Generic placeholder image

Current Medicinal Chemistry

Editor-in-Chief

ISSN (Print): 0929-8673
ISSN (Online): 1875-533X

Review Article

Web-based Tools for Drug Repurposing: Successful Examples of Collaborative Research

Author(s): Quentin Vanhaelen*

Volume 28, Issue 1, 2021

Published on: 28 January, 2020

Page: [181 - 195] Pages: 15

DOI: 10.2174/0929867327666200128111925

Price: $65

Abstract

Computational approaches have been proven to be complementary tools of interest in identifying potential candidates for drug repurposing. However, although the methods developed so far offer interesting opportunities and could contribute to solving issues faced by the pharmaceutical sector, they also come with their constraints. Indeed, specific challenges ranging from data access, standardization and integration to the implementation of reliable and coherent validation methods must be addressed to allow systematic use at a larger scale. In this mini-review, we cover computational tools recently developed for addressing some of these challenges. This includes specific databases providing accessibility to a large set of curated data with standardized annotations, web-based tools integrating flexible user interfaces to perform fast computational repurposing experiments and standardized datasets specifically annotated and balanced for validating new computational drug repurposing methods. Interestingly, these new databases combined with the increasing number of information about the outcomes of drug repurposing studies can be used to perform a meta-analysis to identify key properties associated with successful drug repurposing cases. This information could further be used to design estimation methods to compute a priori assessment of the repurposing possibilities.

Keywords: Drug repurposing, web-based tools, database, computational methods, validation, data integration.

