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Approaches for the Discovery of Small Molecule Ligands Targeting microRNAs

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RNA Therapeutics

Part of the book series: Topics in Medicinal Chemistry ((TMC,volume 27))

Abstract

RNA is essential for life, serving as the intermediate between genomic storage and protein function. As our knowledge of biological systems has grown, so has our understanding of RNA, revealing additional functions of this critical class of biomolecules. One class of RNA, microRNAs (miRNA), highlights the fundamental role of non-coding RNA in higher organisms. miRNAs regulate nearly every biological pathway through targeted translational suppression, and dysregulation of miRNA expression has been implicated in many human disease states. Thus, therapeutically targeting miRNAs with small molecule ligands is of growing importance. Herein we focus on methods employed to discover small molecule miRNA ligands, their successes thus far, and future directions for the field.

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References

  1. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854

    Article  CAS  Google Scholar 

  2. Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75:855–862

    Article  CAS  Google Scholar 

  3. Ruvkun G, Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901–906

    Article  CAS  Google Scholar 

  4. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408:86–89

    Article  CAS  Google Scholar 

  5. Friedman RC, Kai-How Farh K, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19:92–105

    Article  CAS  Google Scholar 

  6. Li Z, Rana TM (2014) Therapeutic targeting of microRNAs: current status and future challenges. Nat Rev Drug Discov 13:622–638

    Article  CAS  Google Scholar 

  7. Roush S, Slack FJ (2008) The let-7 family of microRNAs. Trends Cell Biol 18:505–516

    Article  CAS  Google Scholar 

  8. Han C, Yu Z, Duan Z, Kan Q (2014) Role of microRNA-1 in human cancer and its therapeutic potentials. Biomed Res Int 2014:428371

    Google Scholar 

  9. Ma L (2010) Role of miR-10b in breast cancer metastasis. Breast Cancer Res 12:210

    Article  CAS  Google Scholar 

  10. Pfeffer S, Yang CH, Pfeffer LM (2015) The role of miR-21 in cancer. Drug Dev Res 76:270–277

    Article  CAS  Google Scholar 

  11. Chhabra R, Dubey R, Saini N (2010) Cooperative and individualistic functions of the microRNAs in the miR-23a-27a-24-2 cluster and its implications in human diseases. Mol Cancer 9:232

    Article  CAS  Google Scholar 

  12. Wang Y, Zhang X, Li H, Yu J, Ren X (2013) The role of miRNA-29 family in cancer. Eur J Cell Biol 92:123–128

    Article  CAS  Google Scholar 

  13. Hermeking H (2010) The miR-34 family in cancer and apoptosis. Cell Death Differ 17:193–199

    Article  CAS  Google Scholar 

  14. Guttilla IK, White BA (2009) Coordinate regulation of FOXO1 by miR-27a, miR-96, and miR-182 in breast cancer cells. J Biol Chem 284:23204–23216

    Article  CAS  Google Scholar 

  15. Henke JI, Goergen D, Zheng J, Song Y, Schuttler CG, Fehr C, Junemann C, Niepmann M (2008) microRNA-122 stimulates translation of hepatitis C virus RNA. EMBO J 27:3300–3310

    Article  CAS  Google Scholar 

  16. Gramantieri L, Ferracin M, Fornari F, Veronese A, Sabbioni S, Liu C-G, Calin GA, Giovannini C, Ferrazzi M, Grazi GL, Croce CM, Bolondi L, Negrini M (2007) Cyclin G1 is a target of miR-122, a microRNA frequently down-regulated in human hepatocellular carcinoma. Cancer Res 67:6092–6099

    Article  CAS  Google Scholar 

  17. Ozen M, Creighton CJ, Ozdemir M, Ittmann M (2008) Widespread deregulation of microRNA expression in human prostate cancer. Oncogene 27:1788–1793

    Article  CAS  Google Scholar 

  18. Thum T, Catalucci D, Bauersachs J (2008) MicroRNAs: novel regulators in cardiac development and disease. Cardiovasc Res 79:562–570

    Article  CAS  Google Scholar 

  19. Isobe T, Hisamori S, Hogan DJ, Zabala M, Hendrickson DG, Dalerba P, Cai S, Scheeren F, Kuo AH, Sikandar SS, Lam JS, Qian D, Dirbas FM, Somlo G, Lao K, Brown PO, Clarke MF, Shimono Y (2014) miR-142 regulates the tumorigenicity of human breast cancer stem cells through the canonical WNT signaling pathway. Elife 3:e01977

    Article  Google Scholar 

  20. Faraoni I, Antonetti FR, Cardone J, Bonmassar E (2009) miR-155 gene: a typical multifunctional microRNA. Biochim Biophys Acta 1792:497–505

    Article  CAS  Google Scholar 

  21. Williams AH, Valdez G, Moresi V, Qi X, McAnally J, Elliott JL, Bassel-Duby R, Sanes JR, Olson EN (2009) MicroRNA-206 delays ALS progression and promotes regeneration of neuromuscular synapses in mice. Science 326:1549–1554

    Article  CAS  Google Scholar 

  22. Scarola M, Schoeftner S, Schneider C, Benetti R (2010) miR-335 directly targets Rb1 (pRb/P105) in a proximal connection to P53-dependent stress response. Cancer Res 70:6925–6933

