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Zhang Y, Pan X, Shi T, Gu Z, Yang Z, Liu M, Xu Y, Yang Y, Ren L, Song X, Lin H, Deng K. P450Rdb: A manually curated database of reactions catalyzed by cytochrome P450 enzymes. J Adv Res 2024; 63:35-42. [PMID: 37871773 PMCID: PMC11380020 DOI: 10.1016/j.jare.2023.10.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/03/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023] Open
Abstract
INTRODUCTION Cytochrome P450 enzymes (P450s) are recognized as the most versatile catalysts worldwide, playing vital roles in numerous biological metabolism and biosynthesis processes across all kingdoms of life. Despite the vast number of P450 genes available in databases (over 300,000), only a small fraction of them (less than 0.2 %) have undergone functional characterization. OBJECTIVES To provide a convenient platform with abundant information on P450s and their corresponding reactions, we introduce the P450Rdb database, a manually curated resource compiles literature-supported reactions catalyzed by P450s. METHODS All the P450s and Reactions were manually curated from the literature and known databases. Subsequently, the P450 reactions organized and categorized according to their chemical reaction type and site. The website was developed using HTML and PHP languages, with the MySQL server utilized for data storage. RESULTS The current version of P450Rdb catalogs over 1,600 reactions, involving more than 590 P450s across a diverse range of over 200 species. Additionally, it offers a user-friendly interface with comprehensive information, enabling easy querying, browsing, and analysis of P450s and their corresponding reactions. P450Rdb is free available at http://www.cellknowledge.com.cn/p450rdb/. CONCLUSIONS We believe that this database will significantly promote structural and functional research on P450s, thereby fostering advancements in the fields of natural product synthesis, pharmaceutical engineering, biotechnological applications, agricultural and crop improvement, and the chemical industry.
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Affiliation(s)
- Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xianrun Pan
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianyu Shi
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zhifeng Gu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zhaochang Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Minghao Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yi Xu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yu Yang
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China.
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Kejun Deng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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Deng Y, Wu S, Fan H. Genome-wide pathway-based quantitative multiple phenotypes analysis. PLoS One 2020; 15:e0240910. [PMID: 33175855 PMCID: PMC7657528 DOI: 10.1371/journal.pone.0240910] [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: 04/02/2020] [Accepted: 10/06/2020] [Indexed: 11/18/2022] Open
Abstract
For complex diseases, genome-wide pathway association studies have become increasingly promising. Currently, however, pathway-based association analysis mainly focus on a single phenotype, which may insufficient to describe the complex diseases and physiological processes. This work proposes a combination model to evaluate the association between a pathway and multiple phenotypes and to reduce the run time based on asymptotic results. For a single phenotype, we propose a semi-supervised maximum kernel-based U-statistics (mSKU) method to assess the pathway-based association analysis. For multiple phenotypes, we propose the fisher combination function with dependent phenotypes (FC) to transform the p-values between the pathway and each marginal phenotype individually to achieve pathway-based multiple phenotypes analysis. With real data from the Alzheimer Disease Neuroimaging Initiative (ADNI) study and Human Liver Cohort (HLC) study, the FC-mSKU method allows us to specify which pathways are specific to a single phenotype or contribute to common genetic constructions of multiple phenotypes. If we only focus on single-phenotype tests, we may miss some findings for etiology studies. Through extensive simulation studies, the FC-mSKU method demonstrates its advantages compared with its counterparts.
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Affiliation(s)
- Yamin Deng
- Statistics Center, First Hospital of Shanxi Medical University, Taiyuan, China.,Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Shiman Wu
- Statistics Center, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Huifang Fan
- Statistics Center, First Hospital of Shanxi Medical University, Taiyuan, China
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Insight into the structural and functional analysis of the impact of missense mutation on cytochrome P450 oxidoreductase. J Mol Graph Model 2020; 100:107708. [PMID: 32805558 DOI: 10.1016/j.jmgm.2020.107708] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 01/26/2023]
Abstract
Cytochrome P450 oxidoreductase (POR) is a steroidogenic and drug-metabolizing enzyme. It helps in the NADPH dependent transfer of electrons to cytochrome P450 (CYP) enzymes for their biological activity. In this study, we employed integrative computational approaches to decipher the impact of proline to leucine missense mutation at position 384 (P384L) in the connecting/hinge domain region which is essential for the catalytic activity of POR. Analysis of protein stability using DUET, MUpro, CUPSAT, I-Mutant2.0, iStable and SAAFEC servers predicted that mutation might alter the structural stability of POR. The significant conformational changes induced by the mutation to the POR structure were analyzed by long-range molecular dynamics simulation. The results revealed that missense mutation decreased the conformational stability of POR as compared to wild type (WT). The PCA based FEL analysis described the mutant-specific conformational alterations and dominant motions essential for the biological activity of POR. The LIGPLOT interaction analysis showed the different binding architecture of FMN, FAD, and NADPH as a result of mutation. The increased number of hydrogen bonds in the FEL conformation of WT proved the strong binding of cofactors in the binding pocket as compared to the mutant. The porcupine plot analysis associated with cross-correlation analysis depicted the high-intensity flexible motion exhibited by functionally important FAD and NADPH binding domain regions. The computational findings unravel the impact of mutation at the structural level, which could be helpful in understanding the molecular mechanism of drug metabolism.