[1]
Ashburn, T.T.; Thor, K.B. Drug repositioning: identifying and developing new uses for existing drugs. Nat. Rev. Drug Discov., 2004, 3(8), 673-683.
[http://dx.doi.org/10.1038/nrd1468] [PMID: 15286734]
[2]
Dudley, J.T.; Deshpande, T.; Butte, A.J. Exploiting drug-disease relationships for computational drug repositioning. Brief. Bioinform., 2011, 12(4), 303-311.
[http://dx.doi.org/10.1093/bib/bbr013] [PMID: 21690101]
[3]
DiMasi, J.A.; Grabowski, H.G.; Hansen, R.W. Innovation in the pharmaceutical industry: new estimates of R&D costs. J. Health Econ., 2016, 47, 20-33.
[http://dx.doi.org/10.1016/j.jhealeco.2016.01.012] [PMID: 26928437]
[4]
Graul, A.I.; Revel, L.; Rosa, E.; Cruces, E. Overcoming the obstacles in the pharma/biotech industry: 2008 update. Drug News Perspect., 2009, 22(1), 39-51.
[http://dx.doi.org/10.1358/dnp.2009.22.1.1303817] [PMID: 19209298]
[5]
Schneider, G. Automating drug discovery. Nat. Rev. Drug Discov., 2018, 17(2), 97-113.
[http://dx.doi.org/10.1038/nrd.2017.232] [PMID: 29242609]
[6]
Paul, S.M.; Mytelka, D.S.; Dunwiddie, C.T.; Persinger, C.C.; Munos, B.H.; Lindborg, S.R.; Schacht, A.L. How to improve R&D productivity: the pharmaceutical industry’s grand challenge. Nat. Rev. Drug Discov., 2010, 9(3), 203-214.
[http://dx.doi.org/10.1038/nrd3078] [PMID: 20168317]
[7]
Munos, B.H.; Chin, W.W. How to revive breakthrough innovation in the pharmaceutical industry. Sci. Transl. Med., 2011, 3(89)89cm16
[http://dx.doi.org/10.1126/scitranslmed.3002273] [PMID: 21715677]
[8]
Mignani, S.; Huber, S.; Tomás, H.; Rodrigues, J.; Majoral, J.P. Why and how have drug discovery strategies in pharma changed? What are the new mindsets? Drug Discov. Today, 2016, 21(2), 239-249.
[http://dx.doi.org/10.1016/j.drudis.2015.09.007] [PMID: 26376356]
[9]
Tollman, P.; Morieux, Y.; Murphy, J.K.; Schulze, U.; Identifying, R. D outliers. Nat. Rev. Drug Discov., 2011, 10(9), 653-654.
[http://dx.doi.org/10.1038/nrd3555] [PMID: 21878973]
[10]
Scannell, J.W.; Blanckley, A.; Boldon, H.; Warrington, B. Diagnosing the decline in pharmaceutical R&D efficiency. Nat. Rev. Drug Discov., 2012, 11(3), 191-200.
[http://dx.doi.org/10.1038/nrd3681] [PMID: 22378269]
[11]
Novac, N. Challenges and opportunities of drug repositioning. Trends Pharmacol. Sci., 2013, 34(5), 267-272.
[http://dx.doi.org/10.1016/j.tips.2013.03.004] [PMID: 23582281]
[12]
Mucke, H.A.M. Drug repurposing patent applications October-December 2015. Assay Drug Dev. Technol., 2016, 14(5), 308-312.
[http://dx.doi.org/10.1089/adt.2016.29041.pq4] [PMID: 30909710]
[13]
Naylor, S.; Kaupi, M.J.; Schonfeld, J.M. Therapeutic drug repurposing, repositioning, and rescue: part III- market exclusivity using intellectual property and regulatory pathways. Drug Discov. World, 2015, 16(3), 62-69.
[14]
Vortherms, A.R.; Dang, H.N.; Doyle, R.P. Anticancer conjugates and cocktails based on methotrexate and nucleoside synergism. Clin. Med. Oncol., 2009, 3, 19-26.
[http://dx.doi.org/10.4137/CMO.S2113] [PMID: 20689607]
[15]
Gupta, S.C.; Sung, B.; Prasad, S.; Webb, L.J.; Aggarwal, B.B. Cancer drug discovery by repurposing: teaching new tricks to old dogs. Trends Pharmacol. Sci., 2013, 34(9), 508-517.
[http://dx.doi.org/10.1016/j.tips.2013.06.005] [PMID: 23928289]
[16]
Yildiz, A.; Guleryuz, S.; Ankerst, D.P.; Ongür, D.; Renshaw, P.F. Protein kinase C inhibition in the treatment of mania: a double-blind, placebo-controlled trial of tamoxifen. Arch. Gen. Psychiatry, 2008, 65(3), 255-263.
