Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules

Bioinformatics

Volumn 26, Issue 22, 2010, Pages 2881-2888

  Cheng, Tiejun ^a   Wang, Yanli ^a   Bryant, Stephen H ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG;

ARTICLE; CHEMISTRY; DATA MINING; FACTUAL DATABASE; KNOWLEDGE BASE; LIBRARY; METHODOLOGY; UNITED STATES;

DATA MINING; DATABASES, FACTUAL; KNOWLEDGE BASES; NATIONAL LIBRARY OF MEDICINE (U.S.); PHARMACEUTICAL PREPARATIONS; UNITED STATES;

EID: 78149267865     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq550     Document Type: Article

References (40)

1. Berman, H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
2. Chen, B. and Wild, D.J. (2010) PubChem BioAssays as a data source for predictive models. J. Mol. Graphics Model., 28, 420-426.
3. Chen, B. et al. (2009) PubChem as a source of polypharmacology. J. Chem. Inf. Model., 49, 2044-2055.
4. DiMasi, J.A. et al. (2003) The price of innovation: new estimates of drug development costs. J. Health Econ., 22, 151-185.
5. Guha, R. (2008) Flexible web service infrastructure for the development and deployment of predictive models. J. Chem. Inf. Model., 48, 456-464.
6. Han, L. et al. (2008) Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem. BMC Bioinf., 9, 401.
7. Kanehisa, M. et al. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res., 32, D277-D280.
8. Klausmeyer, P. et al. (2007) Identification of a new natural camptothecin analogue in targeted screening for HIF-1( inhibitors. Planta Med., 73, 49-52.
9. Lee, A.C. et al. (2008) Data mining the NCI60 to predict generalized cytotoxicity. J. Chem. Inf. Model., 48, 1379-1388.
10. Li, Q. et al. (2009) A novel method for mining highly imbalanced high-throughput screening data in PubChem. Bioinformatics, 25, 3310-3316.
11. Park, J. and Liu, A.Y. (2001) JNK phosphorylates the HSF1 transcriptional activation domain: role of JNK in the regulation of the heat shock response. J. Cell. Biochem., 82, 326-338.
12. Paull, K.D. et al. (1989) Display and analysis of patterns of differential activity of drugs against human tumor cell lines: development of mean graph and COMPARE algorithm. J. Natl Cancer Inst., 81, 1088-1092.
13. Ping, Y.-H. et al. (2006) Anticancer effects of low-dose 10-hydroxycamptothecin in human colon cancer. Oncol. Rep., 15, 1273-1279.
14. Pizzolato, J.F. and Saltz, L.B. (2003) The camptothecins. Lancet, 361, 2235-2242.
15. Rabow, A.A. et al. (2002) Mining the National Cancer Institute's tumor-screening database: identification of compounds with similar cellular activities. J. Med. Chem., 45, 818-840.
16. Rapisarda, A. et al. (2002) Identification of small molecule inhibitors of hypoxiainducible factor 1 transcriptional activation pathway. Cancer Res., 62, 4316-4324.
17. Rohrer, S.G. and Baumann, K. (2009) Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data. J. Chem. Inf. Model., 49, 169-184.
18. Seo, J. and Shneiderman, B. (2002) Interactively exploring hierarchical clustering results. IEEE Computer, 35, 80-86.
19. Shannon, P. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
20. Shi, L.M. et al. (1998a) Mining the NCI anticancer drug discovery databases: genetic function approximation for the QSAR Study of anticancer ellipticine analogues. J. Chem. Inf. Comput. Sci., 38, 189-199.
21. Shi, L.M. et al. (1998b) Mining the National Cancer Institute anticancer drug discovery database: cluster analysis of ellipticine analogs with p53-inverse and central nervous system-selective patterns of activity. Mol. Pharmacol., 53, 241-251.
22. Shi, L.M. et al. (1999) Mining and visualizing large anticancer drug discovery databases. J. Chem. Inf. Comput. Sci., 40, 367-379.
23. Shoemaker, R.H. (2006) The NCI60 human tumour cell line anticancer drug screen. Nat. Rev. Cancer., 6, 813-823.
24. Staker, B.L. et al. (2005) Structures of three classes of anticancer agents bound to the human topoisomerase I-DNA covalent complex. J. Med. Chem., 48, 2336-2345.
25. Staker, B.L. et al. (2002) The mechanism of topoisomerase I poisoning by a camptothecin analog. Proc. Nat. Acad. Sci. USA., 99, 15387-15392.
26. van Osdol, W.W. et al. (1994) Use of the Kohonen self-organizing map to study the mechanisms of action of chemotherapeutic agents. J. Natl Cancer Inst., 86, 1853-1859.
27. Wallqvist, A. et al. (2003) Linking the growth inhibition response from the National Cancer Institute's anticancer screen to gene expression levels and other molecular target data. Bioinformatics, 19, 2212-2224.
28. Wang, H. et al. (2007) Chemical data mining of the NCI human tumor cell line database. J. Chem. Inf. Model., 47, 2063-2076.
29. Wang, Y. et al. (2009) PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res., 37, W623-W633.
30. Wang, Y. et al. (2010) An overview of the PubChem BioAssay resource. Nucleic Acids Res., 38, D255-D266.
31. Weinstein, J.N. et al. (1992) Neural computing in cancer drug development: predicting mechanism of action. Science, 258, 447-451.
32. Weinstein, J.N. et al. (1997) An information-intensive approach to the molecular pharmacology of cancer. Science, 275, 343-349.
33. Weis, D.C. et al. (2008) Data mining PubChem using a support vector machine with the signature molecular descriptor: classification of factor XIa inhibitors. J. Mol. Graphics Model., 27, 466-475.
34. Westerheide, S.D. et al. (2006) Triptolide, an inhibitor of the human heat shock response that enhances stress-induced cell death. J. Biol. Chem., 281, 9616-9622.
35. Wethington, S.L. et al. (2008) Key role of topoisomerase I inhibitors in the treatment of recurrent and refractory epithelial ovarian carcinoma. Expert Rev. Anticancer Ther., 8, 819-831.
36. Wishart, D.S. et al. (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res., 34, D668-D672.
37. Wishart, D.S. et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res., 36, D901-D906.
38. Xie, X.-Q. and Chen, J.-Z. (2008) Data mining a small molecule drug screening representative subset from NIH PubChem. J. Chem. Inf. Model., 48, 465-475.
39. Zaharevitz, D.W. et al. (2002) COMPARE: a web accessible tool for investigating mechanisms of cell growth inhibition. J. Mol. Graphics Model., 20, 297-303.
40. Zerhouni, E. (2003) The NIH roadmap. Science, 302, 63-72.