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Structure-Based Drug Design for Cytochrome P450 Family 1 Inhibitors. Bioinorg Chem Appl 2018; 2018:3924608. [PMID: 30147715 PMCID: PMC6083639 DOI: 10.1155/2018/3924608] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/17/2018] [Accepted: 06/20/2018] [Indexed: 12/13/2022] Open
Abstract
Cytochromes P450 are a class of metalloproteins which are responsible for electron transfer in a wide spectrum of reactions including metabolic biotransformation of endogenous and exogenous substrates. The superfamily of cytochromes P450 consists of families and subfamilies which are characterized by a specific structure and substrate specificity. Cytochromes P450 family 1 (CYP1s) play a distinctive role in the metabolism of drugs and chemical procarcinogens. In recent decades, these hemoproteins have been intensively studied with the use of computational methods which have been recently developed remarkably to be used in the process of drug design by the virtual screening of compounds in order to find agents with desired properties. Moreover, the molecular modeling of proteins and ligand docking to their active sites provide an insight into the mechanism of enzyme action and enable us to predict the sites of drug metabolism. The review presents the current status of knowledge about the use of the computational approach in studies of ligand-enzyme interactions for CYP1s. Research on the metabolism of substrates and inhibitors of CYP1s and on the selectivity of their action is particularly valuable from the viewpoint of cancer chemoprevention, chemotherapy, and drug-drug interactions.
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Šink R, Sosič I, Živec M, Fernandez-Menendez R, Turk S, Pajk S, Alvarez-Gomez D, Lopez-Roman EM, Gonzales-Cortez C, Rullas-Triconado J, Angulo-Barturen I, Barros D, Ballell-Pages L, Young RJ, Encinas L, Gobec S. Design, Synthesis, and Evaluation of New Thiadiazole-Based Direct Inhibitors of Enoyl Acyl Carrier Protein Reductase (InhA) for the Treatment of Tuberculosis. J Med Chem 2014; 58:613-24. [DOI: 10.1021/jm501029r] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Roman Šink
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenija
| | - Izidor Sosič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenija
| | - Matej Živec
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenija
| | - Raquel Fernandez-Menendez
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Samo Turk
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenija
| | - Stane Pajk
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenija
| | - Daniel Alvarez-Gomez
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Eva Maria Lopez-Roman
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Carolina Gonzales-Cortez
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Joaquin Rullas-Triconado
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Inigo Angulo-Barturen
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - David Barros
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Lluís Ballell-Pages
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Robert J. Young
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Lourdes Encinas
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Stanislav Gobec
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenija
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Pan Y, Tiong KH, Abd-Rashid BA, Ismail Z, Ismail R, Mak JW, Ong CE. Inhibitory effects of cytochrome P450 enzymes CYP2C8, CYP2C9, CYP2C19 and CYP3A4 by Labisia pumila extracts. JOURNAL OF ETHNOPHARMACOLOGY 2012; 143:586-91. [PMID: 22885070 DOI: 10.1016/j.jep.2012.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 06/29/2012] [Accepted: 07/21/2012] [Indexed: 01/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Labisa pumila (LP), popularly known with its local name, Kacip Fatimah, is a well known herb grown in Indochina and Southeast Asia and is traditionally used to regain energy after giving birth in women. The propensity of LP to cause drug-herb interaction via cytochrome P450 (CYP) enzyme system has not been investigated. AIM OF THE STUDY To evaluate the in vitro inhibitory effects of various LP extracts (aqueous, ethanol, dichloromethane (DCM) and hexane) on cytochrome P450 2C8 (CYP2C8), CYP2C9, CYP2C19 and CYP3A4 activities. MATERIALS AND METHODS Probe substrate-based high performance liquid chromatography (HPLC) methods were established for CYP2C9, CYP2C19 and CYP3A4 whereas a fluorescence-based enzyme assay was established for CYP2C8. The metabolite formations were examined after incubation of probe substrate with respective CYP isoform in the present or absent of LP extracts. The inhibitory effect of LP was characterized with kinetic parameters IC(50) and K(i) values. RESULTS LP extracts showed differential effect of CYP activities with the order of inhibitory potency as follows: dichloromethane>hexane>ethanol>aqueous. This differential effect was only observed in CYP2C isoforms but not CYP3A4. Both the hexane and DCM extracts exhibited moderate to potent inhibition towards CYP2C activities in different modes including non-competitive, competive and mixed-type. The DCM effect was notably strong for CYP2C8 and CYP2C9 showing K(i) values of below 1 μg/ml. The selectivity of LP for CYP2C isoforms rather than CYP3A4 may be attributed to the presence of relatively small, lipophilic yet slightly polar compounds within the LP extracts. CONCLUSIONS The results of our study revealed that phytoconstituents contained in LP, particularly in hexane and dichloromethane extracts, were able to selectively inhibit CYP2C isoforms. The inactivation was characterized by low K(i) values, in particular, in CYP2C8 and CYP2C9. These in vitro data indicate that LB preparations contain constituents that can potently inhibit CYP2C activities and suggest that this herb should be examined for potential pharmacokinetic drug interactions in vivo.
