1
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Guvench O. Water Exchange from the Buried Binding Sites of Cytochrome P450 Enzymes 1A2, 2D6, and 3A4 Correlates with Conformational Fluctuations. Molecules 2024; 29:494. [PMID: 38276571 PMCID: PMC10820051 DOI: 10.3390/molecules29020494] [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: 12/19/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Human cytochrome P450 enzymes (CYPs) are critical for the metabolism of small-molecule pharmaceuticals (drugs). As such, the prediction of drug metabolism by and drug inhibition of CYP activity is an important component of the drug discovery and design process. Relative to the availability of a wide range of experimental atomic-resolution CYP structures, the development of structure-based CYP activity models has been limited. To better characterize the role of CYP conformational fluctuations in CYP activity, we perform multiple microsecond-scale all-atom explicit-solvent molecular dynamics (MD) simulations on three CYP isoforms, 1A2, 2D6, and 3A4, which together account for the majority of CYP-mediated drug metabolism. The MD simulations employ a variety of positional restraints, ranging from keeping all CYP atoms close to their experimentally determined coordinates to allowing full flexibility. We find that, with full flexibility, large fluctuations in the CYP binding sites correlate with efficient water exchange from these buried binding sites. This is especially true for 1A2, which, when restrained to its crystallographic conformation, is unable to exchange water between the binding site and bulk solvent. These findings imply that, in addition to crystal structures, a representative ensemble of conformational states ought to be included when developing structure-based CYP activity models.
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Affiliation(s)
- Olgun Guvench
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, Westbrook College of Health Professions, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA
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2
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Dai Z, Wu Y, Xiong Y, Wu J, Wang M, Sun X, Ding X, Yang L, Sun X, Ge G. CYP1A inhibitors: Recent progress, current challenges, and future perspectives. Med Res Rev 2024; 44:169-234. [PMID: 37337403 DOI: 10.1002/med.21982] [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: 12/09/2022] [Revised: 03/28/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
Mammalian cytochrome P450 1A (CYP1A) are key phase I xenobiotic-metabolizing enzymes that play a distinctive role in metabolic activation or metabolic clearance of a variety of procarcinogens, drugs, and endogenous substances. Human CYP1A subfamily contains two members (hCYP1A1 and hCYP1A2), which are known to catalyze the oxidative activation of some environmental procarcinogens into carcinogenic species. Increasing evidence has demonstrated that CYP1A inhibitor therapies are promising strategies for cancer chemoprevention or overcoming CYP1A-associated drug toxicity and resistance. Herein, we reviewed recent advances in the discovery and characterization of hCYP1A inhibitors, from the discovery approaches to structural features and biomedical applications of hCYP1A inhibitors. The inhibition potentials, inhibition modes, and inhibition constants of all reported hCYP1A inhibitors are comprehensively summarized. Meanwhile, the structural features and structure-activity relationships of different classes of hCYP1A1 and hCYP1A2 inhibitors are analyzed and discussed in depth. Furthermore, the major challenges and future directions for this field are presented and highlighted. Collectively, the information and knowledge presented here will strongly facilitate the researchers to discover and develop more efficacious CYP1A inhibitors for specific purposes, such as chemo-preventive agents or as tool molecules in hCYP1A-related fundamental studies.
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Affiliation(s)
- Ziru Dai
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yue Wu
- Shanghai Frontiers Science Center for TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuan Xiong
- Shanghai Frontiers Science Center for TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jingjing Wu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, China
| | - Min Wang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiao Sun
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xinxin Ding
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, America
| | - Ling Yang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Xiaobo Sun
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center for TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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3
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Di L. Quantitative Translation of Substrate Intrinsic Clearance from Recombinant CYP1A1 to Humans. AAPS J 2023; 25:98. [PMID: 37798423 DOI: 10.1208/s12248-023-00863-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023] Open
Abstract
CYP1A1 is a cytochrome P450 family 1 enzyme that is mostly expressed in the extrahepatic tissues. To understand the CYP1A1 contribution to drug clearance in humans, we examined the in vitro-in vivo extrapolation (IVIVE) of intrinsic clearance (CLint) for a set of drugs that are in vitro CYP1A1 substrates. Despite being strong in vitro CYP1A1 substrates, 82% of drugs gave good IVIVE with predicted CLint within 2-3-fold of the observed values using human liver microsomes and hepatocytes, suggesting they were not in vivo CYP1A1 substrates due to the lack of extrahepatic contribution to CLint. Only three drugs (riluzole, melatonin and ramelteon) that are CYP1A2 substrates yielded significant underprediction of in vivo CLint up to 11-fold. The fold of CLint underprediction was linearly proportional to human recombinant CYP1A1 (rCYP1A1) CLint, indicating they were likely to be in vivo CYP1A1 substrates. Using these three substrates, a calibration curve can be developed to enable direct translation from in vitro rCYP1A1 CLint to in vivo extrahepatic contributions in humans. In vivo CYP1A1 substrates are planar and small, which is consistent with the structure of the active site. This is in contrast to the in vitro substrates, which include large and nonplanar molecules, suggesting rCYP1A1 is more accessible than what is in vivo. The impact of CYP1A1 on first-pass intestinal metabolism was also evaluated and shown to be minimal. This is the first study providing new insights on in vivo translation of CYP1A1 contributions to human clearance using in vitro rCYP1A1 data.
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Affiliation(s)
- Li Di
- Pharmacokinetic, Dynamics and Drug Metabolism, Pfizer Worldwide Research and Development, Groton, Connecticut, 06543, USA.
