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Decembrino D, Cannella D. The thin line between monooxygenases and peroxygenases. P450s, UPOs, MMOs, and LPMOs: A brick to bridge fields of expertise. Biotechnol Adv 2024; 72:108321. [PMID: 38336187 DOI: 10.1016/j.biotechadv.2024.108321] [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: 10/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Many scientific fields, although driven by similar purposes and dealing with similar technologies, often appear so isolated and far from each other that even the vocabularies to describe the very same phenomenon might differ. Concerning the vast field of biocatalysis, a special role is played by those redox enzymes that employ oxygen-based chemistry to unlock transformations otherwise possible only with metal-based catalysts. As such, greener chemical synthesis methods and environmentally-driven biotechnological approaches were enabled over the last decades by the use of several enzymes and ultimately resulted in the first industrial applications. Among what can be called today the environmental biorefinery sector, biomass transformation, greenhouse gas reduction, bio-gas/fuels production, bioremediation, as well as bulk or fine chemicals and even pharmaceuticals manufacturing are all examples of fields in which successful prototypes have been demonstrated employing redox enzymes. In this review we decided to focus on the most prominent enzymes (MMOs, LPMO, P450 and UPO) capable of overcoming the ∼100 kcal mol-1 barrier of inactivated CH bonds for the oxyfunctionalization of organic compounds. Harnessing the enormous potential that lies within these enzymes is of extreme value to develop sustainable industrial schemes and it is still deeply coveted by many within the aforementioned fields of application. Hence, the ambitious scope of this account is to bridge the current cutting-edge knowledge gathered upon each enzyme. By creating a broad comparison, scientists belonging to the different fields may find inspiration and might overcome obstacles already solved by the others. This work is organised in three major parts: a first section will be serving as an introduction to each one of the enzymes regarding their structural and activity diversity, whereas a second one will be encompassing the mechanistic aspects of their catalysis. In this regard, the machineries that lead to analogous catalytic outcomes are depicted, highlighting the major differences and similarities. Finally, a third section will be focusing on the elements that allow the oxyfunctionalization chemistry to occur by delivering redox equivalents to the enzyme by the action of diverse redox partners. Redox partners are often overlooked in comparison to the catalytic counterparts, yet they represent fundamental elements to better understand and further develop practical applications based on mono- and peroxygenases.
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Affiliation(s)
- Davide Decembrino
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
| | - David Cannella
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
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2
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Amisaki T. Multilevel superposition for deciphering the conformational variability of protein ensembles. Brief Bioinform 2024; 25:bbae137. [PMID: 38557679 PMCID: PMC10983786 DOI: 10.1093/bib/bbae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/14/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
The dynamics and variability of protein conformations are directly linked to their functions. Many comparative studies of X-ray protein structures have been conducted to elucidate the relevant conformational changes, dynamics and heterogeneity. The rapid increase in the number of experimentally determined structures has made comparison an effective tool for investigating protein structures. For example, it is now possible to compare structural ensembles formed by enzyme species, variants or the type of ligands bound to them. In this study, the author developed a multilevel model for estimating two covariance matrices that represent inter- and intra-ensemble variability in the Cartesian coordinate space. Principal component analysis using the two estimated covariance matrices identified the inter-/intra-enzyme variabilities, which seemed to be important for the enzyme functions, with the illustrative examples of cytochrome P450 family 2 enzymes and class A $\beta$-lactamases. In P450, in which each enzyme has its own active site of a distinct size, an active-site motion shared universally between the enzymes was captured as the first principal mode of the intra-enzyme covariance matrix. In this case, the method was useful for understanding the conformational variability after adjusting for the differences between enzyme sizes. The developed method is advantageous in small ensemble-size problems and hence promising for use in comparative studies on experimentally determined structures where ensemble sizes are smaller than those generated, for example, by molecular dynamics simulations.
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Affiliation(s)
- Takashi Amisaki
- Department of Biological Regulation, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8503, Japan
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3
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Wang PF, Yang Y, Patel V, Neiner A, Kharasch ED. Natural Products Inhibition of Cytochrome P450 2B6 Activity and Methadone Metabolism. Drug Metab Dispos 2024; 52:252-265. [PMID: 38135504 PMCID: PMC10877711 DOI: 10.1124/dmd.123.001578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 12/24/2023] Open
Abstract
Methadone is cleared predominately by hepatic cytochrome P450 (CYP) 2B6-catalyzed metabolism to inactive metabolites. CYP2B6 also catalyzes the metabolism of several other drugs. Methadone and CYP2B6 are susceptible to pharmacokinetic drug-drug interactions. Use of natural products such as herbals and other botanicals is substantial and growing, and concomitant use of prescription medicines and non-prescription herbals is common and may result in interactions, often precipitated by CYP inhibition. Little is known about herbal product effects on CYP2B6 activity, and CYP2B6-catalyzed methadone metabolism. We screened a family of natural product compounds used in traditional medicines, herbal teas, and synthetic analogs of compounds found in plants, including kavalactones, flavokavains, chalcones and gambogic acid, for inhibition of expressed CYP2B6 activity and specifically inhibition of CYP2B6-mediated methadone metabolism. An initial screen evaluated inhibition of CYP2B6-catalyzed 7-ethoxy-4-(trifluoromethyl) coumarin O-deethylation. Hits were further evaluated for inhibition of racemic methadone metabolism, including mechanism of inhibition and kinetic constants. In order of decreasing potency, the most effective inhibitors of methadone metabolism were dihydromethysticin (competitive, K i 0.074 µM), gambogic acid (noncompetitive, K i 6 µM), and 2,2'-dihydroxychalcone (noncompetitive, K i 16 µM). Molecular modeling of CYP2B6-methadone and inhibitor binding showed substrate and inhibitor binding position and orientation and their interactions with CYP2B6 residues. These results show that CYP2B6 and CYP2B6-catalyzed methadone metabolism are inhibited by certain natural products, at concentrations which may be clinically relevant. SIGNIFICANCE STATEMENT: This investigation identified several natural product constituents which inhibit in vitro human recombinant CYP2B6 and CYP2B6-catalyzed N-demethylation of the opioid methadone. The most potent inhibitors (K i) were dihydromethysticin (0.074 µM), gambogic acid (6 µM) and 2,2'-dihydroxychalcone (16 µM). Molecular modeling of ligand interactions with CYP2B6 found that dihydromethysticin and 2,2'-dihydroxychalcone bound at the active site, while gambogic acid interacted with an allosteric site on the CYP2B6 surface. Natural product constituents may inhibit CYP2B6 and methadone metabolism at clinically relevant concentrations.
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Affiliation(s)
- Pan-Fen Wang
- Department of Anesthesiology, Duke University, Durham, North Carolina (P.-F.W., E.D.K.) and Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri (Y.Y., V.P., A.N.)
| | - Yanming Yang
- Department of Anesthesiology, Duke University, Durham, North Carolina (P.-F.W., E.D.K.) and Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri (Y.Y., V.P., A.N.)
| | - Vishal Patel
- Department of Anesthesiology, Duke University, Durham, North Carolina (P.-F.W., E.D.K.) and Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri (Y.Y., V.P., A.N.)
| | - Alicia Neiner
- Department of Anesthesiology, Duke University, Durham, North Carolina (P.-F.W., E.D.K.) and Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri (Y.Y., V.P., A.N.)
| | - Evan D Kharasch
- Department of Anesthesiology, Duke University, Durham, North Carolina (P.-F.W., E.D.K.) and Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri (Y.Y., V.P., A.N.)
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4
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Wiley AM, Yang J, Madhani R, Nath A, Totah RA. Investigating the association between CYP2J2 inhibitors and QT prolongation: a literature review. Drug Metab Rev 2024; 56:145-163. [PMID: 38478383 DOI: 10.1080/03602532.2024.2329928] [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: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Drug withdrawal post-marketing due to cardiotoxicity is a major concern for drug developers, regulatory agencies, and patients. One common mechanism of cardiotoxicity is through inhibition of cardiac ion channels, leading to prolongation of the QT interval and sometimes fatal arrythmias. Recently, oxylipin signaling compounds have been shown to bind to and alter ion channel function, and disruption in their cardiac levels may contribute to QT prolongation. Cytochrome P450 2J2 (CYP2J2) is the predominant CYP isoform expressed in cardiomyocytes, where it oxidizes arachidonic acid to cardioprotective epoxyeicosatrienoic acids (EETs). In addition to roles in vasodilation and angiogenesis, EETs bind to and activate various ion channels. CYP2J2 inhibition can lower EET levels and decrease their ability to preserve cardiac rhythm. In this review, we investigated the ability of known CYP inhibitors to cause QT prolongation using Certara's Drug Interaction Database. We discovered that among the multiple CYP isozymes, CYP2J2 inhibitors were more likely to also be QT-prolonging drugs (by approximately 2-fold). We explored potential binding interactions between these inhibitors and CYP2J2 using molecular docking and identified four amino acid residues (Phe61, Ala223, Asn231, and Leu402) predicted to interact with QT-prolonging drugs. The four residues are located near the opening of egress channel 2, highlighting the potential importance of this channel in CYP2J2 binding and inhibition. These findings suggest that if a drug inhibits CYP2J2 and interacts with one of these four residues, then it may have a higher risk of QT prolongation and more preclinical studies are warranted to assess cardiovascular safety.
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Affiliation(s)
- Alexandra M Wiley
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Jade Yang
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Rivcka Madhani
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Rheem A Totah
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
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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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Padayachee T, Lamb DC, Nelson DR, Syed K. Structure-Function Analysis of the Biotechnologically Important Cytochrome P450 107 (CYP107) Enzyme Family. Biomolecules 2023; 13:1733. [PMID: 38136604 PMCID: PMC10741444 DOI: 10.3390/biom13121733] [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: 11/03/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Cytochrome P450 monooxygenases (CYPs; P450s) are a superfamily of heme-containing enzymes that are recognized for their vast substrate range and oxidative multifunctionality. CYP107 family members perform hydroxylation and epoxidation processes, producing a variety of biotechnologically useful secondary metabolites. Despite their biotechnological importance, a thorough examination of CYP107 protein structures regarding active site cavity dynamics and key amino acids interacting with bound ligands has yet to be undertaken. To address this research knowledge gap, 44 CYP107 crystal structures were investigated in this study. We demonstrate that the CYP107 active site cavity is very flexible, with ligand binding reducing the volume of the active site in some situations and increasing volume size in other instances. Polar interactions between the substrate and active site residues result in crucial salt bridges and the formation of proton shuttling pathways. Hydrophobic interactions, however, anchor the substrate within the active site. The amino acid residues within the binding pocket influence substrate orientation and anchoring, determining the position of the hydroxylation site and hence direct CYP107's catalytic activity. Additionally, the amino acid dynamics within and around the binding pocket determine CYP107's multifunctionality. This study serves as a reference for understanding the structure-function analysis of CYP107 family members precisely and the structure-function analysis of P450 enzymes in general. Finally, this work will aid in the genetic engineering of CYP107 enzymes to produce novel molecules of biotechnological interest.