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Affiliation(s)
- Yan Pan
- School of Pharmacy and Health Sciences, International Medical University, 126, Jalan 19/155B, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
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DA FONSECA RUTE, MENZIANI MARIACRISTINA, MELO ANDRÉ, RAMOS MARIAJOÃO. Modelling the metabolic action of human and rat CYP1A2 and its relationship with the carcinogenicity of heterocyclic amines. Mol Phys 2009. [DOI: 10.1080/00268970310001603112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- RUTE DA FONSECA
- a REQUIMTE/Departamento de Química, Faculdade de Ciências , Universidade do Porto, Rua do Campo Alegre , 687, 4169-007 , Porto , Portugal
| | | | - ANDRÉ MELO
- a REQUIMTE/Departamento de Química, Faculdade de Ciências , Universidade do Porto, Rua do Campo Alegre , 687, 4169-007 , Porto , Portugal
| | - MARIA JOÃO RAMOS
- a REQUIMTE/Departamento de Química, Faculdade de Ciências , Universidade do Porto, Rua do Campo Alegre , 687, 4169-007 , Porto , Portugal
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Lewis DFV, Ito Y. Human P450s involved in drug metabolism and the use of structural modelling for understanding substrate selectivity and binding affinity. Xenobiotica 2009; 39:625-35. [DOI: 10.1080/00498250903000255] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Lewis DF, Ito Y. Human cytochromes P450 in the metabolism of drugs: new molecular models of enzyme-substrate interactions. Expert Opin Drug Metab Toxicol 2008; 4:1181-6. [PMID: 18721112 DOI: 10.1517/17425255.4.9.1181] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The overall predictive ability of molecular modelling, as applied to the cytochrome P450 (CYP) system, is analysed in the light of current developments in a variety of techniques, including X-ray crystallography, molecular biology, enzyme kinetics, molecular mechanics and dynamics, in relation to its relevance to drug metabolism in humans. This review demonstrates that it is possible to generate realistic models for the major human CYPs, which metabolise xenobiotics that compare favourably with crystal structures, and thus may be used to derive substrate binding energies that agree closely with experimental K(m) values obtained from enzyme kinetics.
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Affiliation(s)
- David Fv Lewis
- University of Surrey, Centre for Toxicology, Faculty of Health and Medical Sciences, Guildford, Surrey, UK.
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Lewis DFV, Lake BG, Dickins M. Quantitative structure-activity relationships within a homologous series of 7-alkoxyresorufins exhibiting activity towards CYP1A and CYP2B enzymes: molecular modelling studies on key members of the resorufin series with CYP2C5-derived models of human CYP1A1, CYP1A2, CYP2B6 and CYP3A4. Xenobiotica 2008; 34:501-13. [PMID: 15277012 DOI: 10.1080/00498250410001691316] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
1. The results of quantitative structure-activity relationships (QSARs) within a homologous series of 7-n-alkoxyresorufins are reported. They are consistent with homology modelling of the relevant P450s involved in their metabolism. 2. QSARs were generated for activities involving CYP1A and CYP2B enzymes with structural descriptors relating to compound planarity and other shape parameters, together with certain features of the n-alkoxyresorufin electronic structure, especially electron densities and superdelocalizabilities. 3. A quadratic relationship between compound lipophilicity and binding to CYP2B enzymes was apparent, and which indicated maximal interaction for 7-pentoxyresorufin. Such indications help to explain enzyme selectivity in terms of optimal alkyl chain length for fitting within the relevant active site region. 4. Calculation of the binding affinities for methoxy-, ethoxy-, pentoxy- and benzyloxy-resorufins towards either CYP1A2 or CYP2B6 enzymes, depending on the 7-alkoxyresorufin agree favourably with experimental values obtained from K(m) determinations.
