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Gutiérrez Rico EM, Kikuchi A, Saito T, Kumondai M, Hishinuma E, Kaneko A, Chan CW, Gitaka J, Nakayoshi T, Oda A, Saito S, Hirasawa N, Hiratsuka M. CYP2D6 genotyping analysis and functional characterization of novel allelic variants in a Ni-Vanuatu and Kenyan population by assessing dextromethorphan O-demethylation activity. Drug Metab Pharmacokinet 2019; 35:89-101. [PMID: 32037159 DOI: 10.1016/j.dmpk.2019.07.003] [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: 03/18/2019] [Revised: 07/03/2019] [Accepted: 07/16/2019] [Indexed: 12/11/2022]
Abstract
While CYP2D6 allele and phenotype frequencies have been extensively studied, currently, very little ethnically specific data is available regarding the East African and South Pacific region, including Kenya and Vanuatu. The absence of information regarding gene polymorphisms and their resulting clinical effects in these populations may hinder treatment strategies and patient outcome. Given the scarceness of CYP2D6 related data in these populations, the purpose of this study was to perform a pharmacogenomic analysis of the Kenyan and Ni-Vanuatu population and ultimately characterize the enzymatic properties of eight novel CYP2D6 variant proteins expressed in 293FT cells in vitro using dextromethorphan as a substrate. Our study revealed a prevalence of functional alleles in both populations a low frequency for decreased function defining genotypes in the Ni-Vanuatu population, with approximately 36% of our Kenyan subjects presenting substrate-dependent decreased function alleles. Additionally, 6 variants (P171L, G306R, V402L, K1, K2, and K3) showed significantly reduced intrinsic clearance compared to wild-type CYP2D6.1. Our findings aid in efforts to bridge the gap between pharmacogenomic analysis and clinical application, by providing useful information in the development of ethnic-specific strategies as well as stressing the importance of population-specific genotyping when conducting multi-regional clinical trials and designing therapeutic strategies.
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Affiliation(s)
- Evelyn Marie Gutiérrez Rico
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Aoi Kikuchi
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Takahiro Saito
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Masaki Kumondai
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Eiji Hishinuma
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8575, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8575, Japan
| | - Akira Kaneko
- Department of Parasitology and Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Chim Wai Chan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | | | | | - Akifumi Oda
- Faculty of Pharmacy, Meijo University, Nagoya 468-8503, Japan
| | - Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8575, Japan
| | - Noriyasu Hirasawa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8575, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai 980-8574, Japan
| | - Masahiro Hiratsuka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8575, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8575, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai 980-8574, Japan.
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Microsecond MD simulations of human CYP2D6 wild-type and five allelic variants reveal mechanistic insights on the function. PLoS One 2018; 13:e0202534. [PMID: 30133539 PMCID: PMC6104999 DOI: 10.1371/journal.pone.0202534] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/03/2018] [Indexed: 11/19/2022] Open
Abstract
Characterization of cytochrome P450 2D6 (CYP2D6) and the impact of the major identified allelic variants on the activity of one of the most dominating drug-metabolising enzymes is essential to increase drug safety and avoid adverse reactions. Microsecond molecular dynamics simulations have been performed to capture the dynamic signatures of this complex enzyme and five allelic variants with diverse enzymatic activity. In addition to the apo simulations, three substrates (bufuralol, veliparib and tamoxifen) and two inhibitors (prinomastat and quinidine) were included to explore their influence on the structure and dynamical features of the enzyme. Our results indicate that the altered enzyme activity can be attributed to changes in the hydrogen bonding network within the active site, and local structural differences in flexibility, position and shape of the binding pocket. In particular, the increased (CYP2D6*53) or the decreased (CYP2D6*17) activity seems to be related to a change in dynamics of mainly the BC loop due to a modified hydrogen bonding network around this region. In addition, the smallest active site volume was found for CYP2D6*4 (no activity). CYP2D6*2 (normal activity) showed no major differences in dynamic behaviour compared to the wild-type.
