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Structural dynamics of the cooperative binding of small inhibitors in human cytochrome P450 2C9. J Mol Graph Model 2022; 113:108151. [DOI: 10.1016/j.jmgm.2022.108151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 11/23/2022]
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2
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Skerratt SE, de Groot MJ, Phillips C. Discovery of a novel binding pocket for CYP 2C9 inhibitors: crystallography, pharmacophore modelling and inhibitor SAR. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00011h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
CYP 2C9 co-crystal structures of compound1(green) in binding mode 1 (CYP 2C9 in green) and compound2(yellow) in binding mode 2 (CYP 2C9 in yellow).
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3
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Tsukada C, Saito T, Maekawa M, Mano N, Oda A, Hirasawa N, Hiratsuka M. Functional characterization of 12 allelic variants of CYP2C8 by assessment of paclitaxel 6α-hydroxylation and amodiaquine N-deethylation. Drug Metab Pharmacokinet 2015; 30:366-73. [PMID: 26427316 DOI: 10.1016/j.dmpk.2015.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 07/14/2015] [Accepted: 07/21/2015] [Indexed: 12/25/2022]
Abstract
Cytochrome P450 2C8 (CYP2C8) is one of the enzymes primarily responsible for the metabolism of many drugs, including paclitaxel and amodiaquine. CYP2C8 genetic variants contribute to interindividual variations in the therapeutic efficacy and toxicity of paclitaxel. Although it is difficult to investigate the enzymatic function of most CYP2C8 variants in vivo, this can be investigated in vitro using recombinant CYP2C8 protein variants. The present study used paclitaxel to evaluate 6α-hydroxylase activity and amodiaquine for the N-deethylase activity of wild-type and 11 CYP2C8 variants resulting in amino acid substitutions in vitro. The wild-type and variant CYP2C8 proteins were heterologously expressed in COS-7 cells. Paclitaxel 6α-hydroxylation and amodiaquine N-deethylation activities were determined by measuring the concentrations of 6α-hydroxypaclitaxel and N-desethylamodiaquine, respectively, and the kinetic parameters were calculated. Compared to the wild-type enzyme (CYP2C8.1), CYP2C8.11 and CYP2C8.14 showed little or no activity with either substrate. In addition, the intrinsic clearance values of CYP2C8.8 and CYP2C8.13 for paclitaxel were 68% and 67% that of CYP2C8.1, respectively. In contrast, the CLint values of CYP2C8.2 and CYP2C8.12 were 1.4 and 1.9 times higher than that of CYP2C8.1. These comprehensive findings could inform for further genotype-phenotype studies on interindividual differences in CYP2C8-mediated drug metabolism.
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Affiliation(s)
- Chiharu Tsukada
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Takahiro Saito
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Masamitsu Maekawa
- Department of Pharmacy, Tohoku University Hospital, Sendai 980-8574, Japan
| | - Nariyasu Mano
- Department of Pharmacy, Tohoku University Hospital, Sendai 980-8574, Japan
| | - Akifumi Oda
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Noriyasu Hirasawa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Masahiro Hiratsuka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan.
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4
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Artese A, Cross S, Costa G, Distinto S, Parrotta L, Alcaro S, Ortuso F, Cruciani G. Molecular interaction fields in drug discovery: recent advances and future perspectives. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1150] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Anna Artese
- Dipartimento di Scienze della Salute; Università degli Studi “Magna Graecia” di Catanzaro; Campus “S. Venuta”; Viale Europa Catanzaro Italy
| | - Simon Cross
- Molecular Discovery Ltd, Pinner; Middlesex London United Kingdom
| | - Giosuè Costa
- Dipartimento di Scienze della Salute; Università degli Studi “Magna Graecia” di Catanzaro; Campus “S. Venuta”; Viale Europa Catanzaro Italy
| | - Simona Distinto
- Dipartimento di Scienze della Vita e dell'Ambiente; Università di Cagliari; Cagliari Italy
| | - Lucia Parrotta
- Dipartimento di Scienze della Salute; Università degli Studi “Magna Graecia” di Catanzaro; Campus “S. Venuta”; Viale Europa Catanzaro Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute; Università degli Studi “Magna Graecia” di Catanzaro; Campus “S. Venuta”; Viale Europa Catanzaro Italy
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute; Università degli Studi “Magna Graecia” di Catanzaro; Campus “S. Venuta”; Viale Europa Catanzaro Italy
| | - Gabriele Cruciani
- Laboratory for Chemometrics and Cheminformatics; Chemistry Department; University of Perugia; Perugia Italy
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5
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Sirci F, Goracci L, Rodríguez D, van Muijlwijk-Koezen J, Gutiérrez-de-Terán H, Mannhold R. Ligand-, structure- and pharmacophore-based molecular fingerprints: a case study on adenosine A1, A2A, A2B, and A3 receptor antagonists. J Comput Aided Mol Des 2012; 26:1247-66. [DOI: 10.1007/s10822-012-9612-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 09/20/2012] [Indexed: 10/27/2022]
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6
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Exploration of the binding of curcumin analogues to human P450 2C9 based on docking and molecular dynamics simulation. J Mol Model 2011; 18:2599-611. [DOI: 10.1007/s00894-011-1275-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 10/09/2011] [Indexed: 11/26/2022]