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Affiliation(s)
- David F V Lewis
- School of Biomedical and Molecular Sciences, University of Surrey, Guildford GU2 7XH, UK.
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Ito Y, Kondo H, Goldfarb PS, Lewis DFV. Analysis of CYP2D6 substrate interactions by computational methods. J Mol Graph Model 2008; 26:947-56. [PMID: 17764997 DOI: 10.1016/j.jmgm.2007.07.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Revised: 07/18/2007] [Accepted: 07/20/2007] [Indexed: 10/23/2022]
Abstract
Cytochrome P450 CYP2D6 is involved in the oxidation of well over 150 drugs and, in general, those which contain a basic nitrogen atom in the molecule. To clarify how the residues of CYP2D6 are utilized for orientating a wide range of its specific substrates and distinguishing them from a variety of other organic compounds, docking studies by AutoDock and molecular dynamics (MD) simulations were conducted. Specific ligands were docked to both the homology model and crystal structures optimally to estimate the site of reaction on the ligand molecule and the binding energy for the complex, which were generally in good agreement with the experimental data. MD simulation for the CYP2D6-propranolol complex was then carried out to reveal the amino acid residues interacting with the substrate at the active site. Phe-120, Glu-216, Asp-301, and Phe-483 are identified as the substrate-binding residues in agreement with previously reported site-directed mutagenesis data and the crystal structure reported recently (PDB code: 2F9Q). As well as these residues, our theoretical prediction suggests that Phe-219 and Glu-222 are also important residues for mediating oxidation of substrates, especially propranolol.
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Affiliation(s)
- Yuko Ito
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-City, Fukuoka 820-8502, Japan.
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Hernandez CE, Kumar S, Liu H, Halpert JR. Investigation of the role of cytochrome P450 2B4 active site residues in substrate metabolism based on crystal structures of the ligand-bound enzyme. Arch Biochem Biophys 2006; 455:61-7. [PMID: 17027909 PMCID: PMC1773018 DOI: 10.1016/j.abb.2006.08.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 08/31/2006] [Accepted: 08/31/2006] [Indexed: 11/25/2022]
Abstract
Based on the X-ray crystal structures of 4-(4-chlorophenyl)imidazole (4-CPI)- and bifonazole (BIF)-bound P450 2B4, eight active site mutants at six positions were created in an N-terminal modified construct termed 2B4dH and characterized for enzyme inhibition and catalysis. I363A showed a >4-fold decrease in differential inhibition by BIF and 4-CPI (IC(50,BIF)/IC(50,4-CPI)). F296A, T302A, I363A, V367A, and V477A showed a 2-fold decreased k(cat) for 7-ethoxy-4-trifluoromethylcoumarin O-deethylation, whereas V367A and V477F showed an altered K(m). T302A, V367L, and V477A showed >4-fold decrease in total testosterone hydroxylation, whereas I363A, V367A, and V477F showed altered stereo- and regioselectivity. Interestingly, I363A showed a 150-fold enhanced k(cat)/K(m) with testosterone, and yielded a new metabolite. Furthermore, testosterone docking into three-dimensional models of selected mutants based on the 4-CPI-bound structure suggested a re-positioning of residues 363 and 477 to yield products. In conclusion, our results suggest that the 4-CPI-bound 2B4dH/H226Y crystal structure is an appropriate model for predicting enzyme catalysis.
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Affiliation(s)
- Cynthia E Hernandez
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-1031, USA
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Lewis DF, Ito Y, Goldfarb PS. Cytochrome P450 structures and their substrate interactions. Drug Dev Res 2006. [DOI: 10.1002/ddr.20040] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Lewis DFV, Ito Y, Lake BG. Metabolism of coumarin by human P450s: a molecular modelling study. Toxicol In Vitro 2005; 20:256-64. [PMID: 16157466 DOI: 10.1016/j.tiv.2005.08.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Revised: 07/08/2005] [Accepted: 08/01/2005] [Indexed: 10/25/2022]
Abstract
The oxidative metabolism of coumarin via several human cytochrome P450 (CYP) enzymes from families CYP1, CYP2 and CYP3 is rationalized in terms of molecular modelling studies carried out on the key interactions with various amino acid residues in the relevant active sites. The findings from modelling by homology with the CYP2C5 crystallographic template are in agreement with the known metabolism of coumarin in human P450s from the CYP1, CYP2 and CYP3 families, which has been published recently, and with independently reported information from site-directed mutagenesis studies.