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Larsen JB, Rasmussen JB. Pharmacogenetic testing revisited: 5' nuclease real-time polymerase chain reaction test panels for genotyping CYP2D6 and CYP2C19. Pharmgenomics Pers Med 2017; 10:115-128. [PMID: 28458572 PMCID: PMC5403119 DOI: 10.2147/pgpm.s131580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Due to their involvement in the metabolization of commonly prescribed psychopharmaceutical drugs, the cytochrome oxidase genes CYP2D6 and CYP2C19 are extensive targets for pharmacogenetic testing. The existence of common allelic variants allows the prediction of a metabolic phenotype based on a genotype result, hereby supplying a clinical tool for optimizing prescription and minimizing adverse effects. In this study, we present the development of two 5' nuclease real-time polymerase chain reaction (PCR) test panels, capable of detecting eight of the most clinically relevant alleles of the CYP2D6 gene (*2, *3, *4, *6, *9, *10, 17, *41) and the three most common nonfunctional alleles of CYP2C19 (*2, *3, *4). The assays have been thoroughly validated using a large collection of reference samples, by parallel testing and by DNA sequencing. The reanalysis of reference samples provided the calculation of the frequency of the CYP2D6*4K allele in a population, not previously reported. Furthermore, original test results from CYP2D6*41, generated based on the presence of the 2850T and the lack of the -1584G single-nucleotide polymorphism (SNP), were compared with genotyping based on the current acknowledged founder SNP 2988G of this allele. These results indicate that up to 17.7% of the patients originally tested as carriers of the CYP2D6*41 allele may have had an incorrect phenotypic result assigned. The two 5' nuclease real-time PCR test panels have subsequently been optimized for use in the clinical laboratory, using a standard real-time PCR instrument and software.
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Fukuyoshi S, Kometani M, Watanabe Y, Hiratsuka M, Yamaotsu N, Hirono S, Manabe N, Takahashi O, Oda A. Molecular Dynamics Simulations to Investigate the Influences of Amino Acid Mutations on Protein Three-Dimensional Structures of Cytochrome P450 2D6.1, 2, 10, 14A, 51, and 62. PLoS One 2016; 11:e0152946. [PMID: 27046024 PMCID: PMC4821567 DOI: 10.1371/journal.pone.0152946] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 03/20/2016] [Indexed: 11/18/2022] Open
Abstract
Many natural mutants of the drug metabolizing enzyme cytochrome P450 (CYP) 2D6 have been reported. Because the enzymatic activities of many mutants are different from that of the wild type, the genetic polymorphism of CYP2D6 plays an important role in drug metabolism. In this study, the molecular dynamics simulations of the wild type and mutants of CYP2D6, CYP2D6.1, 2, 10, 14A, 51, and 62 were performed, and the predictions of static and dynamic structures within them were conducted. In the mutant CYP2D6.10, 14A, and 61, dynamic properties of the F-G loop, which is one of the components of the active site access channel of CYP2D6, were different from that of the wild type. The F-G loop acted as the “hatch” of the channel, which was closed in those mutants. The structure of CYP2D6.51 was not converged by the simulation, which indicated that the three-dimensional structure of CYP2D6.51 was largely different from that of the wild type. In addition, the intramolecular interaction network of CYP2D6.10, 14A, and 61 was different from that of the wild type, and it is considered that these structural changes are the reason for the decrease or loss of enzymatic activities. On the other hand, the static and dynamic properties of CYP2D6.2, whose activity was normal, were not considerably different from those of the wild type.