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7
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Craig IR, Pfleger C, Gohlke H, Essex JW, Spiegel K. Pocket-space maps to identify novel binding-site conformations in proteins. J Chem Inf Model 2011; 51:2666-79. [PMID: 21910474 DOI: 10.1021/ci200168b] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The identification of novel binding-site conformations can greatly assist the progress of structure-based ligand design projects. Diverse pocket shapes drive medicinal chemistry to explore a broader chemical space and thus present additional opportunities to overcome key drug discovery issues such as potency, selectivity, toxicity, and pharmacokinetics. We report a new automated approach to diverse pocket selection, PocketAnalyzer(PCA), which applies principal component analysis and clustering to the output of a grid-based pocket detection algorithm. Since the approach works directly with pocket shape descriptors, it is free from some of the problems hampering methods that are based on proxy shape descriptors, e.g. a set of atomic positional coordinates. The approach is technically straightforward and allows simultaneous analysis of mutants, isoforms, and protein structures derived from multiple sources with different residue numbering schemes. The PocketAnalyzer(PCA) approach is illustrated by the compilation of diverse sets of pocket shapes for aldose reductase and viral neuraminidase. In both cases this allows identification of novel computationally derived binding-site conformations that are yet to be observed crystallographically. Indeed, known inhibitors capable of exploiting these novel binding-site conformations are subsequently identified, thereby demonstrating the utility of PocketAnalyzer(PCA) for rationalizing and improving the understanding of the molecular basis of protein-ligand interaction and bioactivity. A Python program implementing the PocketAnalyzer(PCA) approach is available for download under an open-source license ( http://sourceforge.net/projects/papca/ or http://cpclab.uni-duesseldorf.de/downloads ).
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Affiliation(s)
- Ian R Craig
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, UK.
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8
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Banu H, Renuka N, Vasanthakumar G. Reduced catalytic activity of human CYP2C9 natural alleles for gliclazide: Molecular dynamics simulation and docking studies. Biochimie 2011; 93:1028-36. [DOI: 10.1016/j.biochi.2011.02.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Accepted: 02/16/2011] [Indexed: 11/27/2022]
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9
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Exploration of the binding of proton pump inhibitors to human P450 2C9 based on docking and molecular dynamics simulation. J Mol Model 2010; 17:1941-51. [DOI: 10.1007/s00894-010-0903-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Accepted: 11/11/2010] [Indexed: 01/08/2023]
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10
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Xu C, Mager DE. Quantitative structure–pharmacokinetic relationships. Expert Opin Drug Metab Toxicol 2010; 7:63-77. [DOI: 10.1517/17425255.2011.537257] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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11
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Rocha JR, Freitas RF, Montanari CA. The GRID/CPCA approach in drug discovery. Expert Opin Drug Discov 2010; 5:333-46. [DOI: 10.1517/17460441003652959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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12
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13
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Ahlström MM, Ridderström M, Zamora I. CYP2C9 Structure−Metabolism Relationships: Substrates, Inhibitors, and Metabolites. J Med Chem 2007; 50:5382-91. [DOI: 10.1021/jm070745g] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marie M. Ahlström
- Discovery DMPK and Bioanalytical Chemistry, AstraZeneca R&D Mölndal, SE-431 83 Mölndal, Sweden, Department of Chemistry, Medicinal Chemistry, Göteborg University, SE-412 96 Gothenburg, Sweden, Lead Molecular Design, S.L., Vallés 96-102 (27) E-08190, Sant Cugat del Vallés, Spain, and Institut Municipal d'Investigació Medica (IMIM), Universitat Pompeu Fabra, Doctor Aiguader 80, 08003 Barcelona, Spain
| | - Marianne Ridderström
- Discovery DMPK and Bioanalytical Chemistry, AstraZeneca R&D Mölndal, SE-431 83 Mölndal, Sweden, Department of Chemistry, Medicinal Chemistry, Göteborg University, SE-412 96 Gothenburg, Sweden, Lead Molecular Design, S.L., Vallés 96-102 (27) E-08190, Sant Cugat del Vallés, Spain, and Institut Municipal d'Investigació Medica (IMIM), Universitat Pompeu Fabra, Doctor Aiguader 80, 08003 Barcelona, Spain
| | - Ismael Zamora
- Discovery DMPK and Bioanalytical Chemistry, AstraZeneca R&D Mölndal, SE-431 83 Mölndal, Sweden, Department of Chemistry, Medicinal Chemistry, Göteborg University, SE-412 96 Gothenburg, Sweden, Lead Molecular Design, S.L., Vallés 96-102 (27) E-08190, Sant Cugat del Vallés, Spain, and Institut Municipal d'Investigació Medica (IMIM), Universitat Pompeu Fabra, Doctor Aiguader 80, 08003 Barcelona, Spain
