Toxicological relationships between proteins obtained from protein target predictions of large toxicity databases

Toxicology and Applied Pharmacology

Volumn 231, Issue 2, 2008, Pages 225-234

  Nigsch, Florian ^a   Mitchell, John B O ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Computational toxicology; Protein target prediction; Toxicity; Winnow algorithm

Indexed keywords

ALGORITHM; ARTICLE; DATA BASE; MODEL; MONTE CARLO METHOD; PREDICTION; PROTEIN TARGETING; TOXICITY; TOXICOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; FORECASTING; HUMANS; MODELS, BIOLOGICAL; MONTE CARLO METHOD; PHARMACEUTICAL PREPARATIONS; PROTEINS;

EID: 49549094711     PISSN: 0041008X     EISSN: 10960333     Source Type: Journal    
DOI: 10.1016/j.taap.2008.05.007     Document Type: Article

References (72)

1. Barki-Harrington L., Perrino C., and Rockman H.A. Network integration of the adrenergic system in cardiac hypertrophy. Cardiovasc. Res. 63 3 (2004) 391-402
2. Bender A., Mussa H.Y., Glen R.C., and Reiling S. Molecular similarity searching using atom environments, information-based feature selection, and a naive Bayesian classifier. J. Chem. Inf. Comput. Sci. 44 1 (2004) 170-178
3. Bender A., Jenkins J.L., Glick M., Deng Z., Nettles J.H., and Davies J.W. "Bayes affinity fingerprints" improve retrieval rates in virtual screening and define orthogonal bioactivity space: when are multitarget drugs a feasible concept?. J. Chem. Inf. Model. 46 6 (2006) 2445-2456
4. Bender A., Scheiber J., Glick M., Davies J.W., Azzaoui K., Hamon J., Urban L., Whitebread S., and Jenkins J.L. Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure. Chem. Med. Chem 2 6 (2007) 861-873
5. Benz R.D. Toxicological and clinical computational analysis and the US FDA/CDER. Expert Opin. Drug Metab. Toxicol. 3 1 (2007) 109-124
6. Bhavani S., Nagargadde A., Thawani A., Sridhar V., and Chandra N. Substructure-based support vector machine classifiers for prediction of adverse effects in diverse classes of drugs. J. Chem. Inf. Model. 46 6 (2006) 2478-2486
7. Caldarelli A., Diel P., and Vollmer G. Effect of phytoestrogens on gene expression of carbonic anhydrase II in rat uterus and liver. J. Steroid Biochem. Mol. Biol. 97 3 (2005) 251-256
8. Dagan I., Karov Y., and Roth D. Mistake-driven learning in text-categorization. Proceedings of Empirical Methods in Natural Language Processing (1997) 55-63
9. Drinka P.J., Krause P.F., Nest L.J., and Goodman B.M. Determinants of parathyroid hormone levels in nursing home residents. J. Am. Med. Dir. Assoc. 8 5 (2007) 328-331
10. Elsevier MDL (2007). 2440 Camino Ramon, Suite 300, San Ramon, CA 94583.
11. Everts V., Korper W., Hoeben K.A., Jansen I.D.C., Bromme D., Cleut-jens K.B.J.M., Heeneman S., Peters C., Reinheckel T., Saftig P., and Beertsen W. Osteoclastic bone degradation and the role of different cysteine proteinases and matrix metalloproteinases: differences between calvaria and long bone. J. Bone Miner. Res. 21 9 (2006) 1399-1408
12. Farina C., and Gagliardi S. Selective inhibition of osteoclast vacuolar H()-ATPase. Curr. Pharm. Des. 8 23 (2002) 2033-2048
13. Fliri A.F., Loging W.T., Thadeio P.F., and Volkmann R.A. Biological spectra analysis: Linking biological activity profiles to molecular structure. Proc. Natl. Acad. Sci. U. S. A. 102 2 (2005) 261-266
14. Furuyama N., and Fujisawa Y. Regulation of collagenolytic cysteine protease synthesis by estrogen in osteoclasts. Steroids 65 7 (2000) 371-378
