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Amisaki T. Multilevel superposition for deciphering the conformational variability of protein ensembles. Brief Bioinform 2024; 25:bbae137. [PMID: 38557679 PMCID: PMC10983786 DOI: 10.1093/bib/bbae137] [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: 09/26/2023] [Revised: 02/14/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
The dynamics and variability of protein conformations are directly linked to their functions. Many comparative studies of X-ray protein structures have been conducted to elucidate the relevant conformational changes, dynamics and heterogeneity. The rapid increase in the number of experimentally determined structures has made comparison an effective tool for investigating protein structures. For example, it is now possible to compare structural ensembles formed by enzyme species, variants or the type of ligands bound to them. In this study, the author developed a multilevel model for estimating two covariance matrices that represent inter- and intra-ensemble variability in the Cartesian coordinate space. Principal component analysis using the two estimated covariance matrices identified the inter-/intra-enzyme variabilities, which seemed to be important for the enzyme functions, with the illustrative examples of cytochrome P450 family 2 enzymes and class A $\beta$-lactamases. In P450, in which each enzyme has its own active site of a distinct size, an active-site motion shared universally between the enzymes was captured as the first principal mode of the intra-enzyme covariance matrix. In this case, the method was useful for understanding the conformational variability after adjusting for the differences between enzyme sizes. The developed method is advantageous in small ensemble-size problems and hence promising for use in comparative studies on experimentally determined structures where ensemble sizes are smaller than those generated, for example, by molecular dynamics simulations.
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Affiliation(s)
- Takashi Amisaki
- Department of Biological Regulation, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8503, Japan
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2
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Nair PC, Burns K, Chau N, McKinnon RA, Miners JO. The molecular basis of dapsone activation of CYP2C9-catalyzed nonsteroidal anti-inflammatory drug oxidation. J Biol Chem 2023; 299:105368. [PMID: 37866634 PMCID: PMC10696402 DOI: 10.1016/j.jbc.2023.105368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023] Open
Abstract
Positive heterotropic cooperativity, or "activation," results in an instantaneous increase in enzyme activity in the absence of an increase in protein expression. Thus, cytochrome P450 (CYP) enzyme activation presents as a potential drug-drug interaction mechanism. It has been demonstrated previously that dapsone activates the CYP2C9-catalyzed oxidation of a number of nonsteroidal anti-inflammatory drugs in vitro. Here, we conducted molecular dynamics simulations (MDS) together with enzyme kinetic investigations and site-directed mutagenesis to elucidate the molecular basis of the activation of CYP2C9-catalyzed S-flurbiprofen 4'-hydroxylation and S-naproxen O-demethylation by dapsone. Supplementation of incubations of recombinant CYP2C9 with dapsone increased the catalytic efficiency of flurbiprofen and naproxen oxidation by 2.3- and 16.5-fold, respectively. MDS demonstrated that activation arises predominantly from aromatic interactions between the substrate, dapsone, and the phenyl rings of Phe114 and Phe476 within a common binding domain of the CYP2C9 active site, rather than involvement of a distinct effector site. Mutagenesis of Phe114 and Phe476 abrogated flurbiprofen and naproxen oxidation, and MDS and kinetic studies with the CYP2C9 mutants further identified a pivotal role of Phe476 in dapsone activation. MDS additionally showed that aromatic stacking interactions between two molecules of naproxen are necessary for binding in a catalytically favorable orientation. In contrast to flurbiprofen and naproxen, dapsone did not activate the 4'-hydroxylation of diclofenac, suggesting that the CYP2C9 active site favors cooperative binding of nonsteroidal anti-inflammatory drugs with a planar or near-planar geometry. More generally, the work confirms the utility of MDS for investigating ligand binding in CYP enzymes.
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Affiliation(s)
- Pramod C Nair
- Department of Clinical Pharmacology, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia; FHMRI Cancer Program, Flinders Health and Medical Research Institute, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia.
| | - Kushari Burns
- Department of Clinical Pharmacology, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Nuy Chau
- Department of Clinical Pharmacology, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Ross A McKinnon
- FHMRI Cancer Program, Flinders Health and Medical Research Institute, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - John O Miners
- Department of Clinical Pharmacology, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia; FHMRI Cancer Program, Flinders Health and Medical Research Institute, Flinders University College of Medicine and Public Health, Flinders Medical Centre, Bedford Park, South Australia, Australia
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3
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Takeji S, Okada M, Hayashi S, Kanamaru K, Uno Y, Imaishi H, Uno T. Metabolism of testosterone and progesterone by cytochrome P450 2C19 allelic variants. Biopharm Drug Dispos 2023; 44:420-430. [PMID: 37815926 DOI: 10.1002/bdd.2378] [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: 04/29/2023] [Revised: 08/29/2023] [Accepted: 09/19/2023] [Indexed: 10/12/2023]
Abstract
CYP2C19 is a member of the human microsomal cytochrome P450 (CYP). Significant variation in CYP2C19 levels and activity can be attributed to polymorphisms in this gene. Wildtype CYP2C19 and 13 mutants (CYP2C19.1B, CYP2C19.5A, CYP2C19.5B, CYP2C19.6, CYP2C19.8, CYP2C19.9, CYP2C19.10, CYP2C19.11, CYP2C19.13, CYP2C19.16, CYP2C19.19, CYP2C19.23, CYP2C19.30, and CYP2C19.33) were coexpressed with NADPH-cytochrome P450 reductase in Escherichia coli. Hydroxylase activity toward testosterone and progesterone was also examined. Ten CYP2C19 variants showed Soret peaks (450 nm) typical of P450 in the reduced CO-difference spectra. CYP2C19.11 and CYP2C19.23 showed higher testosterone 11α, 16α-/17- and progesterone 6β-,21-,16α-/17α-hydroxylase activities than CYP2C19.1B. CYP2C19.6, CYP2C19.16, CYP2C19.19, and CYP2C19.30 showed lower activity than CYP2C19.1B. CYP2C19.9, CYP2C19.10. CYP2C19.13, and CYP2C19.33 showed different hydroxylation activities than CYP2C19.1B. These results indicated that CYP2C19 variants have very different substrate specificities for testosterone and progesterone.
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Affiliation(s)
- Shiori Takeji
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Mai Okada
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shu Hayashi
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Kengo Kanamaru
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yuichi Uno
- Department of Plant Resource Science, Faculty of Agriculture, Kobe University, Kobe, Japan
| | - Hiromasa Imaishi
- Functional Analysis of Environmental Genes, Research Center for Environmental, Genomics, Kobe University, Kobe, Japan
| | - Tomohide Uno
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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4
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Chamboko CR, Veldman W, Tata RB, Schoeberl B, Tastan Bishop Ö. Human Cytochrome P450 1, 2, 3 Families as Pharmacogenes with Emphases on Their Antimalarial and Antituberculosis Drugs and Prevalent African Alleles. Int J Mol Sci 2023; 24:ijms24043383. [PMID: 36834793 PMCID: PMC9961538 DOI: 10.3390/ijms24043383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Precision medicine gives individuals tailored medical treatment, with the genotype determining the therapeutic strategy, the appropriate dosage, and the likelihood of benefit or toxicity. Cytochrome P450 (CYP) enzyme families 1, 2, and 3 play a pivotal role in eliminating most drugs. Factors that affect CYP function and expression have a major impact on treatment outcomes. Therefore, polymorphisms of these enzymes result in alleles with diverse enzymatic activity and drug metabolism phenotypes. Africa has the highest CYP genetic diversity and also the highest burden of malaria and tuberculosis, and this review presents current general information on CYP enzymes together with variation data concerning antimalarial and antituberculosis drugs, while focusing on the first three CYP families. Afrocentric alleles such as CYP2A6*17, CYP2A6*23, CYP2A6*25, CYP2A6*28, CYP2B6*6, CYP2B6*18, CYP2C8*2, CYP2C9*5, CYP2C9*8, CYP2C9*9, CYP2C19*9, CYP2C19*13, CYP2C19*15, CYP2D6*2, CYP2D6*17, CYP2D6*29, and CYP3A4*15 are implicated in diverse metabolic phenotypes of different antimalarials such as artesunate, mefloquine, quinine, primaquine, and chloroquine. Moreover, CYP3A4, CYP1A1, CYP2C8, CYP2C18, CYP2C19, CYP2J2, and CYP1B1 are implicated in the metabolism of some second-line antituberculosis drugs such as bedaquiline and linezolid. Drug-drug interactions, induction/inhibition, and enzyme polymorphisms that influence the metabolism of antituberculosis, antimalarial, and other drugs, are explored. Moreover, a mapping of Afrocentric missense mutations to CYP structures and a documentation of their known effects provided structural insights, as understanding the mechanism of action of these enzymes and how the different alleles influence enzyme function is invaluable to the advancement of precision medicine.
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Affiliation(s)
- Chiratidzo R Chamboko
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| | - Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| | - Rolland Bantar Tata
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| | - Birgit Schoeberl
- Translational Medicine, Novartis Institutes for BioMedical Research, 220 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
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Manoj KM, Gideon DA, Bazhin NM, Tamagawa H, Nirusimhan V, Kavdia M, Jaeken L. Na,K-ATPase: A murzyme facilitating thermodynamic equilibriums at the membrane-interface. J Cell Physiol 2023; 238:109-136. [PMID: 36502470 DOI: 10.1002/jcp.30925] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022]
Abstract
The redox metabolic paradigm of murburn concept advocates that diffusible reactive species (DRS, particularly oxygen-centric radicals) are mainstays of physiology, and not mere pathological manifestations. The murburn purview of cellular function also integrates the essential principles of bioenergetics, thermogenesis, homeostasis, electrophysiology, and coherence. In this context, any enzyme that generates/modulates/utilizes/sustains DRS functionality is called a murzyme. We have demonstrated that several water-soluble (peroxidases, lactate dehydrogenase, hemogoblin, etc.) and membrane-embedded (Complexes I-V in mitochondria, Photosystems I/II in chloroplasts, rhodopsin/transducin in rod cells, etc.) proteins serve as murzymes. The membrane protein of Na,K-ATPase (NKA, also known as sodium-potassium pump) is the focus of this article, owing to its centrality in neuro-cardio-musculo electrophysiology. Herein, via a series of critical queries starting from the geometric/spatio-temporal considerations of diffusion/mass transfer of solutes in cells to an update on structural/distributional features of NKA in diverse cellular systems, and from various mechanistic aspects of ion-transport (thermodynamics, osmoregulation, evolutionary dictates, etc.) to assays/explanations of inhibitory principles like cardiotonic steroids (CTS), we first highlight some unresolved problems in the field. Thereafter, we propose and apply a minimalist murburn model of trans-membrane ion-differentiation by NKA to address the physiological inhibitory effects of trans-dermal peptide, lithium ion, volatile anesthetics, confirmed interfacial DRS + proton modulators like nitrophenolics and unsaturated fatty acid, and the diverse classes of molecules like CTS, arginine, oximes, etc. These explanations find a pan-systemic connectivity with the inhibitions/uncouplings of other membrane proteins in cells.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Shoranur-2, Kerala, India
| | - Daniel A Gideon
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Shoranur-2, Kerala, India
| | - Nikolai M Bazhin
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, Russia
| | - Hirohisa Tamagawa
- Department of Mechanical Engineering, Gifu University, Gifu City, Japan
| | - Vijay Nirusimhan
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Shoranur-2, Kerala, India
| | - Mahendra Kavdia
- Department of Biomedical Engineering, Wayne State University, Detroit, Michigan, USA
| | - Laurent Jaeken
- Department of Industrial Sciences and Technology, Karel de Grote-Hogeschool, Antwerp University Association, Antwerp, Belgium
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6
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Zhao FL, Zhang Q, Wang SH, Hong Y, Zhou S, Zhou Q, Geng PW, Luo QF, Yang JF, Chen H, Cai JP, Dai DP. Identification and drug metabolic characterization of four new CYP2C9 variants CYP2C9*72- *75 in the Chinese Han population. Front Pharmacol 2022; 13:1007268. [PMID: 36582532 PMCID: PMC9792615 DOI: 10.3389/fphar.2022.1007268] [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: 07/30/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
Cytochrome 2C9 (CYP2C9), one of the most important drug metabolic enzymes in the human hepatic P450 superfamily, is required for the metabolism of 15% of clinical drugs. Similar to other CYP2C family members, CYP2C9 gene has a high genetic polymorphism which can cause significant racial and inter-individual differences in drug metabolic activity. To better understand the genetic distribution pattern of CYP2C9 in the Chinese Han population, 931 individuals were recruited and used for the genotyping in this study. As a result, seven synonymous and 14 non-synonymous variations were identified, of which 4 missense variants were designated as new alleles CYP2C9*72, *73, *74 and *75, resulting in the amino acid substitutions of A149V, R150C, Q214H and N418T, respectively. When expressed in insect cell microsomes, all four variants exhibited comparable protein expression levels to that of the wild-type CYP2C9 enzyme. However, drug metabolic activity analysis revealed that these variants exhibited significantly decreased catalytic activities toward three CYP2C9 specific probe drugs, as compared with that of the wild-type enzyme. These data indicate that the amino acid substitution in newly designated variants can cause reduced function of the enzyme and its clinical significance still needs further investigation in the future.
