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Mokhosoev IM, Astakhov DV, Terentiev AA, Moldogazieva NT. Cytochrome P450 monooxygenase systems: Diversity and plasticity for adaptive stress response. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 193:19-34. [PMID: 39245215 DOI: 10.1016/j.pbiomolbio.2024.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/21/2024] [Accepted: 09/04/2024] [Indexed: 09/10/2024]
Abstract
Superfamily of cytochromes P450 (CYPs) is composed of heme-thiolate-containing monooxygenase enzymes, which play crucial roles in the biosynthesis, bioactivation, and detoxification of a variety of organic compounds, both endogenic and exogenic. Majority of CYP monooxygenase systems are multi-component and contain various redox partners, cofactors and auxiliary proteins, which contribute to their diversity in both prokaryotes and eukaryotes. Recent progress in bioinformatics and computational biology approaches make it possible to undertake whole-genome and phylogenetic analyses of CYPomes of a variety of organisms. Considerable variations in sequences within and between CYP families and high similarity in secondary and tertiary structures between all CYPs along with dramatic conformational changes in secondary structure elements of a substrate binding site during catalysis have been reported. This provides structural plasticity and substrate promiscuity, which underlie functional diversity of CYPs. Gene duplication and mutation events underlie CYP evolutionary diversity and emergence of novel selectable functions, which provide the involvement of CYPs in high adaptability to changing environmental conditions and dietary restrictions. In our review, we discuss the recent advancements and challenges in the elucidating the evolutionary origin and mechanisms underlying the CYP monooxygenase system diversity and plasticity. Our review is in the view of hypothesis that diversity of CYP monooxygenase systems is translated into the broad metabolic profiles, and this has been acquired during the long evolutionary time to provide structural plasticity leading to high adaptative capabilities to environmental stress conditions.
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Affiliation(s)
| | - Dmitry V Astakhov
- Department of Biochemistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991, Moscow, Russia
| | - Alexander A Terentiev
- Department of Biochemistry and Molecular Biology, N.I. Pirogov Russian National Research Medical University, 117997, Moscow, Russia
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2
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Iori S, Lahtela-Kakkonen M, D'Onofrio C, Maietti F, Mucignat G, Bardhi A, Barbarossa A, Zaghini A, Pauletto M, Dacasto M, Giantin M. New insights into aflatoxin B1 mechanistic toxicology in cattle liver: an integrated approach using molecular docking and biological evaluation in CYP1A1 and CYP3A74 knockout BFH12 cell lines. Arch Toxicol 2024; 98:3097-3108. [PMID: 38834875 PMCID: PMC11324698 DOI: 10.1007/s00204-024-03799-y] [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: 01/29/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024]
Abstract
Aflatoxin B1 (AFB1) is a pro-carcinogenic compound bioactivated in the liver by cytochromes P450 (CYPs). In mammals, CYP1A and CYP3A are responsible for AFB1 metabolism, with the formation of the genotoxic carcinogens AFB1-8,9-epoxide and AFM1, and the detoxified metabolite AFQ1. Due to climate change, AFB1 cereals contamination arose in Europe. Thus, cattle, as other farm animals fed with grains (pig, sheep and broiler), are more likely exposed to AFB1 via feed with consequent release of AFM1 in milk, posing a great concern to human health. However, knowledge about bovine CYPs involved in AFB1 metabolism is still scanty. Therefore, CYP1A1- and CYP3A74-mediated molecular mechanisms of AFB1 hepatotoxicity were here dissected. Molecular docking of AFB1 into CYP1A1 model suggested AFB1 8,9-endo- and 8,9-exo-epoxide, and AFM1 formation, while docking of AFB1 into CYP3A74 pointed to AFB1 8,9-exo-epoxide and AFQ1 synthesis. To biologically confirm these predictions, CYP1A1 and CYP3A74 knockout (KO) BFH12 cell lines were exposed to AFB1. LC-MS/MS investigations showed the abolished production of AFM1 in CYP1A1 KO cells and the strong increase of parent AFB1 in CYP3A74 KO cells; the latter result, coupled to a decreased cytotoxicity, suggested the major role of CYP3A74 in AFB1 8,9-exo-epoxide formation. Finally, RNA-sequencing analysis indirectly proved lower AFB1-induced cytotoxic effects in engineered cells versus naïve ones. Overall, this study broadens the knowledge on AFB1 metabolism and hepatotoxicity in cattle, and it provides the weight of evidence that CYP1A1 and CYP3A74 inhibition might be exploited to reduce AFM1 and AFBO synthesis, AFB1 toxicity, and AFM1 milk excretion.
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Affiliation(s)
- Silvia Iori
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Maija Lahtela-Kakkonen
- School of Pharmacy, University of Eastern Finland, Yliopistonrinne 3, 70210, Kuopio, Finland
| | - Caterina D'Onofrio
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Federica Maietti
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Greta Mucignat
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Anisa Bardhi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Via Tolara di Sopra 50, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Andrea Barbarossa
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Via Tolara di Sopra 50, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Anna Zaghini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Via Tolara di Sopra 50, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy.
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3
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Musyoka K, Chan CW, Gutiérrez Rico EM, Omondi P, Kijogi C, Okai T, Kongere J, Ngara M, Kagaya W, Kanoi BN, Hiratsuka M, Kido Y, Gitaka J, Kaneko A. Genetic variation present in the CYP3A4 gene in Ni-Vanuatu and Kenyan populations in malaria endemicity. Drug Metab Pharmacokinet 2024; 57:101029. [PMID: 39079373 DOI: 10.1016/j.dmpk.2024.101029] [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: 04/11/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 08/21/2024]
Abstract
Cytochrome P450 3A4 (CYP3A4) enzyme is involved in the metabolism of about 30 % of clinically used drugs, including the antimalarials artemether and lumefantrine. CYP3A4 polymorphisms yield enzymatic variants that contribute to inter-individual variation in drug metabolism. Here, we examined CYP3A4 polymorphisms in populations from malaria-endemic islands in Lake Victoria, Kenya, and Vanuatu, to expand on the limited data sets. We used archived dried blood spots collected from 142 Kenyan and 263 ni-Vanuatu adults during cross-sectional malaria surveys in 2013 and 2005-13, respectively, to detect CYP3A4 variation by polymerase chain reaction (PCR) and sequencing. In Kenya, we identified 14 CYP3A4 single nucleotide polymorphisms (SNPs), including the 4713G (CYP3A4∗1B; allele frequency 83.9 %) and 19382A (CYP3A4∗15; 0.7 %) variants that were previously linked to altered metabolism of antimalarials. In Vanuatu, we detected 15 SNPs, including the 4713A (CYP3A4∗1A; 88.6 %) and 25183C (CYP3A4∗18; 0.6 %) variants. Additionally, we detected a rare and novel SNP C4614T (0.8 %) in the 5' untranslated region. A higher proportion of CYP3A4 genetic variance was found among ni-Vanuatu populations (16 %) than among Lake Victoria Kenyan populations (8 %). Our work augments the scarce data sets and contributes to improved precision medicine approaches, particularly to anti-malarial chemotherapy, in East African and Pacific Islander populations.
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Affiliation(s)
- Kelvin Musyoka
- Department of Virology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Chim W Chan
- Department of Parasitology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Evelyn Marie Gutiérrez Rico
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Protus Omondi
- Department of Virology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Caroline Kijogi
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Takatsugu Okai
- Department of Virology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - James Kongere
- Department of Virology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Mtakai Ngara
- Island Malaria Group, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Wataru Kagaya
- Department of Eco-epidemiology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Bernard N Kanoi
- Centre for Research in Infectious Diseases, Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya; Centre for Malaria Elimination, Mount Kenya University, Thika, Kenya
| | - Masahiro Hiratsuka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yasutoshi Kido
- Department of Virology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Jesse Gitaka
- Centre for Research in Infectious Diseases, Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya; Centre for Malaria Elimination, Mount Kenya University, Thika, Kenya
| | - Akira Kaneko
- Department of Parasitology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan; Island Malaria Group, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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4
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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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5
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Zhou TP, Feng J, Wang Y, Li S, Wang B. Substrate Conformational Switch Enables the Stereoselective Dimerization in P450 NascB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations. JACS AU 2024; 4:1591-1604. [PMID: 38665654 PMCID: PMC11040706 DOI: 10.1021/jacsau.4c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024]
Abstract
P450 NascB catalyzes the coupling of cyclo-(l-tryptophan-l-proline) (1) to generate (-)-naseseazine C (2) through intramolecular C-N bond formation and intermolecular C-C coupling. A thorough understanding of its catalytic mechanism is crucial for the engineering or design of P450-catalyzed C-N dimerization reactions. By employing MD simulations, QM/MM calculations, and enhanced sampling, we assessed various mechanisms from recent works. Our study demonstrates that the most favorable pathway entails the transfer of a hydrogen atom from N7-H to Cpd I. Subsequently, there is a conformational change in the substrate radical, shifting it from the Re-face to the Si-face of N7 in Substrate 1. The Si-face conformation of Substrate 1 is stabilized by the protein environment and the π-π stacking interaction between the indole ring and heme porphyrin. The subsequent intermolecular C3-C6' bond formation between Substrate 1 radical and Substrate 2 occurs via a radical attack mechanism. The conformational switch of the Substrate 1 radical not only lowers the barrier of the intermolecular C3-C6' bond formation but also yields the correct stereoselectivity observed in experiments. In addition, we evaluated the reactivity of the ferric-superoxide species, showing it is not reactive enough to initiate the hydrogen atom abstraction from the indole NH group of the substrate. Our simulation provides a comprehensive mechanistic insight into how the P450 enzyme precisely controls both the intramolecular C-N cyclization and intermolecular C-C coupling. The current findings align with the available experimental data, emphasizing the pivotal role of substrate dynamics in governing P450 catalysis.
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Affiliation(s)
- Tai-Ping Zhou
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jianqiang Feng
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yongchao Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shengying Li
- State
Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Binju Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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6
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Ackad EM, Biggers L, Meister M, Kontoyianni M. Equilibrium landscape of ingress/egress channels and gating residues of the Cytochrome P450 3A4. PLoS One 2024; 19:e0298424. [PMID: 38498575 PMCID: PMC10947690 DOI: 10.1371/journal.pone.0298424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 01/24/2024] [Indexed: 03/20/2024] Open
Abstract
The Cytochrome P450 (CYP) enzymes metabolize a variety of drugs, which may potentially lead to toxicity or reduced efficacy when drugs are co-administered. These drug-drug interactions are often manifested by CYP3A4, the most prevalent of all CYP isozymes. We carried out multiple MD simulations employing CAVER to quantify the channels, and Hidden Markov Models (HMM) to characterize the behavior of the gating residues. We discuss channel properties, bottleneck residues with respect to their likelihood to deem the respective channel ingress or egress, gating residues regarding their open or closed states, and channel location relative to the membrane. Channels do not display coordinated motion and randomly transition between different conformations. Gateway residues also behave in a random fashion. Our findings shed light on the equilibrium behavior of the gating residues and channels in the apo state.