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Genome-Wide Identification and Analysis of the Cytochrome B5 Protein Family in Chinese Cabbage ( Brassica rapa L. ssp. Pekinensis). Int J Genomics 2019; 2019:2102317. [PMID: 31871927 PMCID: PMC6913312 DOI: 10.1155/2019/2102317] [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: 03/24/2019] [Accepted: 09/10/2019] [Indexed: 11/18/2022] Open
Abstract
Cytochrome B5 (CB5) family proteins play an important role in various oxidation/reduction reactions in cells as the electron donor and are involved in a variety of biotic and abiotic stress processes. However, the function of the CB5s in Brassica rapa is still unclear. In this study, we carried out genome-wide identification, characterization, and expression analysis of BrCB5s in different tissues under adversities and stresses. It was identified that fifteen BrCB5s were distributed on different chromosomes, which were classified into seven groups (A-G) according to its phylogenetic relationship. Phylogenetic analysis of the CB5 protein sequences from six species showed that the BrCB5s conduct a close evolutionary process with the CB5s of Arabidopsis thaliana and far from those of Oryza sativa. Protein interaction analysis showed that 40 interaction patterns were predicted including two Sucrose Transporter 4 subfamily proteins (SUT 4) and Fatty Acid Hydroxylase 2 protein (FAH 2) can interact with most members of BrCB5s. The expression profile analysis indicated that BrCB5s were differentially expressed in different tissues, and the transcript abundances were significantly different under various abiotic stresses and plant hormone treatments. Our study provides a basis for a better understanding of the characteristics and biological functions of the CB5 family genes in Chinese cabbage during plant development, especially in plant responses to multiple stresses.
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Vik D, Crocoll C, Andersen TG, Burow M, Halkier BA. CB5C affects the glucosinolate profile in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2016; 11:e1160189. [PMID: 27454255 PMCID: PMC5022417 DOI: 10.1080/15592324.2016.1160189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 05/26/2023]
Abstract
Cytochrome b5 (CB5) proteins are small heme-binding proteins, that influence cytochrome P450 activity. While only one CB5 isoform is found in mammals, higher plants have several isoforms of these proteins. The roles of the many CB5 isoforms in plants remain unknown. We hypothesized that CB5 proteins support the cytochrome P450 enzymes of plant specialized metabolism and found CB5C from Arabidopsis thaliana to co-express with glucosinolate biosynthetic genes. We characterized the glucosinolate profiles of 2 T-DNA insertion mutants of CB5C, and found that long-chained aliphatic glucosinolates were reduced in one of the mutant lines - a phenotype that was exaggerated upon methyl-jasmonate treatment. These results support the hypothesis, that CB5C influences glucosinolate biosynthesis, however, the mode of action remains unknown. Furthermore, the mutants differed in their biomass response to methyl jasmonate treatment. Thereby, our results highlight the varying effects of T-DNA insertion sites, as the 2 analyzed alleles show different phenotypes.
