AmineDB: Large scale docking of amines with CYP2D6 and scoring for druglike properties - Towards defining the scope of the chemical defense against foreign amines in humans

Xenobiotica

Volumn 37, Issue 3, 2007, Pages 221-245

  Costache, A D ^a   Trawick, D ^a   Bohl, D ^a   Sem, D S ^a  

^a Marquette University   (United States)

Author keywords

AmineDB; Amines and CYP2D6; CYP2D6; Modeling of CYP2D6; Substrate docking

Indexed keywords

AMINE; CODEINE; CYTOCHROME P450 2D6; FLUOXETINE; LIGAND; PSYCHOTROPIC AGENT; QUINIDINE;

ARTICLE; BAYES THEOREM; BINDING AFFINITY; CORRELATION ANALYSIS; DATA BASE; DRUG BINDING; DRUG BINDING SITE; DRUG METABOLISM; DRUG SPECIFICITY; DRUG STRUCTURE; ENZYME BINDING; IC 50; IONIZATION; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR WEIGHT; SCORING SYSTEM;

AMINES; BAYES THEOREM; BINDING SITES; CYTOCHROME P-450 CYP2D6; DATABASES, FACTUAL; DRUG EVALUATION, PRECLINICAL; HUMANS; LIGANDS; METABOLIC DETOXICATION, PHASE I; PSYCHOTROPIC DRUGS; SUBSTRATE SPECIFICITY; XENOBIOTICS;

EID: 33947314331     PISSN: 00498254     EISSN: 13665928     Source Type: Journal    
DOI: 10.1080/00498250601089162     Document Type: Article

References (71)

