Associating drugs, targets and clinical outcomes into an integrated network affords a new platform for computer-aided drug repurposing

Molecular Informatics

Volumn 30, Issue 2-3, 2011, Pages 100-111

  Oprea, Tudor I ^a,b   Kim Nielsen, Sonny ^b   Ursu, Oleg ^a   Yang, Jeremy J ^a   Taboureau, Olivier ^b   Mathias, Stephen L ^a,b   Kouskoumvekaki, Irene ^b   Sklar, Larry A ^a   Bologa, Cristian G ^a  

^a UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Drug discovery; Drug side effects; Drug targets; Principal component analysis; Text mining

Indexed keywords

DATA MINING; DRUG INTERACTIONS; MULTIVARIANT ANALYSIS;

CLINICAL OUTCOME; COMPUTER-AIDED; DRUG DISCOVERY; DRUG SIDE-EFFECTS; DRUG TARGETS; INTEGRATED NETWORKS; PRINCIPAL-COMPONENT ANALYSIS; REPURPOSING; SIDE EFFECT; TEXT-MINING;

PRINCIPAL COMPONENT ANALYSIS;

ANESTHETIC AGENT; ANTIARRHYTHMIC AGENT; ANTICONVULSIVE AGENT; ANTIDEPRESSANT AGENT; ANTIDIURETIC AGENT; ANTIDOTE; ANTIEMETIC AGENT; ANTIFUNGAL AGENT; ANTIHYPERTENSIVE AGENT; ANTIINFLAMMATORY AGENT; ANTILIPEMIC AGENT; ANTIMIGRAINE AGENT; ANTIPARKINSON AGENT; ANTIULCER AGENT; ANTIVIRUS AGENT; ANXIOLYTIC AGENT; BRONCHODILATING AGENT; CHOLINERGIC RECEPTOR BLOCKING AGENT; IMMUNOSUPPRESSIVE AGENT; LAMOTRIGINE; MUSCLE RELAXANT AGENT; NEUROLEPTIC AGENT; NOOTROPIC AGENT; PHENYTOIN; PREGABALIN; RESPIRATORY STIMULANT AGENT; SEDATIVE AGENT; TOPIRAMATE; UNINDEXED DRUG; ZONISAMIDE;

ANTICONVULSANT ACTIVITY; BIOINFORMATICS; COMPUTER AIDED DESIGN; COMPUTER AIDED DRUG REPURPOSING; COMPUTER NETWORK; CONFERENCE PAPER; DRUG APPROVAL; DRUG INDUSTRY; DRUG INFORMATION; DRUG LABELING; DRUG SURVEILLANCE PROGRAM; DRUG TARGETING; MENTAL DISEASE; PRIORITY JOURNAL;

EID: 79958831734     PISSN: 18681743     EISSN: 18681751     Source Type: Journal    
DOI: 10.1002/minf.201100023     Document Type: Conference Paper

References (70)