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Affiliation(s)
- 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, China,Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Qing Zhang
- Department of Cardiovascular, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuang-Hu 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
- Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Quan Zhou
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, China
| | - Pei-Wu Geng
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, China
| | - Qing-Feng Luo
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jie-Fu Yang
- Department of Cardiovascular, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hao Chen
- Department of Cardiovascular, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China,*Correspondence: Da-Peng Dai, ; Jian-Ping Cai, ; Hao Chen,
| | - 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, China,*Correspondence: Da-Peng Dai, ; Jian-Ping Cai, ; Hao Chen,
| | - 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, China,Peking University Fifth School of Clinical Medicine, Beijing, China,*Correspondence: Da-Peng Dai, ; Jian-Ping Cai, ; Hao Chen,
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7
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The protein conformational basis of isoflavone biosynthesis. Commun Biol 2022; 5:1249. [PMID: 36376429 PMCID: PMC9663428 DOI: 10.1038/s42003-022-04222-x] [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: 05/26/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022] Open
Abstract
Isoflavonoids play important roles in plant defense and also exhibit a range of mammalian health-promoting activities. Their biosynthesis is initiated by two enzymes with unusual catalytic activities; 2-hydroxyisoflavanone synthase (2-HIS), a membrane-bound cytochrome P450 catalyzing a coupled aryl-ring migration and hydroxylation, and 2-hydroxyisoflavanone dehydratase (2-HID), a member of a large carboxylesterase family that paradoxically catalyzes dehydration of 2-hydroxyisoflavanones to isoflavone. Here we report the crystal structures of 2-HIS from Medicago truncatula and 2-HID from Pueraria lobata. The 2-HIS structure reveals a unique cytochrome P450 conformation and heme and substrate binding mode that facilitate the coupled aryl-ring migration and hydroxylation reactions. The 2-HID structure reveals the active site architecture and putative catalytic residues for the dual dehydratase and carboxylesterase activities. Mutagenesis studies revealed key residues involved in substrate binding and specificity. Understanding the structural basis of isoflavone biosynthesis will facilitate the engineering of new bioactive isoflavonoids. The structure and function of two isoflavone biosynthetic enzymes are reported revealing a novel cytochrome P450 conformation and identification of key residues for dual dehydratase and carboxylesterase activities
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8
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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9
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Structural dynamics of the cooperative binding of small inhibitors in human cytochrome P450 2C9. J Mol Graph Model 2022; 113:108151. [DOI: 10.1016/j.jmgm.2022.108151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 11/23/2022]
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10
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Zhao Y, Yu C, Liang W, Atodiresei IL, Patureau FW. TEMPO-mediated late stage photochemical hydroxylation of biaryl sulfonium salts. Chem Commun (Camb) 2022; 58:2846-2849. [PMID: 35129566 DOI: 10.1039/d1cc07057f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The late stage photochemical hydroxylation of biaryl sulfonium salts was enabled with a TEMPO derivative as a simple oxygen source, in metal free conditions. The scope and mechanism of this exceptionally simple synthetic method, which constructs important arylated phenols from aromatic C-H bonds, are herein discussed.
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Affiliation(s)
- Yue Zhao
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany.
| | - Congjun Yu
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany.
| | - Wenjing Liang
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany.
| | - Iuliana L Atodiresei
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany.
| | - Frederic W Patureau
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany.
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11
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Construction of a fused grid-based template system of CYP2C9 and its application. Drug Metab Pharmacokinet 2022; 45:100451. [DOI: 10.1016/j.dmpk.2022.100451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 02/01/2022] [Indexed: 11/24/2022]
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12
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Goldwaser E, Laurent C, Lagarde N, Fabrega S, Nay L, Villoutreix BO, Jelsch C, Nicot AB, Loriot MA, Miteva MA. Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9. PLoS Comput Biol 2022; 18:e1009820. [PMID: 35081108 PMCID: PMC8820617 DOI: 10.1371/journal.pcbi.1009820] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 02/07/2022] [Accepted: 01/10/2022] [Indexed: 11/19/2022] Open
Abstract
Cytochrome P450 2C9 (CYP2C9) is a major drug-metabolizing enzyme that represents 20% of the hepatic CYPs and is responsible for the metabolism of 15% of drugs. A general concern in drug discovery is to avoid the inhibition of CYP leading to toxic drug accumulation and adverse drug-drug interactions. However, the prediction of CYP inhibition remains challenging due to its complexity. We developed an original machine learning approach for the prediction of drug-like molecules inhibiting CYP2C9. We created new predictive models by integrating CYP2C9 protein structure and dynamics knowledge, an original selection of physicochemical properties of CYP2C9 inhibitors, and machine learning modeling. We tested the machine learning models on publicly available data and demonstrated that our models successfully predicted CYP2C9 inhibitors with an accuracy, sensitivity and specificity of approximately 80%. We experimentally validated the developed approach and provided the first identification of the drugs vatalanib, piriqualone, ticagrelor and cloperidone as strong inhibitors of CYP2C9 with IC values <18 μM and sertindole, asapiprant, duvelisib and dasatinib as moderate inhibitors with IC50 values between 40 and 85 μM. Vatalanib was identified as the strongest inhibitor with an IC50 value of 0.067 μM. Metabolism assays allowed the characterization of specific metabolites of abemaciclib, cloperidone, vatalanib and tarafenacin produced by CYP2C9. The obtained results demonstrate that such a strategy could improve the prediction of drug-drug interactions in clinical practice and could be utilized to prioritize drug candidates in drug discovery pipelines.
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Affiliation(s)
- Elodie Goldwaser
- INSERM U1268 « Medicinal Chemistry and Translational Research », UMR 8038 CiTCoM, CNRS—University of Paris, Paris, France
| | | | - Nathalie Lagarde
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, 2 Rue Conté, Hésam Université, Paris, France
| | - Sylvie Fabrega
- Viral Vector for Gene Transfer core facility, Université de Paris—Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Laure Nay
- Viral Vector for Gene Transfer core facility, Université de Paris—Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | | | | | - Arnaud B. Nicot
- INSERM, Nantes Université, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, Nantes, France
| | - Marie-Anne Loriot
- University of Paris, INSERM U1138, Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service de Biochimie, Paris, France
| | - Maria A. Miteva
- INSERM U1268 « Medicinal Chemistry and Translational Research », UMR 8038 CiTCoM, CNRS—University of Paris, Paris, France
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Massively parallel characterization of CYP2C9 variant enzyme activity and abundance. Am J Hum Genet 2021; 108:1735-1751. [PMID: 34314704 DOI: 10.1016/j.ajhg.2021.07.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/28/2021] [Indexed: 12/19/2022] Open
Abstract
CYP2C9 encodes a cytochrome P450 enzyme responsible for metabolizing up to 15% of small molecule drugs, and CYP2C9 variants can alter the safety and efficacy of these therapeutics. In particular, the anti-coagulant warfarin is prescribed to over 15 million people annually and polymorphisms in CYP2C9 can affect individual drug response and lead to an increased risk of hemorrhage. We developed click-seq, a pooled yeast-based activity assay, to test thousands of variants. Using click-seq, we measured the activity of 6,142 missense variants in yeast. We also measured the steady-state cellular abundance of 6,370 missense variants in a human cell line by using variant abundance by massively parallel sequencing (VAMP-seq). These data revealed that almost two-thirds of CYP2C9 variants showed decreased activity and that protein abundance accounted for half of the variation in CYP2C9 function. We also measured activity scores for 319 previously unannotated human variants, many of which may have clinical relevance.
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14
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Feng L, Ning J, Tian X, Wang C, Yu Z, Huo X, Xie T, Zhang B, James TD, Ma X. Fluorescent probes for the detection and imaging of Cytochrome P450. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213740] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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15
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Descriptors of Cytochrome Inhibitors and Useful Machine Learning Based Methods for the Design of Safer Drugs. Pharmaceuticals (Basel) 2021; 14:ph14050472. [PMID: 34067565 PMCID: PMC8156202 DOI: 10.3390/ph14050472] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/16/2022] Open
Abstract
Roughly 2.8% of annual hospitalizations are a result of adverse drug interactions in the United States, representing more than 245,000 hospitalizations. Drug-drug interactions commonly arise from major cytochrome P450 (CYP) inhibition. Various approaches are routinely employed in order to reduce the incidence of adverse interactions, such as altering drug dosing schemes and/or minimizing the number of drugs prescribed; however, often, a reduction in the number of medications cannot be achieved without impacting therapeutic outcomes. Nearly 80% of drugs fail in development due to pharmacokinetic issues, outlining the importance of examining cytochrome interactions during preclinical drug design. In this review, we examined the physiochemical and structural properties of small molecule inhibitors of CYPs 3A4, 2D6, 2C19, 2C9, and 1A2. Although CYP inhibitors tend to have distinct physiochemical properties and structural features, these descriptors alone are insufficient to predict major cytochrome inhibition probability and affinity. Machine learning based in silico approaches may be employed as a more robust and accurate way of predicting CYP inhibition. These various approaches are highlighted in the review.