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Affiliation(s)
- Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920–1192, Japan
| | - Masaharu Kometani
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920–1192, Japan
| | - Yurie Watanabe
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920–1192, Japan
| | - Masahiro Hiratsuka
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6–3 Aoba, Aramaki, Aoba-ku, Sendai, 980–8578, Japan
| | - Noriyuki Yamaotsu
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108–8641, Japan
| | - Shuichi Hirono
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108–8641, Japan
| | - Noriyoshi Manabe
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981–8558, Japan
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981–8558, Japan
| | - Akifumi Oda
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920–1192, Japan
- Institute for Protein Research, Osaka University, 3–2 Yamadaoka, Suita, Osaka, 565–0871, Japan
- * E-mail:
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Xu Q, Wu Z, Yang L, Zhang X, Gai Z, Chen L, He L, Qin S. Functional characterization of CYP2D6 novel allelic variants identified in the Chinese Han population. Pharmacogenomics 2015; 17:119-9. [PMID: 26652007 DOI: 10.2217/pgs.15.148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIM This study was aimed to functionally characterize four novel CYP2D6 alleles identified in Chinese Han population. MATERIALS & METHODS CYP2D6 proteins of wild-type and the four novel variants along with CYP2D6.2 and CYP2D6.10 were heterologously expressed in yeast cells and the kinetic parameters were determined. RESULTS Compared with CYP2D6.1 (frequency in Chinese 24.65%), CYP2D6.X (1.63%), CYP2D6.Y (1.50%), CYP2D6.Z (0.81%), CYP2D6.10 (52.53%) and CYP2D6.75 (0.13%) exhibited low activity at different degrees, whereas the kinetic parameters of CYP2D6.2 (11.06%) were much the same with CYP2D6.1. The novel allele CYP2D6.75 showed decreased enzyme activity. CONCLUSION This is the first study to conduct functional analysis of CYP2D6 four novel alleles in Chinese Han population, which might be helpful for optimizing pharmacotherapy and the design of personalized medicine.
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Affiliation(s)
- Qingqing Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Zhenqiang Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Lun Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | | | - Zhongtao Gai
- Jinan Infectious Disease Hospital, Shandong University, Jinan, China
| | - Lili Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
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Lee SH, Kang S, Dong MS, Park JD, Park J, Rhee S, Ryu DY. Characterization of the Ala62Pro polymorphic variant of human cytochrome P450 1A1 using recombinant protein expression. Toxicol Appl Pharmacol 2015; 285:159-69. [DOI: 10.1016/j.taap.2015.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/11/2015] [Accepted: 04/13/2015] [Indexed: 11/16/2022]
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Bajpai P, Srinivasan S, Ghosh J, Nagy LD, Wei S, Guengerich FP, Avadhani NG. Targeting of splice variants of human cytochrome P450 2C8 (CYP2C8) to mitochondria and their role in arachidonic acid metabolism and respiratory dysfunction. J Biol Chem 2014; 289:29614-30. [PMID: 25160618 DOI: 10.1074/jbc.m114.583062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In this study, we found that the full-length CYP2C8 (WT CYP2C8) and N-terminal truncated splice variant 3 (∼ 44-kDa mass) are localized in mitochondria in addition to the endoplasmic reticulum. Analysis of human livers showed that the mitochondrial levels of these two forms varied markedly. Molecular modeling based on the x-ray crystal structure coordinates of CYP2D6 and CYP2C8 showed that despite lacking the N-terminal 102 residues variant 3 possessed nearly complete substrate binding and heme binding pockets. Stable expression of cDNAs in HepG2 cells showed that the WT protein is mostly targeted to the endoplasmic reticulum and at low levels to mitochondria, whereas variant 3 is primarily targeted to mitochondria and at low levels to the endoplasmic reticulum. Enzyme reconstitution experiments showed that both microsomal and mitochondrial WT CYP2C8 efficiently catalyzed paclitaxel 6-hydroxylation. However, mitochondrial variant 3 was unable to catalyze this reaction possibly because of its inability to stabilize the large 854-Da substrate. Conversely, mitochondrial variant 3 catalyzed the metabolism of arachidonic acid into 8,9-, 11,12-, and 14,15-epoxyeicosatrienoic acids and 20-hydroxyeicosatetraenoic acid when reconstituted with adrenodoxin and adrenodoxin reductase. HepG2 cells stably expressing variant 3 generated higher levels of reactive oxygen species and showed a higher level of mitochondrial respiratory dysfunction. This study suggests that mitochondrially targeted variant 3 CYP2C8 may contribute to oxidative stress in various tissues.
