Rationalizing the role of SAR tolerance for ligand-based virtual screening

Journal of Chemical Information and Modeling

Volumn 51, Issue 4, 2011, Pages 837-842

  Ripphausen, Peter ^a   Nisius, Britta ^a   Wawer, Mathias ^a   Bajorath, Jürgen ^a  

^a UNIVERSITY OF BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINS;

ACTIVE COMPOUNDS; METHODOLOGICAL ASPECTS; MULTIPLE REGIONS; SCREENING TARGETS; STRUCTURE-ACTIVITY RELATIONSHIPS; TARGET LEVELS; TARGET PROTEINS; VIRTUAL SCREENING;

LIGANDS;

G PROTEIN COUPLED RECEPTOR; GLYCOGEN SYNTHASE KINASE 3; GLYCOGEN SYNTHASE KINASE 3 BETA; LIGAND;

ARTICLE; BIOLOGY; COMPUTER GRAPHICS; DRUG ANTAGONISM; DRUG SCREENING; LIBRARY; METHODOLOGY; STRUCTURE ACTIVITY RELATION;

COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DRUG EVALUATION, PRECLINICAL; GLYCOGEN SYNTHASE KINASE 3; LIBRARIES, DIGITAL; LIGANDS; RECEPTORS, G-PROTEIN-COUPLED; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 79955428414     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200064c     Document Type: Article

References (31)

