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Leow JWH, Chan ECY. CYP2J2-mediated metabolism of arachidonic acid in heart: A review of its kinetics, inhibition and role in heart rhythm control. Pharmacol Ther 2024; 258:108637. [PMID: 38521247 DOI: 10.1016/j.pharmthera.2024.108637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 02/06/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
Cytochrome P450 2 J2 (CYP2J2) is primarily expressed extrahepatically and is the predominant epoxygenase in human cardiac tissues. This highlights its key role in the metabolism of endogenous substrates. Significant scientific interest lies in cardiac CYP2J2 metabolism of arachidonic acid (AA), an omega-6 polyunsaturated fatty acid, to regioisomeric bioactive epoxyeicosatrienoic acid (EET) metabolites that show cardioprotective effects including regulation of cardiac electrophysiology. From an in vitro perspective, the accurate characterization of the kinetics of CYP2J2 metabolism of AA including its inhibition and inactivation by drugs could be useful in facilitating in vitro-in vivo extrapolations to predict drug-AA interactions in drug discovery and development. In this review, background information on the structure, regulation and expression of CYP2J2 in human heart is presented alongside AA and EETs as its endogenous substrate and metabolites. The in vitro and in vivo implications of the kinetics of this endogenous metabolic pathway as well as its perturbation via inhibition and inactivation by drugs are elaborated. Additionally, the role of CYP2J2-mediated metabolism of AA to EETs in cardiac electrophysiology will be expounded.
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Affiliation(s)
- Jacqueline Wen Hui Leow
- Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
| | - Eric Chun Yong Chan
- Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore.
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2
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Niwa T. [Metabolic Activities Catalyzed by Human Cytochrome P450 (CYP) 2D6 and CYP3A Subfamily Members and Effect of Various Compounds, Including Endogenous Steroid Hormones, on These Activities]. YAKUGAKU ZASSHI 2024; 144:197-202. [PMID: 38296497 DOI: 10.1248/yakushi.23-00174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
My research focused on the effects of various drugs on (1) dopamine formation from p-tyramine catalyzed by polymorphic cytochrome P450 (CYP or P450) 2D6 variants and (2) endogenous steroid hormone hydroxylation catalyzed by CYP3A subfamily members (CYP3A4, CYP3A5, CYP3A7). The activation (cooperativity) of metabolic reactions catalyzed by P450s was especially emphasized. The effects of various psychotropic agents on dopamine formation from p-tyramine, catalyzed by wild-type CYP2D6.1 and CYP2D6 variants, including CYP2D6.2 (Arg296Cys;Ser486Thr), CYP2D6.10 (Pro34Ser;Ser486Thr), and CYP2D6.39 (Ser486Thr) were compared. Michaelis (Km) and inhibition (Ki) constants of the psychotropic agents in the presence of CYP2D6.10 were higher than those observed in the presence of other CYP2D6 variants. Fluvoxamine, fluoxetine, milnacipran, and haloperidol activated CYP2D6-catalyzed dopamine formation [decreasing the Km and/or increasing the maximal velocity (kcat)], and this activation was CYP2D6 variant-dependent. Regarding the CYP3A subfamily, the effects of various compounds including endogenous steroid hormones on the 6β-hydroxylation of steroid hormones, such as testosterone, progesterone, and cortisol, were determined; it was found that testosterone, dehydroepiandrosterone, and/or α-naphthoflavone activated 6β-hydroxylation of cortisol and/or progesterone, but the effects varied in the presence of different CYP3A subfamily members. Further studies are required to confirm the mechanisms and therapeutic relevance of these activation phenomena.
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Nolte TM. 300-fold higher neuro- and immunotoxicity from low-redox transformation of carbamazepine. Toxicol Rep 2023; 11:319-329. [PMID: 37927955 PMCID: PMC10622881 DOI: 10.1016/j.toxrep.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023] Open
Abstract
Current challenges in (eco)toxicology are in understanding the transformation of (reactive) substances, and how transformation affects toxic modes of action. Empirical assessment of transformation products of, practically an infinite number of substances, via experimentation, is impossible. Predicting transformation products for (benchmarking) compounds from conditions, facilitates risk analyses. This study applied calculus to predict transformation products of an important environmental and medicinal/toxicological marker, carbamazepine. As radicals are ubiquitous in humans and the environment, we looked into radical-mediated transformations of carbamazepine as a benchmark. We calculated proportions of their speciation states as function of redox conditions, which we took as pH and O2 concentration, describing transformation via covalent and ionic interactions. Formation of ring-contracted products with neuro-immunological activity is thermodynamically favored under anaerobic conditions and at low pH. Experimentally observed product distributions and toxicities reflect that pattern. Our predictive method may support toxicity predictions for other substances and conditions 'similar' to the current case study via interpolation. This paves the way for a more coherent, effective and easier risk assessment of transformation products.