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Affiliation(s)
- Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa;
| | - David C. Lamb
- Faculty of Medicine, Health and Life Sciences, Swansea University, Swansea SA2 8PP, UK;
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa;
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7
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Liang S, Zhao W, Chen Y, Lin H, Zhang W, Deng M, Fu L, Zhong X, Zeng S, He B, Qi X, Lü M. A comparative investigation of catalytic mechanism and domain between catechol-O-methyltransferase isoforms by isomeric shikonin and alkannin. Int J Biol Macromol 2023; 242:124758. [PMID: 37150367 DOI: 10.1016/j.ijbiomac.2023.124758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/12/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
The differences in catalytic mechanism and domain between the soluble (S-COMT) and membrane-bound catechol-O-methyltransferase (MB-COMT) are poorly documented due to the unavailable crystal structure of MB-COMT. Considering the enzymatic nature of S-COMT and MB-COMT, the challenge could be solvable by probing the interactions between the enzymes with the ligands with minor differences in structures. Herein, isomeric shikonin and alkannin bearing a R/S -OH group in side chain at the C2 position were used for domain profiling of COMTs. Human and rat liver-derived COMTs showed the differences in inhibitory response (human's IC50 and Ki values for S-COMT < rat's, 5.80-19.56 vs. 19.56-37.47 μM; human's IC50 and Ki values for MB-COMT > rat's) and mechanism (uncompetition vs. noncompetition) towards the two isomers. The inhibition of the two isomers against human and rat S-COMTs was stronger than those for MB-COMTs (S-COMT's IC50 and Ki values < MB-COMT's, 5.80-37.47 vs. 40.01-111.8 μM). Additionally, the inhibition response of alkannin was higher than those of shikonin in no matter human and rat COMTs. Molecular docking stimulation was used for analysis. The inhibitory effects observed in in vitro and in silico tests were confirmed in vivo. These findings would facilitate further COMT-associated basic and applied research.
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Affiliation(s)
- Sicheng Liang
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China; Department of Dermatology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China; The Public Platform of Advanced Detecting Instruments, Public Center of Experimental Technology, Southwest Medical University, Luzhou 646000, China; Human Microecology and Precision Diagnosis and Treatment of Luzhou Key Laboratory, Luzhou 646000, China; Cardiovascular and Metabolic Diseases of Sichuan Key Laboratory, Luzhou 646000, China
| | - Wenjing Zhao
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Yonglan Chen
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Hua Lin
- Technology Center of Chengdu Customs, Chengdu, China
| | - Wei Zhang
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Mingming Deng
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Lu Fu
- The Public Platform of Advanced Detecting Instruments, Public Center of Experimental Technology, Southwest Medical University, Luzhou 646000, China
| | - Xiaolin Zhong
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang University, Hangzhou, China
| | - Bing He
- The Public Platform of Advanced Detecting Instruments, Public Center of Experimental Technology, Southwest Medical University, Luzhou 646000, China
| | - Xiaoyi Qi
- Department of Dermatology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China.
| | - Muhan Lü
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China; Human Microecology and Precision Diagnosis and Treatment of Luzhou Key Laboratory, Luzhou 646000, China; Cardiovascular and Metabolic Diseases of Sichuan Key Laboratory, Luzhou 646000, China.
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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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Gadgoli UB, Sunil Kumar YC, Kumar D. An Insight into the Metabolism of 2,5-Disubstituted Monotetrazole Bearing Bisphenol Structures: Emerging Bisphenol A Structural Congeners. Molecules 2023; 28:molecules28031465. [PMID: 36771130 PMCID: PMC9921896 DOI: 10.3390/molecules28031465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
The non-estrogenic 2,5-disubstituted tetrazole core-bearing bisphenol structures (TbB) are being researched as emerging structural congeners of Bisphenol A, an established industrial endocrine disruptor. However, there is no understanding of TbB's adverse effects elicited via metabolic activation. Therefore, the current study aimed to investigate the metabolism of TbB ligands, with in silico results serving as a guide for in vitro studies. The Cytochrome P450 enzymes (CYP) inhibitory assay of TbB ligands on the seven human liver CYP isoforms (i.e., 1A2, 2A6, 2D6, 2C9, 2C8, 2C19, and 3A4) using human liver microsomes (HLM) revealed TbB ligand 223-3 to have a 50% inhibitory effect on all the CYP isoforms at a 10 μM concentration, except 1A2. The TbB ligand 223-10 inhibited 2B6 and 2C8, whereas the TbB ligand 223-2 inhibited only 2C9. The first-order inactivity rate constant (Kobs) studies indicated TbB ligands 223-3, 223-10 to be time-dependent (TD) inhibitors, whereas the TbB 223-2 ligand did not show such a significant effect. The 223-3 exhibited a TD inhibition for 2C9, 2C19, and 1A2 with Kobs values of 0.0748, 0.0306, and 0.0333 min-1, respectively. On the other hand, the TbB ligand 223-10 inhibited 2C9 in a TD inhibition manner with Kobs value 0.0748 min-1. However, the TbB ligand 223-2 showed no significant TD inhibition effect on the CYPs. The 223-2 ligand biotransformation pathway by in vitro studies in cryopreserved human hepatocytes suggested the clearance via glucuronidation with the predominant detection of only 223-2 derived mono glucuronide as a potential inactive metabolite. The present study demonstrated that the 223-2 ligand did not elicit any significant adverse effect via metabolic activation, thus paving the way for its in vivo drug-drug interactions (DDI) studies.
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Affiliation(s)
- Umesh B. Gadgoli
- Department of Chemistry, M.S. Ramaiah University of Applied Sciences, Bengaluru 560054, Karnataka, India
- Correspondence:
| | - Yelekere C. Sunil Kumar
- Dayanada Sagar Academy of Technology and Management, Kanakapura Rd, Opp. Art of Living International Centre, Udaypura, Bengaluru 560082, Karnataka, India
| | - Deepak Kumar
- Department of Chemistry, M.S. Ramaiah University of Applied Sciences, Bengaluru 560054, Karnataka, India
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Devine AJ, Parnell AE, Back CR, Lees NR, Johns ST, Zulkepli AZ, Barringer R, Zorn K, Stach JEM, Crump MP, Hayes MA, van der Kamp MW, Race PR, Willis CL. The Role of Cytochrome P450 AbyV in the Final Stages of Abyssomicin C Biosynthesis. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202213053. [PMID: 38516347 PMCID: PMC10952897 DOI: 10.1002/ange.202213053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Indexed: 03/23/2024]
Abstract
Abyssomicin C and its atropisomer are potent inhibitors of bacterial folate metabolism. They possess complex polycyclic structures, and their biosynthesis has been shown to involve several unusual enzymatic transformations. Using a combination of synthesis and in vitro assays we reveal that AbyV, a cytochrome P450 enzyme from the aby gene cluster, catalyses a key late-stage epoxidation required for the installation of the characteristic ether-bridged core of abyssomicin C. The X-ray crystal structure of AbyV has been determined, which in combination with molecular dynamics simulations provides a structural framework for our functional data. This work demonstrates the power of combining selective carbon-13 labelling with NMR spectroscopy as a sensitive tool to interrogate enzyme-catalysed reactions in vitro with no need for purification.
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Affiliation(s)
| | | | | | | | | | | | - Rob Barringer
- School of BiochemistryUniversity of BristolBS81TDBristolUK
| | - Katja Zorn
- BioPharmaceuticals R&DAstraZenecaPepparedsleden 143183MölndalSweden
| | - James E. M. Stach
- School of Natural and Environmental SciencesNewcastle UniversityNE17RUNewcastle-upon-TyneUK
| | | | - Martin A. Hayes
- BioPharmaceuticals R&DAstraZenecaPepparedsleden 143183MölndalSweden
| | | | - Paul R. Race
- School of BiochemistryUniversity of BristolBS81TDBristolUK
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11
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Devine AJ, Parnell AE, Back CR, Lees NR, Johns ST, Zulkepli AZ, Barringer R, Zorn K, Stach JEM, Crump MP, Hayes MA, van der Kamp MW, Race PR, Willis CL. The Role of Cytochrome P450 AbyV in the Final Stages of Abyssomicin C Biosynthesis. Angew Chem Int Ed Engl 2023; 62:e202213053. [PMID: 36314667 PMCID: PMC10107801 DOI: 10.1002/anie.202213053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/16/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Abyssomicin C and its atropisomer are potent inhibitors of bacterial folate metabolism. They possess complex polycyclic structures, and their biosynthesis has been shown to involve several unusual enzymatic transformations. Using a combination of synthesis and in vitro assays we reveal that AbyV, a cytochrome P450 enzyme from the aby gene cluster, catalyses a key late-stage epoxidation required for the installation of the characteristic ether-bridged core of abyssomicin C. The X-ray crystal structure of AbyV has been determined, which in combination with molecular dynamics simulations provides a structural framework for our functional data. This work demonstrates the power of combining selective carbon-13 labelling with NMR spectroscopy as a sensitive tool to interrogate enzyme-catalysed reactions in vitro with no need for purification.