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16
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Zhang X, Xu M, Wu Z, Liu G, Tang Y, Li W. Assessment of CYP2C9 Structural Models for Site of Metabolism Prediction. ChemMedChem 2021; 16:1754-1763. [PMID: 33600055 DOI: 10.1002/cmdc.202000964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/07/2021] [Indexed: 11/07/2022]
Abstract
Structure-based prediction of a compound's potential sites of metabolism (SOMs) mediated by cytochromes P450 (CYPs) is highly advantageous in the early stage of drug discovery. However, the accuracy of the SOMs prediction can be influenced by several factors. CYP2C9 is one of the major drug-metabolizing enzymes in humans and is responsible for the metabolism of ∼13 % of clinically used drugs. In this study, we systematically evaluated the effects of protein crystal structure models, scoring functions, heme forms, conserved active-site water molecules, and protein flexibility on SOMs prediction of CYP2C9 substrates. Our results demonstrated that, on average, ChemScore and GlideScore outperformed four other scoring functions: Vina, GoldScore, ChemPLP, and ASP. The performance of the crystal structure models with pentacoordinated heme was generally superior to that of the hexacoordinated iron-oxo heme (referred to as Compound I) models. Inclusion of the conserved active-site water molecule improved the prediction accuracy of GlideScore, but reduced the accuracy of ChemScore. In addition, the effect of the conserved water on SOMs prediction was found to be dependent on the receptor model and the substrate. We further found that one of snapshots from molecular dynamics simulations on the apo form can improve the prediction accuracy when compared to the crystal structural model.
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Affiliation(s)
- Xiaoxiao Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 20023, P. R. China
| | - Minjie Xu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 20023, P. R. China
| | - Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 20023, P. R. China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 20023, P. R. China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 20023, P. R. China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 20023, P. R. China
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17
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Nair PC, Gillani TB, Rawling T, Murray M. Differential inhibition of human CYP2C8 and molecular docking interactions elicited by sorafenib and its major N-oxide metabolite. Chem Biol Interact 2021; 338:109401. [PMID: 33556367 DOI: 10.1016/j.cbi.2021.109401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/12/2021] [Accepted: 01/31/2021] [Indexed: 10/22/2022]
Abstract
The tyrosine kinase inhibitor sorafenib (SOR) is being used increasingly in combination with other anticancer agents like paclitaxel, but this increases the potential for drug toxicity. SOR inhibits several human CYPs, including CYP2C8, which is a major enzyme in the elimination of oncology drugs like paclitaxel and imatinib. It has been reported that CYP2C8 inhibition by SOR in human liver microsomes is potentiated by NADPH-dependent biotransformation. This implicates a SOR metabolite in enhanced inhibition, although the identity of that metabolite is presently unclear. The present study evaluated the capacity of the major N-oxide metabolite of SOR (SNO) to inhibit CYP2C8-dependent paclitaxel 6α-hydroxylation. The IC50 of SNO against CYP2C8 activity was found to be 3.7-fold lower than that for the parent drug (14 μM versus 51 μM). In molecular docking studies, both SOR and SNO interacted with active site residues in CYP2C8, but four additional major hydrogen and halogen bonding interactions were identified between SNO and amino acids in the B-B' loop region and helixes F' and I that comprise the catalytic region of the enzyme. In contrast, the binding of both SOR and SNO to active site residues in the closely related human CYP2C9 enzyme was similar, as were the IC50s determined against CYP2C9-mediated losartan oxidation. These findings suggest that the active metabolite SNO could impair the elimination of coadministered drugs that are substrates for CYP2C8, and mediate toxic adverse events, perhaps in those individuals in whom SNO is formed extensively.
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Affiliation(s)
- Pramod C Nair
- Discipline of Clinical Pharmacology and Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Tina B Gillani
- Pharmacogenomics and Drug Development Group, Discipline of Pharmacology, School of Medical Sciences, Sydney Medical School, University of Sydney, NSW, 2006, Australia
| | - Tristan Rawling
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| | - Michael Murray
- Pharmacogenomics and Drug Development Group, Discipline of Pharmacology, School of Medical Sciences, Sydney Medical School, University of Sydney, NSW, 2006, Australia.
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18
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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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19
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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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20
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Engineered human CYP2C9 and its main polymorphic variants for bioelectrochemical measurements of catalytic response. Bioelectrochemistry 2020; 138:107729. [PMID: 33421896 DOI: 10.1016/j.bioelechem.2020.107729] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022]
Abstract
Polymorphism is an important aspect in drug metabolism responsible for different individual response to drug dosage, often leading to adverse drug reactions. Here human CYP2C9 as well as its polymorphic variants CYP2C9*2 and CYP2C9*3 present in approximately 35% of the Caucasian population have been engineered by linking their gene to the one of D. vulgaris flavodoxin (FLD) that acts as regulator of the electron flow from the electrode surface to the haem. The redox properties of the immobilised proteins were investigated by cyclic voltammetry and electrocatalysis was measured in presence of the largely used anticoagulant drug S-warfarin, marker substrate for CYP2C9. Immobilisation of the CYP2C9-FLD, CYP2C9*2-FLD and CYP2C9*3-FLD on DDAB modified glassy carbon electrodes showed well defined redox couples on the oxygen-free cyclic voltammograms and mid-point potentials of all enzymes were calculated. Electrocatalysis in presence of substrate and quantification of the product formed showed lower catalytic activities for the CYP2C9*3-FLD (2.73 ± 1.07 min-1) and CYP2C9*2-FLD (12.42 ± 2.17 min-1) compared to the wild type CYP2C9-FLD (18.23 ± 1.29 min-1). These differences in activity among the CYP2C9 variants are in line with the reported literature data, and this set the basis for the use of the bio-electrode for the measurement of the different catalytic responses towards drugs very relevant in therapy.
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21
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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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Inhibitory Effect of AB-PINACA, Indazole Carboxamide Synthetic Cannabinoid, on Human Major Drug-Metabolizing Enzymes and Transporters. Pharmaceutics 2020; 12:pharmaceutics12111036. [PMID: 33138123 PMCID: PMC7692329 DOI: 10.3390/pharmaceutics12111036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/19/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022] Open
Abstract
Indazole carboxamide synthetic cannabinoid, AB-PINACA, has been placed into Schedule I of the Controlled Substances Act by the US Drug Enforcement Administration since 2015. Despite the possibility of AB-PINACA exposure in drug abusers, the interactions between AB-PINACA and drug-metabolizing enzymes and transporters that play crucial roles in the pharmacokinetics and efficacy of various substrate drugs have not been investigated. This study was performed to investigate the inhibitory effects of AB-PINACA on eight clinically important human major cytochrome P450s (CYPs) and six uridine 5′-diphospho-glucuronosyltransferases (UGT) in human liver microsomes and the activities of six solute carrier transporters and two efflux transporters in transporter-overexpressing cells. AB-PINACA reversibly inhibited the metabolic activities of CYP2C8 (Ki, 16.9 µM), CYP2C9 (Ki, 6.7 µM), and CYP2C19 (Ki, 16.1 µM) and the transport activity of OAT3 (Ki, 8.3 µM). It exhibited time-dependent inhibition on CYP3A4 (Ki, 17.6 µM; kinact, 0.04047 min−1). Other metabolizing enzymes and transporters such as CYP1A2, CYP2A6, CYP2B6, CYP2D6, UGT1A1, UGT1A3, UGT1A4, UGT1A6, UGT1A9, UGT2B7, OAT1, OATP1B1, OATP1B3, OCT1, OCT2, P-glycoprotein, and BCRP, exhibited only weak interactions with AB-PINACA. These data suggest that AB-PINACA can cause drug-drug interactions with CYP3A4 substrates but that the significance of drug interactions between AB-PINACA and CYP2C8, CYP2C9, CYP2C19, or OAT3 substrates should be interpreted carefully.
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23
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Nair PC, Chau N, McKinnon RA, Miners JO. Arginine-259 of UGT2B7 Confers UDP-Sugar Selectivity. Mol Pharmacol 2020; 98:710-718. [PMID: 33008919 DOI: 10.1124/molpharm.120.000104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/17/2020] [Indexed: 11/22/2022] Open
Abstract
Enzymes of the human UDP-glycosyltransferase (UGT) superfamily typically catalyze the covalent addition of the sugar moiety from a UDP-sugar cofactor to relatively low-molecular weight lipophilic compounds. Although UDP-glucuronic acid (UDP-GlcUA) is most commonly employed as the cofactor by UGT1 and UGT2 family enzymes, UGT2B7 and several other enzymes can use both UDP-GlcUA and UDP-glucose (UDP-Glc), leading to the formation of glucuronide and glucoside conjugates. An investigation of UGT2B7-catalyzed morphine glycosidation indicated that glucuronidation is the principal route of metabolism because the binding affinity of UDP-GlcUA is higher than that of UDP-Glc. Currently, it is unclear which residues in the UGT2B7 cofactor binding domain are responsible for the preferential binding of UDP-GlcUA. Here, molecular dynamics (MD) simulations were performed together with site-directed mutagenesis and enzyme kinetic studies to identify residues within the UGT2B7 binding site responsible for the selective cofactor binding. MD simulations demonstrated that Arg259, which is located within the N-terminal domain, specifically interacts with UDP-GlcUA, whereby the side chain of Arg259 H-bonds and forms a salt bridge with the carboxylate group of glucuronic acid. Consistent with the MD simulations, substitution of Arg259 with Leu resulted in the loss of morphine, 4-methylumbelliferone, and zidovudine glucuronidation activity, but morphine glucosidation was preserved. SIGNIFICANCE STATEMENT: Despite the importance of uridine diphosphate glycosyltransferase (UGT) enzymes in drug and chemical metabolism, cofactor binding interactions are incompletely understood, as is the molecular basis for preferential glucuronidation by UGT1 and UGT2 family enzymes. The study demonstrated that long timescale molecular dynamics (MD) simulations with a UGT2B7 homology model can be used to identify critical binding interactions of a UGT protein with UDP-sugar cofactors. Further, the data provide a basis for the application of MD simulations to the elucidation of UGT-aglycone interactions.
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Affiliation(s)
- Pramod C Nair
- Department of Clinical Pharmacology (P.C.N., N.C., J.O.M.) and Flinders Health and Medical Research Institute (FHMRI) Cancer Program (P.C.N., R.A.M., J.O.M.), Flinders Health and Medical Research Institute, Flinders University College of Medicine and Public Health, Flinders Medical Centre, South Australia, Australia
| | - Nuy Chau
- Department of Clinical Pharmacology (P.C.N., N.C., J.O.M.) and Flinders Health and Medical Research Institute (FHMRI) Cancer Program (P.C.N., R.A.M., J.O.M.), Flinders Health and Medical Research Institute, Flinders University College of Medicine and Public Health, Flinders Medical Centre, South Australia, Australia
| | - Ross A McKinnon
- Department of Clinical Pharmacology (P.C.N., N.C., J.O.M.) and Flinders Health and Medical Research Institute (FHMRI) Cancer Program (P.C.N., R.A.M., J.O.M.), Flinders Health and Medical Research Institute, Flinders University College of Medicine and Public Health, Flinders Medical Centre, South Australia, Australia
| | - John O Miners
- Department of Clinical Pharmacology (P.C.N., N.C., J.O.M.) and Flinders Health and Medical Research Institute (FHMRI) Cancer Program (P.C.N., R.A.M., J.O.M.), Flinders Health and Medical Research Institute, Flinders University College of Medicine and Public Health, Flinders Medical Centre, South Australia, Australia
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Banoth S, Tangutur AD, Anthappagudem A, Ramaiah J, Bhukya B. Cloning and in vivo metabolizing activity study of CYP3A4 on amiodarone drug residues: A possible probiotic and therapeutic option. Pharmacotherapy 2020; 127:110128. [DOI: 10.1016/j.biopha.2020.110128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 10/24/2022]
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25
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Roy H, Nandi S. In-Silico Modeling in Drug Metabolism and Interaction: Current Strategies of Lead Discovery. Curr Pharm Des 2020; 25:3292-3305. [PMID: 31481001 DOI: 10.2174/1381612825666190903155935] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/01/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Drug metabolism is a complex mechanism of human body systems to detoxify foreign particles, chemicals, and drugs through bio alterations. It involves many biochemical reactions carried out by invivo enzyme systems present in the liver, kidney, intestine, lungs, and plasma. After drug administration, it crosses several biological membranes to reach into the target site for binding and produces the therapeutic response. After that, it may undergo detoxification and excretion to get rid of the biological systems. Most of the drugs and its metabolites are excreted through kidney via urination. Some drugs and their metabolites enter into intestinal mucosa and excrete through feces. Few of the drugs enter into hepatic circulation where they go into the intestinal tract. The drug leaves the liver via the bile duct and is excreted through feces. Therefore, the study of total methodology of drug biotransformation and interactions with various targets is costly. METHODS To minimize time and cost, in-silico algorithms have been utilized for lead-like drug discovery. Insilico modeling is the process where a computer model with a suitable algorithm is developed to perform a controlled experiment. It involves the combination of both in-vivo and in-vitro experimentation with virtual trials, eliminating the non-significant variables from a large number of variable parameters. Whereas, the major challenge for the experimenter is the selection and validation of the preferred model, as well as precise simulation in real physiological status. RESULTS The present review discussed the application of in-silico models to predict absorption, distribution, metabolism, and excretion (ADME) properties of drug molecules and also access the net rate of metabolism of a compound. CONCLUSION It helps with the identification of enzyme isoforms; which are likely to metabolize a compound, as well as the concentration dependence of metabolism and the identification of expected metabolites. In terms of drug-drug interactions (DDIs), models have been described for the inhibition of metabolism of one compound by another, and for the compound-dependent induction of drug-metabolizing enzymes.
