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Computational Methods for Drug Repurposing

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Computational Methods for Precision Oncology

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1361))

Abstract

The wealth of knowledge and multi-omics data available in drug research has allowed the rise of several computational methods in the drug discovery field, resulting in a novel and exciting strategy called drug repurposing. Drug repurposing consists in finding new applications for existing drugs. Numerous computational methods perform a high-level integration of different knowledge sources to facilitate the discovery of unknown mechanisms. In this chapter, we present a survey of data resources and computational tools available for drug repositioning.

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References

  1. Sam E, Athri P. Web-based drug repurposing tools: a survey. Brief Bioinform. 2019;20:299–316.

    Article  PubMed  CAS  Google Scholar 

  2. Fiscon G, Paci P. SAveRUNNER: an R-based tool for drug repurposing. BMC Bioinformatics. 2021;22:150.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Jin G, Wong STC. Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. Drug Discov Today. 2014;19:637–44.

    Article  PubMed  Google Scholar 

  4. Gong J, Cai C, Liu X, Ku X, Jiang H, Gao D, Li H. ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method. Bioinformatics. 2013;29:1827–9.

    Article  CAS  PubMed  Google Scholar 

  5. Kringelum J, Kjaerulff SK, Brunak S, Lund O, Oprea TI, Taboureau O. ChemProt-3.0: a global chemical biology diseases mapping. Database. 2016;2016:bav123. https://doi.org/10.1093/database/bav123.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Liu X, Vogt I, Haque T, Campillos M. HitPick: a web server for hit identification and target prediction of chemical screenings. Bioinformatics. 2013;29:1910–2.

    Article  CAS  PubMed  Google Scholar 

  7. Xiao X, Min J-L, Lin W-Z, Liu Z, Cheng X, Chou K-C. iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach. J Biomol Struct Dyn. 2015;33:2221–33.

    Article  CAS  PubMed  Google Scholar 

  8. Abdouli NOA, Al Abdouli NO, Aung Z, Woon WL, Svetinovic D. Tackling class imbalance problem in binary classification using augmented neighborhood cleaning algorithm. In: Kim K, editor. Information science and applications. Lecture notes in electrical engineering. Berlin, Heidelberg: Springer; 2015. p. 827–34.

    Chapter  Google Scholar 

  9. Chawla NV, Bowyer KW, Hall LO, Kegelmeyer WP. SMOTE: Synthetic Minority Over-sampling TEchnique. J Artif Intell Res. 2002;16:321–57.

    Article  Google Scholar 

  10. Awale M, Reymond J-L. The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data. J Cheminform. 2017;9:11.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotechnol. 2007;25:197–206.

    Article  CAS  PubMed  Google Scholar 

  12. Nickel J, Gohlke B-O, Erehman J, Banerjee P, Rong WW, Goede A, Dunkel M, Preissner R. SuperPred: update on drug classification and target prediction. Nucleic Acids Res. 2014;42:W26–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. 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:W32–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Daina A, Michielin O, Zoete V. SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules. Nucleic Acids Res. 2019;47:W357–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Liu X, Gao Y, Peng J, Xu Y, Wang Y, Zhou N, Xing J, Luo X, Jiang H, Zheng M. TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds. Bioinformatics. 2015;31:2049–51.

    Article  CAS  PubMed  Google Scholar 

  16. Wang L, Ma C, Wipf P, Liu H, Su W, Xie X-Q. TargetHunter: an in silico target identification tool for predicting therapeutic potential of small organic molecules based on chemogenomic database. AAPS J. 2013;15:395–406.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Wang J-C, Chu P-Y, Chen C-M, Lin J-H. idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach. Nucleic Acids Res. 2012;40:W393–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Wang C, Hu G, Wang K, Brylinski M, Xie L, Kurgan L. PDID: database of molecular-level putative protein–drug interactions in the structural human proteome. Bioinformatics. 2016;32:579–86.

    Article  CAS  PubMed  Google Scholar 

  19. Li H, Gao Z, Kang L, et al. TarFisDock: a web server for identifying drug targets with docking approach. Nucleic Acids Res. 2006;34:W219–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Cobanoglu MC, Oltvai ZN, Taylor DL, Bahar I. BalestraWeb: efficient online evaluation of drug-target interactions. Bioinformatics. 2015;31:131–3.

    Article  CAS  PubMed  Google Scholar 

  21. Lo Y-C, Senese S, Li C-M, Hu Q, Huang Y, Damoiseaux R, Torres JZ. Large-scale chemical similarity networks for target profiling of compounds identified in cell-based chemical screens. PLoS Comput Biol. 2015;11:e1004153.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Ba-Alawi W, Soufan O, Essack M, Kalnis P, Bajic VB. DASPfind: new efficient method to predict drug-target interactions. J Cheminform. 2016;8:15.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Martínez-Jiménez F, Marti-Renom MA. Ligand-target prediction by structural network biology using nAnnoLyze. PLoS Comput Biol. 2015;11:e1004157.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  24. von Eichborn J, Murgueitio MS, Dunkel M, Koerner S, Bourne PE, Preissner R. PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Res. 2011;39:D1060–6.