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Affiliation(s)
- Andrew J Devine
- School of Chemistry, University of Bristol, BS81TS, Bristol, UK
| | - Alice E Parnell
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Catherine R Back
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Nicholas R Lees
- School of Chemistry, University of Bristol, BS81TS, Bristol, UK
| | - Samuel T Johns
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Ainul Z Zulkepli
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Rob Barringer
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Katja Zorn
- BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University, NE17RU, Newcastle-upon-Tyne, UK
| | - Matthew P Crump
- School of Chemistry, University of Bristol, BS81TS, Bristol, UK
| | - Martin A Hayes
- BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | | | - Paul R Race
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
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12
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Manthalkar L, Bhattacharya S. Evidence-based capacity of natural cytochrome enzyme inhibitors to increase the effectivity of antineoplastic drugs. Discov Oncol 2022; 13:142. [PMID: 36571647 PMCID: PMC9792636 DOI: 10.1007/s12672-022-00605-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/14/2022] [Indexed: 12/27/2022] Open
Abstract
Cytochrome (CYP) enzymes catalyze the metabolism of numerous exogenous and endogenous substrates in cancer therapy leading to significant drug interactions due to their metabolizing effect. CYP enzymes play an important role in the metabolism of essential anticancer medications. They are shown to be overexpressed in tumor cells at numerous locations in the body. This overexpression could be a result of lifestyle factors, presence of hereditary variants of CYP (Bio individuality) and multi-drug resistance. This finding has sparked an interest in using CYP inhibitors to lower their metabolizing activity as a result facilitating anti-cancer medications to have a therapeutic impact. As a result of the cytotoxic nature of synthetic enzyme inhibitors and the increased prevalence of herbal medication, natural CYP inhibitors have been identified as an excellent way to inhibit overexpression sighting their tendency to show less cytotoxicity, lesser adverse drug reactions and enhanced bioavailability. Nonetheless, their effect of lowering the hindrance caused in chemotherapy due to CYP enzymes remains unexploited to its fullest. It has been observed that there is a substantial decrease in first pass metabolism and increase in intestinal absorption of chemotherapeutic drugs like paclitaxel when administered along with flavonoids which help suppress certain specific cytochrome enzymes which play a role in paclitaxel metabolism. This review elaborates on the role and scope of phytochemicals in primary, secondary and tertiary care and how targeted prevention of cancer could be a breakthrough in the field of chemotherapy and oncology. This opens up a whole new area of research for delivery of these natural inhibitors along with anticancer drugs with the help of liposomes, micelles, nanoparticles, the usage of liquid biopsy analysis, artificial intelligence in medicine, risk assessment tools, multi-omics and multi-parametric analysis. Further, the site of action, mechanisms, metabolites involved, experimental models, doses and observations of two natural compounds, quercetin & thymoquinone, and two plant extracts, liquorice & garlic on CYP enzymes have been summarized.
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Affiliation(s)
- Laxmi Manthalkar
- Department of Pharmaceutics, School of Pharmacy & Technology Management, SVKM'S NMIMS Deemed-to-be University, Shirpur, 425405, Maharashtra, India
| | - Sankha Bhattacharya
- Department of Pharmaceutics, School of Pharmacy & Technology Management, SVKM'S NMIMS Deemed-to-be University, Shirpur, 425405, Maharashtra, India.
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13
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Qiu M, Liang X, Deng S, Li Y, Ke Y, Wang P, Mei H. A unified GCNN model for predicting CYP450 inhibitors by using graph convolutional neural networks with attention mechanism. Comput Biol Med 2022; 150:106177. [PMID: 36242811 DOI: 10.1016/j.compbiomed.2022.106177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/19/2022] [Accepted: 10/01/2022] [Indexed: 11/17/2022]
Abstract
Undesirable drug-drug interactions (DDIs) may lead to serious adverse side effects when more than two drugs are administered to a patient simultaneously. One of the most common DDIs is caused by unexpected inhibition of a specific human cytochrome P450 (CYP450), which plays a dominant role in the metabolism of the co-administered drugs. Therefore, a unified and reliable method for predicting the potential inhibitors of CYP450 family is extremely important in drug development. In this work, graph convolutional neural network (GCN) with attention mechanism and 1-D convolutional neural network (CNN) were used to extract the features of CYP ligands and the binding sites of CYP450 respectively, which were then combined to establish a unified GCN-CNN (GCNN) model for predicting the inhibitors of 5 dominant CYP isoforms, i.e., 1A2, 2C9, 2C19, 2D6, and 3A4. Overall, the established GCNN model showed good performances on the test samples and achieved better performances than the recently proposed iCYP-MFE model by using the same datasets. Based on the heat-map analysis of the resulting molecular graphs, the key structural determinants of the CYP inhibitors were further explored.
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Affiliation(s)
- Minyao Qiu
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing, 400044, China; College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Xiaoqi Liang
- College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Siyao Deng
- College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Yufang Li
- College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Yanlan Ke
- College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Pingqing Wang
- College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Hu Mei
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing, 400044, China; College of Bioengineering, Chongqing University, Chongqing, 400044, China.
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14
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Wang PF, Sharma A, Montana M, Neiner A, Juriga L, Reddy KN, Tallchief D, Blood J, Kharasch ED. Methadone pharmacogenetics in vitro and in vivo: Metabolism by CYP2B6 polymorphic variants and genetic variability in paediatric disposition. Br J Clin Pharmacol 2022; 88:4881-4893. [PMID: 35538637 PMCID: PMC10908252 DOI: 10.1111/bcp.15393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 04/06/2022] [Accepted: 04/22/2022] [Indexed: 11/02/2022] Open
Abstract
AIMS Methadone metabolism and clearance are determined principally by polymorphic cytochrome P4502B6 (CYP2B6). Some CYP2B6 allelic variants affect methadone metabolism in vitro and disposition in vivo. We assessed methadone metabolism by CYP2B6 minor variants in vitro. We also assessed the influence of CYP2B6 variants, and P450 oxidoreductase (POR) and CYP2C19 variants, on methadone clearance in surgical patients in vivo. METHODS CYP2B6 and P450 oxidoreductase variants were coexpressed with cytochrome b5 . The metabolism of methadone racemate and enantiomers was measured at therapeutic concentrations and intrinsic clearances were determined. Adolescents receiving methadone for surgery were genotyped for CYP2B6, CYP2C19 and POR, and methadone clearance and metabolite formation clearance were determined. RESULTS In vitro, CYP2B6.4 was more active than wild-type CYP2B6.1. CYPs 2B6.5, 2B6.6, 2B6.7, 2B6.9, 2B6.17, 2B6.19 and 2B6.26 were less active. CYPs 2B6.16 and 2B6.18 were inactive. CYP2B6.1 expressed with POR variants POR.28, POR.5 and P228L had lower rates of methadone metabolism than wild-type reductase. In vivo, methadone clinical clearance decreased linearly with the number of CYP2B6 slow metabolizer alleles, but was not different in CYP2C19 slow or rapid metabolizer phenotypes, or in carriers of the POR*28 allele. CONCLUSIONS Several CYP2B6 and POR variants were slow metabolizers of methadone in vitro. Polymorphisms in CYP2B6, but not CYP2C19 or P450 reductase, affected methadone clearance in vivo. CYP2B6 polymorphisms 516G>T and 983T>C code for canonical loss of function variants and should be assessed when considering genetic influences on clinical methadone disposition. These complementary translational in vitro and in vivo results inform on pharmacogenetic variability affecting methadone disposition in patients.
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Affiliation(s)
- Pan-Fen Wang
- Department of Anesthesiology, Duke University, Durham, NC, USA
| | - Anshuman Sharma
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
| | - Michael Montana
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alicia Neiner
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Kavya Narayana Reddy
- Department of Pediatric Anesthesiology, Arkansas Children's Hospital, Little Rock, AK, USA
| | - Dani Tallchief
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jane Blood
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Evan D Kharasch
- Department of Anesthesiology, Duke University, Durham, NC, USA
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15
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Feng L, Tian X, Yao D, Yu Z, Huo X, Tian Z, Ning J, Cui J, James TD, Ma X. A practical strategy to develop isoform-selective near-infrared fluorescent probes for human cytochrome P450 enzymes. Acta Pharm Sin B 2022; 12:1976-1986. [PMID: 35847500 PMCID: PMC9279627 DOI: 10.1016/j.apsb.2021.11.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 01/08/2023] Open
Affiliation(s)
- Lei Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116023, China
- College of Pharmacy, the National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, Dalian Medical University, Dalian 116044, China
| | - Xiangge Tian
- College of Pharmacy, the National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, Dalian Medical University, Dalian 116044, China
| | - Dahong Yao
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen 518060, China
| | - Zhenlong Yu
- College of Pharmacy, the National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, Dalian Medical University, Dalian 116044, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian 116023, China
- College of Pharmacy, the National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, Dalian Medical University, Dalian 116044, China
| | - Zhenhao Tian
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Jing Ning
- College of Pharmacy, the National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, Dalian Medical University, Dalian 116044, China
- Corresponding authors. Tel.: +86 411 86110419.
| | - Jingnan Cui
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Tony D. James
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian 116023, China
- College of Pharmacy, the National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, Dalian Medical University, Dalian 116044, China
- Corresponding authors. Tel.: +86 411 86110419.
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16
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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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17
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Wang Z, Paragas EM, Nagar S, Korzekwa K. Complex Cytochrome P450 Kinetics Due to Multisubstrate Binding and Sequential Metabolism. Part 1. Theoretical Considerations. Drug Metab Dispos 2021; 49:1090-1099. [PMID: 34503952 PMCID: PMC11022900 DOI: 10.1124/dmd.121.000553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/06/2021] [Indexed: 11/22/2022] Open
Abstract
Complexities in P450-mediated metabolism kinetics include multisubstrate binding, multiple-product formation, and sequential metabolism. Saturation curves and intrinsic clearances were simulated for single-substrate and multisubstrate models using derived velocity equations and numerical solutions of ordinary differential equations (ODEs). Multisubstrate models focused on sigmoidal kinetics because of their dramatic impact on clearance predictions. These models were combined with multiple-product formation and sequential metabolism, and simulations were performed with random error. Use of single-substrate models to characterize multisubstrate data can result in inaccurate kinetic parameters and poor clearance predictions. Comparing results for use of standard velocity equations with ODEs clearly shows that ODEs are more versatile and provide better parameter estimates. It would be difficult to derive concentration-velocity relationships for complex models, but these relationships can be easily modeled using numerical methods and ODEs. SIGNIFICANCE STATEMENT: The impact of multisubstrate binding, multiple-product formation, and sequential metabolism on the P450 kinetics was investigated. Numerical methods are capable of characterizing complicated P450 kinetics.
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Affiliation(s)
- Zeyuan Wang
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Erickson M Paragas
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Swati Nagar
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
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18
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Massively parallel characterization of CYP2C9 variant enzyme activity and abundance. Am J Hum Genet 2021; 108:1735-1751. [PMID: 34314704 DOI: 10.1016/j.ajhg.2021.07.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/28/2021] [Indexed: 12/19/2022] Open
Abstract
CYP2C9 encodes a cytochrome P450 enzyme responsible for metabolizing up to 15% of small molecule drugs, and CYP2C9 variants can alter the safety and efficacy of these therapeutics. In particular, the anti-coagulant warfarin is prescribed to over 15 million people annually and polymorphisms in CYP2C9 can affect individual drug response and lead to an increased risk of hemorrhage. We developed click-seq, a pooled yeast-based activity assay, to test thousands of variants. Using click-seq, we measured the activity of 6,142 missense variants in yeast. We also measured the steady-state cellular abundance of 6,370 missense variants in a human cell line by using variant abundance by massively parallel sequencing (VAMP-seq). These data revealed that almost two-thirds of CYP2C9 variants showed decreased activity and that protein abundance accounted for half of the variation in CYP2C9 function. We also measured activity scores for 319 previously unannotated human variants, many of which may have clinical relevance.