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Affiliation(s)
- Harekrishna Roy
- Nirmala College of Pharmacy, Mangalagiri, Guntur, Affiliated to Acharya Nagarjuna University, Andhra Pradesh-522503, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research, Affiliated to Uttarakhand Technical University, Kashipur-244713, India
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26
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McDonald MG, Henderson LM, Ray S, Yeung CK, Johnson AL, Kowalski JP, Hanenberg H, Wiek C, Thummel KE, Rettie AE. Heterologous Expression and Functional Characterization of Novel CYP2C9 Variants Identified in the Alaska Native People. J Pharmacol Exp Ther 2020; 374:233-240. [PMID: 32423989 DOI: 10.1124/jpet.120.265850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/12/2020] [Indexed: 01/27/2023] Open
Abstract
CYP2C9 is a major form of human liver cytochrome P450 that is responsible for the oxidative metabolism of several widely used low-therapeutic index drugs, including (S)-warfarin and phenytoin. In a cohort of Alaska Native people, ultrarare or novel CYP2C9 protein variants, M1L (rs114071557), N218I (rs780801862), and P279T (rs182132442, CYP2C9*29), are expressed with higher frequencies than the well characterized CYP2C9*2 and CYP2C9*3 alleles. We report here on their relative expression in lentivirus-infected HepG2 cells and the functional characterization of purified reconstituted enzyme variants expressed in Escherichia coli toward (S)-warfarin, phenytoin, flurbiprofen, and (S)-naproxen. In the infected HepG2 cells, robust mRNA and protein expression were obtained for wild-type, N218I, and P279T variants, but as expected, the M1L variant protein was not translated in this liver-derived cell line. His-tagged wild-type protein and the N218I and P279T variants, but not M1L, expressed well in E. coli and were highly purified after affinity chromatography. Upon reconstitution with cytochrome P450 oxidoreductase and cytochrome b5, the N218I and P279T protein variants metabolized (S)-warfarin, phenytoin, flurbiprofen, and (S)-naproxen to the expected monohydroxylated or O-demethylated metabolites. Steady-state kinetic analyses revealed that the relative catalytic efficiency ratios of (S)-warfarin metabolism by the P279T and N218I variants were 87% and 24%, respectively, of wild-type CYP2C9 protein. A similar rank ordering was observed for metabolism of phenytoin, flurbiprofen, and (S)-naproxen. We conclude that carriers of the variant N218I and, especially, the M1L alleles would be at risk of exacerbated therapeutic effects from drugs that rely on CYP2C9 for their metabolic clearance. SIGNIFICANCE STATEMENT: Novel gene variants of CYP2C9-M1L, and N218I, along with P279T (CYP2C9*29)-are expressed in Alaska Native people at relatively high frequencies. In vitro characterization of their functional effects revealed that each variant confers reduced catalytic efficiency toward several substrates, including the low-therapeutic index drugs (S)-warfarin and phenytoin. These data provide the first functional information for new, common CYP2C9 variants in this understudied population. The data may help guide dose adjustments in allele carriers, thus mitigating potential healthcare disparities.
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Affiliation(s)
- Matthew G McDonald
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Lindsay M Henderson
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Sutapa Ray
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Catherine K Yeung
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Amanda L Johnson
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - John P Kowalski
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Helmut Hanenberg
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Constanze Wiek
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Kenneth E Thummel
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Allan E Rettie
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
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Mustafa G, Nandekar PP, Mukherjee G, Bruce NJ, Wade RC. The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics. Sci Rep 2020; 10:7284. [PMID: 32350331 PMCID: PMC7190701 DOI: 10.1038/s41598-020-64129-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 04/13/2020] [Indexed: 11/24/2022] Open
Abstract
The simulation of membrane proteins requires compatible protein and lipid force fields that reproduce the properties of both the protein and the lipid bilayer. Cytochrome P450 enzymes are bitopic membrane proteins with a transmembrane helical anchor and a large cytosolic globular domain that dips into the membrane. As such, they are representative and challenging examples of membrane proteins for simulations, displaying features of both peripheral and integral membrane proteins. We performed molecular dynamics simulations of three cytochrome P450 isoforms (2C9, 2C19 and 1A1) in a 2-oleoyl-1-palmitoyl-sn-glycerol-3-phosphocholine bilayer using two AMBER force field combinations: GAFF-LIPID with ff99SB for the protein, and LIPID14 with ff14SB for the protein. Comparison of the structural and dynamic properties of the proteins, the lipids and the protein-membrane interactions shows differing sensitivity of the cytochrome P450 isoforms to the choice of force field, with generally better agreement with experiment for the LIPID14 + ff14SB combination.
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Affiliation(s)
- Ghulam Mustafa
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,B-Zell-Immunologie (D130), German Cancer Research Center, Deutsches Krebsforschungszentrum (DKF), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Prajwal P Nandekar
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120, Heidelberg, Germany.,Schrodinger Inc. #147, 3rd Floor, Jawaharlal Nehru main road, Above State Bank of India, Channasandra, 5th Stage, RR Nagar, Bengaluru, 560098, India
| | - Goutam Mukherjee
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120, Heidelberg, Germany
| | - Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. .,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120, Heidelberg, Germany. .,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, INF 368, 69120, Heidelberg, Germany.
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28
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Mendieta-Wejebe JE, Silva-Trujillo A, Bello M, Mendoza-Figueroa HL, Galindo-Alvarez NL, Albores A, Tamay-Cach F, Rosales-Hernández MC, Romero-Castro A, Correa-Basurto J. Exploring the biotransformation of N-(2-hydroxyphenyl)-2-propylpentanamide (an aryl valproic acid derivative) by CYP2C11, using in silico predictions and in vitro studies. J Pharm Pharmacol 2020; 72:938-955. [PMID: 32307724 DOI: 10.1111/jphp.13270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/21/2020] [Indexed: 01/22/2023]
Abstract
OBJECTIVES N-(2-hydroxyphenyl)-2-propylpentanamide (HO-AAVPA), a derivative of valproic acid (VPA), has been proposed as a potential anticancer agent due to its improved antiproliferative effects in some cancer cell lines. Although there is evidence that VPA is metabolized by cytochrome P450 2C11 rat isoform, HO-AAVPA CYP-mediated metabolism has not yet been fully explored. Therefore, in this work, the biotransformation of HO-AAVPA by CYP2C11 was investigated. METHODS Kinetic parameters and spectral interaction between HO-AAVPA and CYP were evaluated using rat liver microsomes. The participation of CYP2C11 in metabolism of HO-AAVPA was confirmed by cimetidine (CIM) inhibition assay. Docking and molecular dynamics simulations coupled to MMGBSA methods were used in theoretical study. KEY FINDINGS HO-AAVPA is metabolized by CYP enzymes (KM = 38.94 µm), yielding a hydroxylated metabolite according to its HPLC retention time (5.4 min) and MS analysis (252.2 m/z). In addition, CIM inhibition in rat liver microsomes (Ki = 59.23 µm) confirmed that CYP2C11 is mainly involved in HO-AAVPA metabolism. Furthermore, HO-AAVPA interacts with CYP2C11 as a type I ligand. HO-AAVPA is stabilized at the CYP2C11 ligand recognition site through a map of interactions similar to other typical CYP2C11 substrates. CONCLUSION Therefore, rat liver CYP2C11 isoform is able to metabolize HO-AAVPA.
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Affiliation(s)
- Jessica Elena Mendieta-Wejebe
- Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Arianna Silva-Trujillo
- Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Humberto L Mendoza-Figueroa
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Norma Lizeth Galindo-Alvarez
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Arnulfo Albores
- Sección de Toxicología, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Ciudad de México, México
| | - Feliciano Tamay-Cach
- Laboratorio de Investigación Bioquímica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | | | | | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
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29
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Manoj KM. Murburn concept: a paradigm shift in cellular metabolism and physiology. Biomol Concepts 2020; 11:7-22. [PMID: 31961793 DOI: 10.1515/bmc-2020-0002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/02/2020] [Indexed: 12/26/2022] Open
Abstract
Two decades of evidence-based exploratory pursuits in heme-flavin enzymology led to the formulation of a new biological electron/moiety transfer paradigm, called murburn concept. Murburn is a novel literary abstraction from "mured burning" or "mild unrestricted burning". This concept was invoked to explain the longstanding conundrum of maverick physiological dose responses and also applied to remodel the prevailing understanding of drug metabolism and cellular respiration. A conglomeration of simple ideas grounded in the known principles of thermodynamics and reaction chemistry, murburn concept invokes catalytic/functional roles for diffusible reactive species or radicals. Hitherto, diffusible reactive species were primarily seen as toxic agents of chaos, non-conducible to the maintenance of life-order. Since the murburn paradigm offers a distinctly different perspective for several biological phenomena, researchers holding conventional views of cellular metabolism pose a direct conflict of interests to the advancement of murburn concept. Murburn schemes are poised to integrate numerous metabolic motifs with holistic physiological outcomes; redefining pursuits in biology and medicine. To advance this agenda, I present a brief account of murburn concept and point out how redundant ideas are still advocated in some prestigious journals.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation,Snehatheeram, Kulappully, Shoranur-2 (PO), Kerala,India-679122
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30
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Preclinical toxicity of innovative molecules: In vitro, in vivo and metabolism prediction. Chem Biol Interact 2020; 315:108896. [DOI: 10.1016/j.cbi.2019.108896] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/19/2019] [Accepted: 11/08/2019] [Indexed: 11/22/2022]
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31
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Quiroga I, Scior T. Induced fit for cytochrome P450 3A4 based on molecular dynamics. ADMET & DMPK 2019; 7:252-266. [PMID: 35359616 PMCID: PMC8963583 DOI: 10.5599/admet.729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/19/2019] [Indexed: 11/18/2022]
Abstract
The present study aims at numerically describing to what extent substrate - enzyme complexes in solution may change over time as a natural process of conformational changes for a liganded enzyme in comparison to those movements which occur independently from substrate interaction, i.e. without a ligand. To this end, we selected structurally known pairs of liganded / unliganded CYP450 3A4 enzymes with different geometries hinting at induced fit events. We carried out molecular dynamics simulations (MD) comparing the trajectories in a “cross-over” protocol: (i) we added the ligand to the unliganded crystal form which should adopt geometries similar to the known geometry of the liganded crystal structure during MD, and – conversely – (ii) we removed the bound ligand form the known liganded complex to test if a geometry similar to the known unliganded (apo-) form can be adopted during MD. To compare continues changes we measured root means square deviations and frequencies. Results for case (i) hint at larger conformational changes required for accepting the substrate during its approach to final position – in contrast to case (ii) when mobility is fairly reduced by ligand binding (strain energy). In conclusion, a larger conformational sampling prior to ligand binding and the freezing-in (rigidity) of conformations for bound ligands can be interpreted as two conditions linked to induced-fit.