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Affiliation(s)
- Tom M. Nolte
- Department of Environmental Science, Institute for Water and Wetland Research, Radboud, University Nijmegen, 6500 GL Nijmegen, the Netherlands
- Eidgenössische Technische Hochschule (ETH) Zurich, Laboratory of Inorganic Chemistry, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
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4
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Atypical kinetics of cytochrome P450 enzymes in pharmacology and toxicology. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:131-176. [PMID: 35953154 DOI: 10.1016/bs.apha.2022.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Atypical kinetics are observed in metabolic reactions catalyzed by cytochrome P450 enzymes (P450). Yet, this phenomenon is regarded as experimental artifacts in some instances despite increasing evidence challenging the assumptions of typical Michaelis-Menten kinetics. As P450 play a major role in the metabolism of a wide range of substrates including drugs and endogenous compounds, it becomes critical to consider the impact of atypical kinetics on the accuracy of estimated kinetic and inhibitory parameters which could affect extrapolation of pharmacological and toxicological implications. The first half of this book chapter will focus on atypical non-Michaelis-Menten kinetics (e.g. substrate inhibition, biphasic and sigmoidal kinetics) as well as proposed underlying mechanisms supported by recent insights in mechanistic enzymology. In particular, substrate inhibition kinetics in P450 as well as concurrent drug inhibition of P450 in the presence of substrate inhibition will be further discussed. Moreover, mounting evidence has revealed that despite the high degree of sequence homology between CYP3A isoforms (i.e. CYP3A4 and CYP3A5), they have the propensities to exhibit vastly different susceptibilities and potencies of mechanism-based inactivation (MBI) with a common drug inhibitor. These experimental observations pertaining to the presence of these atypical isoform- and probe substrate-specific complexities in CYP3A isoforms by several clinically-relevant drugs will therefore be expounded and elaborated upon in the second half of this book chapter.
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5
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Denisov IG, Grinkova YV, McLean MA, Camp T, Sligar SG. Midazolam as a Probe for Heterotropic Drug-Drug Interactions Mediated by CYP3A4. Biomolecules 2022; 12:853. [PMID: 35740978 PMCID: PMC9221276 DOI: 10.3390/biom12060853] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
Human cytochrome P450 CYP3A4 is involved in the processing of more than 35% of current pharmaceuticals and therefore is responsible for multiple drug-drug interactions (DDI). In order to develop a method for the detection and prediction of the possible involvement of new drug candidates in CYP3A4-mediated DDI, we evaluated the application of midazolam (MDZ) as a probe substrate. MDZ is hydroxylated by CYP3A4 in two positions: 1-hydroxy MDZ formed at lower substrate concentrations, and up to 35% of 4-hydroxy MDZ at high concentrations. The ratio of the formation rates of these two products (the site of metabolism ratio, SOM) was used as a measure of allosteric heterotropic interactions caused by effector molecules using CYP3A4 incorporated in lipid nanodiscs. The extent of the changes in the SOM in the presence of effectors is determined by chemical structure and is concentration-dependent. MD simulations of CYP3A4 in the lipid bilayer suggest that experimental results can be explained by the movement of the F-F' loop and concomitant changes in the shape and volume of the substrate-binding pocket. As a result of PGS binding at the allosteric site, several residues directly contacting MDZ move away from the substrate molecule, enabling the repositioning of the latter for minor product formation.
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Affiliation(s)
- Ilia G. Denisov
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (I.G.D.); (Y.V.G.); (M.A.M.); (T.C.)
| | - Yelena V. Grinkova
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (I.G.D.); (Y.V.G.); (M.A.M.); (T.C.)
| | - Mark A. McLean
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (I.G.D.); (Y.V.G.); (M.A.M.); (T.C.)
| | - Tyler Camp
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (I.G.D.); (Y.V.G.); (M.A.M.); (T.C.)
| | - Stephen G. Sligar
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (I.G.D.); (Y.V.G.); (M.A.M.); (T.C.)
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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6
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Tooker BC, Kandel SE, Work HM, Lampe JN. Pseudomonas aeruginosa cytochrome P450 CYP168A1 is a fatty acid hydroxylase that metabolizes arachidonic acid to the vasodilator 19-HETE. J Biol Chem 2022; 298:101629. [PMID: 35085556 PMCID: PMC8913318 DOI: 10.1016/j.jbc.2022.101629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/08/2022] [Accepted: 01/20/2022] [Indexed: 01/08/2023] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic human pathogen that is highly prevalent in individuals with cystic fibrosis (CF). A major problem in treating CF patients infected with P. aeruginosa is the development of antibiotic resistance. Therefore, the identification of novel P. aeruginosa antibiotic drug targets is of the utmost urgency. The genome of P. aeruginosa contains four putative cytochrome P450 enzymes (CYPs) of unknown function that have never before been characterized. Analogous to some of the CYPs from Mycobacterium tuberculosis, these P. aeruginosa CYPs may be important for growth and colonization of CF patients’ lungs. In this study, we cloned, expressed, and characterized CYP168A1 from P. aeruginosa and identified it as a subterminal fatty acid hydroxylase. Spectral binding data and computational modeling of substrates and inhibitors suggest that CYP168A1 has a large, expansive active site and preferentially binds long chain fatty acids and large hydrophobic inhibitors. Furthermore, metabolic experiments confirm that the enzyme is capable of hydroxylating arachidonic acid, an important inflammatory signaling molecule present in abundance in the CF lung, to 19-hydroxyeicosatetraenoic acid (19-HETE; Km = 41 μM, Vmax = 220 pmol/min/nmol P450), a potent vasodilator, which may play a role in the pathogen’s ability to colonize the lung. Additionally, we found that the in vitro metabolism of arachidonic acid is subject to substrate inhibition and is also inhibited by the presence of the antifungal agent ketoconazole. This study identifies a new metabolic pathway in this important human pathogen that may be of utility in treating P. aeruginosa infections.