1. Bertelsen KM, Venkatakrishnan K, von Moltke LL, Obach RS, Greenblatt DJ. 2003. Apparent mechanism-based inhibition of human CYP2D6 in vitro by paroxetine: Comparison with fluoxetine and quinidine. Drug Metabolism and Disposition 31:289-293.
2. Bertilsson L, Dahl ML, Dalen P, Al-Shurbaji A. 2002. Molecular genetics of CYP2D6: Clinical relevance with focus on psychotropic drugs. British Journal of Clinical Pharmacology 53:111-122.
3. Bezeley P, Prithivi S, Struble CA, Povinelli R, Sem DS. 2006. Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: Predicting affinity and conformational sampling. Journal of Chemical Information and Modeling 46:2698-2708.
4. Casabianca LB, de Dios AC. 2006. Relationship between NMR shielding and heme binding strength for a series of 7-substituted quinolines. Journal of Physical Chemistry A 110:7787-7792.
5. Cohen LH, Remley MJ, Raunig D, Vaz ADN. 2003. In Vitro drug interactions of Cytochrome P450: An evaluation of fluorogenic to conventional substrates. Drug Metabolism and Disposition 31:1005-1015.
6. de Graaf C, Oostenbrink C, Keizers PH, van der Wijst T, Jongejan A, Vermeulen NP. 2006. Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking. Journal of Medicinal Chemistry 49:2417-2430.
7. de Groot MJ, Ackland MJ, Horne VA, Alex AA, Jones BC. 1999a. Novel approach to predicting P450-mediated drug metabolism: Development of a combined protein and pharmacophore model for CYP2D6. Journal of Medicinal Chemistry 42:1515-1524.
8. de Groot MJ, Ackland MJ, Horne VA, Alex AA, Jones BC. 1999b. A novel approach to predicting P450 mediated drug metabolism. CYP2D6 catalyzed N-dealkylation reactions and qualitative metabolite predictions using a combined protein and pharmacophore model for CYP2D6. Journal of Medicinal Chemistry 42:4062-4070.
9. de Groot MJ, Bijloo GJ, Martens BJ, van Acker FA, Vermeulen NP. 1997. A refined substrate model for human cytochrome P450 2D6. Chemical Research in Toxicology 10:41-48.
10. de Groot MJ, Vermeulen NP, Kramer JD, van Acker FA, Donne-Op den Kelder GM. 1996. A three-dimensional protein model for human cytochrome P450 2D6 based on the crystal structures of P450 101, P450 102, and P450 108. Chemical Research in Toxicology 9:1079-1091.
11. Dewar MJS, Hashmall JA, Venier CG. 1968. Ground states of conjugated molecules. IX. Hydrocarbon radicals and radical ions. Journal of the American Chemical Society 90:1953-1957.
12. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP. 1985. AM1: A new general purpose quantum mechanical molecular model. Journal of the American Chemical Society 107:3902-3909.
13. Ekins S, Bravi G, Binkley S, Gillespie JS, Ring BJ, Wikel JH, Wrighton SA. 1999. Three and four dimensionalquantitative structure activity relationship (3D/4D-QSAR) analyses of CYP2D6 inhibitors. Pharmacogenetics 9:477-489.
14. Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP. 1997. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. Journal of Computer-aided Molecular Design 11:425-445.
15. Ellis SW, Hayhurst GP, Smith G, Lightfoot T, Wong MM, Simula AP, Ackland MJ, Sternberg MJ, Lennard MS, Tucker GT, et al. 1995. Evidence that aspartic acid 301 is a critical substrate-contact residue in the active site of cytochrome P450 2D6. Journal of Biological Chemistry 270:29055-29058.
16. Flanagan JU, Marechal JD, Ward R, Kemp CA, McLaughlin LA, Sutcliffe MJ, Roberts GC, Paine MJ, Wolf CR. 2004. Phe120 contributes to the regiospecificity of cytochrome P450 2D6: Mutation leads to the formation of a novel dextromethorphan metabolite. Biochemical Journal 380:353-360.
17. Ghose AK, Viswanadhan VN, Wendoloski JJ. 1998. Prediction of hydrophobic (lipophilic) properties of small organic molecules using fragment methods: An analysis of AlogP and ClogP methods. Journal of Physical Chemistry A 102:3762-3772.
18. Guengerich FP, Miller GP, Hanna IH, Martin MV, Leger S, Black C, Chauret N, Silva JM, Trimble LA, Yergey JA, et al. 2002. Diversity in the oxidation of substrates by cytochrome P450 2D6: Lack of an obligatory role of aspartate 301-substrate electrostatic bonding. Biochemistry 41:11025-11034.
19. Guex N, Peitsch MC. 1997. SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modelling. Electrophoresis 18:2714-2723.
20. Hassan M, Brown RD, Varma-O'Brien, Rogers D. 2006. Cheminformatics analysis and learning in a data pipelining environment, Molecular Diversity 10:283-299.
21. Hayhurst GP, Harlow J, Chowdry J, Gross E, Hilton E, Lennard MS, Tucker GT, Ellis SW. 2001. Influence of phenylalanine-481 substitutions on the catalytic activity of cytochrome P450 2D6. Biochemical Journal 355:373-379.
22. Irwin JJ, Shoichet BK. 2005. ZINC - a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling 45:177-182.
