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Feng Y, Gong C, Zhu J, Liu G, Tang Y, Li W. Unraveling the Ligand-Binding Sites of CYP3A4 by Molecular Dynamics Simulations with Solvent Probes. J Chem Inf Model 2024; 64:3451-3464. [PMID: 38593186 DOI: 10.1021/acs.jcim.4c00089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Cytochrome P450 3A4 (CYP3A4) is one of the most important drug-metabolizing enzymes in the human body and is well known for its complicated, atypical kinetic characteristics. The existence of multiple ligand-binding sites in CYP3A4 has been widely recognized as being capable of interfering with the active pocket through allosteric effects. The identification of ligand-binding sites other than the canonical active site above the heme is especially important for understanding the atypical kinetic characteristics of CYP3A4 and the intriguing association between the ligand and the receptor. In this study, we first employed mixed-solvent molecular dynamics (MixMD) simulations coupled with the online computational predictive tools to explore potential ligand-binding sites in CYP3A4. The MixMD approach demonstrates better performance in dealing with the receptor flexibility compared with other computational tools. From the sites identified by MixMD, we then picked out multiple sites for further exploration using ensemble docking and conventional molecular dynamics (cMD) simulations. Our results indicate that three extra sites are suitable for ligand binding in CYP3A4, including one experimentally confirmed site and two novel sites.
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Affiliation(s)
- Yanjun Feng
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Changda Gong
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jieyu Zhu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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2
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Yumoto Y, Endo T, Harada H, Kobayashi K, Nakabayashi T, Abe Y. High-throughput assay to simultaneously evaluate activation of CYP3A and the direct and time-dependent inhibition of CYP3A, CYP2C9, and CYP2D6 using liquid chromatography-tandem mass spectrometry. Xenobiotica 2024; 54:45-56. [PMID: 38265764 DOI: 10.1080/00498254.2024.2308818] [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: 10/25/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024]
Abstract
In the early stages of drug discovery, adequate evaluation of the potential drug-drug interactions (DDIs) of drug candidates is important. Several CYP3A activators are known to lead to underestimation of DDIs. These compounds affect midazolam 1'-hydroxylation but not midazolam 4-hydroxylation.We used both metabolic reactions of midazolam to evaluate the activation and inhibition of CYP3A activators simultaneously. For our CYP inhibition assay using cocktail probe substrates, simultaneous liquid chromatography-tandem mass spectrometry monitoring of 1'-hydroxymidazolam and 4-hydroxymidazolam for CYP3A was established in addition to monitoring of 4-hydroxydiclofenac and 1'-hydroxybufuralol for CYP2C9 and CYP2D6.The results of our cocktail inhibition assay were well correlated with those of a single inhibition assay, as were the estimated inhibition parameters for typical CYP3A inhibitors. In our assay, a proprietary compound that activated midazolam 1'-hydroxylation and tended to inhibit 4-hydroxylation was evaluated along with known CYP3A activators. All compounds were well characterised by comparison of the results of midazolam 1'- and 4-hydroxylation.In conclusion, our CYP cocktail inhibition assay can detect CYP3A activation and assess the direct and time-dependent inhibition potentials for CYP3A, CYP2C9, and CYP2D6. This method is expected to be very efficient in the early stages of drug discovery.
