Drug repositioning beyond the low-hanging fruits

Nosengo, 2016, Can you teach old drugs new tricks?, Nature, 534, 314, 10.1038/534314a Santos, 2017, A comprehensive map of molecular drug targets, Nature reviews Drug discovery, 16, 19, 10.1038/nrd.2016.230 Yildirim, 2007, Drug-target network, Nat Biotechnol, 25, 1119, 10.1038/nbt1338 Sawada, 2015, Target-based drug repositioning using large-scale chemical–protein interactome data, J Chem Inf Model, 55, 2717, 10.1021/acs.jcim.5b00330 Duran-Frigola, 2014, A chemo-centric view of human health and disease, Nat Commun, 5, 5676, 10.1038/ncomms6676 Yang, 2011, Systematic drug repositioning based on clinical side-effects, PLoS One, 6, e28025, 10.1371/journal.pone.0028025 Novac, 2013, Challenges and opportunities of drug repositioning, Trends Pharmacol Sci, 34, 267, 10.1016/j.tips.2013.03.004 Hartmaier, 2017, High-throughput genomic profiling of adult solid tumors reveals novel insights into cancer pathogenesis, Cancer Res, 77, 2464, 10.1158/0008-5472.CAN-16-2479 Oprea, 2012, Drug repurposing: far beyond new targets for old drugs, AAPS J, 14, 759, 10.1208/s12248-012-9390-1 Frail, 2015, Pioneering government-sponsored drug repositioning collaborations: progress and learning, Nat Rev Drug Discov, 14, 833, 10.1038/nrd4707 Sun, 2015, A comparative study of disease genes and drug targets in the human protein interactome, BMC Bioinforma, 16, S1, 10.1186/1471-2105-16-S5-S1 Guney, 2016, Network-based in silico drug efficacy screening, Nat Commun, 7, 10331, 10.1038/ncomms10331 Gaulton, 2017, The chembl database in 2017, Nucleic Acids Res, 45, D945, 10.1093/nar/gkw1074 Law, 2014, Drugbank 4.0: shedding new light on drug metabolism, Nucleic acids Res, 42, D1091, 10.1093/nar/gkt1068 Finan, 2017, The druggable genome and support for target identification and validation in drug development, Sci Transl Med, 9, eaag1166, 10.1126/scitranslmed.aag1166 Schenone, 2013, Target identification and mechanism of action in chemical biology and drug discovery, Nat Chem Biol, 9, 232, 10.1038/nchembio.1199 Neira, 2017, Identification of a drug targeting an intrinsically disordered protein involved in pancreatic adenocarcinoma, Scientific Rep, 7, 39732, 10.1038/srep39732 Duran-Frigola, 2013, Structural systems pharmacology: the role of 3d structures in next-generation drug development, Chem Biol, 20, 674, 10.1016/j.chembiol.2013.03.004 Mendez-Lucio, 2014, Toward drug repurposing in epigenetics: olsalazine as a hypomethylating compound active in a cellular context, ChemMedChem, 9, 560, 10.1002/cmdc.201300555 Weinstein, 2013, The cancer genome atlas pan-cancer analysis project, Nat Genet, 45, 1113, 10.1038/ng.2764 Rubio-Perez, 2015, In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities, Cancer Cell, 27, 382, 10.1016/j.ccell.2015.02.007 Kopetz, 2015, Phase ii pilot study of vemurafenib in patients with metastatic braf-mutated colorectal cancer, J Clin Oncol, 33, 4032, 10.1200/JCO.2015.63.2497 Biankin, 2015, Patient-centric trials for therapeutic development in precision oncology, Nature, 526, 361, 10.1038/nature15819 Mullard, 2015, Nci-match trial pushes cancer umbrella trial paradigm, Nat Rev Drug Discov, 14, 513, 10.1038/nrd4694 Sottoriva, 2015, A big bang model of human colorectal tumor growth, Nat Genet, 47, 209, 10.1038/ng.3214 Jaeger, 2017, Quantification of pathway crosstalk reveals novel synergistic drug combinations for breast cancer, Cancer Res, 77, 459, 10.1158/0008-5472.CAN-16-0097 