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Affiliation(s)
- Edward Michael Ackad
- Department of Physics, Southern Illinois University Edwardsville, Edwardsville, IL, United States of America
| | - Laurence Biggers
- Department of Internal Medicine at UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Mary Meister
- University of Illinois College of Medicine, Chicago, IL, United States of America
| | - Maria Kontoyianni
- Department of Pharmaceutical Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, United States of America
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7
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Fu T, Zhang H, Zheng Q. Assessing the role of residue Phe108 of cytochrome P450 3A4 in allosteric effects of midazolam metabolism. Phys Chem Chem Phys 2024; 26:8807-8814. [PMID: 38421040 DOI: 10.1039/d3cp05270b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Cytochrome P450 3A4 (CYP3A4) is involved in the metabolism of more drugs in clinical use than any other xenobiotic-metabolizing enzyme. CYP3A4-mediated drug metabolism is usually allosterically modulated by substrate concentration (homotropic allostery) and other drugs (heterotropic allostery), exhibiting unusual kinetic profiles and regiospecific metabolism. Recent studies suggest that residue Phe108 (F108) of CYP3A4 may have an important role in drug metabolism. In this work, residue mutations were coupled with well-tempered metadynamics simulations to assess the importance of F108 in the allosteric effects of midazolam metabolism. Comparing the simulation results of the wild-type and mutation systems, we identify that the π-π interaction and steric effect between the F108 side chain and midazolam is favorable for the stable binding of substrate in the active site. F108 also plays an important role in the transition of substrate binding mode, which mainly induces the transition of substrate binding mode by forming π-π interactions with multiple aromatic rings of the substrate. Moreover, the side chain of F108 is closely related to the radius and depth of the 2a and 2f channels, and F108 may further regulate drug metabolism by affecting the pathway, orientation, or time of substrate entry into the CYP3A4 active site or product egress from the active site. Altogether, we suggest that F108 affects drug metabolism and regulatory mechanisms by affecting substrate binding stability, binding mode transition, and channel characteristics of CYP3A4. Our findings could promote the understanding of complicated allosteric mechanisms in CYP3A4-mediated drug metabolism, and the knowledge could be used for drug development and disease treatment.
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Affiliation(s)
- Tingting Fu
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, China.
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Hongxing Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Qingchuan Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, China.
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
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8
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Qi Y, Yang H, Wang S, Zou L, Zhao F, Zhang Q, Hong Y, Luo Q, Zhou Q, Geng P, Chen H, Ji F, Cai J, Dai D. Identification and Functional Assessment of Eight CYP3A4 Allelic Variants *39-*46 Detected in the Chinese Han Population. Drug Metab Dispos 2024; 52:218-227. [PMID: 38195522 DOI: 10.1124/dmd.123.001542] [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: 09/20/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Cytochrome P450 3A4 (CYP3A4), a key enzyme, is pivotal in metabolizing approximately half of the drugs used clinically. The genetic polymorphism of the CYP3A4 gene significantly influences individual variations in drug metabolism, potentially leading to severe adverse drug reactions (ADRs). In this study, we conducted a genetic analysis on CYP3A4 gene in 1163 Chinese Han individuals to identify the genetic variations that might affect their drug metabolism capabilities. For this purpose, a multiplex polymerase chain reaction (PCR) amplicon sequencing technique was developed, enabling us to perform the genotyping of CYP3A4 gene efficiently and economically on a large scale. As a result, a total of 14 CYP3A4 allelic variants were identified, comprising six previously reported alleles and eight new nonsynonymous variants that were nominated as new allelic variants *39-*46 by the PharmVar Association. Further, functional assessments of these novel CYP3A4 variants were undertaken by coexpressing them with cytochromes P450 oxidoreductase (CYPOR) in Saccharomyces cerevisiae microsomes. Immunoblot analysis indicated that with the exception of CYP3A4.40 and CYP3A4.45, the protein expression levels of most new variants were similar to that of the wild-type CYP3A4.1 in yeast cells. To evaluate their catalytic activities, midazolam was used as a probe drug. The results showed that variant CYP3A4.45 had almost no catalytic activity, whereas the other variants exhibited significantly reduced drug metabolism abilities. This suggests that the majority of the CYP3A4 variants identified in the Chinese population possess markedly altered capacities for drug metabolism. SIGNIFICANCE STATEMENT: In this study, we established a multiplex polymerase chain reaction (PCR) amplicon sequencing method and detected the maximum number of new CYP3A4 variants in a single ethnic population. Additionally, we performed the functional characterizations of these eight novel CYP3A4 allele variants in vitro. This study not only contributes to the understanding of CYP3A4 genetic polymorphism in the Chinese Han population but also holds substantial reference value for their potential clinical applications in personalized medicine.
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Affiliation(s)
- Yuying Qi
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hang Yang
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuanghu Wang
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lili Zou
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fangling Zhao
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Qing Zhang
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yun Hong
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Qingfeng Luo
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Quan Zhou
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Peiwu Geng
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hao Chen
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fusui Ji
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jianping Cai
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Dapeng Dai
- Peking University Fifth School of Clinical Medicine, Beijing, China (Y.Q., H.Y., D.D.); The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China (H.Y., F.Z., J.C.); Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, China (S.W., Q.Z., P.G.); and Department of Cardiology (L.Z., Q.Z., H.C., F.J.) and Department of Gastroenterology (Y.H., Q.L.), Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
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9
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Sahil M, Singh T, Ghosh S, Mondal J. 3site Multisubstrate-Bound State of Cytochrome P450cam. J Am Chem Soc 2023; 145:23488-23502. [PMID: 37867463 DOI: 10.1021/jacs.3c06144] [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: 10/24/2023]
Abstract
We identified a multisubstrate-bound state, hereby referred as a 3site state, in cytochrome P450cam via integrating molecular dynamics simulation with nuclear magnetic resonance (NMR) pseudocontact shift measurements. The 3site state is a result of simultaneous binding of three camphor molecules in three locations around P450cam: (a) in a well-established "catalytic" site near heme, (b) in a kink-separated "waiting" site along channel-1, and (c) in a previously reported "allosteric" site at E, F, G, and H helical junctions. These three spatially distinct binding modes in the 3site state mutually communicate with each other via homotropic allostery and act cooperatively to render P450cam functional. The 3site state shows a significantly superior fit with NMR pseudo contact shift (PCS) data with a Q-score of 0.045 than previously known bound states and consists of D251 free of salt-bridges with K178 and R186, rendering the enzyme functionally primed. To date, none of the reported cocomplex of P450cam with its redox partner putidaredoxin (pdx) has been able to match solution NMR data and controversial pdx-induced opening of P450cam's channel-1 remains a matter of recurrent discourse. In this regard, inclusion of pdx to the 3site state is able to perfectly fit the NMR PCS measurement with a Q-score of 0.08 and disfavors the pdx-induced opening of channel-1, reconciling previously unexplained remarkably fast hydroxylation kinetics with a koff of 10.2 s-1. Together, our findings hint that previous experimental observations may have inadvertently captured the 3site state as an in vitro solution state, instead of the catalytic state alone, and provided a distinct departure from the conventional understanding of cytochrome P450.
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Affiliation(s)
- Mohammad Sahil
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Tejender Singh
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Soumya Ghosh
- Tata Institute of Fundamental Research, Hyderabad 500046, India
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10
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Liu S, Zheng Q, Bai F. Differences of Atomic-Level Interactions between Midazolam and Two CYP Isoforms 3A4 and 3A5. Molecules 2023; 28:6900. [PMID: 37836743 PMCID: PMC10574787 DOI: 10.3390/molecules28196900] [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: 07/16/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
CYP 3A4 and CYP 3A5 are two important members of the human cytochrome P450 family. Although their overall structures are similar, the local structures of the active site are different, which directly leads to obvious individual differences in drug metabolic efficacy and toxicity. In this work, midazolam (MDZ) was selected as the probe substrate, and its interaction with two proteins, CYP 3A4 and CYP 3A5, was studied by molecular dynamics simulation (MD) along with the calculation of the binding free energy. The results show that two protein-substrate complexes have some similarities in enzyme-substrate binding; that is, in both complexes, Ser119 forms a high occupancy hydrogen bond with MDZ, which plays a key role in the stability of the interaction between MDZ and the enzymes. However, the complex formed by CYP 3A4 and MDZ is more stable, which may be attributed to the sandwich structure formed by the fluorophenyl group of the substrate with Leu216 and Leu482. Our study interprets the binding differences between two isoform-substrate complexes and reveals a structure-function relationship from the atomic perspective, which is expected to provide a theoretical basis for accurately measuring the effectiveness and toxicity of drugs for individuals in the era of precision medicine.
