A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators

Proteins: Structure, Function and Genetics

Volumn 59, Issue 2, 2005, Pages 205-220

  Yang, Jinn Moon ^a   Shen, Tsai Wei ^a  

^a NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

Author keywords

Estrogen receptor; Evolutionary approach; Hot spots; Pharmacophore based scoring function; SERMs; Virtual screening

Indexed keywords

11 [4 [[5 [(4,4,5,5,5 PENTAFLUOROPENTYL)SULFONYL]PENTYL]OXY]PHENYL]ESTRADIOL; 4 HYDROXYTAMOXIFEN; ACOLBIFENE; ESTROGEN RECEPTOR; LIGAND; LY 326315; LY 357489; N BUTYL 11 (3,17BETA DIHYDROXYESTRA 1,3,5(10) TRIEN 7ALPHA YL) N METHYLUNDECANAMIDE; NAFOXIDINE; PHENOL DERIVATIVE; RALOXIFENE; SELECTIVE ESTROGEN RECEPTOR MODULATOR; UNCLASSIFIED DRUG; ZK 11901;

ACCURACY; ARTICLE; DATA BASE; DRUG BINDING SITE; DRUG SCREENING; EMPIRICISM; EVOLUTION; LIGAND BINDING; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN TARGETING; SCORING SYSTEM;

BINDING SITES; DATABASES, FACTUAL; DATABASES, PROTEIN; ESTROGEN ANTAGONISTS; ESTROGEN RECEPTOR MODULATORS; ESTROGENS; EVOLUTION, MOLECULAR; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; RECEPTORS, ESTROGEN; USER-COMPUTER INTERFACE;

EID: 16344377697     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20387     Document Type: Article

References (35)

1. Lyne PD. Structure-based virtual screening: an overview. Drug Discov Today 2002;7:1047-1055.
2. Shoichet BK, McGovern SL, Wei B, Irwin J. Lead discovery using molecular docking. Curr Opin Chem Biol 2002;6:439-446.
3. Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, Connolly DT, Shoichet BK. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem 2002;45:2213-2221.
4. Kubinyi H. QSAR and 3-D QSAR in drug design: 1. Methodology. Drug Discov Today 1997;2:457-467.
5. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecular-ligand interactions. J Mol Biol 1982;161:269-288.
6. Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997;267:727-748.
7. Kramer B, Rarey M, Lengauer T. Evaluation of the FlexX incremental construction algorithm for protein-ligand docking. Proteins 1999;37:228-241.
8. Ewing TJ, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 2001;15:411-428.
9. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J Comput Chem 1998;19:1639-1662.
10. Yang J-M, Chen C-C. GEMDOCK: a generic evolutionary method for molecular docking. Proteins 2004;55:288-304.
11. Gohlke H, Hendlich M, Klebe G. Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 2000;295: 337-356.
12. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta SJ, Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 1984;106: 765-784.
13. Gehlhaar DK, Verkhivker GM, Rejto P, Sherman CJ, Fogel DB, Fogel LJ, Freer ST. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Chem Biol 1995;2:317-324.
14. Bissantz C, Folkers G, Rognan D. Protein-based virtual screening of chemical databases: 1. Evaluation of different docking/scoring combinations. J Med Chem 2000;43:4759-4767.
15. Stahl M, Rarey M. Detailed analysis of scoring functions for virtual screening. J Med Chem 2001;44:1035-1042.
16. Langer T, Krovat EM. Chemical feature-based pharmacophores and virtual library screening for discovery of new leads. Curr Opin Drug Discov Dev 2003;6:370-376.
17. Fradera X, Knegtel RMA, Mestres J. Similarity-driven flexible ligand docking. Proteins 2000;40:623-637.
18. Hindle SA, Rarey M, Buning C, Lengauer T. Flexible docking under pharmacophore type constraints. J Comput Aided Mol Des 2002;16:129-149.
19. Pegg SC-H, Haresco JJ, Kuntz ID. A genetic algorithm for structure-based de novo design. J Comput Aided Mol Des 2001;15: 911-933.
20. Muegge I, Martin YC, Hajduk PJ, Fesik SW. Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. J Med Chem 1999;42:2498-2503.
21. Yang J-M. Development and evaluation of a generic evolutionary method for protein-ligand docking. J Comput Chem 2004;25:843-857.
22. Good AC, Cheney DL, Sitkoff DF, Tokarski JS, Stouch TR, Bassolino DA, Krystek SR, Li Y, Mason JS, Perkins TD. Analysis and optimization of structure-based virtual screening protocols: 2. Examination of docked ligand orientation sampling methodology: mapping a pharmacophore for success. J Mol Graph Model 2003;22:31-40.
23. Joseph-McCarthy D, Thomas BEI, Belmarsh M, Moustakas D, Alvarez JC. Pharmacophore-based molecular docking to account for ligand flexibility. Proteins 2003;51:172-188.
24. Miller CP. SERMs: evolutionary chemistry, revolutionary biology. Curr Pharm Des 2002;8:2089-2111.
25. Dutertre M, Smith CL. Molecular mechanisms of selective estrogen receptor modulator (SERM) action. J Pharmacol Exp Ther 2000;295:431-437.
26. Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, Agard DA, Greene GL. The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 1998;95:927-937.
27. van Lipzig MM, ter Laak AM, Jongejan A, Vermeulen NP, Wamelink M, Geerke D, Meerman JH. Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method. J Med Chem 2004;47:1018-1030.
28. Warnmark A, Treuter E, Gustafsson JA, Hubbard RE, Brzozowski AM, Pike AC. Interaction of transcriptional intermediary factor 2 nuclear receptor box peptides with the coactivator binding site of estrogen receptor alpha. J Biol Chem 2002;277:21862-21868.
29. Brzozowski AM, Pike AC, Dauter Z, Hubbard RE, Bonn T, Engstroem O, Oehman L, Greene GL, Gustafsson JA, Carlquist M. Molecular basis of agonism and antagonism in the oestrogen receptor. Nature 1997;389:753-758.
30. Renaud J, Bischoff SF, Buhl T, Floersheim P, Fournier B, Halleux C, Kallen J, Keller H, Schlaeppi JM, Stark W. Estrogen receptor modulators: identification and structure-activity relationships of potent ER-alpha-selective tetrahydroisoquinoline ligands. J Med Chem 2003;46:2945-2957.
31. Gust R, Keilitz R, Schmidt K. Synthesis, structural evaluation, and estrogen receptor interaction of 2,3-diarylpiperazines. J Med Chem 2002;45:2325-2337.
32. Garg R, Kapur S, Hansch C. Radical toxicity of phenols: a reference point for obtaining perspective in the formulation of QSAR. Med Res Rev 2001;21:73-82.
33. Fisher LS, Guner OF. Seeking novel leads through structure-based pharmacophore design. J Braz Chem Soc 2002;13:777-787.
34. Sadowski J, Gasteiger J, Klebe G. Comparison of automatic three-dimensional model builders using 639 X-ray structures. J Chem Inform Comput Sci 1994;34:1000-1008.
35. Jain AN. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem 2003;46: 499-511.