Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors

Journal of Chemical Information and Modeling

Volumn 46, Issue 6, 2006, Pages 2324-2332

  Renner, Steffen ^a   Schwab, Christof H ^b   Gasteiger, Johann ^c   Schneider, Gisbert ^a  

^a GOETHE UNIVERSITY   (Germany)

^b Molecular Networks GmbH   (Germany)

^c UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; CONFORMATIONS; CORRELATION METHODS; CRYSTAL STRUCTURE; DATABASE SYSTEMS; DRUG THERAPY;

CONFORMATIONAL FLEXIBILITY; CORRELATION VECTORS; PHARMACOPHORE SEARCHING; VIRTUAL SCREENING;

MOLECULAR DYNAMICS;

LIGAND; PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; CONFORMATION; CRYSTALLIZATION; METHODOLOGY; PLIABILITY; PROTEIN DATABASE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STATISTICAL MODEL; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; CHEMISTRY; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; LIGANDS; MODELS, STATISTICAL; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; PLIABILITY; PROTEINS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SOFTWARE;

EID: 33750434190     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050075s     Document Type: Article

References (32)

1. Virtual Screening for Bioactive Molecules; Böhm, H.-J., Schneider, G., Eds.; Wiley-VCH: Weinheim, New York, 2000.
2. Schneider, G.; Böhm, H.-J. Virtual Screening and Fast Automated Docking Methods. Drug Discovery Today 2002, 7, 64-70.
3. Perola, E.; Charifson, P. S. Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding. J. Med. Chem. 2004, 47, 2499-2510.
4. Boström, J. Reproducing the Conformation of Protein-Bound Ligands: A Critical Evaluation of Several Popular Conformational Searching Tools. J. Comput.-Aided Mol. Des. 2002, 15, 1137-1152.
5. Schwab, C. H. Conformational Analysis and Searching. In Handbook of Cheminformatics; Gasteiger, J., Ed.; Wiley-VCH: Weinheim, New York, 2003; pp 262-301.
6. Carhart, R. E.; Smith, D. H.; Venkataraghavan, R. Atom Pairs as Molecular Features in Structure-Activity Studies: Definition and Applications. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.
7. Schneider, G.; Neidhart, W.; Giller, T.; Schmid, G. "Scaffold- Hopping" by Topological Pharmacophore Search: A Contribution to Virtual Screening. Angew. Chem., Int. Ed. 1999, 58, 2894-2896.
8. Moreau, G.; Broto, P. The Autocorrelation of a Topological Structure: A New Molecular Descriptor. Nouv. J. Chim. 1980, 4, 359-360.
9. Wagener, M.; Sadowski, J.; Gasteiger, J. Autocorrelation of Molecular Surface Properties for Modeling Corticosteroid Binding Globulin and Cytosolic Ah Receptor Activity by Neural Networks. J. Am. Chem. Soc. 1995, 117, 7769-7775.
10. Fechner, U.; Franke, L.; Renner, S.; Schneider, P.; Schneider, G. Comparison of Correlation Vector Methods for Ligand-Based Similar ity Searching. J. Comput.-Aided Mol. Des. 2003, 17, 687-698.
11. Renner, S.; Noeske, T.; Parsons, C. G.; Schneider, P.; Weil, T.; Schneider, G. New Allosteric Modulators of Metabotropic Glutamate Receptor 5 (mGhiR5) Found by Ligand-Based Virtual Screening. ChemBioChem 2005, 6, 620-625.
12. Sheridan, R. P.; Miller, M. D.; Underwood, D. J.; Kearsley, S. K. Chemical Similarity Using Geometrie Atom Pair Descriptors. J. Chem. Inf. Comput Sci. 1996, 36, 128-136.
13. Renner, S.; Ludwig, V.; Boden, O.; Scheffer, U.; Göbel, M.; Schneider, G. New Inhibitors of the Tat-TAR RNA Interaction Found with a "Fuzzy" Pharmacophore Model. ChemBioChem 2005, 6, 1119-1125.
14. Renner, S.; Schneider, G. Scaffold-Hopping Potential of Ligand-Based Similarity Concepts. ChemMedChem 2006, 1, 181-185.
15. Renner, S.; Schneider, G. Fuzzy Pharmacophore Models from Molecular Alignments for Correlation-Vector Based Virtual Screening. J. Med. Chem. 2004, 47, 4653-4664.
16. Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures. J. Med. Chem. 2004, 47, 2977-2980.
17. Schneider, P.; Schneider, G. Collection of Bioactive Reference Compounds for Focused Library Design. QSAR Comb. Sci. 2003, 22, 713-718.
18. Sadowski, J.; Gasteiger, J.; Klebe, G. Comparison of Automatic Three-Dimensional Model Builders Using 639 X-Ray Structures. J. Chem. Inf. Comput. Sci. 1994, 34, 1000-1008.
19. (b) CORINA is available from Molecular Networks GmbH, Erlangen, Germany (http://www.mol-net.com).
20. ROTATE is available from Molecular Networks GmbH, Erlangen, Germany (www.mol-net.com).
21. MOE, Molecular Operating Environment. Distributor is available from Chemical Computing Group, Montreal, Canada (www.chemcomp.com).
22. Klebe, G.; Mietzner, T. A Fast and Efficient Method to Generate Biologically Relevant Conformations. J. Comput.-Aided Mol. Des. 1994, 8, 583-606.
23. (b) Klebe, G.; Mietzner, T.; Weber, F. Different Approaches Toward an Automatic Structural Alignment of Drug Molecules: Applications to Sterol Mimics, Thrombin and Thermolysin Inhibitors. J. Comput.-Aided Mol. Des. 1999, 13, 35-49.
24. Allen, F. H.; Kennard, O.; Watson, D. G. Crystallographic Databases: Search and Retrieval of Information from the Cambridge Structural Database. In Structure Correlation; Bürgi, H.-B., Dunitz, J. D., Eds; Wiley-VCH: Weinheim, New York, 1994; Vol. 1, pp 71-110.
25. (b) The Cambridge Structural Database (CSD) is available from Cambridge Crystallographic Data Centre, Cambridge, U.K. (www.ccdc.cam.ac.uk).
26. Klebe, G. Structure Correlation and Ligand/Receptor Interactions. In Structure Correlation; Bürgi, H.-B., Dunitz, J. D., Eds.; Wiley-VCH: Weinheim, New York, 1994; Vol. 2, pp 543-603.
27. Personal communications, Jens Sadowski, AstraZeneca R&D Mölndal, Sweden (MATCH3D was developed at the Computer-Chemie-Centrum, University of Erlangen-Nürnberg, Germany).
28. Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. Macromodel - An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics. J. Comput. Chem. 1990, 11, 440-467.
29. (b) MacroModel is available from Schrödinger LLC, Portland, OR, U.S.A. (www.schrodinger.com).
30. Boström, J.; Greenwood, J. R.; Gottfries, J. Assessing the Performance of OMEGA with Respect to Retrieving Bioactive Conformations. J. Mol. Graphics Modell. 2003, 21, 449-462.
31. (b) OMEGA is available from OpenEye Scientific Software, Santa Fe, NM. U.S.A. (www.eyesopen.com).
32. Zauhar, R. J.; Moyna, G.; Tian, L.; Li, Z.; Welsh, W. J. Shape Signatures: A New Approach to Computer-Aided Ligand- and Receptor-Based Drug Design. J. Med. Chem. 2003, 46, 5674-5690.