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19
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Bin Jardan YA, Ahad A, Raish M, Ahmad A, Alam MA, Al-Mohizea AM, Al-Jenoobi FI. Assessment of glibenclamide pharmacokinetics in poloxamer 407-induced hyperlipidemic rats. Saudi Pharm J 2021; 29:719-723. [PMID: 34400867 PMCID: PMC8347666 DOI: 10.1016/j.jsps.2021.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
The aim of the present research was to describe the consequences of hyperlipidemia (HL) on the pharmacokinetics of glibenclamide (Gb) in poloxamer 407-induced hyperlipidemic rats. Rats were given intraperitoneal dose of poloxamer 407 to cause hyperlipidemia. A single oral dose of Gb (10 mg/Kg) was given to normal and HL rats. The Cmax and tmax after oral dose of Gb in normal rats were 340.10 µg/ml and 3.67 h, respectively. Whereas, the Cmax and tmax after oral dose of Gb in HL rats were noted as 773.39 µg/ml and 2.50 h respectively. The AUC value of Gb was found considerably higher in the HL rats. While the plasma clearance (CL) after oral dose of Gb was 2.53 ml/h and 1.39 ml/h in normal and HL rats respectively. The improved plasma concentration of Gb following oral dosing in rats with HL seems to be due to a direct influence on hepatic clearance or metabolizing enzymes. In conclusion, the Gb pharmacokinetics was considerably affected by the HL in rats. Such findings play an important role for predicting the alterations in the pharmacokinetics of drugs including GB, in cases having hyperlipidemia.
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Affiliation(s)
- Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
- Corresponding author.
| | - Abdul Ahad
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohammad Raish
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Ajaz Ahmad
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohd Aftab Alam
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Abdullah M. Al-Mohizea
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Fahad I. Al-Jenoobi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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20
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Functional Characterization of 21 Rare Allelic CYP1A2 Variants Identified in a Population of 4773 Japanese Individuals by Assessing Phenacetin O-Deethylation. J Pers Med 2021; 11:jpm11080690. [PMID: 34442334 PMCID: PMC8401128 DOI: 10.3390/jpm11080690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022] Open
Abstract
Cytochrome P450 1A2 (CYP1A2), which accounts for approximately 13% of the total hepatic cytochrome content, catalyzes the metabolic reactions of approximately 9% of frequently used drugs, including theophylline and olanzapine. Substantial inter-individual differences in enzymatic activity have been observed among patients, which could be caused by genetic polymorphisms. Therefore, we functionally characterized 21 novel CYP1A2 variants identified in 4773 Japanese individuals by determining the kinetic parameters of phenacetin O-deethylation. Our results showed that most of the evaluated variants exhibited decreased or no enzymatic activity, which may be attributed to potential structural alterations. Notably, the Leu98Gln, Gly233Arg, Ser380del Gly454Asp, and Arg457Trp variants did not exhibit quantifiable enzymatic activity. Additionally, three-dimensional (3D) docking analyses were performed to further understand the underlying mechanisms behind variant pharmacokinetics. Our data further suggest that despite mutations occurring on the protein surface, accumulating interactions could result in the impairment of protein function through the destabilization of binding regions and changes in protein folding. Therefore, our findings provide additional information regarding rare CYP1A2 genetic variants and how their underlying effects could clarify discrepancies noted in previous phenotypical studies. This would allow the improvement of personalized therapeutics and highlight the importance of identifying and characterizing rare variants.
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21
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A Physiologically Based Pharmacokinetic and Drug-Drug Interaction Model for the CB2 Agonist Lenabasum. Eur J Drug Metab Pharmacokinet 2021; 46:513-525. [PMID: 34143391 DOI: 10.1007/s13318-021-00693-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND AND OBJECTIVES Lenabasum is a synthetic agonist of the cannabinoid receptor type 2 (CB2) with anti-inflammatory and antifibrotic properties. Utilizing Simcyp, we developed a physiologically based pharmacokinetic (PBPK) model based on physicochemical properties, cell culture data, and cytochrome P450 (CYP) phenotyping, inhibition, and induction data. METHODS Clinical data from healthy volunteers treated with 20 mg of lenabasum in a single ascending dose (SAD) study were used for model development. The model was verified using lenabasum SAD (10 and 40 mg) data as well as multiple dose (20 mg three times per day) data. Lenabasum is a CYP substrate, and the model predicted lenabasum clearance of 51% by CYP2C9, 37% by CYP2C8, and 12% by CYP3A4. Lenabasum is also an inhibitor of these isozymes. RESULTS The model accurately described the area under the plasma concentration-time curve (AUC) and maximum plasma concentration (Cmax) for lenabasum within 1.19-fold and 1.25-fold accuracy, respectively, of the observed clinical values. The simulations of CYP inducers predicted that the strongest interaction would occur with rifampin, with the AUC decreasing to 0.36 of the control value, whereas the simulations of CYP inhibitors predicted that the greatest effect would occur with fluconazole, with a 1.43-fold increase in AUC. CONCLUSIONS Our model is a useful tool for predicting the pharmacokinetics of lenabasum and adjustments to its dosing in possible drug-drug interaction scenarios.
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22
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Feng L, Ning J, Tian X, Wang C, Yu Z, Huo X, Xie T, Zhang B, James TD, Ma X. Fluorescent probes for the detection and imaging of Cytochrome P450. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213740] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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23
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Descriptors of Cytochrome Inhibitors and Useful Machine Learning Based Methods for the Design of Safer Drugs. Pharmaceuticals (Basel) 2021; 14:ph14050472. [PMID: 34067565 PMCID: PMC8156202 DOI: 10.3390/ph14050472] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/16/2022] Open
Abstract
Roughly 2.8% of annual hospitalizations are a result of adverse drug interactions in the United States, representing more than 245,000 hospitalizations. Drug-drug interactions commonly arise from major cytochrome P450 (CYP) inhibition. Various approaches are routinely employed in order to reduce the incidence of adverse interactions, such as altering drug dosing schemes and/or minimizing the number of drugs prescribed; however, often, a reduction in the number of medications cannot be achieved without impacting therapeutic outcomes. Nearly 80% of drugs fail in development due to pharmacokinetic issues, outlining the importance of examining cytochrome interactions during preclinical drug design. In this review, we examined the physiochemical and structural properties of small molecule inhibitors of CYPs 3A4, 2D6, 2C19, 2C9, and 1A2. Although CYP inhibitors tend to have distinct physiochemical properties and structural features, these descriptors alone are insufficient to predict major cytochrome inhibition probability and affinity. Machine learning based in silico approaches may be employed as a more robust and accurate way of predicting CYP inhibition. These various approaches are highlighted in the review.
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24
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Chen J, Liu J, Huang Y, Li R, Ma C, Zhang B, Wu F, Yu W, Zuo X, Liang Y, Wang Q. Insights into oral bioavailability enhancement of therapeutic herbal constituents by cytochrome P450 3A inhibition. Drug Metab Rev 2021; 53:491-507. [PMID: 33905669 DOI: 10.1080/03602532.2021.1917598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Herbal plants typically have complex compositions and diverse mechanisms. Among them, bioactive constituents with relatively high exposure in vivo are likely to exhibit therapeutic efficacy. On the other hand, their bioavailability may be influenced by the synergistic effects of different bioactive components. Cytochrome P450 3A (CYP3A) is one of the most abundant CYP enzymes, responsible for the metabolism of 50% of approved drugs. In recent years, many therapeutic herbal constituents have been identified as CYP3A substrates. It is more evident that CYP3A inhibition derived from the herbal formula plays a critical role in improving the oral bioavailability of therapeutic constituents. CYP3A inhibition may be the mechanism of the synergism of herbal formula. In this review, we explored the multiplicity of CYP3A, summarized herbal monomers with CYP3A inhibitory effects, and evaluated herb-mediated CYP3A inhibition, thereby providing new insights into the mechanisms of CYP3A inhibition-mediated oral herb bioavailability.
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Affiliation(s)
- Junmei Chen
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jinman Liu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yueyue Huang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ruoyu Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Cuiru Ma
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Beiping Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fanchang Wu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wenqian Yu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xue Zuo
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yong Liang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
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Paroxetine-Overview of the Molecular Mechanisms of Action. Int J Mol Sci 2021; 22:ijms22041662. [PMID: 33562229 PMCID: PMC7914979 DOI: 10.3390/ijms22041662] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/31/2021] [Accepted: 02/04/2021] [Indexed: 12/20/2022] Open
Abstract
In the 21st century and especially during a pandemic, the diagnosis and treatment of depression is an essential part of the daily practice of many family doctors. It mainly affects patients in the age category 15–44 years, regardless of gender. Anxiety disorders are often diagnosed in children and adolescents. Social phobias can account for up to 13% of these diagnoses. Social anxiety manifests itself in fear of negative social assessment and humiliation, which disrupts the quality of social functioning. Treatment of the above-mentioned disorders is based on psychotherapy and pharmacotherapy. Serious side effects or mortality from antidepressant drug overdose are currently rare. Recent studies indicate that paroxetine (ATC code: N06AB), belonging to the selective serotonin reuptake inhibitors, has promising therapeutic effects and is used off-label in children and adolescents. The purpose of this review is to describe the interaction of paroxetine with several molecular targets in various points of view including the basic chemical and pharmaceutical properties. The central point of the review is focused on the pharmacodynamic analysis based on the molecular mechanism of binding paroxetine to various therapeutic targets.