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Affiliation(s)
- Prachi Bajpai
- From the Department of Animal Biology and Mari Lowe Center for Comparative Oncology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 and
| | - Satish Srinivasan
- From the Department of Animal Biology and Mari Lowe Center for Comparative Oncology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 and
| | - Jyotirmoy Ghosh
- From the Department of Animal Biology and Mari Lowe Center for Comparative Oncology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 and
| | - Leslie D Nagy
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Shouzou Wei
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - F Peter Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Narayan G Avadhani
- From the Department of Animal Biology and Mari Lowe Center for Comparative Oncology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 and
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Crystal structure of aldoxime dehydratase and its catalytic mechanism involved in carbon-nitrogen triple-bond synthesis. Proc Natl Acad Sci U S A 2013; 110:2810-5. [PMID: 23382199 DOI: 10.1073/pnas.1200338110] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aldoxime dehydratase (OxdA), which is a unique heme protein, catalyzes the dehydration of an aldoxime to a nitrile even in the presence of water in the reaction mixture. Unlike the utilization of H(2)O(2) or O(2) as a mediator of catalysis by other heme-containing enzymes (e.g., P450), OxdA is notable for the direct binding of a substrate to the heme iron. Here, we determined the crystal structure of OxdA. We then constructed OxdA mutants in which each of the polar amino acids lying within ∼6 Å of the iron atom of the heme was converted to alanine. Among the purified mutant OxdAs, S219A had completely lost and R178A exhibited a reduction in the activity. Together with this finding, the crystal structural analysis of OxdA and spectroscopic and electrostatic potential analyses of the wild-type and mutant OxdAs suggest that S219 plays a key role in the catalysis, forming a hydrogen bond with the substrate. Based on the spatial arrangement of the OxdA active site and the results of a series of mutagenesis experiments, we propose the detailed catalytic mechanism of general aldoxime dehydratases: (i) S219 stabilizes the hydroxy group of the substrate to increase its basicity; (ii) H320 acts as an acid-base catalyst; and (iii) R178 stabilizes the heme, and would donate a proton to and accept one from H320.
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Teh LK, Bertilsson L. Pharmacogenomics of CYP2D6: molecular genetics, interethnic differences and clinical importance. Drug Metab Pharmacokinet 2011; 27:55-67. [PMID: 22185816 DOI: 10.2133/dmpk.dmpk-11-rv-121] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
CYP2D6 has received intense attention since the beginning of the pharmacogenetic era in the 1970s. This is because of its involvement in the metabolism of more than 25% of the marketed drugs, the large geographical and inter-ethnic differences in the genetic polymorphism and possible drug-induced toxicity. Many interesting reviews have been published on CYP2D6 and this review aims to reinstate the importance of the genetic polymorphism of CYP2D6 in different populations as well as some clinical implications and important drug interactions.
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Affiliation(s)
- Lay Kek Teh
- Pharmacogenomics Centre PROMISE, Faculty of Pharmacy, Universiti Teknologi MARA, Selangor DE, Malaysia.
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10
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Lee IS, Kim D. Polymorphic metabolism by functional alterations of human cytochrome P450 enzymes. Arch Pharm Res 2011; 34:1799-816. [PMID: 22139682 DOI: 10.1007/s12272-011-1103-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 08/24/2011] [Indexed: 10/14/2022]
Abstract
The study of cytochrome P450 pharmacogenomics is of particular interest because of its promise in the development of rational means to optimize drug therapy with respect to patient's genotype to ensure maximum efficacy with minimal adverse effects. Drug metabolizing P450 enzymes are polymorphic and are the main phase I enzymes responsible for the metabolism of clinical drugs. Therefore, polymorphisms in the P450s have the most impact on the fate of clinical drugs in phase I metabolism since almost 80% of drugs in use today are metabolized by these enzymes. Predictive genotyping for P450 enzymes for a more effective therapy will be routine for specific drugs in the future. In this review, we discuss the current knowledge of polymorphic metabolism by functional alterations in nonsynonymous SNPs of P450 1A2, 2A6, 2C8, 2C9, 2C19, 2D6, and 3A4 enzymes.