[http://dx.doi.org/10.1001/archgenpsychiatry.2007.43] [PMID: 18316672]
[17]
Nishimura, Y.; Tagawa, M.; Ito, H.; Tsuruma, K.; Hara, H. Overcoming obstacles to drug repositioning in Japan. Front. Pharmacol., 2017, 8, 729.
[http://dx.doi.org/10.3389/fphar.2017.00729] [PMID: 29075191]
[18]
Yarchoan, M.; Arnold, S.E. Repurposing diabetes drugs for brain insulin resistance in Alzheimer disease. Diabetes, 2014, 63(7), 2253-2261.
[http://dx.doi.org/10.2337/db14-0287] [PMID: 24931035]
[19]
Mucke, H.A.M. Drug repurposing for vascular dementia: overview and current developments. Future Neurol., 2016, 11(3), 215-225.
[http://dx.doi.org/10.2217/fnl-2016-0001 ]
[20]
Lee, H.M.; Kim, Y. drug repurposing is a new opportunity for developing drugs against neuropsychiatric disorders. Schizophr. Res. Treatment, 2016.
[http://dx.doi.org/doi:10.1155/2016/6378137] [PMID: 27073698]
[21]
Is there a place for duloxetine? Drug Ther. Bull., 2007, 45(4), 29-32.
[http://dx.doi.org/10.1136/dtb.2007.45429] [PMID: 17451072]
[22]
Ho, L.Y.; Mok, C.C.; To, C.H.; Anselm, M.; Cheung, M.Y.; Yu, K.L. Rituximab for refractory rheumatoid arthritis: a 24-week open-label prospective study. Open Rheumatol. J., 2007, 1, 1-4.
[http://dx.doi.org/10.2174/1874312900701010001] [PMID: 19088893]
[23]
O’Donnell, E.F.; Koch, D.C.; Bisson, W.H.; Jang, H.S.; Kolluri, S.K. The aryl hydrocarbon receptor mediates raloxifene-induced apoptosis in estrogen receptor-negative hepatoma and breast cancer cells. Cell Death Dis., 2014, 5(1)e1038
[http://dx.doi.org/10.1038/cddis.2013.549] [PMID: 24481452]
[24]
Ayzenberg, I.; Hoepner, R.; Kleiter, I. Fingolimod for multiple sclerosis and emerging indications: appropriate patient selection, safety precautions, and special considerations. Ther. Clin. Risk Manag., 2016, 12, 261-272.
[http://dx.doi.org/10.2147/tcrm.s65558] [PMID: 26929636]
[25]
McMahon, C.G. Efficacy of dapoxetine in the treatment of premature ejaculation. Clin. Med. Insights Reprod. Health, 2011, 5, 25-39.
[http://dx.doi.org/10.4137/CMRH.S7337] [PMID: 24453509]
[26]
Smith, S.M.; Meyer, M.; Trinkley, K.E. Phentermine/topiramate for the treatment of obesity. Ann. Pharmacother., 2013, 47(3), 340-349.
[http://dx.doi.org/10.1345/aph.1R501] [PMID: 23482732]
[27]
Comte-Perret, S.; Zanchi, A.; Gomez, F. Long-term low-dose ketoconazole treatment in bilateral macronodular adrenal hyperplasia. Endocrinol. Diabetes Metab. Case Rep., 2014, 2014140083
[http://dx.doi.org/10.1530/EDM-14-0083] [PMID: 25535576]
[28]
Mazumdar, D.; Banerjee, S.; Bhattacharya, A.; Das, T. Repurposing of aspirin to regress tumor from its ‘Root’ - the cancer stem cells. Austin J. Pharmacol. Ther., 2017, 5(2), 1096.
[29]
Jin, G.; Wong, S.T.C. Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. Drug Discov. Today, 2014, 19(5), 637-644.
[http://dx.doi.org/10.1016/j.drudis.2013.11.005] [PMID: 24239728]
[30]
Snell, T.W.; Johnston, R.K.; Srinivasan, B.; Zhou, H.; Gao, M.; Skolnick, J. Repurposing FDA-approved drugs for anti-aging therapies. Biogerontology, 2016, 17(5-6), 907-920.
[http://dx.doi.org/10.1007/s10522-016-9660-x] [PMID: 27484416]
[31]
Kato, S.; Moulder, S.L.; Ueno, N.T.; Wheler, J.J.; Meric-Bernstam, F.; Kurzrock, R.; Janku, F. Challenges and perspective of drug repurposing strategies in early phase clinical trials. Oncoscience, 2015, 2(6), 576-580.
[http://dx.doi.org/10.18632/oncoscience.173] [PMID: 26244164]
[32]