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26
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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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27
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Molecular determinant of substrate binding and specificity of cytochrome P450 2J2. Sci Rep 2020; 10:22267. [PMID: 33335233 PMCID: PMC7746748 DOI: 10.1038/s41598-020-79284-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022] Open
Abstract
Cytochrome P450 2J2 (CYP2J2) is responsible for the epoxidation of endogenous arachidonic acid, and is involved in the metabolism of exogenous drugs. To date, no crystal structure of CYP2J2 is available, and the proposed structural basis for the substrate recognition and specificity in CYP2J2 varies with the structural models developed using different computational protocols. In this study, we developed a new structural model of CYP2J2, and explored its sensitivity to substrate binding by molecular dynamics simulations of the interactions with chemically similar fluorescent probes. Our results showed that the induced-fit binding of these probes led to the preferred active poses ready for the catalysis by CYP2J2. Divergent conformational dynamics of CYP2J2 due to the binding of each probe were observed. However, a stable hydrophobic clamp composed of residues I127, F310, A311, V380, and I487 was identified to restrict any substrate access to the active site of CYP2J2. Molecular docking of a series of compounds including amiodarone, astemizole, danazol, ebastine, ketoconazole, terfenadine, terfenadone, and arachidonic acid to CYP2J2 confirmed the role of those residues in determining substrate binding and specificity of CYP2J2. In addition to the flexibility of CYP2J2, the present work also identified other factors such as electrostatic potential in the vicinity of the active site, and substrate strain energy and property that have implications for the interpretation of CYP2J2 metabolism.
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28
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Dixit VA, Warwicker J, Visser SP. How Do Metal Ions Modulate the Rate‐Determining Electron‐Transfer Step in Cytochrome P450 Reactions? Chemistry 2020; 26:15270-15281. [DOI: 10.1002/chem.202003024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmacy Birla Institute of Technology and Sciences Pilani (BITS-Pilani) Vidya Vihar Campus 41 Pilani 333031 Rajasthan India
| | - Jim Warwicker
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M17DN United Kingdom
- Department of Chemistry The University of Manchester Oxford Road Manchester M139PL United Kingdom
| | - Sam P. Visser
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M17DN United Kingdom
- Department of Chemical Engineering and Analytical Science The University of Manchester Oxford Road Manchester M13 9PL United Kingdom
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29
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Li J, Zhou Y, Tang Y, Li W, Tu Y. Dissecting the Structural Plasticity and Dynamics of Cytochrome P450 2B4 by Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:5026-5035. [PMID: 32808774 DOI: 10.1021/acs.jcim.0c00482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The plasticity of cytochromes P450 (P450s) is known to contribute significantly to their catalytic capacity of metabolizing various substrates. Although numerous studies have been performed, factors governing the plasticity and dynamics of P450s are still not fully understood. In this study, taking CYP2B4 as an example, we dissect the protein plasticity and dynamics in different environments. CYP2B4 is featured by a high degree of plasticity, which exhibits open, closed, and intermediate states. By analyzing the CYP2B4 crystal structures, we identified the structural features for the closed, open, and intermediate states. Interestingly, formation of the dimer structure was found in the open and intermediate states. The subsequent molecular dynamics (MD) simulations of the open structure in water confirmed the importance of the dimer form in stabilizing the open conformations. MD simulations of the closed and open structures in the membrane environment and the free energies for opening the F-G cassette obtained from the umbrella sampling calculations indicate that the membrane environment is important for stabilizing the F-G cassette. The dynamical network analysis indicates that Asp105 on the B-C loop plays an important role in transiting the structure from the open to the intermediate state. Our results thus unveil the mechanisms of dimer formation and open-to-intermediate transition for CYP2B4 in the water and membrane environments.
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Affiliation(s)
- Junhao Li
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Yang Zhou
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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30
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β-Naphthoflavone and Ethanol Reverse Mitochondrial Dysfunction in A Parkinsonian Model of Neurodegeneration. Int J Mol Sci 2020; 21:ijms21113955. [PMID: 32486438 PMCID: PMC7312836 DOI: 10.3390/ijms21113955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/29/2020] [Accepted: 05/30/2020] [Indexed: 12/04/2022] Open
Abstract
The 1-methyl-4-phenylpyridinium (MPP+) is a parkinsonian-inducing toxin that promotes neurodegeneration of dopaminergic cells by directly targeting complex I of mitochondria. Recently, it was reported that some Cytochrome P450 (CYP) isoforms, such as CYP 2D6 or 2E1, may be involved in the development of this neurodegenerative disease. In order to study a possible role for CYP induction in neurorepair, we designed an in vitro model where undifferentiated neuroblastoma SH-SY5Y cells were treated with the CYP inducers β-naphthoflavone (βNF) and ethanol (EtOH) before and during exposure to the parkinsonian neurotoxin, MPP+. The toxic effect of MPP+ in cell viability was rescued with both βNF and EtOH treatments. We also report that this was due to a decrease in reactive oxygen species (ROS) production, restoration of mitochondrial fusion kinetics, and mitochondrial membrane potential. These treatments also protected complex I activity against the inhibitory effects caused by MPP+, suggesting a possible neuroprotective role for CYP inducers. These results bring new insights into the possible role of CYP isoenzymes in xenobiotic clearance and central nervous system homeostasis.
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31
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Modification of the lead molecule: Tryptophan and piperidine appended triazines reversing inflammation and hyeperalgesia in rats. Bioorg Med Chem 2020; 28:115246. [PMID: 31843462 DOI: 10.1016/j.bmc.2019.115246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/23/2019] [Accepted: 11/29/2019] [Indexed: 11/20/2022]
Abstract
The structural optimization of the molecules making them to fit into the active site pocket of COX-2 occupying the same space as covered by the natural substrate arachidonic acid helped in the emergence of compound 10 as an efficacious anti-inflammatory agent. Selective for COX-2 over COX-1, compound 10 exhibited IC50 0.02 µM for COX-2 and reversed acetic acid induced inflammation in rats by 73% when used at 10 mg kg-1 dose and the same dose of the compound also rescued the animals from inflammatory phase of formalin induced hyperalgesia. As evidenced by the results of molecular modeling studies supported by the nuclear Overhauser enhancement data, the appropriate geometry of the molecule in the active site pocket of COX-2 contributing to its H-bond/hydrophobic interactions with Ser530, Trp387 and Tyr385 seems responsible for the enzyme inhibitory activity of the compound.
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32
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33
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Wang PF, Neiner A, Kharasch ED. Efavirenz Metabolism: Influence of Polymorphic CYP2B6 Variants and Stereochemistry. Drug Metab Dispos 2019; 47:1195-1205. [PMID: 31324697 DOI: 10.1124/dmd.119.086348] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/10/2019] [Indexed: 01/11/2023] Open
Abstract
Efavirenz (more specifically the S-enantiomer) is a cornerstone antiretroviral therapy for treatment of HIV infection. The major primary metabolite is S-8-hydroxyefavirenz, which does not have antiretroviral activity but is neurotoxic. Cytochrome P450 2B6 (CYP2B6) is the major enzyme catalyzing S-8-hydroxyefavirenz formation. CYP2B6 genetics and drug interactions are major determinants of clinical efavirenz disposition and dose adjustment. In addition, as a prototypic CYP2B6 substrate, S-efavirenz and analogs can inform on the structure, activity, catalytic mechanisms, and stereoselectivity of CYP2B6. Metabolism of R-efavirenz by CYP2B6 remains unexplored. This investigation assessed S-efavirenz metabolism by clinically relevant CYP2B6 genetic variants. This investigation also evaluated R-efavirenz hydroxylation by wild-type CYP2B6.1 and CYP2B6 variants. S-Efavirenz 8-hydroxylation by wild-type CYP2B6.1 and variants exhibited positive cooperativity and apparent cooperative substrate inhibition. On the basis of Clmax values, relative activities for S-efavirenz 8-hydroxylation were in the order CYP2B6.4 > CYP2B6.1 ≈ CYP2B6.5 ≈ CYP2B6.17 > CYP2B6.6 ≈ CYP2B6.7 ≈ CYP2B6.9 ≈ CYP2B6.19 ≈ CYP2B6.26; CYP2B6.16 and CYP2B6.18 showed minimal activity. Rates of R-efavirenz metabolism were approximately 1/10 those of S-efavirenz for wild-type CYP2B6.1 and variants. On the basis of Clmax values, there was 14-fold enantioselectivity (S > R-efavirenz) for wild-type CYP2B6.1, and 5- to 22-fold differences for other CYP2B6 variants. These results show that both CYP2B6 516G > T (CYP2B6*6 and CYP2B6*9) and 983T > C (CYP2B6*16 and CYP2B6*18) polymorphisms cause canonical diminishment or loss-of-function variants for S-efavirenz 8-hydroxylation, provide a mechanistic basis for known clinical pharmacogenetic differences in efavirenz disposition, and may predict additional clinically important variant alleles. Efavirenz is the most stereoselective CYP2B6 drug substrate yet identified and may be a useful probe for the CYP2B6 active site and catalytic mechanisms. SIGNIFICANCE STATEMENT: Clinical disposition of the antiretroviral S-efavirenz is affected by CYP2B6 polymorphisms. Expressed CYP2B6 with 516G>T (CYP2B6*6 and CYP2B6*9), and 983T>C (CYP2B6*16 and CYP2B6*18) polymorphisms had a diminishment or loss of function for efavirenz 8-hydroxylation. This provides a mechanistic basis for efavirenz clinical pharmacogenetics and may predict additional clinically important variant alleles. Efavirenz metabolism showed both cooperativity and cooperative substrate inhibition. With greater than 10-fold enantioselectivity (S- vs. R- metabolism), efavirenz is the most stereoselective CYP2B6 drug substrate yet identified. These findings may provide mechanistic insights.
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Affiliation(s)
- Pan-Fen Wang
- Department of Anesthesiology, Duke University School of Medicine, Durham, North Carolina
| | - Alicia Neiner
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri.
| | - Evan D Kharasch
- Department of Anesthesiology, Duke University School of Medicine, Durham, North Carolina
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34
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Analysis of the Molecular Interactions between Cytochromes P450 3A4 and 1A2 and Aflatoxins: A Docking Study. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9122467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Mycotoxins known as aflatoxins (AF) are produced as a secondary metabolite by some species of Aspergillus fungi. They are considered carcinogenic, hepatotoxic, teratogenic, and mutagenic. In this study, the molecular structure, chemical reactivity, and charge transfer values of AFB1, B2, G1, and G2 were analyzed using density functional theory. Different methodologies—B3LYP/6-311G(d,p) and M06-2X/6-311G(d,p)—were applied for geometrical calculations. Chemical reactivity parameters were used in the calculation of charge transfer values during the interaction between protein and ligand. The binding energy, the electrostatic interactions, and the amino acids of the active site were determined by molecular docking analysis between AF and cytochromes P450 (3A4 and 1A2), employing different PDB files (CYP3A4:1TQN, 2V0M, 4NY4 and 1W0E, and CYP1A2:2HI4). Molecular docking analysis indicated that the central rings of the AF are involved in the interaction with the HEM group of the active site. The differences in the molecular structure of the AF affect their position regarding the HEM group. The resulting configurations presented considerable variation in the amino acids and the position of the coupling. The charge transfer values showed that there is oxidative damage inside the active site and that the HEM group is responsible for the main charge transferences.