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Affiliation(s)
- Im-Soon Lee
- Department of Biological Sciences and Center for Biotechnology Research in UBITA, Konkuk University, Seoul 143-701, Korea
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Abstract
The cytochrome P450 (CYP) superfamily is one of the most important groups of enzymes involved in drug metabolism. It is responsible for the metabolism of a large number of drugs. Many CYP isoforms are expressed polymorphically, and catalytic alterations of allelic variant proteins can affect the metabolic activities of many drugs. The CYP2D6, CYP2C9, CYP2C19, and CYP2B6 genes are particularly polymorphic, whereas CYP1A1, CYP1A2, CYP2E1, and CYP3A4 are relatively well conserved without common functional polymorphisms. In vitro studies using cDNA expression systems are useful tools for evaluating functional alterations of the allelic variants of CYP, particularly for low-frequency alleles. Recombinant CYPs have been successfully expressed in bacteria, yeast, baculoviruses, and several mammalian cells. Determination of CYP variant-mediated kinetic parameters (Km and Vmax) in vitro can be useful for predicting drug dosing and clearance in humans. This review focuses on the advantages and disadvantages of the various cDNA-expression systems used to determine the kinetic parameters for CYP allelic variants, the methods for determining the kinetic parameters, and the findings of in vitro studies on highly polymorphic CYPs, including CYP2D6, CYP2C9, CYP2C19, and CYP2B6.
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Affiliation(s)
- Masahiro Hiratsuka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.
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12
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Seripa D, Pilotto A, Panza F, Matera MG, Pilotto A. Pharmacogenetics of cytochrome P450 (CYP) in the elderly. Ageing Res Rev 2010; 9:457-74. [PMID: 20601196 DOI: 10.1016/j.arr.2010.06.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 05/28/2010] [Accepted: 06/01/2010] [Indexed: 12/22/2022]
Abstract
The genetics of cytochrome P450 (CYP) is a very active area of multidisciplinary research, overlapping the interest of medicine, biology and pharmacology, being the CYP enzyme system responsible for the metabolism of more than 80% of the commercially available drugs. Variations in CYP encoding genes are responsible for inter-individual differences in CYP production or function, with severe clinical consequences as therapeutic failures (TFs) and adverse drug reactions (ADRs), being ADRs worldwide primary causes of morbidity and mortality in elderly people. In fact, the prevalence of both TFs and ADRs strongly increased in the presence of multiple pharmacological treatments, a common status in subjects aging 65 years and over. The present article explored some basic concepts of human genetics that have important implications in the genetics of CYP. An attempted to transfer these basic concepts to the genetic data reported by the Home Page of The Human Cytochrome P450 (CYP) Allele Nomenclature Committee was also made, focusing on the current knowledge of CYP genetics. The status of what we know and what we need to know is the base for the clinical applications of pharmacogenetics, in which personalized drug treatments constituted the main aim, in particular in patients attending a geriatric ward.
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Affiliation(s)
- Davide Seripa
- Geriatric Unit & Gerontology-Geriatrics Research Laboratory, Department of Medical Sciences, IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013 San Giovanni Rotondo (FG), Italy.