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Affiliation(s)
- Daniel Vik
- Department of Plant and Environmental Sciences, DynaMo Center of Excellence & Copenhagen Plant Science Center, University of Copenhagen, Denmark
| | - Christoph Crocoll
- Department of Plant and Environmental Sciences, DynaMo Center of Excellence & Copenhagen Plant Science Center, University of Copenhagen, Denmark
| | | | - Meike Burow
- Department of Plant and Environmental Sciences, DynaMo Center of Excellence & Copenhagen Plant Science Center, University of Copenhagen, Denmark
| | - Barbara Ann Halkier
- Department of Plant and Environmental Sciences, DynaMo Center of Excellence & Copenhagen Plant Science Center, University of Copenhagen, Denmark
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Lietzow J, Golchert J, Homuth G, Völker U, Jonas W, Köhrle J. 3,5-T2 alters murine genes relevant for xenobiotic, steroid, and thyroid hormone metabolism. J Mol Endocrinol 2016; 56:311-23. [PMID: 26903510 DOI: 10.1530/jme-15-0159] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 02/22/2016] [Indexed: 12/18/2022]
Abstract
The endogenous thyroid hormone (TH) metabolite 3,5-diiodo-l-thyronine (3,5-T2) acts as a metabolically active substance affecting whole-body energy metabolism and hepatic lipid handling in a desirable manner. Considering possible adverse effects regarding thyromimetic action of 3,5-T2 treatment in rodents, the current literature remains largely controversial. To obtain further insights into molecular mechanisms and to identify novel target genes of 3,5-T2 in liver, we performed a microarray-based liver tissue transcriptome analysis of male lean and diet-induced obese euthyroid mice treated for 4 weeks with a dose of 2.5 µg/g bw 3,5-T2 Our results revealed that 3,5-T2 modulates the expression of genes encoding Phase I and Phase II enzymes as well as Phase III transporters, which play central roles in metabolism and detoxification of xenobiotics. Additionally, 3,5-T2 changes the expression of TH responsive genes, suggesting a thyromimetic action of 3,5-T2 in mouse liver. Interestingly, 3,5-T2 in obese but not in lean mice influences the expression of genes relevant for cholesterol and steroid biosynthesis, suggesting a novel role of 3,5-T2 in steroid metabolism of obese mice. We concluded that treatment with 3,5-T2 in lean and diet-induced obese male mice alters the expression of genes encoding hepatic xenobiotic-metabolizing enzymes that play a substantial role in catabolism and inactivation of xenobiotics and TH and are also involved in hepatic steroid and lipid metabolism. The administration of this high dose of 3,5-T2 might exert adverse hepatic effects. Accordingly, the conceivable use of 3,5-T2 as pharmacological hypolipidemic agent should be considered with caution.
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Affiliation(s)
- Julika Lietzow
- Institut für Experimentelle EndokrinologieCharité - Universitätsmedizin Berlin, Berlin, Germany
| | - Janine Golchert
- Interfaculty Institute for Genetics and Functional GenomicsDepartment of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional GenomicsDepartment of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional GenomicsDepartment of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Wenke Jonas
- Department of Experimental DiabetologyGerman Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany German Center for Diabetes Research (DZD)Helmholtz Center Munich, Neuherberg, Germany
| | - Josef Köhrle
- Institut für Experimentelle EndokrinologieCharité - Universitätsmedizin Berlin, Berlin, Germany
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Tomková M, Panda SP, Šeda O, Baxová A, Hůlková M, Siler Masters BS, Martásek P. Genetic variations in NADPH-CYP450 oxidoreductase in a Czech Slavic cohort. Pharmacogenomics 2015; 16:205-15. [PMID: 25712184 DOI: 10.2217/pgs.14.169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Estimating polymorphic allele frequencies of the NADPH-CYP450 oxidoreductase (POR) gene in a Czech Slavic population. METHODS The POR gene was analyzed in 322 individuals from a control cohort by sequencing and high resolution melting analysis. RESULTS We identified seven unreported SNP genetic variations, including two SNPs in the 5' flanking region (g.4965C>T and g.4994G>T), one intronic variant (c.1899-20C>T), one synonymous SNP (p.20Ala=) and three nonsynonymous SNPs (p.Thr29Ser, p.Pro384Leu and p.Thr529Met). The p.Pro384Leu variant exhibited reduced enzymatic activities compared with wild-type. CONCLUSION New POR variant identification indicates the number of uncommon variants might be specific for each subpopulation being investigated, particularly germane to the singular role that POR plays in providing reducing equivalents to all CYP450s in the endoplasmic reticulum. Original submitted 15 September 2014; Revision submitted 17 November 2014.