Naik, R.R.; Luo, T.; Kohandel, M.; Bapat, S.A. Tumor deconstruction as a tool for advanced drug screening and repositioning. Pharmacol. Res., 2016, 111, 815-819.
[http://dx.doi.org/10.1016/j.phrs.2016.07.018] [PMID: 27431330]
[33]
Shim, J.S.; Liu, J.O. Recent advances in drug repositioning for the discovery of new anticancer drugs. Int. J. Biol. Sci., 2014, 10(7), 654-663.
[http://dx.doi.org/10.7150/ijbs.9224] [PMID: 25013375]
[34]
Heckman-Stoddard, B.M.; Gandini, S.; Puntoni, M.; Dunn, B.K.; DeCensi, A.; Szabo, E. Repurposing old drugs to chemoprevention: the case of metformin. Semin. Oncol., 2016, 43(1), 123-133.
[http://dx.doi.org/10.1053/j.seminoncol.2015.09.009] [PMID: 26970131]
[35]
Gilbert, D.C.; Vale, C.; Haire, R.; Coyle, C.; Langley, R.E. Repurposing vitamin D as an anticancer drug. Clin. Oncol. (R. Coll. Radiol.), 2016, 28(1), 36-41.
[http://dx.doi.org/10.1016/j.clon.2015.10.004] [PMID: 26520788]
[36]
Guney, E.; Menche, J.; Vidal, M.; Barábasi, A.L. Network-based in silico drug efficacy screening. Nat. Commun., 2016, 7, 10331.
[http://dx.doi.org/10.1038/ncomms10331] [PMID: 26831545]
[37]
Kaplan, W.; Wirtz, V.; Mantel, A.; Batrice, P.S.U. Priority Medicines for Europe and the World Update 2013; World Health Organization: Geneva, Switzerland, 2013.
[38]
Hodos, R.A.; Kidd, B.A.; Shameer, K.; Readhead, B.P.; Dudley, J.T. In silico methods for drug repurposing and pharmacology. Wiley Interdiscip. Rev. Syst. Biol. Med., 2016, 8(3), 186-210.
[http://dx.doi.org/10.1002/wsbm.1337] [PMID: 27080087]
[39]
Wu, Z.; Wang, Y.; Chen, L. Network-based drug repositioning. Mol. Biosyst., 2013, 9(6), 1268-1281.
[http://dx.doi.org/10.1039/c3mb25382a] [PMID: 23493874]
[40]
Chen, B.; Butte, A.J. Leveraging big data to transform target selection and drug discovery. Clin. Pharmacol. Ther., 2016, 99(3), 285-297.
[http://dx.doi.org/10.1002/cpt.318] [PMID: 26659699]
[41]
Zou, J.; Zheng, M.W.; Li, G.; Su, Z.G. Advanced systems biology methods in drug discovery and translational biomedicine. BioMed Res. Int., 2013, 2013742835
[http://dx.doi.org/10.1155/2013/742835] [PMID: 24171171]
[42]
Prathipati, P.; Mizuguchi, K. Systems biology approaches to a rational drug discovery paradigm. Curr. Top. Med. Chem., 2016, 16(9), 1009-1025.
[http://dx.doi.org/10.2174/1568026615666150826114524] [PMID: 26306988]
[43]
Lavecchia, A.; Cerchia, C. In silico methods to address polypharmacology: current status, applications and future perspectives. Drug Discov. Today, 2016, 21(2), 288-298.
[http://dx.doi.org/10.1016/j.drudis.2015.12.007] [PMID: 26743596]
[44]
Cichonska, A.; Rousu, J.; Aittokallio, T. Identification of drug candidates and repurposing opportunities through compound-target interaction networks. Expert Opin. Drug Discov., 2015, 10(12), 1333-1345.
[http://dx.doi.org/10.1517/17460441.2015.1096926] [PMID: 26429153]
[45]
Fu, C.; Jin, G.; Gao, J.; Zhu, R.; Ballesteros-Villagrana, E.; Wong, S.T. DrugMap Central: an online query and visualization tool to facilitate drug repositioning studies. Bioinformatics, 2013, 29(14), 1834-1836.
[http://dx.doi.org/10.1093/bioinformatics/btt279] [PMID: 23681121]
[46]
Luo, H.; Chen, J.; Shi, L.; Mikailov, M.; Zhu, H.; Wang, K.; He, L.; Yang, L. DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical-protein interactome. Nucleic Acids Res, 2011, 39(Web Server issue), 492-498.
[http://dx.doi.org/10.1093/nar/gkr299 ] [PMID: 21558322]
[47]