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Affiliation(s)
- David F V Lewis
- School of Biomedical and Molecular Sciences, University of Surrey, Stag Hill, Guildford, Surrey GU2 7XH, UK.
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Abstract
Advances in bioinformatics and protein modeling algorithms, in addition to the enormous increase in experimental protein structure information, have aided in the generation of databases that comprise homology models of a significant portion of known genomic protein sequences. Currently, 3D structure information can be generated for up to 56% of all known proteins. However, there is considerable controversy concerning the real value of homology models for drug design. This review provides an overview of the latest developments in this area and includes selected examples of successful applications of the homology modeling technique to pharmaceutically relevant questions. In addition, the strengths and limitations of the application of homology models during all phases of the drug discovery process are discussed.
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Takahashi S, Zhao Y, O’Maille PE, Greenhagen BT, Noel JP, Coates RM, Chappell J. Kinetic and molecular analysis of 5-epiaristolochene 1,3-dihydroxylase, a cytochrome P450 enzyme catalyzing successive hydroxylations of sesquiterpenes. J Biol Chem 2005; 280:3686-96. [PMID: 15522862 PMCID: PMC2859954 DOI: 10.1074/jbc.m411870200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The final step of capsidiol biosynthesis is catalyzed by 5-epiaristolochene dihydroxylase (EAH), a cytochrome P450 enzyme that catalyzes the regio- and stereospecific insertion of two hydroxyl moieties into the bicyclic sesquiterpene 5-epiaristolochene (EA). Detailed kinetic studies using EA and the two possible monohydroxylated intermediates demonstrated the release of 1beta-hydroxy-EA ((OH)EA) at high EA concentrations and a 10-fold catalytic preference for 1beta(OH)EA versus 3alpha(OH)EA, indicative of a preferred reaction order of hydroxylation at C-1, followed by that at C-3. Sequence alignments and homology modeling identified active-site residues tested for their contribution to substrate specificity and overall enzymatic activity. Mutants EAH-S368C and EAH-S368V exhibited wild-type catalytic efficiencies for 1beta(OH)EA biosynthesis, but were devoid of the successive hydroxylation activity for capsidiol biosynthesis. In contrast to EAH-S368C, EAH-S368V catalyzed the relative equal biosynthesis of 1beta(OH)EA, 2beta(OH)EA, and 3beta(OH)EA from EA with wild-type efficiency. Moreover, EAH-S368V converted approximately 1.5% of these monohydroxylated products to their respective ketone forms. Alanine and threonine mutations at position 368 were significantly compromised in their conversion rates of EA to capsidiol and correlated with 3.6- and 5.7-fold increases in their Km values for the 1beta(OH)EA intermediate, respectively. A role for Ile486 in the successive hydroxylations of EA was also suggested by the EAH-I468A mutant, which produced significant amounts 1beta(OH)EA, but negligible amounts of capsidiol from EA. The altered product profile of the EAH-I486A mutant correlated with a 3.6-fold higher Km for EA and a 4.4-fold slower turnover rate (kcat) for 1beta(OH)EA. These kinetic and mutational studies were correlated with substrate docking predictions to suggest how Ser368 and Ile486 might contribute to active-site topology, substrate binding, and substrate presentation to the oxo-Fe-heme reaction center.