15. Gardner M.J., van der Meulen M.C.H., Carson J., Zelken J., Ricciardi B.F., Wright T.M., Lane J.M., and Bostrom M.P. Role of parathyroid hormone in the mechanosensitivity of fracture healing. J. Orthop. Res. 25 11 (2007) 1474-1480
16. Goodwin G.A., and Barr G.A. Behavioral and heart rate effects of infusing kainic acid into the dorsal midbrain during early development in the rat. Dev. Brain Res. 107 1 (1998) 11-20
17. Goren M.Z., Onat F., and Berkman K. Participation of NMDA and kainate receptors of paraventricular nucleus in cardiovascular responses to glutamate receptor agonist. Eur. J. Pharmacol. 388 1 (2000) 77-84
18. Goss P., and von Eichel L. Summary of aromatase inhibitor trials: the past and future. J. Steroid Biochem. Mol. Biol. 106 1-5 (2007) 40-48
19. Herz J. The LDL receptor gene family: (un)expected signal transducers in the brain. Neuron 29 3 (2001) 571-581
20. Herz J., and Bock H.H. Lipoprotein receptors in the nervous system. Annu. Rev. Biochem. 71 (2002) 405-434
21. Johnson D.E., and Rodgers A.D. Computational toxicology: heading toward more relevance in drug discovery and development. Curr. Opin. Drug Discov. Devel. 9 1 (2006) 29-37
22. Johnson P.H., Walker R.P., Jones S.W., Stephens K., Meurer J., Zajchowski D.A., Luke M.M., Eeckman F., Tan Y., Wong L., Parry G., Morgan T.K., McCarrick M.A., and Monforte J. Multiplex gene expression analysis for high-throughput drug discovery: screening and analysis of compounds affecting genes overexpressed in cancer cells. Mol. Cancer Ther. 1 14 (2002) 1293-1304
23. Keiser M.J., Roth B.L., Armbruster B.N., Ernsberger P., Irwin J.J., and Shoichet B.K. Relating protein pharmacology by ligand chemistry. Nat. Biotechnol. 25 2 (2007) 197-206
24. Lagunin A., Stepanchikova A., Filimonov D., and Poroikov V. PASS: prediction of activity spectra for biologically active substances. Bioinformatics 16 8 (2000) 747-748
25. Lee K.H., Finnigan-Bunick C., Bahr J., and Bunick D. Estrogen regulation of ion transporter messenger RNA levels in mouse efferent ductules are mediated differentially through estrogen receptor (ER) alpha and ER beta. Biol. Reprod. 65 5 (2001) 1534-1541
26. MacLean M.R. Pulmonary hypertension and the serotonin hypothesis: where are we now?. Int. J. Clin. Pract. 156 (2007) 27-31 Suppl
27. Mantey S.A., Coy D.H., Pradhan T.K., Igarashi H., Rizo I.M., Shen L., Hou W., Hocart S.J., and Jensen R.T. Rational design of a peptide agonist that interacts selectively with the orphan receptor, bombesin receptor subtype 3. J. Biol. Chem. 276 12 (2001) 9219-9229
28. Mayer M.L. Glutamate receptors at atomic resolution. Nature 440 7083 (2006) 456-462
29. Merchenthaler I. Estrogen stimulates galanin expression within luteinizing hormone-releasing hormone-immunoreactive (LHRH-i) neurons via estrogen receptor-beta (ERbeta) in the female rat brain. Neuropeptides 39 3 (2005) 341-343
30. Mitchell group website (2008). http://www-mitchell.ch.cam.ac.uk/flo/targetpred/ (accessed 17/01/2008).
31. Mizunashi K., Furukawa Y., Katano K., and Abe K. Effect of omeprazole, an inhibitor of H,K()-ATPase, on bone resorption in humans. Calcif. Tissue Int. 53 1 (1993) 21-25
32. Molecule File Converter (2008). Version 5.0.0, (C) 1999-2008 ChemAxon Ltd., 2007, ChemAxon (http://www.chemaxon.com/ accessed 17/01/08).
33. Morphy R., Kay C., and Rankovic Z. From magic bullets to designed multiple ligands. Drug Discov. Today 9 15 (2004) 641-651
