Systematic drug repositioning for a wide range of diseases with integrative analyses of phenotypic and molecular data

Journal of Chemical Information and Modeling

Volumn 55, Issue 2, 2015, Pages 446-459

  Iwata, Hiroaki ^a   Sawada, Ryusuke ^a   Mizutani, Sayaka ^b   Yamanishi, Yoshihiro ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG INTERACTIONS; FORECASTING;

COMPREHENSIVE PREDICTION; DISEASE ASSOCIATIONS; DISEASE-CAUSING GENE; ENVIRONMENTAL FACTORS; INTEGRATIVE ANALYSIS; INTERNATIONAL CLASSIFICATION OF DISEASE; PHARMACEUTICAL SCIENCE; STRUCTURE SIMILARITY;

DIAGNOSIS;

ANTINEOPLASTIC AGENT; BIOLOGICAL MARKER; DRUG;

ALGORITHM; ARTIFICIAL NEURAL NETWORK; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DATA MINING; DISEASES; DRUG REPOSITIONING; ENVIRONMENT; GENETICS; HIGH THROUGHPUT SCREENING; HUMAN; INTERNATIONAL CLASSIFICATION OF DISEASES; NEOPLASMS; PHENOTYPE; PROCEDURES; REPRODUCIBILITY;

ALGORITHMS; ANTINEOPLASTIC AGENTS; BIOMARKERS; CLUSTER ANALYSIS; DATA MINING; DISEASE; DRUG REPOSITIONING; ENVIRONMENT; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; INTERNATIONAL CLASSIFICATION OF DISEASES; NEOPLASMS; NEURAL NETWORKS (COMPUTER); PHARMACEUTICAL PREPARATIONS; PHENOTYPE; REPRODUCIBILITY OF RESULTS;

EID: 84923348557     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci500670q     Document Type: Article

References (74)