    Article  CAS  Google Scholar 

  23. Staedel C, Varon C, Nguyen PH, Vialet B, Chambonnier L, Rousseau B, Soubeyran I, Evrary S, Couillaud F, Darfeuille F (2015) Inhibition of gastric tumor cell growth using seed-targeting LNA as specific, long-lasting microRNA inhibitors. Mol Ther Nucleic Acids 4:e246

    Article  CAS  Google Scholar 

  24. Hu W, Chan CS, Wu R, Zhang C, Sun Y, Song JS, Tang LH, Levine AJ, Feng Z (2010) Negative regulation of tumor suppressor P53 by microRNA miR-504. Mol Cell 38:689–699

    Article  CAS  Google Scholar 

  25. Pang F, Zha R, Zhao Y, Wang Q, Chen D, Zhang Z, Chen T, Yao M, Gu J, He X (2014) MiR-525-3p enhances the migration and invasion of liver cancer cells by downregulating ZNF395. PLoS One 9:e90867

    Article  CAS  Google Scholar 

  26. Haga CL, Velagapudi SP, Strivelli JR, Yang W-Y, Disney MD, Phinney DG (2015) Small molecule inhibition of miR-544 biogenesis disrupts adaptive responses to hypoxia by modulating ATM-mTOR signaling. ACS Chem Biol 10:2267–2276

    Article  CAS  Google Scholar 

  27. Lin S, Gregory RI (2015) MicroRNA biogenesis pathways in cancer. Nat Rev Cancer 15:321–333

    Article  CAS  Google Scholar 

  28. Ha M, Kim VN (2014) Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15:509–524

    Article  CAS  Google Scholar 

  29. Mack GS (2007) MicroRNA gets down to business. Nat Biotechnol 25:631–638

    Article  CAS  Google Scholar 

  30. Wang V, Wu W (2009) MicroRNA-based therapeutics for cancer. BioDrugs 23:15–23

    Article  Google Scholar 

  31. Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S, Shimuzu M, Rattan S, Bullrich F, Negrini M, Croce CM (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci U S A 101:2999–3004

    Article  CAS  Google Scholar 

  32. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR (2005) MicroRNA expression profiles classify human cancers. Nature 435:834–838

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  34. Franceschini A, Meier R, Casanova A, Kreibich S, Daga N, Andritschke D, Dilling S, Ramo P, Emmenlauer M, Kaufmann A, Conde-Alvarez R, Low SH, Pelkmans L, Helenius A, Hardt W-D, Dehio C, von Mering C (2014) Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens. Proc Natl Acad Sci U S A 111:4548–4553

    Article  CAS  Google Scholar 

  35. White PJ, Anastasopoulos F, Pouton CW, Boyd BJ (2009) Overcoming biological barriers to in vivo efficacy of antisense oligonucleotides. Expert Rev Mol Med 11:e10

    Article  Google Scholar 

  36. Thomas JR, Hergenrother PJ (2008) Targeting RNA with small molecules. Chem Rev 108:1171–1224

    Article  CAS  Google Scholar 

  37. Guan L, Disney MD (2012) Recent advances in developing small molecules targeting RNA. ACS Chem Biol 7:73–86

    Article  CAS  Google Scholar 

  38. Connelly CM, Moon MH, Schneekloth Jr JS (2016) The emerging role of RNA as a therapeutic target for small molecules. Cell Chem Biol 23:1077–1090

    Article  CAS  Google Scholar 

  39. Disney MD (2013) Rational design of chemical genetic probes of RNA function and lead therapeutics targeting repeating transcripts. Drug Discov Today 18:1228–1236

    Article  CAS  Google Scholar 

  40. Werstuck G, Green MR (1998) Controlling gene expression in living cells through small molecule-RNA interactions. Science 282:296–298

    Article  CAS  Google Scholar 

  41. Sparano BA, Koide K (2007) Fluorescent sensors for specific RNA: a general paradigm using chemistry and combinatorial biology. J Am Chem Soc 129:4785–4794

    Article  CAS  Google Scholar 

  42. Paige JS, Wu KY, Jaffrey SR (2011) RNA mimics of green fluorescent protein. Science 333:642–646

    Article  CAS  Google Scholar 

  43. Serganov A, Nudler E (2013) A decade of riboswitches. Cell 152:17–24

    Article  CAS  Google Scholar 

  44. Terasaka N, Futai K, Katoh T, Suga H (2016) A human microRNA precursor binding to folic acid discovered by small RNA transcriptomic SELEX. RNA 22:1918–1928

    CAS  Google Scholar 

  45. Connelly CM, Thomas M, Deiters A (2012) High-throughput luciferase reporter assay for small-molecule inhibitors of microRNA function. J Biomol Screen 17:822–828

    Article  CAS  Google Scholar 

  46. Connelly CM, Deiters A (2014) Cellular microRNA sensors based on luciferase reporters. Methods Mol Biol 1095:135–146

    Article  CAS  Google Scholar 

  47. Connelly CM, Deiters A (2014) Identification of inhibitors of microRNA function from small molecule screens. Methods Mol Biol 1095:147–156