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35
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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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36
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Ning J, Liu T, Dong P, Wang W, Ge G, Wang B, Yu Z, Shi L, Tian X, Huo X, Feng L, Wang C, Sun C, Cui J, James TD, Ma X. Molecular Design Strategy to Construct the Near-Infrared Fluorescent Probe for Selectively Sensing Human Cytochrome P450 2J2. J Am Chem Soc 2019; 141:1126-1134. [PMID: 30525564 DOI: 10.1021/jacs.8b12136] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cytochrome P450 2J2 (CYP2J2), a key enzyme responsible for oxidative metabolism of various xenobiotics and endogenous compounds, participates in a diverse array of physiological and pathological processes in humans. Its biological role in tumorigenesis and cancer diagnosis remains poorly understood, owing to the lack of molecular tools suitable for real-time monitoring CYP2J2 in complex biological systems. Using molecular design principles, we were able to modify the distance between the catalytic unit and metabolic recognition moiety, allowing us to develop a CYP2J2 selective fluorescent probe using a near-infrared fluorophore ( E)-2-(2-(6-hydroxy-2, 3-dihydro-1 H-xanthen-4-yl)vinyl)-3,3-dimethyl-1-propyl-3 H-indol-1-ium iodide (HXPI). To improve the reactivity and isoform specificity, a self-immolative linker was introduced to the HXPI derivatives in order to better fit the narrow substrate channel of CYP2J2, the modification effectively shortened the spatial distance between the metabolic moiety ( O-alkyl group) and catalytic center of CYP2J2. After screening a panel of O-alkylated HXPI derivatives, BnXPI displayed the best combination of specificity, sensitivity and applicability for detecting CYP2J2 in vitro and in vivo. Upon O-demethylation by CYP2J2, a self-immolative reaction occurred spontaneously via 1,6-elimination of p-hydroxybenzyl resulting in the release of HXPI. Allowing BnXPI to be successfully used to monitor CYP2J2 activity in real-time for various living systems including cells, tumor tissues, and tumor-bearing animals. In summary, our practical strategy could help the development of a highly specific and broadly applicable tool for monitoring CYP2J2, which offers great promise for exploring the biological functions of CYP2J2 in tumorigenesis.
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Affiliation(s)
- Jing Ning
- College of Integrative Medicine, The National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, College of Pharmacy , Dalian Medical University , Dalian 116044 , China.,State Key Laboratory of Fine Chemicals, Dalian University of Technology , Dalian 116024 , China
| | - Tao Liu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology , Dalian 116024 , China
| | - Peipei Dong
- College of Integrative Medicine, The National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, College of Pharmacy , Dalian Medical University , Dalian 116044 , China
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Sino-Pakistan TCM and Ethnomedicine Research 8 Center, School of Pharmacy , Hunan University of Chinese Medicine , Changsha 410208 , China
| | - Guangbo Ge
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine , Shanghai 201203 , China
| | - Bo Wang
- College of Integrative Medicine, The National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, College of Pharmacy , Dalian Medical University , Dalian 116044 , China
| | - Zhenlong Yu
- College of Integrative Medicine, The National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, College of Pharmacy , Dalian Medical University , Dalian 116044 , China
| | - Lei Shi
- College of Integrative Medicine, The National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, College of Pharmacy , Dalian Medical University , Dalian 116044 , China
| | - Xiangge Tian
- College of Integrative Medicine, The National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, College of Pharmacy , Dalian Medical University , Dalian 116044 , China
| | - Xiaokui Huo
- College of Integrative Medicine, The National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, College of Pharmacy , Dalian Medical University , Dalian 116044 , China
| | - Lei Feng
- College of Integrative Medicine, The National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, College of Pharmacy , Dalian Medical University , Dalian 116044 , China.,State Key Laboratory of Fine Chemicals, Dalian University of Technology , Dalian 116024 , China
| | - Chao Wang
- College of Integrative Medicine, The National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, College of Pharmacy , Dalian Medical University , Dalian 116044 , China
| | - Chengpeng Sun
- College of Integrative Medicine, The National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, College of Pharmacy , Dalian Medical University , Dalian 116044 , China
| | - Jingnan Cui
- State Key Laboratory of Fine Chemicals, Dalian University of Technology , Dalian 116024 , China
| | - Tony D James
- Department of Chemistry , University of Bath , Bath BA2 7AY , United Kingdom
| | - Xiaochi Ma
- College of Integrative Medicine, The National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, College of Pharmacy , Dalian Medical University , Dalian 116044 , China
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37
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Fernandez-Abascal J, Ripullone M, Valeri A, Leone C, Valoti M. β-Naphtoflavone and Ethanol Induce Cytochrome P450 and Protect towards MPP⁺ Toxicity in Human Neuroblastoma SH-SY5Y Cells. Int J Mol Sci 2018; 19:ijms19113369. [PMID: 30373287 PMCID: PMC6274691 DOI: 10.3390/ijms19113369] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/26/2018] [Accepted: 10/26/2018] [Indexed: 12/13/2022] Open
Abstract
Cytochrome P450 (CYP) isozymes vary their expression depending on the brain area, the cell type, and the presence of drugs. Some isoforms are involved in detoxification and/or toxic activation of xenobiotics in central nervous system. However, their role in brain metabolism and neurodegeneration is still a subject of debate. We have studied the inducibility of CYP isozymes in human neuroblastoma SH-SY5Y cells, treated with β-naphtoflavone (β-NF) or ethanol (EtOH) as inducers, by qRT-PCR, Western blot (WB), and metabolic activity assays. Immunohistochemistry was used to localize the isoforms in mitochondria and/or endoplasmic reticulum (ER). Tetrazolium (MTT) assay was performed to study the role of CYPs during methylphenyl pyridine (MPP+) exposure. EtOH increased mRNA and protein levels of CYP2D6 by 73% and 60% respectively. Both β-NF and EtOH increased CYP2E1 mRNA (4- and 1.4-fold, respectively) and protein levels (64% both). The 7-ethoxycoumarin O-deethylation and dextromethorphan O-demethylation was greater in treatment samples than in controls. Furthermore, both treatments increased by 22% and 18%, respectively, the cell viability in MPP+-treated cells. Finally, CYP2D6 localized at mitochondria and ER. These data indicate that CYP is inducible in SH-SY5Y cells and underline this in vitro system for studying the role of CYPs in neurodegeneration.
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Affiliation(s)
- Jesus Fernandez-Abascal
- Dipartimento di Scienze della Vita, Università di Siena, Via Aldo Moro 2, 53100 Siena, Italy.
| | - Mariantonia Ripullone
- Dipartimento di Scienze della Vita, Università di Siena, Via Aldo Moro 2, 53100 Siena, Italy.
| | - Aurora Valeri
- Molecular Horizon srl, Via Montelino 32, Bettona, 06084 Perugia, Italy.
| | - Cosima Leone
- Dipartimento di Scienze della Vita, Università di Siena, Via Aldo Moro 2, 53100 Siena, Italy.
| | - Massimo Valoti
- Dipartimento di Scienze della Vita, Università di Siena, Via Aldo Moro 2, 53100 Siena, Italy.
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38
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Bapiro TE, Sykes A, Martin S, Davies M, Yates JWT, Hoch M, Rollison HE, Jones B. Complete Substrate Inhibition of Cytochrome P450 2C8 by AZD9496, an Oral Selective Estrogen Receptor Degrader. Drug Metab Dispos 2018; 46:1268-1276. [PMID: 29921707 DOI: 10.1124/dmd.118.081539] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/14/2018] [Indexed: 12/21/2022] Open
Abstract
AZD9496 ((E)-3-(3,5-difluoro-4-((1R,3R)-2-(2-fluoro-2-methylpropyl)-3-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indol-1-yl)phenyl)acrylic acid) is an oral selective estrogen receptor degrader currently in clinical development for treatment of estrogen receptor-positive breast cancer. In a first-in-human phase 1 study, AZD9496 exhibited dose nonlinear pharmacokinetics, the mechanistic basis of which was investigated in this study. The metabolism kinetics of AZD9496 were studied using human liver microsomes (HLMs), recombinant cytochrome P450s (rP450s), and hepatocytes. In addition, modeling approaches were used to gain further mechanistic insights. CYP2C8 was predominantly responsible for biotransformation of AZD9496 to its two main metabolites whose rate of formation with increasing AZD9496 concentrations exhibited complete substrate inhibition in HLM, rCYP2C8, and hepatocytes. Total inhibition by AZD9496 of amodiaquine N-deethylation, a specific probe of CYP2C8 activity, confirmed the completeness of this inhibition. The commonly used substrate inhibition model analogous to uncompetitive inhibition fit poorly to the data. However, using the same model but without constraints on the number of molecules occupying the inhibitory binding site (i.e., nS1ES) provided a significantly better fit (F test, P< 0.005). With the improved model, up to three AZD9496 molecules were predicted to bind the inhibitory site of CYP2C8. In contrast to previous studies showing substrate inhibition of P450s to be partial, our results demonstrate complete substrate inhibition of CYP2C8 via binding of more than one molecule of AZD9496 to the inhibitory site. As CYP2C8 appears to be the sole isoform catalyzing formation of the main metabolites, the substrate inhibition might explain the observed dose nonlinearity in the clinic at higher doses.