Pihan, E.; Colliandre, L.; Guichou, J.F.; Douguet, D. e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design. Bioinformatics, 2012, 28(11), 1540-1541.
[http://dx.doi.org/10.1093/bioinformatics/bts186] [PMID: 22539672]
[48]
Lee, H.S.; Bae, T.; Lee, J.H.; Kim, D.G.; Oh, Y.S.; Jang, Y.; Kim, J.T.; Lee, J.J.; Innocenti, A.; Supuran, C.T.; Chen, L.; Rho, K.; Kim, S. Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug. BMC Syst. Biol., 2012, 6, 80.
[http://dx.doi.org/10.1186/1752-0509-6-80] [PMID: 22748168]
[49]
von Eichborn, J.; Murgueitio, M.S.; Dunkel, M.; Koerner, S.; Bourne, P.E.; Preissner, R. PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Res., 2011, 39(Database issue), D1060-D1066.
[http://dx.doi.org/10.1093/nar/gkq1037] [PMID: 21071407]
[50]
Nagaraj, A.B.; Wang, Q.Q.; Joseph, P.; Zheng, C.; Chen, Y.; Kovalenko, O.; Singh, S.; Armstrong, A.; Resnick, K.; Zanotti, K.; Waggoner, S.; Xu, R.; DiFeo, A. Using a novel computational drug-repositioning approach (DrugPredict) to rapidly identify potent drug candidates for cancer treatment. Oncogene, 2018, 37(3), 403-414.
[http://dx.doi.org/10.1038/onc.2017.328] [PMID: 28967908]
[51]
Shameer, K.; Readhead, B.; Dudley, J.T. Computational and experimental advances in drug repositioning for accelerated therapeutic stratification. Curr. Top. Med. Chem., 2015, 15(1), 5-20.
[http://dx.doi.org/10.2174/1568026615666150112103510] [PMID: 25579574]
[52]
Alaimo, S.; Giugno, R.; Pulvirenti, A. Recommendation techniques for drug-target interaction prediction and drug repositioning. Methods Mol. Biol., 2016, 1415, 441-462.
[http://dx.doi.org/10.1007/978-1-4939-3572-7_23] [PMID: 27115647]
[53]
González-Díaz, H.; Prado-Prado, F.; García-Mera, X.; Alonso, N.; Abeijón, P.; Caamaño, O.; Yáñez, M.; Munteanu, C.R.; Pazos, A.; Dea-Ayuela, M.A.; Gómez-Muñoz, M.T.; Garijo, M.M.; Sansano, J.; Ubeira, F.M. MIND-BEST: Web server for drugs and target discovery; design, synthesis, and assay of MAO-B inhibitors and theoretical-experimental study of G3PDH protein from Trichomonas gallinae. J. Proteome Res., 2011, 10(4), 1698-1718.
[http://dx.doi.org/10.1021/pr101009e] [PMID: 21184613]
[54]
Vanhaelen, Q.; Mamoshina, P.; Aliper, A.M.; Artemov, A.; Lezhnina, K.; Ozerov, I.; Labat, I.; Zhavoronkov, A. Design of efficient computational workflows for in silico drug repurposing. Drug Discov. Today, 2017, 22(2), 210-222.
[http://dx.doi.org/10.1016/j.drudis.2016.09.019] [PMID: 27693712]
[55]
Jahchan, N.S.; Dudley, J.T.; Mazur, P.K.; Flores, N.; Yang, D.; Palmerton, A.; Zmoos, A.F.; Vaka, D.; Tran, K.Q.; Zhou, M.; Krasinska, K.; Riess, J.W.; Neal, J.W.; Khatri, P.; Park, K.S.; Butte, A.J.; Sage, J. A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. Cancer Discov., 2013, 3(12), 1364-1377.
[http://dx.doi.org/10.1158/2159-8290.CD-13-0183] [PMID: 24078773]
[56]
Putin, E.; Mamoshina, P.; Aliper, A.; Korzinkin, M.; Moskalev, A.; Kolosov, A.; Ostrovskiy, A.; Cantor, C.; Vijg, J.; Zhavoronkov, A. Deep biomarkers of human aging: Application of deep neural networks to biomarker development. Aging (Albany NY), 2016, 8(5), 1021-1033.
[http://dx.doi.org/10.18632/aging.100968] [PMID: 27191382]
[57]
Aliper, A.; Plis, S.; Artemov, A.; Ulloa, A.; Mamoshina, P.; Zhavoronkov, A. Deep learning applications for predicting pharmacological properties of drugs and drug repurposing using transcriptomic data. Mol. Pharm., 2016, 13(7), 2524-2530.
[http://dx.doi.org/10.1021/acs.molpharmaceut.6b00248] [PMID: 27200455]