34. Nidhi, Glick M., Davies J.W., and Jenkins J.L. Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases. J. Chem. Inf. Model. 46 3 (2006) 1124-1133
35. Nigsch F., and Mitchell J.B.O. How to Winnow actives from inactives: introducing molecular orthogonal sparse bigrams (MOSBs) and multiclass Winnow. J. Chem. Inf. Model. 48 2 (2008) 306-318
36. Nigsch F., Klaffke W., and Miret S. In vitro models for processes involved in intestinal absorption. Expert Opin. Drug Metab. Toxicol. 3 4 (2007) 545-556
37. Nigsch, F., Bender, A., Jenkins, J.L., Mitchell, J.B.O., (submitted for publication). Ligand-Target Prediction Using Winnow and Naïve Bayesian Algorithms and the Implications of Overall Performance Statistics. J. Chem. Inf. Model.
38. Olah M., Mracec M., Ostopovici L., Rad R., Bora A., Hadaruga N., Olah I., Banda M., Simon Z., and Oprea T.I. WOMBAT: World of Molecular Bioactivity. Cheminformatics in Drug Discovery (2004), Wiley-VCH, New York
39. Paolini G.V., Shapland R.H.B., van Hoorn W.P., Mason J.S., and Hopkins A.L. Global mapping of pharmacological space. Nat. Biotechnol. 24 7 (2006) 805-815
40. Piotrowski P.L., Sumpter B.G., Malling H.V., Wassom J.S., Lu P.Y., Brothers R.A., Sega G.A., Martin S.A., and Parang M. A toxicity evaluation and predictive system based on neural networks and wavelets. J. Chem. Inf. Model. 47 2 (2007) 676-685
41. Pole J.C.M., Gold L.I., Orton T., Huby R., and Carmichael P.L. Gene expression changes induced by estrogen and selective estrogen receptor modulators in primary-cultured human endometrial cells: signals that distinguish the human carcinogen tamoxifen. Toxicology 206 1 (2005) 91-109
42. Poroikov V., Filimonov D., Lagunin A., Gloriozova T., and Zakharov A. PASS: identification of probable targets and mechanisms of toxicity. SAR QSAR Environ. Res. 18 1-2 (2007) 101-110
43. R Development Core Team (2007). R: A Language and Envi-ronment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
44. Rabaglio M., Aebi S., and Castiglione-Gertsch M. Controversies of adjuvant endocrine treatment for breast cancer and recommendations of the 2007 St Gallen conference. Lancet Oncol. 8 10 (2007) 940-949
45. Richard A.M., Gold L.S., and Nicklaus M.C. Chemical structure indexing of toxicity data on the internet: moving toward a flat world. Curr. Opin. Drug Discov. Devel. 9 3 (2006) 314-325
46. Schuffenhauer A., Floersheim P., Acklin P., and Jacoby E. Similarity metrics for ligands reflecting the similarity of the target proteins. J. Chem. Inf. Comput. Sci. 43 2 (2003) 391-405
47. Scripture C.D., and Figg W.D. Drug interactions in cancer therapy. Nat. Rev. Cancer 6 7 (2006) 546-558
48. Sheridan R.P., and Kearsley S.K. Why do we need so many chemical similarity search methods? Drug Discov. Today 7 17 (2002) 903-911
49. Sheridan R.P., and Shpungin J. Calculating similarities between biological activities in the MDL Drug Data Report database. J. Chem. Inf. Comput. Sci. 44 2 (2004) 727-740
50. Smout A.J.P.M. The patient with GORD and chronically recurrent problems. Best Pract. Res. Clin. Gastroenterol. 21 3 (2007) 365-378
51. Song F., Wisithphrom K., Zhou J., and Windsor L.J. Matrix metalloproteinase dependent and independent collagen degradation. Front. Biosci. 11 (2006) 3100-3120
52. Sriraman V., and Richards J.S. Cathepsin L gene expression and promoter activation in rodent granulosa cells. Endocrinology 145 2 (2004) 582-591
