365
11 Computational Toxicology in Drug Discovery: Opportunities and Limitations
40. Fung M, Thornton A, Mybeck K et al (2001) Evaluation of the characteristics of safety withdrawal of prescription drugs from worldwide pharmaceutical markets-1960 to 1999*. Drug
Inf J 35:293–317. doi:10.1177/009286150103500134
41. Stephens MDB (2004) Introduction. In: Talbot J, Waller P (eds) Stephens detect. New adverse drug react., 5th edn. Wiley, Chichester, pp 1–91
42. MRTD database. http://www.epa.gov/ncct/dsstox/sdf_fdamdd.html. Accessed 8 May 2013
43. Mitchell JA, Warner TD (2005) Discontinuation of Vioxx. The Lancet 365:27–28.
doi:10.1016/S0140-6736(04)17659-9
44. Whitebread S, Hamon J, Bojanic D, Urban L (2005) Keynote review: in vitro safety pharmacology profiling: an essential tool for successful drug development. Drug Discov Today
10:1421–1433. doi:10.1016/S1359-6446(05)03632-9
45. Lagunin A, Filimonov D, Poroikov V (2010) Multi-targeted natural products evaluation
based on biological activity prediction with PASS. Curr Pharm Des 16:1703–1717
46. Breckenridge A (1996) A clinical pharmacologist’s view of drug toxicity. Br J Clin Pharmacol 42:53–58
47. Lazarou J, Pomeranz BH, Corey PN (1998) Incidence of adverse drug reactions in hospitalized patients: a meta-analysis of prospective studies. JAMA J Am Med Assoc 279:1200–1205
48. Ji ZL, Wang Y, Yu L et al (2006) In silico search of putative adverse drug reaction related proteins as a potential tool for facilitating drug adverse effect prediction. Toxicol Lett 164:104–
112. doi:10.1016/j.toxlet.2005.11.017
49. Chen YZ, Zhi DG (2001) Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins 43:217–226
50. Ji ZL, Han LY, Yap CW et al (2003) Drug Adverse Reaction Target Database (DART): proteins related to adverse drug reactions. Drug Saf Int J Med Toxicol Drug Exp 26:685–690
51. Poroikov V, Filimonov D, Lagunin A et al (2007) PASS: identification of probable targets and mechanisms of toxicity. SAR QSAR Environ Res 18:101–110.
doi:10.1080/10629360601054032
52. Filimonov DA, Zakharov AV, Lagunin AA, Poroikov VV (2009) QNA-based “Star Track”
QSAR approach. SAR QSAR Environ Res 20:679–709. doi:10.1080/10629360903438370
53. Sadym A, Lagunin A, Filimonov D, Poroikov V (2003) Prediction of biological activity spectra via the Internet. SAR QSAR Environ Res 14:339–347. doi:10.1080/10629360310001623
935
54. Lagunin AA, Zakharov AV, Filimonov DA, Poroikov VV (2007) A new approach to QSAR modelling of acute toxicity. SAR QSAR Environ Res 18:285–298.
doi:10.1080/10629360701304253
55. Kokurkina GV, Dutov MD, Shevelev SA et al (2011) Synthesis, antifungal activity and
QSAR study of 2-arylhydroxynitroindoles. Eur J Med Chem 46:4374–4382. doi:10.1016/j.
ejmech.2011.07.008
56. Zakharov AV, Peach ML, Sitzmann M et al (2012) Computational tools and resources for
metabolism-related property predictions. 2. Application to prediction of half-life time in human liver microsomes. Future Med Chem 4:1933–1944. doi:10.4155/fmc.12.152
57. Zakharov AV, Lagunin AA, Filimonov DA, Poroikov VV (2012) Quantitative prediction of
antitarget interaction profiles for chemical compounds. Chem Res Toxicol 25:2378–2385.
doi:10.1021/tx300247r
58. Overington JP, Al-Lazikani B, Hopkins AL (2006) How many drug targets are there? Nat Rev
Drug Discov 5:993–996. doi:10.1038/nrd2199
59. Lounkine E, Keiser MJ, Whitebread S et al (2012) Large-scale prediction and testing of drug
activity on side-effect targets. Nature 486:361–367. doi:10.1038/nature11159
60. Ivanov SM, Lagunin AA, Zakharov AV et al (2013) Computer search for molecular mechanisms of ulcerogenic action of non-steroidal anti-inflammatory drugs. Biochem Mosc Suppl
Ser B Biomed Chem 7:40–45. doi:10.1134/S199075081301006X
61. Yang L, Wang K, Chen J et al (2011) Exploring off-targets and off-systems for adverse drug
reactions via chemical-protein interactome-clozapine-induced agranulocytosis as a case
study. PLoS Comput Biol 7:e1002016. doi:10.1371/journal.pcbi.1002016
11 Computational Toxicology in Drug Discovery: Opportunities and Limitations
40. Fung M, Thornton A, Mybeck K et al (2001) Evaluation of the characteristics of safety withdrawal of prescription drugs from worldwide pharmaceutical markets-1960 to 1999*. Drug
Inf J 35:293–317. doi:10.1177/009286150103500134
41. Stephens MDB (2004) Introduction. In: Talbot J, Waller P (eds) Stephens detect. New adverse drug react., 5th edn. Wiley, Chichester, pp 1–91