1. DiMasi, J. A.; Hansen, R. W.; Grabowski, H. G. The price of innovation: New estimates of drug development costs J. Health Econ. 2003, 22, 151-185
2. Ashburn, T. T.; Thor, K. B. Drug repositioning: Identifying and developing new uses for existing drugs Nat. Rev. Drug Discovery 2004, 3, 673-683
3. Chong, C. R.; Sullivan, D. J. New uses for old drugs Nature 2007, 448, 645-646
4. Hopkins, A. L.; Mason, J. S.; Overington, J. P. Can we rationally design promiscuous drugs? Curr. Opin. Struct. Biol. 2006, 16, 127-136
5. Nacher, J. C.; Schwartz, J. M. Modularity in protein complex and drug interactions reveals new polypharmacological properties PLoS One 2012, 7, e30028
6. Csermely, P.; Korcsmáros, T.; Kiss, H. J.; London, G.; Nussinov, R. Structure and dynamics of molecular networks: A novel paradigm of drug discovery. A comprehensive review Pharmacol. Ther. 2013, 138, 333-408
7. Novac, N. Challenges and opportunities of drug repositioning Trends Pharmacol. Sci. 2013, 34, 267-272
8. Whitebread, S.; Hamon, J.; Bojanic, D.; Urban, L. Keynote review: In vitro safety pharmacology profiling: an essential tool for successful drug development Drug discovery today 2005, 10, 1421-1433
9. Blagg, J. Structure-activity relationships for in vitro and in vivo toxicity Annu. Rep. Med. Chem. 2006, 41, 353
10. Terstappen, G. C.; Reggiani, A. In silico research in drug discovery Trends Pharmacol. Sci. 2001, 22, 23-26
11. Lamb, J.; Crawford, E. D.; Peck, D.; Modell, J. W.; Blat, I. C.; Wrobel, M. J.; Lerner, J.; Brunet, J.-P.; Subramanian, A.; Ross, K. N.; Reich, M.; Hieronymus, H.; Wei, G.; Armstrong, S. A.; Haggarty, S. J.; Clemons, P. A.; Wei, R.; Carr, S. A.; Lander, E. S.; Golub, T. R. The Connectivity Map: Using gene-expression signatures to connect small molecules, genes, and disease Science 2006, 313, 1929-1935
12. Hu, G.; Agarwal, P. Human disease-drug network based on genomic expression profiles PLoS One 2009, 4, e6536
13. Chiang, A. P.; Butte, A. J. Systematic evaluation of drug-disease relationships to identify leads for novel drug uses Clin. Pharmacol. Ther. 2009, 86, 507-510
14. Iorio, F.; Bosotti, R.; Scacheri, E.; Belcastro, V.; Mithbaokar, P.; Ferriero, R.; Murino, L.; Tagliaferri, R.; Brunetti-Pierri, N.; Isacchi, A.; Bernardo, D. d. Discovery of drug mode of action and drug repositioning from transcriptional responses Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 14621-14626
15. Sirota, M.; Dudley, J. T.; Kim, J.; Chiang, A. P.; Morgan, A. A.; Sweet-Cordero, A.; Sage, J.; Butte, A. J. Discovery and preclinical validation of drug indications using compendia of public gene expression data Sci. Transl. Med. 2011, 3, 96ra77-96ra77
16. Ye, H.; Tang, K.; Yang, L.; Cao, Z.; Li, Y. Study of drug function based on similarity of pathway fingerprint Protein & cell 2012, 3, 132-139
17. Zhao, S.; Li, S. A co-module approach for elucidating drug-disease associations and revealing their molecular basis Bioinformatics 2012, 28, 955-961
18. Ye, H.; Liu, Q.; Wei, J. Construction of drug network based on side effects and its application for drug repositioning PLoS One 2014, 9, e87864
19. Gottlieb, A.; Stein, G. Y.; Ruppin, E.; Sharan, R. PREDICT: A method for inferring novel drug indications with application to personalized medicine Mol. Syst. Biol. 2011, 7, 496
20. Yang, L.; Agarwal, P. Systematic drug repositioning based on clinical side-effects PLoS One 2011, 6, e28025
21. Wang, Y.; Chen, S.; Deng, N.; Wang, Y. Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data PLoS One 2013, 8, e78518
22. Napolitano, F.; Zhao, Y.; Moreira, V. M.; Tagliaferri, R.; Kere, J.; DAmato, M.; Greco, D. Drug repositioning: A machine-learning approach through data integration J. Cheminformatics 2013, 5, 30
23. Hamosh, A.; Scott, A. F.; Amberger, J.; Bocchini, C.; Valle, D.; McKusick, V. A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders Nucleic Acids Res. 2002, 30, 52-55