    Article  CAS  Google Scholar 

  48. Gumireddy K, Young DD, Xiong X, Hogenesch JB, Huang Q, Deiters A (2008) Small-molecule inhibitors of microRNA miR-21 function. Angew Chem Int Ed 47:7482–7484

    Article  CAS  Google Scholar 

  49. Volinia S, Calin GA, Liu C-G, Ambs S, Cimmino A, Petrocca F, Visone R, Iorio M, Roldo C, Ferracin M, Prueitt RL, Yanaihara N, Lanza G, Scarpa A, Vecchione A, Negrini M, Harris CC, Croce CM (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 103:2257–2261

    Article  CAS  Google Scholar 

  50. Selcuklu SD, Donoghue MTA, Spillane C (2009) miR-21 as a key regulator of oncogenic processes. Biochem Soc Trans 37:918–925

    Article  CAS  Google Scholar 

  51. Krichevsky AM, Gabriely G (2009) miR-21: a small multi-faceted RNA. J Cell Mol Med 13:39–53

    Article  CAS  Google Scholar 

  52. Jazbutyte V, Thum T (2010) MicroRNA-21: from cancer to cardiovascular disease. Curr Drug Targets 11:926–935

    Article  CAS  Google Scholar 

  53. Esquela-Kerscher A, Slack FJ (2006) Oncomirs – microRNAs with a role in cancer. Nat Rev Cancer 6:259–269

    Article  CAS  Google Scholar 

  54. Medina PP, Nolde M, Slack FJ (2010) OncomiR addiction in an in vivo model of microRNA-21-induced pre-B-cell lymphoma. Nature 467:86–90

    Article  CAS  Google Scholar 

  55. Cheng CJ, Slack FJ (2012) The duality of oncomiR addiction in the maintenance and treatment of cancer. Cancer J 18:232–237

    Article  Google Scholar 

  56. Jiang C-S, Wang X-M, Zhang S-Q, Meng L-S, Zhu W-H, Xu J, Lu S-M (2015) Discovery of 4-benzoylamino-N-(prop-2-yn-1-yl)benzamides as novel microRNA-21 inhibitors. Bioorg Med Chem 23:6510–6519

    Article  CAS  Google Scholar 

  57. Naro Y, Thomas M, Stephens MD, Connelly CM, Deiters A (2015) Aryl amide small-molecule inhibitors of microRNA miR-21 function. Bioorg Med Chem Lett 25:4793–4796

    Article  CAS  Google Scholar 

  58. Young DD, Connelly CM, Grohmann C, Deiters A (2010) Small molecule modifiers of microRNA miR-122 function for the treatment of hepatitis C virus infection and hepatocellular carcinoma. J Am Chem Soc 132:7976–7981

    Article  CAS  Google Scholar 

  59. Jopling CL, Yi M-K, Lancaster AM, Lemon SM, Sarnow P (2005) Modulation of hepatits C virus RNA abundance by a liver-specific microRNA. Science 309:1577–1581

    Article  CAS  Google Scholar 

  60. Lanford RE, Hildebrandt-Eriksen ES, Petri A, Persson R, Lindow M, Munk ME, Kauppinen S, Orum H (2010) Therapeutic silencing of microRNA-122 in primates with chronic hepatits C virus infection. Science 327:198–201

    Article  CAS  Google Scholar 

  61. Janssen HLA, Reesink HW, Lawitz EJ, Zeuzem S, Rodriguez-Torres M, Patel K, van der Meer AJ, Patrick AK, Chen A, Zhou Y, Persson R, King BD, Kauppinen S, Levin AA, Hodges MR (2013) Treatment of HCV infection by targeting microRNA. N Engl J Med 368:1685–1694

    Article  CAS  Google Scholar 

  62. van der Ree MH, van der Meer AJ, de Bruijne J, Maan R, van Vliet A, Welzel TM, Zeuzem S, Lawitz EJ, Rodriguez-Torres M, Kupcova V, Wiercinska-Drapalo A, Hodges MR, Janssen HLA, Reesink HW (2014) Long-term safety and efficacy of microRNA-targeted therapy in chronic hepatitis C patients. Antivir Res 111:53–59

    Article  CAS  Google Scholar 

  63. Ottosen S, Parsley TB, Yang L, Zeh K, van Doom L-J, van der Veer E, Raney AK, Hodges MR, Patrick AK (2014) In vitro antiviral activity and preclinical and clincal resistance profile of miravirsen, a novel anti-hepatitis C virus therapeutic targeting the human factor miR-122. Antimicrob Agents Chemother 59:599–608

    Article  CAS  Google Scholar 

  64. van der Ree MH, van der Meer AJ, van Nuenen AC, de Bruijne J, Ottosen S, Janssen HLA, Kootstra NA, Reesink HW (2015) Miravirsen dosing in chronic hepatits C patients results in decreased microRNA-122 levels without affecting other microRNAs in plasma. Aliment Pharmacol Ther 43:102–113

    Google Scholar 

  65. Wiggins JF, Ruffino L, Kelnar K, Omotola M, Patrawala L, Brown D, Bader AG (2010) Development of a lung cancer therapeutic based on the tumor suppressor microRNA-34. Cancer Res 70:5923–5930