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Wang B, Yang LP, Zhang XZ, Huang SQ, Bartlam M, Zhou SF. New insights into the structural characteristics and functional relevance of the human cytochrome P450 2D6 enzyme. Drug Metab Rev 2010; 41:573-643. [PMID: 19645588 DOI: 10.1080/03602530903118729] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To date, the crystal structures of at least 12 human CYPs (1A2, 2A6, 2A13, 2C8, 2C9, 2D6, 2E1, 2R1, 3A4, 7A1, 8A1, and 46A1) have been determined. CYP2D6 accounts for only a small percentage of all hepatic CYPs (< 2%), but it metabolizes approximately 25% of clinically used drugs with significant polymorphisms. CYP2D6 also metabolizes procarcinogens and neurotoxins, such as 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, 1,2,3,4-tetrahydroquinoline, and indolealkylamines. Moreover, the enzyme utilizes hydroxytryptamines and neurosteroids as endogenous substrates. Typical CYP2D6 substrates are usually lipophilic bases with an aromatic ring and a nitrogen atom, which can be protonated at physiological pH. Substrate binding is generally followed by oxidation (5-7 A) from the proposed nitrogen-Asp301 interaction. A number of homology models have been constructed to explore the structural features of CYP2D6, while antibody studies also provide useful structural information. Site-directed mutagenesis studies have demonstrated that Glu216, Asp301, Phe120, Phe481, and Phe483 play important roles in determining the binding of ligands to CYP2D6. The structure of human CYP2D6 has been recently determined and shows the characteristic CYP fold observed for other members of the CYP superfamily. The lengths and orientations of the individual secondary structural elements in the CYP2D6 structure are similar to those seen in other human CYP2 members, such as CYP2C9 and 2C8. The 2D6 structure has a well-defined active-site cavity located above the heme group with a volume of approximately 540 A(3), which is larger than equivalent cavities in CYP2A6 (260 A(3)), 1A2 (375 A(3)), and 2E1 (190 A(3)), but smaller than those in CYP3A4 (1385 A(3)) and 2C8 (1438 A(3)). Further studies are required to delineate the molecular mechanisms involved in CYP2D6 ligand interactions and their implications for drug development and clinical practice.
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Affiliation(s)
- Bo Wang
- Department of Pediatrics, Guangdong Women and Children's Hospital, Guangzhou, China
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14
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Affiliation(s)
- Shu-Feng Zhou
- Discipline of Chinese Medicine, School of Health Sciences, RMIT University, Victoria, Australia.
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15
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Zhou SF, Liu JP, Chowbay B. Polymorphism of human cytochrome P450 enzymes and its clinical impact. Drug Metab Rev 2009; 41:89-295. [PMID: 19514967 DOI: 10.1080/03602530902843483] [Citation(s) in RCA: 502] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pharmacogenetics is the study of how interindividual variations in the DNA sequence of specific genes affect drug response. This article highlights current pharmacogenetic knowledge on important human drug-metabolizing cytochrome P450s (CYPs) to understand the large interindividual variability in drug clearance and responses in clinical practice. The human CYP superfamily contains 57 functional genes and 58 pseudogenes, with members of the 1, 2, and 3 families playing an important role in the metabolism of therapeutic drugs, other xenobiotics, and some endogenous compounds. Polymorphisms in the CYP family may have had the most impact on the fate of therapeutic drugs. CYP2D6, 2C19, and 2C9 polymorphisms account for the most frequent variations in phase I metabolism of drugs, since almost 80% of drugs in use today are metabolized by these enzymes. Approximately 5-14% of Caucasians, 0-5% Africans, and 0-1% of Asians lack CYP2D6 activity, and these individuals are known as poor metabolizers. CYP2C9 is another clinically significant enzyme that demonstrates multiple genetic variants with a potentially functional impact on the efficacy and adverse effects of drugs that are mainly eliminated by this enzyme. Studies into the CYP2C9 polymorphism have highlighted the importance of the CYP2C9*2 and *3 alleles. Extensive polymorphism also occurs in other CYP genes, such as CYP1A1, 2A6, 2A13, 2C8, 3A4, and 3A5. Since several of these CYPs (e.g., CYP1A1 and 1A2) play a role in the bioactivation of many procarcinogens, polymorphisms of these enzymes may contribute to the variable susceptibility to carcinogenesis. The distribution of the common variant alleles of CYP genes varies among different ethnic populations. Pharmacogenetics has the potential to achieve optimal quality use of medicines, and to improve the efficacy and safety of both prospective and currently available drugs. Further studies are warranted to explore the gene-dose, gene-concentration, and gene-response relationships for these important drug-metabolizing CYPs.