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Affiliation(s)
- Shuhui Liu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China;
- School and Hospital of Stomatology, Jilin University, Changchun 130023, China
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China;
| | - Fuquan Bai
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China;
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11
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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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12
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Zhang J, Liu F, Suo Y, Tong D, Hu J, Lyu H, Liao J, Wang J, Wang J, Xu C. The "outsized" role of the I-helix kink in human Cytochrome P450s. Clin Transl Med 2023; 13:e1378. [PMID: 37712170 PMCID: PMC10502461 DOI: 10.1002/ctm2.1378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023] Open
Affiliation(s)
- Jingjing Zhang
- Department of NephrologyShenzhen Key Laboratory of Kidney DiseasesShenzhen Clinical Research Centre for GeriatricsShenzhen People's Hospital, The First Affiliated HospitalSouthern University of Science and TechnologyShenzhenP. R. China
- Integrated Chinese and Western Medicine Postdoctoral Research StationJinan UniversityGuangzhouP. R. China
| | - Fengting Liu
- Department of NephrologyShenzhen Key Laboratory of Kidney DiseasesShenzhen Clinical Research Centre for GeriatricsShenzhen People's Hospital, The First Affiliated HospitalSouthern University of Science and TechnologyShenzhenP. R. China
| | - Yaran Suo
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, Artemisinin Research Centerand Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingP. R. China
| | - Dudu Tong
- Department of NephrologyShenzhen Key Laboratory of Kidney DiseasesShenzhen Clinical Research Centre for GeriatricsShenzhen People's Hospital, The First Affiliated HospitalSouthern University of Science and TechnologyShenzhenP. R. China
| | - Jinyu Hu
- Department of NephrologyShenzhen Key Laboratory of Kidney DiseasesShenzhen Clinical Research Centre for GeriatricsShenzhen People's Hospital, The First Affiliated HospitalSouthern University of Science and TechnologyShenzhenP. R. China
| | - Hai‐Ning Lyu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, Artemisinin Research Centerand Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingP. R. China
| | - Jingjing Liao
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, Artemisinin Research Centerand Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingP. R. China
| | - Jiaqi Wang
- School of Pharmaceutical Sciences (Shenzhen)Shenzhen Campus of Sun Yat‐sen UniversityShenzhenP. R. China
| | - Jigang Wang
- Department of NephrologyShenzhen Key Laboratory of Kidney DiseasesShenzhen Clinical Research Centre for GeriatricsShenzhen People's Hospital, The First Affiliated HospitalSouthern University of Science and TechnologyShenzhenP. R. China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, Artemisinin Research Centerand Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingP. R. China
| | - Chengchao Xu
- Department of NephrologyShenzhen Key Laboratory of Kidney DiseasesShenzhen Clinical Research Centre for GeriatricsShenzhen People's Hospital, The First Affiliated HospitalSouthern University of Science and TechnologyShenzhenP. R. China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, Artemisinin Research Centerand Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingP. R. China
- College of Integrative MedicineLaboratory of PathophysiologyKey Laboratory of Integrative Medicine on Chronic DiseasesFujian University of Traditional Chinese MedicineFuzhouP. R. China
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13
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Paço L, Hackett JC, Atkins WM. Nanodisc-embedded cytochrome P450 P3A4 binds diverse ligands by distributing conformational dynamics to its flexible elements. J Inorg Biochem 2023; 244:112211. [PMID: 37080138 PMCID: PMC10175226 DOI: 10.1016/j.jinorgbio.2023.112211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/12/2023] [Accepted: 04/03/2023] [Indexed: 04/22/2023]
Abstract
Cytochrome P450 3A4 (CYP3A4) metabolizes a wide range of drugs and toxins. Interactions of CYP3A4 with ligands are difficult to predict due to promiscuity and conformational flexibility. To better understand CYP3A4 conformational responses to ligands we use hydrogen deuterium exchange mass spectrometry (HDX-MS) to investigate the effect of ligands on nanodisc-embedded CYP3A4. For a subset of CYP3A4-ligand complexes, differences in the low-frequency modes derived by principal component analyses of molecular dynamics trajectories mirrored the HDX-MS results. The effects of ligands are distributed to flexible elements of CYP3A4 between stretches of secondary structure. The largest effects occur in the F- and G-helices, where most ligands increase the flexibility of the F-helix and connecting loops and decrease the flexibility of the C-term of the G-helix. Most ligands affect the E-F-G, CD and HI regions of the protein. Ligand-dependent differences are observed in the A"-A' loop, BC region, E-helix, K-β1 region, proximal loop, and C-term loop. Correlated HDX responses were observed in the CD region and the C-term of the G-helix that were most pronounced for Type II ligands. Collectively, the HDX and molecular dynamics results suggest that CYP3A4 accommodates diverse binding partners by propagating local backbone fluctuations from the binding site onto the flexible regions of the enzyme via long-range interactions that are differentially modulated by ligands. In contrast to the paradigm wherein ligands decrease protein dynamics at their binding site, a wide range of ligands modestly increase CYP3A4 dynamics throughout the protein including effects remote from the active site.
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Affiliation(s)
- Lorela Paço
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, United States of America
| | - John C Hackett
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States of America
| | - William M Atkins
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, United States of America.
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14
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Lawson R, Čechová P, Zarrouk E, Javellaud J, Bazgier V, Otyepka M, Trouillas P, Picard N, Marquet P, Saint-Marcoux F, El Balkhi S. Metabolic interactions of benzodiazepines with oxycodone ex vivo and toxicity depending on usage patterns in an animal model. Br J Pharmacol 2023; 180:829-842. [PMID: 34855983 DOI: 10.1111/bph.15765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 09/16/2021] [Accepted: 11/03/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND AND PURPOSE Opioids and benzodiazepines are frequently combined in medical as well as in non-medical contexts. At high doses, such combinations often result in serious health complications attributed to pharmacodynamics interactions. Here, we investigate the contribution of the metabolic interactions between oxycodone, diazepam and diclazepam (a designer benzodiazepine) in abuse/overdose conditions through ex vivo, in vivo and in silico approaches. EXPERIMENTAL APPROACH A preparation of pooled human liver microsomes was used to study oxycodone metabolism in the presence or absence of diazepam or diclazepam. In mice, diazepam or diclazepam was concomitantly administered with oxycodone to mimic acute intoxication. Diclazepam was introduced on Day 10 in mice continuously infused with oxycodone for 15 days to mimic chronic intoxication. In silico modelling was used to study the molecular interactions of the three drugs with CYP3A4 and 2D6. KEY RESULTS In mice, in acute conditions, both diazepam and diclazepam inhibited the metabolism of oxycodone. In chronic conditions and at pharmacologically equivalent doses, diclazepam drastically enhanced the production of oxymorphone. In silico, the affinity of benzodiazepines was higher than oxycodone for CYP3A4, inhibiting oxycodone metabolism through CYP3A4. Oxycodone metabolism is likely to be diverted towards CYP2D6. CONCLUSION AND IMPLICATIONS Acute doses of diazepam or diclazepam result in the accumulation of oxycodone, whereas chronic administration induces the accumulation of oxymorphone, the toxic metabolite. This suggests that overdoses of opioids in the presence of benzodiazepines are partly due to metabolic interactions, which in turn explain the patterns of toxicity dependent on usage. LINKED ARTICLES This article is part of a themed issue on Advances in Opioid Pharmacology at the Time of the Opioid Epidemic. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v180.7/issuetoc.
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Affiliation(s)
- Roland Lawson
- University of Limoges, IPPRITT, Limoges, France.,INSERM, IPPRITT, U1248, Limoges, France
| | - Petra Čechová
- Regional Center of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Olomouc, Czechia
| | - Eliès Zarrouk
- University of Limoges, IPPRITT, Limoges, France.,INSERM, IPPRITT, U1248, Limoges, France
| | - James Javellaud
- University of Limoges, IPPRITT, Limoges, France.,INSERM, IPPRITT, U1248, Limoges, France
| | - Václav Bazgier
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Olomouc, Czechia
| | - Patrick Trouillas
- University of Limoges, IPPRITT, Limoges, France.,INSERM, IPPRITT, U1248, Limoges, France.,Regional Center of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Olomouc, Czechia
| | - Nicolas Picard
- University of Limoges, IPPRITT, Limoges, France.,INSERM, IPPRITT, U1248, Limoges, France.,Department of Pharmacology, Toxicology and Pharmacovigilance, CHU Limoges, Limoges, France
| | - Pierre Marquet
- University of Limoges, IPPRITT, Limoges, France.,INSERM, IPPRITT, U1248, Limoges, France.,Department of Pharmacology, Toxicology and Pharmacovigilance, CHU Limoges, Limoges, France
| | - Franck Saint-Marcoux
- University of Limoges, IPPRITT, Limoges, France.,INSERM, IPPRITT, U1248, Limoges, France.,Department of Pharmacology, Toxicology and Pharmacovigilance, CHU Limoges, Limoges, France
| | - Souleiman El Balkhi
- INSERM, IPPRITT, U1248, Limoges, France.,Department of Pharmacology, Toxicology and Pharmacovigilance, CHU Limoges, Limoges, France
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15
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High hepatic and plasma exposures of atorvastatin in subjects harboring impaired cytochrome P450 3A4∗16 modeled after virtual administrations and possibly associated with statin intolerance found in the Japanese adverse drug event report database. Drug Metab Pharmacokinet 2023; 49:100486. [PMID: 36746706 DOI: 10.1016/j.dmpk.2022.100486] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/13/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]
Abstract
Drug interactions between atorvastatin and cytochrome P450 (P450) 3A substrates/inhibitors lead to an increased incidence of skeletal muscle or hepatic toxicity. However, in this survey, among 483 Japanese subjects administered atorvastatin alone, more than half (258) experienced statin intolerance and were unable to continue using the drug. Although many factors underly atorvastatin toxicity, the intrinsic clearance rate might be a contributing causal factor. The impaired P450 3A4 p.Thr185Ser variant, CYP3A4∗16 (rs12721627), has been identified in East Asians with an allele frequency of 2.2%. Pharmacokinetically modeled plasma concentrations of atorvastatin increased after a virtual oral dose of 40 mg in CYP3A4∗16 homozygotes; the maximum concentration and area under the concentration curve, respectively, were 3.3-fold and 4.2-fold those in subjects homozygous for CYP3A4∗1. In subjects with CYP3A4∗16/∗16, the virtual hepatic concentrations of atorvastatin after daily doses of 10 mg for a week were similar to or higher than the plasma concentrations. These results suggest that the estimated high virtual plasma and hepatic exposures obtained by pharmacokinetic modeling in subjects harboring impaired allele CYP3A4∗16 may be one of the causal factors for statin intolerance in a manner similar to the well-known drug interactions caused by co-administrations of CYP3A inhibitors.
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16
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Denison M, Ahrens JJ, Dunbar MN, Warmahaye H, Majeed A, Turro C, Kocarek TA, Sevrioukova IF, Kodanko JJ. Dynamic Ir(III) Photosensors for the Major Human Drug-Metabolizing Enzyme Cytochrome P450 3A4. Inorg Chem 2023; 62:3305-3320. [PMID: 36758158 PMCID: PMC10268476 DOI: 10.1021/acs.inorgchem.3c00059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Probing the activity of cytochrome P450 3A4 (CYP3A4) is critical for monitoring the metabolism of pharmaceuticals and identifying drug-drug interactions. A library of Ir(III) probes that detect occupancy of the CYP3A4 active site were synthesized and characterized. These probes show selectivity for CYP3A4 inhibition, low cellular toxicity, Kd values as low as 9 nM, and are highly emissive with lifetimes up to 3.8 μs in cell growth media under aerobic conditions. These long emission lifetimes allow for time-resolved gating to distinguish probe from background autofluorescence from growth media and live cells. X-ray crystallographic analysis revealed structure-activity relationships and the preference or indifference of CYP3A4 toward resolved stereoisomers. Ir(III)-based probes show emission quenching upon CYP3A4 binding, then emission increases following displacement with CYP3A4 inhibitors or substrates. Importantly, the lead probes inhibit the activity of CYP3A4 at concentrations as low as 300 nM in CYP3A4-overexpressing HepG2 cells that accurately mimic human hepatic drug metabolism. Thus, the Ir(III)-based agents show promise as novel chemical tools for monitoring CYP3A4 active site occupancy in a high-throughput manner to gain insight into drug metabolism and drug-drug interactions.
