use in drug discovery. ACTA ACUST UNITED AC 2008; 13:343-53. [PMID: 18474896 DOI: 10.1177/1087057108317480] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The potential for metabolism-related drug-drug interactions by new chemical entities is assessed by monitoring the impact of these compounds on cytochrome P450 (CYP) activity using well-characterized CYP substrates. The conventional gold standard approach for in vitro evaluation of CYP inhibitory potential uses pooled human liver microsomes (HLM) in conjunction with prototypical drug substrates, often quantified by LC-MS/MS. However, fluorescent CYP inhibition assays, which use recombinantly expressed CYPs and fluorogenic probe substrates, have been employed in early drug discovery to provide low-cost, high-throughput assessment of new chemical entities. Despite its greatly enhanced throughput, this approach has been met with mixed success in predicting the data obtained with the conventional gold standard approach (HLM+LC-MS). The authors find that the predictivity of fluorogenic assays for the major CYP isoforms 3A4 and 2D6 may depend on the quality of the test compounds. Although the structurally more optimized marketed drugs yielded acceptable correlations between the fluorogenic and HLM+LC-MS/MS assays for CYPs 3A4, 2D6, and 2C9 (r2 = 0.5-0.7; p < 0.005), preoptimization, early discovery compounds yielded poorer correlations (r2 < or = 0.2) for 2 of these major isoforms, CYPs 3A4 and 2D6. Potential reasons for the observed differences are discussed.
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Affiliation(s)
- Leslie Bell
- ADME Profiling Cambridge, Metabolism and Pharmacokinetics, Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA.
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44
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Zhang W, Lim LY. Effects of Spice Constituents on P-Glycoprotein-Mediated Transport and CYP3A4-Mediated Metabolism in Vitro. Drug Metab Dispos 2008; 36:1283-90. [DOI: 10.1124/dmd.107.019737] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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45
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Nath A, Fernández C, Lampe JN, Atkins WM. Spectral resolution of a second binding site for Nile Red on cytochrome P4503A4. Arch Biochem Biophys 2008; 474:198-204. [PMID: 18395506 DOI: 10.1016/j.abb.2008.03.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 03/11/2008] [Accepted: 03/15/2008] [Indexed: 11/30/2022]
Abstract
Nile Red is sequentially metabolized by cytochrome P4503A4 to the N-monoethyl and N-desethyl products, which typifies the metabolism of many amine containing drugs. Sequential metabolism of a single substrate results in complex kinetics that confound predictive models of drug clearance. As a fluorescent model for drugs which undergo sequential metabolism, Nile Red provides the opportunity to monitor drug-CYP interactions wherein the fluorescent properties of Nile Red could, in principle, be exploited to determine individual rate and equilibrium constants for the individual reactions. Previously, it was shown that Nile Red binds at the active site and fluoresces (K(D) approximately 50nM) with maximum emission at approximately 620nm, but it was unclear whether a red-shifted emission, at approximately 660nm, consisted of only free Nile Red or Nile Red bound at a second site on the protein. Here, equilibrium binding studies, including 'reverse titrations' spanning low ratios of CYP3A4/Nile Red, indicate two binding sites for Nile Red with a contribution to the 'red emission' greater than can be accounted for by free Nile Red. Singular value decomposition affords basis spectra for both spectral components and fits well to the experimentally determined concentration dependence of Nile Red emission. In addition, the red spectral component, with an apparent K(D)=2.2muM, is selectively eliminated by titration with the known allosteric effectors of CYP3A4, alpha-napthoflavone and testosterone. Furthermore, the double mutant L2311F/D214E, previously demonstrated to perturb a peripheral allosteric site, lacks the red-emitting Nile Red binding site, but retains the blue-emitting site. Together these data indicate that a second Nile Red site competes with other effectors of CYP3A4 at a site that results in Nile Red emission at 660nm.