    Article  CAS  Google Scholar 

  66. Adams BD, Parsons C, Slack FJ (2016) The tumor-suppressive and potential therapeutic functions of miR-34a in epithelial carcinomas. Expert Opin Ther Targets 20:737–753

    Article  CAS  Google Scholar 

  67. Daige CL, Wiggins JF, Priddy L, Nelligan-Davis T, Zhao J, Brown D (2014) Systemic delivery of a miR-34a mimic as a potential therapeutic for liver cancer. Mol Cancer Ther 13:2352–2360

    Article  CAS  Google Scholar 

  68. Xiao Z, Li CH, Chan SL, Xu F, Feng L, Wang Y, Jiang JD, Sung JJY, Cheng CHK, Chen Y (2014) A small-molecule modulator of the tumor-suppressor miR34a inhibits the growth of hepatocellular carcinoma. Cancer Res 74:6236–6247

    Article  CAS  Google Scholar 

  69. Tan S-B, Huang C, Chen X, Wu Y, Zhou M, Zhang C, Zhang Y (2013) Small molecular inhibitors of miR-1 identified from photocycloadducts of acetylenes with 2-methoxy-1,4-napthalenequinone. Bioorg Med Chem 21:6124–6131

    Article  CAS  Google Scholar 

  70. Tan S-B, Li J, Chen X, Zhang W, Zhang D, Zhang C, Li D, Zhang Y (2014) Small molecule inhibitor of myogenic microRNAs leads to a discovery of miR-221/222-myoD-myomiRs regulatory pathway. Chem Biol 21:1265–1270

    Article  CAS  Google Scholar 

  71. Chen X, Huang C, Zhang W, Wu Y, Chen X, Zhang C-Y, Zhang Y (2012) A universal activator of microRNAs identified from photoreaction products. Chem Commun 48:6432–6433

    Article  CAS  Google Scholar 

  72. Shan G, Li Y, Zhang J, Li W, Szulwach KE, Duan R, Faghihi MA, Khalil AM, Lu L, Paroo Z, Chan AWS, Shi Z, Liu Q, Wahlestedt C, He C, Jin P (2008) A small molecule enhances RNA interference and promotes microRNA processing. Nat Biotechnol 26:933–940

    Article  CAS  Google Scholar 

  73. Melo S, Villanueva A, Moutinho C (2011) Small molecule enoxacin is a cancer-specific growth inhibitor that acts by enhancing TAR RNA-binding protein 2-mediated microRNA processing. Proc Natl Acad Sci U S A 108:4394–4300

    Article  CAS  Google Scholar 

  74. Shum D, Bhinder B, Radu C, Farazi T, Landthaler M, Tuschl T, Calder P, Ramirez CN, Djaballah H (2012) An image-based biosensor assay strategy to screen for modulators of the microRNA 21 biogenesis pathway. Comb Chem High Throughput Screen 15:529–541

    Article  CAS  Google Scholar 

  75. Watashi K, Yeung ML, Starost MF, Hosmane RS, Jeang K-T (2010) Identification of small molecules that suppress microRNA function and reverse tumorigenesis. J Biol Chem 285:24707–24716

    Article  CAS  Google Scholar 

  76. Bose D, Jayaraj G, Suryawanshi H, Agarwala P, Pore SK, Banerjee R, Maiti S (2012) The tuberculosis drug streptomycin as a potential cancer therapeutic: inhibition of miR-21 function by directly targeting its precursor. Angew Chem Int Ed 51:1019–1023

    Article  CAS  Google Scholar 

  77. Lorenz DA, Song JM, Garner AL (2015) High-throughput platform assay technology for the discovery of pre-microRNA-selective small molecule probes. Bioconjug Chem 26:19–23

    Article  CAS  Google Scholar 

  78. Tran TPA, Vo DD, Di Giorgio A, Duca M (2015) Ribosome-targeting antibiotics as inhibitors of oncogenic microRNAs biogenesis: old scaffolds for new perspectives in RNA targeting. Bioorg Med Chem 23:5334–5344

    Article  CAS  Google Scholar 

  79. Nahar S, Ranjan N, Ray A, Arya DP, Maiti S (2015) Potent inhibition of miR-27a by neomycin-benzimidazole conjugates. Chem Sci 6:5837–5846

    Article  CAS  Google Scholar 

  80. Bose D, Jayaraj GG, Kumar S, Maiti S (2013) A molecule-beacon-based screen for small molecule inhibitors of miRNA maturation. ACS Chem Biol 8:930–938

    Article  CAS  Google Scholar 

  81. MacBeath G, Koehler AN, Schreiber SL (1999) Printing small molecule as microarrays and detecting protein-ligand interactions en mass. J Am Chem Soc 121:7967–7968

    Article  CAS  Google Scholar 

  82. Hong JA, Neel DV, Wassaf D, Caballero F, Koehler AN (2014) Recent discoveries and applications involving small-molecule microarrays. Curr Opin Chem Biol 18:21–28

