Hopkins AL. Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol. 2008;4(11):682–90.
Article
CAS
PubMed
Google Scholar
Jin G, Wong ST. Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. Drug Discov Today. 2014;19(5):637–44.
Article
PubMed
Google Scholar
Ekins S, Mestres J, Testa B. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. Br J Pharmacol. 2007;152(1):9–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kolb P, Ferreira RS, Irwin JJ, Shoichet BK. Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol. 2009;20(4):429–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Swamidass SJ. Mining small-molecule screens to repurpose drugs. Brief Bioinform. 2011;12(4):327–35.
Article
CAS
PubMed
Google Scholar
Alaimo S, Pulvirenti A, Giugno R, Ferro A. Drug–target interaction prediction through domain-tuned network-based inference. Bioinformatics. 2013;29(16):2004–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang L, Agarwal P. Systematic drug repositioning based on clinical side-effects. PLoS One. 2011;6(12):e28025.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bisgin H, Liu Z, Kelly R, Fang H, Xu X, Tong W. Investigating drug repositioning opportunities in FDA drug labels through topic modeling. BMC Bioinf. 2012;13(15):S6.
Article
Google Scholar
Sanseau P, Agarwal P, Barnes MR, Pastinen T, Richards JB, Cardon LR, Mooser V. Use of genome-wide association studies for drug repositioning. Nat Biotechnol. 2012;30(4):317–20.
Article
CAS
PubMed
Google Scholar
Qu XA, Rajpal DK. Applications of Connectivity Map in drug discovery and development. Drug Discov Today. 2012;17(23):1289–98.
Article
CAS
PubMed
Google Scholar
Lussier YA, Chen JL. The emergence of genome-based drug repositioning. Sci Transl Med. 2011;3(96):96ps35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao H, Jin G, Cui K, Ren D, Liu T, Chen P, Wong S, Li F, Fan Y, Rodriguez A. Novel modeling of cancer cell signaling pathways enables systematic drug repositioning for distinct breast cancer metastases. Cancer Res. 2013;73(20):6149–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Iorio F, Bosotti R, Scacheri E, Belcastro V, Mithbaokar P, Ferriero R, Murino L, Tagliaferri R, Brunetti-Pierri N, Isacchi A. Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc Natl Acad Sci. 2010;107(33):14621–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Basbaum AI, Fields HL. Endogenous Pain Control-Systems - Brain-Stem Spinal Pathways and Endorphin Circuitry. Annu Rev Neurosci. 1984;7:309–38.
Article
CAS
PubMed
Google Scholar
Vane JR, Botting RM. The mechanism of action of aspirin. Thromb Res. 2003;110(5–6):255–8.
Article
CAS
PubMed
Google Scholar
Paterson JR, Baxter G, Dreyer JS, Halket JM, Flynn R, Lawrence JR. Salicylic Acid sans Aspirin in Animals and Man: Persistence in Fasting and Biosynthesis from Benzoic Acid. J Agric Food Chem. 2008;56(24):11648–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dobson PD, Patel Y, Kell DB. Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries. Drug Discov Today. 2009;14(1–2):31–40.
Article
CAS
PubMed
Google Scholar
Kell DB. Implications of endogenous roles of transporters for drug discovery: hitchhiking and metabolite-likeness. Nat Rev Drug Discov. 2016;15(2):143.
Article
CAS
PubMed
Google Scholar
O’Hagan S, Swainston N, Handl J, Kell DB. A ‘rule of 0.5′ for the metabolite-likeness of approved pharmaceutical drugs. Metabolomics. 2015;11(2):340.
Article
Google Scholar
Gfeller D, Grosdidier A, Wirth M, Daina A, Michielin O, Zoete V. SwissTargetPrediction: a web server for target prediction of bioactive small molecules. Nucleic Acids Res. 2014;42(W1):W32–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yao Z-J, Dong J, Che Y-J, Zhu M-F, Wen M, Wang N-N, Wang S, Lu A-P, Cao D-S. TargetNet: a web service for predicting potential drug–target interaction profiling via multi-target SAR models. J Comput Aided Mol Des. 2016;30(5):413–24.
Article
CAS
PubMed
Google Scholar
Rao SN, Head MS, Kulkarni A, LaLonde JM. Validation studies of the site-directed docking program LibDock. J Chem Inf Model. 2007;47(6):2159–71.