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Affiliation(s)
- Yu Yumoto
- Central Research Laboratories, Kissei Pharmaceutical Co., Ltd, Azumino, Nagano, Japan
| | - Takuro Endo
- Central Research Laboratories, Kissei Pharmaceutical Co., Ltd, Azumino, Nagano, Japan
| | - Hiroshi Harada
- Central Research Laboratories, Kissei Pharmaceutical Co., Ltd, Azumino, Nagano, Japan
| | - Kaoru Kobayashi
- Central Research Laboratories, Kissei Pharmaceutical Co., Ltd, Azumino, Nagano, Japan
| | - Takeshi Nakabayashi
- Central Research Laboratories, Kissei Pharmaceutical Co., Ltd, Azumino, Nagano, Japan
| | - Yoshikazu Abe
- Central Research Laboratories, Kissei Pharmaceutical Co., Ltd, Azumino, Nagano, Japan
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3
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Rougée LRA, Bedwell DW, Hansen K, Abraham TL, Hall SD. Impact of Heterotropic Allosteric Modulation on the Time-Dependent Inhibition of Cytochrome P450 3A4. Drug Metab Dispos 2023; 51:1372-1380. [PMID: 37524542 DOI: 10.1124/dmd.123.001382] [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: 05/02/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023] Open
Abstract
The current study was designed to investigate the influence of allosteric effectors on the metabolism of the prototypical cytochrome P450 (CYP) 3A4 substrate midazolam (MDZ), and on the determination in vitro time-dependent inhibition (TDI) of CYP3A4 using human liver microsomes (HLM). As the concentration of midazolam increased to 250 µM in HLMs, homotropic cooperativity resulted in a decrease in the 1'-hydroxymidazolam to 4-hydroxymidazolam ratio to a maximum of 1.1. The presence of varying concentrations of testosterone, progesterone (PGS), or carbamazepine (CBZ) in HLMs with MDZ could recapitulate the effect of homotropic cooperativity such that the formation rates of the 1'hydroxymidazolam and 4-hydroxymidazolam were equal even at low concentrations of MDZ. The presence of PGS (10 or 100 µM) and CBZ (100 or 1000 µM) in in vitro TDI determination of four known CYP3A4 time-dependent inactivators (clarithromycin, troleandomycin, mibefradil, raloxifene) simultaneously decreased potency and inactivation rate constant, resulting in fold changes in inactivation efficiency on average of 1.6-fold and 13-fold for the low and high concentrations of allosteric modulator tested, respectively. The formation of a metabolic-intermediate complex (MIC) for clarithromycin and troleandomycin decreased in the presence of the allosteric modulators in a concentration-dependent manner, reaching a new steady state formation that could not be overcome with increased incubation time. Maximum reduction of the MIC formed by clarithromycin was up to ∼91%, while troleandomycin MIC decreased up to ∼31%. These findings suggest that the absence of endogenous allosteric modulators may contribute to the poor translation of HLM-based drug-drug interaction predictions. SIGNIFICANCE STATEMENT: The reported overprediction of in vitro human liver microsome time-dependent inhibition of CYP3A4 and observed drug interactions in vivo remains an issue in drug development. We provide characterization of allosteric modulators on the CYP3A4 metabolism of the prototypical substrate midazolam, demonstrating the ability of the modulators to recapitulate the homotropic cooperativity of midazolam. Furthermore, we demonstrate that allosteric heterotropic cooperativity of CYP3A4 can impact the time-dependent inhibition kinetics of known mechanisms-based inhibitors, providing a potential mechanism to explain the overprediction.
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Affiliation(s)
- Luc R A Rougée
- Lilly Research Laboratories; Eli Lilly and Company, Indianapolis, Indiana
| | - David W Bedwell
- Lilly Research Laboratories; Eli Lilly and Company, Indianapolis, Indiana
| | - Kasi Hansen
- Lilly Research Laboratories; Eli Lilly and Company, Indianapolis, Indiana
| | - Trent L Abraham
- Lilly Research Laboratories; Eli Lilly and Company, Indianapolis, Indiana
| | - Stephen D Hall
- Lilly Research Laboratories; Eli Lilly and Company, Indianapolis, Indiana
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4
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Liu J, Kandel SE, Lampe JN, Scott EE. Human cytochrome P450 3A7 binding four copies of its native substrate dehydroepiandrosterone 3-sulfate. J Biol Chem 2023; 299:104993. [PMID: 37392852 PMCID: PMC10388207 DOI: 10.1016/j.jbc.2023.104993] [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: 04/19/2023] [Revised: 06/05/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
Human fetal cytochrome P450 3A7 (CYP3A7) is involved in both xenobiotic metabolism and the estriol biosynthetic pathway. Although much is understood about cytochrome P450 3A4 and its role in adult drug metabolism, CYP3A7 is poorly characterized in terms of its interactions with both categories of substrates. Herein, a crystallizable mutated form of CYP3A7 was saturated with its primary endogenous substrate dehydroepiandrosterone 3-sulfate (DHEA-S) to yield a 2.6 Å X-ray structure revealing the unexpected capacity to simultaneously bind four copies of DHEA-S. Two DHEA-S molecules are located in the active site proper, one in a ligand access channel, and one on the hydrophobic F'-G' surface normally embedded in the membrane. While neither DHEA-S binding nor metabolism exhibit cooperative kinetics, the current structure is consistent with cooperativity common to CYP3A enzymes. Overall, this information suggests that mechanism(s) of CYP3A7 interactions with steroidal substrates are complex.