    Article  CAS  Google Scholar 

  83. Abulwerdi FA, Schneekloth Jr JS (2016) Microarray-based technologies for the discovery of selective, RNA-binding molecules. Methods 103:188–195

    Article  CAS  Google Scholar 

  84. Connelly CM, Boer RE, Moon MH, Gareiss P, Schneekloth JS Jr (2017) Discovery of inhibitors of microRNA-21 processing using small molecule microarrays. ACS Chem Biol 12:435–443

    Article  CAS  Google Scholar 

  85. Chirayil S, Chirayil R, Luebke KJ (2009) Discovering ligands for a microRNA precursor with peptoid microarrays. Nucleic Acids Res 37:5486–5497

    Article  CAS  Google Scholar 

  86. Chirayil R, Wu Q, Amezcua C, Luebke KJ (2014) NMR characterization of an oligonucleotide model of the MiR-21 pre-element. PLoS One 9:e108231

    Article  CAS  Google Scholar 

  87. Diaz JP, Chirayil R, Chirayil S, Tom M, Head KJ, Luebke KJ (2014) Association of a peptoid ligand with the apical loop of pri-miR-21 inhibits cleavage by Drosha. RNA 20:528–539

    Article  CAS  Google Scholar 

  88. Carlson CB, Beal PA (2002) Points of attachment and sequence of immobilized peptide-acridine conjugates control affinity for nucleic acids. J Am Chem Soc 124:8510–8511

    Article  CAS  Google Scholar 

  89. Disney MD, Seeberger PH (2004) Aminoglycoside microarray to explore interactions of antibiotics with RNAs and proteins. Chem Eur J 10:3308–3314

    Article  CAS  Google Scholar 

  90. Pai J, Hyun S, Hyun JY, Park S-H, Kim W-J, Bae S-H, Kim N-K, Yu J, Shin I (2016) Screening of pre-miRNA-155 binding peptides for apoptosis inducing activity using peptide microarrays. J Am Chem Soc 138:857–867

    Article  CAS  Google Scholar 

  91. Eis PS, Tam W, Sun L, Chadburn A, Li Z, Gomez MF, Lund E, Dahlberg JE (2005) Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc Natl Acad Sci U S A 102:3627–3632

    Article  CAS  Google Scholar 

  92. Hyun S, Han A, Jo MH, Hohng S, Yu J (2014) Dicer nuclease-promoted production of Let7a-1 microRNA is enhanced in the presence of tryptophan-containing amphiphilic peptides. Chembiochem 15:1651–1659

    Article  CAS  Google Scholar 

  93. Bose D, Nahar S, Rai MK, Ray A, Chakraborty K, Maiti S (2010) Selective inhibition of miR-21 by phage display screened peptide. Nucleic Acids Res 43:4342–4352

    Article  CAS  Google Scholar 

  94. Nahar S, Bose D, Pal S, Chakraborty TK, Maiti S (2015) Cyclic cationic peptides containing sugar amino acids selectively distinguishes and inhibits maturation of pre-miRNAs of the same family. Nucleic Acid Ther 25:323–329

    Article  CAS  Google Scholar 

  95. Krishnamurthy M, Simon K, Orendt AM, Beal PA (2007) Macrocyclic helix-threading peptides for targeting RNA. Angew Chem Int Ed 46:7044–7047

    Article  CAS  Google Scholar 

  96. Chen Y, Yang F, Zubovic L, Pavelitz T, Yang W, Godin K, Walker M, Zheng S, Macchi P, Varani G (2016) Targeting inhibition of oncogenic miR-21 maturation with designed RNA-binding proteins. Nat Chem Biol 12:717–723

    Article  CAS  Google Scholar 

  97. Velagapudi SP, Disney MD (2014) Two-dimensional combinatorial screening enables the bottom-up design of a microRNA-10b inhibitor. Chem Commun 50:3027–3029

    Article  CAS  Google Scholar 

  98. Disney MD, Labuda LP, Paul DJ, Poplawski SG, Pushechnikov A, Tran T, Velagapudi SP, Wu M, Childs-Disney JL (2008) Two-dimensional combinatorial screening identifies specific aminoglycoside-RNA internal loop partners. J Am Chem Soc 130:11185–11194

    Article  CAS  Google Scholar 

  99. Velagapudi SP, Seedhouse SJ, Disney MD (2010) Structure-activity relationships through sequencing (StARTS) defines optimal and suboptimal RNA motif targets for small molecules. Angew Chem Int Ed 49:3816–3818

    Article  CAS  Google Scholar 

  100. Ma L, Teruya-Feldstein J, Weinberg RA (2007) Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature 449:682–687

    Article  CAS  Google Scholar 

  101. Ma L, Reinhardt F, Pan E, Soutschek J, Bhat B, Marcusson EG, Teruya-Feldstein J, Bell GW, Weinberg RA (2010) Therapeutic silencing of miR-10b inhibits metastasis in a mouse mammary tumor model. Nat Biotechnol 28:341–347