Article
CAS
PubMed
Google Scholar
Morowitz HJ, Kostelnik JD, Yang J, Cody GD. The origin of intermediary metabolism. P Natl Acad Sci USA. 2000;97(14):7704–8.
Article
CAS
Google Scholar
Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, Liu YF, Djoumbou Y, Mandal R, Aziat F, Dong E, et al. HMDB 3.0-The Human Metabolome Database in. Nucleic Acids Res 2013. 2013;41(D1):D801–7.
Article
CAS
Google Scholar
Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, et al. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 2013;41(D1):D456–63.
Article
CAS
PubMed
Google Scholar
Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han LY, He JE, He SQ, Shoemaker BA, et al. PubChem Substance and Compound databases. Nucleic Acids Res. 2016;44(D1):D1202–13.
Article
PubMed
Google Scholar
Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006;34:D668–72.
Article
CAS
PubMed
Google Scholar
Riniker S, Landrum GA. Open-source platform to benchmark fingerprints for ligand-based virtual screening. J Cheminformatics. 2013;5(1):26.
Durant JL, Leland BA, Henry DR, Nourse JG. Reoptimization of MDL keys for use in drug discovery. J Chem Inf Comp Sci. 2002;42(6):1273–80.
Article
CAS
Google Scholar
Willett P. Similarity-based virtual screening using 2D fingerprints. Drug Discov Today. 2006;11(23–24):1046–53.
Article
CAS
PubMed
Google Scholar
Maggiora G, Vogt M, Stumpfe D, Bajorath J. Molecular Similarity in Medicinal Chemistry: Miniperspective. J Med Chem. 2013;57(8):3186–204.
Article
PubMed
Google Scholar
Warnes MGR, Bolker B, Bonebakker L: Package ‘gplots’. Various R Programming Tools for Plotting Data 2016
Team RC. R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2016. URL https://www.R-project.org/.
Google Scholar
Brewer CA, MacEachren AM, Pickle LW, Herrmann D. Mapping mortality: Evaluating color schemes for choropleth maps. Ann Assoc Am Geogr. 1997;87(3):411–38.
Article
Google Scholar
Consortium U. UniProt: a hub for protein information. Nucleic Acids Res. 2015;43(D1):D204–12.
Article
Google Scholar
Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D. BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res. 2004;32:D431–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, et al. A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013;31(5):419.
Article
CAS
PubMed
Google Scholar
Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000;28(1):27–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davies JF, Delcamp TJ, Prendergast NJ, Ashford VA, Freisheim JH, Kraut J. Crystal-Structures of Recombinant Human Dihydrofolate-Reductase Complexed with Folate and 5-Deazafolate. Biochemistry-Us. 1990;29(40):9467–79.
Article
CAS
Google Scholar
Phan J, Koli S, Minor W, Dunlap RB, Berger SH, Lebioda L. Human thymidylate synthase is in the closed conformation when complexed with dUMP and raltitrexed, an antifolate drug. Biochemistry-Us. 2001;40(7):1897–902.
Article
CAS
Google Scholar
Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioinformatics. 2005;21(20):3940–1.
Article
CAS
PubMed
Google Scholar
Fluss R, Faraggi D, Reiser B. Estimation of the Youden index and its associated cutoff point. Biometrical J. 2005;47(4):458–72.
Article
Google Scholar
Cole PD, Zebala JA, Kamen BA. Antimetabolites: A new perspective. Drug Discovery Today: Therapeutic Strategies. 2006;2(4):337–42.
Google Scholar
Tsukihara H, Tsunekuni K, Takechi T. Folic Acid- Metabolizing Enzymes Regulate the Antitumor Effect of 5-Fluoro-2′- Deoxyuridine in Colorectal Cancer Cell Lines. PLoS One. 2016;11(9):e0163961.
Article
PubMed
PubMed Central
Google Scholar
Bouchard J, Momparler R. Incorporation of 5- Aza-2′-deoxycytidine-5′-triphosphate into DNA. Interactions with mammalian DNA polymerase alpha and DNA methylase. Mol Pharmacol. 1983;24(1):109–14.