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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: 5] [Impact Index Per Article: 5.0] [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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Abstract
Cytochrome P450 (CYP450) is a major drug-metabolizing enzyme system mainly distributed in liver microsomes and involved in the metabolism of many endogenous substances (such as fatty acids and arachidonic acids), and exogenous compounds (such as drugs, toxicants, carcinogens, and procarcinogens). Due to the similarity in structures and catalytic functions between CYP450 isoforms, the lack of effective selective detection tools greatly limits the understanding and the research of their respective physiological roles in living organisms. Until now, several small-molecular fluorescent probes have been employed for selective detection and monitoring of CYP450s (Cytochrome P450 enzymes) in vitro or in vivo owing to the tailored properties, biodegradability, and high temporal and spatial resolution imaging in situ. In this review, we summarize the recent advances in fluorescent probes for CYP450s (including CYP1, CYP2, and CYP3 families), and we discuss and focus on their identification mechanisms, general probe design strategies, and bioimaging applications. We also highlight the potential challenges and prospects of designing new generations of fluorescent probes in CYP450 studies, which will further enhance the diversity, practicality, and clinical feasibility of research into CYP450.
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6
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Park H, Brahma R, Shin J, Cho K. Prediction of human cytochrome
P450
inhibition using bio‐selectivity induced deep neural network. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hyejin Park
- AzothBio, Rm. DA724 Hyundai Knowledge Industry Center Hanam‐si Gyeonggi‐do Republic of Korea
| | - Rahul Brahma
- School of Systems Biomedical Science Soongsil University Seoul Republic of Korea
| | - Jae‐Min Shin
- AzothBio, Rm. DA724 Hyundai Knowledge Industry Center Hanam‐si Gyeonggi‐do Republic of Korea
| | - Kwang‐Hwi Cho
- School of Systems Biomedical Science Soongsil University Seoul Republic of Korea
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7
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8
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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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9
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Zhang F, Huang J, He RJ, Wang L, Huo PC, Guan XQ, Fang SQ, Xiang YW, Jia SN, Ge GB. Herb-drug interaction between Styrax and warfarin: Molecular basis and mechanism. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2020; 77:153287. [PMID: 32739573 DOI: 10.1016/j.phymed.2020.153287] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Styrax, one of the most famous folk medicines, has been frequently used for the treatment of cardiovascular diseases and skin problems in Asia and Africa. It is unclear whether Styrax or Styrax-related herbal medicines may trigger clinically relevant herb-drug interactions. PURPOSE This study was carried out to investigate the inhibitory effects of Styrax on human cytochrome P450 enzymes (CYPs) and to clarify whether this herb may modulate the pharmacokinetic behavior of the CYP-substrate drug warfarin when co-administered. STUDY DESIGN The inhibitory effects of Styrax on CYPs were assayed in human liver microsomes (HLM), while the pharmacokinetic interactions between Styrax and warfarin were investigated in rats. The bioactive constituents in Styrax with strong CYP3A inhibitory activity were identified and their inhibitory mechanisms were carefully investigated. METHODS The inhibitory effects of Styrax on human CYPs were assayed in vitro, while the pharmacokinetic interactions between Styrax and warfarin were studied in rats. Fingerprinting analysis of Styrax coupled with LC-TOF-MS/MS profiling and CYP inhibition assays were used to identify the constituents with strong CYP3A inhibitory activity. The inhibitory mechanism of oleanonic acid (the most potent CYP3A inhibitor occurring in Styrax) against CYP3A4 was investigated by a panel of inhibition kinetics analyses and in silico analysis. RESULTS In vitro assays demonstrated that Styrax extract strongly inhibited human CYP3A and moderately inhibited six other tested human CYPs, as well as potently inhibited warfarin 10-hydroxylation in liver microsomes from both humans and rats. In vivo assays demonstrated that compared with warfarin given individually in rats, Styrax (100 mg/kg) significantly prolonged the plasma half-life of warfarin by 2.3-fold and increased the AUC(0-inf) of warfarin by 2.7-fold when this herb was co-administrated with warfarin (2 mg/kg) in rats. Two LC fractions were found with strong CYP3A inhibitory activity and the major constituents in these fractions were characterized by LC-TOF-MS/MS. Five pentacyclic triterpenoid acids (including epibetulinic acid, betulinic acid, betulonic acid, oleanonic acid and maslinic acid) present in Styrax were potent CYP3A inhibitors, and oleanonic acid was a competitive inhibitor against CYP3A-mediated testosterone 6β-hydroxylation. CONCLUSION Styrax and the pentacyclic triterpenoid acids occurring in this herb strongly modulate the pharmacokinetic behavior of warfarin via inhibition of CYP3A.
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Affiliation(s)
- Feng Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jian Huang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Pharmacology and Toxicology Division, Shanghai Institute of Food and Drug Control, Shanghai, China
| | - Rong-Jing He
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lu Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Peng-Chao Huo
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiao-Qing Guan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Sheng-Quan Fang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200473, China
| | - Yan-Wei Xiang
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shou-Ning Jia
- Qinghai Hospital of Traditional Chinese Medicine, Xining, China
| | - Guang-Bo Ge
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200473, China.
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10
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Edamatsu H, Yagawa M, Ikushiro S, Sakaki T, Nakagawa Y, Miyagawa H, Akamatsu M. Identification and in silico prediction of metabolites of tebufenozide derivatives by major human cytochrome P450 isoforms. Bioorg Med Chem 2020; 28:115429. [PMID: 32201191 DOI: 10.1016/j.bmc.2020.115429] [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: 01/14/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 11/18/2022]
Abstract
Cytochrome P450 (CYP) enzymes constitute a superfamily of heme-containing monooxygenases. CYPs are involved in the metabolism of many chemicals such as drugs and agrochemicals. Therefore, examining the metabolic reactions by each CYP isoform is important to elucidate their substrate recognition mechanisms. The clarification of these mechanisms may be useful not only for the development of new drugs and agrochemicals, but also for risk assessment of chemicals. In our previous study, we identified the metabolites of tebufenozide, an insect growth regulator, formed by two human CYP isoforms: CYP3A4 and CYP2C19. The accessibility of each site of tebufenozide to the reaction center of CYP enzymes and the susceptibility of each hydrogen atom for metabolism by CYP enzymes were evaluated by a docking simulation and hydrogen atom abstraction energy estimation at the density functional theory level, respectively. In this study, the same in silico prediction method was applied to the metabolites of tebufenozide derivatives by major human CYPs (CYP1A2, 2C9, 2C19, 2D6, and 3A4). In addition, the production rate of the metabolites by CYP3A4 was quantitively analyzed by frequency based on docking simulation and hydrogen atom abstraction energy using the classical QSAR approach. Then, the obtained QSAR model was applied to predict the sites of metabolism and the metabolite production order by each CYP isoform.