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Affiliation(s)
- Madeline Denison
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, United States
| | - Justin J Ahrens
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, United States
| | - Marilyn N Dunbar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Habon Warmahaye
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Aliza Majeed
- Institute of Environmental Health Sciences, Wayne State University, 6135 Woodward Avenue, Integrative Biosciences Center, Room 2126, Detroit, Michigan 48202, United States
| | - Claudia Turro
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Thomas A Kocarek
- Institute of Environmental Health Sciences, Wayne State University, 6135 Woodward Avenue, Integrative Biosciences Center, Room 2126, Detroit, Michigan 48202, United States
| | - Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Jeremy J Kodanko
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, Michigan 48202, United States
- Barbara Ann Karmanos Cancer Institute, Detroit, Michigan 48201, United States
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17
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Fu T, Zhang H, Zheng Q. Molecular Insights into the Heterotropic Allosteric Mechanism in Cytochrome P450 3A4-Mediated Midazolam Metabolism. J Chem Inf Model 2022; 62:5762-5770. [PMID: 36342224 DOI: 10.1021/acs.jcim.2c01264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cytochrome P450 3A4 (CYP3A4) is the main P450 enzyme for drug metabolism and drug-drug interactions (DDIs), as it is involved in the metabolic process of approximately 50% of drugs. A detailed mechanistic elucidation of DDIs mediated by CYP3A4 is commonly believed to be critical for drug optimization and rational use. Here, two typical probes, midazolam (MDZ, substrate) and testosterone (TST, allosteric effector), are used to investigate the molecular mechanism of CYP3A4-mediated heterotropic allosteric interactions, through conventional molecular dynamics (cMD) and well-tempered metadynamics (WT-MTD) simulations. Distance monitoring shows that TST can stably bind in two potential peripheral sites (Site 1 and Site 2) of CYP3A4. The binding of TST at these two sites can induce conformational changes in CYP3A4 flexible loops on the basis of conformational analysis, thereby promoting the transition of the MDZ binding mode and affecting the ratio of MDZ metabolites. According to the results of the residue interaction network, multiple allosteric communication pathways are identified that can provide vivid and applicable insights into the heterotropic allostery of TST on MDZ metabolism. Comparing the regulatory effects and the communication pathways, the allosteric effect caused by TST binding in Site 2 seems to be more pronounced than in Site 1. Our findings could provide a deeper understanding of CYP3A4-mediated heterotropic allostery at the atomic level and would be helpful for rational drug use as well as the design of new allosteric modulators.
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Affiliation(s)
- Tingting Fu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Hongxing Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130023, China
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Changes in Alprazolam Metabolism by CYP3A43 Mutants. Biomedicines 2022; 10:biomedicines10123022. [PMID: 36551778 PMCID: PMC9775082 DOI: 10.3390/biomedicines10123022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/03/2022] [Accepted: 11/06/2022] [Indexed: 11/25/2022] Open
Abstract
Alprazolam is a triazolobenzodiazepine which is most commonly used in the short-term management of anxiety disorders, often in combination with antipsychotics. The four human members of the CYP3A subfamily are mainly responsible for its metabolism, which yields the main metabolites 4-hydroxyalprazolam and α-hydroxyalprazolam. We performed a comparison of alprazolam metabolism by all four CYP3A enzymes upon recombinant expression in the fission yeast Schizosaccharomyces pombe. CYP3A4 and CYP3A5 show the highest 4-hydroxyalprazolam production rates, while CYP3A5 alone is the major producer of α-hydroxyalprazolam. For both metabolites, CYP3A7 and CYP3A43 show lower activities. Computational simulations rationalize the difference in preferred oxidation sites observed between the exemplary enzymes CYP3A5 and CYP3A43. Investigations of the alprazolam metabolites formed by three previously described CYP3A43 mutants (L293P, T409R, and P340A) unexpectedly revealed that they produce 4-hydroxy-, but not α-hydroxyalprazolam. Instead, they all also make a different metabolite, which is 5-N-O alprazolam. With respect to 4-hydroxyalprazolam, the mutants showed fourfold (T409R) to sixfold (L293P and P340A) higher production rates compared to the wild-type (CYP3A43.1). In the case of 5-N-O alprazolam, the production rates were similar for the three mutants, while no formation of this metabolite was found in the wild-type incubation.
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Alshabani LA, Kumar A, Willcocks SJ, Srithiran G, Bhakta S, Estrada DF, Simons C. Synthesis, biological evaluation and computational studies of pyrazole derivatives as Mycobacterium tuberculosis CYP121A1 inhibitors. RSC Med Chem 2022; 13:1350-1360. [PMID: 36426236 PMCID: PMC9667784 DOI: 10.1039/d2md00155a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/12/2022] [Indexed: 07/25/2023] Open
Abstract
A series of imidazole and triazole diarylpyrazole derivatives were prepared using an efficient 5-step synthetic scheme and evaluated for binding affinity with Mycobacterium tuberculosis (Mtb) CYP121A1 and antimycobacterial activity against Mtb H37Rv. Antimycobacterial susceptibility was measured using the spot-culture growth inhibition assay (SPOTi): the imidazoles displayed minimum inhibitory concentration (MIC90) in the range of 3.95-12.03 μg mL-1 (10.07-33.19 μM) with 11f the most active, while the triazoles displayed MIC90 in the range of 4.35-25.63 μg mL-1 (11.88-70.53 μM) with 12b the most active. Assessment of binding affinity using UV-vis spectroscopy showed that for the imidazole series, the propyloxy (11f) and isopropyloxy (11h) derivatives of the 4-chloroaryl pyrazoles displayed Mtb CYP121A1 type II binding affinity with K d 11.73 and 17.72 μM respectively compared with the natural substrate cYY (K d 12.28 μM), while in the triazole series, only the methoxy substitution with the 4-chloroaryl pyrazole (12b) showed good type II Mtb CYP121A1 binding affinity (K d 5.13 μM). Protein-detected 1D 19F-NMR spectroscopy as an orthogonal strategy was used to evaluate ligand binding independent of perturbations at the haem. For imidazole and triazole compounds, perturbations were more intense than cYY indicating tighter binding and confirming that ligand coordination occurs in the substrate-binding pocket despite very modest changes in UV-vis absorbance, consistent with computational studies and the demonstrated potential anti-tuberculosis properties of these compounds.
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Affiliation(s)
- Lama A Alshabani
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University King Edward VII Avenue Cardiff CF10 3NB UK
| | - Amit Kumar
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Science, University at Buffalo Buffalo New York-14203 USA
| | - Sam J Willcocks
- Department of Infection Biology, The London School of Hygiene and Tropical Medicine London WC1E 7HT UK
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London London WC1E 7HX UK
| | - Gayathri Srithiran
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London London WC1E 7HX UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London London WC1E 7HX UK
| | - D Fernando Estrada
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Science, University at Buffalo Buffalo New York-14203 USA
| | - Claire Simons
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University King Edward VII Avenue Cardiff CF10 3NB UK
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20
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Mateev E, Balkanska-Mitkova T, Peikova L, Dimitrova M, Kondeva-Burdina M. In vitro and in silico inhibition performance of choline against CYP1A2, CYP2D6 and CYP3A4. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2144452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Emilio Mateev
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria
| | - Tony Balkanska-Mitkova
- Department of Pharmacology, Pharmacotherapy and Toxicology, Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria
| | - Lily Peikova
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria
| | - Maria Dimitrova
- Department of Organization and Economics of Pharmacy, Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria
| | - Magdalena Kondeva-Burdina
- Department of Pharmacology, Pharmacotherapy and Toxicology, Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria
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21
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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 Y, Shi J, Dai D, Cai J, Wang S, Hong Y, Zhou S, Zhao F, Zhou Q, Geng P, Zhou Y, Xu X, Luo Q. Evaluation of commonly used cardiovascular drugs in inhibiting vonoprazan metabolism in vitro and in vivo. Front Pharmacol 2022; 13:909168. [PMID: 36052128 PMCID: PMC9424819 DOI: 10.3389/fphar.2022.909168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
As a novel acid-suppressing drug, vonoprazan shows the potential to replace traditional proton-pump inhibitors. With its widespread use, some adverse effects that require further study have emerged due to drug–drug interactions. Our study is the first experiment that evaluated the drug–drug interactions of eleven common cardiovascular drugs that inhibit vonoprazan metabolism in vitro and in vivo. Rat liver microsome incubation and molecular simulation docking were applied to explore the inhibition mechanism. Amlodipine and nifedipine showed inhibitory effects on vonoprazan metabolism in both rat and human liver microsomes in the first evaluation part in vitro. The inhibition mechanism analysis results demonstrated that amlodipine and nifedipine might inhibit the metabolism of vonoprazan by a mixed type of competitive and non-competitive inhibition. However, the pharmacokinetic data of the vonoprazan prototype revealed that amlodipine affected vonoprazan in vivo while nifedipine did not. Thus, more attention should be paid when amlodipine is prescribed with vonoprazan. Furthermore, the changes in its carboxylic acid metabolites MI hinted at a complex situation. Molecular simulation suggested the CYP2B6 enzyme may contribute more to this than CYP3A4, and further inhibitory experiments preliminarily verified this speculation. In conclusion, the use of vonoprazan with cardiovascular drugs, especially amlodipine, should receive particular attention in clinical prescriptions.
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Affiliation(s)
- Yiran Wang
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Jihua Shi
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Dapeng Dai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Jianping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Shuanghu Wang
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, China
| | - Yun Hong
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Zhou
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Fangling Zhao
- Peking University Fifth School of Clinical Medicine, Beijing, China
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Quan Zhou
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, China
| | - Peiwu Geng
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, China
| | - Yunfang Zhou
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, China
| | - Xue Xu
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Qingfeng Luo
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Qingfeng Luo,
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23
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Kabir M, Padilha EC, Shah P, Huang R, Sakamuru S, Gonzalez E, Ye L, Hu X, Henderson MJ, Xia M, Xu X. Identification of Selective CYP3A7 and CYP3A4 Substrates and Inhibitors Using a High-Throughput Screening Platform. Front Pharmacol 2022; 13:899536. [PMID: 35847040 PMCID: PMC9283723 DOI: 10.3389/fphar.2022.899536] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/27/2022] [Indexed: 11/26/2022] Open
Abstract
Cytochrome P450 (CYP) 3A7 is one of the major xenobiotic metabolizing enzymes in human embryonic, fetal, and newborn liver. CYP3A7 expression has also been observed in a subset of the adult population, including pregnant women, as well as in various cancer patients. The characterization of CYP3A7 is not as extensive as other CYPs, and health authorities have yet to provide guidance towards DDI assessment. To identify potential CYP3A7-specific molecules, we used a P450-Glo CYP3A7 enzyme assay to screen a library of ∼5,000 compounds, including FDA-approved drugs and drug-like molecules, and compared these screening data with that from a P450-Glo CYP3A4 assay. Additionally, a subset of 1,000 randomly selected compounds were tested in a metabolic stability assay. By combining the data from the qHTS P450-Glo and metabolic stability assays, we identified several chemical features important for CYP3A7 selectivity. Halometasone was chosen for further evaluation as a potential CYP3A7-selective inhibitor using molecular docking. From the metabolic stability assay, we identified twenty-two CYP3A7-selective substrates over CYP3A4 in supersome setting. Our data shows that CYP3A7 has ligand promiscuity, much like CYP3A4. Furthermore, we have established a large, high-quality dataset that can be used in predictive modeling for future drug metabolism and interaction studies.