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Affiliation(s)
- Brian C Tooker
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado, Aurora, Colorado, USA
| | - Sylvie E Kandel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado, Aurora, Colorado, USA
| | - Hannah M Work
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado, Aurora, Colorado, USA
| | - Jed N Lampe
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado, Aurora, Colorado, USA.
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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8
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Leow JWH, Verma RK, Lim ABH, Fan H, Chan ECY. Atypical kinetics of cytochrome P450 2J2: Epoxidation of arachidonic acid and reversible inhibition by xenobiotic inhibitors. Eur J Pharm Sci 2021; 164:105889. [PMID: 34044117 DOI: 10.1016/j.ejps.2021.105889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/04/2021] [Accepted: 05/20/2021] [Indexed: 01/08/2023]
Abstract
Extrahepatic CYP2J2 metabolism of arachidonic acid (AA) to bioactive regioisomeric epoxyeicosatrienoic acids (EETs) is implicated in both physiological and pathological conditions. Here, we aimed to characterize atypical substrate inhibition kinetics of this endogenous metabolic pathway and its reversible inhibition by xenobiotic inhibitors when AA is used as the physiologically-relevant substrate vis-à-vis conventional probe substrate astemizole (AST). As compared to typical Michaelis-Menten kinetics observed for AST, complete substrate inhibition was observed for CYP2J2 metabolism of AA to 14,15-EET whereby velocity of the reaction declined significantly at concentrations of AA above 20-30 µM with an estimated substrate inhibition constant (Ks) of 31 µM. In silico sequential docking of two AA substrates to orthosteric (OBS) and adjacent secondary binding sites (SBS) within a 3-dimensional homology model of CYP2J2 revealed favorable and comparable binding poses of glide-scores -3.1 and -3.8 respectively. Molecular dynamics (MD) simulations ascertained CYP2J2 conformational stability with dual AA substrate binding as time-dependent root mean squared deviation (RMSD) of protein Cα atoms and ligand heavy atoms stabilized to a plateau in all but one trajectory (n=6). The distance between heme-iron and ω6 (C14, C15) double bond of AA in OBS also increased from 7.5 ± 1.4 Å to 8.5 ± 1.8 Å when CYP2J2 was simulated with only AA in OBS versus the presence of AA in both OBS and SBS (p<0.001), supporting the observed in vitro substrate inhibition phenomenon. Poor correlation was observed between inhibitory constants (Ki) determined for a panel of nine competitive and mixed mode xenobiotic inhibitors against CYP2J2 metabolism of AA as compared to AST, whereby 4 out of 9 drugs had a greater than 5-fold difference between Ki values. Nonlinear Eadie-Hofstee plots illustrated that complete substrate inhibition of CYP2J2 by AA was not attenuated even at high concentrations of xenobiotic inhibitors which further corroborates that CYP2J2 may accommodate three or more ligands simultaneously. In light of the atypical kinetics, our results highlight the importance of using physiologically-relevant substrates in in vitro enzymatic inhibition assays for the characterization of xenobiotic-endobiotic interactions which is applicable to other complex endogenous metabolic pathways beyond CYP2J2 metabolism of AA to EETs. The accurate determination of Ki would further facilitate the association of xenobiotic-endobiotic interactions to observed therapeutic or toxic outcomes.
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Affiliation(s)
- Jacqueline Wen Hui Leow
- Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore 117543
| | - Ravi Kumar Verma
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Amos Boon Hao Lim
- Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore 117543
| | - Hao Fan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Eric Chun Yong Chan
- Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore 117543.
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9
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Ducharme J, Polic V, Thibodeaux CJ, Auclair K. Combining Small-Molecule Bioconjugation and Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) to Expose Allostery: the Case of Human Cytochrome P450 3A4. ACS Chem Biol 2021; 16:882-890. [PMID: 33913317 DOI: 10.1021/acschembio.1c00084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report a novel approach to study allostery which combines the use of carefully selected bioconjugates and hydrogen-deuterium exchange mass spectrometry (HDX-MS). This strategy avoids issues related to weak substrate binding and ligand relocalization. The utility of our method is demonstrated using human cytochrome P450 3A4 (CYP3A4), the most important drug-metabolizing enzyme. Allosteric activation and inhibition of CYP3A4 by pharmaceuticals is an important mechanism of drug interactions. We performed HDX-MS analysis on several CYP3A4-effector bioconjugates, some of which mimic the allosteric effect of positive effectors, while others show activity enhancement even though the label does not occupy the allosteric pocket (agonistic) or do not show activation while still blocking the allosteric site (antagonistic). This allowed us to better define the position of the allosteric site, the protein structural dynamics associated with allosteric activation, and the presence of coexisting conformers.