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Affiliation(s)
- Jinghan Liu
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Sylvie E Kandel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, Colorado, USA
| | - Jed N Lampe
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, Colorado, USA
| | - Emily E Scott
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Departments of Pharmacology, Biological Chemistry and Programs in Chemical Biology and Biophysics, University of Michigan, Ann Arbor, Michigan, USA.
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Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site. Int J Mol Sci 2022; 23:ijms232012591. [PMID: 36293445 PMCID: PMC9604483 DOI: 10.3390/ijms232012591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 11/29/2022] Open
Abstract
Cytochrome P450 3A4 (CYP3A4) is a major human drug-metabolizing enzyme, notoriously known for its extreme substrate promiscuity, allosteric behavior, and implications in drug–drug interactions. Despite extensive investigations, the mechanism of ligand binding to CYP3A4 is not fully understood. We determined the crystal structure of CYP3A4 complexed with fluorol, a small fluorescent dye that can undergo hydroxylation. In the structure, fluorol associates to the substrate channel, well suited for the binding of planar polyaromatic molecules bearing polar groups, through which stabilizing H-bonds with the polar channel residues, such as Thr224 and Arg372, can be established. Mutagenesis, spectral, kinetic, and functional data confirmed the involvement but not strict requirement of Thr224 for the association of fluorol. Collectively, our data identify the substrate channel as a high-affinity ligand binding site and support the notion that hydrophobic ligands first dock to the nearby peripheral surface, before migrating to the channel and, subsequently, into the active site.
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Wang Z, Zeng Y, Jia H, Yang N, Liu M, Jiang M, Zheng Y. Bioconversion of vitamin D 3 to bioactive calcifediol and calcitriol as high-value compounds. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:109. [PMID: 36229827 PMCID: PMC9563128 DOI: 10.1186/s13068-022-02209-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022]
Abstract
Biological catalysis is an important approach for the production of high-value-added compounds, especially for products with complex structures. Limited by the complex steps of chemical synthesis and low yields, the bioconversion of vitamin D3 (VD3) to calcifediol and calcitriol, which are natural steroid products with high added value and significantly higher biological activity compared to VD3, is probably the most promising strategy for calcifediol and calcitriol production, and can be used as an alternative method for chemical synthesis. The conversion efficiency of VD3 to calcifediol and calcitriol has continued to rise in the past few decades with the help of several different VD3 hydroxylases, mostly cytochrome P450s (CYPs), and newly isolated strains. The production of calcifediol and calcitriol can be systematically increased in different ways. Specific CYPs and steroid C25 dehydrogenase (S25DH), as VD3 hydroxylases, are capable of converting VD3 to calcifediol and calcitriol. Some isolated actinomycetes have also been exploited for fermentative production of calcifediol and calcitriol, although the VD3 hydroxylases of these strains have not been elucidated. With the rapid development of synthetic biology and enzyme engineering, quite a lot of advances in bioproduction of calcifediol and calcitriol has been achieved in recent years. Therefore, here we review the successful strategies of promoting VD3 hydroxylation and provide some perspective on how to further improve the bioconversion of VD3 to calcifediol and calcitriol.