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Affiliation(s)
- Mária Tomková
- Department of Pediatrics, First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
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Varma MVS, Scialis RJ, Lin J, Bi YA, Rotter CJ, Goosen TC, Yang X. Mechanism-based pharmacokinetic modeling to evaluate transporter-enzyme interplay in drug interactions and pharmacogenetics of glyburide. AAPS JOURNAL 2014; 16:736-48. [PMID: 24839071 DOI: 10.1208/s12248-014-9614-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 04/26/2014] [Indexed: 11/30/2022]
Abstract
The purpose of this study is to characterize the involvement of hepato-biliary transport and cytochrome-P450 (CYP)-mediated metabolism in the disposition of glyburide and predict its pharmacokinetic variability due to drug interactions and genetic variations. Comprehensive in vitro studies suggested that glyburide is a highly permeable drug with substrate affinity to multiple efflux pumps and to organic anion transporting polypeptide (OATP)1B1 and OATP2B1. Active hepatic uptake was found to be significantly higher than the passive uptake clearance (15.8 versus 5.3 μL/min/10(6)-hepatocytes), using the sandwich-cultured hepatocyte model. In vitro, glyburide is metabolized (intrinsic clearance, 52.9 μL/min/mg-microsomal protein) by CYP3A4, CYP2C9, and CYP2C8 with fraction metabolism of 0.53, 0.36, and 0.11, respectively. Using these in vitro data, physiologically based pharmacokinetic models, assuming rapid-equilibrium between blood and liver compartments or permeability-limited hepatic disposition, were built to describe pharmacokinetics and evaluate drug interactions. Permeability-limited model successfully predicted glyburide interactions with rifampicin and other perpetrator drugs. Conversely, model assuming rapid-equilibrium mispredicted glyburide interactions, overall, suggesting hepatic uptake as the primary rate-determining process in the systemic clearance of glyburide. Further modeling and simulations indicated that the impairment of CYP2C9 function has a minimal effect on the systemic exposure, implying discrepancy in the contribution of CYP2C9 to glyburide clearance.
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Affiliation(s)
- Manthena V S Varma
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Groton, Connecticut, USA,
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Rowland A, Mangoni AA. Cytochrome P450 and ischemic heart disease: current concepts and future directions. Expert Opin Drug Metab Toxicol 2013; 10:191-213. [PMID: 24274646 DOI: 10.1517/17425255.2014.859675] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The P450 enzymes (P450s) mediate the biotransformation of several drugs, steroid hormones, eicosanoids, cholesterol, vitamins, fatty acids and bile acids, many of which affect cardiovascular homeostasis. Experimental studies have demonstrated that several P450s modulate important steps in the pathogenesis of ischemic heart disease (IHD). AREAS COVERED This article discusses the current knowledge on i) the expression of P450s in cardiovascular and renal tissues; ii) the role of P450s in the pathophysiology of IHD, in particular the modulation of blood pressure and cardiac hypertrophy, coronary arterial tone, ischemia-reperfusion injury and the metabolism of cardiovascular drugs; iii) the available evidence from observational studies on the association between P450 gene polymorphisms and risk of myocardial infarction (MI); and iv) suggestions for further research in this area. EXPERT OPINION P450s exert important modulatory effects in experimental models of IHD and MI. However, observational studies have provided conflicting results on the association between P450 genetic polymorphisms and MI. Further, adequately powered studies are required to ascertain the biological and clinical impact of P450s on clinical IHD end-points, that is, fatal and nonfatal MI, revascularization and long-term outcomes post MI. Pharmacogenetic substudies of recently completed cardiovascular clinical trials might represent an alternative strategy in this context.
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Affiliation(s)
- Andrew Rowland
- Flinders University, School of Medicine, Department of Clinical Pharmacology , Bedford Park, SA 5042 , Australia
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Panda SP, Guntur AR, Polusani SR, Fajardo RJ, Gakunga PT, Roman LJ, Masters BS. Conditional deletion of cytochrome p450 reductase in osteoprogenitor cells affects long bone and skull development in mice recapitulating antley-bixler syndrome: role of a redox enzyme in development. PLoS One 2013; 8:e75638. [PMID: 24086598 PMCID: PMC3783497 DOI: 10.1371/journal.pone.0075638] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 08/17/2013] [Indexed: 12/15/2022] Open
Abstract
NADPH-cytochrome P450 oxidoreductase (POR) is the primary electron donor for cytochromes P450, dehydrocholesterol reductase, heme oxygenase, and squalene monooxygenase. Human patients with specific mutations in POR exhibit severe developmental malformations including disordered steroidogenesis, sexual ambiguities and various bone defects, similar to those seen in patients with Antley-Bixler syndrome (ABS). To probe the role of POR during bone development, we generated a conditional knockout mouse (CKO) by cross breeding Porlox/lox and Dermo1 Cre mice. CKO mice were smaller than their littermate controls and exhibited significant craniofacial and long bone abnormalities. Differential staining of the CKO mice skull bases shows premature fusion of the sphenooccipital and basioccipital-exoccipital synchondroses. Class III malocclusion was noted in adult knockout mice with an unusual overgrowth of the lower incisors. Shorter long bones were observed along with a reduction in the bone volume fraction, measured by microCT, in the Por-deleted mice compared to age- and sex-matched littermate controls. Concerted up- or down-regulation of proteins in the FGF signaling pathway observed by immunohistochemistry in the tibia samples of CKO mice compared to wild type controls shows a decrease in the FGF signaling pathway. To our knowledge, this is the first report of a mouse model that recapitulates both skull and long bone defects upon Por deletion, offering an approach to study the sequelae of POR mutations. This unique model demonstrates that P450 metabolism in bone itself is potentially important for proper bone development, and that an apparent link exists between the POR and FGF signaling pathways, begging the question of how an oxidation-reduction flavoprotein affects developmental and cellular signaling processes.