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Affiliation(s)
- Hiroaki Edamatsu
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masataka Yagawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shinichi Ikushiro
- Faculty of Engineering, Toyama Prefectural University, 5180, Kurokawa, Imizu-shi, Toyama 939-0398, Japan
| | - Toshiyuki Sakaki
- Faculty of Engineering, Toyama Prefectural University, 5180, Kurokawa, Imizu-shi, Toyama 939-0398, Japan
| | - Yoshiaki Nakagawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hisashi Miyagawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Miki Akamatsu
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan.
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11
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Dmitriev AV, Lagunin AA, Karasev DА, Rudik AV, Pogodin PV, Filimonov DA, Poroikov VV. Prediction of Drug-Drug Interactions Related to Inhibition or Induction of Drug-Metabolizing Enzymes. Curr Top Med Chem 2019; 19:319-336. [PMID: 30674264 DOI: 10.2174/1568026619666190123160406] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/02/2019] [Accepted: 01/07/2019] [Indexed: 02/07/2023]
Abstract
Drug-drug interaction (DDI) is the phenomenon of alteration of the pharmacological activity of a drug(s) when another drug(s) is co-administered in cases of so-called polypharmacy. There are three types of DDIs: pharmacokinetic (PK), pharmacodynamic, and pharmaceutical. PK is the most frequent type of DDI, which often appears as a result of the inhibition or induction of drug-metabolising enzymes (DME). In this review, we summarise in silico methods that may be applied for the prediction of the inhibition or induction of DMEs and describe appropriate computational methods for DDI prediction, showing the current situation and perspectives of these approaches in medicinal and pharmaceutical chemistry. We review sources of information on DDI, which can be used in pharmaceutical investigations and medicinal practice and/or for the creation of computational models. The problem of the inaccuracy and redundancy of these data are discussed. We provide information on the state-of-the-art physiologically- based pharmacokinetic modelling (PBPK) approaches and DME-based in silico methods. In the section on ligand-based methods, we describe pharmacophore models, molecular field analysis, quantitative structure-activity relationships (QSAR), and similarity analysis applied to the prediction of DDI related to the inhibition or induction of DME. In conclusion, we discuss the problems of DDI severity assessment, mention factors that influence severity, and highlight the issues, perspectives and practical using of in silico methods.
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Affiliation(s)
| | - Alexey A Lagunin
- Institute of Biomedical Chemistry, Moscow, Russian Federation.,Pirogov Russian National Research Medical University, Moscow, RussiaN Federation
| | | | | | - Pavel V Pogodin
- Institute of Biomedical Chemistry, Moscow, Russian Federation
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12
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Zhang J, Chai X, He XP, Kim HJ, Yoon J, Tian H. Fluorogenic probes for disease-relevant enzymes. Chem Soc Rev 2019; 48:683-722. [PMID: 30520895 DOI: 10.1039/c7cs00907k] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Traditional biochemical methods for enzyme detection are mainly based on antibody-based immunoassays, which lack the ability to monitor the spatiotemporal distribution and, in particular, the in situ activity of enzymes in live cells and in vivo. In this review, we comprehensively summarize recent progress that has been made in the development of small-molecule as well as material-based fluorogenic probes for sensitive detection of the activities of enzymes that are related to a number of human diseases. The principles utilized to design these probes as well as their applications are reviewed. Specific attention is given to fluorogenic probes that have been developed for analysis of the activities of enzymes including oxidases and reductases, those that act on biomacromolecules including DNAs, proteins/peptides/amino acids, carbohydrates and lipids, and those that are responsible for translational modifications. We envision that this review will serve as an ideal reference for practitioners as well as beginners in relevant research fields.
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Affiliation(s)
- Junji Zhang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd., Shanghai 200237, P. R. China.
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13
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Ai CZ, Man HZ, Saeed Y, Chen DC, Wang LH, Jiang YZ. Computational insight into crucial binding features for metabolic specificity of cytochrome P450 17A1. INFORMATICS IN MEDICINE UNLOCKED 2019. [DOI: 10.1016/j.imu.2019.100172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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14
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Parmentier Y, Pothier C, Hewitt N, Vincent L, Caradec F, Liu J, Lin F, Trancart MM, Guillet F, Bouaita B, Chesne C, Walther B. Direct and quantitative evaluation of the major human CYP contribution (fmCYP) to drug clearance using the in vitro Silensomes™ model. Xenobiotica 2018; 49:22-35. [PMID: 29297729 DOI: 10.1080/00498254.2017.1422156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
1. We have applied the concept of using MBIs to produce CYP-Silensomes to quantify the contribution of the major CYPs to drug metabolism (fmCYP). 2. The target CYPs were extensively and selectivity inhibited by the selected MBIs, while non-target CYPs were inhibited by less than 20% of the homologous control activities. Only CYP2D6-Silensomes exhibited a CYP2B6 inhibition that could be easily and efficiently encountered by subtracting the fmCYP2B6 measured using CYP2B6-Silensomes to adjust the fmCYP2D6. 3. To validate the use of a panel of 6 CYP-Silensomes, we showed that the fmCYP values of mono- and multi-CYP metabolised drugs were well predicted, with 70% within ± 15% accuracy. Moreover, the correlation with observed fmCYP values was higher than that for rhCYPs, which were run in parallel using the same drugs (<45% within ±15% accuracy). Moreover, the choice of the RAF substrate in rhCYP predictions was shown to affect the accuracy of the fmCYP measurement. 4. These results support the use of CYP1A2-, CYP2B6-, CYP2C8-, CYP2C9-, CYP2D6 and CYP3A4-Silensomes to accurately predict fmCYP values during the in vitro enzyme phenotyping assays in early, as well as in development, phases of drug development.