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Affiliation(s)
- Julie Ducharme
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Vanja Polic
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Christopher J. Thibodeaux
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
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Denisov IG, Grinkova YV, Camp T, McLean MA, Sligar SG. Midazolam as a Probe for Drug-Drug Interactions Mediated by CYP3A4: Homotropic Allosteric Mechanism of Site-Specific Hydroxylation. Biochemistry 2021; 60:1670-1681. [PMID: 34015213 DOI: 10.1021/acs.biochem.1c00161] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We developed an efficient and sensitive probe for drug-drug interactions mediated by human CYP3A4 by using midazolam (MDZ) as a probe substrate. Using global analysis of four parameters over several experimental data sets, we demonstrate that the first MDZ molecule (MDZ1) binds with high affinity at the productive site near the heme iron and gives only hydroxylation at the 1 position (1OH). The second midazolam molecule (MDZ2) binds at an allosteric site at the membrane surface and perturbs the position and mobility of MDZ1 such that the minor hydroxylation product at the 4 position (4OH) is formed in a 1:2 ratio (35%). No increase in catalytic rate is observed after the second MDZ binding. Hence, the site of the 1OH:4OH metabolism ratio is a sensitive probe for drugs, such as progesterone, that bind with high affinity to the allosteric site and serve as effectors. We observe similar changes in the MDZ 1OH:4OH ratio in the presence of progesterone (PGS), suggesting a direct communication between the active and allosteric sites. Mutations introduced into the F-F' loop indicate that residues F213 and D214 are directly involved in allosteric interactions leading to MDZ homotropic cooperativity, and these same residues, together with L211, are involved in heterotropic allosteric interactions in which PGS is the effector and MDZ the substrate. Molecular dynamics simulations provide a mechanistic picture of the origin of this cooperativity. These results show that the midazolam can be used as a sensitive probe for drug-drug interactions in human P450 CYP3A4.
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11
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Niwa T, Toyota M, Kawasaki H, Ishii R, Sasaki S. Comparison of the Stimulatory and Inhibitory Effects of Steroid Hormones and α-Naphthoflavone on Steroid Hormone Hydroxylation Catalyzed by Human Cytochrome P450 3A Subfamilies. Biol Pharm Bull 2021; 44:579-584. [PMID: 33790108 DOI: 10.1248/bpb.b20-00987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The inhibitory and stimulatory effects of steroid hormones and related compounds on the hydroxylation activity at the 6β-position of two steroid hormones, progesterone and testosterone, by CYP3A4, polymorphically expressed CYP3A5, and fetal CYP3A7 were compared to clarify the catalytic properties of the predominant forms of the human CYP3A subfamily. Hydroxylation activities of progesterone and testosterone by CYP3A4, CYP3A5, and CYP3A7 were estimated using HPLC. The Michaelis constants (Km) for progesterone 6β-hydroxylation by CYP3A5 were markedly decreased in the presence of dehydroepiandrosterone (DHEA) and α-naphthoflavone (ANF), whereas progesterone and DHEA competitively inhibited testosterone 6β-hydroxylation mediated by CYP3A4, and progesterone competitively inhibited CYP3A5-mediated activity, which was weaker than that for CYP3A4. ANF noncompetitively inhibited testosterone 6β-hydroxylation mediated by both CYP3A4 and CYP3A5. Progesterone and testosterone 6β-hydroxylation mediated by CYP3A7 was inhibited or unaffected by DHEA, pregnenolone, and ANF. These results suggested that DHEA and ANF stimulated progesterone 6β-hydroxylation by CYP3A5 but not by CYP3A4 and CYP3A7; however, progesterone, DHEA, and ANF inhibited testosterone 6β-hydroxylation mediated by all CYP3A subfamily members. The inhibitory/stimulatory pattern of steroid-steroid interactions is different among CYP3A subfamily members and CYP3A5 is the most sensitive in terms of activation among the CYP3A subfamily members investigated.
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12
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Discovery of a Regulatory Subunit of the Yeast Fatty Acid Synthase. Cell 2020; 180:1130-1143.e20. [DOI: 10.1016/j.cell.2020.02.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/23/2019] [Accepted: 02/12/2020] [Indexed: 11/23/2022]
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13
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Atypical Michaelis-Menten kinetics in cytochrome P450 enzymes: A focus on substrate inhibition. Biochem Pharmacol 2019; 169:113615. [DOI: 10.1016/j.bcp.2019.08.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022]
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14
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Guengerich FP. Kinetic Modeling of Steady-State Situations in Cytochrome P450 Enzyme Reactions. Drug Metab Dispos 2019; 47:1232-1239. [PMID: 31427434 DOI: 10.1124/dmd.119.088732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/14/2019] [Indexed: 12/18/2022] Open
Abstract
In the course of investigations of the kinetics of individual reactions of cytochrome P450 (P450) enzymes, a number of points about the complexity of P450 enzyme kinetics have become apparent. Several of these are of particular relevance to work with P450 enzymes in the course of drug development and lead optimization, particularly with regard to estimating in vitro kinetic parameters and dealing with enzyme inhibitors. Modern simulation modeling has been applied to situations involving issues of preincubation time with moderate strength and strong inhibitors, inhibition by tightly bound ligands that have been identified in P450 enzymes, extensive substrate depletion, P450 reactions with a rate-limiting step after product formation, and the consumption of an inhibitor during a reaction by either a P450 enzyme being monitored or another one in a mixture. The results all follow from first principles, and simulations reveal the extent of their significance in various settings. The order of addition of substrate and inhibitors can change the apparent outcome (inhibition constant, K i), and the effect of the order is more pronounced with a stronger inhibitor. Substrate depletion alters parameters (Michaelis constant, K m) and can generate apparently sigmoidal plots. A rate-limiting step after product formation lowers the apparent K m and distorts K i Consumption of an inhibitor during a reaction affects K i and differs depending on which enzyme is involved. The results are relevant with P450 enzymes and other enzymes as well. SIGNIFICANCE STATEMENT: Kinetic simulations have been used to address several potential problems in enzyme kinetic analysis. Although the simulations done here are general for enzyme reactions, several problems addressed here are particularly relevant to cytochrome P450 reactions encountered in drug development work.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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15