24. The ICD-10 Classification of Mental and Behavioural Disorders: Clinical Descriptions and Diagnostic Guidelines; World Health Organization: Geneva, 1992.
25. Kanehisa, M.; Goto, S.; Furumichi, M.; Tanabe, M.; Hirakawa, M. KEGG for representation and analysis of molecular networks involving diseases and drugs Nucleic Acids Res. 2010, 38, D355-D360
26. Chen, B.; Wild, D.; Guha, R. PubChem as a source of polypharmacology J. Chem. Inf. Model. 2009, 49, 2044-2055
27. Kanehisa, M.; Araki, M.; Goto, S.; Hattori, M.; Hirakawa, M.; Itoh, M.; Katayama, T.; Kawashima, S.; Okuda, S.; Tokimatsu, T.; Yamanishi, Y. KEGG for linking genomes to life and the environment Nucleic Acids Res. 2008, 36, D480-D484
28. Papadakis, M. A.; McPhee, S. J.; Rabow, M. W. CURRENT Medical Diagnosis and Treatment 2014; McGraw-Hill Medical: New York, 2013.
29. Tabei, Y.; Pauwels, E.; Stoven, V.; Takemoto, K.; Yamanishi, Y. Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers Bioinformatics 2012, 28, i487-i494
30. Fan, R.-E.; Chang, K.-W.; Hsieh, C.-J.; Wang, X.-R.; Lin, C.-J. LIBLINEAR: A library for large linear classification J. Mach. Learn. Res. 2008, 9, 1871-1874
31. Takarabe, M.; Kotera, M.; Nishimura, Y.; Goto, S.; Yamanishi, Y. Drug target prediction using adverse event report systems: A pharmacogenomic approach Bioinformatics 2012, 28, i611-i618.
32. Iwata, H.; Mizutani, S.; Tabei, Y.; Kotera, M.; Goto, S.; Yamanishi, Y. Inferring protein domains associated with drug side effects based on drug-target interaction network BMC Syst. Biol. 2013, 7, 1-11
33. Tanimoto, T. T. An Elementary Mathematical Theory of Classification and Prediction; International Business Machines Corporation: New York, 1958.
34. Campillos, M.; Kuhn, M.; Gavin, A. C.; Jensen, L. J.; Bork, P. Drug target identification using side-effect similarity Science 2008, 321, 263-266
35. Kuhn, M.; Campillos, M.; Letunic, I.; Jensen, L. J.; Bork, P. A side effect resource to capture phenotypic effects of drugs Mol. Syst. Biol. 2010, 6, 343
36. Whirl-Carrillo, M.; McDonagh, E.; Hebert, J.; Gong, L.; Sangkuhl, K.; Thorn, C.; Altman, R.; Klein, T. E. Pharmacogenomics knowledge for personalized medicine Clin. Pharmacol. Ther. 2012, 92, 414-417
37. Nacher, J. C.; Schwartz, J.-M. A global view of drug-therapy interactions BMC pharmacology 2008, 8, 5
38. Knox, C.; Law, V.; Jewison, T.; Liu, P.; Ly, S.; Frolkis, A.; Pon, A.; Banco, K.; Mak, C.; Neveu, V.; Djoumbou, Y.; Eisner, R.; Guo, A. C.; Wishart, D. S. DrugBank 3.0: A comprehensive resource for omics research on drugs Nucleic Acids Res. 2011, 39, D1035-D1041
39. Kuhn, M.; Szklarczyk, D.; Pletscher-Frankild, S.; Blicher, T. H.; von Mering, C.; Jensen, L. J.; Bork, P. STITCH 4: Integration of protein-chemical interactions with user data Nucleic Acids Res. 2013, 42, D401-D407
40. Liu, T.; Lin, Y.; Wen, X.; Jorissen, R. N.; Gilson, M. K. BindingDB: A web-accessible database of experimentally determined protein-ligand binding affinities Nucleic Acids Res. 2007, 35, D198-D201
41. Gunther, S.; Kuhn, M.; Dunkel, M.; Campillos, M.; Senger, C.; Petsalaki, E.; Ahmed, J.; Urdiales, E. G.; Gewiess, A.; Jensen, L. J.; Schneider, R.; Skoblo, R.; Russell, R. B.; Bourne, P. E.; Bork, P.; Preissner, R. SuperTarget and Matador: Resources for exploring drug-target relationships Nucleic Acids Res. 2008, 36, D919-D922
42. Gaulton, A.; Bellis, L. J.; Bento, A. P.; Chambers, J.; Davies, M.; Hersey, A.; Light, Y.; McGlinchey, S.; Michalovich, D.; Al-Lazikani, B.; Overington, J. P. ChEMBL: a large-scale bioactivity database for drug discovery Nucleic Acids Res. 2012, 40, D1100-D1107
43. Lin, S. F.; Xiao, K. T.; Huang, Y. T.; Chiu, C. C.; Soo, V. W. Analysis of adverse drug reactions using drug and drug target interactions and graph-based methods Artif. Intell. Med. 2010, 48, 161-166