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Affiliation(s)
- Tashinga E Bapiro
- Oncology (T.E.B., A.S., S.M., M.D., J.W.T.Y., B.J.), Quantitative Clinical Pharmacology, Early Clinical Development (M.H.), and Drug Safety and Metabolism (H.E.R.), IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Andy Sykes
- Oncology (T.E.B., A.S., S.M., M.D., J.W.T.Y., B.J.), Quantitative Clinical Pharmacology, Early Clinical Development (M.H.), and Drug Safety and Metabolism (H.E.R.), IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Scott Martin
- Oncology (T.E.B., A.S., S.M., M.D., J.W.T.Y., B.J.), Quantitative Clinical Pharmacology, Early Clinical Development (M.H.), and Drug Safety and Metabolism (H.E.R.), IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Michael Davies
- Oncology (T.E.B., A.S., S.M., M.D., J.W.T.Y., B.J.), Quantitative Clinical Pharmacology, Early Clinical Development (M.H.), and Drug Safety and Metabolism (H.E.R.), IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - James W T Yates
- Oncology (T.E.B., A.S., S.M., M.D., J.W.T.Y., B.J.), Quantitative Clinical Pharmacology, Early Clinical Development (M.H.), and Drug Safety and Metabolism (H.E.R.), IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Matthias Hoch
- Oncology (T.E.B., A.S., S.M., M.D., J.W.T.Y., B.J.), Quantitative Clinical Pharmacology, Early Clinical Development (M.H.), and Drug Safety and Metabolism (H.E.R.), IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Helen E Rollison
- Oncology (T.E.B., A.S., S.M., M.D., J.W.T.Y., B.J.), Quantitative Clinical Pharmacology, Early Clinical Development (M.H.), and Drug Safety and Metabolism (H.E.R.), IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Barry Jones
- Oncology (T.E.B., A.S., S.M., M.D., J.W.T.Y., B.J.), Quantitative Clinical Pharmacology, Early Clinical Development (M.H.), and Drug Safety and Metabolism (H.E.R.), IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
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Šrejber M, Navrátilová V, Paloncýová M, Bazgier V, Berka K, Anzenbacher P, Otyepka M. Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners. J Inorg Biochem 2018; 183:117-136. [DOI: 10.1016/j.jinorgbio.2018.03.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/16/2018] [Accepted: 03/01/2018] [Indexed: 01/08/2023]
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Ligand Access Channels in Cytochrome P450 Enzymes: A Review. Int J Mol Sci 2018; 19:ijms19061617. [PMID: 29848998 PMCID: PMC6032366 DOI: 10.3390/ijms19061617] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/27/2018] [Accepted: 05/28/2018] [Indexed: 12/22/2022] Open
Abstract
Quantitative structure-activity relationships may bring invaluable information on structural elements of both enzymes and substrates that, together, govern substrate specificity. Buried active sites in cytochrome P450 enzymes are connected to the solvent by a network of channels exiting at the distal surface of the protein. This review presents different in silico tools that were developed to uncover such channels in P450 crystal structures. It also lists some of the experimental evidence that actually suggest that these predicted channels might indeed play a critical role in modulating P450 functions. Amino acid residues at the entrance of the channels may participate to a first global ligand recognition of ligands by P450 enzymes before they reach the buried active site. Moreover, different P450 enzymes show different networks of predicted channels. The plasticity of P450 structures is also important to take into account when looking at how channels might play their role.
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Increased Phenacetin Oxidation upon the L382V Substitution in Cytochrome P450 1A2 is Associated with Altered Substrate Binding Orientation. Int J Mol Sci 2018; 19:ijms19061580. [PMID: 29799514 PMCID: PMC6032418 DOI: 10.3390/ijms19061580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 05/23/2018] [Accepted: 05/23/2018] [Indexed: 11/22/2022] Open
Abstract
Leucine382 of cytochrome P450 1A2 (CYP1A2) plays an important role in binding and O-dealkylation of phenacetin, with the L382V mutation increasing substrate oxidation (Huang and Szklarz, 2010, Drug Metab. Dispos. 38:1039–1045). This was attributed to altered substrate binding orientation, but no direct experimental evidence had been available. Therefore, in the current studies, we employed nuclear magnetic resonance (NMR) longitudinal (T1) relaxation measurements to investigate phenacetin binding orientations within the active site of CYP1A2 wild type (WT) and mutants. Paramagnetic relaxation time (T1P) for each proton of phenacetin was calculated from the T1 value obtained from the enzymes in ferric and ferrous-CO state in the presence of phenacetin, and used to model the orientation of phenacetin in the active site. All aromatic protons of phenacetin were nearly equidistant from the heme iron (6.34–8.03 Å). In contrast, the distance between the proton of the –OCH2– group, which is abstracted during phenacetin oxidation, and the heme iron, was much shorter in the L382V (5.93 Å) and L382V/N312L (5.96 Å) mutants compared to the N312L mutant (7.84 Å) and the wild type enzyme (6.55 Å), consistent with modeling results. These studies provide direct evidence for the molecular mechanism underlying increased oxidation of phenacetin upon the L382V mutation.
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Li X, Xu Y, Lai L, Pei J. Prediction of Human Cytochrome P450 Inhibition Using a Multitask Deep Autoencoder Neural Network. Mol Pharm 2018; 15:4336-4345. [DOI: 10.1021/acs.molpharmaceut.8b00110] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiang Li
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Youjun Xu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Luhua Lai
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jianfeng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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Don CG, Smieško M. Out‐compute drug side effects: Focus on cytochrome P450 2D6 modeling. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Charleen G. Don
- Department of Pharmaceutical SciencesUniversity of BaselBaselSwitzerland
| | - Martin Smieško
- Department of Pharmaceutical SciencesUniversity of BaselBaselSwitzerland
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Lim DS, Lim DH, Lee JH, Oh ET, Keum YS. Structure-Oxidative Metabolism Relationships of Substituted Flavones by Aspergillus niger. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:3056-3064. [PMID: 28322046 DOI: 10.1021/acs.jafc.7b00390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Aspergillus niger is a rich source of oxidative enzymes, which are important for many industrial applications. However, systematic evaluation of their metabolic characteristics is limited. In this study, structure-dependent metabolism of flavones by Aspergillus niger were investigated with synthetic substrates. Metabolic inhibitor studies suggested that cytochrome P450s are the major enzymes in oxidative metabolism. The reactions include ring hydroxylation, O-demethylation, sulfone/sulfoxide formation, and oxidation of alkyls to carboxy groups. Initial oxidative metabolism occurred almost exclusively at 4'-substituents. 4'-Halogenated- and 3',5'-dihalogenated analogues were stable against biodegradation. Hydrophilic flavones were more rapidly metabolized than lipophilic analogues. Molecular widths of the A and B ring were important determinants of the position of metabolic oxidation and biotransformation rate. The structure-metabolism relationship analysis indicates that the shape of the B ring was the most important parameter of biotransformation. The electrostatic environment of the same ring also affected the transformation. Additionally, the results showed that the B ring may preferentially be oriented toward the catalytic center.
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Affiliation(s)
- Da-Som Lim
- Department of Crop Science, Konkuk University , 1 Hwayang-dong, Gwanjin-Gu, Seoul 143-701, Republic of Korea
| | - Do-Hyung Lim
- Department of Crop Science, Konkuk University , 1 Hwayang-dong, Gwanjin-Gu, Seoul 143-701, Republic of Korea
| | - Ji-Ho Lee
- Department of Crop Science, Konkuk University , 1 Hwayang-dong, Gwanjin-Gu, Seoul 143-701, Republic of Korea
| | - Eun-Tae Oh
- Department of Crop Science, Konkuk University , 1 Hwayang-dong, Gwanjin-Gu, Seoul 143-701, Republic of Korea
| | - Young-Soo Keum
- Department of Crop Science, Konkuk University , 1 Hwayang-dong, Gwanjin-Gu, Seoul 143-701, Republic of Korea
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45
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Ollikainen E, Liu D, Kallio A, Mäkilä E, Zhang H, Salonen J, Santos HA, Sikanen TM. The impact of porous silicon nanoparticles on human cytochrome P450 metabolism in human liver microsomes in vitro. Eur J Pharm Sci 2017; 104:124-132. [PMID: 28366651 DOI: 10.1016/j.ejps.2017.03.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/08/2017] [Accepted: 03/28/2017] [Indexed: 02/05/2023]
Abstract
Engineered nanoparticles are increasingly used as drug carriers in pharmaceutical formulations. This study focuses on the hitherto unaddressed impact of porous silicon (PSi) nanoparticles on human cytochrome P450 (CYP) metabolism, which is the major detoxification route of most pharmaceuticals and other xenobiotics. Three different surface chemistries, including thermally carbonized PSi (TCPSi), aminopropylsilane-modified TCPSi (APTES-TCPSi) and alkyne-terminated thermally hydrocarbonized PSi (Alkyne-THCPSi), were compared for their effects on the enzyme kinetics of the major CYP isoforms (CYP1A2, CYP2A6, CYP2D6, and CYP3A4) in human liver microsomes (HLM) in vitro. The enzyme kinetic parameters, Km and Vmax, and the intrinsic clearance (CLint) were determined using FDA-recommended, isoenzyme-specific model reactions with and without PSi nanoparticles. Data revealed statistically significant alterations of most isoenzyme activities in HLM in the presence of nanoparticles at 1mg/ml concentration, and polymorphic CYP2D6 was the most vulnerable to enzyme inhibition. However, the observed CYP2D6 inhibition was shown to be dose-dependent in case of TCPSi and Alkyne-THCPSi nanoparticles and attenuated at the concentrations below 1μg/ml. Adsorption of the probe substrates onto the hydrophobic Alkyne-THCPSi particles was also observed and taken into account in the determination of the kinetic parameters. Three polymer additives commonly used in pharmaceutical nanoformulations (Pluronics F68 and F127, and polyvinylalcohol) were also separately screened for their effects on CYP isoenzyme activities. These polymers had less effect on the enzyme kinetic parameters, and resulted in increased activity rather than enzyme inhibition, in contrast to the PSi nanoparticles. Although the chosen subcellular model (HLM) is not able to predict the cellular disposition of PSi nanoparticles in hepatocytes and thus provides limited information of probability of CYP interactions in vivo, the present study suggests that mechanistic interactions by the PSi nanoparticles or the polymer stabilizers may appear if these are effectively uptaken by the hepatocytes.