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Affiliation(s)
- Zheyi Wang
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049 China
| | - Yan Zeng
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Hongmin Jia
- China Animal Husbandry Industry Co. Ltd, Beijing, 100095 China
| | - Niping Yang
- grid.256885.40000 0004 1791 4722School of Life Sciences, Hebei University, No. 180 Wusi Dong Road, Baoding, 071002 China
| | - Mengshuang Liu
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049 China
| | - Mingyue Jiang
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049 China
| | - Yanning Zheng
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101 China
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7
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Bergström H, Lindahl A, Warnqvist A, Diczfalusy U, Ekström L, Björkhem‐Bergman L. Studies on CYP3A activity during the menstrual cycle as measured by urinary 6β-hydroxycortisol/cortisol. Pharmacol Res Perspect 2021; 9:e00884. [PMID: 34664787 PMCID: PMC8525181 DOI: 10.1002/prp2.884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/29/2021] [Accepted: 09/29/2021] [Indexed: 11/26/2022] Open
Abstract
The 6β-OH-cortisol/cortisol ratio (6β-OHC/C) in urine is an endogenous marker of drug-metabolizing enzyme cytochrome P450 3A (CYP3A). The primary aim of this single center, prospective, non-interventional cohort study, was to investigate the variability of 6β-OHC/C during the menstrual cycle. In addition, possible associations between the CYP3A activity and sex hormones, gut microbiota metabolite trimethylamine-N-Oxide (TMAO) and microRNA-27b, respectively, were investigated. Serum and urinary samples from healthy, regularly menstruating women followed for two menstrual cycles were analyzed. Twenty-six complete menstrual cycles including follicular, ovulatory, and luteal phase were defined based on hormone analyses in serum. 6β-OHC/C were analyzed in urine and sex hormones, TMAO and miRNA-27b were analyzed in serum at the same time points. 6β-OHC/C did not vary between the follicular, ovulatory, or luteal phases. There was a difference in the relative miRNA-27b expression between the follicular and ovulatory phase (p = .03). A significant association was found between 6β-OHC/C and progesterone during the follicular (p = .005) and ovulatory (p = .01) phases (n = 26 for each phase). In addition, a significant association was found between the ratio and TMAO during the ovulatory (p = .02) and luteal (p = .002) phases. 6β-OHC/C and gut microbiota TMAO were significantly associated (p = .003) when evaluating all values, for all phases (n = 78). Interestingly, the finding of an association between 6β-OHC/C in urine and levels of TMAO in serum suggest that gut microbiota may affect CYP3A activity.
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Affiliation(s)
- Helena Bergström
- Department of NeurobiologyCare Sciences and Society (NVS)Division of Clinical GeriatricsKarolinska InstitutetHuddingeSweden
| | - Anna Lindahl
- Department of Laboratory MedicineDivision of Clinical ChemistryKarolinska InstitutetStockholmSweden
- Department of Clinical ChemistryKarolinska University LaboratoryKarolinska University HospitalStockholmSweden
| | - Anna Warnqvist
- Department of Environmental MedicineDivision of BiostatisticsKarolinska InstitutetStockholmSweden
| | - Ulf Diczfalusy
- Department of Laboratory MedicineDivision of Clinical ChemistryKarolinska InstitutetStockholmSweden
- Department of Clinical ChemistryKarolinska University LaboratoryKarolinska University HospitalStockholmSweden
| | - Lena Ekström
- Department of Laboratory MedicineDivision of Clinical PharmacologyKarolinska InstitutetKarolinska University HospitalStockholmSweden
| | - Linda Björkhem‐Bergman
- Department of NeurobiologyCare Sciences and Society (NVS)Division of Clinical GeriatricsKarolinska InstitutetHuddingeSweden
- Department of Palliative MedicineStockholms SjukhemStockholmSweden
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8
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Zhang L, Wang Q. Harnessing P450 Enzyme for Biotechnology and Synthetic Biology. Chembiochem 2021; 23:e202100439. [PMID: 34542923 DOI: 10.1002/cbic.202100439] [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: 08/21/2021] [Revised: 09/18/2021] [Indexed: 12/29/2022]
Abstract
Cytochrome P450 enzymes (P450s, CYPs) catalyze the oxidative transformation of a wide range of organic substrates. Their functions are crucial to xenobiotic metabolism and steroid transformation in humans and other organisms. The enzymes are promising for synthetic biology applications but limited by several drawbacks including low turnover rates, poor stability, the dependance of expensive cofactors and redox partners, and the narrow substrate scope. To conquer these obstacles, emerging strategies including substrate engineering, usage of decoy and decoy-based small molecules auxiliaries, designing of artificial enzyme cascades and the incorporation of materials have been explored based on the unique properties of P450s. These strategies can be applied to a wide range of P450s and can be combined with protein engineering to improve the enzymatic activities. This minireview will focus on some recent developments of these strategies which have been used to leverage P450 catalysis. Remaining challenges and future opportunities will also be discussed.