53. Standardizer (2007). Version 3.2.10. Standardizer was used for structure canonicalization and transformation, ChemAxon (http://www.chemaxon.com/ accessed 17/01/08).
54. Steindl T.M., Schuster D., Laggner C., and Langer T. Parallel screening: a novel concept in pharmacophore modeling and virtual screening. J. Chem. Inf. Model. 46 5 (2006) 2146-2157
55. Thibodeau P.A., Bissonnette N., Bédard S.K., Hunting D., and Paquette B. Induction by estrogens of methotrexate resistance in MCF-7 breast cancer cells. Carcinogenesis 19 9 (1998) 1545-1552
56. Tripos (2007). Inc., St. Louis, Missouri, U.S.A.
57. Tuukkanen, J., and Väänänen H.K. Omeprazole, a specific inhibitor of H+-K+-ATPase, inhibits bone resorption in vitro. Calcif. Tissue Int. 38 2 (1986) 123-125
58. Ulrich D., and Bettler B. GABA(B) receptors: synaptic functions and mechanisms of diversity. Curr. Opin. Neurobiol. 17 3 (2007) 298-303
59. Vedani A., Descloux A.V., Spreafico M., and Ernst B. Predicting the toxic potential of drugs and chemicals in silico: a model for the peroxisome proliferator-activated receptor gamma (PPAR gamma). Toxicol. Lett. 173 1 (2007) 17-23
60. Vestergaard P., Rejnmark L., and Mosekilde L. Proton pump inhibitors, histamine H2 receptor antagonists, and other antacid medications and the risk of fracture. Calcif. Tissue Int. 79 2 (2006) 76-83
61. Virág L., and Szabó C. The therapeutic potential of poly(ADP-ribose) polymerase inhibitors. Pharmacol. Rev. 54 3 (2002) 375-429
62. von Korff M., and Sander T. Toxicity-indicating structural patterns. J. Chem. Inf. Model. 46 2 (2006) 536-544
63. von Lindern M., Boer L., Wessely O., Parker M., and Beug H. The transactivation domain AF-2 but not the DNA-binding domain of the estrogen receptor is required to inhibit differentiation of avian erythroid progenitors. Mol. Endocrinol. 12 2 (1998) 263-277
64. Weir M.R. Effects of renin-angiotensin system inhibition on end-organ protection: can we do better?. Clin. Ther. 29 9 (2007) 1803-1824
65. Wermuth C.G. Selective optimization of side activities: another way for drug discovery. J. Med. Chem. 47 6 (2004) 1303-1314
66. Winum J.Y., Vullo D., Casini A., Montero J.L., Scozzafava A., and Supuran C.T. Carbonic anhydrase inhibitors. Inhibition of cytosolic isozymes I and II and transmembrane, tumor-associated isozyme IX with sulfamates including EMATE also acting as steroid sulfatase inhibitors. J. Med. Chem. 46 11 (2003) 2197-2204
67. Yang Y.X., Lewis J.D., Epstein S., and Metz D.C. Long-term proton pump inhibitor therapy and risk of hip fracture. JAMA 296 24 (2006) 2947-2953
68. Zaccolo M., and Movsesian M.A. cAMP and cGMP sig-naling cross-talk: role of phosphodiesterases and implications for cardiac pathophysiology. Circ. Res. 100 11 (2007) 1569-1578
69. Zaichuk T., Ivancic D., Scholtens D., Schiller C., and Khan S.A. Tissue-specific transcripts of human steroid sulfatase are under control of estrogen signaling pathways in breast carcinoma. J. Steroid Biochem. Mol. Biol. 105 1-5 (2007) 76-84
70. Zaidi M. Modularity of osteoclast behaviour and "mode-specific" inhibition of osteoclast function. Biosci. Rep. 10 6 (1990) 547-556
71. Zeng C., Zhang M., Asico L.D., Eisner G.M., and Jose P.A. The dopaminergic system in hypertension. Clin. Sci. (Lond) 112 12 (2007) 583-597
72. Zimmerman G., and Soreq H. Termination and beyond: acetylcholinesterase as a modulator of synaptic transmission. Cell Tissue Res. 326 2 (2006) 655-669