44. Wong, N. S.; Buckman, R. A.; Clemons, M.; Verma, S.; Dent, S.; Trudeau, M. E.; Roche, K.; Ebos, J.; Kerbel, R.; DeBoer, G. E.; Sutherland, D. J.; Emmenegger, U.; Slingerland, J.; Gardner, S.; Pritchard, K. I. Phase I/II trial of metronomic chemotherapy with daily dalteparin and cyclophosphamide, twice-weekly methotrexate, and daily prednisone as therapy for metastatic breast cancer using vascular endothelial growth factor and soluble vascular endothelial growth factor receptor levels as markers of response J. Clin. Oncol. 2010, 28, 723-730
45. Nozawa, S.; Engvall, E.; Kano, S.; Kurihara, S.; Fishman, W. H. Sodium butyrate produces concordant expression of early placental alkaline phosphatase, pregnancy-specific beta1-glycoprotein and human chorionic gonadotropin beta-subunit in a newly established uterine cervical cancer cell line (SKG-IIIa) Int. J. Cancer 1983, 32, 267-272
46. Boll, B.; Bredenfeld, H.; Gorgen, H.; Halbsguth, T.; Eich, H. T.; Soekler, M.; Markova, J.; Keller, U.; Graeven, U.; Kremers, S.; Geissler, M.; Trenn, G.; Fuchs, M.; Tresckow, B. v.; Eichenauer, D. A.; Borchmann, P.; Engert, A. Phase 2 study of PVAG (prednisone, vinblastine, doxorubicin, gemcitabine) in elderly patients with early unfavorable or advanced stage Hodgkin lymphoma Blood 2011, 118, 6292-6298
47. Yardley, D. A.; Zubkus, J.; Daniel, B.; Inhorn, R.; Lane, C. M.; Vazquez, E. R.; Naot, Y.; Burris, H. A., III; Hainsworth, J. D. A phase II trial of dose-dense neoadjuvant gemcitabine, epirubicin, and albumin-bound paclitaxel with pegfilgrastim in the treatment of patients with locally advanced breast cancer Clin. Breast Cancer 2010, 10, 367-372
48. Moore, C. M.; Lamzabi, I.; Bartels, A. K.; Jakate, S.; Van Thiel, D. H. Colonic diffuse large B-cell lymphoma in a liver transplant patient with historically very low tacrolimus levels Case Rep. Transplant. 2012, 2012, 952359
49. Buske, C.; Hoster, E.; Dreyling, M.; Eimermacher, H.; Wandt, H.; Metzner, B.; Fuchs, R.; Bittenbring, J.; Woermann, B.; Hohloch, K.; Hess, G.; Ludwig, W. D.; Schimke, J.; Schmitz, S.; Kneba, M.; Reiser, M.; Graeven, U.; Klapper, W.; Unterhalt, M.; Hiddemann, W. The addition of rituximab to front-line therapy with CHOP (R-CHOP) results in a higher response rate and longer time to treatment failure in patients with lymphoplasmacytic lymphoma: results of a randomized trial of the German Low-Grade Lymphoma Study Group (GLSG) Leukemia 2008, 23, 153-161
50. Haarstad, H.; Jacobsen, A. B.; Schjølseth, S. A.; Risberg, T.; Fossa, S. D. Interferon-α, 5-FU and prednisone in metastatic renal cell carcinoma: A phase II study Ann. Oncol. 1994, 5, 245-248
51. Legros, L.; Guilhot, J.; Huault, S.; Mahon, F.; Preudhomme, C.; Guilhot, F.; Hueber, A. Interferon decreases VEGF levels in patients with chronic myeloid leukemia treated with imatinib Leuk. Res. 2014, 38, 662-665
52. Kim, M. Y.; Sposto, R.; Swaika, A.; Asano, H.; Alamgir, A.; Chanan Khan, A.; Ailawadhi, S. Pharmacoeconomic implications of lenalidomide maintenance therapy in multiple myeloma Oncology 2014, 87, 224-231
53. Chauncey, T. R.; Gundacker, H.; Shadman, M.; List, A. F.; Dakhil, S. R.; Erba, H. P.; Slovak, M. L.; Chen, I.; Willman, C. L.; Kopecky, K. J.; Appelbaum, F. R. Sequential phase II Southwest Oncology Group studies (S0112 and S0301) of daunorubicin and cytarabine by continuous infusion, without and with ciclosporin, in older patients with previously untreated acute myeloid leukaemia Br. J. Hamaetol. 2010, 148, 48-58
54. Newcomb, P.; Trentham-Dietz, A.; Hampton, J. Bisphosphonates for osteoporosis treatment are associated with reduced breast cancer risk Br. J. Cancer 2010, 102, 799-802
55. Hue, T. F.; Cummings, S. R.; Cauley, J. A.; Bauer, D. C.; Ensrud, K. E.; Barrett-Connor, E.; Black, D. M. Effect of bisphosphonate use on risk of postmenopausal breast cancer: Results from the randomized clinical trials of alendronate and zoledronic acid JAMA Intern. Med. 2014, 174, 1550-1557
56. Lee, M. V.; Fong, E. M.; Singer, F. R.; Guenette, R. S. Bisphosphonate treatment inhibits the growth of prostate cancer cells Cancer Res. 2001, 61, 2602-2608