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Wang PF, Neiner A, Kharasch ED. Efavirenz Metabolism: Influence of Polymorphic CYP2B6 Variants and Stereochemistry. Drug Metab Dispos 2019; 47:1195-1205. [PMID: 31324697 DOI: 10.1124/dmd.119.086348] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/10/2019] [Indexed: 01/11/2023] Open
Abstract
Efavirenz (more specifically the S-enantiomer) is a cornerstone antiretroviral therapy for treatment of HIV infection. The major primary metabolite is S-8-hydroxyefavirenz, which does not have antiretroviral activity but is neurotoxic. Cytochrome P450 2B6 (CYP2B6) is the major enzyme catalyzing S-8-hydroxyefavirenz formation. CYP2B6 genetics and drug interactions are major determinants of clinical efavirenz disposition and dose adjustment. In addition, as a prototypic CYP2B6 substrate, S-efavirenz and analogs can inform on the structure, activity, catalytic mechanisms, and stereoselectivity of CYP2B6. Metabolism of R-efavirenz by CYP2B6 remains unexplored. This investigation assessed S-efavirenz metabolism by clinically relevant CYP2B6 genetic variants. This investigation also evaluated R-efavirenz hydroxylation by wild-type CYP2B6.1 and CYP2B6 variants. S-Efavirenz 8-hydroxylation by wild-type CYP2B6.1 and variants exhibited positive cooperativity and apparent cooperative substrate inhibition. On the basis of Clmax values, relative activities for S-efavirenz 8-hydroxylation were in the order CYP2B6.4 > CYP2B6.1 ≈ CYP2B6.5 ≈ CYP2B6.17 > CYP2B6.6 ≈ CYP2B6.7 ≈ CYP2B6.9 ≈ CYP2B6.19 ≈ CYP2B6.26; CYP2B6.16 and CYP2B6.18 showed minimal activity. Rates of R-efavirenz metabolism were approximately 1/10 those of S-efavirenz for wild-type CYP2B6.1 and variants. On the basis of Clmax values, there was 14-fold enantioselectivity (S > R-efavirenz) for wild-type CYP2B6.1, and 5- to 22-fold differences for other CYP2B6 variants. These results show that both CYP2B6 516G > T (CYP2B6*6 and CYP2B6*9) and 983T > C (CYP2B6*16 and CYP2B6*18) polymorphisms cause canonical diminishment or loss-of-function variants for S-efavirenz 8-hydroxylation, provide a mechanistic basis for known clinical pharmacogenetic differences in efavirenz disposition, and may predict additional clinically important variant alleles. Efavirenz is the most stereoselective CYP2B6 drug substrate yet identified and may be a useful probe for the CYP2B6 active site and catalytic mechanisms. SIGNIFICANCE STATEMENT: Clinical disposition of the antiretroviral S-efavirenz is affected by CYP2B6 polymorphisms. Expressed CYP2B6 with 516G>T (CYP2B6*6 and CYP2B6*9), and 983T>C (CYP2B6*16 and CYP2B6*18) polymorphisms had a diminishment or loss of function for efavirenz 8-hydroxylation. This provides a mechanistic basis for efavirenz clinical pharmacogenetics and may predict additional clinically important variant alleles. Efavirenz metabolism showed both cooperativity and cooperative substrate inhibition. With greater than 10-fold enantioselectivity (S- vs. R- metabolism), efavirenz is the most stereoselective CYP2B6 drug substrate yet identified. These findings may provide mechanistic insights.
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Affiliation(s)
- Pan-Fen Wang
- Department of Anesthesiology, Duke University School of Medicine, Durham, North Carolina
| | - Alicia Neiner
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri.
| | - Evan D Kharasch
- Department of Anesthesiology, Duke University School of Medicine, Durham, North Carolina
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16
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Theoretical explanation for the pharmaceutical incompatibility through the cooperativity effect of the drug-drug intermolecular interactions in the phenobarbital∙∙∙paracetamol∙∙∙H 2O complex. J Mol Model 2019; 25:181. [PMID: 31175465 DOI: 10.1007/s00894-019-4060-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 04/30/2019] [Indexed: 02/08/2023]
Abstract
In order to reveal the essence of the pharmaceutical incompatibility, the cooperativity effects of the drug-drug intermolecular π∙∙∙π and H∙∙∙O H-bonding interactions involving hydration were evaluated in the phenobarbital∙∙∙paracetamol∙∙∙H2O complex at the M06-2X/6-311++G** and MP2/6-311++G** levels. The thermodynamic cooperativity effects were also investigated by the statistical thermodynamic method. The results show that the π∙∙∙π stacking ternary complexes with the moderate anti-cooperativity effects are dominant in controling the aggregation process of phenobarbital, paracetamol, and H2O, as is confirmed by the atoms-in-molecules (AIM) and reduced density gradient (RDG) analyses. Therefore, it can be inferred that the anti-cooperativity effect plays an important role in forming the pharmaceutical incompatibility, and thus a deduction on the formation process of the pharmaceutical incompatibility between phenobarbital and paracetamol, with the hydration effect, is given. Several valuable models that relate the features of molecular surface electrostatic potentials or their statistical parameters, such as the surface areas, average values ([Formula: see text]), variances ([Formula: see text], [Formula: see text] and [Formula: see text]), and product of [Formula: see text] and electrostatic balance parameter (ν) ([Formula: see text]ν), to the values of the cooperativity effects were predicted. The formation of the pharmaceutical incompatibility is a thermodynamic cooperativity process driven by the enthalpy change. Graphical abstract Anti-cooperativity effect plays an important role in forming the pharmaceutical incompatibility.