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Affiliation(s)
- Shu-Feng Zhou
- School of Health Sciences, RMIT University, Bundoora, Victoria, Australia.
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Pang GSY, Wang J, Wang Z, Lee CGL. Predicting potentially functional SNPs in drug-response genes. Pharmacogenomics 2009; 10:639-53. [DOI: 10.2217/pgs.09.12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
SNPs are known to contribute to variations in drug response and there are more than 14 million polymorphisms spanning the human genome. However, not all of these SNPs are functional. It would be impractical and costly to evaluate every individual SNP for functionality experimentally. Consequently, one of the major challenges for researchers has been to seek out functional SNPs from all the SNPs in the human genome. In silico or bioinformatic methods are economical, less labor intensive, yet powerful approaches to filter out potentially functional SNPs in drug-response genes for further study. This allows researchers to prioritize which SNPs to subsequently evaluate experimentally for drug-response studies, as well as potentially providing insights into possible mechanisms underlying how SNPs may affect drug-response genes.
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Affiliation(s)
- Grace SY Pang
- Division of Medical Sciences, National Cancer Center, Level 6, Lab 5, 11 Hospital Drive, Singapore 169610, Singapore
| | | | - Zihua Wang
- Division of Medical Sciences, National Cancer Center, Level 6, Lab 5, 11 Hospital Drive, Singapore 169610, Singapore
- National University of Singapore, Singapore
| | - Caroline GL Lee
- Division of Medical Sciences, National Cancer Center, Level 6, Lab 5, 11 Hospital Drive, Singapore 169610, Singapore
- National University of Singapore, Singapore
- DUKE-NUS Graduate Medical School, Singapore
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Zhang WY, Tu YB, Haining RL, Yu AM. Expression and functional analysis of CYP2D6.24, CYP2D6.26, CYP2D6.27, and CYP2D7 isozymes. Drug Metab Dispos 2008; 37:1-4. [PMID: 18838503 DOI: 10.1124/dmd.108.023663] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The objectives of this study were to compare the drug-metabolizing activity of human CYP2D6.24 (I297L), CYP2D6.26 (I369T), and CYP2D6.27 (E410K) allelic isoforms with wild-type CYP2D6.1 and to express the CYP2D7 protein derived from an indel polymorphism (CYP2D7 138delT) and investigate its possible codeine O-demethylase activity. Successful creation of individual cDNAs corresponding to CYP2D6*24 (2853 A>C), CYP2D6*26 (3277 T>C), and CYP2D6*27 (3853 G>A) allelic variants and CYP2D7 was achieved via molecular cloning. The corresponding proteins, CYP2D6.24, CYP2D6.26, CYP2D6.27, and CYP2D7, were expressed in insect cells by using a baculovirus-mediated expression system. All CYP2D proteins showed the empirical carbon monoxide difference spectra. We were surprised to find that the CYP2D7 protein was detected mainly in mitochondrial fractions, whereas all CYP2D6 allelic isoforms were present in the microsomal fraction. Furthermore, CYP2D7 did not produce any morphine from codeine. In contrast, CYP2D6.24, CYP2D6.26, and CYP2D6.27 allelic isoforms all showed active drug-metabolizing activities toward both codeine and dextromethorphan O-demethylation. Whereas CYP2D6.24 exhibited the highest intrinsic clearance in dextromethorphan O-demethylation (approximately 6-fold higher than that by CYP2D6.1), it had the lowest enzyme efficiency in codeine O-demethylation (approximately 50% lower than that by CYP2D6.1). Overall, the enzymatic consequences of CYP2D6 allelic isozymes are substrate dependent. These data would help preclinical and clinical assessments of the metabolic elimination of drugs that are mediated by human CYP2D enzyme.
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Affiliation(s)
- Wei-Yan Zhang
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, USA
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