1. Geppert, H.; Vogt, M.; Bajorath, J. Current Trends in Ligand-based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation J. Chem. Inf. Model. 2010, 50, 205-216
2. Eckert, H.; Bajorath, J. Molecular Similarity Analysis in Virtual Screening: Foundations, Limitations and Novel Approaches Drug Discovery Today 2007, 12, 225-233
3. Wassermann, A. M.; Wawer, M.; Bajorath, J. Activity Landscape Representations for Structure-Activity Relationship Analysis J. Med. Chem. 2010, 53, 8209-8223
4. Ripphausen, P.; Nisius, B.; Bajorath, J. State-of-the-Art in Ligand-based Virtual Screening. Drug Discovery Today, in press, doi:10.1016/j.drudis.2011. 02.011.
5. Liu, T.; Lin, Y.; Wen, X.; Jorissen, R. N.; Gilson, M. K. BindingDB: a Web-Accessible Database of Experimentally Determined Protein-Ligand Binding Affinities Nucleic Acids Res. 2007, 35, D198-D201
6. ChEMBL; European Bioinformatics Institute (EBI): Cambridge, U.K., 2010; http://www.ebi.ac.uk/chembl/. (Accessed January 10, 2011).
7. Willett, P. Searching Techniques for Databases of Two- and Three-dimensional Structures J. Med. Chem. 2005, 48, 1-17
8. Rogers, D.; Hahn, M. Extended-Connectivity Fingerprints J. Chem. Inf. Model. 2010, 50, 742-754
9. Scitegic Pipeline Pilot, student ed.; Accelrys, Inc.: San Diego, CA, 2010.
10. Wawer, M.; Bajorath, J. Extracting SAR Information from a Large Collection of Anti-Malarial Screening Hits by NSG-SPT Analysis ACS Med. Chem. Lett. 2011, 2, 201-206
11. Wawer, M.; Peltason, L.; Weskamp, N.; Teckentrup, A.; Bajorath, J. Structure-Activity Relationship Anatomy by Network-like Similarity Graphs and Local Structure-Activity Relationship Indices J. Med. Chem. 2008, 51, 6075-6084
12. Peltason, L.; Bajorath, J. SAR Index: Quantifying the Nature of Structure-Activity Relationships J. Med. Chem. 2007, 50, 5571-5578 (Pubitemid 350106013)
13. Fruchterman, T. M. J.; Reingold, E. M. Graph Drawing by Force-Directed Placement Software - Practice and Experience 1991, 21, 1129-1164
14. Csardi, G. igraph library, version 0.5.5; XXX: Budapest, Hungary, 2009; http://igraph.sourceforge.net/. (Accessed December 16, 2010).
15. Bates, D.; Chambers, J.; R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2010.
16. Franke, L.; Schwarz, O.; Müller-Kuhrt, L.; Hoernig, C.; Fischer, L.; George, S.; Tanrikulu, Y.; Schneider, P.; Werz, O.; Steinhilber, D.; Schneider, G. Identification of Natural-Product-Derived Inhibitors of 5-Lipoxygenase Activity by Ligand-Based Virtual Screening J. Med. Chem. 2007, 50, 2640-2646 (Pubitemid 46896071)
17. Chaudhaery, S. S.; Roy, K. K.; Shakya, N.; Saxena, G.; Sammi, S. R.; Nazir, A.; Nath, C.; Saxena, A. K. Novel Carbamates as Orally Active Acetylcholinesterase Inhibitors Found to Improve Scopolamine-Induced Cognition Impairment: Pharmacophore-Based Virtual Screening, Synthesis, and Pharmacology J. Med. Chem. 2010, 53, 6490-6505
18. Neves, M. A. C.; Dinis, T. C. P.; Colombo, G.; Sa e Melo, M. L. An Efficient Steroid Pharmacophore-Based Strategy to Identify New Aromatase Inhibitors Eur. J. Med. Chem. 2009, 44, 4121-4127
19. Foloppe, N.; Benwell, K.; Brooks, T. D.; Kennett, G.; Knight, A. R.; Misra, A.; Monck, N. J. T. Discovery and Functional Evaluation of Diverse Novel Human CB1 Receptor Ligands Bioorg. Med. Chem. Lett. 2009, 19, 4183-4190
20. Moree, W. J.; Kataoka, K.; Ramirez-Weinhouse, M. M.; Shiota, T.; Imai, M.; Sudo, M.; Tsutumi, T.; Endo, N.; Muroga, Y.; Hada, T.; Tanaka, H.; Morita, T.; Greene, J.; Barnum, D.; Saunders, J.; Kato, Y.; Myers, P. L.; Tarby, C. M. Small Molecule Antagonists Of the CCR2b Receptor. Part 2: Discovery Process and Initial Structure-Activity Relationships of Diamine Derivatives Bioorg. Med. Chem. Lett. 2004, 14, 5413-5416 (Pubitemid 39348936)
21. Byvatov, E.; Sasse, B. C.; Stark, H.; Schneider, G. From Virtual to Real Screening for D3 Dopamine Receptor Ligands ChemBioChem 2005, 6, 997-999 (Pubitemid 40825338)
22. Enyedy, I. J.; Sakamuri, S.; Zaman, W. A.; Johnson, K. M.; Wang, S. Pharmacophore-Based Discovery of Substituted Pyridines as Novel Dopamine Transporter Inhibitors Bioorg. Med. Chem. Lett. 2003, 13, 513-517 (Pubitemid 36259725)
23. Funk, O. F.; Kettmann, V.; Drimal, J.; Langer, T. Chemical Function Based Pharmacophore Generation of Endothelin-A Selective Receptor Antagonists J. Med. Chem. 2004, 47, 2750-2760 (Pubitemid 38656728)
24. Narum., L.; Norskov-Lauritsen, L.; Olesen, P. Scaffold Hopping and Optimization towards Libraries of Glycogen Synthase Kinase-3 Inhibitors Bioorg. Med. Chem. Lett. 2002, 12, 1525-1528 (Pubitemid 34521927)
25. Shoda, M.; Harada, T.; Kogami, Y.; Tsujita, R.; Akashi, H.; Kouji, H.; Stahura, F. L.; Xue, L.; Bajorath, J. Identification of Structurally Diverse Growth Hormone Secretagogue Agonists by Virtual Screening and Structure-Activity Relationship Analysis of 2-Formylaminoacetamide Derivates J. Med. Chem. 2004, 47, 4286-4290 (Pubitemid 39045434)
26. Al-Sha'er, M. A.; Taha, M. O. Elaborate Ligand-Based Modeling Reveals New Nanomolar Heat Shock Protein 90α Inhibitors J. Chem. Inf. Model. 2010, 50, 1706-1723
27. Tang, H.; Wang, X. S.; Huang, X.-P.; Roth, B. L.; Butler, K. V.; Kozikowski, A. P.; Jung, M.; Tropsha, A. Novel Inhibitors of Human Histone Deacetylase (HDAC) Identified by QSAR Modeling of Known Inhibitors, Virtual Screening, and Experimental Validation J. Chem. Inf. Model. 2009, 49, 461-476
28. Hajjo, R.; Grulke, C. M.; Golbraikh, A.; Setola, V.; Huang, X.-P.; Roth, B. L.; Tropsha, A. Development, Validation, and Use of Quantitative Structure-Activity Relationship Models of 5-Hydroxytryptamine (2B) Receptor Ligands to Identify Novel Receptor Binders and Putative Valvulopathic Compounds among Common Drugs J. Med. Chem. 2010, 53, 7573-7586
29. Koide, Y.; Uemoto, K.; Hasegawa, T.; Sada, T.; Murakami, A.; Takasugi, H.; Sakurai, A.; Mochizuki, N.; Takahashi, A.; Nishida, A. Pharmacophore-Based Design of Sphingosine-3 Receptor Antagonists That Include a 3,4- Dialkoxybenzophenone Scaffold J. Med. Chem. 2007, 50, 442-454 (Pubitemid 46239779)
30. Lescot, E.; Sopkova-de Oliveira Santos, J.; Dubessy, C.; Oulyadi, H.; Lesnard, A.; Vaudry, H.; Bureau, R.; Rault, S. Definition of New Pharmacophores for Nonpeptide Antagonists of Human Urotensin-II. Comparison with the 3D-structure of Human Urotensin-II and URP J. Chem. Inf. Model. 2007, 47, 602-612 (Pubitemid 46615961)
31. Peukert, S.; Brendel, J.; Pirard, B.; Strübing, C.; Kleemann, H.-W.; Böhme, T.; Hemmerle, H. Pharmacophore-Based Search, Synthesis, and Biological Evaluation of Anthranilic Amides as Novel Blockers of the Kv1.5 Channel Bioorg. Med. Chem. Lett. 2004, 14, 2823-2827 (Pubitemid 38569744)