1. J. Drews, Drug Discov. Today 1998, 3, 491-494.
2. T. Olsson, T. I. Oprea, Curr. Op. Drug Discov. Dev. 2001, 4, 308-313.
3. J. A. DiMasi, R. W. Hansen, H. G. Grabowski, J. Health Econ. 2003, 22, 151-185.
4. C. P. Adams, V. V. Brantner, Health Affairs 2006, 25, 420-428.
5. C. P. Austin, L. S. Brady, T. R. Insel, F. S. Collins, Science 2004, 306, 1138-1139.
6. CTSA: http://www.ncrr.nih.gov/clinical-research-resources/clinical-and- translational-science-awards/
7. F. S. Collins, Science 2010, 327, 36-37.
8. M. S. Boguski, K. D. Mandl, V. P. Sukhatme, Science 2009, 324, 1394-1395.
9. J. H. Toney, J. I. Fasick, S. Singh, C. Beyrer, D. J. Sullivan Jr. , Science 2009, 325, 1139-1140.
10. C. R. Chong, D. J. Sullivan Jr. , Nature 2007, 448, 645-646.
11. M. Campillos, M. Kuhn, A. C. Gavin, L. J. Jensen, P. Bork, Science 2008, 321, 263-266.
12. M. J. Keiser, V. Setola, J. J. Irwin, C. Laggner, A. I. Abbas, S. J. Hufeisen, N. H. Jensen, M. B. Kuijer, R. C. Matos, T. B. Tran, R. Whaley, R. A. Glennon, J. Hert, K. L. H. Thomas, D. D. Edwards, B. K. Shoichet, B. L. Roth, Nature 2009, 462, 175-181.
13. T. T. Ashburn, K. B. Thor, Nature Rev. Drug Discov. 2004, 3, 673-683.
14. C. L. Campbell, S. Smyth, G. Montalescot, S. R. Steinhubl, JAMA 2007, 297, 2018-2024.
15. The FDA-approved label for Zyrtec D 12 hour can be accessed at http://www.accessdata.fda.gov/drugsatfda-docs/label/2004/19835slr016, 21150slr005,30346slr011-zyrtec-lbl.pdf
16. D. R. Lara, J. Alzheimers Dis. 2010, 20, S239-S248.
17. M. J. Glade, Nutrition 2010, 26, 932-938.
18. D. J. Henderson-Smart, A. G. De Paoli, Cochrane Database Syst. Rev. 2010, 12, CD000140.
19. The FDA Guidance for the Industry with respect to 505(b)(2) is available at http://www.fda.gov/downloads/Drugs/Guidance ComplianceRegulatoryInformation/ Guidances/ucm079345.pdf
20. The Hatch-Waxman Amendments are at http://www.fdli.org/pubs/Journal Online/54-2/art2.pdf
21. CTSA research volunteers: https://www.researchmatch.org/
22. CTSA IP: http://www.ctsaip.org/
23. CTSA Portal: http://www.ctsapharmaportal.org/
24. G. V. Paolini, R. H. B. Shapland, W. P. van Hoorn, J. S. Mason, A. L. Hopkins, Nature Biotechnol. 2006, 24, 805-815.
25. M. A. Yildirim, K. I. Goh, M. E. Cusick, A. L. Barabasi, M. Vidal, Nature Biotechnol. 2007, 25, 1119-1126.
26. I. Vogt, J. Mestres, Mol. Inf. 2010, 29, 10-14.
27. J. Mestres, E. Gregori-Puigjané S. Valverde, R. V. Solé, Nature Biotechnol. 2008, 26, 983-984.
28. The PubChem Portal is http://pubchem.ncbi.nlm.nih.gov/.
29. Prestwick Chemical Library information at http://www.prestwickchemical. fr/index.php?pa=26
30. DailyMed can be accessed at http://dailymed.nlm.nih.gov/dailymed/.
31. DrugBank is available at http://www.drugbank.ca/.
32. T. Berners-Lee, J. Hendler, O. Lassila, Sci. Am. 2001, 284, 34-43.
33. R. Vaz, T. Klabunde, Antitargets. Wiley-VCH, Weinheim, 2008.
34. M. Olah, R. Rad, L. Ostopovici, A. Bora, N. Hadaruga, D. Hadaruga, R. Moldovan, A. Fulias, M. Mracec, T. I. Oprea, in Chemical Biology: From Small Molecules to Systems Biology and Drug Design (Eds: S. L. Schreiber, T. M. Kapoor, G. Wess), Wiley-VCH, Weinheim, 2007, pp. 760-786.
35. PDSP is available at http://pdsp.med.unc.edu/.
36. J. R. Proudfoot, Bioorg. Med. Chem. Lett. 2005, 15, 1087-1090.
37. M. Vieth, J. J. Sutherland, J. Med. Chem. 2006, 49, 3451-3453.
