Latent hit series hidden in high-throughput screening data

Journal of Medicinal Chemistry

Volumn 55, Issue 3, 2012, Pages 1161-1170

  Varin, Thibault ^a   Didiot, Marie Cecile ^a   Parker, Christian N ^a   Schuffenhauer, Ansgar ^a  

^a NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BENZALKONIUM CHLORIDE; DIMETHYL SULFOXIDE; GENOMIC RNA; RESAZURIN;

ARTICLE; CELL ASSAY; CELL GROWTH; CELL PROLIFERATION; CELL VIABILITY; CONTROLLED STUDY; ENCEPHALOMYOCARDITIS VIRUS; HIGH THROUGHPUT SCREENING; INTERNAL RIBOSOME ENTRY SITE; LUMINESCENCE; NONHUMAN; PROSPECTIVE STUDY; PROTEIN EXPRESSION; PROTEIN PROCESSING;

CELL LINE, TUMOR; CELL SURVIVAL; DATABASES, FACTUAL; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; ENCEPHALOMYOCARDITIS VIRUS; GENES, REPORTER; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; LUCIFERASES, FIREFLY; PROTEIN BIOSYNTHESIS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RIBOSOMES; RNA, VIRAL; VIRUS INTERNALIZATION;

EID: 84856854230     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm201328e     Document Type: Article

References (31)