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Affiliation(s)
- Yannick Parmentier
- a Department of Biopharmaceutical Research , Technologie Servier , Orléans Cedex , France
| | - Corinne Pothier
- a Department of Biopharmaceutical Research , Technologie Servier , Orléans Cedex , France
| | | | - Ludwig Vincent
- a Department of Biopharmaceutical Research , Technologie Servier , Orléans Cedex , France
| | - Fabrice Caradec
- a Department of Biopharmaceutical Research , Technologie Servier , Orléans Cedex , France
| | - Jia Liu
- c SIMM-SERVIER Joint Biopharmacy Laboratory, Shanghai Institute of Materia Medica , Shanghai , China
| | - Feifei Lin
- c SIMM-SERVIER Joint Biopharmacy Laboratory, Shanghai Institute of Materia Medica , Shanghai , China
| | | | | | | | | | - Bernard Walther
- a Department of Biopharmaceutical Research , Technologie Servier , Orléans Cedex , France
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15
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Liu HW, Chen L, Xu C, Li Z, Zhang H, Zhang XB, Tan W. Recent progresses in small-molecule enzymatic fluorescent probes for cancer imaging. Chem Soc Rev 2018; 47:7140-7180. [DOI: 10.1039/c7cs00862g] [Citation(s) in RCA: 515] [Impact Index Per Article: 85.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An overview of recent advances in small-molecule enzymatic fluorescent probes for cancer imaging, including design strategies and cancer imaging applications.
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Affiliation(s)
- Hong-Wen Liu
- Molecular Science and Biomedicine Laboratory (MBL)
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Collaborative Innovation Center for Chemistry and Molecular Medicine
- Hunan University
| | - Lanlan Chen
- Molecular Science and Biomedicine Laboratory (MBL)
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Collaborative Innovation Center for Chemistry and Molecular Medicine
- Hunan University
| | - Chengyan Xu
- Molecular Science and Biomedicine Laboratory (MBL)
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Collaborative Innovation Center for Chemistry and Molecular Medicine
- Hunan University
| | - Zhe Li
- Molecular Science and Biomedicine Laboratory (MBL)
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Collaborative Innovation Center for Chemistry and Molecular Medicine
- Hunan University
| | - Haiyang Zhang
- Molecular Science and Biomedicine Laboratory (MBL)
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Collaborative Innovation Center for Chemistry and Molecular Medicine
- Hunan University
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory (MBL)
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Collaborative Innovation Center for Chemistry and Molecular Medicine
- Hunan University
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL)
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Collaborative Innovation Center for Chemistry and Molecular Medicine
- Hunan University
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16
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Dai ZR, Feng L, Jin Q, Cheng H, Li Y, Ning J, Yu Y, Ge GB, Cui JN, Yang L. A practical strategy to design and develop an isoform-specific fluorescent probe for a target enzyme: CYP1A1 as a case study. Chem Sci 2016; 8:2795-2803. [PMID: 28553516 PMCID: PMC5426458 DOI: 10.1039/c6sc03970g] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/16/2016] [Indexed: 12/21/2022] Open
Abstract
The development of isoform-specific probe(s) for a target enzyme with multiple homologs is always challenging. Herein, a practical strategy was used to design and develop an isoform-specific probe for CYP1A1, a key cytochrome P450 isoenzyme involved in xenobiotic metabolism and bioactivation. On the basis of the subtle differences in 3D structure and substrate preference between CYP1A1 and its homolog CYP1A2, we proposed that it was possible to design a CYP1A1-specific probe via local modification of the reaction site on known CYP1A substrates. To validate this hypothesis, 4-hydroxy-1,8-naphthalimide (HN) was selected as the basic fluorophore due to its excellent optical properties, while a series of O-alkylated HN derivatives were prepared to evaluate their specificity towards CYP1A1. Our results revealed that the introduction of a chloroethyl to HN could get the best isoform selectivity towards CYP1A1 over other CYPs including CYP1A2. The newly developed probe NBCeN exhibited excellent specificity, high sensitivity, and a ratiometric fluorescence response following CYP1A1-catalyzed O-dechloroethylation. NBCeN was successfully used to real-time monitor the activity of CYP1A1 in complex biological samples and to rapidly screen CYP1A1 modulators in living systems. NBCeN could also be used for two-photon imaging of intracellular CYP1A1 in living cells and tissues with high ratiometric imaging resolution and deep tissue penetration. All these findings demonstrated that local modification of non-specific substrates was a practical strategy to develop an isoform-specific probe for a target isoenzyme, while NBCeN could serve as a specific imaging tool to explore the biological functions of CYP1A1 in complex biological systems.