42. MRTD database. http://www.epa.gov/ncct/dsstox/sdf_fdamdd.html. Accessed 8 May 2013
43. Mitchell JA, Warner TD (2005) Discontinuation of Vioxx. The Lancet 365:27–28.
doi:10.1016/S0140-6736(04)17659-9
44. Whitebread S, Hamon J, Bojanic D, Urban L (2005) Keynote review: in vitro safety pharmacology profiling: an essential tool for successful drug development. Drug Discov Today
10:1421–1433. doi:10.1016/S1359-6446(05)03632-9
45. Lagunin A, Filimonov D, Poroikov V (2010) Multi-targeted natural products evaluation
based on biological activity prediction with PASS. Curr Pharm Des 16:1703–1717
46. Breckenridge A (1996) A clinical pharmacologist’s view of drug toxicity. Br J Clin Pharmacol 42:53–58
47. Lazarou J, Pomeranz BH, Corey PN (1998) Incidence of adverse drug reactions in hospitalized patients: a meta-analysis of prospective studies. JAMA J Am Med Assoc 279:1200–1205
48. Ji ZL, Wang Y, Yu L et al (2006) In silico search of putative adverse drug reaction related proteins as a potential tool for facilitating drug adverse effect prediction. Toxicol Lett 164:104–
112. doi:10.1016/j.toxlet.2005.11.017
49. Chen YZ, Zhi DG (2001) Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins 43:217–226
50. Ji ZL, Han LY, Yap CW et al (2003) Drug Adverse Reaction Target Database (DART): proteins related to adverse drug reactions. Drug Saf Int J Med Toxicol Drug Exp 26:685–690
51. Poroikov V, Filimonov D, Lagunin A et al (2007) PASS: identification of probable targets and mechanisms of toxicity. SAR QSAR Environ Res 18:101–110.
doi:10.1080/10629360601054032
52. Filimonov DA, Zakharov AV, Lagunin AA, Poroikov VV (2009) QNA-based “Star Track”
QSAR approach. SAR QSAR Environ Res 20:679–709. doi:10.1080/10629360903438370
53. Sadym A, Lagunin A, Filimonov D, Poroikov V (2003) Prediction of biological activity spectra via the Internet. SAR QSAR Environ Res 14:339–347. doi:10.1080/10629360310001623
935
54. Lagunin AA, Zakharov AV, Filimonov DA, Poroikov VV (2007) A new approach to QSAR modelling of acute toxicity. SAR QSAR Environ Res 18:285–298.
doi:10.1080/10629360701304253
55. Kokurkina GV, Dutov MD, Shevelev SA et al (2011) Synthesis, antifungal activity and
QSAR study of 2-arylhydroxynitroindoles. Eur J Med Chem 46:4374–4382. doi:10.1016/j.
ejmech.2011.07.008
56. Zakharov AV, Peach ML, Sitzmann M et al (2012) Computational tools and resources for
metabolism-related property predictions. 2. Application to prediction of half-life time in human liver microsomes. Future Med Chem 4:1933–1944. doi:10.4155/fmc.12.152
57. Zakharov AV, Lagunin AA, Filimonov DA, Poroikov VV (2012) Quantitative prediction of
antitarget interaction profiles for chemical compounds. Chem Res Toxicol 25:2378–2385.
doi:10.1021/tx300247r
58. Overington JP, Al-Lazikani B, Hopkins AL (2006) How many drug targets are there? Nat Rev
Drug Discov 5:993–996. doi:10.1038/nrd2199
59. Lounkine E, Keiser MJ, Whitebread S et al (2012) Large-scale prediction and testing of drug
activity on side-effect targets. Nature 486:361–367. doi:10.1038/nature11159
60. Ivanov SM, Lagunin AA, Zakharov AV et al (2013) Computer search for molecular mechanisms of ulcerogenic action of non-steroidal anti-inflammatory drugs. Biochem Mosc Suppl
Ser B Biomed Chem 7:40–45. doi:10.1134/S199075081301006X
61. Yang L, Wang K, Chen J et al (2011) Exploring off-targets and off-systems for adverse drug
reactions via chemical-protein interactome-clozapine-induced agranulocytosis as a case
study. PLoS Comput Biol 7:e1002016. doi:10.1371/journal.pcbi.1002016