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Affiliation(s)
- Israel Quiroga
- Faculty of Chemical Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Pue., Mexico
| | - Thomas Scior
- Faculty of Chemical Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Pue., Mexico
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32
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Wasukan N, Kuno M, Maniratanachote R. Molecular Docking as a Promising Predictive Model for Silver Nanoparticle-Mediated Inhibition of Cytochrome P450 Enzymes. J Chem Inf Model 2019; 59:5126-5134. [PMID: 31714078 DOI: 10.1021/acs.jcim.9b00572] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cytochrome P450 (CYP) enzymes are responsible for oxidative metabolisms of a large number of xenobiotics. In this study, we investigated interactions of silver nanoparticles (AgNPs) and silver ions (Ag+) with six CYP isoforms, namely, CYP1A2, CYP2C9, CYP2C19, CYP2D6, CYP2E1, and CYP3A4, within CYP-specific inhibitor-binding pockets by molecular docking and quantum mechanical (QM) calculations. The docking results revealed that the Ag3 cluster, not Ag+, interacted with key amino acids of CYP2C9, CYP2C19, and CYP2D6 within a distance of about 3 Å. Moreover, the QM analysis confirmed that the amino acid residues of these CYP enzymes strongly interacted with the Ag3 cluster, providing more insight into the mechanism of the potential inhibition of CYP enzyme activities. Interestingly, these results are consistent with previous in vitro data indicating that AgNPs inhibited activities of CYP2C and CYP2D in rat liver microsomes. It is suggested that the Ag3 cluster is a minimal unit of AgNPs for in silico modeling. In summary, we demonstrated that molecular docking, together with QM analysis, is a promising tool to predict AgNP-mediated CYP inhibition. These methods are useful for deeper understanding of reaction mechanisms and could be used for other nanomaterials.
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Affiliation(s)
- Nootcharin Wasukan
- National Science and Technology Development Agency (NSTDA) , 111 Thailand Science Park , Khlong Luang , Pathum Thani 12120 , Thailand
| | - Mayuso Kuno
- Department of Chemistry, Faculty of Science , Srinakharinwirot University , Sukhumwit 23 , Wattana District, Bangkok 10110 , Thailand
| | - Rawiwan Maniratanachote
- National Science and Technology Development Agency (NSTDA) , 111 Thailand Science Park , Khlong Luang , Pathum Thani 12120 , Thailand
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33
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Mustafa G, Nandekar PP, Bruce NJ, Wade RC. Differing Membrane Interactions of Two Highly Similar Drug-Metabolizing Cytochrome P450 Isoforms: CYP 2C9 and CYP 2C19. Int J Mol Sci 2019; 20:ijms20184328. [PMID: 31487853 PMCID: PMC6770661 DOI: 10.3390/ijms20184328] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/31/2019] [Accepted: 09/01/2019] [Indexed: 12/22/2022] Open
Abstract
The human cytochrome P450 (CYP) 2C9 and 2C19 enzymes are two highly similar isoforms with key roles in drug metabolism. They are anchored to the endoplasmic reticulum membrane by their N-terminal transmembrane helix and interactions of their cytoplasmic globular domain with the membrane. However, their crystal structures were determined after N-terminal truncation and mutating residues in the globular domain that contact the membrane. Therefore, the CYP-membrane interactions are not structurally well-characterized and their dynamics and the influence of membrane interactions on CYP function are not well understood. We describe herein the modeling and simulation of CYP 2C9 and CYP 2C19 in a phospholipid bilayer. The simulations revealed that, despite high sequence conservation, the small sequence and structural differences between the two isoforms altered the interactions and orientations of the CYPs in the membrane bilayer. We identified residues (including K72, P73, and I99 in CYP 2C9 and E72, R73, and H99 in CYP 2C19) at the protein-membrane interface that contribute not only to the differing orientations adopted by the two isoforms in the membrane, but also to their differing substrate specificities by affecting the substrate access tunnels. Our findings provide a mechanistic interpretation of experimentally observed effects of mutagenesis on substrate selectivity.
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Affiliation(s)
- Ghulam Mustafa
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Prajwal P Nandekar
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany.
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany.
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34
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Exploring the Chemical Space of Cytochrome P450 Inhibitors Using Integrated Physicochemical Parameters, Drug Efficiency Metrics and Decision Tree Models. COMPUTATION 2019. [DOI: 10.3390/computation7020026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The cytochrome P450s (CYPs) play a central role in the metabolism of various endogenous and exogenous compounds including drugs. CYPs are vulnerable to inhibition and induction which can lead to adverse drug reactions. Therefore, insights into the underlying mechanism of CYP450 inhibition and the estimation of overall CYP inhibitor properties might serve as valuable tools during the early phases of drug discovery. Herein, we present a large data set of inhibitors against five major metabolic CYPs (CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4) for the evaluation of important physicochemical properties and ligand efficiency metrics to define property trends across various activity levels (active, efficient and inactive). Decision tree models for CYP inhibition were developed with an accuracy >90% for both the training set and 10-folds cross validation. Overall, molecular weight (MW), hydrogen bond acceptors/donors (HBA/HBD) and lipophilicity (clogP/logPo/w) represent important physicochemical descriptors for CYP450 inhibitors. However, highly efficient CYP inhibitors show mean MW, HBA, HBD and logP values between 294.18–482.40,5.0–8.2,1–7.29 and 1.68–2.57, respectively. Our results might help in optimization of toxicological profiles associated with new chemical entities (NCEs), through a better understanding of inhibitor properties leading to CYP-mediated interactions.
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Nagayoshi H, Murayama N, Kakimoto K, Tsujino M, Takenaka S, Katahira J, Lim YR, Kim D, Yamazaki H, Komori M, Guengerich FP, Shimada T. Oxidation of Flavone, 5-Hydroxyflavone, and 5,7-Dihydroxyflavone to Mono-, Di-, and Tri-Hydroxyflavones by Human Cytochrome P450 Enzymes. Chem Res Toxicol 2019; 32:1268-1280. [PMID: 30964977 DOI: 10.1021/acs.chemrestox.9b00078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biologically active plant flavonoids, including 5,7-dihydroxyflavone (57diOHF, chrysin), 4',5,7-trihydroxyflavone (4'57triOHF, apigenin), and 5,6,7-trihydroxyflavone (567triOHF, baicalein), have important pharmacological and toxicological significance, e.g., antiallergic, anti-inflammatory, antioxidative, antimicrobial, and antitumorgenic properties. In order to better understand the metabolism of these flavonoids in humans, we examined the oxidation of flavone, 5-hydroxyflavone (5OHF), and 57diOHF to various products by human cytochrome P450 (P450 or CYP) and liver microsomal enzymes. Individual human P450s and liver microsomes oxidized flavone to 6-hydroxyflavone, small amounts of 5OHF, and 11 other monohydroxylated products at different rates and also produced several dihydroxylated products (including 57diOHF and 7,8-dihydroxyflavone) from flavone. We also found that 5OHF was oxidized by several P450 enzymes and human liver microsomes to 57diOHF and further to 567triOHF, but the turnover rates in these reactions were low. Interestingly, both CYP1B1.1 and 1B1.3 converted 57diOHF to 567triOHF at turnover rates (on the basis of P450 contents) of >3.0 min-1, and CYP1A1 and 1A2 produced 567triOHF at rates of 0.51 and 0.72 min-1, respectively. CYP2A13 and 2A6 catalyzed the oxidation of 57diOHF to 4'57triOHF at rates of 0.7 and 0.1 min-1, respectively. Our present results show that different P450s have individual roles in oxidizing these phytochemical flavonoids and that these reactions may cause changes in their biological and toxicological properties in mammals.
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Affiliation(s)
- Haruna Nagayoshi
- Osaka Institute of Public Health , 1-3-69 Nakamichi , Higashinari-ku , Osaka 537-0025 , Japan
| | - Norie Murayama
- Laboratory of Drug Metabolism and Pharmacokinetics , Showa Pharmaceutical University , Machida , Tokyo 194-8543 , Japan
| | - Kensaku Kakimoto
- Osaka Institute of Public Health , 1-3-69 Nakamichi , Higashinari-ku , Osaka 537-0025 , Japan
| | - Masaki Tsujino
- Osaka Institute of Public Health , 1-3-69 Nakamichi , Higashinari-ku , Osaka 537-0025 , Japan
| | - Shigeo Takenaka
- Graduate School of Comprehensive Rehabilitation , Osaka Prefecture University , 3-7-30 , Habikino , Osaka 583-8555 , Japan
| | - Jun Katahira
- Laboratory of Cellular and Molecular Biology, Veterinary Sciences , Osaka Prefecture University , 1-58 Rinku-Orai-Kita , Izumisano , Osaka 598-8531 , Japan
| | - Young-Ran Lim
- Department of Biological Sciences , Konkuk University , Seoul 05029 , Korea
| | - Donghak Kim
- Department of Biological Sciences , Konkuk University , Seoul 05029 , Korea
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics , Showa Pharmaceutical University , Machida , Tokyo 194-8543 , Japan
| | - Masayuki Komori
- Laboratory of Cellular and Molecular Biology, Veterinary Sciences , Osaka Prefecture University , 1-58 Rinku-Orai-Kita , Izumisano , Osaka 598-8531 , Japan
| | - F Peter Guengerich
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States
| | - Tsutomu Shimada
- Laboratory of Cellular and Molecular Biology, Veterinary Sciences , Osaka Prefecture University , 1-58 Rinku-Orai-Kita , Izumisano , Osaka 598-8531 , Japan
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36
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Nair PC, McKinnon RA, Miners JO. Computational Prediction of the Site(s) of Metabolism and Binding Modes of Protein Kinase Inhibitors Metabolized by CYP3A4. Drug Metab Dispos 2019; 47:616-631. [DOI: 10.1124/dmd.118.085167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/18/2019] [Indexed: 01/13/2023] Open
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37
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Derayea SM, Tsujino H, Oyama Y, Ishikawa Y, Yamashita T, Uno T. Investigation on drug-binding in heme pocket of CYP2C19 with UV-visible and resonance Raman spectroscopies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 209:209-216. [PMID: 30399481 DOI: 10.1016/j.saa.2018.10.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/23/2018] [Accepted: 10/25/2018] [Indexed: 06/08/2023]
Abstract
Cytochrome P450 (CYP) is a class of heme-containing enzymes which mainly catalyze a monooxygenation reaction of various chemicals, and hence CYP plays a key role in the drug metabolism. Although CYP2C19 isoform is a minor hepatic CYP, it metabolizes clinically important drugs such as omeprazole and S‑mephenytoin. In this work, the interaction of purified CYP2C19 WT (CYP2C19) with seven drugs (phenytoin, S‑mephenytoin, omeprazole, lansoprazole, cimetidine, propranolol, and warfarin) was investigated using spectroscopic methods. The binding of each drug and the induced structural change in the heme distal environment were evaluated. Ferric form of CYP2C19 was revealed to contain a six-coordinate low-spin heme with a water molecule as a sixth ligand in a distal site, and the addition of each drug caused varied minor fraction of five-coordinate heme. It was suggested that the ligated water molecule was partly moved away from the heme distal environment and that the degree of water removal was dependent on the type of drugs. The effect on the coordination was varied with the studied drugs with wide variation in the dissociation constants from 2.6 μM for lansoprazole to 5400 μM for warfarin. Phenytoin and S‑mephenytoin showed that binding to CYP2C19 occurred in a stepwise manner and that the coordination of a water molecule was facilitated in the second binding step. In the ferrous CO-bound state, ν(FeCO) stretching mode was clearly observed at 471 cm-1 in the absence of drugs. The Raman line was greatly up-shifted by omeprazole (487 cm-1) and lansoprazole (477 cm-1) but was minimally affected by propranolol, phenytoin, and S‑mephenytoin. These results indicate that slight chemical modification of a drug greatly affects the heme distal environments upon binding.