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Affiliation(s)
- Zi-Ru Dai
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ; .,Graduate School of Chinese Academy of Sciences , Beijing , China
| | - Lei Feng
- State Key Laboratory of Fine Chemicals , Dalian University of Technology , Dalian , China
| | - Qiang Jin
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ; .,Graduate School of Chinese Academy of Sciences , Beijing , China
| | - Hailing Cheng
- Cancer Institute , The Second Hospital of Dalian Medical University , Dalian , China
| | - Yan Li
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ;
| | - Jing Ning
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ;
| | - Yang Yu
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ;
| | - Guang-Bo Ge
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ; .,State Key Laboratory of Fine Chemicals , Dalian University of Technology , Dalian , China
| | - Jing-Nan Cui
- State Key Laboratory of Fine Chemicals , Dalian University of Technology , Dalian , China
| | - Ling Yang
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ;
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17
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Ferreira RS, Chivittz CDC, Santos GSD, Zanette J. Cytochrome P450 1A mRNA in the guppy Phalloceros caudimaculatus and response to beta-naphthoflavone and environmental samples. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 181:86-93. [PMID: 27821351 DOI: 10.1016/j.aquatox.2016.10.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/20/2016] [Accepted: 10/24/2016] [Indexed: 06/06/2023]
Abstract
The cytochrome P450 1A (CYP1A) mRNA is induced by environmental contaminants such as PAHs, PCBs and dioxins. The present study cloned the CYP1A transcript from the guppy Phalloceros caudimaculatus, which represents a potential fish for toxicological studies in South America. The newly identified CYP1A encodes a protein with 521 amino acids that shared 96-70% identity with other fishes. The characterization of organ- and time-dependent induction of CYP1A using RT-qPCR was evaluated after waterborne exposure to beta-naphthoflavone (BNF; 1μM). The minimum exposure time that elicited significant CYP1A induction was 1h for liver, gill, gut, brain, anal fin and fingerlings; 2h for dorsal fin; and 4h for kidney and tail fin. CYP1A tended to reach peak induction in the first few hours (4h-8h) of experiment in most organs, although levels remained induced until the end of the experiment (96h). Validation of CYP1A use in environmental sample was performed by exposing P. caudimaculatus to elutriate made from sediment of three streams located in adjacent areas of the Patos Lagoon Estuary (RS, Brazil). CYP1A in liver, gills and anal fin was induced by elutriate made from urban (S1) and industrial (S2) sites; and not induced by a reference site located 22 Km from potential contaminant sources, suggesting that environmental contamination plays a role in this induction. The results suggest that fins could be used for CYP1A biomarker analysis and employed in non-lethal biopsy methods for environmental monitoring. The responsiveness of the newly identified CYP1A to BNF and elutriate indicates that the guppy P. caudimaculatus could be used for environmental toxicology investigations in South American environments.
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Affiliation(s)
- Roger Stacke Ferreira
- Instituto de Ciências Biológicas (ICB), Universidade Federal do Rio Grande (FURG), Rio Grande, RS 96203-900, Brazil; Programa de Pós-graduação em Biologia de Ambientes Aquáticos Continentais (PPGBAC), Universidade Federal do Rio Grande (FURG), Rio Grande, RS 96203-900, Brazil
| | - Cíntia da Cruz Chivittz
- Instituto de Ciências Biológicas (ICB), Universidade Federal do Rio Grande (FURG), Rio Grande, RS 96203-900, Brazil; Programa de Pós-graduação em Biologia de Ambientes Aquáticos Continentais (PPGBAC), Universidade Federal do Rio Grande (FURG), Rio Grande, RS 96203-900, Brazil
| | - Guilherme Senna Dos Santos
- Instituto de Ciências Biológicas (ICB), Universidade Federal do Rio Grande (FURG), Rio Grande, RS 96203-900, Brazil
| | - Juliano Zanette
- Instituto de Ciências Biológicas (ICB), Universidade Federal do Rio Grande (FURG), Rio Grande, RS 96203-900, Brazil; Programa de Pós-graduação em Biologia de Ambientes Aquáticos Continentais (PPGBAC), Universidade Federal do Rio Grande (FURG), Rio Grande, RS 96203-900, Brazil.
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18
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Nakayama SMM, Ikenaka Y, Hayami A, Mizukawa H, Darwish WS, Watanabe KP, Kawai YK, Ishizuka M. Characterization of equine cytochrome P450: role of CYP3A in the metabolism of diazepam. J Vet Pharmacol Ther 2016; 39:478-87. [DOI: 10.1111/jvp.12303] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 01/29/2016] [Indexed: 11/29/2022]
Affiliation(s)
- S. M. M. Nakayama
- Laboratory of Toxicology; Department of Environmental Veterinary Sciences; Graduate School of Veterinary Medicine; Hokkaido University; Kita-ku Sapporo Japan
| | - Y. Ikenaka
- Laboratory of Toxicology; Department of Environmental Veterinary Sciences; Graduate School of Veterinary Medicine; Hokkaido University; Kita-ku Sapporo Japan
- Water Research Group; Unit for Environmental Sciences and Management; North-West University; Potchefstroom South Africa
| | - A. Hayami
- Laboratory of Toxicology; Department of Environmental Veterinary Sciences; Graduate School of Veterinary Medicine; Hokkaido University; Kita-ku Sapporo Japan
| | - H. Mizukawa
- Department of Environmental Veterinary Sciences; Graduate School of Veterinary Medicine; Hokkaido University; Kita-ku Sapporo Japan
| | - W. S. Darwish
- Laboratory of Toxicology; Department of Environmental Veterinary Sciences; Graduate School of Veterinary Medicine; Hokkaido University; Kita-ku Sapporo Japan
- Food Control Department; Faculty of Veterinary Medicine; Zagazig University; Zagazig Egypt
| | - K. P. Watanabe
- Laboratory of Toxicology; Department of Environmental Veterinary Sciences; Graduate School of Veterinary Medicine; Hokkaido University; Kita-ku Sapporo Japan
| | - Y. K. Kawai
- Laboratory of Toxicology; Department of Environmental Veterinary Sciences; Graduate School of Veterinary Medicine; Hokkaido University; Kita-ku Sapporo Japan
- Diagnostic Center for Animal Health and Food Safety; Obihiro University of Agriculture and Veterinary Medicine; Obihiro Japan
| | - M. Ishizuka
- Laboratory of Toxicology; Department of Environmental Veterinary Sciences; Graduate School of Veterinary Medicine; Hokkaido University; Kita-ku Sapporo Japan