38. SciFinder is available at https://scifinder.cas.org/scifinder/
39. The UniProt Consortium, Nucl. Acids Res. 2010, 38, D142-D148.
40. O. Taboureau, S. K. Nielsen, K. Audouze, N. Weinhold, D. Edsgärd, F. S. Roque, I. Kouskoumvekaki, A. Bora, R. Curpan, T. S. Jensen, S. Brunak, T. I. Oprea, Nucl. Acids Res. 2011, 39, D367-D372.
41. A. J. Harmar, R. A. Hills, E. M. Rosser, M. Jones, O. P. Buneman, D. R. Dunbar, S. D. Greenhill, V. A. Hale, J. L. Sharman, T. I. Bonner, W. A. Catterall, A. P. Davenport, P. Delagrange, C. T. Dollery, S. M. Foord, G. A. Gutman, V. Laudet, R. R. Neubig, E. H. Ohlstein, R. W. Olsen, J. Peters, J. P. Pin, R. R. Ruffolo, D. B. Searls, M. W. Wright, M. Spedding, Nucl. Acids Res. 2009, 37, D680-D685.
42. The IUPHAR Database is http://www.iuphar-db.org/index.jsp.
43. The ChemblDB Databases are at http://www.ebi.ac.uk/chembldb/index.php.
44. J. W. Black, W. A. M. Duncan, R. G. Shanks, Br. J. Pharmacol. 1965, 25, 577-591.
45. JChem and other ChemAxon software are available from ChemAxon at http://www.chemaxon.com/product/jc-base.html.
46. OEChem and other OpenEye software are available fromOpenEye Scientific Software at http://www.eyesopen.com/.
47. R. Garcia-Serna, O. Ursu, T. I. Oprea, J. Mestres, Bioinformatics 2010, 26, 985-986.
48. The iPHACE interface from IMIM, http://cgl.imim.es/iphace/main.php, is mirrored at UNM, http://agave.health.unm.edu/ iphace/main.php.
49. The IUPHAR Database linked to Wikipedia, iPHACE and PharmKGB in May 2010.
50. The U.S. Food and Drug Administration on-line search interface, "Drugs@FDA" service, can be accessed at http://www.accessdata.fda.gov/ scripts/cder/drugsatfda/.
51. EMA products authorized for human use can be accessed at http://www.ema.europa.eu/htms/human/epar/a.htm.
52. WHO Essential Medicines are listed at http://www.who.int/topics/ essential-medicines/en/.
53. TGA Medicines are found at http://www.tga.gov.au/
54. PDR is available at http://www.pdr.net/
55. Martindale is available at http://medicinescomplete.com/mc/martindale/ current/
56. AHFS is available at http://medicinescomplete.com/mc/ahfs/current/
57. M. Kuhn, M. Campillos, I. Letunic, L. J. Jensen, P. Bork, Mol. Systems Biol. 2010, 6, 343.
58. I. Feinerer, K. Hornik, D. Meyer, J. Stat. Software 2008, 25, 1-54.
59. J. E. Jackson, A Users Guide to Principal Components, Wiley, New York, 1991.
60. Simca software is available from Umetrics at http://www.umetrics.com/
61. T. Kohonen, Proc. IEEE 1990, 78, 1464-1480.
62. The Spotfire Data Analysis Module is available from TIBCO at http://spotfire.tibco.com/
63. X. Wang, G. Hripcsak, M. Markatou, C. Friedman, J. Am. Med. Inform. Assoc. 2009, 16, 328-337.
64. R. Garcia-Serna, J. Mestres Expert Opin. Drug Metab. Toxicol. 2010, 6, 1253-1263.
65. P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, T. Ideker, Genome Res. 2003, 13, 2498-2504.
66. Cytoscape can be downloaded from http://www.cytoscape.org.
67. B. Chen, X. Dong, D. Jiao, H. Wang, Q. Zhu, Y. Ding, D. J. Wild, BMC Bioinformatics 2010, 11, 255.
68. H. W. Mewes, B. Wachinger, V. Stémpflen, Pharmacopsychiatry 2010, 43, S2-S8.
69. M. Kuhn, D. Szklarczyk, A. Franceschini, M. Campillos, C. von Mering, L. J. Jensen, A. Beyer, P. Bork, Nucl. Acids Res. 2009, 10.1093/nar/gkp937.
70. STITCH, http://stitch.embl.de/.