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Affiliation(s)
- Sayed M Derayea
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan; Analytical Chemistry Department, Faculty of Pharmacy, Minia University, Minia, Egypt.
| | - Hirofumi Tsujino
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan
| | - Yukiko Oyama
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Kumamoto 862-0973, Japan
| | - Yoshinobu Ishikawa
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Taku Yamashita
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, 11-68 Koshien-Kyubancho, Nishinomiya 663-8179, Japan
| | - Tadayuki Uno
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan
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Devarajan S, Moon I, Ho MF, Larson NB, Neavin DR, Moyer AM, Black JL, Bielinski SJ, Scherer SE, Wang L, Weinshilboum RM, Reid JM. Pharmacogenomic Next-Generation DNA Sequencing: Lessons from the Identification and Functional Characterization of Variants of Unknown Significance in CYP2C9 and CYP2C19. Drug Metab Dispos 2019; 47:425-435. [PMID: 30745309 DOI: 10.1124/dmd.118.084269] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/15/2019] [Indexed: 02/06/2023] Open
Abstract
CYP2C9 and CYP2C19 are highly polymorphic pharmacogenes; however, clinically actionable genetic variability in drug metabolism due to these genes has been limited to a few common alleles. The identification and functional characterization of less-common open reading frame sequence variation might help to individualize therapy with drugs that are substrates for the enzymes encoded by these genes. The present study identified seven uncharacterized variants each in CYP2C9 and CYP2C19 using next-generation sequence data for 1013 subjects, and functionally characterized the encoded proteins. Constructs were created and transiently expressed in COS-1 cells for the assay of protein concentration and enzyme activities using fluorometric substrates and liquid chromatography- tandem mass spectrometry with tolbutamide (CYP2C9) and (S)-mephenytoin (CYP2C19) as prototypic substrates. The results were compared with the SIFT, Polyphen, and Provean functional prediction software programs. Cytochrome P450 oxidoreductase (CPR) activities were also determined. Positive correlations were observed between protein content and fluorometric enzyme activity for variants of CYP2C9 (P < 0.05) and CYP2C19 (P < 0.0005). However, CYP2C9 709G>C and CYP2C19 65A>G activities were much lower than predicted based on protein content. Substrate intrinsic clearance values for CYP2C9 218C>T, 343A>C, and CYP2C19 337G>A, 518C>T, 556C>T, and 557G>A were less than 25% of wild-type allozymes. CPR activity levels were similar for all variants. In summary, sequencing of CYP2C9 and CYP2C19 in 1013 subjects identified low-frequency variants that had not previously been functionally characterized. In silico predictions were not always consistent with functional assay results. These observations emphasize the need for high-throughput methods for pharmacogene variant mutagenesis and functional characterization.
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Affiliation(s)
- Sandhya Devarajan
- Departments of Molecular Pharmacology and Experimental Therapeutics (S.D., I.M., M.-F.H., L.W., R.M.W., J.M.R.) and Health Sciences Research (N.B.L., S.J.B.), Personalized Genomics Laboratory, Department of Laboratory Medicine and Pathology (A.M.M., J.L.B.), and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences (D.R.N.), Mayo Clinic, Rochester, Minnesota; and Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas (S.E.S.)
| | - Irene Moon
- Departments of Molecular Pharmacology and Experimental Therapeutics (S.D., I.M., M.-F.H., L.W., R.M.W., J.M.R.) and Health Sciences Research (N.B.L., S.J.B.), Personalized Genomics Laboratory, Department of Laboratory Medicine and Pathology (A.M.M., J.L.B.), and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences (D.R.N.), Mayo Clinic, Rochester, Minnesota; and Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas (S.E.S.)
| | - Ming-Fen Ho
- Departments of Molecular Pharmacology and Experimental Therapeutics (S.D., I.M., M.-F.H., L.W., R.M.W., J.M.R.) and Health Sciences Research (N.B.L., S.J.B.), Personalized Genomics Laboratory, Department of Laboratory Medicine and Pathology (A.M.M., J.L.B.), and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences (D.R.N.), Mayo Clinic, Rochester, Minnesota; and Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas (S.E.S.)
| | - Nicholas B Larson
- Departments of Molecular Pharmacology and Experimental Therapeutics (S.D., I.M., M.-F.H., L.W., R.M.W., J.M.R.) and Health Sciences Research (N.B.L., S.J.B.), Personalized Genomics Laboratory, Department of Laboratory Medicine and Pathology (A.M.M., J.L.B.), and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences (D.R.N.), Mayo Clinic, Rochester, Minnesota; and Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas (S.E.S.)
| | - Drew R Neavin
- Departments of Molecular Pharmacology and Experimental Therapeutics (S.D., I.M., M.-F.H., L.W., R.M.W., J.M.R.) and Health Sciences Research (N.B.L., S.J.B.), Personalized Genomics Laboratory, Department of Laboratory Medicine and Pathology (A.M.M., J.L.B.), and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences (D.R.N.), Mayo Clinic, Rochester, Minnesota; and Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas (S.E.S.)
| | - Ann M Moyer
- Departments of Molecular Pharmacology and Experimental Therapeutics (S.D., I.M., M.-F.H., L.W., R.M.W., J.M.R.) and Health Sciences Research (N.B.L., S.J.B.), Personalized Genomics Laboratory, Department of Laboratory Medicine and Pathology (A.M.M., J.L.B.), and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences (D.R.N.), Mayo Clinic, Rochester, Minnesota; and Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas (S.E.S.)
| | - John L Black
- Departments of Molecular Pharmacology and Experimental Therapeutics (S.D., I.M., M.-F.H., L.W., R.M.W., J.M.R.) and Health Sciences Research (N.B.L., S.J.B.), Personalized Genomics Laboratory, Department of Laboratory Medicine and Pathology (A.M.M., J.L.B.), and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences (D.R.N.), Mayo Clinic, Rochester, Minnesota; and Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas (S.E.S.)
| | - Suzette J Bielinski
- Departments of Molecular Pharmacology and Experimental Therapeutics (S.D., I.M., M.-F.H., L.W., R.M.W., J.M.R.) and Health Sciences Research (N.B.L., S.J.B.), Personalized Genomics Laboratory, Department of Laboratory Medicine and Pathology (A.M.M., J.L.B.), and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences (D.R.N.), Mayo Clinic, Rochester, Minnesota; and Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas (S.E.S.)
| | - Steven E Scherer
- Departments of Molecular Pharmacology and Experimental Therapeutics (S.D., I.M., M.-F.H., L.W., R.M.W., J.M.R.) and Health Sciences Research (N.B.L., S.J.B.), Personalized Genomics Laboratory, Department of Laboratory Medicine and Pathology (A.M.M., J.L.B.), and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences (D.R.N.), Mayo Clinic, Rochester, Minnesota; and Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas (S.E.S.)
| | - Liewei Wang
- Departments of Molecular Pharmacology and Experimental Therapeutics (S.D., I.M., M.-F.H., L.W., R.M.W., J.M.R.) and Health Sciences Research (N.B.L., S.J.B.), Personalized Genomics Laboratory, Department of Laboratory Medicine and Pathology (A.M.M., J.L.B.), and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences (D.R.N.), Mayo Clinic, Rochester, Minnesota; and Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas (S.E.S.)
| | - Richard M Weinshilboum
- Departments of Molecular Pharmacology and Experimental Therapeutics (S.D., I.M., M.-F.H., L.W., R.M.W., J.M.R.) and Health Sciences Research (N.B.L., S.J.B.), Personalized Genomics Laboratory, Department of Laboratory Medicine and Pathology (A.M.M., J.L.B.), and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences (D.R.N.), Mayo Clinic, Rochester, Minnesota; and Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas (S.E.S.)
| | - Joel M Reid
- Departments of Molecular Pharmacology and Experimental Therapeutics (S.D., I.M., M.-F.H., L.W., R.M.W., J.M.R.) and Health Sciences Research (N.B.L., S.J.B.), Personalized Genomics Laboratory, Department of Laboratory Medicine and Pathology (A.M.M., J.L.B.), and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences (D.R.N.), Mayo Clinic, Rochester, Minnesota; and Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas (S.E.S.)
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Xu LH, Du YL. Rational and semi-rational engineering of cytochrome P450s for biotechnological applications. Synth Syst Biotechnol 2018; 3:283-290. [PMID: 30533540 PMCID: PMC6263019 DOI: 10.1016/j.synbio.2018.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 01/08/2023] Open
Abstract
The cytochrome P450 enzymes are ubiquitous heme-thiolate proteins performing regioselective and stereoselective oxygenation reactions in cellular metabolism. Due to their broad substrate scope and catalytic versatility, P450 enzymes are also attractive candidates for many industrial and biopharmaceutical applications. For particular uses, enzyme properties of P450s can be further optimized through directed evolution, rational, and semi-rational engineering approaches, all of which introduce mutations within the P450 structures. In this review, we describe the recent applications of these P450 engineering approaches and highlight the key regions and residues that have been identified using such approaches. These “hotspots” lie within critical functional areas of the P450 structure, including the active site, the substrate access channel, and the redox partner interaction interface.
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Affiliation(s)
- Lian-Hua Xu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Corresponding author.
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Corresponding author.