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19
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Yang X, Atkinson K, Di L. Novel Cytochrome P450 Reaction Phenotyping for Low-Clearance Compounds Using the Hepatocyte Relay Method. Drug Metab Dispos 2015; 44:460-5. [DOI: 10.1124/dmd.115.067876] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/22/2015] [Indexed: 11/22/2022] Open
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20
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Dai ZR, Ge GB, Feng L, Ning J, Hu LH, Jin Q, Wang DD, Lv X, Dou TY, Cui JN, Yang L. A Highly Selective Ratiometric Two-Photon Fluorescent Probe for Human Cytochrome P450 1A. J Am Chem Soc 2015; 137:14488-95. [DOI: 10.1021/jacs.5b09854] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Zi-Ru Dai
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guang-Bo Ge
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State
Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Lei Feng
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State
Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Jing Ning
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Liang-Hai Hu
- Research
Center for Drug Metabolism, College of Life Science, Jilin University, Changchun 130012, China
| | - Qiang Jin
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Dan-Dan Wang
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xia Lv
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Tong-Yi Dou
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jing-Nan Cui
- State
Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Ling Yang
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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21
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Shirotani N, Togawa M, Ikushiro S, Sakaki T, Harada T, Miyagawa H, Matsui M, Nagahori H, Mikata K, Nishioka K, Hirai N, Akamatsu M. Identification and in silico prediction of metabolites of the model compound, tebufenozide by human CYP3A4 and CYP2C19. Bioorg Med Chem 2015; 23:6594-601. [PMID: 26404412 DOI: 10.1016/j.bmc.2015.09.019] [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] [Received: 07/28/2015] [Revised: 09/09/2015] [Accepted: 09/11/2015] [Indexed: 10/23/2022]
Abstract
The metabolites of tebufenozide, a model compound, formed by the yeast-expressed human CYP3A4 and CYP2C19 were identified to clarify the substrate recognition mechanism of the human cytochrome P450 (CYP) isozymes. We then determined whether tebufenozide metabolites may be predicted in silico. Hydrogen abstraction energies were calculated with the density functional theory method B3LYP/6-31G(∗). A docking simulation was performed using FRED software. Several alkyl sites of tebufenozide were hydroxylated by CYP3A4 whereas only one site was modified by CYP2C19. The accessibility of each site of tebufenozide to the reaction center of CYP enzymes and the susceptibility of each hydrogen atom for metabolism by CYP enzymes were evaluated by a docking simulation and hydrogen abstraction energy estimation, respectively.
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Affiliation(s)
- Naoki Shirotani
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Moe Togawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shinichi Ikushiro
- Faculty of Engineering, Toyama Prefectural University, 5180, Kurokawa, Imizu-shi, Toyama 939-0398, Japan
| | - Toshiyuki Sakaki
- Faculty of Engineering, Toyama Prefectural University, 5180, Kurokawa, Imizu-shi, Toyama 939-0398, Japan
| | - Toshiyuki Harada
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hisashi Miyagawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayoshi Matsui
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd, 1-98, Kasugade-naka 3-chome, Konohana-ku, Osaka 554-8558, Japan
| | - Hirohisa Nagahori
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd, 1-98, Kasugade-naka 3-chome, Konohana-ku, Osaka 554-8558, Japan
| | - Kazuki Mikata
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd, 1-98, Kasugade-naka 3-chome, Konohana-ku, Osaka 554-8558, Japan
| | - Kazuhiko Nishioka
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd, 1-98, Kasugade-naka 3-chome, Konohana-ku, Osaka 554-8558, Japan
| | - Nobuhiro Hirai
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Miki Akamatsu
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan.
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22
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Wu JJ, Ge GB, He YQ, Wang P, Dai ZR, Ning J, Hu LH, Yang L. Gomisin A is a Novel Isoform-Specific Probe for the Selective Sensing of Human Cytochrome P450 3A4 in Liver Microsomes and Living Cells. AAPS JOURNAL 2015; 18:134-45. [PMID: 26361765 DOI: 10.1208/s12248-015-9827-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/31/2015] [Indexed: 10/23/2022]
Abstract
Nearly half of prescription medicines are metabolized by human cytochrome P450 (CYP) 3A. CYP3A4 and 3A5 are two major isoforms of human CYP3A and share most of the substrate spectrum. A very limited previous study distinguished the activity of CYP3A4 and CYP3A5, identifying the challenge in predicting CYP3A-mediated drug clearance and drug-drug interaction. In the present study, we introduced gomisin A (GA) with a dibenzocyclooctadiene skeleton as a novel selective probe of CYP3A4. The major metabolite of GA was fully characterized as 8-hydroxylated GA by LC-MS and NMR. CYP3A4 was assigned as the predominant isozyme involved in GA 8-hydroxylation by reaction phenotyping assays, chemical inhibition assays, and correlation studies. GA 8-hydroxylation in both recombinant human CYP3A4 and human liver microsomes followed classic Michaelis-Menten kinetics. The intrinsic clearance values indicated that CYP3A4 contributed 12.8-fold more than CYP3A5 to GA 8-hydroxylation. Molecular docking studies indicated different hydrogen bonds and π-π interactions between CYP3A4 and CYP3A5, which might result in the different catalytic activity for GA 8-hydroxylation. Furthermore, GA exhibited a stronger inhibitory activity towards CYP3A4 than CYP3A5, which further suggested a preferred selectivity of CYP3A4 for the transformation of GA. More importantly, GA has been successfully applied to selectively monitor the modulation of CYP3A4 activities by the inducer rifampin in hepG2 cells, which is consistent with the level change of CYP3A4 mRNA expression. In summary, our results suggested that GA could be used as a novel probe for the selective sensing of CYP3A4 in tissue and cell preparations.