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Affiliation(s)
- Abhinav Nath
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610, USA
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46
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Cheng D, Harris D, Reed JR, Backes WL. Inhibition of CYP2B4 by 2-ethynylnaphthalene: evidence for the co-binding of substrate and inhibitor within the active site. Arch Biochem Biophys 2007; 468:174-82. [PMID: 17967439 PMCID: PMC2121586 DOI: 10.1016/j.abb.2007.07.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2007] [Revised: 07/21/2007] [Accepted: 07/25/2007] [Indexed: 10/22/2022]
Abstract
2-ethynylnaphthalene (2EN) is an effective mechanism-based inhibitor of CYP2B4. There are two inhibitory components: (1) irreversible inactivation of CYP2B4 (a typical time-dependent inactivation), and (2) a reversible component. The reversible component was unusual in that the degree of inhibition was not simply a characteristic of the enzyme-inhibitor interaction, but dependent on the size of the substrate molecule used to monitor residual activity. The effect of 2EN on the metabolism of seven CYP2B4 substrates showed that it was not an effective reversible inhibitor of substrates containing a single aromatic ring; substrates with two fused rings were competitively inhibited by 2EN; and larger substrates were non-competitively inhibited. Energy-based docking studies demonstrated that, with increasing substrate size, the energy of 2EN and substrate co-binding in the active site became unfavorable precisely at the point where 2EN became a competitive inhibitor. Hierarchical docking revealed potential allosteric inhibition sites separate from the substrate binding site.
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Affiliation(s)
- Dongmei Cheng
- Department of Pharmacology and Experimental Therapeutics, and The Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, 533 Bolivar Street, New Orleans, LA 70112, USA
| | - Danni Harris
- Molecular Research Institute, Mountain View, CA 94043
| | - James R. Reed
- Department of Pharmacology and Experimental Therapeutics, and The Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, 533 Bolivar Street, New Orleans, LA 70112, USA
| | - Wayne L. Backes
- Department of Pharmacology and Experimental Therapeutics, and The Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, 533 Bolivar Street, New Orleans, LA 70112, USA
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47
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Fishelovitch D, Hazan C, Hirao H, Wolfson HJ, Nussinov R, Shaik S. QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding. J Phys Chem B 2007; 111:13822-32. [PMID: 18020326 PMCID: PMC2596655 DOI: 10.1021/jp076401j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome P450 3A4 is involved in the metabolism of 50% of all swallowed drugs. The enzyme functions by means of a high-valent iron-oxo species, called compound I (Cpd I), which is formed after entrance of the substrate to the active site. We explored the features of Cpd I using hybrid quantum mechanical/molecular mechanical calculations on various models that are either substrate-free or containing one and two molecules of diazepam as a substrate. Mössbauer parameters of Cpd I were computed. Our major finding shows that without the substrate, Cpd I tends to elongate its Fe-S bond, localize the radical on the sulfur, and form hydrogen bonds with A305 and T309, which may hypothetically lead to Cpd I consumption by H-abstraction. However, the positioning of diazepam close to Cpd I, as enforced by the effector molecule, was found to strengthen the NH...S interactions of the conserved I443 and G444 residues with the proximal cysteinate ligand. These interactions are known to stabilize the Fe-S bond, and as such, the presence of the substrate leads to a shorter Fe-S bond and it prevents the localization of the radical on the sulfur. This diazepam-Cpd I stabilization was manifested in the 1W0E conformer. The effector substrate did not influence Cpd I directly but rather by positioning the active substrate close to Cpd I, thus displacing the hydrogen bonds with A305 and T309, and thereby giving preference to substrate oxidation. It is hypothesized that these effects on Cpd I, promoted by the restrained substrate, may be behind the special metabolic behavior observed in cases of multiple substrate binding (also called cooperative binding). This restraint constitutes a mechanism whereby substrates stabilize Cpd I sufficiently long to affect monooxygenation by P450s at the expense of Cpd I destruction by the protein residues.
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Affiliation(s)
- Dan Fishelovitch
- Department of Human Genetics, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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48
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Cameron MD, Wen B, Roberts AG, Atkins WM, Campbell AP, Nelson SD. Cooperative binding of acetaminophen and caffeine within the P450 3A4 active site. Chem Res Toxicol 2007; 20:1434-41. [PMID: 17894464 DOI: 10.1021/tx7000702] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acetaminophen (N-acetyl-p-aminophenol, APAP) is a commonly used analgesic/antipyretic. When oxidized by P450, a toxic APAP metabolite is generated. Human P450 3A4 was expressed in Escherichia coli , purified, and reconstituted using artificial liposomes. Oxidation of APAP by P450 3A4, as detected by the formation of its glutathione adduct, was found to exhibit negative homotropic cooperativity with a Hill coefficient of 0.7. In the presence of caffeine, the observed kinetics were close to classical Michaelis-Menten kinetics with a Hill coefficient approaching 1. In order to probe for a potential repositioning of APAP within the P450 3A4 pocket in the presence of caffeine, NMR T1 paramagnetic relaxation techniques were used to calculate distances from the P450 3A4 heme iron to protons of APAP alone and in the presence of caffeine. Both APAP and caffeine were found to bind at the active site in proximity to the heme iron. When APAP was incubated with P450 3A4, the acetamido group of APAP was found to be closest to the heme iron consistent with the amide group of APAP weakly associating with the heme iron. The addition of caffeine disrupted the ability of APAP to coordinate with the heme iron of P450 3A4 and enhanced the rate of oxidation to its toxic metabolite.