    Article  CAS  Google Scholar 

  102. Davies BP, Arenz C (2006) A homogeneous assay for microRNA maturation. Angew Chem Int Ed 45:5550–5552

    Article  CAS  Google Scholar 

  103. Davies BP, Arenz C (2008) A fluorescence probe for assaying microRNA maturation. Bioorg Med Chem 16:49–55

    Article  CAS  Google Scholar 

  104. Vo DD, Staedel C, Zehnacker L, Benhida R, Darfeuille F, Duca M (2014) Targeting the production of oncogenic microRNAs with multimodal synthetic small molecules. ACS Chem Biol 9:711–721

    Article  CAS  Google Scholar 

  105. Comley J (2003) Assay interference a limiting factor in HTS? Drug Discov World 4:91–98

    Google Scholar 

  106. Imbert P-E, Unterreiner V, Siebert D, Gubler H, Parker C, Gabriel D (2007) Recommendations for the reduction of compound artifacts in time-resolved fluorescence resonance energy transfer assays. Assay Drug Dev Technol 5:363–372

    Article  CAS  Google Scholar 

  107. MacRae IJ, Zhou Z, Doudna JA (2007) Structural determinants of RNA recognition and cleavage by Dicer. Nat Struct Mol Biol 14:934–940

    Article  CAS  Google Scholar 

  108. Feng Y, Zhang X, Graves P, Zeng Y (2012) A comprehensive analysis of precursor microRNA cleavage by human Dicer. RNA 18:2083–2092

    Article  CAS  Google Scholar 

  109. Klemm CM, Berthelmann A, Neubacher S, Arenz C (2009) Short and efficient synthesis of alkyne-modified amino glycoside building blocks. Eur J Org Chem 17:2788–2794

    Article  CAS  Google Scholar 

  110. Vo DD, Tran TPA, Staedel C, Benhida R, Darfeuille F, Di Giorgio A, Duca M (2016) Oncogenic microRNAs biogenesis as a drug target: structure-activity relationship studies on new aminoglycoside conjugates. Chemistry 22:5350–5362

    Article  CAS  Google Scholar 

  111. Judson RL, Babiarz JE, Venere M, Blelloch R (2009) Embryonic stem cell-specific microRNAs promote induced pluripotency. Nat Biotechnol 27:459–461

    Article  CAS  Google Scholar 

  112. Wang Y, Blelloch R (2009) Cell cycle regulation by microRNAs in embryonic stem cells. Cancer Res 69:4093–4096

    Article  CAS  Google Scholar 

  113. Podolska K, Sedlak D, Bartunek P, Svoboda P (2014) Fluorescence-based high-throughput screening of Dicer cleavage activity. J Biomol Screen 19:417–426

    Article  CAS  Google Scholar 

  114. Tran T, Disney MD (2012) Identifying the preferred RNA motifs and chemotypes that interact by probing millions of combinations. Nat Commun 3:1125

    Article  CAS  Google Scholar 

  115. Zhang J, Umemoto S, Nakatani K (2010) Fluorescent indicator displacement assay for ligand-RNA interactions. J Am Chem Soc 132:3660–3661

    Article  CAS  Google Scholar 

  116. Maiti M, Nauwelaerts K, Herdewijn P (2012) Pre-microRNA binding aminoglycosides and antitumor drugs as inhibitors of Dicer catalyzed microRNA processing. Bioorg Med Chem Lett 22:1709–1711

    Article  CAS  Google Scholar 

  117. Murata A, Fukuzumi T, Umemoto S, Nakatani K (2013) Xanthone derivatives as potential inhibitors of miRNA processing by human Dicer: targeting secondary structures of pre-miRNA by small molecules. Bioorg Med Chem Lett 23:252–255

    Article  CAS  Google Scholar 

  118. Murata A, Harada Y, Fukuzumi T, Nakatani K (2013) Fluorescent indicator displacement assay of ligands targeting 10 microRNA precursors. Bioorg Med Chem 21:7101–7106

    Article  CAS  Google Scholar 

  119. Fukuzumi T, Murata A, Aikawa H, Harada Y, Nakatani K (2015) Exploratory study on the RNA-binding structural motifs by library screening targeting pre-miR-29a. Chemistry 21:16859–16867

    Article  CAS  Google Scholar 

  120. Murata A, Otabe T, Zhang J, Nakatani K (2016) BZDANP, a small-molecule modulator of pre-miR-29a maturation by Dicer. ACS Chem Biol 11:2790–2796

    Article  CAS  Google Scholar 

  121. Watkins D, Jiang L, Nahar S, Maiti S, Arya DP (2015) A pH sensitive high-throughput assay for miRNA binding of a peptide-aminoglycoside (PA) library. PLoS One 10:e0144251

    Article  CAS  Google Scholar 

  122. Lorenz DA, Garner AL (2016) A click chemistry-based microRNA maturation assay optimized for high-throughput screening. Chem Commun 52:8267–8270

    Article  CAS  Google Scholar 

  123. Garner AL, Janda KD (2010) cat-ELCCA: a robust method to monitor the fatty acid acyltransferase activity of ghrelin O-acyltransferase (GOAT). Angew Chem Int Ed 49:9630–9634

    Article  CAS  Google Scholar 

  124. Garner AL, Janda KD (2011) A small molecule antagonist of ghrelin O-acyltransferase (GOAT). Chem Commun 47:7512–7514