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40
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Uno T, Nakano R, Kitagawa R, Okada M, Kanamaru K, Takenaka S, Uno Y, Imaishi H. Metabolism of steroids by cytochrome P450 2C9 variants. Biopharm Drug Dispos 2018; 39:371-377. [DOI: 10.1002/bdd.2153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 07/25/2018] [Accepted: 07/31/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Tomohide Uno
- Biological Chemistry; Faculty of Agriculture, Kobe University; Nada-ku, Kobe Hyogo Japan
| | - Ryosuke Nakano
- Biological Chemistry; Faculty of Agriculture, Kobe University; Nada-ku, Kobe Hyogo Japan
| | - Risa Kitagawa
- Biological Chemistry; Faculty of Agriculture, Kobe University; Nada-ku, Kobe Hyogo Japan
| | - Mai Okada
- Biological Chemistry; Faculty of Agriculture, Kobe University; Nada-ku, Kobe Hyogo Japan
| | - Kengo Kanamaru
- Biological Chemistry; Faculty of Agriculture, Kobe University; Nada-ku, Kobe Hyogo Japan
| | - Shinji Takenaka
- Environmental Microbiology, Faculty of Agriculture; Kobe University; Nada-ku, Kobe Hyogo Japan
| | - Yuichi Uno
- Department of Plant Resource Science, Faculty of Agriculture; Kobe University; Nada-ku, Hyogo Japan
| | - Hiromasa Imaishi
- Laboratory of Response to Environmental Materials; Division of Signal Responses, Biosignal Research Center, Kobe University; Nada-ku, Kobe Hyogo Japan
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41
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Sausville LN, Gangadhariah MH, Chiusa M, Mei S, Wei S, Zent R, Luther JM, Shuey MM, Capdevila JH, Falck JR, Guengerich FP, Williams SM, Pozzi A. The Cytochrome P450 Slow Metabolizers CYP2C9*2 and CYP2C9*3 Directly Regulate Tumorigenesis via Reduced Epoxyeicosatrienoic Acid Production. Cancer Res 2018; 78:4865-4877. [PMID: 30012669 PMCID: PMC6125168 DOI: 10.1158/0008-5472.can-17-3977] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/31/2018] [Accepted: 07/11/2018] [Indexed: 01/02/2023]
Abstract
Increased expression of cytochrome P450 CYP2C9, together with elevated levels of its products epoxyeicosatrienoic acids (EET), is associated with aggressiveness in cancer. Cytochrome P450 variants CYP2C9*2 and CYP2C9*3 encode proteins with reduced enzymatic activity, and individuals carrying these variants metabolize drugs more slowly than individuals with wild-type CYP2C9*1, potentially affecting their response to drugs and altering their risk of disease. Although genetic differences in CYP2C9-dependent oxidation of arachidonic acid (AA) have been reported, the roles of CYP2C9*2 and CYP2C9*3 in EET biosynthesis and their relevance to disease are unknown. Here, we report that CYP2C9*2 and CYP2C9*3 metabolize AA less efficiently than CYP2C9*1 and that they play a role in the progression of non-small cell lung cancer (NSCLC) via impaired EET biosynthesis. When injected into mice, NSCLC cells expressing CYP2C9*2 and CYP2C9*3 produced lower levels of EETs and developed fewer, smaller, and less vascularized tumors than cells expressing CYP2C9*1. Moreover, endothelial cells expressing these two variants proliferated and migrated less than cells expressing CYP2C*1. Purified CYP2C9*2 and CYP2C9*3 exhibited attenuated catalytic efficiency in producing EETs, primarily due to impaired reduction of these two variants by NADPH-P450 reductase. Loss-of-function SNPs within CYP2C9*2 and CYP2C9*3 were associated with improved survival in female cases of NSCLC. Thus, decreased EET biosynthesis represents a novel mechanism whereby CYPC29*2 and CYP2C9*3 exert a direct protective role in NSCLC development.Significance: These findings report single nucleotide polymorphisms in the human CYP2C9 genes, CYP2C9*2 and CYP2C9*3, exert a direct protective role in tumorigenesis by impairing EET biosynthesis. Cancer Res; 78(17); 4865-77. ©2018 AACR.
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Affiliation(s)
- Lindsay N Sausville
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Mahesha H Gangadhariah
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Pathobiology, Cleveland Clinic, Cleveland, Ohio
| | - Manuel Chiusa
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Shaojun Mei
- Diabetes Research and Training Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Shouzuo Wei
- Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Roy Zent
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Veterans Affairs Hospital, Nashville, Tennessee
| | - James M Luther
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Megan M Shuey
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jorge H Capdevila
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John R Falck
- Division of Chemistry, University of Texas Southwestern Medical Center, Dallas, Texas
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Ambra Pozzi
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
- Veterans Affairs Hospital, Nashville, Tennessee
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42
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Geronimo I, Denning CA, Heidary DK, Glazer EC, Payne CM. Molecular Determinants of Substrate Affinity and Enzyme Activity of a Cytochrome P450 BM3 Variant. Biophys J 2018; 115:1251-1263. [PMID: 30224054 DOI: 10.1016/j.bpj.2018.08.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 12/29/2022] Open
Abstract
Cytochrome P450BM3 catalyzes the hydroxylation and/or epoxidation of fatty acids, fatty amides, and alcohols. Protein engineering has produced P450BM3 variants capable of accepting drug molecules normally metabolized by human P450 enzymes. The enhanced substrate promiscuity has been attributed to the greater flexibility of the lid of the substrate channel. However, it is not well understood how structurally different and highly polar drug molecules can stably bind in the active site nor how the activity and coupling efficiency of the enzyme may be affected by the lack of enzyme-substrate complementarity. To address these important aspects of non-native small molecule binding, this study investigated the binding of drug molecules with different size, charge, polar surface area, and human P450 affinity on the promiscuous R47L/F87V/L188Q/E267V/F81I pentuple mutant of P450BM3. Binding free energy data and energy decomposition analysis showed that pentuple mutant P450BM3 stably binds (i.e., negative ΔGb°) a broad range of substrate and inhibitor types because dispersion interactions with active site residues overcome unfavorable repulsive and electrostatic effects. Molecular dynamics simulations revealed that 1) acidic substrates tend to disrupt the heme propionate A-K69 salt bridge, which may reduce heme oxidizing ability, and 2) the lack of complementarity leads to high substrate mobility and water density in the active site, which may lead to uncoupling. These factors must be considered in future developments of P450BM3 as a biocatalyst in the large-scale production of drug metabolites.
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Affiliation(s)
- Inacrist Geronimo
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky
| | | | - David K Heidary
- Department of Chemistry, University of Kentucky, Lexington, Kentucky
| | - Edith C Glazer
- Department of Chemistry, University of Kentucky, Lexington, Kentucky.
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky.
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43
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Elfaki I, Mir R, Almutairi FM, Duhier FMA. Cytochrome P450: Polymorphisms and Roles in Cancer, Diabetes and Atherosclerosis. Asian Pac J Cancer Prev 2018; 19:2057-2070. [PMID: 30139042 PMCID: PMC6171375 DOI: 10.22034/apjcp.2018.19.8.2057] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cytochromes P450s (CYPs) constitute a superfamily of enzymes that catalyze the metabolism of drugs and other substances. Endogenous substrates of CYPs include eicosanoids, estradiol, arachidonic acids, cholesterol, vitamin D and neurotransmitters. Exogenous substrates of CYPs include the polycyclic aromatic hydrocarbons and about 80% of currently used drugs. Some isoforms can activate procarcinogens to ultimate carcinogens. Genetic polymorphisms of CYPs may affect the enzyme catalytic activity and have been reported among different populations to be associated with various diseases and adverse drug reactions. With regard of drug metabolism, phenotypes for CYP polymorphism range from ultrarapid to poor metabolizers. In this review, we discuss some of the most clinically important CYPs isoforms (CYP2D6, CYP2A6, CYP2C19, CYP2C9, CYP1B1 and CYP1A2) with respect to gene polymorphisms and drug metabolism. Moreover, we review the role of CYPs in renal, lung, breast and prostate cancers and also discuss their significance for atherosclerosis and type 2 diabetes mellitus.
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Affiliation(s)
- Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, Kingdom of Saudi Arabia.
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44
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Arendse LB, Blackburn JM. Effects of polymorphic variation on the thermostability of heterogenous populations of CYP3A4 and CYP2C9 enzymes in solution. Sci Rep 2018; 8:11876. [PMID: 30089838 PMCID: PMC6082832 DOI: 10.1038/s41598-018-30195-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/23/2018] [Indexed: 12/11/2022] Open
Abstract
The effect of non-synonymous single nucleotide polymorphisms (SNPs) on cytochrome P450 (CYP450) drug metabolism is currently poorly understood due to the large number of polymorphisms, the diversity of potential substrates and the complexity of CYP450 function. Previously we carried out in silico studies to explore the effect of SNPs on CYP450 function, using in silico calculations to predict the effect of mutations on protein stability. Here we have determined the effect of eight CYP3A4 and seven CYP2C9 SNPs on the thermostability of proteins in solution to test these predictions. Thermostability assays revealed distinct CYP450 sub-populations with only 65–70% of wild-type CYP3A4 and CYP2C9 susceptible to rapid heat-induced P450 to P420 conversion. CYP3A4 mutations G56D, P218R, S222P, I223R, L373F and M445T and CYP2C9 mutations V76M, I359L and I359T were destabilising, increasing the proportion of protein sensitive to the rapid heat-induced P450 to P420 conversion and/or reducing the half-life of this conversion. CYP2C9 Q214L was the only stabilising mutation. These results corresponded well with the in silico protein stability calculations, confirming the value of these predictions and together suggest that the changes in thermostability result from destabilisation/stabilisation of the protein fold, changes in the haem-binding environment or effects on oligomer formation/conformation.
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Affiliation(s)
- Lauren B Arendse
- Institute for Infectious Disease & Molecular Medicine, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, South Africa
| | - Jonathan M Blackburn
- Institute for Infectious Disease & Molecular Medicine, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, South Africa.
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45
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Gottardi M, Tyzack JD, Bender A, Cedergreen N. Can the inhibition of cytochrome P450 in aquatic invertebrates due to azole fungicides be estimated with in silico and in vitro models and extrapolated between species? AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 201:11-20. [PMID: 29859403 DOI: 10.1016/j.aquatox.2018.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Azole fungicides, designed to halt fungal growth by specific inhibition of fungal cytochrome P450 (CYP51), inhibit cytochrome P450s involved in the metabolism of xenobiotics in several non-target organisms thus raising environmental concern. The present study investigates the degree by which inhibition strengths of azoles toward cytochrome P450 in rat liver, the insect Chironomus riparius larvae and the snail Lymnaea stagnalis can be extrapolated from estimated in silico affinities. Azoles' affinities toward human cytochrome P450 isoforms involved in xenobiotic metabolism (CYP3A4, CYP2C9 and CYP2D6) as well as fungal CYP51 were estimated with a ligand-protein docking model based on the ChemScore scoring function. Estimated affinities toward the selected enzymatic structures correlated strongly with measured inhibition strengths in rat liver (ChemScore vs. logIC50 among cytochrome P450 isoforms: -0.662 < r < -0.891, n = 17 azoles), while weaker correlations were found for C. riparius larvae (-0.167 < r < -0.733, n = 9) and L. stagnalis (-0.084 < r < -0.648, n = 8). Inhibition strengths toward C. riparius and rat liver activities were found to be highly correlated to each other (r: 0.857) while no significant relationship was found between either of the species and L. stagnalis. The inhibition of cytochrome P450 due to azole fungicides could be estimated in vitro and to a lesser extent in silico for C. riparius but not for L. stagnalis, possibly due to different enzymatic susceptibility toward azole inhibition among the species.
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Affiliation(s)
- Michele Gottardi
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Jonathan D Tyzack
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Nina Cedergreen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark.
