Chemoinformatics profiling of ionic liquids-uncovering structure-cytotoxicity relationships with network-like similarity graphs

Toxicological Sciences

Volumn 138, Issue 1, 2014, Pages 191-204

  Cruz Monteagudo, Maykel ^a,b   Cordeiro, Maria Natália Dias Soeiro ^a  

^a UNIVERSITY OF PORTO   (Portugal)

^b CENTRAL UNIVERSITY OF LAS VILLAS   (Cuba)

Author keywords

Cytotoxicity; Focused combinatorial library design; Ionic liquids; Network similarity graphs; SAR mining; SAR pathways; SAR trees; Structure cytotoxicity relationships

Indexed keywords

CYTOTOXICITY; FOCUSED COMBINATORIAL LIBRARY DESIGN; IONIC LIQUIDS; NETWORK SIMILARITY GRAPHS; SAR MINING; SAR PATHWAYS; SAR TREES; STRUCTURE-CYTOTOXICITY RELATIONSHIPS.;

COMPUTER GRAPHICS; COMPUTER SIMULATION; DATA MINING; IONIC LIQUIDS; MODELS, CHEMICAL; NEURAL NETWORKS (COMPUTER); STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84894311153     PISSN: 10966080     EISSN: 10960929     Source Type: Journal    
DOI: 10.1093/toxsci/kft210     Document Type: Article

References (36)

