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Prediction of Non-coding RNAs as Drug Targets

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Non-coding RNAs in Complex Diseases

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1094))

Abstract

MiRNA is a class of small non-coding RNA molecule that regulates gene expression at post-transcriptional level. Increasing evidences show aberrant expression of miRNAs in a variety of diseases. Targeting the dysregulated miRNAs with small molecule drugs has become a novel therapeutics for many human diseases, especially cancers. In this chapter, we introduced a series of computational studies for prediction of small molecule and miRNA associations. Based on different hypotheses, such as transcriptional response similarity, functional consistence or network closeness, the small molecule-miRNA networks were constructed and further analyzed. In addition, several resources that collected experimentally validated relationships or computational predicted associations between small molecules and miRNAs were provided. Collectively, these computational frameworks and databases pave a new way for miRNA-targeted therapy and drug repositioning.

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References

  1. Drews J, Ryser S (1997) The role of innovation in drug development. Nat Biotechnol 15(13):1318–1319

    Article  CAS  PubMed  Google Scholar 

  2. Overington JP, Al-Lazikani B, Hopkins AL (2006) How many drug targets are there? Nat Rev Drug Discov 5(12):993–996

    Article  CAS  PubMed  Google Scholar 

  3. Hopkins AL, Groom CR (2002) The druggable genome. Nat Rev Drug Discov 1(9):727–730

    Article  CAS  PubMed  Google Scholar 

  4. Garzon R, Marcucci G, Croce CM (2010) Targeting microRNAs in cancer: rationale, strategies and challenges. Nat Rev Drug Discov 9(10):775–789

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Schmidt MF (2014) Drug target miRNAs: chances and challenges. Trends Biotechnol 32(11):578–585

    Article  CAS  PubMed  Google Scholar 

  6. Ling H, Fabbri M, Calin GA (2013) MicroRNAs and other non-coding RNAs as targets for anticancer drug development. Nat Rev Drug Discov 12(11):847–865

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Gebert LF et al (2014) Miravirsen (SPC3649) can inhibit the biogenesis of miR-122. Nucleic Acids Res 42(1):609–621

    Article  CAS  PubMed  Google Scholar 

  8. Lanford RE et al (2010) Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science 327(5962):198–201

    Article  CAS  PubMed  Google Scholar 

  9. Bose D et al (2012) The tuberculosis drug streptomycin as a potential cancer therapeutic: inhibition of miR-21 function by directly targeting its precursor. Angew Chem Int Ed Eng 51(4):1019–1023

    Article  CAS  Google Scholar 

  10. Monroig Pdel C et al (2015) Small molecule compounds targeting miRNAs for cancer therapy. Adv Drug Deliv Rev 81:104–116

    Article  CAS  PubMed  Google Scholar 

  11. Vo DD et al (2014) Targeting the production of oncogenic microRNAs with multimodal synthetic small molecules. ACS Chem Biol 9(3):711–721

    Article  CAS  PubMed  Google Scholar 

  12. Jamal S, Periwal V, Scaria V (2012) Computational analysis and predictive modeling of small molecule modulators of microRNA. J Cheminform 4(1):16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Zhang S et al (2010) Targeting microRNAs with small molecules: from dream to reality. Clin Pharmacol Ther 87(6):754–758

    Article  CAS  PubMed  Google Scholar 

  14. Bose D et al (2013) A molecular-beacon-based screen for small molecule inhibitors of miRNA maturation. ACS Chem Biol 8(5):930–938

    Article  CAS  PubMed  Google Scholar 

  15. Sirota M et al (2011) Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med 3(96):96ra77

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Dudley JT et al (2011) Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med 3(96):96ra76

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Iorio F et al (2010) Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc Natl Acad Sci U S A 107(33):14621–14626

    Article  PubMed  PubMed Central  Google Scholar 

  18. Jiang W et al (2012) Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses. Sci Rep 2:282

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Lamb J et al (2006) The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313(5795):1929–1935

    Article  CAS  PubMed  Google Scholar 

  20. Rhodes DR et al (2007) Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 9(2):166–180

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Meng F et al (2016) Psmir: a database of potential associations between small molecules and miRNAs. Sci Rep 6:19264

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Wang J et al (2016) Identification of associations between small molecule drugs and miRNAs based on functional similarity. Oncotarget 7(25):38658–38669

    PubMed  PubMed Central  Google Scholar 

  23. Frohlich H et al (2007) GOSim – an R-package for computation of information theoretic GO similarities between terms and gene products. BMC Bioinformatics 8:166

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Alexa A, Rahnenfuhrer J, Lengauer T (2006) Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22(13):1600–1607

    Article  CAS  PubMed  Google Scholar 

  25. Yu G et al (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 26(7):976–978

    Article  CAS  PubMed  Google Scholar 

  26. Lv Y et al (2015) Identifying novel associations between small molecules and miRNAs based on integrated molecular networks. Bioinformatics 31(22):3638–3644

    Article  CAS  PubMed  Google Scholar 

  27. Liu X et al (2013) SM2miR: a database of the experimentally validated small molecules’ effects on microRNA expression. Bioinformatics 29(3):409–411

    Article  CAS  PubMed  Google Scholar 

  28. Yang Q et al (2011) miREnvironment database: providing a bridge for microRNAs, environmental factors and phenotypes. Bioinformatics 27(23):3329–3330

    Article  CAS  PubMed  Google Scholar 

  29. Barh D, Bhat D, Viero C (2010) miReg: a resource for microRNA regulation. J Integr Bioinform 7(1):144

    Article  Google Scholar 

  30. Rukov JL et al (2014) Pharmaco-miR: linking microRNAs and drug effects. Brief Bioinform 15(4):648–659

    Article  CAS  PubMed  Google Scholar 

  31. Wahlestedt C (2013) Targeting long non-coding RNA to therapeutically upregulate gene expression. Nat Rev Drug Discov 12(6):433–446

    Article  CAS  PubMed  Google Scholar 

  32. Wheeler TM et al (2012) Targeting nuclear RNA for in vivo correction of myotonic dystrophy. Nature 488(7409):111–115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Correspondence to Wei Jiang .

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Jiang, W., Lv, Y., Wang, S. (2018). Prediction of Non-coding RNAs as Drug Targets. In: Li, X., Xu, J., Xiao, Y., Ning, S., Zhang, Y. (eds) Non-coding RNAs in Complex Diseases. Advances in Experimental Medicine and Biology, vol 1094. Springer, Singapore. https://doi.org/10.1007/978-981-13-0719-5_11

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