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Affiliation(s)
- Satya P. Panda
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas, United States of America
- * E-mail: ; (BSM)
| | - Anyonya R. Guntur
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Srikanth R. Polusani
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Roberto J. Fajardo
- Department of Orthopedics, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Peter T. Gakunga
- Department of Developmental Dentistry, Division of Orthodontics, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Linda J. Roman
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Bettie Sue Masters
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas, United States of America
- * E-mail: ; (BSM)
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Ahmed ISA, Chamberlain C, Craven RJ. S2RPgrmc1: the cytochrome-related sigma-2 receptor that regulates lipid and drug metabolism and hormone signaling. Expert Opin Drug Metab Toxicol 2012; 8:361-70. [DOI: 10.1517/17425255.2012.658367] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Yáñez JA, Wang SW, Knemeyer IW, Wirth MA, Alton KB. Intestinal lymphatic transport for drug delivery. Adv Drug Deliv Rev 2011; 63:923-42. [PMID: 21689702 PMCID: PMC7126116 DOI: 10.1016/j.addr.2011.05.019] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 10/15/2010] [Accepted: 01/26/2011] [Indexed: 12/16/2022]
Abstract
Intestinal lymphatic transport has been shown to be an absorptive pathway following oral administration of lipids and an increasing number of lipophilic drugs, which once absorbed, diffuse across the intestinal enterocyte and while in transit associate with secretable enterocyte lipoproteins. The chylomicron-associated drug is then secreted from the enterocyte into the lymphatic circulation, rather than the portal circulation, thus avoiding the metabolically-active liver, but still ultimately returning to the systemic circulation. Because of this parallel and potentially alternative absorptive pathway, first-pass metabolism can be reduced while increasing lymphatic drug exposure, which opens the potential for novel therapeutic modalities and allows the implementation of lipid-based drug delivery systems. This review discusses the physiological features of the lymphatics, enterocyte uptake and metabolism, links between drug transport and lipid digestion/re-acylation, experimental model (in vivo, in vitro, and in silico) of lymphatic transport, and the design of lipid- or prodrug-based drug delivery systems for enhancing lymphatic drug transport.
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Structural basis for human NADPH-cytochrome P450 oxidoreductase deficiency. Proc Natl Acad Sci U S A 2011; 108:13486-91. [PMID: 21808038 DOI: 10.1073/pnas.1106632108] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
NADPH-cytochrome P450 oxidoreductase (CYPOR) is essential for electron donation to microsomal cytochrome P450-mediated monooxygenation in such diverse physiological processes as drug metabolism (approximately 85-90% of therapeutic drugs), steroid biosynthesis, and bioactive metabolite production (vitamin D and retinoic acid metabolites). Expressed by a single gene, CYPOR's role with these multiple redox partners renders it a model for understanding protein-protein interactions at the structural level. Polymorphisms in human CYPOR have been shown to lead to defects in bone development and steroidogenesis, resulting in sexual dimorphisms, the severity of which differs significantly depending on the degree of CYPOR impairment. The atomic structure of human CYPOR is presented, with structures of two naturally occurring missense mutations, V492E and R457H. The overall structures of these CYPOR variants are similar to wild type. However, in both variants, local disruption of H bonding and salt bridging, involving the FAD pyrophosphate moiety, leads to weaker FAD binding, unstable protein, and loss of catalytic activity, which can be rescued by cofactor addition. The modes of polypeptide unfolding in these two variants differ significantly, as revealed by limited trypsin digestion: V492E is less stable but unfolds locally and gradually, whereas R457H is more stable but unfolds globally. FAD addition to either variant prevents trypsin digestion, supporting the role of the cofactor in conferring stability to CYPOR structure. Thus, CYPOR dysfunction in patients harboring these particular mutations may possibly be prevented by riboflavin therapy in utero, if predicted prenatally, or rescued postnatally in less severe cases.