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Affiliation(s)
- Md Kabir
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- Department of Pharmacology, The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Elias C. Padilha
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Pranav Shah
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Ruili Huang
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Srilatha Sakamuru
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Eric Gonzalez
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- Novartis Institutes for BioMedical Research, Cambridge, MA, United States
| | - Lin Ye
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Xin Hu
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Mark J. Henderson
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Menghang Xia
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- *Correspondence: Menghang Xia, ; Xin Xu,
| | - Xin Xu
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- *Correspondence: Menghang Xia, ; Xin Xu,
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24
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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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25
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Hong Y, Dai DP, Cai JP, Wang SH, Wang YR, Zhao FL, Zhou S, Zhou Q, Geng PW, Zhou YF, Xu X, Shi JH, Luo QF. Effects of Simvastatin on the Metabolism of Vonoprazan in Rats Both in vitro and in vivo. Drug Des Devel Ther 2022; 16:1779-1789. [PMID: 35707687 PMCID: PMC9191837 DOI: 10.2147/dddt.s365610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/02/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Yun Hong
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People’s Republic of China
| | - Da-Peng Dai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, People’s Republic of China
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, People’s Republic of China
| | - Shuang-Hu Wang
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, 323020, People’s Republic of China
| | - Yi-Ran Wang
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People’s Republic of China
- Peking University Fifth School of Clinical Medicine, Beijing, 100730, People’s Republic of China
| | - Fang-Ling Zhao
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, People’s Republic of China
- Peking University Fifth School of Clinical Medicine, Beijing, 100730, People’s Republic of China
| | - Shan Zhou
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, People’s Republic of China
| | - Quan Zhou
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, 323020, People’s Republic of China
| | - Pei-Wu Geng
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, 323020, People’s Republic of China
| | - Yun-Fang Zhou
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, 323020, People’s Republic of China
| | - Xue Xu
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People’s Republic of China
| | - Ji-Hua Shi
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People’s Republic of China
| | - Qing-Feng Luo
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People’s Republic of China
- Correspondence: Qing-Feng Luo, Department of Gastroenterology, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People’s Republic of China, Tel + 86 138 1151 9095, Email
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26
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Koulgi S, Jani V, Phukan S, Sonavane U, Joshi R, Kamboj RK, Palle V. A Deep Dive into the Conformational Dynamics of CYP3A4 : Understanding the Binding of Homotropic and Non‐homotropic Ligands for Mitigating Drug‐Drug interaction (DDI). ChemistrySelect 2022. [DOI: 10.1002/slct.202200249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shruti Koulgi
- High Performance Computing – Medical and Bioinformatics Applications Group Centre for Development of Advanced Computing C–DAC Innovation Park, Panchawati, Pashan Pune 411 008 India
| | - Vinod Jani
- High Performance Computing – Medical and Bioinformatics Applications Group Centre for Development of Advanced Computing C–DAC Innovation Park, Panchawati, Pashan Pune 411 008 India
| | - Samiron Phukan
- Lupin Limited (Research Park), Nande Village Pune 412115 India
| | - Uddhavesh Sonavane
- High Performance Computing – Medical and Bioinformatics Applications Group Centre for Development of Advanced Computing C–DAC Innovation Park, Panchawati, Pashan Pune 411 008 India
| | - Rajendra Joshi
- High Performance Computing – Medical and Bioinformatics Applications Group Centre for Development of Advanced Computing C–DAC Innovation Park, Panchawati, Pashan Pune 411 008 India
| | | | - Venkata Palle
- Lupin Limited (Research Park), Nande Village Pune 412115 India
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27
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Ridhwan MJM, Bakar SIA, Latip NA, Ghani NA, Ismail NH. A Comprehensive Analysis of Human CYP3A4 Crystal Structures as a Potential Tool for Molecular Docking-Based Site of Metabolism and Enzyme Inhibition Studies. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2022; 21:259-285. [DOI: 10.1142/s2737416522300012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The notable ability of human liver cytochrome P450 3A4 (CYP3A4) to metabolize diverse xenobiotics encourages researchers to explore in-depth the mechanism of enzyme action. Numerous CYP3A4 protein crystal structures have been deposited in protein data bank (PDB) and are majorly used in molecular docking analysis. The quality of the molecular docking results depends on the three-dimensional CYP3A4 protein crystal structures from the PDB. Present review endeavors to provide a brief outline of some technical parameters of CYP3A4 PDB entries as valuable information for molecular docking research. PDB entries between 22 April 2004 and 2 June 2021 were compiled and the active sites were thoroughly observed. The present review identified 76 deposited PDB entries and described basic information that includes CYP3A4 from human genetic, Escherichia coli (E. coli) use for protein expression, crystal structure obtained from X-ray diffraction method, taxonomy ID 9606, Uniprot ID P08684, ligand–protein structure description, co-crystal ligand, protein site deposit and resolution ranges between 1.7[Formula: see text]Å and 2.95[Formula: see text]Å. The observation of protein–ligand interactions showed the various residues on the active site depending on the ligand. The residues Ala305, Ser119, Ala370, Phe304, Phe108, Phe213 and Phe215 have been found to frequently interact with ligands from CYP3A4 PDB. Literature surveys of 17 co-crystal ligands reveal multiple mechanisms that include competitive inhibition, noncompetitive inhibition, mixed-mode inhibition, mechanism-based inhibition, substrate with metabolite, inducer, or combination modes of action. This overview may help researchers choose a trustworthy CYP3A4 protein structure from the PDB database to apply the protein in molecular docking analysis for drug discovery.
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Affiliation(s)
- Mohamad Jemain Mohamad Ridhwan
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam 40450, Selangor, Malaysia
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
| | - Syahrul Imran Abu Bakar
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam 40450, Selangor, Malaysia
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
| | - Normala Abd Latip
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
| | - Nurunajah Ab Ghani
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam 40450, Selangor, Malaysia
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
| | - Nor Hadiani Ismail
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam 40450, Selangor, Malaysia
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
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28
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Fu T, Zheng Q, Zhang H. Investigation of the molecular and mechanistic basis for the regioselective metabolism of midazolam by cytochrome P450 3A4. Phys Chem Chem Phys 2022; 24:8104-8112. [PMID: 35319551 DOI: 10.1039/d2cp00232a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cytochrome P450 3A4 (CYP3A4) is the most important P450 enzyme for drug metabolism and drug-drug interaction, due to it being responsible for the biotransformation of approximately 50% of clinically used drugs. Advance knowledge of the molecular and mechanistic basis of CYP3A4 regioselective metabolism is beneficial for understanding the production of metabolites, and may allow personalized metabolic pathways or designing pathway-specific therapeutics. In this work, we focus on investigating the ligand-receptor interactions, substrate conformational transition, and key factors regulating the specificity of metabolic pathways using midazolam (MDZ) as a probe. Here, three types of substrate-binding conformations related to the diversity of MDZ metabolites are identified. The results also suggest that an allosteric site for MDZ is located near the F'-helix, A-anchor, and C-terminal loop of CYP3A4. The presence of an effector in the allosteric site can accelerate the conformational transition of the substrate via modulating a "sandwich" structure, and may affect the proportion of metabolites at high substrate concentration. We hope that the results can improve the understanding of the CYP3A4 structure and function, and provide a new perspective for drug development.
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Affiliation(s)
- Tingting Fu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China.
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China. .,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130023, China
| | - Hongxing Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China.
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29
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Krenc D, Na-Bangchang K. Spectroscopic observations of β-eudesmol binding to human cytochrome P450 isoforms 3A4 and 1A2, but not to isoforms 2C9, 2C19 and 2D6. Xenobiotica 2022; 52:199-208. [PMID: 35139770 DOI: 10.1080/00498254.2022.2037168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
β-Eudesmol is a sesquiterpenoid component o Atractylodes lancea with cytotoxic activity against cholangiocarcinoma. Its lipophilic nature makes β-eudesmol a likely substrate of human cytochrome P450 (P450) enzymes.Using ligand-binding difference spectroscopy, the affinities of this compound to recombinant CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4 were investigated in Escherichia coli membrane preparations.CYP3A4 showed a type I spectral change, with a binding constant Ks of 77 ± 23 (mean ± SD) μM at 0.5 μM P450 (Ks/[P450] ≈ 155). The reference substrate testosterone and the inhibitor fluconazole bound to the enzyme with apparent affinities of 86 ± 4 μM (type I) and 21 μM (type II), respectively. β-Eudesmol was bound to CYP3A4 in a non-cooperative manner (Hill coefficient n ≈ 0.8). CYP1A2 showed reverse type I difference spectra with either β-eudesmol or caffeine. The CYP1A2 affinity for β-eudesmol was higher (0.23 mM) than for caffeine (0.37 mM) but lower than for phenacetin (0.11 mM, type I). β-Eudesmol did not bind significantly to CYP2C9, CYP2C19, and CYP2D6.Confirmation of metabolic activity and studies on the involvement of other human P450 isoforms studies are required. Double-beam spectrometry is needed to validate Ks measurements made with a plate reader.
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Affiliation(s)
- Dawid Krenc
- Chulabhorn International College of Medicine, Thammasat University, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Kesara Na-Bangchang
- Graduate Program in Bioclinical Sciences, Chulabhorn International College of Medicine, Thammasat University, Khlong Luang, Pathum Thani, 12120, Thailand.,Center of Excellence in Pharmacology and Molecular Biology of Malaria and Cholangiocarcinoma, Chulabhorn International College of Medicine, Thammasat University, Khlong Luang, Pathum Thani, 12120, Thailand.,Drug Discovery and Development Center, Thammasat University, Khlong Luang, Pathum Thani, 12120, Thailand
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30
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Paragas EM, Wang Z, Korzekwa K, Nagar S. Complex Cytochrome P450 Kinetics Due to Multisubstrate Binding and Sequential Metabolism. Part 2. Modeling of Experimental Data. Drug Metab Dispos 2021; 49:1100-1108. [PMID: 34503953 PMCID: PMC11022889 DOI: 10.1124/dmd.121.000554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/30/2021] [Indexed: 11/22/2022] Open
Abstract
Three CYP3A4 substrates, midazolam, ticlopidine, and diazepam, display non-Michaelis-Menten kinetics, form multiple primary metabolites, and are sequentially metabolized to secondary metabolites. We generated saturation curves for these compounds and analyzed the resulting datasets using a number of single-substrate and multisubstrate binding models. These models were parameterized using rate equations and numerical solutions of the ordinary differential equations. Multisubstrate binding models provided results superior to single-substrate models, and simultaneous modeling of multiple metabolites provided better results than fitting the individual datasets independently. Although midazolam datasets could be represented using standard two-substrate models, more complex models that include explicit enzyme-product complexes were needed to model the datasets for ticlopidine and diazepam. In vivo clearance predictions improved markedly with the use of in vitro parameters from the complex models versus the Michaelis-Menten equation. The results highlight the need to use sufficiently complex kinetic schemes instead of the Michaelis-Menten equation to generate accurate kinetic parameters. SIGNIFICANCE STATEMENT: The metabolism of midazolam, ticlopidine, and diazepam by CYP3A4 results in multiple metabolites and sequential metabolism. This study evaluates the use of rate equations and numerical methods to characterize the in vitro enzyme kinetics. Use of complex cytochrome P450 kinetic models is necessary to obtain accurate parameter estimates for predicting in vivo disposition.