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Affiliation(s)
- Shunji Takahashi
- Plant Physiology, Biochemistry, and Molecular Biology Program, Agronomy Department, University of Kentucky, Lexington, Kentucky, 40546-0312
| | - Yuxin Zhao
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801
| | - Paul E. O’Maille
- Salk Institute for Biological Studies, La Jolla, California 92037
| | - Bryan T. Greenhagen
- Plant Physiology, Biochemistry, and Molecular Biology Program, Agronomy Department, University of Kentucky, Lexington, Kentucky, 40546-0312
| | - Joseph P. Noel
- Salk Institute for Biological Studies, La Jolla, California 92037
| | - Robert M. Coates
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801
| | - Joe Chappell
- Plant Physiology, Biochemistry, and Molecular Biology Program, Agronomy Department, University of Kentucky, Lexington, Kentucky, 40546-0312
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Oda A, Yamaotsu N, Hirono S. Studies of Binding Modes of (S)-Mephenytoin to Wild Types and Mutants of Cytochrome P450 2C19 and 2C9 Using Homology Modeling and Computational Docking. Pharm Res 2004; 21:2270-8. [PMID: 15648259 DOI: 10.1007/s11095-004-7680-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
PURPOSE This study investigated the structural features of CYP2C19 complexed with (S)-mephenytoin, using computational methods. In addition to wild-type CYP2C19 proteins (1A and 1B), which have selective 4-hydroxylase activities of (S)-mephenytoin, CYP2C19 mutants were also studied, together with a wild type and artificial mutants of CYP2C19. METHODS Three-dimensional structures of wild-type and mutant proteins of CYP2C19 and CYP2C9 were estimated from homology modeling using the crystal structure of rabbit CYP2C5 as a reference. The binding mode of (S)-mephenytoin to CYP2C19 was investigated using computational docking. RESULTS The results reproduced the specific bindings between (S)-mephenytoin and the wild types of CYP2C19. Our findings suggest that Asp293 of CYP2C19 plays an important role in the binding of (S)-mephenytoin, which was surrounded by Vall13 and Ala297, and points the phenyl ring at the heme iron. In addition the wild types of CYP2C19, the computational docking studies also accounted for the experimental activities of CYP2C19 mutants, and wild-type and mutant CYP2C19 proteins. CONCLUSIONS These results confirm that the predicted three-dimensional structure of the CYP2C19-(S)-mephenytoin complex is reasonable, and that this strategy is useful for investigating complex structures. Virtual screening for drug discovery can also be carried out using these methods.
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Affiliation(s)
- Akifumi Oda
- Discovery Laboratories, Toyama Chemical Co Ltd, 2-4-1 Shimookui, Toyama 930-8508, Japan.
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Lewis DFV. Quantitative structure-activity relationships (QSARs) within the cytochrome P450 system: QSARs describing substrate binding, inhibition and induction of P450s. Inflammopharmacology 2004; 11:43-73. [PMID: 15035734 DOI: 10.1163/156856003321547112] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Quantitative structure-activity relationships (QSARs) within substrates, inducers and inhibitors of cytochromes P450 involved in xenobiotic metabolism are reported, together with QSARs associated with induction, inhibition and metabolic rate. The importance of frontier orbitals and shape descriptors, such as planarity (estimated by the area/depth(2) parameter) and rectangularity (estimated by the length/width parameter) is discussed, particularly in the context of the COMPACT system which discriminates between several P450 families associated with the activation and detoxication of xenobiotics. The use of parameters, particularly those derived from homology modelling of mammalian (especially human) P450s that are involved in exogenous metabolism, in generating QSARs for P450 substrates is discussed in the context of explaining differences in the binding affinities of human P450 substrates which are pharmacologically active.
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Affiliation(s)
- David F V Lewis
- School of Biomedical and Life Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK.
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Jalas JR, Seetharaman M, Hecht SS, Murphy SE. Molecular modelling of CYP2A enzymes: application to metabolism of the tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Xenobiotica 2004; 34:515-33. [PMID: 15277013 DOI: 10.1080/00498250410001713131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
1. Tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is a lung carcinogen in a variety of animal models and a putative human lung carcinogen. Its tumorigenic potential is unmasked via cytochrome P450 (CYP)-mediated hydroxylation of the carbon atoms adjacent to the nitroso moiety (i.e. alpha-hydroxylation). Therefore, elucidation of enzyme-substrate interactions that facilitate alpha-hydroxylation is important to gain insight into the tumorigenic mechanism of NNK and to develop potent inhibitors of this detrimental reaction. 2. Molecular models of CYP2A enzymes from mice, rats and humans that are catalysts of NNK bioactivation were constructed and used, in conjunction with docking experiments, to identify active-site residues that make important substrate contacts. 3. Docking studies revealed that hydrophobic residues at positions 117, 209, 365 and 481, among others, play critical roles in orienting NNK in the active site to effect alpha-hydroxylation. These molecular models were then used to rationalize the stereo- and regioselectivity, as well as the efficiency, of CYP2A-mediated NNK metabolism.