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17
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Denisov IG, Grinkova YV, Nandigrami P, Shekhar M, Tajkhorshid E, Sligar SG. Allosteric Interactions in Human Cytochrome P450 CYP3A4: The Role of Phenylalanine 213. Biochemistry 2019; 58:1411-1422. [PMID: 30785734 DOI: 10.1021/acs.biochem.8b01268] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of Phe213 in the allosteric mechanism of human cytochrome P450 CYP3A4 was studied using a combination of progesterone (PGS) and carbamazepine (CBZ) as probe substrates. We expressed, purified, and incorporated into POPC Nanodiscs three mutants, F213A, F213S, and F213Y, and compared them with wild-type (WT) CYP3A4 by monitoring spectral titration, the rate of NADPH oxidation, and steady-state product turnover rates with pure substrates and substrate mixtures. All mutants demonstrated higher activity with CBZ, lower activity with PGS, and a reduced level of activation of CBZ epoxidation by PGS, which was most pronounced in the F213A mutant. Using all-atom molecular dynamics simulations, we compared the dynamics of WT CYP3A4 and the F213A mutant incorporated into the lipid bilayer and the effect of the presence of the PGS molecule at the allosteric peripheral site and evaluated the critical role of Phe213 in mediating the heterotropic allosteric interactions in CYP3A4.
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18
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Ren T, Yang M, Xiao M, Zhu J, Xie W, Zuo Z. Time-dependent inhibition of carbamazepine metabolism by piperine in anti-epileptic treatment. Life Sci 2019; 218:314-323. [DOI: 10.1016/j.lfs.2018.12.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/31/2018] [Accepted: 12/31/2018] [Indexed: 11/25/2022]
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19
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Lin H, Yang J, Wang D, Hao G, Dong J, Wang Y, Yang W, Wu J, Zhan C, Yang G. Molecular insights into the mechanism of 4‐hydroxyphenylpyruvate dioxygenase inhibition: enzyme kinetics, X‐ray crystallography and computational simulations. FEBS J 2019; 286:975-990. [DOI: 10.1111/febs.14747] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/29/2018] [Accepted: 01/09/2019] [Indexed: 02/03/2023]
Affiliation(s)
- Hong‐Yan Lin
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health Chemical Biology Center College of Chemistry Central China Normal University Wuhan China
| | - Jing‐Fang Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health Chemical Biology Center College of Chemistry Central China Normal University Wuhan China
| | - Da‐Wei Wang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health Chemical Biology Center College of Chemistry Central China Normal University Wuhan China
| | - Ge‐Fei Hao
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health Chemical Biology Center College of Chemistry Central China Normal University Wuhan China
| | - Jiang‐Qing Dong
- MOE Key Laboratory of Protein Sciences Tsinghua‐Peking Center for Life Sciences School of Life Sciences Tsinghua University Beijing China
| | - Yu‐Xia Wang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health Chemical Biology Center College of Chemistry Central China Normal University Wuhan China
| | - Wen‐Chao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health Chemical Biology Center College of Chemistry Central China Normal University Wuhan China
| | - Jia‐Wei Wu
- MOE Key Laboratory of Protein Sciences Tsinghua‐Peking Center for Life Sciences School of Life Sciences Tsinghua University Beijing China
| | - Chang‐Guo Zhan
- Department of Pharmaceutical Sciences College of Pharmacy University of Kentucky Lexington KY USA
| | - Guang‐Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health Chemical Biology Center College of Chemistry Central China Normal University Wuhan China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
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20
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Somasundar Y, Shen LQ, Hoane AG, Tang LL, Mills MR, Burton AE, Ryabov AD, Collins TJ. Structural, Mechanistic, and Ultradilute Catalysis Portrayal of Substrate Inhibition in the TAML–Hydrogen Peroxide Catalytic Oxidation of the Persistent Drug and Micropollutant, Propranolol. J Am Chem Soc 2018; 140:12280-12289. [DOI: 10.1021/jacs.8b08108] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yogesh Somasundar
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Longzhu Q. Shen
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, U.K
| | - Alexis G. Hoane
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Liang L. Tang
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Matthew R. Mills
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Abigail E. Burton
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Alexander D. Ryabov
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Terrence J. Collins
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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21
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Affiliation(s)
- Yujie Liang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Xu Qiu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
- State Key Laboratory of Organometallic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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22
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Ewert J, Glück C, Strasdeit H, Fischer L, Stressler T. Influence of the metal ion on the enzyme activity and kinetics of PepA from Lactobacillus delbrueckii. Enzyme Microb Technol 2018; 110:69-78. [DOI: 10.1016/j.enzmictec.2017.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/13/2017] [Accepted: 10/10/2017] [Indexed: 10/18/2022]
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23
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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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24
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Kandel SE, Han LW, Mao Q, Lampe JN. Digging Deeper into CYP3A Testosterone Metabolism: Kinetic, Regioselectivity, and Stereoselectivity Differences between CYP3A4/5 and CYP3A7. Drug Metab Dispos 2017; 45:1266-1275. [PMID: 28986474 DOI: 10.1124/dmd.117.078055] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/04/2017] [Indexed: 01/22/2023] Open
Abstract
The metabolism of testosterone to 6β-hydroxytestosterone (6β-OH-T) is a commonly used assay to evaluate human CYP3A enzyme activities. However, previous reports have indicated that CYP3A7 also produces 2α-hydroxytestosterone (2α-OH-T) and that a 2α-OH-T/6β-OH-T ratio may be a unique endogenous biomarker of the activity of the enzyme. Until now, the full metabolite and kinetic profile for testosterone hydroxylation by CYP3A7 has not been fully examined. To this end, we performed a complete kinetic analysis of the 6β-OH-T, 2α-OH-T, and 2β-hydroxytestosterone metabolites for recombinant Supersome CYP3A4, CYP3A5, and CYP3A7 enzymes and monitored metabolism in fetal and adult human liver microsomes for comparison. In general, a decrease in the velocity of the reaction was observed between CYP3A4 and the two other enzymes, with CYP3A7 showing the lowest metabolic capacity. Interestingly, we found that the 2α-OH-T/6β-OH-T ratio varied with substrate concentration when testosterone was incubated with CYP3A7, suggesting that this ratio would likely not function well as a biomarker for CYP3A7 activity. In silico docking studies revealed at least two different binding modes for testosterone between CYP3A4 and CYP3A7. In CYP3A4, the most energetically favorable docking mode places testosterone in a position with the methyl groups directed toward the heme iron, which is more favorable for oxidation at C6β, whereas for CYP3A7 the testosterone methyl groups are positioned away from the heme, which is more favorable for an oxidation event at C2α In conclusion, our data indicate an alternative binding mode for testosterone in CYP3A7 that favors the 2α-hydroxylation, suggesting significant structural differences in its active site compared with CYP3A4/5.