[58]
Bloom, B.E. Creating new economic incentives for repurposing generic drugs for unsolved diseases using social finance. Assay Drug Dev. Technol., 2015, 13(10), 606-611.
[http://dx.doi.org/10.1089/adt.2015.29015.beddrrr] [PMID: 26284286]
[59]
Mucke, H.A.; Mucke, E. Sources and targets for drug repurposing: landscaping transitions in therapeutic space. Assay Drug Dev. Technol., 2015, 13(6), 319-324.
[http://dx.doi.org/10.1089/adt.2015.29009.hmedrrr] [PMID: 26241211]
[60]
Shameer, K.; Glicksberg, B.S.; Hodos, R.; Johnson, K.W.; Badgeley, M.A.; Readhead, B.; Tomlinson, M.S.; O’Connor, T.; Miotto, R.; Kidd, B.A.; Chen, R.; Ma’ayan, A.; Dudley, J.T. Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. Brief. Bioinform., 2018, 19(4), 656-678.
[http://dx.doi.org/10.1093/bib/bbw136] [PMID: 28200013]
[61]
Ursu, O.; Holmes, J.; Knockel, J.; Bologa, C.G.; Yang, J.J.; Mathias, S.L.; Nelson, S.J.; Oprea, T.I. DrugCentral: online drug compendium. Nucleic Acids Res., 2017, 45(D1), D932-D939.
[http://dx.doi.org/10.1093/nar/gkw993] [PMID: 27789690]
[62]
Koscielny, G.; An, P.; Carvalho-Silva, D.; Cham, J.A.; Fumis, L.; Gasparyan, R.; Hasan, S.; Karamanis, N.; Maguire, M.; Papa, E.; Pierleoni, A.; Pignatelli, M.; Platt, T.; Rowland, F.; Wankar, P.; Bento, A.P.; Burdett, T.; Fabregat, A.; Forbes, S.; Gaulton, A.; Gonzalez, C.Y.; Hermjakob, H.; Hersey, A.; Jupe, S.; Kafkas, Ş.; Keays, M.; Leroy, C.; Lopez, F.J.; Magarinos, M.P.; Malone, J.; McEntyre, J.; Munoz-Pomer Fuentes, A.; O’Donovan, C.; Papatheodorou, I.; Parkinson, H.; Palka, B.; Paschall, J.; Petryszak, R.; Pratanwanich, N.; Sarntivijal, S.; Saunders, G.; Sidiropoulos, K.; Smith, T.; Sondka, Z.; Stegle, O.; Tang, Y.A.; Turner, E.; Vaughan, B.; Vrousgou, O.; Watkins, X.; Martin, M.J.; Sanseau, P.; Vamathevan, J.; Birney, E.; Barrett, J.; Dunham, I. Open targets: a platform for therapeutic target identification and validation. Nucleic Acids Res., 2017, 45(D1), D985-D994.
[http://dx.doi.org/doi:10.1093/nar/gkw1055] [PMID: 27899665]
[63]
Corsello, S.M.; Bittker, J.A.; Liu, Z.; Gould, J.; McCarren, P.; Hirschman, J.E.; Johnston, S.E.; Vrcic, A.; Wong, B.; Khan, M.; Asiedu, J.; Narayan, R.; Mader, C.C.; Subramanian, A.; Golub, T.R. The drug repurposing hub: a next-generation drug library and information resource. Nat. Med., 2017, 23(4), 405-408.
[http://dx.doi.org/10.1038/nm.4306] [PMID: 28388612]
[64]
Cho, S.J. COMBINE: a novel drug discovery platform designed to capture insight and experience of users. arXiv, 2017, arXiv-1711.
[65]
Brown, A.S.; Kong, S.W.; Kohane, I.S.; Patel, C.J. ksRepo: a generalized platform for computational drug repositioning. BMC Bioinformatics, 2016, 17, 78.
[http://dx.doi.org/10.1186/s12859-016-0931-y] [PMID: 26860211]
[66]
Lee, B.K.; Tiong, K.H.; Chang, J.K.; Liew, C.S.; Abdul Rahman, Z.A.; Tan, A.C.; Khang, T.F.; Cheong, S.C. DeSigN: connecting gene expression with therapeutics for drug repurposing and development. BMC Genomics, 2017, 18(Suppl. 1), 934.
[http://dx.doi.org/10.1186/s12864-016-3260-7] [PMID: 28198666]
[67]
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(5795), 1929-1935.
[http://dx.doi.org/10.1126/science.1132939] [PMID: 17008526]
[68]
Moosavinasab, S.; Patterson, J.; Strouse, R.; Rastegar-Mojarad, M.; Regan, K.; Payne, P.R.O.; Huang, Y.; Lin, S.M. ‘RE:fine drugs’: an interactive dashboard to access drug repurposing opportunities. Database (Oxford), 2016, 2016baw083