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Affiliation(s)
- Elisa Ollikainen
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Dongfei Liu
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Arttu Kallio
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Ermei Mäkilä
- Laboratory of Industrial Physics, Department of Physics and Astronomy, University of Turku, Turku, Finland
| | - Hongbo Zhang
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland; Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Jarno Salonen
- Laboratory of Industrial Physics, Department of Physics and Astronomy, University of Turku, Turku, Finland
| | - Hélder A Santos
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Tiina M Sikanen
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
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46
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Davydov DR, Yang Z, Davydova N, Halpert JR, Hubbell WL. Conformational Mobility in Cytochrome P450 3A4 Explored by Pressure-Perturbation EPR Spectroscopy. Biophys J 2016; 110:1485-1498. [PMID: 27074675 DOI: 10.1016/j.bpj.2016.02.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 12/04/2015] [Accepted: 02/15/2016] [Indexed: 11/18/2022] Open
Abstract
We used high hydrostatic pressure as a tool for exploring the conformational landscape of human cytochrome P450 3A4 (CYP3A4) by electron paramagnetic resonance and fluorescence spectroscopy. Site-directed incorporation of a luminescence resonance energy transfer donor-acceptor pair allowed us to identify a pressure-dependent equilibrium between two states of the enzyme, where an increase in pressure increased the spatial separation between the two distantly located fluorophores. This transition is characterized by volume change (ΔV°) and P1/2 values of -36.8 ± 5.0 mL/mol and 1.45 ± 0.33 kbar, respectively, which corresponds to a Keq° of 0.13 ± 0.06, so that only 15% of the enzyme adopts the pressure-promoted conformation at ambient pressure. This pressure-promoted displacement of the equilibrium is eliminated by the addition of testosterone, an allosteric activator. Using site-directed spin labeling, we demonstrated that the pressure- and testosterone-sensitive transition is also revealed by pressure-induced changes in the electron paramagnetic resonance spectra of a nitroxide side chain placed at position 85 or 409 of the enzyme. Furthermore, we observed a pressure-induced displacement of the emission maxima of a solvatochromic fluorophore (7-diethylamino-3-((((2-maleimidyl)ethyl)amino)carbonyl) coumarin) placed at the same positions, which suggests a relocation to a more polar environment. Taken together, the results reveal an effector-dependent conformational equilibrium between open and closed states of CYP3A4 that involves a pronounced change at the interface between the region of α-helices A/A' and the meander loop of the enzyme, where residues 85 and 409 are located. Our study demonstrates the high potential of pressure-perturbation strategies for studying protein conformational landscapes.
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Affiliation(s)
- Dmitri R Davydov
- Department of Chemistry, Washington State University, Pullman, Washington; V. N. Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, Russia.
| | - Zhongyu Yang
- Jules Stein Eye Institute, University of California, Los Angeles, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Nadezhda Davydova
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - James R Halpert
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Wayne L Hubbell
- Jules Stein Eye Institute, University of California, Los Angeles, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
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47
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Shah MB, Liu J, Huo L, Zhang Q, Dearing MD, Wilderman PR, Szklarz GD, Stout CD, Halpert JR. Structure-Function Analysis of Mammalian CYP2B Enzymes Using 7-Substituted Coumarin Derivatives as Probes: Utility of Crystal Structures and Molecular Modeling in Understanding Xenobiotic Metabolism. Mol Pharmacol 2016; 89:435-45. [PMID: 26826176 DOI: 10.1124/mol.115.102111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/20/2016] [Indexed: 01/09/2023] Open
Abstract
Crystal structures of CYP2B35 and CYP2B37 from the desert woodrat were solved in complex with 4-(4-chlorophenyl)imidazole (4-CPI). The closed conformation of CYP2B35 contained two molecules of 4-CPI within the active site, whereas the CYP2B37 structure demonstrated an open conformation with three 4-CPI molecules, one within the active site and the other two in the substrate access channel. To probe structure-function relationships of CYP2B35, CYP2B37, and the related CYP2B36, we tested the O-dealkylation of three series of related substrates-namely, 7-alkoxycoumarins, 7-alkoxy-4-(trifluoromethyl)coumarins, and 7-alkoxy-4-methylcoumarins-with a C1-C7 side chain. CYP2B35 showed the highest catalytic efficiency (kcat/KM) with 7-heptoxycoumarin as a substrate, followed by 7-hexoxycoumarin. In contrast, CYP2B37 showed the highest catalytic efficiency with 7-ethoxy-4-(trifluoromethyl)coumarin (7-EFC), followed by 7-methoxy-4-(trifluoromethyl)coumarin (7-MFC). CYP2B35 had no dealkylation activity with 7-MFC or 7-EFC. Furthermore, the new CYP2B-4-CPI-bound structures were used as templates for docking the 7-substituted coumarin derivatives, which revealed orientations consistent with the functional studies. In addition, the observation of multiple -Cl and -NH-π interactions of 4-CPI with the aromatic side chains in the CYP2B35 and CYP2B37 structures provides insight into the influence of such functional groups on CYP2B ligand binding affinity and specificity. To conclude, structural, computational, and functional analysis revealed striking differences between the active sites of CYP2B35 and CYP2B37 that will aid in the elucidation of new structure-activity relationships.
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Affiliation(s)
- Manish B Shah
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - Jingbao Liu
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - Lu Huo
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - Qinghai Zhang
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - M Denise Dearing
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - P Ross Wilderman
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - Grazyna D Szklarz
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - C David Stout
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
| | - James R Halpert
- School of Pharmacy, University of Connecticut, Storrs, Connecticut (M.B.S., J.L., L.H., P.R.W., J.R.H.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (Q.Z., C.D.S.); Department of Biology, University of Utah, Salt Lake City, Utah (M.D.D.); and Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (G.D.S.)
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48
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Estrada DF, Laurence JS, Scott EE. Cytochrome P450 17A1 Interactions with the FMN Domain of Its Reductase as Characterized by NMR. J Biol Chem 2015; 291:3990-4003. [PMID: 26719338 DOI: 10.1074/jbc.m115.677294] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 11/06/2022] Open
Abstract
To accomplish key physiological processes ranging from drug metabolism to steroidogenesis, human microsomal cytochrome P450 enzymes require the sequential input of two electrons delivered by the FMN domain of NADPH-cytochrome P450 reductase. Although some human microsomal P450 enzymes can instead accept the second electron from cytochrome b5, for human steroidogenic CYP17A1, the cytochrome P450 reductase FMN domain delivers both electrons, and b5 is an allosteric modulator. The structural basis of these key but poorly understood protein interactions was probed by solution NMR using the catalytically competent soluble domains of each protein. Formation of the CYP17A1·FMN domain complex induced differential line broadening of the NMR signal for each protein. Alterations in the exchange dynamics generally occurred for residues near the surface of the flavin mononucleotide, including 87-90 (loop 1), and for key CYP17A1 active site residues. These interactions were modulated by the identity of the substrate in the buried CYP17A1 active site and by b5. The FMN domain outcompetes b5 for binding to CYP17A1 in the three-component system. These results and comparison with previous NMR studies of the CYP17A1·b5 complex suggest a model of CYP17A1 enzyme regulation.
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Affiliation(s)
- D Fernando Estrada
- From the Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045 and
| | - Jennifer S Laurence
- the Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047
| | - Emily E Scott
- From the Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045 and
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Iavicoli I, Leso V, Schulte PA. Biomarkers of susceptibility: State of the art and implications for occupational exposure to engineered nanomaterials. Toxicol Appl Pharmacol 2015; 299:112-24. [PMID: 26724381 DOI: 10.1016/j.taap.2015.12.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 12/07/2015] [Accepted: 12/21/2015] [Indexed: 11/25/2022]
Abstract
Rapid advances and applications in nanotechnology are expected to result in increasing occupational exposure to nano-sized materials whose health impacts are still not completely understood. Scientific efforts are required to identify hazards from nanomaterials and define risks and precautionary management strategies for exposed workers. In this scenario, the definition of susceptible populations, which may be at increased risk of adverse effects may be important for risk assessment and management. The aim of this review is to critically examine available literature to provide a comprehensive overview on susceptibility aspects potentially affecting heterogeneous responses to nanomaterials workplace exposure. Genetic, genotoxic and epigenetic alterations induced by nanomaterials in experimental studies were assessed with respect to their possible function as determinants of susceptibility. Additionally, the role of host factors, i.e. age, gender, and pathological conditions, potentially affecting nanomaterial toxicokinetic and health impacts, were also analysed. Overall, this review provides useful information to obtain insights into the nanomaterial mode of action in order to identify potentially sensitive, specific susceptibility biomarkers to be validated in occupational settings and addressed in risk assessment processes. The findings of this review are also important to guide future research into a deeper characterization of nanomaterial susceptibility in order to define adequate risk communication strategies. Ultimately, identification and use of susceptibility factors in workplace settings has both scientific and ethical issues that need addressing.
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Affiliation(s)
- Ivo Iavicoli
- Department of Public Health, Division of Occupational Medicine, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy.
| | - Veruscka Leso
- Institute of Public Health, Section of Occupational Medicine, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy.
| | - Paul A Schulte
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 4676 Columbia Parkway, MS C-14, Cincinnati, OH 45226, USA.
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50
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Burkhardt T, Letzel T, Drewes JE, Grassmann J. Comprehensive assessment of Cytochrome P450 reactions: A multiplex approach using real-time ESI-MS. Biochim Biophys Acta Gen Subj 2015; 1850:2573-81. [PMID: 26409144 DOI: 10.1016/j.bbagen.2015.09.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 09/01/2015] [Accepted: 09/22/2015] [Indexed: 01/14/2023]
Abstract
BACKGROUND The detailed analysis of Cytochrome P450 (CYP) catalyzed reactions is of great interest, since those are of importance for biotechnical applications, drug interaction studies and environmental research. Often cocktail approaches are carried out in order to monitor several CYP activities in a single experiment. Commonly in these approaches product formation is detected and IC50 values are determined. METHODS In the present work, the reactions of two different CYP isoforms were monitored using real-time electrospray ionization mass spectrometry. Multiplex experiments using the highly specific CYP2A6 with its corresponding substrate coumarin as well as the highly promiscuous CYP3A4 with testosterone were conducted. Product formation and substrate depletion were simultaneously monitored and compared to the single CYP experiments. The diffusion-controlled rate of reaction and conversion rates that are used as parameters to assess the enzymatic activity were calculated for all measurements conducted. RESULTS Differences in conversion rates and the theoretical rate of reaction that were observed for single CYP and multiplex experiments, respectively, reveal the complexity of the underlying mechanisms. Findings of this study imply that there might be distinct deviations between product formation and substrate degradation when mixtures are used. CONCLUSIONS Detailed results indicate that for a comprehensive assessment of these enzymatic reactions both product and substrate should be considered. GENERAL SIGNIFICANCE The direct hyphenation of enzymatic reactions to mass spectrometry allows for a comprehensive assessment of enzymatic behavior. Due to the benefits of this technique, the entire system which includes substrate, product and intermediates can be investigated. Thus, besides IC50 values further information regarding the enzymatic behavior offers the opportunity for a more detailed insight.
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Affiliation(s)
- Therese Burkhardt
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall, 85748 Garching, Germany.
| | - Thomas Letzel
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall, 85748 Garching, Germany.
| | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall, 85748 Garching, Germany.
| | - Johanna Grassmann
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall, 85748 Garching, Germany.
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