    Article  CAS  Google Scholar 

  125. Zhang J-H, Chung TDY, Oldenburg KR (1999) A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen 4:67–73

    Article  CAS  Google Scholar 

  126. Mustoe AM, Brooks III CL, Al-Hashimi HM (2014) Hierarchy of RNA functional dynamics. Annu Rev Biochem 83:441–466

    Article  CAS  Google Scholar 

  127. Turner DH, Sugimoto N, Freier SM (1988) RNA structure prediction. Annu Rev Biophys Biophys Chem 17:167–192

    Article  CAS  Google Scholar 

  128. Parisien M, Major F (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452:51–55

    Article  CAS  Google Scholar 

  129. Disney MD, Winkelsas AM, Velagapudi SP, Southern M, Fallahi M, Childs-Disney JL (2016) Inforna 2.0: a platform for the sequence-based design of small molecules targeting structured RNAs. ACS Chem Biol 11:1720–1728

    Article  CAS  Google Scholar 

  130. Velagapudi SP, Gallo SM, Disney MD (2014) Sequence-based design of bioactive small molecules that target precursor microRNAs. Nat Chem Biol 10:291–297

    Article  CAS  Google Scholar 

  131. Liu B, Childs-Disney JL, Znosko BM, Wang D, Fallahi M, Gallo SM, Disney MD (2016) Analysis of secondary structural elements in human microRNA hairpin precursors. BMC Bioinformatics 17:112

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  133. Wehler T, Brenk R (2017) Structure-based discovery of small molecules binding to RNA. Topics Med Chem. doi:10.1007/7355_2016_29

  134. Shi Z, Zhang J, Qian X, Han L, Zhang K, Chen L, Liu J, Ren Y, Yang M, Zhang A, Pu P, Kang C (2013) AC1MMYR2, an inhibitor of Dicer-mediated biogenesis of oncomir miR-21, reverses epithelial-mesenchymal transition and suppresses tumor growth and progression. Cancer Res 73:5519–5531

    Article  CAS  Google Scholar 

  135. Ren Y, Zhou X, Liu X, Jia H-H, Zhao X-H, Wang Q-X, Han L, Song X, Zhu Z-Y, Sun T, Jiao H-X, Tian W-P, Yang Y-Q, Zhao X-L, Zhang L, Mei M, Kang C-S (2016) Reprogramming carcinoma associated fibroblasts by AC1MMYR2 impedes tumor metastasis and improves chemotherapy efficacy. Cancer Lett 374:96–106

    Article  CAS  Google Scholar 

  136. Childs-Disney JL, Wu M, Pushechnikov A, Aminova O, Disney MD (2007) A small molecule microarray platform to select RNA internal loop-ligand interactions. ACS Chem Biol 2:745–754

    Article  CAS  Google Scholar 

  137. Velagapudi SP, Seedhouse SJ, French J, Disney MD (2011) Defining the RNA internal loops preferred by benzimidazole derivatives via 2D combinatorial screening and computational analysis. J Am Chem Soc 133:10111–10118

    Article  CAS  Google Scholar 

  138. Disney MD, Angelbello AJ (2016) Rational design of small molecules targeting oncogenic noncoding RNAs from sequence. Acc Chem Res 49:2698–2704

    Article  CAS  Google Scholar 

  139. Costales MG, Childs-Disney JL, Disney MD (2017) Computational tools for design of selective small molecules targeting RNA: from small molecule microarray to chemical similarity searching. Topics Med Chem. doi:10.1007/7355_2016_21

  140. Dambal S, Shah M, Mihelich B, Nonn L (2015) The microRNA-183 cluster: the family that plays together stay together. Nucleic Acids Res 43:7173–7188

    Article  CAS  Google Scholar 

  141. Costales MG, Rzuczek SG, Disney MD (2016) Comparison of small molecules and oligonucleotides that target a toxic, non-coding RNA. Bioorg Med Chem Lett 26:2605–2609

    Article  CAS  Google Scholar 

  142. Velagapudi SP, Cameron MD, Haga CL, Rosenberg LH, Lafitte M, Duckett DR, Phinney DG, Disney MD (2016) Design of a small molecule against an oncogenic noncoding RNA. Proc Natl Acad Sci U S A 113:5898–5903

    Article  CAS  Google Scholar 

  143. Haga CL, Phinney DG (2012) MicroRNAs in the imprinted DLK1-DIO3 region repress the epithelial-to-mesenchymal transition by targeting the TWIST1 protein signaling network. J Biol Chem 287:42695–42707

    Article  CAS  Google Scholar 

  144. Childs-Disney JL, Disney MD (2016) Small molecule targeting of a microRNA associated with hepatocellular carcinoma. ACS Chem Biol 11:375–380

    Article  CAS  Google Scholar 

  145. Mei H-Y, Mack DP, Galan AA, Halim NS, Heldsinger A, Loo JA, Moreland DW, Sannes-Lowery KA, Sharmeen L, Truong HN, Czarnik AW (1997) Discovery of selective, small-molecule inhibitors of RNA complexes – I. The Tat protein/TAR RNA complexes required for HIV-1 transcription. Bioorg Med Chem 5:1173–1184