    Article  CAS  Google Scholar 

  25. Gallo K, Goede A, Eckert A, Moahamed B, Preissner R, Gohlke B-O. PROMISCUOUS 2.0: a resource for drug-repositioning. Nucleic Acids Res. 2021;49:D1373–80.

    Article  CAS  PubMed  Google Scholar 

  26. Chen B, Ding Y, Wild DJ. Assessing drug target association using semantic linked data. PLoS Comput Biol. 2012;8:e1002574.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P. STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res. 2014;42:D401–7.

    Article  CAS  PubMed  Google Scholar 

  28. Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P. STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res. 2012;40:D876–80.

    Article  CAS  PubMed  Google Scholar 

  29. Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M. STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data. Nucleic Acids Res. 2016;44:D380–4.

    Article  CAS  PubMed  Google Scholar 

  30. Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P. STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Res. 2010;38:D552–6.

    Article  CAS  PubMed  Google Scholar 

  31. Alaimo S, Bonnici V, Cancemi D, Ferro A, Giugno R, Pulvirenti A. DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference. BMC Syst Biol. 2015;9(Suppl 3):S4.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Alaimo S, Pulvirenti A, Giugno R, Ferro A. Drug-target interaction prediction through domain-tuned network-based inference. Bioinformatics. 2013;29:2004–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Chen B, Ma L, Paik H, Sirota M, Wei W, Chua M-S, So S, Butte AJ. Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets. Nat Commun. 2017;8:16022.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Konc J, Janezic D. ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins. Nucleic Acids Res. 2012;40:W214–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Ito J-I, Tabei Y, Shimizu K, Tsuda K, Tomii K. PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Res. 2012;40:D541–8.

    Article  CAS  PubMed  Google Scholar 

  36. Ito J-I, Ikeda K, Yamada K, Mizuguchi K, Tomii K. PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. Nucleic Acids Res. 2015;43:D392–8.

    Article  CAS  PubMed  Google Scholar 

  37. Brown AS, Patel CJ. MeSHDD: literature-based drug-drug similarity for drug repositioning. J Am Med Inform Assoc. 2017;24:614–8.

    Article  PubMed  Google Scholar 

  38. Moosavinasab S, Patterson J, Strouse R, Rastegar-Mojarad M, Regan K, Payne PRO, Huang Y, Lin SM. “RE:fine drugs”: an interactive dashboard to access drug repurposing opportunities. Database. 2016;2016:baw083. https://doi.org/10.1093/database/baw083.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Madhukar NS, Khade PK, Huang L, Gayvert K, Galletti G, Stogniew M, Allen JE, Giannakakou P, Elemento O. A Bayesian machine learning approach for drug target identification using diverse data types. Nat Commun. 2019;10:5221.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  40. Subramanian A, Narayan R, Corsello SM, et al. A next generation connectivity map: L1000 platform and the first 1,000,000 profiles. Cell. 2017;171:1437–1452.e17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Lamb J, Crawford ED, Peck D, et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006;313:1929–35.

    Article  CAS  PubMed  Google Scholar 

  42. Lee BKB, Tiong KH, Chang JK, Liew CS, Abdul Rahman ZA, Tan AC, Khang TF, Cheong SC. DeSigN: connecting gene expression with therapeutics for drug repurposing and development. BMC Genomics. 2017;18:934.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  43. Louhimo R, Laakso M, Belitskin D, Klefström J, Lehtonen R, Hautaniemi S. Data integration to prioritize drugs using genomics and curated data. BioData Min. 2016;9:21.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Carrella D, Napolitano F, Rispoli R, Miglietta M, Carissimo A, Cutillo L, Sirci F, Gregoretti F, Di Bernardo D. Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis. Bioinformatics. 2014;30:1787–8.

    Article  CAS  PubMed  Google Scholar 

  45. Setoain J, Franch M, Martínez M, Tabas-Madrid D, Sorzano COS, Bakker A, Gonzalez-Couto E, Elvira J, Pascual-Montano A. NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning. Nucleic Acids Res. 2015;43:W193–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Yu H, Choo S, Park J, Jung J, Kang Y, Lee D. Prediction of drugs having opposite effects on disease genes in a directed network. BMC Syst Biol. 2016;10:S2. https://doi.org/10.1186/s12918-015-0243-2.

    Article  CAS  Google Scholar 

  47. Duan Q, Reid SP, Clark NR, et al. L1000CDS2: LINCS L1000 characteristic direction signatures search engine. npj Syst Biol Appl. 2016;2:16015. https://doi.org/10.1038/npjsba.2016.15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Musa A, Ghoraie LS, Zhang S-D, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform. 2018;19:506–23.

    CAS  PubMed  Google Scholar 

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Correspondence to Alfredo Pulvirenti .

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Rapicavoli, R., Alaimo, S., Ferro, A., Pulvirenti, A. (2022). Computational Methods for Drug Repurposing. In: Laganà, A. (eds) Computational Methods for Precision Oncology. Advances in Experimental Medicine and Biology, vol 1361. Springer, Cham. https://doi.org/10.1007/978-3-030-91836-1_7

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