CAS
PubMed
Google Scholar
Hollenbach PW, Nguyen AN, Brady H, Williams M, Ning Y, Richard N, Krushel L, Aukerman SL, Heise C, MacBeth KJ. A comparison of azacitidine and decitabine activities in acute myeloid leukemia cell lines. e9001. 2010;5(2).
Hartsough MT, Clare SE, Mair M, Elkahloun AG, Sgroi D, Osborne CK, Clark G, Steeg PS. Elevation of breast carcinoma Nm23-H1 metastasis suppressor gene expression and reduced motility by DNA methylation inhibition. Cancer Res. 2001;61(5):2320–7.
CAS
PubMed
Google Scholar
Cook GJ, Caudell DL, Elford HL, Pardee TS. The efficacy of the ribonucleotide reductase inhibitor didox in preclinical models of AML. PLoS One. 2014;9(11):e112619.
Article
PubMed
PubMed Central
Google Scholar
Schäfer A, Schomacher L, Barreto G, Döderlein G, Niehrs C. Gemcitabine functions epigenetically by inhibiting repair mediated DNA demethylation. PLoS One. 2010;5(11):e14060.
Article
PubMed
PubMed Central
Google Scholar
Cuny GD, Suebsuwong C, Ray SS: Inosine-5′-monophosphate dehydrogenase (IMPDH) inhibitors: a patent and scientific literature review (2002–2016). Expert Opinion on Therapeutic Patents 2017(just-accepted).
Lee S-Y, Perotti A, De Jonghe S, Herdewijn P, Hanck T, Müller CE. Thiazolo [3, 2-a] benzimidazol-3 (2H)-one derivatives: Structure–activity relationships of selective nucleotide pyrophosphatase/phosphodiesterase1 (NPP1) inhibitors. Bioorg Med Chem. 2016;24(14):3157–65.
Article
CAS
PubMed
Google Scholar
Shemesh E, Deroma L, Bembi B, Deegan P, Hollak C, Weinreb NJ, Cox TM. Enzyme replacement and substrate reduction therapy for Gaucher disease. Cochrane Db Syst Rev. 2015;(3):CD010324.
Cox TM, Aerts JMFG, Andria G, Beck M, Belmatoug N, Bembi B, Chertkoff R, Vom Dahl S, Elstein D, Erikson A, et al. The role of the iminosugar N-butyldeoxynojirimycin (miglustat) in the management of type I (non-neuronopathic) Gaucher disease: A position statement. J Inherit Metab Dis. 2003;26(6):513–26.
Article
CAS
PubMed
Google Scholar
Sanchez-Olle G, Duque J, Egido-Gabas M, Casas J, Lluch M, Chabas A, Grinberg D, Vilageliu L. Promising results of the chaperone effect caused by iminosugars and aminocyclitol derivatives on mutant glucocerebrosidases causing Gaucher disease. Blood Cell Mol Dis. 2009;42(2):159–66.
Article
CAS
Google Scholar
Cox T, Aerts JM, Andria G, Beck M, Belmatoug N, Bembi B, Chertkoff R, Vom Dahl S, Elstein D, Erikson A. The role of the iminosugar N-butyldeoxynojirimycin (miglustat) in the management of type I (non-neuronopathic) Gaucher disease: a position statement. J Inherit Metab Dis. 2003;26(6):513–26.
Article
CAS
PubMed
Google Scholar
Parenti G, Fecarotta S, la Marce G, Rossi B, Ascione S, Donati MA, Morandis LO, Ravaglia S, Pichiecchio A, Ombrone D, et al. A Chaperone Enhances Blood alpha-Glucosidase Activity in Pompe Disease Patients Treated With Enzyme Replacement Therapy. Mol Ther. 2014;22(11):2004–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rigat B, Mahuran D. Diltiazem, a L-type Ca2+ channel blocker, also acts as a pharmacological chaperone in Gaucher patient cells. Mol Genet Metab. 2009;96(4):225–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bendikov-Bar I, Maor G, Filocamo M, Horowitz M. Ambroxol as a pharmacological chaperone for mutant glucocerebrosidase. Blood Cell Mol Dis. 2013;50(2):141–5.
Article
CAS
Google Scholar
Mele BH, Citro V, Andreotti G, Cubellis MV. Drug repositioning can accelerate discovery of pharmacological chaperones. Orphanet J Rare Dis. 2015;10:55.