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Affiliation(s)
- Jing-Jing Wu
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China.,Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Guang-Bo Ge
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yu-Qi He
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Ping Wang
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Zi-Ru Dai
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China.,Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, China
| | - Jing Ning
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Liang-Hai Hu
- Research Center for Drug Metabolism, College of Life Science, Jilin University, Changchun, 130012, China
| | - Ling Yang
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China.
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23
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Dai ZR, Ai CZ, Ge GB, He YQ, Wu JJ, Wang JY, Man HZ, Jia Y, Yang L. A Mechanism-Based Model for the Prediction of the Metabolic Sites of Steroids Mediated by Cytochrome P450 3A4. Int J Mol Sci 2015; 16:14677-94. [PMID: 26133240 PMCID: PMC4519866 DOI: 10.3390/ijms160714677] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 11/16/2022] Open
Abstract
Early prediction of xenobiotic metabolism is essential for drug discovery and development. As the most important human drug-metabolizing enzyme, cytochrome P450 3A4 has a large active cavity and metabolizes a broad spectrum of substrates. The poor substrate specificity of CYP3A4 makes it a huge challenge to predict the metabolic site(s) on its substrates. This study aimed to develop a mechanism-based prediction model based on two key parameters, including the binding conformation and the reaction activity of ligands, which could reveal the process of real metabolic reaction(s) and the site(s) of modification. The newly established model was applied to predict the metabolic site(s) of steroids; a class of CYP3A4-preferred substrates. 38 steroids and 12 non-steroids were randomly divided into training and test sets. Two major metabolic reactions, including aliphatic hydroxylation and N-dealkylation, were involved in this study. At least one of the top three predicted metabolic sites was validated by the experimental data. The overall accuracy for the training and test were 82.14% and 86.36%, respectively. In summary, a mechanism-based prediction model was established for the first time, which could be used to predict the metabolic site(s) of CYP3A4 on steroids with high predictive accuracy.
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Affiliation(s)
- Zi-Ru Dai
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chun-Zhi Ai
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Guang-Bo Ge
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yu-Qi He
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Jing-Jing Wu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Jia-Yue Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Hui-Zi Man
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yan Jia
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ling Yang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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24
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Olsen L, Oostenbrink C, Jørgensen FS. Prediction of cytochrome P450 mediated metabolism. Adv Drug Deliv Rev 2015; 86:61-71. [PMID: 25958010 DOI: 10.1016/j.addr.2015.04.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 03/30/2015] [Accepted: 04/27/2015] [Indexed: 10/23/2022]
Abstract
Cytochrome P450 enzymes (CYPs) form one of the most important enzyme families involved in the metabolism of xenobiotics. CYPs comprise many isoforms, which catalyze a wide variety of reactions, and potentially, a large number of different metabolites can be formed. However, it is often hard to rationalize what metabolites these enzymes generate. In recent years, many different in silico approaches have been developed to predict binding or regioselective product formation for the different CYP isoforms. These comprise ligand-based methods that are trained on experimental CYP data and structure-based methods that consider how the substrate is oriented in the active site or/and how reactive the part of the substrate that is accessible to the heme group is. We will review key aspects for various approaches that are available to predict binding and site of metabolism (SOM), what outcome can be expected from the predictions, and how they could potentially be improved.
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25
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Raunio H, Kuusisto M, Juvonen RO, Pentikäinen OT. Modeling of interactions between xenobiotics and cytochrome P450 (CYP) enzymes. Front Pharmacol 2015; 6:123. [PMID: 26124721 PMCID: PMC4464169 DOI: 10.3389/fphar.2015.00123] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/29/2015] [Indexed: 01/01/2023] Open
Abstract
The adverse effects to humans and environment of only few chemicals are well known. Absorption, distribution, metabolism, and excretion (ADME) are the steps of pharmaco/toxicokinetics that determine the internal dose of chemicals to which the organism is exposed. Of all the xenobiotic-metabolizing enzymes, the cytochrome P450 (CYP) enzymes are the most important due to their abundance and versatility. Reactions catalyzed by CYPs usually turn xenobiotics to harmless and excretable metabolites, but sometimes an innocuous xenobiotic is transformed into a toxic metabolite. Data on ADME and toxicity properties of compounds are increasingly generated using in vitro and modeling (in silico) tools. Both physics-based and empirical modeling approaches are used. Numerous ligand-based and target-based as well as combined modeling methods have been employed to evaluate determinants of CYP ligand binding as well as predicting sites of metabolism and inhibition characteristics of test molecules. In silico prediction of CYP–ligand interactions have made crucial contributions in understanding (1) determinants of CYP ligand binding recognition and affinity; (2) prediction of likely metabolites from substrates; (3) prediction of inhibitors and their inhibition potency. Truly predictive models of toxic outcomes cannot be created without incorporating metabolic characteristics; in silico methods help producing such information and filling gaps in experimentally derived data. Currently modeling methods are not mature enough to replace standard in vitro and in vivo approaches, but they are already used as an important component in risk assessment of drugs and other chemicals.