23. Islam SA, Wolf CR, Lennard MS, Sternberg MJ. 1991. A three-dimensional molecular template for substrates of human cytochrome P450 involved in debrisoquine 4-hydroxylation. Carcinogenesis 12:2211-2219.
24. Jones G, Willett P, Glen RC, Leach AR, Taylor R. 1997. Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology 267:727-748.
25. Keizers PH, de Graaf C, de Kanter FJ, Oostenbrink C, Feenstra KA, Commandeur JN, Vermeulen NP. 2005. Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-N-alkylamphetamines: In silico predictions and experimental validation. Journal of Medicinal Chemistry 48:6117-6127.
26. Kemp CA, Flanagan JU, van Eldik AJ, Marechal JD, Wolf CR, Roberts GC, Paine MJ, Sutcliffe MJ. 2004. Validation of model of cytochrome P450 2D6: An in silico tool for predicting metabolism and inhibition. Journal of Medicinal Chemistry 47:5340-5346.
27. Kirton SB, Kemp CA, Tomkinson NP, St-Gallay S, Sutcliffe MJ. 2002. Impact of incorporating the 2C5 crystal structure into comparative models of cytochrome P450 2D6. Proteins 49:216-231.
28. Koymans LM, Vermeulen NP, Baarslag A, Donne-Op den Kelder GM. 1993. A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building. Journal of Computer-aided Molecular Design 7:281-289.
29. Koymans L, Vermeulen NP, van Acker SA, te Koppele JM, Heykants JJ, Lavrijsen K, Meuldermans W, Donne-Op den Kelder GM. 1992. A predictive model for substrates of cytochrome P450-debrisoquine (2D6). Chemical Research in Toxicology 5:211-219.
30. Leed A, DuBay K, Ursos LM, Sears D, De Dios AC, Roepe PD. 2002. Solution structures of antimalarial drug-heme complexes. Biochemistry 41:10245-10255.
31. Lemberger L, Bergstrom RF, Wolen RL, Farid NA, Enas GC, Aronoff GR. 1985. Fluoxetine: Clinical pharmacology and physiologic disposition. Journal of Clinical Psychiatry 46:14-19.
32. Lewis DFV. 2001. Guide to cytochromes P450 structure and function. New York: Taylor & Francis.
33. Lewis DFV. 2003. Human cytochromes P450 associated with the phase 1 metabolism of drugs and other xenobiotics: A compilation of substrates and inhibitors of the CYP1, CYP2 and CYP3 families. Current Medicinal Chemistry 10:1955-1972.
34. Lewis DF, Eddershaw PJ, Goldfarb PS, Tarbit MH. 1997. Molecular modelling of cytochrome P4502D6 (CYP2D6) based on an alignment with CYP102: Structural studies on specific CYP2D6 substrate metabolism. Xenobiotica 27:319-339.
35. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. 2001. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews 46:1-26.
36. Lussenburg BM, Keizers PH, de Graaf C, Hidestrand M, Ingelman-Sundberg M, Vermeulen NP, Commandeur JN. 2005. The role of phenylalanine 483 in cytochrome P450 2D6 is strongly substrate dependent. Biochemical Pharmacology 70:1253-1261.
37. McLaughlin LA, Paine MJ, Kemp CA, Marechal JD, Flanagan JU, Ward CJ, Sutcliffe MJ, Roberts GC, Wolf CR. 2005. Why is quinidine an inhibitor of cytochrome P450 2D6? The role of key active-site residues in quinidine binding. Journal of Biological Chemistry 280:38617-38624.
38. Meyer UA, Gut J, Kronbach T, Skoda C, Meier UT, Catin T, Dayer P. 1996. The molecular mechanisms of two common polymorphisms of drug oxidation - evidence for functional changes in cytochrome P-450 isozymes catalysing bufuralol and mephenytoin oxidation. Xenobiotica 16:449-464.
39. Michalets EL. 1998. Update: Clinically significant cytochrome P-450 drug interactions. Pharmacotherapy 18:84-112.
40. Modi S, Paine MJ, Sutcliffe MJ, Lian LY, Primrose WU, Wolf CR, Roberts GC. 1996. A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding. Biochemistry 35:4540-4550.
41. Morgan HL. 1965. The generation of a unique machine description for chemical structures - A technique developed at Chemical Abstract Service. Journal of Chemical Documentation 2:107-113.
42. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. 1998. Automated docking using a lamarckian genetic algorithm and empirical binding free energy function. Journal of Computational Chemistry 19:1639-1662.
43. Mortimer O, Persson K, Ladona MG, Spalding D, Zanger UM, Meyer UA, Rane A. 1990. Polymorphic formation of morphine from codeine in poor and extensive metabolizers of dextromethorphan: Relationship to the presence of immunoidentified cytochrome P-450IID1. Clinical Pharmacology and Therapeutics 47:27-35.
44. Olah MM, Bologa CG, Oprea TI. 2004. Strategies for compound selection. Current Drug Discovery Technologies 1:211-220.
45. Ortiz de Montellano P. 2005. Structure, function and biochemistry. 3rd ed. New York: Plenum Press.
46. Paine MJ, McLaughlin LA, Flanagan JU, Kemp CA, Sutcliffe MJ, Roberts GC, Wolf CR. 2003. Residues glutamate 216 and aspartate 301 are key determinants of substrate specificity and product regioselectivity in cytochrome P450 2D6. Journal of Biological Chemistry 278:4021-4027.