1. Anastas, P. A. and Warner, J. C. (1998). Green Chemistry: Theory and Practice. Oxford University Press, Oxford, UK.
2. Arning, J., Stolte, S., Boschen, A., Stock, F., Pitner, W.-R., Welz-Biermann, U., Jastorff, B., and Ranke, J. (2008). Qualitative and quantitative structure activity relationships for the inhibitory effects of cationic head groups, functionalised side chains and anions of ionic liquids on acetylcholinesterase. Green Chem. 10, 47-58.
3. Chem Axon. (2012a). J. Chem. for Excel, 5.10.2.725.
4. ChemAxon. (2012b). Marvin View, 5.10.2.
5. Cruz-Monteagudo, M., Ancede-Gallardo, E., Jorge, M., and Cordeiro, M. N. D. S. (2013). Chemoinformatics profiling of ionic liquids - Automatic and chemically interpretable cytotoxicity profiling, virtual screening and cytotoxicophore identification. Tox. Sci. doi:10.1093/toxsci/kft209
6. Durant, J. L., Leland, B. A., Henry, D. R., and Nourse, J. G. (2002). Reoptimization of MDL keys for use in drug discovery. J. Chem. Inf. Comput. Sci. 42, 1273-1280.
7. Frade, R. F., and Afonso, C. A. (2010). Impact of ionic liquids in environment and humans: an overview. Hum. Exp. Toxicol. 29, 1038-1054.
8. Hough, W. L., Smiglak, M., Rodriguez, H., Swatloski, R. P., Spear, S. K., Daly, D. T., Pernak, J., Grisel, J. E., Carliss, R. D., Soutullo, et al.. (2007). The third evolution of ionic liquids: active pharmaceutical ingredients. New J. Chem. 31, 1429-1436.
9. Lounkine, E., Wawer, M., Wassermann, A. M., and Bajorath, J. (2010). SARANEA: a freely available program to mine structure-activity andstructure-selectivity relationship information in compound data sets. J. Chem. Inf. Model. 50, 68-78.
10. Maggiora, G. M. (2006). On outliers and activity cliffs-why QSAR often disappoints. J. Chem. Inf. Model. 46, 1535.
11. Peltason, L., and Bajorath, J. (2007). SAR index: quantifying the nature of structure-activity relationships. J. Med. Chem. 50, 5571-5578.
12. Pham, T. P., Cho, C. W., and Yun, Y. S. (2010). Environmental fate and toxicity of ionic liquids: a review. Water Res. 44, 352-372.
13. Ranke, J., Cox, M., Muller, A., Schmidt, C., and Beyersmann, D. (2006). Sorption, cellular distribution, and cytotoxicity of imidazolium ionic liquids in mammalian cells - influence of lipophilicity. Toxicol. Environ. Chem. 88, 273-285.
14. Ranke, J., Molter, K., Stock, F., Bottin-Weber, U., Poczobutt, J., Hoffmann, J., Ondruschka, B., Filser, J., and Jastorff, B. (2004). Biological effects of imidazolium ionic liquids with varying chain lengths in acute Vibrio fischeri and WST-1 cell viability assays. Ecotoxicol. Environ. Saf. 58, 396-404.
15. Ranke, J., Muller, A., Bottin-Weber, U., Stock, F., Stolte, S., Arning, J., Stormann, R., and Jastorff, B. (2007a). Lipophilicity parameters for ionic liquid cations and their correlation to in vitro cytotoxicity. Ecotoxicol. Environ. Saf. 67, 430-438.
16. Ranke, J., Stolte, S., Stormann, R., Arning, J., and Jastorff, B. (2007b). Design of sustainable chemical products-the example of ionic liquids. Chem. Rev. 107, 2183-2206.
17. Rogers, R. D., and Seddon, K. R. (2003). Ionic Liquids as Green Solvents: Progress and Prospects. American Chemical Society, Washington DC.
18. Schuller, A., Schneider, G., and Byvatov, E. (2003). SMILIB: rapid assembly of combinatorial libraries in SMILES notation. QSAR Comb Sci. 22, 719-721.
19. Sheldon, R. A. (2005). Green solvents for sustainable organic synthesis: state of the art. Green Chem. 7, 267-278.
20. Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., and Willighagen, E. (2003). The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics. J. Chem. Inf. Comput. Sci. 43, 493-500.
21. Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., and Willighagen, E. L. (2006). Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. Curr. Pharm. Des. 12, 2111-2120.
22. Stock, F., Hoffmann, J., Ranke, J., Styrmann, R., Ondruschka, B., and Jastorff, B. (2004). Effects of ionic liquids on the acetylcholinesterase? a structure?activity relationship consideration. Green Chem. 6, 286-290.
23. Stolte, S., Arning, J., Bottin-Weber, U., Matzke, M., Stock, F., Thiele, K., Uerdingen, M., Welz-Biermann, U., Jastorff, B., and Ranke, J. (2006). Anion effects on the cytotoxicity of ionic liquids. Green Chem. 8, 621-629.
24. Stolte, S., Arning, J., Bottin-Weber, U., Muller, A., Pitner, W.-R., Welz-Biermann, U., Jastorff, B., and Ranke, J. (2007). Effects of different head groups and functionalised side chains on the cytotoxicity of ionic liquids. Green Chem. 9, 760-767.
25. Stumpfe, D., and Bajorath, J. (2012). Methods for SAR visualization. RSC Adv. 2, 369-378.
26. Varnek, A., Fourches, D., Hoonakker, F., and Solov'ev, V. P. (2005). Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures. J. Comput. Aided. Mol. Des. 19, 693-703.
27. Varnek, A., Fourches, D., Horvath, D., Klimchuk, O., Gaudin, C., Vayer, P., Solov'ev, V., Hoonakker, F., Tetko, I., and Gilles, M. (2008). ISIDA - platform for virtual screening based on fragment and pharmacophoric descriptors. Curr. Comput. Aided Drug Des. 4, 191-198.
28. Wassermann, A. M., Wawer, M., and Bajorath, J. (2010). Activity landscape representations for structure-activity relationship analysis. J. Med. Chem. 53, 8209-8223.
29. Wasserscheid, P., and Welton, T. (2003). Ionic Liquids in Synthesis. Wiley-VCH, Weinheim, Germany.
30. Wawer, M., and Bajorath, J. (2009). Systematic extraction of structure-activity relationship information from biological screening data. ChemMedChem 4, 1431-1438.
31. Wawer, M., and Bajorath, J. (2011). Extracting SAR information from a large collection of anti-malarial screening hits by NSG-SPT analysis. ACS Med. Chem. Lett. 2, 201-206.
32. Wawer, M., Lounkine, E., Wassermann, A. M., and Bajorath, J. (2010). Data structures and computational tools for the extraction of SAR information from large compound sets. Drug Discov. Today 15, 630-639.
33. Wawer, M., Peltason, L., and Bajorath, J. (2009). Elucidation of structure-activity relationship pathways in biological screening data. J. Med. Chem. 52, 1075-1080.
34. Wawer, M., Peltason, L., Weskamp, N., Teckentrup, A., and Bajorath, J. (2008). Structure-activity relationship anatomy by network-like similarity graphs and local structure-activity relationship indices. J. Med. Chem. 51, 6075-6084.
35. Welton, T. (1999). Room-Temperature Ionic Liquids. Solvents for Synthesis and Catalysis. Chem. Rev. 99, 2071-2084.
36. Zhao, D., Liao, Y., and Zhang, Z. (2007). Toxicity of ionic liquids. CLEAN 35, 42-48.