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Affiliation(s)
- Libo Zhang
- Department of Chemistry and Biochemistry University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA.,Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Qian Wang
- Department of Chemistry and Biochemistry University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
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9
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Ducharme J, Sevrioukova IF, Thibodeaux CJ, Auclair K. Structural Dynamics of Cytochrome P450 3A4 in the Presence of Substrates and Cytochrome P450 Reductase. Biochemistry 2021; 60:2259-2271. [PMID: 34196520 DOI: 10.1021/acs.biochem.1c00178] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450 3A4 (CYP3A4) is the most important drug-metabolizing enzyme in humans and has been associated with harmful drug interactions. The activity of CYP3A4 is known to be modulated by several compounds and by the electron transfer partner, cytochrome P450 reductase (CPR). The underlying mechanism of these effects, however, is poorly understood. We have used hydrogen-deuterium exchange mass spectrometry to investigate the impact of binding of CPR and of three different substrates (7-benzyloxy-4-trifluoromethyl-coumarin, testosterone, and progesterone) on the conformational dynamics of CYP3A4. Here, we report that interaction of CYP3A4 with substrates or with the oxidized or reduced forms of CPR leads to a global rigidification of the CYP3A4 structure. This was evident from the suppression of deuterium exchange in several regions of CYP3A4, including regions known to be involved in protein-protein interactions (helix C) and substrate binding and specificity (helices B' and E, and loop K/β1). Furthermore, the bimodal isotopic distributions observed for some CYP3A4-derived peptides were drastically impacted upon binding to CPR and/or substrates, suggesting the existence of stable CYP3A4 conformational populations that are perturbed by ligand/CPR binding. The results have implications for understanding the mechanisms of ligand binding, allostery, and catalysis in CYP enzymes.
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Affiliation(s)
- Julie Ducharme
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Christopher J Thibodeaux
- 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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10
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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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11
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Dangi B, Davydova NY, Maldonado MA, Abbasi A, Vavilov NE, Zgoda VG, Davydov DR. Effects of alcohol-induced increase in CYP2E1 content in human liver microsomes on the activity and cooperativity of CYP3A4. Arch Biochem Biophys 2021; 698:108677. [PMID: 33197431 PMCID: PMC7856178 DOI: 10.1016/j.abb.2020.108677] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/15/2020] [Accepted: 11/08/2020] [Indexed: 12/23/2022]
Abstract
We investigate the effect of the alcohol-induced increase in the content of CYP2E1 in human liver microsomes (HLM) on the function of CYP3A4. Membrane incorporation of the purified CYP2E1 into HLM considerably increases the rate of metabolism of 7-benzyloxyquinoline (BQ) and attenuates the homotropic cooperativity observed with this CYP3A4-specific substrate. It also eliminates the activating effect of α-naphthoflavone (ANF) seen in some HLM samples. To probe the physiological relevance of these effects, we compared three pooled preparations of HLM from normal donors (HLM-N) with a pooled preparation from ten heavy alcohol consumers (HLM-A). The composition of the P450 pool in all samples was characterized by the mass-spectrometric determination of 11 cytochrome P450 species. The fractional content of CYP2E1 in HLM-A was from 2.0 to 3.4 times higher than in HLM-N. In contrast, the content of CYP3A4 in HLM-A was the lowest among all samples. Despite that, HLM-A exhibited a much higher metabolism rate and a lower homotropic cooperativity with BQ, similar to CYP2E1-enriched HLM-N. To substantiate the involvement of interactions between CYP2E1 and CYP3A4 in these effects, we probed hetero-association of these proteins in CYP3A4-containing Supersomes™ with a technique employing CYP2E1 labeled with BODIPY-618 maleimide. These experiments evinced the interactions between the two enzymes and revealed an inhibitory effect of ANF on their association. Our results demonstrate that the functional properties of CYP3A4 are fundamentally dependent on the composition of the cytochrome P450 ensemble and suggest a possible impact of chronic alcohol exposure on the pharmacokinetics of drugs metabolized by CYP3A4.
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Affiliation(s)
- Bikash Dangi
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Nadezhda Y Davydova
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Marc A Maldonado
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Armina Abbasi
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | | | - Victor G Zgoda
- Institute of Biomedical Chemistry, Moscow, 119121, Russia; Skolkovo Institute of Science and Technology, 143025, Skolkovo, Moscow Region, Russia
| | - Dmitri R Davydov
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA.
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