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Šrejber M, Navrátilová V, Paloncýová M, Bazgier V, Berka K, Anzenbacher P, Otyepka M. Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners. J Inorg Biochem 2018; 183:117-136. [DOI: 10.1016/j.jinorgbio.2018.03.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/16/2018] [Accepted: 03/01/2018] [Indexed: 01/08/2023]
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47
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Louet M, Labbé CM, Fagnen C, Aono CM, Homem-de-Mello P, Villoutreix BO, Miteva MA. Insights into molecular mechanisms of drug metabolism dysfunction of human CYP2C9*30. PLoS One 2018; 13:e0197249. [PMID: 29746595 PMCID: PMC5944999 DOI: 10.1371/journal.pone.0197249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
Cytochrome P450 2C9 (CYP2C9) metabolizes about 15% of clinically administrated drugs. The allelic variant CYP2C9*30 (A477T) is associated to diminished response to the antihypertensive effects of the prodrug losartan and affected metabolism of other drugs. Here, we investigated molecular mechanisms involved in the functional consequences of this amino-acid substitution. Molecular dynamics (MD) simulations performed for the active species of the enzyme (heme in the Compound I state), in the apo or substrate-bound state, and binding energy analyses gave insights into altered protein structure and dynamics involved in the defective drug metabolism of human CYP2C9.30. Our data revealed an increased rigidity of the key Substrate Recognition Sites SRS1 and SRS5 and shifting of the β turn 4 of SRS6 toward the helix F in CYP2C9.30. Channel and binding substrate dynamics analyses showed altered substrate channel access and active site accommodation. These conformational and dynamic changes are believed to be involved in the governing mechanism of the reduced catalytic activity. An ensemble of representative conformations of the WT and A477T mutant properly accommodating drug substrates were identified, those structures can be used for prediction of new CYP2C9 and CYP2C9.30 substrates and drug-drug interactions.
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Affiliation(s)
- Maxime Louet
- Université Paris Diderot, Sorbonne Paris Cité, Inserm UMR-S 973, Molécules Thérapeutiques In silico, Paris, France
- INSERM, U973, Paris, France
| | - Céline M. Labbé
- Université Paris Diderot, Sorbonne Paris Cité, Inserm UMR-S 973, Molécules Thérapeutiques In silico, Paris, France
- INSERM, U973, Paris, France
| | - Charline Fagnen
- Université Paris Diderot, Sorbonne Paris Cité, Inserm UMR-S 973, Molécules Thérapeutiques In silico, Paris, France
- INSERM, U973, Paris, France
- Université Pierre et Marie Curie, Sorbonne Universités, UMR 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Paris, France
| | - Cassiano M. Aono
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas, Santo André, Brazil
| | - Paula Homem-de-Mello
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas, Santo André, Brazil
| | - Bruno O. Villoutreix
- Université Paris Diderot, Sorbonne Paris Cité, Inserm UMR-S 973, Molécules Thérapeutiques In silico, Paris, France
- INSERM, U973, Paris, France
| | - Maria A. Miteva
- Université Paris Diderot, Sorbonne Paris Cité, Inserm UMR-S 973, Molécules Thérapeutiques In silico, Paris, France
- INSERM, U973, Paris, France
- * E-mail:
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48
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Tan BH, Ahemad N, Pan Y, Palanisamy UD, Othman I, Yiap BC, Ong CE. Cytochrome P450 2C9-natural antiarthritic interactions: Evaluation of inhibition magnitude and prediction from in vitro data. Biopharm Drug Dispos 2018; 39:205-217. [PMID: 29488228 DOI: 10.1002/bdd.2127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/10/2018] [Accepted: 02/18/2018] [Indexed: 11/08/2022]
Abstract
Many dietary supplements are promoted to patients with osteoarthritis (OA) including the three naturally derived compounds, glucosamine, chondroitin and diacerein. Despite their wide spread use, research on interaction of these antiarthritic compounds with human hepatic cytochrome P450 (CYP) enzymes is limited. This study aimed to examine the modulatory effects of these compounds on CYP2C9, a major CYP isoform, using in vitro biochemical assay and in silico models. Utilizing valsartan hydroxylase assay as probe, all forms of glucosamine and chondroitin exhibited IC50 values beyond 1000 μM, indicating very weak potential in inhibiting CYP2C9. In silico docking postulated no interaction with CYP2C9 for chondroitin and weak bonding for glucosamine. On the other hand, diacerein exhibited mixed-type inhibition with IC50 value of 32.23 μM and Ki value of 30.80 μM, indicating moderately weak inhibition. Diacerein's main metabolite, rhein, demonstrated the same mode of inhibition as diacerein but stronger potency, with IC50 of 6.08 μM and Ki of 1.16 μM. The docking of both compounds acquired lower CDOCKER interaction energy values, with interactions dominated by hydrogen and hydrophobic bondings. The ranking with respect to inhibition potency for the investigated compounds was generally the same in both in vitro enzyme assay and in silico modeling with order of potency being diacerein/rhein > various glucosamine/chondroitin forms. In vitro-in vivo extrapolation of inhibition kinetics (using 1 + [I]/Ki ratio) demonstrated negligible potential of diacerein to cause interaction in vivo, whereas rhein was predicted to cause in vivo interaction, suggesting potential interaction risk with the CYP2C9 drug substrates.
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Affiliation(s)
- Boon Hooi Tan
- Division of Applied Biomedical Sciences and Biotechnology, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Yan Pan
- Department of Biomedical Science, University of Nottingham Malaysia Campus, Semenyih, Selangor, Malaysia
| | - Uma Devi Palanisamy
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Iekhsan Othman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Beow Chin Yiap
- School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia
| | - Chin Eng Ong
- School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia
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49
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Joshi P, Sonawane VR, Williams IS, McCann GJP, Gatchie L, Sharma R, Satti N, Chaudhuri B, Bharate SB. Identification of karanjin isolated from the Indian beech tree as a potent CYP1 enzyme inhibitor with cellular efficacy via screening of a natural product repository. MEDCHEMCOMM 2018; 9:371-382. [PMID: 30108931 PMCID: PMC6083783 DOI: 10.1039/c7md00388a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 01/05/2018] [Indexed: 12/16/2022]
Abstract
CYP1A1 is thought to mediate carcinogenesis in oral, lung and epithelial cancers. In order to identify a CYP1A1 inhibitor from an edible plant, 394 natural products in the IIIM's natural product repository were screened, at 10 μM concentration, using CYP1A1-Sacchrosomes™ (i.e. microsomal enzyme isolated from recombinant baker's yeast). Twenty-seven natural products were identified that inhibited 40-97% of CYP1A1's 7-ethoxyresorufin-O-deethylase activity. The IC50 values of the 'hits', belonging to different chemical scaffolds, were determined. Their selectivity was studied against a panel of 8 CYP-Sacchrosomes™. In order to assess cellular efficacy, the 'hits' were screened for their capability to inhibit CYP enzymes expressed within live recombinant human embryonic kidney (HEK293) cells from plasmids encoding specific CYP genes (1A2, 1B1, 2C9, 2C19, 2D6, 3A4). Isopimpinellin (IN-475; IC50, 20 nM) and karanjin (IN-195; IC50, 30 nM) showed the most potent inhibition of CYP1A1 in human cells. Isopimpinellin is found in celery, parsnip, fruits and in the rind and pulp of limes whereas different parts of the Indian beech tree, which contain karanjin, have been used in traditional medicine. Both isopimpinellin and karanjin negate the cellular toxicity of CYP1A1-mediated benzo[a]pyrene. Molecular docking and molecular dynamic simulations with CYP isoforms rationalize the observed trends in the potency and selectivity of isopimpinellin and karanjin.
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Affiliation(s)
- Prashant Joshi
- Medicinal Chemistry Division , CSIR-Indian Institute of Integrative Medicine , Canal Road , Jammu-180001 , India . ; ; Tel: +91 191 2569111
- Academy of Scientific & Innovative Research (AcSIR) , CSIR-Indian Institute of Integrative Medicine , Canal Road , Jammu-180001 , India
| | - Vinay R Sonawane
- Leicester School of Pharmacy , De Montfort University , Leicester , LE1 9BH , UK .
| | - Ibidapo S Williams
- Leicester School of Pharmacy , De Montfort University , Leicester , LE1 9BH , UK .
- CYP Design Limited, Innovation Centre , 49 Oxford Street , Leicester , LE1 5XY , UK
| | - Glen J P McCann
- Leicester School of Pharmacy , De Montfort University , Leicester , LE1 9BH , UK .
| | - Linda Gatchie
- Leicester School of Pharmacy , De Montfort University , Leicester , LE1 9BH , UK .
- CYP Design Limited, Innovation Centre , 49 Oxford Street , Leicester , LE1 5XY , UK
| | - Rajni Sharma
- Academy of Scientific & Innovative Research (AcSIR) , CSIR-Indian Institute of Integrative Medicine , Canal Road , Jammu-180001 , India
- Natural Product Chemistry Division , CSIR-Indian Institute of Integrative Medicine , Canal Road , Jammu-180001 , India
| | - Naresh Satti
- Natural Product Chemistry Division , CSIR-Indian Institute of Integrative Medicine , Canal Road , Jammu-180001 , India
| | - Bhabatosh Chaudhuri
- Leicester School of Pharmacy , De Montfort University , Leicester , LE1 9BH , UK .
| | - Sandip B Bharate
- Medicinal Chemistry Division , CSIR-Indian Institute of Integrative Medicine , Canal Road , Jammu-180001 , India . ; ; Tel: +91 191 2569111
- Academy of Scientific & Innovative Research (AcSIR) , CSIR-Indian Institute of Integrative Medicine , Canal Road , Jammu-180001 , India
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50
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Cui YL, Xu F, Wu R. Molecular dynamics investigations of regioselectivity of anionic/aromatic substrates by a family of enzymes: a case study of diclofenac binding in CYP2C isoforms. Phys Chem Chem Phys 2018; 18:17428-39. [PMID: 27302079 DOI: 10.1039/c6cp01128d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The CYP2C subfamily is of particular importance in the metabolism of drugs, food toxins, and procarcinogens. Like other P450 subfamilies, 2C enzymes share a high sequence identity, but significantly contribute in different ways to hepatic capacity to metabolize drugs. They often metabolize the same substrate to more than one product with different catalytic sites. Because it is challenging to characterize experimentally, much still remains unknown about the reason for why the substrate regioselectivity of these closely related subfamily members is different. Here, we have investigated the structural features of CYP2C8, CYP2C9, and CYP2C19 bound with their shared substrate diclofenac to elucidate the underlying molecular mechanism for the substrate regioselectivity of CYP2C subfamily enzymes. The obtained results demonstrate how a sequence divergence for the active site residues causes heterogeneous variations in the secondary structures and in major tunnel selections, and further affects the shape and chemical properties of the substrate-binding site. Structural analysis and free energy calculations showed that the most important determinants of regioselectivity among the CYP2C isoforms are the geometrical features of the active sites, as well as the hydrogen bonds and the hydrophobic interactions, mainly presenting as the various locations of Arg108 and substitutions of Phe205 for Ile205 in CYP2C8. The MM-GB/SA calculations combined with PMF results accord well with the experimental KM values, bridging the gap between the theory and the experimentally observed results of binding affinity differences. The present study provides important insights into the structure-function relationships of CYP2C subfamily enzymes, the knowledge of ligand binding characteristics and key residue contributions could guide future experimental and computational work on the synthesis of drugs with better pharmacokinetic properties so that CYP interactions could be avoided.
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Affiliation(s)
- Ying-Lu Cui
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Fang Xu
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China and Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA.
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