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Kjellander B, Masimirembwa CM, Zamora I. Exploration of Enzyme−Ligand Interactions in CYP2D6 & 3A4 Homology Models and Crystal Structures Using a Novel Computational Approach. J Chem Inf Model 2007; 47:1234-47. [PMID: 17381082 DOI: 10.1021/ci600561v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New crystal structures of human CYP2D6 and CYP3A4 have recently been reported, and in this study, we wanted to compare them with previously used homology models with respect to predictions of site of metabolism and ligand-enzyme interactions. The data set consisted of a family of synthetic opioid analgesics with the aim to cover both CYP2D6 and CYP3A4, as most of these compounds are metabolized by both isoforms. The program MetaSite was used for the site of metabolism predictions, and the results were validated by experimental assessment of the major metabolites formed with recombinant CYP450s. This was made on a selection of 14 compounds in the data set. The prediction rates for MetaSite were 79-100% except for the CYP3A4 homology model, which picked the correct site in half of the cases. Despite differences in orientation of some important amino acids in the active sites, the MetaSite-predicted sites were the same for the different structures, with the exception of the CYP3A4 homology model. Further exploration of interactions with ligands was done by docking substrates/inhibitors in the different structures with the docking program GLUE. To address the challenge in interpreting patterns of enzyme-ligand interactions for the large number of different docking poses, a new computational tool to handle the results from the dockings was developed, in which the output highlights the relative importance of amino acids in CYP450-substrate/inhibitor interactions. The method is based on calculations of the interaction energies for each pose with the surrounding amino acids. For the CYP3A4 structures, this method was compared with consensus principal component analysis (CPCA), a commonly used method for structural comparison to evaluate the usefulness of the new method. The results from the two methods were comparable with each other, and the highlighted amino acids resemble those that were identified to have a different orientation in the compared structures. The new method has clear advantages over CPCA in that it is far simpler to interpret and there is no need for protein alignment. The methodology enables structural comparison but also gives insights on important amino acid substrate/inhibitor interactions and can therefore be very useful when suggesting modifications of new chemical entities to improve their metabolic profiles.
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Affiliation(s)
- Britta Kjellander
- Discovery DMPK & Bioanalytical Chemisty Department, AstraZeneca R&D Mölndal, SE-431 81, Sweden.
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15
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Seifert A, Tatzel S, Schmid RD, Pleiss J. Multiple molecular dynamics simulations of human p450 monooxygenase CYP2C9: The molecular basis of substrate binding and regioselectivity toward warfarin. Proteins 2006; 64:147-55. [PMID: 16639745 DOI: 10.1002/prot.20951] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
To examine the molecular basis of activity and regioselectivity of the clinically important human microsomal cytochrome P450 (CYP) monooxygenase 2C9 toward its substrate warfarin, 22 molecular dynamics simulations (3-5 ns each) were performed in the presence and absence of warfarin. The resulting trajectories revealed a stable protein core and mobile surface elements. This mobility leads to the formation of two surface channels in the region between F-G loop, B' helix/B-B' loop, beta(1)-sheet, and between helices F and I and the turn in the C-terminal antiparallel beta-sheet in the presence of warfarin. Besides the nonproductive state of the CYP2C9 warfarin complex captured in the crystal structure, three additional states were observed. These states differ in the shape of the substrate binding cavity and the position of the warfarin molecule relative to heme. In one of these states, the 7- and 6-positions of warfarin contact the heme with a marked geometrical preference for position 7 over position 6. This modeling result is consistent with experimentally determined regioselectivity (71 and 22% hydroxylation in positions 7 and 6, respectively). Access to the heme group is limited by the core amino acids Ala297, Leu362, Leu366, and Thr301, which therefore are expected to have a major impact on regioselectivity. In addition, modeling predicts that autoactivation of warfarin is sterically hindered. Our study demonstrates how the combination of mobile surface and rigid core leads to interesting properties: a broad substrate profile and simultaneously a high regioselectivity.
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Affiliation(s)
- Alexander Seifert
- Institute of Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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16
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Chapter 10 Cytochrome P450 Enzymes: Computational Approaches to Substrate Prediction. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/s1574-1400(06)02010-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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17
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Chapter 13 Principal Components Analysis: A Review of its Application on Molecular Dynamics Data. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2006. [DOI: 10.1016/s1574-1400(06)02013-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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18
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de Graaf C, Vermeulen NPE, Feenstra KA. Cytochrome P450 in Silico: An Integrative Modeling Approach. J Med Chem 2005; 48:2725-55. [PMID: 15828810 DOI: 10.1021/jm040180d] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chris de Graaf
- Leiden/Amsterdam Center for Drug Research, Division of Molecular Toxicology, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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