Drugs, non-drugs, and disease category specificity: Organ effects by ligand pharmacology

SAR and QSAR in Environmental Research

Volumn 24, Issue 4, 2013, Pages 319-331

  Garcia Sosa A T ^a   Maran, U ^a  

^a UNIVERSITY OF TARTU   (Estonia)

Author keywords

Bayesian; chemical library; drug design; organ; specificity; toxicity

Indexed keywords

CLASSIFICATION (OF INFORMATION); DRUG INTERACTIONS; LIBRARIES; MOLECULAR BIOLOGY;

BAYESIAN; BAYESIAN CLASSIFIER; CHEMICAL LIBRARIES; CHEMICAL SPACE; DRUG DESIGN; MOLECULAR PROPERTIES; ORGAN; PROPERTY; SPECIFICITY; STATISTICALLY SIGNIFICANT DIFFERENCE;

LIGANDS;

DRUG;

CHEMISTRY; DRUG DESIGN; ISOLATION AND PURIFICATION; MOLECULAR BIOLOGY; PHARMACOLOGY; PHYSICAL CHEMISTRY; PROCEDURES; STATISTICAL MODEL;

CHEMISTRY; DRUG DESIGN; MODELS, STATISTICAL; MOLECULAR BIOLOGY; PHARMACEUTICAL PREPARATIONS; PHARMACOLOGY; PHYSICOCHEMICAL PHENOMENA;

EID: 84891510691     PISSN: 1062936X     EISSN: 1029046X     Source Type: Journal    
DOI: 10.1080/1062936X.2013.773373     Document Type: Article

References (30)