    Article  CAS  Google Scholar 

  146. Mei H-Y, Cui M, Heldsinger A, Lemrow SM, Loo JA, Sannes-Lowery KA, Sharmeen L, Czarnik AW (1998) Inhibitors of protein-RNA complexation that target RNA: specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules. Biochemistry 37:14204–14212

    Article  CAS  Google Scholar 

  147. Stelzer AC, Frank AT, Kratz JD, Swanson MD, Gonzalez-Hernandez MJ, Lee J, Andricioaei I, Markovitz DM, Al-Hashimi HM (2011) Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. Nat Chem Biol 7:553–559

    Article  CAS  Google Scholar 

  148. Naryshkin NA, Weetall M, Dakka A, Narasimhan J, Zhao X, Feng Z, Ling KKY, Karp GM, Qi H, Woll MG, Chen G, Zhang N, Gabbeta V, Vazirani P, Bhattacharyya A, Furia B, Risher N, Sheedy J, Kong R, Ma J, Turpoff A, Lee C-S, Zhang X, Moon Y-C, Trifillis P, Welch EM, Colacino JM, Babiak J, Almstead NG, Peltz SW, Eng LA, Chen KS, Mull JL, Lynes MS, Rubin LL, Fontoura P, Santarelli L, Haehnke D, McCarthy KD, Schmucki R, Ebeling M, Sivaramakrishnan M, Ko C-P, Paushkin SV, Ratni H, Gerlach I, Ghosh A, Metzger F (2014) Motor neuron disease. SMN2 splicing modifiers improve motor function and longevity in mice with spinal muscular atrophy. Science 345:688–693

    Article  CAS  Google Scholar 

  149. Palacino J, Swalley SE, Song C, Cheung AK, Shu L, Zhang X, Van Hoosear M, Shin Y, Chin DN, Keller CG, Beibel M, Renaud NA, Smith TM, Salcius M, Shi X, Hild M, Servais R, Jain M, Deng L, Bullock C, McLellan M, Schuierer S, Murphy L, Blommers MJJ, Blaustein C, Berenshteyn F, Lacoste A, Thomas JR, Roma G, Michaud GA, Tseng BS, Porter JA, Myer VE, Tallarico JA, Hamann LG, Curtis D, Fishman MC, Dietrich WF, Dales NA, Sivasankaran R (2015) SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice. Nat Chem Biol 11:511–517

    Article  CAS  Google Scholar 

  150. Tan GS, Chiu C-H, Garchow BG, Metzler D, Diamond SL, Kiriakidou M (2012) Small molecule inhibition of RISC loading. ACS Chem Biol 7:403–410

    Article  CAS  Google Scholar 

  151. Schmidt MF, Korb O, Abell C (2013) MicroRNA-specific Argonaute 2 protein inhibitors. ACS Chem Biol 8:2122–2126

    Article  CAS  Google Scholar 

  152. Masciarelli S, Quaranta R, Iosue I, Colotti G, Padula F, Varchi G, Fazi F, Del Rio A (2014) A small-molecule targeting the microRNA binding domain of Argonaute 2 improves the retinoic acid differentiation response of the acute promyelocytic leukemia cell line NB4. ACS Chem Biol 9:1674–1679

    Article  CAS  Google Scholar 

  153. Hesse M, Arenz C (2016) A rapid and versatile assay for Ago2-mediated cleavage by using branched rolling circle amplification. Chembiochem 17:304–307

    Article  CAS  Google Scholar 

  154. Lin S, Gregory RI (2015) Identification of small molecule inhibitors of Zcchc11 TUTase activity. RNA Biol 12:792–800

    Article  Google Scholar 

  155. Roos M, Pradere U, Ngondo RP, Behera A, Allegrini S, Civenni G, Zagalak JA, Marchand J-R, Menzi M, Towbin H, Scheuermann J, Neri D, Caflisch A, Catapano CV, Claudo C, Hall J (2016) A small-molecule inhibitor of Lin28. ACS Chem Biol 11:2773–2781

    Article  CAS  Google Scholar 

  156. Lightfoot HL, Miska EA, Balasubramanian S (2016) Identification of small molecule inhibitors of the Lin28-mediated blockage of pre-let-7g processing. Org Biomol Chem 14:10208–10216

    Article  CAS  Google Scholar 

  157. Lim D, Byun WG, Koo JY, Park H, Park SB (2016) Discovery of a small-molecule inhibitor of protein-microRNA interaction using binding assay with a site-specifically labeled Lin28. J Am Chem Soc 138:13630–13638

    Article  CAS  Google Scholar 

  158. Hermann T (2017) Viral RNA targets and their small molecule ligands. Topics Med Chem. doi:10.1007/7355_2016_20

  159. Wirmer J, Westhof E (2006) Molecular contacts between antibiotics and the 30S ribosomal particle. Methods Enzymol 415:180–202

    Article  CAS  Google Scholar 

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Lorenz, D.A., Garner, A.L. (2017). Approaches for the Discovery of Small Molecule Ligands Targeting microRNAs. In: Garner, A. (eds) RNA Therapeutics. Topics in Medicinal Chemistry, vol 27. Springer, Cham. https://doi.org/10.1007/7355_2017_3

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