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Affiliation(s)
- Erickson M Paragas
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Zeyuan Wang
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Swati Nagar
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
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31
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Wang Z, Paragas EM, Nagar S, Korzekwa K. Complex Cytochrome P450 Kinetics Due to Multisubstrate Binding and Sequential Metabolism. Part 1. Theoretical Considerations. Drug Metab Dispos 2021; 49:1090-1099. [PMID: 34503952 PMCID: PMC11022900 DOI: 10.1124/dmd.121.000553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/06/2021] [Indexed: 11/22/2022] Open
Abstract
Complexities in P450-mediated metabolism kinetics include multisubstrate binding, multiple-product formation, and sequential metabolism. Saturation curves and intrinsic clearances were simulated for single-substrate and multisubstrate models using derived velocity equations and numerical solutions of ordinary differential equations (ODEs). Multisubstrate models focused on sigmoidal kinetics because of their dramatic impact on clearance predictions. These models were combined with multiple-product formation and sequential metabolism, and simulations were performed with random error. Use of single-substrate models to characterize multisubstrate data can result in inaccurate kinetic parameters and poor clearance predictions. Comparing results for use of standard velocity equations with ODEs clearly shows that ODEs are more versatile and provide better parameter estimates. It would be difficult to derive concentration-velocity relationships for complex models, but these relationships can be easily modeled using numerical methods and ODEs. SIGNIFICANCE STATEMENT: The impact of multisubstrate binding, multiple-product formation, and sequential metabolism on the P450 kinetics was investigated. Numerical methods are capable of characterizing complicated P450 kinetics.
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Affiliation(s)
- Zeyuan Wang
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Erickson M Paragas
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Swati Nagar
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
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32
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Zuo Y, Shi Y, Zhang F, Guan F, Zhang J, Feyereisen R, Fabrick JA, Yang Y, Wu Y. Genome mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm. PLoS Genet 2021; 17:e1009680. [PMID: 34252082 PMCID: PMC8297932 DOI: 10.1371/journal.pgen.1009680] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/22/2021] [Accepted: 06/23/2021] [Indexed: 01/08/2023] Open
Abstract
The evolution of insecticide resistance represents a global constraint to agricultural production. Because of the extreme genetic diversity found in insects and the large numbers of genes involved in insecticide detoxification, better tools are needed to quickly identify and validate the involvement of putative resistance genes for improved monitoring, management, and countering of field-evolved insecticide resistance. The avermectins, emamectin benzoate (EB) and abamectin are relatively new pesticides with reduced environmental risk that target a wide number of insect pests, including the beet armyworm, Spodoptera exigua, an important global pest of many crops. Unfortunately, field resistance to avermectins recently evolved in the beet armyworm, threatening the sustainable use of this class of insecticides. Here, we report a high-quality chromosome-level assembly of the beet armyworm genome and use bulked segregant analysis (BSA) to identify the locus of avermectin resistance, which mapped on 15-16 Mbp of chromosome 17. Knockout of the CYP9A186 gene that maps within this region by CRISPR/Cas9 gene editing fully restored EB susceptibility, implicating this gene in avermectin resistance. Heterologous expression and in vitro functional assays further confirm that a natural substitution (F116V) found in the substrate recognition site 1 (SRS1) of the CYP9A186 protein results in enhanced metabolism of EB and abamectin. Hence, the combined approach of coupling gene editing with BSA allows for the rapid identification of metabolic resistance genes responsible for insecticide resistance, which is critical for effective monitoring and adaptive management of insecticide resistance.
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Affiliation(s)
- Yayun Zuo
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Institute of Pesticide Science, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yu Shi
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Feng Zhang
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Fang Guan
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jianpeng Zhang
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - René Feyereisen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeffrey A. Fabrick
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, Arizona, United States of America
| | - Yihua Yang
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- * E-mail: (YY); (YW)
| | - Yidong Wu
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- * E-mail: (YY); (YW)
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33
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Wei J, Liu Y. Mechanistic Insights into the P450 TleB-Catalyzed Unusual Intramolecular C-N Bond Formation Involved in the Biosynthesis of Indolactam V. J Chem Inf Model 2021; 61:3638-3648. [PMID: 34240606 DOI: 10.1021/acs.jcim.1c00542] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Indolactam V, a known biosynthetic precursor of indolactam alkaloids, is the main pharmacophore of this family and exhibits potential protein kinase C activation. A key step in the biosynthesis of indolactam V is the formation of an indole-fused nine-membered lactam core by intramolecular C-N bond formation. In this work, we report a computational study of the unique cytochrome P450 TleB enzyme-catalyzed direct and selective C-H bond amination reaction that can generate indolactam V from the dipeptide N-methylvalyl-tryptophanol. By performing molecular dynamics simulations and quantum-mechanical/molecular-mechanical calculations, we revealed that the C-H bond amination involves one step of proton transfer from N1-H of the indole ring to the FeIV═O unit, one step of hydrogen abstraction of N13-H in the side chain of the substrate by the FeIV-OH unit, and diradical coupling, in which two conformational changes of the side chain of the substrate are necessary. In the enzyme-substrate complex of TleB, the N-H bond of the indole ring of the substrate forms a strong hydrogen bond with the FeIV═O unit in compound I, and the porphyrin radical cation accepts an electron from the substrate to form the closed-shell electronic configuration. Thus, compound I in the enzyme-substrate complex cannot be described as FeIV═O coupled to a porphyrin radical cation, which is different from those of other P450 enzymes. Besides, two stages of conformational changes of the side chains of the substrate may increase the relative energies of reaction intermediates by 10-12 kcal/mol. From the structure point of view, it is the rotatable long side chain of the substrate and the large flexible active pocket of TleB that make the intramolecular diradical coupling feasible. Our findings may provide useful information to further understand the Tleb-catalyzed intramolecular C-H bond amination and the other bio-catalyzed intramolecular diradical coupling.
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Affiliation(s)
- Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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34
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Structural Basis for the Diminished Ligand Binding and Catalytic Ability of Human Fetal-Specific CYP3A7. Int J Mol Sci 2021; 22:ijms22115831. [PMID: 34072457 PMCID: PMC8198134 DOI: 10.3390/ijms22115831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
Cytochrome P450 3A7 (CYP3A7) is a fetal/neonatal liver enzyme that participates in estriol synthesis, clearance of all-trans retinoic acid, and xenobiotic metabolism. Compared to the closely related major drug-metabolizing enzyme in adult liver, CYP3A4, the ligand binding and catalytic capacity of CYP3A7 are substantially reduced. To better understand the structural basis for these functional differences, the 2.15 Å crystal structure of CYP3A7 has been solved. Comparative analysis of CYP3A enzymes shows that decreased structural plasticity rather than the active site microenvironment defines the ligand binding ability of CYP3A7. In particular, a rotameric switch in the gatekeeping amino acid F304 triggers local and long-range rearrangements that transmit to the F-G fragment and alter its interactions with the I-E-D-helical core, resulting in a more rigid structure. Elongation of the β3-β4 strands, H-bond linkage in the substrate channel, and steric constraints in the C-terminal loop further increase the active site rigidity and limit conformational ensemble. Collectively, these structural distinctions lower protein plasticity and change the heme environment, which, in turn, could impede the spin-state transition essential for optimal reactivity and oxidation of substrates.
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35
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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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36
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Chen J, Liu J, Huang Y, Li R, Ma C, Zhang B, Wu F, Yu W, Zuo X, Liang Y, Wang Q. Insights into oral bioavailability enhancement of therapeutic herbal constituents by cytochrome P450 3A inhibition. Drug Metab Rev 2021; 53:491-507. [PMID: 33905669 DOI: 10.1080/03602532.2021.1917598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Herbal plants typically have complex compositions and diverse mechanisms. Among them, bioactive constituents with relatively high exposure in vivo are likely to exhibit therapeutic efficacy. On the other hand, their bioavailability may be influenced by the synergistic effects of different bioactive components. Cytochrome P450 3A (CYP3A) is one of the most abundant CYP enzymes, responsible for the metabolism of 50% of approved drugs. In recent years, many therapeutic herbal constituents have been identified as CYP3A substrates. It is more evident that CYP3A inhibition derived from the herbal formula plays a critical role in improving the oral bioavailability of therapeutic constituents. CYP3A inhibition may be the mechanism of the synergism of herbal formula. In this review, we explored the multiplicity of CYP3A, summarized herbal monomers with CYP3A inhibitory effects, and evaluated herb-mediated CYP3A inhibition, thereby providing new insights into the mechanisms of CYP3A inhibition-mediated oral herb bioavailability.
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Affiliation(s)
- Junmei Chen
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jinman Liu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yueyue Huang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ruoyu Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Cuiru Ma
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Beiping Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fanchang Wu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wenqian Yu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xue Zuo
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yong Liang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
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37
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Li J, Chen Y, Tang Y, Li W, Tu Y. Homotropic Cooperativity of Midazolam Metabolism by Cytochrome P450 3A4: Insight from Computational Studies. J Chem Inf Model 2021; 61:2418-2426. [PMID: 33884878 PMCID: PMC8278384 DOI: 10.1021/acs.jcim.1c00266] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Human cytochrome
P450 3A4 (CYP3A4) is responsible for the metabolism
of ∼50% clinically used drugs. Midazolam (MDZ) is a commonly
used sedative drug and serves as a marker substrate for the CYP3A4
activity assessment. MDZ is metabolized by CYP3A4 to two hydroxylation
products, 1′-OH-MDZ and 4-OH-MDZ. It has been reported that
the ratio of 1′-OH-MDZ and 4-OH-MDZ is dependent on the MDZ
concentration, which reflects the homotropic cooperative behavior
in MDZ metabolism by CYP3A4. Here, we used quantum chemistry (QC),
molecular docking, conventional molecular dynamics (cMD), and Gaussian
accelerated molecular dynamics (GaMD) approaches to investigate the
mechanism of the interactions between CYP3A4 and MDZ. QC calculations
suggest that C1′ is less reactive for hydroxylation than C4,
which is a pro-chirality carbon. However, the 4-OH-MDZ product is
likely to be racemic due to the chirality inversion in the rebound
step. The MD simulation results indicate that MDZ at the peripheral
allosteric site is not stable and the binding modes of the MDZ molecules
at the productive site are in line with the experimental observations.
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Affiliation(s)
- Junhao Li
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Yue Chen
- 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
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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38
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Surface hydrophobics mediate functional dimerization of CYP121A1 of Mycobacterium tuberculosis. Sci Rep 2021; 11:394. [PMID: 33431984 PMCID: PMC7801616 DOI: 10.1038/s41598-020-79545-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 11/28/2022] Open
Abstract
Tuberculosis is caused by the pathogenic bacterium Mycobacterium tuberculosis (Mtb) and remains the leading cause of death by infection world-wide. The Mtb genome encodes a disproportionate number of twenty cytochrome P450 enzymes, of which the essential enzyme cytochrome P450 121A1 (CYP121A1) remains a target of drug design efforts. CYP121A1 mediates a phenol coupling reaction of the tyrosine dipeptide cyclo-L-Tyr-L-Tyr (cYY). In this work, a structure and function investigation of dimerization was performed as an overlooked feature of CYP121A1 function. This investigation showed that CYP121A1 dimers form via intermolecular contacts on the distal surface and are mediated by a network of solvent-exposed hydrophobic residues. Disruption of CYP121A1 dimers by site-directed mutagenesis leads to a partial loss of specificity for cYY, resulting in an approximate 75% decrease in catalysis. 19F labeling and nuclear magnetic resonance of the enzyme FG-loop was also combined with protein docking to develop a working model of a functional CYP121A1 dimer. The results obtained suggest that participation of a homodimer interface in substrate selectivity represents a novel paradigm of substrate binding in CYPs, while also providing important mechanistic insight regarding a relevant drug target in the development of novel anti-tuberculosis agents.