1. Keiser, M.J., Irwin, J.J. and Shoichet, B.K. 2010. The chemical basis of pharmacology. Biochemistry, 49: 10267 - 10276.
2. World Health Organization, Anatomical Therapeutic Chemical Classification [online], 2012. Available at www.whocc.no/atc/structure_and_principles/
3. Garcia-Sosa, A.T. and Mancera, R.L. 2010. Free energy calculations of mutations involving a tightly bound water molecule and ligand substitutions in a ligand-protein complex. Mol. Inf., 29: 589 - 600.
4. Panagiotou, G. and Taboureau, O. 2012. The impact of network biology in pharmacology and toxicology. SAR QSAR Environ. Res., 23: 221 - 235.
5. Curtis, C., Shah, S., Chin, S.-F., Turashvili, G., Rueda, O.M., Dunning, M.J., Speed, D., Lynch, A.G., Samarajiwa, S., Yuan, Y., Graf, S., Ha, G., Haffari, G., Bashashati, A., Russell, R., McKinney, S., METABRIC Group, Langerød, A., Green, A., Provenzano, E., Wishart, G., Pinder, S., Watson, P., Markowetz, F., Murphy, L., Ellis, I., Purushotham, A., Børresen-Dale, A.-L., Brenton, J.D., Tavarel, S., Caldas, C. and Aparicio, S. 2012. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature, 486: 346 - 352.
6. Garcia-Sosa, A.T., Maran, U. and Hetenyi, C. 2012. Molecular property filters describing pharmacokinetics and drug binding. Curr. Med. Chem., 19: 1646 - 1662.
7. Garcia-Sosa, A.T., Oja, M., Hetenyi, C. and Maran, U. 2012. Disease-specific differentiation between drugs and non-drugs using principal component analysis of their molecular descriptor space. Mol. Inf., 31: 369 - 383.
8. Garcia-Sosa, A.T., Oja, M., Hetenyi, C. and Maran, U. 2012. DrugLogit: Logistic discrimination between drugs and non-drugs including disease-specificity by assigning probabilities based on molecular properties. J. Chem Inf. Model., 52: 2165 - 2180.
9. Campillos, M., Kuhn, M., Gavin, A.-C., Jensen, L.J. and Bork, P. 2008. Drug target identification using side-effect similarity. Science, 321: 263 - 266.
10. Nidhi, Glick, M., Davies, J.W. and Jenkins, J.L. 2006. Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases. J. Chem. Inf. Model., 46: 1124 - 1133.
11. Azzaoui, K., Hamon, J., Faller, B., Whitebread, S., Jacoby, E., Bender, A., Jenkins, J.L. and Urban, L. 2007. Modeling promiscuity based on in vitro safety pharmacology profiling data. ChemMedChem, 2: 874 - 880.
12. Wang, R., Fang, X., Lu, Y. and Wang, S. 2004. The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J. Med. Chem., 47: 2977 - 2980.
13. Zhang, J.-W., Aizawa, M., Amari, S., Iwasawa, Y., Nakano, T. and Nakata, K. 2004. Development of KiBank, a database supporting structure- based drug design. Comput. Biol. Chem., 28: 401 - 407.
14. Ababou, A. and Ladbury, J.E. 2007. Survey of the year 2005: Literature on applications of isothermal titration calorimetry. J. Mol. Recognit., 20: 4 - 14.
15. Wishart, D.S., Knox, C., Guo, A.C., Shrivastava, S., Hassanali, M., Stothard, P., Chang, Z. and Woolsey, J. 2006. DrugBank: A Knowledgebase for Drugs, Drug Actions and Drug Targets. Nucleic Acids Res., 34: D668 - D672.
16. Shanghai Institute of Organic Chemistry, PDBbind database version 2009; software available at http://www.pdbbind-cn.org/
17. i Database; available at http://pdsp.med.unc.edu/pdsp.php
18. Cheng, T., Zhao, Y., Li, X., Lin, F., Xu, Y., Zhang, X., Li, Y. and Wang, R. 2007. Computation of octanol-water partition coefficients by guiding an additive model with knowledge. J. Chem. Inf. Model., 47: 2140 - 2148.
19. ChemAxon, Marvin Beans version 5.6.0.1; software available at http://www.chemaxon.com
20. Kuntz, I.D., Chen, K., Sharp, K.A. and Kollman, P.A. 1999. The maximal affinity of ligands. Proc. Natl. Acad. Sci. U. S. A., 96: 9997 - 10002.
21. Hopkins, A.L. and Groom, C.R. 2004. Ligand efficiency: A useful metric for lead selection. Drug Discovery Today, 9: 430 - 431.
22. Garcia-Sosa, A.T., Sild, S. and Maran, U. 2009. Docking and virtual screening using distributed grid technology. QSAR Comb. Sci., 28: 815 - 821.
23. Garcia-Sosa, A.T., Hetényi, C. and Maran, U. 2010. Drug efficiency indices for improvement of molecular docking scoring functions. J. Comput. Chem., 31: 174 - 184.
24. Garcia-Sosa, A.T., Sild, S., Takkis, K. and Maran, U. 2011. Combined approach using ligand efficiency, cross-docking, and antitarget hits for wild-type and drug-resistant Y181C HIV-1 reverse transcriptase. J. Chem. Inf. Model., 51: 2595 - 2611.
25. Hetenyi, C., Maran, U., Garcia-Sosa, A.T. and Karelson, M. 2007. Structure-based calculation of drug efficiency indices. Bioinformatics, 23: 2678 - 2685.
26. R Development Core Team, R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna; software available at http://www.R-project.org
27. Crawshaw, J. and Chambers, J. 2001. A Concise Course in Advanced Level Statistics, Cheltenham, U.K: Nelson Thornes.
28. Mathews, B.W. 1975. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405: 442 - 451.
29. Mizuno, S., Yamaguchi, T., Fukushima, A., Matsuyama, Y. and Ohasi, Y. 2005. Overlap coefficient for assessing the similarity of pharmacokinetic data between ethnically different populations. Clinical Trials, 2: 174 - 181.
30. Lipinski, C., Lombardo, F., Dominy, B.W. and Feeney, P.J. 1997. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Delivery Rev., 23: 3 - 25.