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Affiliation(s)
- Hannu Raunio
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland Kuopio, Finland
| | - Mira Kuusisto
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland Kuopio, Finland ; Computational Bioscience Laboratory, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä Jyväskylä, Finland
| | - Risto O Juvonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland Kuopio, Finland
| | - Olli T Pentikäinen
- Computational Bioscience Laboratory, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä Jyväskylä, Finland
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26
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Hegedüs C, Hegedüs T, Sarkadi B. The Role of ABC Multidrug Transporters in Resistance to Targeted Anticancer Kinase Inhibitors. RESISTANCE TO TARGETED ANTI-CANCER THERAPEUTICS 2015. [DOI: 10.1007/978-3-319-09801-2_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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27
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Schmidt T, Bergner A, Schwede T. Modelling three-dimensional protein structures for applications in drug design. Drug Discov Today 2014; 19:890-7. [PMID: 24216321 PMCID: PMC4112578 DOI: 10.1016/j.drudis.2013.10.027] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 10/10/2013] [Accepted: 10/31/2013] [Indexed: 12/22/2022]
Abstract
A structural perspective of drug target and anti-target proteins, and their molecular interactions with biologically active molecules, largely advances many areas of drug discovery, including target validation, hit and lead finding and lead optimisation. In the absence of experimental 3D structures, protein structure prediction often offers a suitable alternative to facilitate structure-based studies. This review outlines recent methodical advances in homology modelling, with a focus on those techniques that necessitate consideration of ligand binding. In this context, model quality estimation deserves special attention because the accuracy and reliability of different structure prediction techniques vary considerably, and the quality of a model ultimately determines its usefulness for structure-based drug discovery. Examples of G-protein-coupled receptors (GPCRs) and ADMET-related proteins were selected to illustrate recent progress and current limitations of protein structure prediction. Basic guidelines for good modelling practice are also provided.
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Affiliation(s)
- Tobias Schmidt
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
| | - Andreas Bergner
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 4056 Basel, Switzerland.
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28
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Abstract
INTRODUCTION Metabolism is one of the most important clearance pathways representing the major clearance route of 75% drugs. The four most common drug metabolizing enzymes (DME) that contribute significantly to elimination pathways of new chemical entities are cytochrome P450s, UDP-glucuronosyltransferases, aldehyde oxidase and sulfotransferases. Accurate prediction of human in vivo clearance by these enzymes, using both in vitro and in vivo tools, is critical for the success of drug candidates in human translation. AREAS COVERED Important recent advances of key DME are reviewed and highlighted in the following areas: major isoforms, tissue distribution, generic polymorphism, substrate specificity, species differences, mechanism of catalysis, in vitro-in vivo extrapolation and the importance of using optimal assay conditions and relevant animal models. EXPERT OPINION Understanding the clearance mechanism of a compound is the first step toward successful prediction of human clearance. It is critical to apply appropriate in vitro and in vivo methodologies and physiologically based models in human translation. While high-confidence prediction for P450-mediated clearance has been achieved, the accuracy of human clearance prediction is significantly lower for other enzyme classes. More accurate predictive methods and models are being developed to address these challenges.
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Affiliation(s)
- Li Di
- Pfizer, Inc., Pharmacokinetics, Dynamics and Metabolism , Groton, CT 06340 , USA +1 860 715 6172 ;
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Liu W, Liu H, Sun H, Dong D, Ma Z, Wang Y, Wu B. Metabolite elucidation of the Hsp90 inhibitor SNX-2112 using ultraperformance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS). Xenobiotica 2013; 44:455-64. [DOI: 10.3109/00498254.2013.853849] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Elens L, van Gelder T, Hesselink DA, Haufroid V, van Schaik RHN. CYP3A4*22: promising newly identified CYP3A4 variant allele for personalizing pharmacotherapy. Pharmacogenomics 2013; 14:47-62. [PMID: 23252948 DOI: 10.2217/pgs.12.187] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Many studies have attempted to explain the interindividual variability observed in drug metabolism by assessing the impact of SNPs in genes implicated in drug absorption, distribution, metabolism and excretion pathways. Particular attention has been paid to the CYP450s. CYP3A4 is the main CYP isoform in human liver and intestine and is involved in the metabolism of many drugs. Its activity, however, is characterized by widespread variation in the general population, which is thought to have a genetic basis. A new CYP3A4 allele (CYP3A4*22; rs35599367 C>T in intron 6) with a frequency of 5-7% in the Caucasian population was recently discovered through its association with low hepatic CYP3A4 expression and CYP3A4 activity, and showing effects on statin, tacrolimus and cyclosporine metabolism. This review will summarize the current literature on phenotypes linked to this new promising CYP3A4 genetic marker SNP and discusses the potential clinical relevance.
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Affiliation(s)
- Laure Elens
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, Rotterdam, The Netherlands
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Wilderman PR, Shah MB, Jang HH, Stout CD, Halpert JR. Structural and thermodynamic basis of (+)-α-pinene binding to human cytochrome P450 2B6. J Am Chem Soc 2013; 135:10433-40. [PMID: 23786449 PMCID: PMC3754432 DOI: 10.1021/ja403042k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite recent advances in atomic-level understanding of drug and inhibitor interactions with human cytochromes P450, the decades-old questions of chemical and structural determinants of hydrocarbon binding are still unanswered. (+)-α-Pinene is a monoterpene hydrocarbon that is widely distributed in the environment and a potent P450 2B inhibitor. Therefore, a combined biophysical and structural analysis of human P450 2B6 interactions with (+)-α-pinene was undertaken to elucidate the basis of the very high affinity binding. Binding of (+)-α-pinene to the P450 active site was demonstrated by a Type I spectral shift. Thermodynamics of ligand binding were explored using isothermal titration calorimetry and compared to those of P450 2A6, which is much less flexible than 2B6 based on comparison of multiple X-ray crystal structures. Consistent with expectation, entropy is the major driving force for hydrocarbon binding to P450 2A6, as evidenced by the calorimetric results. However, formation of the 2B6-(+)-α-pinene complex has a significant enthalpic component. A 2.0 Å resolution crystal structure of this enzyme-ligand complex reveals that the highly plastic 2B6 utilizes previously unrecognized rearrangements of protein motifs. The results indicate that the specific components of enthalpic contribution to ligand binding are closely tied to the degree of enzyme flexibility.
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Affiliation(s)
- P Ross Wilderman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States.
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Human cytosolic glutathione transferases: structure, function, and drug discovery. Trends Pharmacol Sci 2012; 33:656-68. [DOI: 10.1016/j.tips.2012.09.007] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 11/19/2022]
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