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Affiliation(s)
- Michael D Cameron
- Department of Medicinal Chemistry, University of Washington, Seattle 98195, USA
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49
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Roberts AG, Atkins WM. Energetics of heterotropic cooperativity between alpha-naphthoflavone and testosterone binding to CYP3A4. Arch Biochem Biophys 2007; 463:89-101. [PMID: 17459328 PMCID: PMC2062487 DOI: 10.1016/j.abb.2007.03.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Revised: 03/09/2007] [Accepted: 03/10/2007] [Indexed: 11/17/2022]
Abstract
Cytochrome P450 3A4 (CYP3A4) is involved in the metabolism of a majority of drugs. Heterotropic cooperativity of drug binding to CYP3A4 was examined with the flavanoid, alpha-naphthoflavone (ANF) and the steroid, testosterone (TST). UV-vis and EPR spectroscopy of CYP3A4 show that ANF binding to CYP3A4 occurs with apparent negative cooperativity and that there are at least two binding sites: (1) a relatively tight spin-state insensitive binding site (CYP.ANF) and (2) a relatively low affinity spin-state sensitive binding site (CYP.ANF.ANF). Since binding to the spin-state insensitive binding site is considerably tighter for ANF than TST, the spin-state insensitive binding site could be occupied by ANF, while titrating TST at the other site(s). The spin-state insensitive binding site of ANF appears to compete with the spin-state insensitive binding site of TST. The formation of the spin-state insensitive CYP.ANF complex is strongly temperature dependent, when compared to the formation of the CYP.TST complex, suggesting that the formation of the CYP3A4.ANF complex leads to long-range conformational changes within the protein. When the CYP.ANF complex is titrated with TST, the formation of CYP.ANF.TST is favored by 3:1 over the formation of CYP.TST.TST, suggesting that there is an allosteric interaction between ANF and TST. A model of heterotropic cooperativity of CYP3A4 is presented, where the spin-state insensitive binding of ANF occurs at the same peripheral binding site of CYP3A4 as TST.
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Affiliation(s)
- Arthur G. Roberts
- Department of Medicinal Chemistry; Box 357610, University of Washington, Seattle, WA 98195-7610
| | - William M. Atkins
- Department of Medicinal Chemistry; Box 357610, University of Washington, Seattle, WA 98195-7610
- Corresponding Author: Tel: (206) 685-0379; FAX: (206) 685-3252;
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50
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Isin EM, Guengerich FP. Multiple Sequential Steps Involved in the Binding of Inhibitors to Cytochrome P450 3A4. J Biol Chem 2007; 282:6863-74. [PMID: 17200113 DOI: 10.1074/jbc.m610346200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 (P450) 3A4 is an extensively studied human enzyme involved in the metabolism of >50% of drugs. The mechanism of the observed homotropic and heterotropic cooperativity in P450 3A4-catalyzed oxidations is not well understood, and together with the cooperative behavior, a detailed understanding of interaction of drug inhibitors with P450 3A4 is important in predicting clinical drug-drug interactions. The interactions of P450 3A4 with several structurally diverse inhibitors were investigated using both kinetic and thermodynamic approaches to resolve the steps involved in binding of these ligands. The results of pre-steady-state absorbance and fluorescence experiments demonstrate that inhibitor binding is clearly a multistep process, even more complex than the binding of substrates. Based on spectrophotometric equilibrium binding titrations as well as isothermal titration calorimetry experiments, the stoichiometry of binding appears to be 1:1 in the concentration ranges studied. Using a sequential-mixing stopped-flow approach, we were also able to show that the observed multiphasic binding kinetics is the result of sequential events as opposed to the existence of multiple enzyme populations in dynamic equilibrium that interact with ligands at different rates. We propose a three-step minimal model for inhibitor binding, developed with kinetic simulations, consistent with our previously reported model for the binding of substrates, although it is possible that even more steps are involved.
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Affiliation(s)
- Emre M Isin
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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