1. Frearson, J. A.; Collie, I. T. HTS and hit finding in academia: from chemical genomics to drug discovery Drug Discovery Today 2009, 14, 1150-1158
2. Mayr, L. M.; Bojanic, D. Novel trends in high-throughput screening Curr. Opin. Pharmacol. 2009, 9, 580-588
3. Mayr, L. M.; Fuerst, P. The future of high-throughput screening J. Biomol. Screening 2008, 13, 443-448 (Pubitemid 351905082)
4. Macarron, R.; Banks, N. M.; Bojanic, D.; Burns, D. J.; Cirovic, D. A.; Garyantes, T.; Green, D. V. S.; Hertzberg, R. P.; Janzen, W. P.; Paslay, J. W.; Schopfer, U.; Sittampalam, G. S. Impact of high-throughput screening in biomedical research Nat. Rev. Drug Discovery 2011, 10, 188-195
5. Varin, T.; Gubler, H.; Parker, C. N.; Zhang, J. H.; Raman, P.; Ertl, P.; Schuffenhauer, A. Compound set enrichment: A novel approach to analysis of primary HTS data J. Chem. Inf. Model. 2010, 50, 2067-2078
6. Inglese, J.; Auld, D. S.; Jadhav, A.; Johnson, R. L.; Simeonov, A.; Yasgar, A.; Zheng, W.; Austin, C. P. Quantitative high-throughput screening: A titration-based approach that efficiently identifies biological activities in large chemical libraries Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 11473-11478 (Pubitemid 44182476)
7. Kauvar, L. M.; Higgins, D. L.; Villar, H. O.; Sportsman, J. R.; Engqvistgoldstein, A.; Bukar, R.; Bauer, K. E.; Dilley, H.; Rocke, D. M. Predicting ligand-binding to proteins by affinity fingerprinting Chem. Biol. 1995, 2, 107-118
8. Hsu, N.; Cai, D. Y.; Damodaran, K.; Gomez, R. F.; Keck, J. G.; Laborde, E.; Lum, R. T.; Macke, T. J.; Martin, G.; Schow, S. R.; Simon, R. J.; Villar, H. O.; Wick, M. M.; Beroza, P. Novel cyclooxygenase-1 inhibitors discovered using affinity fingerprints J. Med. Chem. 2004, 47, 4875-4880 (Pubitemid 39238262)
9. Beroza, P.; Damodaran, K.; Lum, R. T. Target-related affinity profiling: Telik's lead discovery technology Curr. Top. Med. Chem. 2005, 5, 371-381 (Pubitemid 40753874)
10. Mestres, J.; Veeneman, G. H. Identification of "latent hits" in compound screening collections J. Med. Chem. 2003, 46, 3441-3444 (Pubitemid 36909817)
11. Wilk, W; Zimmermann, T. J.; Kaiser, M.; Waldmann, H. Principles, implementation, and application of biology-oriented synthesis (BIOS) Biol. Chem. 2010, 391, 491-497
12. Andrews, K. M.; Cramer, R. D. Toward general methods of targeted library design: topomer shape similarity searching with diverse structures as queries J. Med. Chem. 2000, 43, 1723-1740 (Pubitemid 30305006)
13. Boehm, M.; Wu, T. Y.; Claussen, H.; Lemmen, C. Similarity searching and scaffold hopping in synthetically accessible combinatorial chemistry spaces J. Med. Chem. 2008, 51, 2468-2480 (Pubitemid 351628508)
14. Varin, T.; Schuffenhauer, A.; Ertl, P.; Renner, S. Mining for bioactive scaffolds with scaffold network: improved compound set enrichment from primary screening data J. Chem. Inf. Model. 2011, 51, 1528-1538
15. National Center for Biotechnology Information. PubChem BioassayDatabase; AID=893, source=Scripps Research Institute Molecular ScreeningCenter, http://pubchem.ncbi.nlm.nih.gov/assay/assay/assay.cgi?aid=893 (accessed June, 17, 2010).
16. National Center for Biotechnology Information. PubChem BioassayDatabase; AID=886, source=Scripps Research Institute Molecular ScreeningCenter, http://pubchem.ncbi.nlm.nih.gov/assay/assay/assay.cgi?aid=886 (accessed January, 11, 2010).
17. Didiot, M. C.; Serafini, S.; Pfeifer, M. J.; King, F. J.; Parker, C. N. Multiplexed reporter gene assays: monitoring the cell viability and the compound kinetics on luciferase activity J. Biomol. Screening 2011, 16, 786-793
18. Abdi, H. The Bonferonni and Sidak corrections for multiple comparisons. In Encyclopedia of Measurement and Statistics, 1 st ed.; Salkind, N. J., Ed.; Sage Publications: Thousand Oaks, CA, 2007; Vol. 1, pp 103-107 (available at http://www.utdallas.edu/~herve/Abdi-Bonferroni2007-pretty.pdf, accessed Aug 13, 2008).
19. Johnson, M. A.; Maggiora, G. M., Eds. Concepts and Applications of Molecular Similarity; Wiley: New York, 1990.
20. Renner, S.; van Otterlo, W. A.; Dominguez Seoane, M.; Möcklinghoff, S.; Hofmann., B.; Wetzel, S.; Schuffenhauer, A.; Ertl, P.; Oprea, T. I.; Steinhilber, D.; Brunsveld, L.; Rauh, D.; Waldmann, H. Bioactivity-guided mapping and navigation of chemical space Nat. Chem. Biol. 2009, 5, 585-592
21. Yan, S. F.; Asatryan, H.; Li, J.; Zhou, Y. Y. Novel statistical approach for primary high-throughput screening hit selection J. Chem. Inf. Model. 2005, 45, 1784-1790 (Pubitemid 41784752)
22. Glick, M.; Jenkins, J. L.; Nettles, J, H.; Hitchings, H.; Davies, J. W. Enrichment of high-throughput screening data with increasing levels of noise using support vector machines, recursive partitioning, and Laplacian-modified naive Bayesian classifiers J. Chem. Inf. Model. 2006, 46, 193-200 (Pubitemid 43282114)
23. Yan, S. F.; King, F. J.; He, Y.; Caldwell, J. S.; Zhou, Y. Y. Learning from the data: Mining of large high-throughput screening databases J. Chem. Inf. Model. 2006, 46, 2381-2395 (Pubitemid 46008112)
24. Lajiness, M.; Watson, I. Dissimilarity-based approaches to compound acquisition Curr. Opin. Chem. Biol. 2008, 12, 3
25. Lipkin, M. J.; Stevens, A. P.; Livingstone, D. J.; Harris, C. J. How large does a compound screening collection need to be? Comb. Chem. High Throughput Screening 2008, 11, 482-493 (Pubitemid 351969365)
26. Schreyer, S. K.; Parker, C. N.; Maggiora, G. M. Data shaving: A novel strategy for analysis of high throughput screening data J. Chem. Inf. Comput. Sci. 2003, 44, 470-479
27. Nilakantan, R.; Immermann, F.; Haraki, K. A novel approach to combinatorial library design Comb. Chem. High Throughput Screening 2002, 5, 105-110 (Pubitemid 34475162)
28. Grover, G. S.; Turner, B. A.; Parker, C. N.; Meier, J.; Lala, D. S.; Lee, P. H. Multiplexing nuclear receptors for agonist identification in a cell-based reporter gene high-throughput screen J. Biomol. Screening 2002, 8, 239-246
29. Lyer, P.; Stumpfe, D.; Bajorath, J. Molecular mechanism-based network-like similarity graphs reveal relationships between different types of receptor ligands and structural changes that determine agonistic, inverse-agonistic, and antagonistic effects J. Chem. Inf. Model. 2011, 51, 1281-1286
30. Zhang, J. H.; Chung, T. D.; Oldenburg, K. R. A simple statistical parameter for use in evaluation and validation of high throughput screening assays J. Biomol. Screening 1999, 4, 67-73 (Pubitemid 29278954)
31. Pipeline Pilot, version 8.0. Accelrys Software Inc., San Diego, CA, 2010. http://accelrys.com/products/pipeline-pilot/.