Integrating high-content screening and ligand-target prediction to identify mechanism of action

Nature Chemical Biology

Volumn 4, Issue 1, 2008, Pages 59-68

  Young, Daniel W ^a,b,c   Bender, Andreas ^a   Hoyt, Jonathan ^a   McWhinnie, Elizabeth ^a   Chirn, Gung Wei ^a   Tao, Charles Y ^a   Tallarico, John A ^a   Labow, Mark ^a   Jenkins, Jeremy L ^a   Mitchison, Timothy J ^b   Feng, Yan ^a  

^a NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c Wolf   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL CYCLE REGULATION; DRUG DETERMINATION; FACTORIAL ANALYSIS; HIGH THROUGHPUT SCREENING; LIGAND BINDING; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; SPECTROFLUOROMETRY; STRUCTURE ACTIVITY RELATION;

EID: 37249026328     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.2007.53     Document Type: Article

References (47)

1. Haggarty, S.J. The principle of complementarity: chemical versus biological space. Curr. Opin. Chem. Biol. 9, 296-303 (2005).
2. Nichols, A. High content screening as a screening tool in drug discovery. Methods Mol. Biol. 356, 379-387 (2007).
3. Lang, P., Yeow, K., Nichols, A. & Scheer, A. Cellular imaging in drug discovery. Nat. Rev. Drug Discov. 5, 343-356 (2006).
4. Mitchison, T.J. Small-molecule screening and profiling by using automated microscopy. ChemBioChem 6, 33-39 (2005).
5. Blake, R.A. Target validation in drug discovery. Methods Mol. Biol. 356, 367-377 (2007).
6. Eggert, U.S. & Mitchison, T.J. Small molecule screening by imaging. Curr. Opin. Chem. Biol. 10, 232-237 (2006).
7. Carpenter, A. et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006).
8. Giuliano, K.A., Haskins, J.R. & Taylor, D.L. Advances in high content screening for drug discovery. Assay Drug Dev. Technol. 1, 565-577 (2003).
9. Lee, S. & Howell, B.J. High-content screening: emerging hardware and software technologies. Methods Enzymol. 414, 468-483 (2006).
10. Spearman, C. "General intelligence", objectively determined and measured. Am. J. Psychol. 15, 201-293 (1904).
11. Carroll, J.B. & Schweiker, R.F. Factor analysis in educational research. Rev. Educ. Res. 21, 368-388 (1951).
12. Floyd, F.J. & Widaman, K.F. Factor analysis in the development and refinement of clinical assessment instruments. Psychol. Assess. 7, 286-299 (1995).
13. Malinowski, E.R. Factor Analysis in Chemistry 1-432 (John Wiley and Sons, Inc., New York, 2002).
14. Stewart, D.W. The application and misapplication of factor analysis in marketing research. J. Mark. Res. 18, 51-62 (1981).
15. Tinsley, H.E.A. & Tinsley, D.J. Uses of factor analysis in counseling psychology research. J. Couns. Psychol. 34, 414-424 (1987).
16. Johnson, R.A. & Wichern, D.W. Applied Multivariate Statistical Analysis 426-542 (Prentice Hall, Inc., Upper Saddle River, New Jersey, USA, 2002).
17. Bender, A. & Glen, R.C. Molecular similarity: a key technique in molecular informatics. Org. Biomol. Chem. 2, 3204-3218 (2004).
18. Johnson, M., Lajiness, M. & Maggiora, G. Molecular similarity: a basis for designing drug screening programs. Prog. Clin. Biol. Res. 291, 167-171 (1989).
19. Maggiora, G.M. On outliers and activity cliffs-why QSAR often disappoints. J. Chem. Inf. Model. 46, 1535 (2006).
20. Hert, J. et al. New methods for ligand-based virtual screening: use of data fusion and machine learning to enhance the effectiveness of similarity searching. J. Chem. Inf. Model. 46, 462-470 (2006).
21. Carrieri, A., Centeno, N.B., Rodrigo, J., Sanz, F. & Carotti, A. Theoretical evidence of a salt bridge disruption as the initiating process for the alpha1d-adrenergic receptor activation: a molecular dynamics and docking study. Proteins 43, 382-394 (2001).
22. Schaper, K. Free-Wilson-type analysis of non-additive substituent effects on THPB dopamine receptor affinity using artificial neural networks. Quant. Struct. Act. Relat. 18, 354-360 (1999).
23. Gräfe, U. et al. Aurantimycins, new depsipeptide antibiotics from Streptomyces aurantiacus IMET 43917. Production, isolation, structure elucidation, and biological activity. J. Antibiot. (Tokyo) 48, 119-125 (1995).