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Affiliation(s)
- Sylvie E Kandel
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas (S.E.K., J.N.L.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (L.W.H., Q.M.); and The University of Kansas Liver Center, Kansas City, Kansas (J.N.L.)
| | - Lyrialle W Han
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas (S.E.K., J.N.L.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (L.W.H., Q.M.); and The University of Kansas Liver Center, Kansas City, Kansas (J.N.L.)
| | - Qingcheng Mao
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas (S.E.K., J.N.L.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (L.W.H., Q.M.); and The University of Kansas Liver Center, Kansas City, Kansas (J.N.L.)
| | - Jed N Lampe
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas (S.E.K., J.N.L.); Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (L.W.H., Q.M.); and The University of Kansas Liver Center, Kansas City, Kansas (J.N.L.)
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25
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Ducharme J, Auclair K. Use of bioconjugation with cytochrome P450 enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [PMID: 28625736 DOI: 10.1016/j.bbapap.2017.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bioconjugation, defined as chemical modification of biomolecules, is widely employed in biological and biophysical studies. It can expand functional diversity and enable applications ranging from biocatalysis, biosensing and even therapy. This review summarizes how chemical modifications of cytochrome P450 enzymes (P450s or CYPs) have contributed to improving our understanding of these enzymes. Genetic modifications of P450s have also proven very useful but are not covered in this review. Bioconjugation has served to gain structural information and investigate the mechanism of P450s via photoaffinity labeling, mechanism-based inhibition (MBI) and fluorescence studies. P450 surface acetylation and protein cross-linking have contributed to the investigation of protein complexes formation involving P450 and its redox partner or other P450 enzymes. Finally, covalent immobilization on polymer surfaces or electrodes has benefited the areas of biocatalysis and biosensor design. 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)
- Julie Ducharme
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
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26
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Tietz DR, Podust LM, Sherman DH, Pochapsky TC. Solution Conformations and Dynamics of Substrate-Bound Cytochrome P450 MycG. Biochemistry 2017; 56:2701-2714. [PMID: 28488849 DOI: 10.1021/acs.biochem.7b00291] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
MycG is a P450 monooxygenase that catalyzes the sequential hydroxylation and epoxidation of mycinamicin IV (M-IV), the last two steps in the biosynthesis of mycinamicin II, a macrolide antibiotic isolated from Micromonospora griseorubida. The crystal structure of MycG with M-IV bound was previously determined but showed the bound substrate in an orientation that did not rationalize the observed regiochemistry of M-IV hydroxylation. Nuclear magnetic resonance paramagnetic relaxation enhancements provided evidence of an orientation of M-IV in the MycG active site more compatible with the observed chemistry, but substrate-induced changes in the enzyme structure were not characterized. We now describe the use of amide 1H-15N residual dipolar couplings as experimental restraints in solvated "soft annealing" molecular dynamics simulations to generate solution structural ensembles of M-IV-bound MycG. Chemical shift perturbations, hydrogen-deuterium exchange, and 15N relaxation behavior provide insight into the dynamic and electronic perturbations in the MycG structure in response to M-IV binding. The solution and crystallographic structures are compared, and the possibility that the crystallographic orientation of bound M-IV represents an inhibitory mode is discussed.