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Mutations of human cytochrome P450 reductase differentially modulate heme oxygenase-1 activity and oligomerization. Arch Biochem Biophys 2011; 513:42-50. [PMID: 21741353 DOI: 10.1016/j.abb.2011.06.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/14/2011] [Accepted: 06/16/2011] [Indexed: 01/26/2023]
Abstract
Genetic variations in POR, encoding NADPH-cytochrome P450 oxidoreductase (CYPOR), can diminish the function of numerous cytochromes P450, and also have the potential to block degradation of heme by heme oxygenase-1 (HO-1). Purified full-length human CYPOR, HO-1, and biliverdin reductase were reconstituted in lipid vesicles and assayed for NADPH-dependent conversion of heme to bilirubin. Naturally-occurring human CYPOR variants queried were: WT, A115V, Y181D, P228L, M263V, A287P, R457H, Y459H, and V492E. All CYPOR variants exhibited decreased bilirubin production relative to WT, with a lower apparent affinity of the CYPOR-HO-1 complex than WT. Addition of FMN or FAD partially restored the activities of Y181D, Y459H, and V492E. When mixed with WT CYPOR, only the Y181D CYPOR variant inhibited heme degradation by sequestering HO-1, whereas Y459H and V492E were unable to inhibit HO-1 activity suggesting that CYPOR variants might have differential binding affinities with redox partners. Titrating the CYPOR-HO-1 complex revealed that the optimal CYPOR:HO-1 ratio for activity was 1:2, lending evidence in support of productive HO-1 oligomerization, with higher ratios of CYPOR:HO-1 showing decreased activity. In conclusion, human POR mutations, shown to impact P450 activities, also result in varying degrees of diminished HO-1 activity, which may further complicate CYPOR deficiency.
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13C-labeled indolequinone-DTPA-Gd conjugate for NMR probing cytochrome:P450 reductase-mediated one-electron reduction. Bioorg Med Chem Lett 2011; 21:790-3. [DOI: 10.1016/j.bmcl.2010.11.105] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 11/16/2010] [Accepted: 11/20/2010] [Indexed: 11/19/2022]
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Yang X, Zhang B, Molony C, Chudin E, Hao K, Zhu J, Gaedigk A, Suver C, Zhong H, Leeder JS, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich RG, Slatter JG, Schadt EE, Kasarskis A, Lum PY. Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver. Genome Res 2010; 20:1020-36. [PMID: 20538623 DOI: 10.1101/gr.103341.109] [Citation(s) in RCA: 207] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Liver cytochrome P450s (P450s) play critical roles in drug metabolism, toxicology, and metabolic processes. Despite rapid progress in the understanding of these enzymes, a systematic investigation of the full spectrum of functionality of individual P450s, the interrelationship or networks connecting them, and the genetic control of each gene/enzyme is lacking. To this end, we genotyped, expression-profiled, and measured P450 activities of 466 human liver samples and applied a systems biology approach via the integration of genetics, gene expression, and enzyme activity measurements. We found that most P450s were positively correlated among themselves and were highly correlated with known regulators as well as thousands of other genes enriched for pathways relevant to the metabolism of drugs, fatty acids, amino acids, and steroids. Genome-wide association analyses between genetic polymorphisms and P450 expression or enzyme activities revealed sets of SNPs associated with P450 traits, and suggested the existence of both cis-regulation of P450 expression (especially for CYP2D6) and more complex trans-regulation of P450 activity. Several novel SNPs associated with CYP2D6 expression and enzyme activity were validated in an independent human cohort. By constructing a weighted coexpression network and a Bayesian regulatory network, we defined the human liver transcriptional network structure, uncovered subnetworks representative of the P450 regulatory system, and identified novel candidate regulatory genes, namely, EHHADH, SLC10A1, and AKR1D1. The P450 subnetworks were then validated using gene signatures responsive to ligands of known P450 regulators in mouse and rat. This systematic survey provides a comprehensive view of the functionality, genetic control, and interactions of P450s.
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Affiliation(s)
- Xia Yang
- Rosetta Inpharmatics, LLC, Merck & Co., Inc., Seattle, Washington 98109, USA.