Rios-Colon, 2017, Targeting the stress oncoprotein ledgf/p75 to sensitize chemoresistant prostate cancer cells to taxanes, Oncotarget, 8, 24915, 10.18632/oncotarget.15323 Maitra, 2015, Repurposing-a ray of hope in tackling extensively drug resistance in tuberculosis, Int J Infect Dis, 32, 50, 10.1016/j.ijid.2014.12.031 Ferreira, 2016, Drug repositioning approaches to parasitic diseases: a medicinal chemistry perspective, Drug Discov Today, 21, 1699, 10.1016/j.drudis.2016.06.021 Calain, 2016, The ebola clinical trials: a precedent for research ethics in disasters, J Med Ethics Kharkar, 2016, Discovery of anti-ebola drugs: a computational drug repositioning case study, RSC Adv, 6, 26329, 10.1039/C6RA01704E Ekins, 2016, Open drug discovery for the zika virus, F1000Res, 5, 150, 10.12688/f1000research.8013.1 Mitjà, 2012, Single-dose azithromycin versus benzathine benzylpenicillin for treatment of yaws in children in Papua New Guinea: an open-label, non-inferiority, randomised trial, Lancet, 379, 342, 10.1016/S0140-6736(11)61624-3 Asiedu, 2014, Eradication of yaws: historical efforts and achieving who's 2020 target, PLoS Neglected Trop Dis, 8, e3016, 10.1371/journal.pntd.0003016 Law, 2013, Drug repurposing: a better approach for infectious disease drug discovery?, Curr Opin Immunol, 25, 588, 10.1016/j.coi.2013.08.004 Lamb, 2006, The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease, Science, 313, 1929, 10.1126/science.1132939 Peck, 2006, A method for high-throughput gene expression signature analysis, Genome Biol, 7, R61, 10.1186/gb-2006-7-7-r61 Barrett, 2013, Ncbi geo: archive for functional genomics data sets–update, Nucleic acids Res, 41, D991 Liberzon, 2015, The molecular signatures database (msigdb) hallmark gene set collection, Cell Syst, 1, 417, 10.1016/j.cels.2015.12.004 Chen, 2013, Enrichr: interactive and collaborative html5 gene list enrichment analysis tool, BMC Bioinforma, 14, 128, 10.1186/1471-2105-14-128 Dudley, 2011, Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease, Sci Transl Med, 3, 96ra76, 10.1126/scitranslmed.3002648 Sirota, 2011, Discovery and preclinical validation of drug indications using compendia of public gene expression data, Sci Transl Med, 3, 96ra77, 10.1126/scitranslmed.3001318 Crockett, 2014, Topiramate use does not reduce flares of inflammatory bowel disease, Dig Dis Sci, 59, 1535, 10.1007/s10620-014-3040-7 Iorio, 2013, Transcriptional data: a new gateway to drug repositioning?, Drug Discov Today, 18, 350, 10.1016/j.drudis.2012.07.014 Farooq, 2009, P38 mitogen-activated protein kinase stabilizes smn mrna through rna binding protein hur, Hum Mol Genet, 18, 4035, 10.1093/hmg/ddp352 Zhao, 2014, Predicting cooperative drug effects through the quantitative cellular profiling of response to individual drugs, CPT Pharmacometrics Syst Pharmacol, 3, e102, 10.1038/psp.2013.79 Duan, 2016, L1000cds2: lincs l1000 characteristic direction signatures search engine, npj Syst Biol Appl, 2, 16015, 10.1038/npjsba.2016.15 Iorio, 2010, Discovery of drug mode of action and drug repositioning from transcriptional responses, Proc Natl Acad Sci U. S. A, 107, 14621, 10.1073/pnas.1000138107 Engreitz, 2011, Profilechaser: searching microarray repositories based on genome-wide patterns of differential expression, Bioinformatics, 27, 3317, 10.1093/bioinformatics/btr548 Gholami, 2013, Global proteome analysis of the nci-60 cell line panel, Cell Rep, 4, 609, 10.1016/j.celrep.2013.07.018 