47. Peitsch MC. 1996. ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. Biochemical Society Transactions 24:274-279.
48. Rowland P, Blaney FE, Smyth MG, Jones JJ, Leydon VR, Oxbrow AK, Lewis CJ, Tennant MG, Modi S, Eggleston DS, et al. 2006. Crystal structure of human cytochrome P450 2D6. Journal of Biological Chemistry 281:7614-7622.
49. Sadowski J. 2004. 3D structure generation. In: Gasteiger J, editor. Handbook of chemoinformaticsfrom data to knowledge. Weinheim: Wiley-VCH.
50. Sadowski J, Gasteiger J. 1993. From atoms and bonds to three-dimensional atomic coordinates: Automatic model builders. Chemical Reviews 93:2567-2581.
51. Schenkman JB, Sligar SG, Cinti DL. 1981. Substrate interaction with cytochrome P-450. Pharmacology and Therapeutics 12:43-71.
52. Schoch GA, Yano JK, Wester MR, Griffin KJ, Stout CD, Johnson EF. 2004. Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. Journal of Biological Chemistry 279:9497-9503.
53. Schwede T, Kopp J, Guex N, Peitsch MC. 2003. SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Research 31:3381-3385.
54. Slaughter RL, Edwards DJ. 1995. Recent advances: The cytochrome P450 enzymes. Annals of Pharmacotherapy 29:619-624.
55. Spina E, Avenoso A, Scordo MG, Ancione M, Madia A, Gatti G, Perucca E. 2002. Inhibition of risperidone metabolism by fluoxetine in patients with schizophrenia: A clinically relevant pharmacokinetic drug interaction. Journal of Clinical Psychopharmacology 22:419-423.
56. Strausberg RL, Schreiber SL. 2003. From knowing to controlling: A path from genomics to drugs using small molecule probes. Science 300:294-295.
57. Trubetskoy OV, Gibson JR, Marks BD. 2005. Highly miniaturized formats for in vitro drug metabolism assays using Vivid® fluorescent substrates and recombinant human cytochrome P450 enzymes. Journal of Biomolecular Screening 10:55-66.
58. Venhorst J, Onderwater RC, Meerman JH, Commandeur JN, Vermeulen NP. 2000. Influence of N-substitution of 7-methoxy-4-(aminomethyl)-coumarin on cytochrome P450 metabolism and selectivity. Drug Metabolism and Disposition 28:1524-1532.
59. Venhorst J, ter Laak AM, Commandeur JN, Funae Y, Hiroi T, Vermeulen NP. 2003. Homology modeling of rat and human cytochrome P450 2D (CYP2D) isoforms and computational rationalization of experimental ligandbinding specificities. Journal of Medicinal Chemistry 46:74-86.
60. Walsh P. (Editor) 2003. Physician's desk reference. New Jersey: Medical Economics and Thomson Healthcare.
61. Wang R, Lai L, Wang S. 2002. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. Journal of Computer-aided Molecular Design 16:11-26.
62. Wang R, Lu Y, Wang S. 2003. Comparative evaluation of 11 scoring functions for molecular docking. Journal of Medicinal Chemistry 46:2287-2303.
63. Wester MR, Yano JK, Schoch GA, Yang C, Griffin KJ, Stout CD, Johnson EF. 2004. The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0-Å resolution. Journal of Biological Chemistry 279:35630-35637.
64. Williams PA, Cosme J, Ward A, Angove HC, Matak Vinkovic D, Jhoti H. 2003. Crystal structure of human cytochrome P450 2C9 with bound warfarin. Nature 424:464-468.
65. Williams PA, Cosme J, Vinkovic DM, Ward A, Angove HC, Day PJ, Vonrhein C, Tickle IJ, Jhoti H. 2004. Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone. Science 305:683-686.
66. Wolff T, Distlerath LM, Worthington MT, Groopman JD, Hammons GJ, Kadlubar FF, Prough RA, Martin MV, Guengerich FP. 1985. Substrate specificity of human liver cytochrome P-450 debrisoquine 4-hydroxylase probed using immunochemical inhibition and chemical modeling. Cancer Research 45:2116-2122.
67. Xia X, Maliski EG, Gallant P, Rogers D. 2004. Classification of kinase inhibitors using a Bayesian model. Journal of Medicinal Chemistry 47:4463-4470.
68. Yano JK, Wester MR, Schoch GA, Griffin KJ, Stout CD, Johnson EF. 2004. The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-Å resolution. Journal of Biological Chemistry 279:38091-38094.
69. Yano JK, Hsu MH, Griffin KJ, Stout CD, Johnson EF. 2005. Structures of human microsomal cytochrome P450 2A6 complexed with coumarin and methoxsalen. Nature Structural and Molecular Biology 12:822-823.
70. Yao H, Costache AD, Sem DS. 2004. Chemical proteomic tool for ligand mapping of CYP anti-targets: An NMR-compatible 3D QSAR descriptor in the heme-based coordinate system. Journal of Chemical Information and Computer Science 44:1456-1465.
71. Zanger UM, Raimundo S, Eichelbaum M. 2004. Cytochrome P450 2D6: Overview and update on pharmacology, genetics, biochemistry. Naunyn-Schmiedebergs Archives of Pharmacology 369:23-37.