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Prediction of the Effects of Genetic Polymorphism on the Pharmacokinetics of CYP2C9 Substrates from In Vitro Data. Pharm Res 2008; 26:822-35. [DOI: 10.1007/s11095-008-9781-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Accepted: 11/04/2008] [Indexed: 11/25/2022]
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Hart SN, Zhong XB. P450 oxidoreductase: genetic polymorphisms and implications for drug metabolism and toxicity. Expert Opin Drug Metab Toxicol 2008; 4:439-52. [PMID: 18433346 DOI: 10.1517/17425255.4.4.439] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Cytochrome P450 oxidoreductase (POR) is the only electron donor for all microsomal cytochrome P450 monooxygenases (CYP), some of which are phase I drug-metabolizing enzymes, responsible for oxidation of more than 80% of drugs. OBJECTIVES To provide a more thorough understanding of the genetic factors influencing drug metabolism, we address the role of genetic polymorphisms in the POR gene, and their implications for drug metabolism and cytotoxicity. METHODS The scope of this review is intended to cover polymorphisms currently identified in the POR gene, assess their functional significance on POR activity, and address their impact on CYP-mediated drug metabolism. POR is also responsible for directly metabolizing several anticancer prodrugs via a 1-electron reduction reaction, so the effect of POR polymorphisms on the direct bioactivation of drugs is also considered. RESULTS/CONCLUSION POR is a polymorphic enzyme that can affect CYP-mediated drug metabolism as well as direct bioactivation of prodrugs. Genetic polymorphisms in the POR gene may help to explain altered drug-metabolizing phenotypes.
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Affiliation(s)
- Steven N Hart
- University of Kansas Medical Center, Department of Pharmacology, Toxicology, and Therapeutics, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA
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Impairment of human CYP1A2-mediated xenobiotic metabolism by Antley-Bixler syndrome variants of cytochrome P450 oxidoreductase. Arch Biochem Biophys 2008; 475:93-9. [PMID: 18455494 DOI: 10.1016/j.abb.2008.04.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 04/14/2008] [Accepted: 04/15/2008] [Indexed: 01/08/2023]
Abstract
Y459H and V492E mutations of cytochrome P450 reductase (CYPOR) cause Antley-Bixler syndrome due to diminished binding of the FAD cofactor. To address whether these mutations impaired the interaction with drug-metabolizing CYPs, a bacterial model of human liver expression of CYP1A2 and CYPOR was implemented. Four models were generated: POR(null), POR(wt), POR(YH), and POR(VE), for which equivalent CYP1A2 and CYPOR levels were confirmed, except for POR(null), not containing any CYPOR. The mutant CYPORs were unable to catalyze cytochrome c and MTT reduction, and were unable to support EROD and MROD activities. Activity was restored by the addition of FAD, with V492E having a higher apparent FAD affinity than Y459H. The CYP1A2-activated procarcinogens, 2-aminoanthracene, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, and 2-amino-3-methylimidazo(4,5-f)quinoline, were significantly less mutagenic in POR(YH) and POR(VE) models than in POR(wt), indicating that CYP1A2, and likely other drug-metabolizing CYPs, are impaired by ABS-related POR mutations as observed in the steroidogenic CYPs.
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20
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Martinez VG, Williams KJ, Stratford IJ, Clynes M, O'Connor R. Overexpression of cytochrome P450 NADPH reductase sensitises MDA 231 breast carcinoma cells to 5-fluorouracil: possible mechanisms involved. Toxicol In Vitro 2007; 22:582-8. [PMID: 18191533 DOI: 10.1016/j.tiv.2007.11.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Revised: 11/16/2007] [Accepted: 11/28/2007] [Indexed: 11/17/2022]
Abstract
Activity of cytochromes P450 is highly dependent on cytochrome P450 NADPH reductase (P450R), but this enzyme can also metabolise drugs on its own. MDA 231 breast adenocarcinoma cells transfected with human P450R (MDA R4) or an empty vector (MDA EV) were exposed to a series of commonly used chemotherapeutic drugs. Overexpression of P450R did not affect cell sensitivity to cisplatin, mitoxantrone, paclitaxel, docetaxel, vincristine or etoposide. However, MDA R4 cells showed increased sensitivity to mitomycin C (6.6-fold) and also to 5-fluorouracil (2.8-fold). In vitro toxicity assays where mitomycin C, 5-fluorouracil and vincristine were preincubated with microsomes expressing recombinant P450R showed that this effect was not a result of direct metabolism by P450R. Levels of NADPH were considerably decreased in MDA R4 as compared to MDA EV cells, while reactive oxygen species (ROS) production was increased in MDA R4 cells in basal conditions, showing no significant further increase after treatment with mitomycin C or 5-fluorouracil. P450R overexpression appears therefore to be detrimental to MDA 231 cells, depleting NADPH and increasing ROS levels; the increased oxidative stress observed in MDA R4 cells might explain the enhanced sensitivity to 5-fluorouracil. Expression of this enzyme in tumour cells might therefore modulate response to 5-fluorouracil.