24. Matsumoto, N. et al. Diperamycin, a new antimicrobial antibiotic produced by Streptomyces griseoaurantiacus MK393-AF2. I. Taxonomy, fermentation, isolation, physico-chemical properties and biological activities. J. Antibiot. (Tokyo) 51, 1087-1092 (1998).
25. Yuan, Y., Men, H. & Lee, C. Total synthesis of kendomycin: a macro-C-glycosidation approach. J. Am. Chem. Soc. 126, 14720-14721 (2004).
26. Manabe, T., Yoshimori, T., Henomatsu, N. & Tashiro, Y. Inhibitors of vacuolar-type H(+)-ATPase suppresses proliferation of cultured cells. J. Cell. Physiol. 157, 445-452 (1993).
27. Kawashima, J. et al. Antitumor activity of heptelidic acid chlorohydrin. J. Antibiot. (Tokyo) 47, 1562-1563 (1994).
28. Samuelsson, M.K., Pazirandeh, A., Davani, B. & Okret, S. p57Kip2, a glucocorticoid-induced inhibitor of cell cycle progression in HeLa cells. Mol. Endocrinol. 12, 1811-1822 (1999).
29. Bielawski, K., Winnicka, K. & Bielawska, A. Inhibition of DNA topoisomerases I and II, and growth inhibition of breast cancer MCF-7 cells by ouabain, digoxin and proscillaridin A. Biol. Pharm. Bull. 29, 1493-1497 (2006).
30. Ramirez-Ortega, M. et al. Proliferation and apoptosis of HeLa cells induced by in vitro stimulation with digitalis. Eur. J. Pharmacol. 534, 71-76 (2006).
31. Pauw, P.G., Kaffer, C.R., Petersen, R.J., Semerad, S.A. & Williams, D.C. Inhibition of myogenesis by ouabain: effect on protein synthesis. In Vitro Cell. Dev. Biol. Anim. 36, 133-138 (2000).
32. Schweighoffer, T. et al. Cytometric analysis of DNA replication inhibited by emetine and cyclosporin A. Histochemistry 96, 93-97 (1991).
33. Horiuchi, S. et al. Expression of progesterone receptor B is associated with G0/G1 arrest of the cell cycle and growth inhibition in NIH3T3 cells. Exp. Cell Res. 305, 233-243 (2005).
34. Owen, G.I., Richer, J.K., Tung, L., Takimoto, G. & Horwitz, K. Progesterone regulates transcription of the p21(WAF1) cyclin-dependent kinase inhibitor gene through Sp1 and CBP/p300. J. Biol. Chem. 273, 10696-10701 (1998).
35. Nidhi, G., Glick, M., Davies, J.W. & Jenkins, J.L. Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases. J. Chem. Inf. Model. 46, 1124-1133 (2006).
36. Checchi, P.M., Nettles, J.H., Zhou, J., Snyder, J.P. & Joshi, H.C. Microtubule-interacting drugs for cancer treatment. Trends Pharmacol. Sci. 24, 361-365 (2003).
37. Li, L. et al. Antitumor agents 155. Synthesis and biological evaluation of 3′,6,7-substituted 2-phenyl-4-quinolones as antimicrotubule agents. J. Med. Chem. 37, 3400-3407 (1994).
38. Shi, Q., Chen, K., Morris-Natschke, S.L. & Lee, K.H. Recent progress in the development of tubulin inhibitors as antimitotic antitumor agents. Curr. Pharm. Des. 4, 219-248 (1998).
39. Tong, Y.G. et al. Pseudolarix acid B, a new tubulin-binding agent, inhibits angiogenesis by interacting with a novel binding site on tubulin. Mol. Pharmacol. 69, 1226-1233 (2006).
40. Clemons, P.A. Complex phenotypic assays in high-throughput screening. Curr. Opin. Chem. Biol. 8, 334-338 (2004).
41. Loo, L.H., Wu, L.F. & Altschuler, S.J. Image-based multivariate profiling of drug responses from single cells. Nat. Methods 4, 445-453 (2007).
42. Olah, M. et al. in Chemoinformatics in Drug Discovery WOMBAT: World of Molecular Bioactivity (ed. Oprea, T.I.) 223-239 (Wiley-VCH, New York, 2004).
43. Jenkins, J.L., Bender, A. & Davies, J.W. In silico target fishing: predicting biological targets from chemical structure. Drug Discov. Today Technol. 3, 413-421 (2007).
44. Bender, A. & Glen, R.C. A discussion of measures of enrichment in virtual screening: comparing the information content of descriptors with increasing levels of sophistication. J. Chem. Inf. Model. 45, 1369-1375 (2005).
45. Bender, A., Mussa, H.Y., Reiling, S. & Glen, R.C. Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance. J. Chem. Inf. Model. 44, 1708-1718 (2004).
46. Glen, R.C. et al. Circular fingerprints: flexible molecular descriptors with applications from physical chemistry to ADME. IDrugs 9, 199-204 (2006).
47. Nettles, J.H. et al. Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors. J. Med. Chem. 49, 6802-6810 (2006).