[http://dx.doi.org/10.1093/database/baw083] [PMID: 27189611]
[69]
Sanseau, P.; Agarwal, P.; Barnes, M.R.; Pastinen, T.; Richards, J.B.; Cardon, L.R.; Mooser, V. Use of genome-wide association studies for drug repositioning. Nat. Biotechnol., 2012, 30(4), 317-320.
[http://dx.doi.org/10.1038/nbt.2151] [PMID: 22491277]
[70]
Andronis, C.; Sharma, A.; Virvilis, V.; Deftereos, S.; Persidis, A. Literature mining, ontologies and information visualization for drug repurposing. Brief. Bioinform., 2011, 12(4), 357-368.
[http://dx.doi.org/10.1093/bib/bbr005] [PMID: 21712342]
[71]
Tari, L.; Vo, N.; Liang, S.; Patel, J.; Baral, C.; Cai, J. Identifying novel drug indications through automated reasoning. PLoS One, 2012, 7(7)e40946
[http://dx.doi.org/10.1371/journal.pone.0040946] [PMID: 22911721]
[72]
Tari, L.B.; Patel, J.H. Systematic drug repurposing through text mining. Methods Mol. Biol., 2014, 1159, 253-267.
[http://dx.doi.org/10.1007/978-1-4939-0709-0_14] [PMID: 24788271]
[73]
Xu, R.; Wang, Q. Combining automatic table classification and relationship extraction in extracting anticancer drug-side effect pairs from full-text articles. J. Biomed. Inform., 2015, 53, 128-135.
[http://dx.doi.org/10.1016/j.jbi.2014.10.002] [PMID: 25445920]
[74]
Yang, H.T.; Ju, J.H.; Wong, Y.T.; Shmulevich, I.; Chiang, J.H. Literature-based discovery of new candidates for drug repurposing. Brief. Bioinform., 2017, 18(3), 488-497.
[http://dx.doi.org/10.1093/bib/bbw030] [PMID: 27113728]
[75]
Brown, A.S.; Patel, C.J. A review of validation strategies for computational drug repositioning. Brief. Bioinform., 2018, 19(1), 174-177.
[http://dx.doi.org/10.1093/bib/bbw110] [PMID: 27881429]
[76]
Wu, H.; Huang, J.; Zhong, Y.; Huang, Q. DrugSig: A resource for computational drug repositioning utilizing gene expression signatures. PLoS One, 2017, 12(5)e0177743
[http://dx.doi.org/10.1371/journal.pone.0177743] [PMID: 28562632]
[77]
Liu, H.; Sun, J.; Guan, J.; Zheng, J.; Zhou, S. Improving compound-protein interaction prediction by building up highly credible negative samples. Bioinformatics, 2015, 31(12), i221-i229.
[http://dx.doi.org/10.1093/bioinformatics/btv256] [PMID: 26072486]
[78]
Brown, A.S.; Patel, C.J. A standard database for drug repositioning. Sci. Data, 2017, 4170029
[http://dx.doi.org/10.1038/sdata.2017.29] [PMID: 28291243]
[79]
Vanhaelen, Q., Ed.; Computational Methods for Drug Repurposing, MIMB, 1903; Humana Press: New York, 2019.
[http://dx.doi.org/doi:10.1007/978-1-4939-8955-3]
[80]
Sagers, J.E.; Brown, A.S.; Vasilijic, S.; Lewis, R.M.; Sahin, M.I.; Landegger, L.D.; Perlis, R.H.; Kohane, I.S.; Welling, D.B.; Patel, C.J.; Stankovic, K.M. Computational repositioning and preclinical validation of mifepristone for human vestibular schwannoma. Sci. Rep., 2018, 8(1), 5437.
[http://dx.doi.org/10.1038/s41598-018-23609-7] [PMID: 29615643]
[81]
Hurle, M.R.; Yang, L.; Xie, Q.; Rajpal, D.K.; Sanseau, P.; Agarwal, P. Computational drug repositioning: from data to therapeutics. Clin. Pharmacol. Ther., 2013, 93(4), 335-341.
[http://dx.doi.org/10.1038/clpt.2013.1] [PMID: 23443757]
[82]
Zhu, F.; Li, X.X.; Yang, S.Y.; Chen, Y.Z. Clinical success of drug targets prospectively predicted by in silico study. Trends Pharmacol. Sci., 2018, 39(3), 229-231.
[http://dx.doi.org/10.1016/j.tips.2017.12.002] [PMID: 29295742]

Rights & Permissions Print Export Cite as
© 2022 Bentham Science Publishers | Privacy Policy