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Affiliation(s)
- Vanesa G Martinez
- National Institute for Cellular Biotechnology (NICB), Dublin City University, Glasnevin, Dublin 9, Ireland.
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21
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Kang HS, Angers M, Beak JY, Wu X, Gimble JM, Wada T, Xie W, Collins JB, Grissom SF, Jetten AM. Gene expression profiling reveals a regulatory role for ROR alpha and ROR gamma in phase I and phase II metabolism. Physiol Genomics 2007; 31:281-94. [PMID: 17666523 DOI: 10.1152/physiolgenomics.00098.2007] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Retinoid-related orphan receptors alpha (ROR alpha) and gamma (ROR gamma) are both expressed in liver; however, their physiological functions in this tissue have not yet been clearly defined. The ROR alpha1 and ROR gamma 1 isoforms, but not ROR alpha 4, show an oscillatory pattern of expression during circadian rhythm. To obtain insight into the physiological functions of ROR receptors in liver, we analyzed the gene expression profiles of livers from WT, ROR alpha-deficient staggerer (sg) mice (ROR alpha(sg/sg)), ROR gamma(-/-), and ROR alpha(sg/sg)ROR gamma(-/-) double knockout (DKO) mice by microarray analysis. DKO mice were generated to study functional redundancy between ROR alpha and ROR gamma. These analyses demonstrated that ROR alpha and ROR gamma affect the expression of a number of genes. ROR alpha and ROR gamma are particularly important in the regulation of genes encoding several phase I and phase II metabolic enzymes, including several 3beta-hydroxysteroid dehydrogenases, cytochrome P450 enzymes, and sulfotransferases. In addition, our results indicate that ROR alpha and ROR gamma each affect the expression of a specific set of genes but also exhibit functional redundancy. Our study shows that ROR alpha and ROR gamma receptors influence the regulation of several metabolic pathways, including those involved in the metabolism of steroids, bile acids, and xenobiotics, suggesting that RORs are important in the control of metabolic homeostasis.
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MESH Headings
- Animals
- Bile Acids and Salts/metabolism
- Cells, Cultured/metabolism
- Circadian Rhythm/genetics
- Cytochrome P-450 Enzyme System/metabolism
- Female
- Gene Expression Profiling
- Hepatocytes/metabolism
- Lipid Metabolism/genetics
- Liver/metabolism
- Metabolic Networks and Pathways/genetics
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Neurologic Mutants
- Nuclear Receptor Subfamily 1, Group F, Member 1
- Nuclear Receptor Subfamily 1, Group F, Member 3
- Receptors, Cytoplasmic and Nuclear/deficiency
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/physiology
- Receptors, Retinoic Acid/deficiency
- Receptors, Retinoic Acid/genetics
- Receptors, Retinoic Acid/physiology
- Receptors, Thyroid Hormone/deficiency
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/physiology
- Recombinant Fusion Proteins/metabolism
- Steroids/metabolism
- Trans-Activators/deficiency
- Trans-Activators/genetics
- Trans-Activators/physiology
- Transfection
- Xenobiotics/metabolism
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Affiliation(s)
- Hong Soon Kang
- Cell Biology Section, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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Testa B, Krämer SD. The biochemistry of drug metabolism--an introduction: Part 2. Redox reactions and their enzymes. Chem Biodivers 2007; 4:257-405. [PMID: 17372942 DOI: 10.1002/cbdv.200790032] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review continues a general presentation of the metabolism of drugs and other xenobiotics started in a recent issue of Chemistry & Biodiversity. This Part 2 presents the numerous oxidoreductases involved, their nomenclature, relevant biochemical properties, catalytic mechanisms, and the very diverse reactions they catalyze. Many medicinally, environmentally, and toxicologically relevant examples are presented and discussed. Cytochromes P450 occupy a majority of the pages of Part 2, but a large number of relevant oxidoreductases are also considered, e.g., flavin-containing monooxygenases, amine oxidases, molybdenum hydroxylases, peroxidases, and the innumerable dehydrogenases/reductases.
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Affiliation(s)
- Bernard Testa
- Department of Pharmacy, University Hospital Centre (CHUV), Rue du Bugnon, CH-1011 Lausanne.
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