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Affiliation(s)
- J R Jalas
- Department of Chemistry, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, MN 55455, USA
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Abstract
The human cytochrome P450 (CYP) complement of heme-thiolate enzymes is reviewed. Of the 57 individual P450s characterized in Homo sapiens thus far, it is apparent that approximately one-half are associated with the metabolism of drugs and other xenobiotics, whereas the other half have endogenous functions in steroid, prostanoid, eicosanoid and fatty acid metabolism. This review covers the extent of enzyme functionality for the known human P450s, focusing primarily on their role in the Phase I metabolism of foreign compounds, which involves the CYP1, CYP2 and CYP3 families.
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Affiliation(s)
- David F V Lewis
- School of Biomedical and Molecular Sciences, University of Surrey, UK.
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Hlavica P, Schulze J, Lewis DFV. Functional interaction of cytochrome P450 with its redox partners: a critical assessment and update of the topology of predicted contact regions. J Inorg Biochem 2003; 96:279-97. [PMID: 12888264 DOI: 10.1016/s0162-0134(03)00152-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The problem of donor-acceptor recognition has been the most important and intriguing one in the area of P450 research. The present review outlines the topological background of electron-transfer complex formation, showing that the progress in collaborative investigations, combining physical techniques with chemical-modification and immunolocalization studies as well as site-directed mutagenesis experiments, has increasingly enabled the substantiation of hypothetical work resulting from homology modelling of P450s. Circumstantial analysis reveals the contact regions for redox proteins to cluster on the proximal face of P450s, constituting parts of the highly conserved, heme-binding core fold. However, more variable structural components located in the periphery of the hemoprotein molecules also participate in donor docking. The cross-reactivity of electron carriers, purified from pro- and eukaryotic sources, with a diversity of P450 species points at a possible evolutionary conservation of common anchoring domains. While electrostatic mechanisms appear to dominate orientation toward each other of the redox partners to generate pre-collisional encounter complexes, hydrophobic forces are likely to foster electron transfer events by through-bonding or pi-stacking interactions. Moreover, electron-tunneling pathways seem to be operative as well. The availability of new P450 crystal structures together with improved validation strategies will undoubtedly permit the production of increasingly satisfactory three-dimensional donor-acceptor models serving to better understand the molecular principles governing functional association of the redox proteins.
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Affiliation(s)
- P Hlavica
- Walther-Straub-Institut für Pharmakologie und Toxikologie, Nussbaumstrasse 26, D-80336, Munich, Germany.
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Kumar S, Scott EE, Liu H, Halpert JR. A rational approach to Re-engineer cytochrome P450 2B1 regioselectivity based on the crystal structure of cytochrome P450 2C5. J Biol Chem 2003; 278:17178-84. [PMID: 12609983 DOI: 10.1074/jbc.m212515200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The regioselectivity for progesterone hydroxylation by cytochrome P450 2B1 was re-engineered based on the x-ray crystal structure of cytochrome P450 2C5. 2B1 is a high K(m) progesterone 16alpha-hydroxylase, whereas 2C5 is a low K(m) progesterone 21-hydroxylase. Initially, nine individual 2B1 active-site residues were changed to the corresponding 2C5 residues, and the mutants were purified from an Escherichia coli expression system and assayed for progesterone hydroxylation. At 150 microm progesterone, I114A, F297G, and V363L showed 5-15% of the 21-hydroxylase activity of 2C5, whereas F206V showed high activity for an unknown product and a 13-fold decrease in K(m). Therefore, a quadruple mutant, I114A/F206V/F297G/V363L (Q), was constructed that showed 60% of 2C5 progesterone 21-hydroxylase activity and 57% regioselectivity. Based on their 2C5-like testosterone hydroxylation profiles, S294D and I477F alone and in combination were added to the quadruple mutant. All three mutants showed enhanced regioselectivity (70%) for progesterone 21-hydroxylation, whereas only Q/I477F had a higher k(cat). Finally, the remaining three single mutants, V103I, V367L, and G478V, were added to Q/I477F and Q/S294D/I477F, yielding seven additional multiple mutants. Among these, Q/V103I/S294D/I477F showed the highest k(cat) (3-fold higher than that of 2C5) and 80% regioselectivity for progesterone 21-hydroxylation. Docking of progesterone into a three-dimensional model of this mutant indicated that 21-hydroxylation is favored. In conclusion, a systematic approach to convert P450 regioselectivity across subfamilies suggests that active-site residues are mainly responsible for regioselectivity differences between 2B1 and 2C5 and validates the reliability of 2B1 models based on the crystal structure of 2C5.
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Affiliation(s)
- Santosh Kumar
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555-1031, USA.
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