Barretina, 2012, The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity, Nature, 483, 603, 10.1038/nature11003 Garnett, 2012, Systematic identification of genomic markers of drug sensitivity in cancer cells, Nature, 483, 570, 10.1038/nature11005 Iorio, 2016, A landscape of pharmacogenomic interactions in cancer, Cell, 166, 740, 10.1016/j.cell.2016.06.017 Jaeger, 2015, Drug sensitivity in cancer cell lines is not tissue-specific, Mol Cancer, 14, 40, 10.1186/s12943-015-0312-6 Geeleher, 2016, Consistency in large pharmacogenomic studies, Nature, 540, E1, 10.1038/nature19838 Haibe-Kains, 2013, Inconsistency in large pharmacogenomic studies, Nature, 504, 389, 10.1038/nature12831 Medico, 2015, The molecular landscape of colorectal cancer cell lines unveils clinically actionable kinase targets, Nat Commun, 6, 7002, 10.1038/ncomms8002 Suresh, 2016, St Onge RP: systematic mapping of chemical-genetic interactions in saccharomyces cerevisiae, Cold Spring Harb Protoc, 2016, 10.1101/pdb.top077701 Zlotkowski, 2013, Small-molecule mechanism of action studies in caenorhabditis elegans, Chembiochem, 14, 2338, 10.1002/cbic.201300399 Laggner, 2011, Chemical informatics and target identification in a zebrafish phenotypic screen, Nat Chem Biol, 8, 144, 10.1038/nchembio.732 Nelson, 2017, Mosaic: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action, bioRxiv van Leeuwen, 2016, Exploring genetic suppression interactions on a global scale, Science, 354, 10.1126/science.aag0839 Wildenhain, 2015, Prediction of synergism from chemical-genetic interactions by machine learning, Cell Syst, 1, 383, 10.1016/j.cels.2015.12.003 Rastegar-Mojarad, 2015, Opportunities for drug repositioning from phenome-wide association studies, Nat Biotechnol, 33, 342, 10.1038/nbt.3183 Melnikova, 2012, Rare diseases and orphan drugs, Nat Rev Drug Discov, 11, 267, 10.1038/nrd3654 Hu, 2016, Network biology concepts in complex disease comorbidities, Nat Rev Genet, 17, 615, 10.1038/nrg.2016.87 Zhou, 2014, Human symptoms-disease network, Nat Commun, 5, 4212, 10.1038/ncomms5212 Menche, 2015, Disease networks. Uncovering disease-disease relationships through the incomplete interactome, Science, 347, 1257601, 10.1126/science.1257601 Goh, 2007, The human disease network, Proc Natl Acad Sci U. S. A, 104, 8685, 10.1073/pnas.0701361104 Bordbar, 2014, Constraint-based models predict metabolic and associated cellular functions, Nat Rev Genet, 15, 107, 10.1038/nrg3643 Nguyen, 2016, Actikerall™ (5-fluorouracil 0.5% and salicylic acid 10%) topical solution for patient-directed treatment of actinic keratoses, Skin Ther Lett, 21, 1 Oprea, 2015, Computational and practical aspects of drug repositioning, Assay Drug Dev Technol, 13, 299, 10.1089/adt.2015.29011.tiodrrr Moosavinasab, 2016, ‘Re:Fine drugs’: an interactive dashboard to access drug repurposing opportunities, Database, 2016, 10.1093/database/baw083 Luo, 2011, Drar-cpi: a server for identifying drug repositioning potential and adverse drug reactions via the chemical-protein interactome, Nucleic Acids Res, 39, W492, 10.1093/nar/gkr299 Fu, 2013, Drugmap central: an on-line query and visualization tool to facilitate drug repositioning studies, Bioinformatics, 29, 1834, 10.1093/bioinformatics/btt279 Lee, 2012, Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug, BMC Syst Biol, 6, 80, 10.1186/1752-0509-6-80 Brown, 2016, A review of validation strategies for computational drug repositioning, Brief Bioinform