57. Blake, S. J.; Hughes, T. P.; Lyons, A. B. Drug-interaction studies evaluating T-cell proliferation reveal distinct activity of dasatinib and imatinib in combination with cyclosporine A Exp. Hematol. 2012, 40, 612-621
58. Schmidt, C.; Fetscher, S.; Gorg, C.; Kornek, P.; Nusch, A.; Kegel, T.; Kellermann, L.; Hiddemann, W.; Fingerle-Rowson, G.; Dreyling, M. Treatment of indolent lymphoma in Germany: Results of a representative population-based survey Clin. Lymphoma, Myeloma Leuk. 2011, 11, 204-211
59. Costa, D.; De Castro, R.; Kara-Jose, N. Case-control study of subconjunctival triamcinolone acetonide injection vs intravenous methylprednisolone pulse in the treatment of endothelial corneal allograft rejection Eye 2008, 23, 708-714
60. Roberti, I.; Geffner, S.; Vyas, S. Successful rescue of refractory acute antibody-mediated renal allograft rejection with splenectomy: A case report Pediatr. Transplant. 2012, 16, E49-E52
61. Feurle, G. E.; Moos, V.; Blaker, H.; Loddenkemper, C.; Moter, A.; Stroux, A.; Marth, T.; Schneider, T. Intravenous ceftriaxone, followed by 12 or three months of oral treatment with trimethoprim-sulfamethoxazole in Whipples disease J. Infect. 2013, 66, 263-270
62. Boulos, A.; Rolain, J. M.; Raoult, D. Antibiotic susceptibility of Tropheryma whipplei in MRC5 cells Antimicrob. Agents Chemother. 2004, 48, 747-752
63. Kalimuddin, S.; Sessions, O. M.; Hou, Y.; Ooi, E. E.; Sim, D.; Cumaraswamy, S.; Tan, T. E.; Lai, S. H.; Low, C. Y. Successful clearance of human parainfluenza virus type 2 viraemia with intravenous ribavirin and immunoglobulin in a patient with acute myocarditis J. Clin. Virol. 2013, 56, 37-40
64. Penduka, D.; Mosa, R.; Simelane, M.; Basson, A.; Okoh, A.; Opoku, A. Evaluation of the anti-Listeria potentials of some plant-derived triterpenes Ann. Clin. Microbiol. Antimicrob. 2014, 13, 37
65. Chhetri, U.; Shrestha, S.; Pradhan, R.; Shrestha, A.; Adhikari, N.; Thorson, S.; Pollard, A.; Murdoch, D.; Kelly, D. Clinical profile of invasive pneumococcal disease in Patan Hospital, Nepal Kathmandu Univ. Med. J. 2012, 9, 45-49
66. Hawkins, C.; Farr, M.; Morris, C.; Hoare, A.; Williamson, N. Detection by electron microscope of rod-shaped organisms in synovial membrane from a patient with the arthritis of Whipples disease Ann. Rheum. Dis. 1976, 35, 502-509
67. Takahira, N.; Shindo, M.; Tanaka, K.; Soma, K.; Ohwada, T.; Itoman, M. Treatment outcome of nonclostridial gas gangrene at a level 1 trauma center J. Orthop. Trauma 2002, 16, 12-17
68. Ganesh Kumar, A.; Kothari, V.; Krishnan, A.; Karnad, D. Benzathine penicillin, metronidazole and benzyl penicillin in the treatment of tetanus: A randomized, controlled trial Ann. Trop. Med. Parasitol. 2004, 98, 59-63
69. Dearment, M. C.; Woodward, T. A.; Menke, D. M.; Brazis, P. W.; Bancroft, L. W.; Persellin, S. T. Whipples disease with destructive arthritis, abdominal lymphadenopathy, and central nervous system involvement J. Rheumatol. 2003, 30, 1347-1350
70. Kanakry, C. G.; Ganguly, S.; Zahurak, M.; Bolanos-Meade, J.; Thoburn, C.; Perkins, B.; Fuchs, E. J.; Jones, R. J.; Hess, A. D.; Luznik, L. Aldehyde dehydrogenase expression drives human regulatory T cell resistance to posttransplantation cyclophosphamide Sci. Transl. Med. 2013, 5, 211ra157-211ra157
71. Bures, J.; Kopácová, M.; Douda, T.; Bártová, J.; Toms, J.; Rejchrt, S.; Tacheci, I. Whipples disease: Our own experience and review of the literature. Gastroenterol. Res. Pract. 2013, 2013.
72. Aziz, K. U.; Patel, N.; Sadullah, T.; Tasneem, H.; Thawerani, H.; Talpur, S. Acute viral myocarditis: Role of immunosuppression: A prospective randomised study Cardiol. Young 2010, 20, 509-515
73. Kanda, T.; Nagaoka, H.; Kaneko, K.; Wilson, J. E.; McManus, B. M.; Imai, S.; Suzuki, T.; Murata, K.; Kobayashi, I. Synergistic effects of tacrolimus and human interferon-alpha A/D in murine viral myocarditis J. Pharmacol. Exp. Ther. 1995, 274, 487-493
74. Chuang, Y. G.; Young, C.; Chen, C. W. Vibrio vulnificus infection Scand. J. Infect. Dis. 1989, 21, 721-726