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39
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Molecular probes for human cytochrome P450 enzymes: Recent progress and future perspectives. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213600] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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40
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Estrada DF, Kumar A, Campomizzi CS, Jay N. Crystal Structures of Drug-Metabolizing CYPs. Methods Mol Biol 2021; 2342:171-192. [PMID: 34272695 PMCID: PMC10813703 DOI: 10.1007/978-1-0716-1554-6_7] [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] [Indexed: 06/13/2023]
Abstract
The complex enzyme kinetics displayed by drug-metabolizing cytochrome P450 enzymes (CYPs) (see Chapter 9 ) can, in part, be explained by an examination of their crystallographic protein structures. Fortunately, despite low sequence similarity between different families of drug-metabolizing CYPs, there exists a high degree of structural homology within the superfamily. This similarity in the protein fold allows for a direct comparison of the structural features of CYPs that contribute toward differences in substrate binding, heterotropic and homotropic cooperativity, and genetic variability in drug metabolism. In this chapter, we first provide an overview of the nomenclature and the role of structural features that are common in all CYPs. We then apply these definitions to understand the different substrate specificities and functions in the CYP3A, CYP2C, and CYP2D families of enzymes.
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Affiliation(s)
| | - Amit Kumar
- Department of Biochemistry, University at Buffalo, Buffalo, NY, USA
| | | | - Natalie Jay
- Department of Biochemistry, University at Buffalo, Buffalo, NY, USA
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Kumondai M, Gutiérrez Rico EM, Hishinuma E, Ueda A, Saito S, Saigusa D, Tadaka S, Kinoshita K, Nakayoshi T, Oda A, Abe A, Maekawa M, Mano N, Hirasawa N, Hiratsuka M. Functional Characterization of 40 CYP3A4 Variants by Assessing Midazolam 1'-Hydroxylation and Testosterone 6 β-Hydroxylation. Drug Metab Dispos 2020; 49:212-220. [PMID: 33384383 DOI: 10.1124/dmd.120.000261] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/24/2020] [Indexed: 12/17/2022] Open
Abstract
CYP3A4 is among the most abundant liver and intestinal drug-metabolizing cytochrome P450 enzymes, contributing to the metabolism of more than 30% of clinically used drugs. Therefore, interindividual variability in CYP3A4 activity is a frequent cause of reduced drug efficacy and adverse effects. In this study, we characterized wild-type CYP3A4 and 40 CYP3A4 variants, including 11 new variants, detected among 4773 Japanese individuals by assessing CYP3A4 enzymatic activities for two representative substrates (midazolam and testosterone). The reduced carbon monoxide-difference spectra of wild-type CYP3A4 and 31 CYP3A4 variants produced with our established mammalian cell expression system were determined by measuring the increase in maximum absorption at 450 nm after carbon monoxide treatment. The kinetic parameters of midazolam and testosterone hydroxylation by wild-type CYP3A4 and 29 CYP3A4 variants (K m , k cat , and catalytic efficiency) were determined, and the causes of their kinetic differences were evaluated by three-dimensional structural modeling. Our findings offer insight into the mechanism underlying interindividual differences in CYP3A4-dependent drug metabolism. Moreover, our results provide guidance for improving drug administration protocols by considering the information on CYP3A4 genetic polymorphisms. SIGNIFICANCE STATEMENT: CYP3A4 metabolizes more than 30% of clinically used drugs. Interindividual differences in drug efficacy and adverse-effect rates have been linked to ethnicity-specific differences in CYP3A4 gene variants in Asian populations, including Japanese individuals, indicating the presence of CYP3A4 polymorphisms resulting in the increased expression of loss-of-function variants. This study detected alterations in CYP3A4 activity due to amino acid substitutions by assessing the enzymatic activities of coding variants for two representative CYP3A4 substrates.
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Affiliation(s)
- Masaki Kumondai
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Evelyn Marie Gutiérrez Rico
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Eiji Hishinuma
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Akiko Ueda
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Sakae Saito
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Daisuke Saigusa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Shu Tadaka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Kengo Kinoshita
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Tomoki Nakayoshi
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Akifumi Oda
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Ai Abe
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Masamitsu Maekawa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Nariyasu Mano
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Noriyasu Hirasawa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Masahiro Hiratsuka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
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Molecular determinant of substrate binding and specificity of cytochrome P450 2J2. Sci Rep 2020; 10:22267. [PMID: 33335233 PMCID: PMC7746748 DOI: 10.1038/s41598-020-79284-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022] Open
Abstract
Cytochrome P450 2J2 (CYP2J2) is responsible for the epoxidation of endogenous arachidonic acid, and is involved in the metabolism of exogenous drugs. To date, no crystal structure of CYP2J2 is available, and the proposed structural basis for the substrate recognition and specificity in CYP2J2 varies with the structural models developed using different computational protocols. In this study, we developed a new structural model of CYP2J2, and explored its sensitivity to substrate binding by molecular dynamics simulations of the interactions with chemically similar fluorescent probes. Our results showed that the induced-fit binding of these probes led to the preferred active poses ready for the catalysis by CYP2J2. Divergent conformational dynamics of CYP2J2 due to the binding of each probe were observed. However, a stable hydrophobic clamp composed of residues I127, F310, A311, V380, and I487 was identified to restrict any substrate access to the active site of CYP2J2. Molecular docking of a series of compounds including amiodarone, astemizole, danazol, ebastine, ketoconazole, terfenadine, terfenadone, and arachidonic acid to CYP2J2 confirmed the role of those residues in determining substrate binding and specificity of CYP2J2. In addition to the flexibility of CYP2J2, the present work also identified other factors such as electrostatic potential in the vicinity of the active site, and substrate strain energy and property that have implications for the interpretation of CYP2J2 metabolism.
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Das A, Weigle AT, Arnold WR, Kim JS, Carnevale LN, Huff HC. CYP2J2 Molecular Recognition: A New Axis for Therapeutic Design. Pharmacol Ther 2020; 215:107601. [PMID: 32534953 PMCID: PMC7773148 DOI: 10.1016/j.pharmthera.2020.107601] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/28/2020] [Indexed: 12/11/2022]
Abstract
Cytochrome P450 (CYP) epoxygenases are a special subset of heme-containing CYP enzymes capable of performing the epoxidation of polyunsaturated fatty acids (PUFA) and the metabolism of xenobiotics. This dual functionality positions epoxygenases along a metabolic crossroad. Therefore, structure-function studies are critical for understanding their role in bioactive oxy-lipid synthesis, drug-PUFA interactions, and for designing therapeutics that directly target the epoxygenases. To better exploit CYP epoxygenases as therapeutic targets, there is a need for improved understanding of epoxygenase structure-function. Of the characterized epoxygenases, human CYP2J2 stands out as a potential target because of its role in cardiovascular physiology. In this review, the early research on the discovery and activity of epoxygenases is contextualized to more recent advances in CYP epoxygenase enzymology with respect to PUFA and drug metabolism. Additionally, this review employs CYP2J2 epoxygenase as a model system to highlight both the seminal works and recent advances in epoxygenase enzymology. Herein we cover CYP2J2's interactions with PUFAs and xenobiotics, its tissue-specific physiological roles in diseased states, and its structural features that enable epoxygenase function. Additionally, the enumeration of research on CYP2J2 identifies the future needs for the molecular characterization of CYP2J2 to enable a new axis of therapeutic design.
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Affiliation(s)
- Aditi Das
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Computational Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Bioengineering, Neuroscience Program, Beckman Institute for Advanced Science and Technology, Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
| | - Austin T Weigle
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - William R Arnold
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Justin S Kim
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Lauren N Carnevale
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Hannah C Huff
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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Cheong EJY, Nair PC, Neo RWY, Tu HT, Lin F, Chiong E, Esuvaranathan K, Fan H, Szmulewitz RZ, Peer CJ, Figg WD, Chai CLL, Miners JO, Chan ECY. Slow-, Tight-Binding Inhibition of CYP17A1 by Abiraterone Redefines Its Kinetic Selectivity and Dosing Regimen. J Pharmacol Exp Ther 2020; 374:438-451. [PMID: 32554434 DOI: 10.1124/jpet.120.265868] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/11/2020] [Indexed: 12/18/2022] Open
Abstract
Substantial evidence underscores the clinical efficacy of inhibiting CYP17A1-mediated androgen biosynthesis by abiraterone for treatment of prostate oncology. Previous structural analysis and in vitro assays revealed inconsistencies surrounding the nature and potency of CYP17A1 inhibition by abiraterone. Here, we establish that abiraterone is a slow-, tight-binding inhibitor of CYP17A1, with initial weak binding preceding the subsequent slow isomerization to a high-affinity CYP17A1-abiraterone complex. The in vitro inhibition constant of the final high-affinity CYP17A1-abiraterone complex ( ( K i * = 0.39 nM )yielded a binding free energy of -12.8 kcal/mol that was quantitatively consistent with the in silico prediction of -14.5 kcal/mol. Prolonged suppression of dehydroepiandrosterone (DHEA) concentrations observed in VCaP cells after abiraterone washout corroborated its protracted CYP17A1 engagement. Molecular dynamics simulations illuminated potential structural determinants underlying the rapid reversible binding characterizing the two-step induced-fit model. Given the extended residence time (42 hours) of abiraterone within the CYP17A1 active site, in silico simulations demonstrated sustained target engagement even when most abiraterone has been eliminated systemically. Subsequent pharmacokinetic-pharmacodynamic (PK-PD) modeling linking time-dependent CYP17A1 occupancy to in vitro steroidogenic dynamics predicted comparable suppression of downstream DHEA-sulfate at both 1000- and 500-mg doses of abiraterone acetate. This enabled mechanistic rationalization of a clinically reported PK-PD disconnect, in which equipotent reduction of downstream plasma DHEA-sulfate levels was achieved despite a lower systemic exposure of abiraterone. Our novel findings provide the impetus for re-evaluating the current dosing paradigm of abiraterone with the aim of preserving PD efficacy while mitigating its dose-dependent adverse effects and financial burden. SIGNIFICANCE STATEMENT: With the advent of novel molecularly targeted anticancer modalities, it is becoming increasingly evident that optimal dose selection must necessarily be predicated on mechanistic characterization of the relationships between target exposure, drug-target interactions, and pharmacodynamic endpoints. Nevertheless, efficacy has always been perceived as being exclusively synonymous with affinity-based measurements of drug-target binding. This work demonstrates how elucidating the slow-, tight-binding inhibition of CYP17A1 by abiraterone via in vitro and in silico analyses was pivotal in establishing the role of kinetic selectivity in mediating time-dependent CYP17A1 engagement and eventually downstream efficacy outcomes.