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Affiliation(s)
| | - Larissa M Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California , San Diego, California 92093, United States
| | - David H Sherman
- Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109-2216, United States
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27
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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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28
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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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29
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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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30
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Aukema KG, Escalante DE, Maltby MM, Bera AK, Aksan A, Wackett LP. In Silico Identification of Bioremediation Potential: Carbamazepine and Other Recalcitrant Personal Care Products. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:880-888. [PMID: 27977154 DOI: 10.1021/acs.est.6b04345] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Emerging contaminants are principally personal care products not readily removed by conventional wastewater treatment and, with an increasing reliance on water recycling, become disseminated in drinking water supplies. Carbamazepine, a widely used neuroactive pharmaceutical, increasingly escapes wastewater treatment and is found in potable water. In this study, a mechanism is proposed by which carbamazepine resists biodegradation, and a previously unknown microbial biodegradation was predicted computationally. The prediction identified biphenyl dioxygenase from Paraburkholderia xenovorans LB400 as the best candidate enzyme for metabolizing carbamazepine. The rate of degradation described here is 40 times greater than the best reported rates. The metabolites cis-10,11-dihydroxy-10,11-dihydrocarbamazepine and cis-2,3-dihydroxy-2,3-dihydrocarbamazepine were demonstrated with the native organism and a recombinant host. The metabolites are considered nonharmful and mitigate the generation of carcinogenic acridine products known to form when advanced oxidation methods are used in water treatment. Other recalcitrant personal care products were subjected to prediction by the Pathway Prediction System and tested experimentally with P. xenovorans LB400. It was shown to biodegrade structurally diverse compounds. Predictions indicated hydrolase or oxygenase enzymes catalyzed the initial reactions. This study highlights the potential for using the growing body of enzyme-structural and genomic information with computational methods to rapidly identify enzymes and microorganisms that biodegrade emerging contaminants.
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Affiliation(s)
- Kelly G Aukema
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Diego E Escalante
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Meghan M Maltby
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Asim K Bera
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Alptekin Aksan
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
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Wei Y, Niu L, Liu X, Zhou H, Dong H, Kong D, Li Y, Li Q. Spectroscopic studies and molecular docking on the interaction of organotin antitumor compound bis[2,4-difluoro-N-(hydroxy-⟨κ⟩O)benzamidato-⟨κ⟩O]diphenyltin(IV) with human cytochrome P450 3A4 protease. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 163:154-161. [PMID: 27049867 DOI: 10.1016/j.saa.2016.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/11/2016] [Accepted: 03/15/2016] [Indexed: 06/05/2023]
Abstract
A novel organotin DFDPT was synthesized and characterized by elemental analysis, IR, (1)H, (13)C, (119)Sn, NMR techniques,etc. In order to investigate profoundly the relationship between DFDPT with human CYP3A4 proteaset and anticancer molecular mechanism of DFDPT, the intercalative mode of binding of DFDPT with CYP3A4 under physiological conditions were comprehensively evaluated using steady state, synchronous, three-dimensional fluorescence spectroscopy,circular dichroism and molecular docking. Fluorescence emission data showed that CYP3A4 fluorescence affected by DFDPT was a static quenching procedure, which implied that DFDPT-CYP3A4 complex had been formed. Apparent binding constants Kb of CYP3A4 with compound at 298 and 310K were 2.51×10(7) and 3.09×10(5), respectively. The binding sites number n was 1.64 and 1.22, respectively. The thermodynamic parameters ΔH and ΔS of the DFDPT-CYP3A4 complex were negative, which indicated that their interaction was driven mainly by hydrogen bonding and van der Waals force. The binding of DFDPT-CYP3A4 was spontaneous process in which ΔG was negative. The synchronous results showed DFDPT induced conformational changes of CYP3A4 protein. Three-dimensional fluorescence and circular dichroism spectra results also revealed conformation of CYP3A4 protein had been possible changed in the presence of DFDPT. Molecular docking was used to study the interaction orientation between DFDPT and CYP3A4 protease. The results indicated that DFDPT interacted with a panel of amino acids in the active sites of CYP3A4 protein mainly through formation of hydrogen bond. Furthermore, the predicted binding mode of DFDPT into CYP3A4 appeared to adopt an orientation with interactions among Arg105, Ser119 and Thr309.
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Affiliation(s)
- Ying Wei
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, PR China
| | - Lin Niu
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, PR China
| | - Xinxin Liu
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, PR China
| | - Hongyan Zhou
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, PR China
| | - Hongzhou Dong
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, PR China
| | - Depeng Kong
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, PR China
| | - Yunlan Li
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, PR China.
| | - Qingshan Li
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, PR China.
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32
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Nair PC, McKinnon RA, Miners JO. Cytochrome P450 structure–function: insights from molecular dynamics simulations. Drug Metab Rev 2016; 48:434-52. [DOI: 10.1080/03602532.2016.1178771] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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33
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Quesne MG, Senthilnathan D, Singh D, Kumar D, Maldivi P, Sorokin AB, de Visser SP. Origin of the Enhanced Reactivity of μ-Nitrido-Bridged Diiron(IV)-Oxo Porphyrinoid Complexes over Cytochrome P450 Compound I. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02720] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Matthew G. Quesne
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Dhurairajan Senthilnathan
- Univ. Grenoble Alpes, INAC-SCIB, Reconnaissance
Ionique et Chimie de Coordination, F-38000 Grenoble, France
- Center for
Computational Chemistry, CRD, PRIST University, Vallam, Thanjavur, Tamilnadu 613403, India
| | - Devendra Singh
- Department
of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow, Uttar Pradesh 226025, India
| | - Devesh Kumar
- Department
of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow, Uttar Pradesh 226025, India
| | - Pascale Maldivi
- Univ. Grenoble Alpes, INAC-SCIB, Reconnaissance
Ionique et Chimie de Coordination, F-38000 Grenoble, France
- CEA, INAC-SCIB, F-38000 Grenoble, France
| | - Alexander B. Sorokin
- Institut
de Recherches sur la Catalyse et l’Environnement de Lyon (IRCELYON),
UMR 5256, CNRS-Université Lyon 1, 2, av. A. Einstein, 69626 Villeurbanne, France
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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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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