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Affiliation(s)
- Eleanor Jing Yi Cheong
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - Pramod C Nair
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - Rebecca Wan Yi Neo
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - Ho Thanh Tu
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - Fu Lin
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - Edmund Chiong
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - Kesavan Esuvaranathan
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - Hao Fan
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - Russell Z Szmulewitz
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - Cody J Peer
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - William D Figg
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - Christina Li Lin Chai
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - John O Miners
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
| | - Eric Chun Yong Chan
- Department of Pharmacy, Faculty of Science (E.J.Y.C., R.W.Y.N., H.T.T., C.L.L.C., E.C.Y.C.) and Department of Biological Sciences (H.F.), National University of Singapore, Singapore, Singapore; Department of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, Australia (P.C.N., J.O.M.); Bioinformatics Institute, Biotransformation Innovation Platform (BioTrans) (F.L.) and Bioinformatics Institute (H.F.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Surgery, National University Health System, Singapore, Singapore (E.C., K.E.); Department of Urology, National University Hospital, Singapore, Singapore (E.C., K.E.); Centre for Computational Biology, DUKE-NUS Medical School, Singapore, Singapore (H.F.); The University of Chicago, Chicago, Illinois (R.Z.S.); National Cancer Institute, Rockville, Maryland (C.J.P., W.D.F.); and National University Cancer Institute, Singapore (NCIS), NUH Medical Centre (NUHMC), Singapore, Singapore (E.C.Y.C.)
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Zárate-Pérez F, Hackett JC. Conformational selection is present in ligand binding to cytochrome P450 19A1 lipoprotein nanodiscs. J Inorg Biochem 2020; 209:111120. [PMID: 32464592 DOI: 10.1016/j.jinorgbio.2020.111120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/28/2020] [Accepted: 05/16/2020] [Indexed: 11/25/2022]
Abstract
Cytochromes P450 (CYPs) display remarkable plasticity in their ability to bind substrates and catalyze a broad array of chemical reactions. Herein we evaluate binding of androstenedione, testosterone, and 7-hydroxyflavone to CYP19A1, also known as aromatase, in phospholipid nanodiscs by stopped-flow UV-vis spectroscopy. Exponential fitting of the kinetic traces supports the possibility of a multi-step binding mechanism. Subsequent global fitting of the data to the solutions of the coupled differential equations describing the fundamental mechanisms of induced fit and conformational selection, consistently support presence of the latter. To our knowledge, this is the first discrimination of conformational selection from induced fit for a mono-disperse CYP in a native-like membrane environment. In addition, 7-hydroxyflavone binds to CYP19A1 nanodiscs with comparable affinity to the substrates and induces an unusual spectral response likely attributable to hydrogen bonding to, rather than displacement of the heme-coordinated water molecule.
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Affiliation(s)
- Francisco Zárate-Pérez
- Department of Physiology and Biophysics and The Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, United States of America
| | - John C Hackett
- Department of Physiology and Biophysics and The Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, United States of America.
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Li J, Tang Y, Li W, Tu Y. Mechanistic Insights into the Regio- and Stereoselectivities of Testosterone and Dihydrotestosterone Hydroxylation Catalyzed by CYP3A4 and CYP19A1. Chemistry 2020; 26:6214-6223. [PMID: 32049373 PMCID: PMC7318132 DOI: 10.1002/chem.201905272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/22/2020] [Indexed: 12/27/2022]
Abstract
The hydroxylation of nonreactive C-H bonds can be easily catalyzed by a variety of metalloenzymes, especially cytochrome P450s (P450s). The mechanism of P450 mediated hydroxylation has been intensively studied, both experimentally and theoretically. However, understanding the regio- and stereoselectivities of substrates hydroxylated by P450s remains a great challenge. Herein, we use a multi-scale modeling approach to investigate the selectivity of testosterone (TES) and dihydrotestosterone (DHT) hydroxylation catalyzed by two important P450s, CYP3A4 and CYP19A1. For CYP3A4, two distinct binding modes for TES/DHT were predicted by dockings and molecular dynamics simulations, in which the experimentally identified sites of metabolism of TES/DHT can access to the catalytic center. The regio- and stereoselectivities of TES/DHT hydroxylation were further evaluated by quantum mechanical and ONIOM calculations. For CYP19A1, we found that sites 1β, 2β and 19 can access the catalytic center, with the intrinsic reactivity 2β>1β>19. However, our ONIOM calculations indicate that the hydroxylation is favored at site 19 for both TES and DHT, which is consistent with the experiments and reflects the importance of the catalytic environment in determining the selectivity. Our study unravels the mechanism underlying the selectivity of TES/DHT hydroxylation mediated by CYP3A4 and CYP19A1 and is helpful for understanding the selectivity of other substrates that are hydroxylated by P450s.
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Affiliation(s)
- Junhao Li
- Department of Theoretical Chemistry and BiologyKTH Royal Institute of TechnologyRoslagstullsbacken 1510691StockholmSweden
| | - Yun Tang
- Shanghai Key Laboratory of New Drug DesignEast China University of Science and TechnologyMeilong Road 130200237ShanghaiP.R. China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug DesignEast China University of Science and TechnologyMeilong Road 130200237ShanghaiP.R. China
| | - Yaoquan Tu
- Department of Theoretical Chemistry and BiologyKTH Royal Institute of TechnologyRoslagstullsbacken 1510691StockholmSweden
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47
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Atkins WM. Mechanisms of promiscuity among drug metabolizing enzymes and drug transporters. FEBS J 2020; 287:1306-1322. [PMID: 31663687 PMCID: PMC7138722 DOI: 10.1111/febs.15116] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/04/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Detoxication, or 'drug-metabolizing', enzymes and drug transporters exhibit remarkable substrate promiscuity and catalytic promiscuity. In contrast to substrate-specific enzymes that participate in defined metabolic pathways, individual detoxication enzymes must cope with substrates of vast structural diversity, including previously unencountered environmental toxins. Presumably, evolution selects for a balance of 'adequate' kcat /KM values for a wide range of substrates, rather than optimizing kcat /KM for any individual substrate. However, the structural, energetic, and metabolic properties that achieve this balance, and hence optimize detoxication, are not well understood. Two features of detoxication enzymes that are frequently cited as contributions to promiscuity include the exploitation of highly reactive versatile cofactors, or cosubstrates, and a high degree of flexibility within the protein structure. This review examines these intuitive mechanisms in detail and clarifies the contributions of the classic ligand binding models 'induced fit' (IF) and 'conformational selection' (CS) to substrate promiscuity. The available literature data for drug metabolizing enzymes and transporters suggest that IF is exploited by these promiscuous detoxication enzymes, as it is with substrate-specific enzymes, but the detoxication enzymes uniquely exploit 'IFs' to retain a wide range of substrates at their active sites. In contrast, whereas CS provides no catalytic advantage to substrate-specific enzymes, promiscuous enzymes may uniquely exploit it to recruit a wide range of substrates. The combination of CS and IF, for recruitment and retention of substrates, can potentially optimize the promiscuity of drug metabolizing enzymes and drug transporters.
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Affiliation(s)
- William M. Atkins
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWAUSA
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48
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Wright WC, Chenge J, Wang J, Girvan HM, Yang L, Chai SC, Huber AD, Wu J, Oladimeji PO, Munro AW, Chen T. Clobetasol Propionate Is a Heme-Mediated Selective Inhibitor of Human Cytochrome P450 3A5. J Med Chem 2020; 63:1415-1433. [PMID: 31965799 PMCID: PMC7087482 DOI: 10.1021/acs.jmedchem.9b02067] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The human cytochrome P450 (CYP) enzymes CYP3A4 and CYP3A5 metabolize most drugs and have high similarities in their structure and substrate preference. Whereas CYP3A4 is predominantly expressed in the liver, CYP3A5 is upregulated in cancer, contributing to drug resistance. Selective inhibitors of CYP3A5 are, therefore, critical to validating it as a therapeutic target. Here we report clobetasol propionate (clobetasol) as a potent and selective CYP3A5 inhibitor identified by high-throughput screening using enzymatic and cell-based assays. Molecular dynamics simulations suggest a close proximity of clobetasol to the heme in CYP3A5 but not in CYP3A4. UV-visible spectroscopy and electron paramagnetic resonance analyses confirmed the formation of an inhibitory type I heme-clobetasol complex in CYP3A5 but not in CYP3A4, thus explaining the CYP3A5 selectivity of clobetasol. Our results provide a structural basis for selective CYP3A5 inhibition, along with mechanistic insights, and highlight clobetasol as an important chemical tool for target validation.
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Affiliation(s)
- William C. Wright
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
- Integrated Biomedical Sciences Program, University of
Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Jude Chenge
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Jingheng Wang
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Hazel M. Girvan
- Manchester Institute of Biotechnology, School of Natural
Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN,
UK
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Sergio C. Chai
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Andrew D. Huber
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Peter O. Oladimeji
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of Natural
Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN,
UK
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
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49
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Bai J, Li L, Zhao S, Fan X, Zhang J, Hu M, Chen Y, Sun Y, Wang B, Jin J, Wang X, Zhang D, Hu J, Li Y. Heterotropic activation of flavonoids on cytochrome P450 3A4: A case example of alleviating dronedarone-induced cytotoxicity. Toxicol Lett 2020; 319:187-196. [DOI: 10.1016/j.toxlet.2019.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022]
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50
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Yadav J, Paragas E, Korzekwa K, Nagar S. Time-dependent enzyme inactivation: Numerical analyses of in vitro data and prediction of drug-drug interactions. Pharmacol Ther 2020; 206:107449. [PMID: 31836452 PMCID: PMC6995442 DOI: 10.1016/j.pharmthera.2019.107449] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cytochrome P450 (CYP) enzyme kinetics often do not conform to Michaelis-Menten assumptions, and time-dependent inactivation (TDI) of CYPs displays complexities such as multiple substrate binding, partial inactivation, quasi-irreversible inactivation, and sequential metabolism. Additionally, in vitro experimental issues such as lipid partitioning, enzyme concentrations, and inactivator depletion can further complicate the parameterization of in vitro TDI. The traditional replot method used to analyze in vitro TDI datasets is unable to handle complexities in CYP kinetics, and numerical approaches using ordinary differential equations of the kinetic schemes offer several advantages. Improvement in the parameterization of CYP in vitro kinetics has the potential to improve prediction of clinical drug-drug interactions (DDIs). This manuscript discusses various complexities in TDI kinetics of CYPs, and numerical approaches to model these complexities. The extrapolation of CYP in vitro TDI parameters to predict in vivo DDIs with static and dynamic modeling is discussed, along with a discussion on current gaps in knowledge and future directions to improve the prediction of DDI with in vitro data for CYP catalyzed drug metabolism.
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Affiliation(s)
- Jaydeep Yadav
- Amgen Inc., 360 Binney Street, Cambridge, MA 02142, United States; Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States
| | - Erickson Paragas
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States
| | - Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States
| | - Swati Nagar
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States.
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