Polypharmacology in Drug Design and Discovery—Basis for Rational Design of Multitarget Drugs

  • Chapter
  • First Online:
Polypharmacology

Abstract

Chapter 3 through Chap. 11 introduces the current status of clinical applications of polypharmacology to disease therapy. This chapter will describe the applications of polypharmacology to drug discovery, mainly from the theoretical account. Specifically, it will explain the theoretical basis for the rational design of new drugs of the “single agent on multiple targets for single disease” category, or the rational design of MTD drugs. Seven essential strategies for MTD drug discovery, including sequence-based epigenetic drugs, sequence-based small-molecule drugs, function-based epigenetic drugs, function-based small-molecule drugs, function-based macromolecule drugs, naturally occurring MTD drugs, and repurposed MTD drugs, will be described in detail with real examples. The contents of this chapter lay the foundation for better understanding of Section II chapters on the methodologies of MTD polypharmacology-based drug discovery and development. Several new concepts on the rational design and discovery of MTDs are proposed by us and presented in this chapter.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
EUR 29.95
Price includes VAT (Germany)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
EUR 117.69
Price includes VAT (Germany)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
EUR 160.49
Price includes VAT (Germany)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
EUR 160.49
Price includes VAT (Germany)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. SoRelle R. Who Owns you DNA? Who Will own it? Circulation. 2000;101:e67–8.

    CAS  PubMed  Google Scholar 

  2. Anderson WF. Human gene therapy. Nature. 1998;392:25–30.

    CAS  PubMed  Google Scholar 

  3. Otsu M, Candotti F. Gene therapy in infants with severe combined immunodeficiency. BioDrugs. 2002;16:229–39.

    Article  CAS  PubMed  Google Scholar 

  4. Baekelandt V, De Strooper B, Nuttin B, et al. Gene therapeutic strategies for neurodegenerative diseases. Curr Opin Mol Ther. 2000;2:540–54.

    CAS  PubMed  Google Scholar 

  5. Galanis E, Russell S. Cancer gene therapy clinical trials: Lessons for the future. Br J Cancer. 2001;85:1432–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Tomaselli D, Lucidi A, Rotili D, et al. Epigenetic polypharmacology: A new frontier for epi-drug discovery. Med Res Rev. 2020;40(1):190–244.

    Article  CAS  PubMed  Google Scholar 

  7. Bird A. Perceptions of epigenetics. Nature. 2007;447(7143):396–8.

    Article  CAS  PubMed  Google Scholar 

  8. Ledford H. Language: Disputed definitions. Nature. 2008;455(7216):1023–8.

    Article  PubMed  CAS  Google Scholar 

  9. Chandler VL. Paramutation: from maize to mice. Cell. 2007;128(4):641–5.

    Article  CAS  PubMed  Google Scholar 

  10. Dupont C, Armant DR, Brenner CA. Epigenetics: definition, mechanisms and clinical perspective. Seminars Reprod Med. 2009;27(5):351–7.

    Article  CAS  Google Scholar 

  11. Franci G, Miceli M, Altucci L. Targeting epigenetic networks with polypharmacology: A new avenue to tackle cancer. Epigenomics. 2010;2(6):731–42.

    Article  CAS  PubMed  Google Scholar 

  12. Ptak C, Petronis A. Epigenetics and complex disease: from etiology to new therapeutics. Annu Rev Pharmacol Toxicol. 2008;48:257–76.

    Article  CAS  PubMed  Google Scholar 

  13. Ganesan A, Arimondo PB, Rots MG, et al. The timeline of epigenetic drug discovery: From reality to dreams. Clin Epigenetics. 2019;11(1):174.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Heerboth S, Lapinska K, Snyder N, et al. Use of epigenetic drugs in disease: an overview. Genet Epigenet. 2014;6:9–19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Benedetti R, Conte M, Iside C, et al. Epigenetic-based therapy: From single- to multi-target approaches. Int J Biochem Cell Biol. 2015;69:121–31.

    Article  CAS  PubMed  Google Scholar 

  16. Ganesan A. Multitarget Drugs: An epigenetic epiphany. ChemMedChem. 2016;11(12):1227–41.

    Article  CAS  PubMed  Google Scholar 

  17. de Lera AR, Ganesan A. Epigenetic polypharmacology: from combination therapy to multitargeted drugs. Clin Epigenetics. 2016;8:105.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  18. Mann BS, Johnson JR, Cohen MH, et al. Approval summary: vorinostat for treatment of advanced primary cutaneous T-cell lymphoma. Oncologist. 2007;12:1247–52.

    Article  CAS  PubMed  Google Scholar 

  19. Mikaelsson MA, Miller CA. The path to epigenetic treatment of memory disorders. Neurobiol Learn Mem. 2011;96:13–8.

    Article  PubMed  PubMed Central  Google Scholar 

  20. Kaminskas E, Farrell AT, Wang Y-C, et al. FDA drug approval summary: azacitidine (5-azacytidine, Vidaza™) for injectable suspension. Oncologist. 2005;10:176–82.

    Article  CAS  PubMed  Google Scholar 

  21. Cheng JC, Matsen CB, Gonzales FA, et al. Inhibition of DNA methylation and reactivation of silenced genes by zebularine. J Natl Cancer Inst. 2003;95:399–409.

    Article  CAS  PubMed  Google Scholar 

  22. Amato RJ. Inhibition of DNA methylation by antisense oligonucleotide MG98 as cancer therapy. Clin Genitourin Cancer. 2007;5:422–6.

    Article  CAS  PubMed  Google Scholar 

  23. Jamieson AC, Miller JC, Pabo CO. Drug discovery with engineered zinc-finger proteins. Nat Rev Drug Discov. 2003;2(5):361–8.

    Article  CAS  PubMed  Google Scholar 

  24. Bhan A, Soleimani M, Mandal SS. Long noncoding RNA and cancer: A new paradigm. Cancer Res. 2017;77(15):3965–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Khalil AM, Guttman M, Huarte M, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci. 2009;106:11667–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Guttman M, Amit I, Garber M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009;458:223–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Matsui M, Corey DR. Non-coding RNAs as drug targets. Nat Rev Drug Discov. 2017;16(3):167–79.

    Article  CAS  PubMed  Google Scholar 

  28. Esteller M. Non-coding RNAs in human disease. Nat Rev Genet. 2011;12(12):861–74.

    Article  CAS  PubMed  Google Scholar 

  29. Rupaimoole R, Slack FJ. MicroRNA therapeutics: Towards a new era for the management of cancer and other diseases. Nat Rev Drug Discov. 2017;16:203–22.

    Article  CAS  PubMed  Google Scholar 

  30. Harries LW. RNA biology provides new therapeutic targets for human disease. Front Genet. 2019;10:1–12.

    Article  CAS  Google Scholar 

  31. Rani A, O’Shea A, Ianov L, et al. miRNA in circulating microvesicles as biomarkers for age-related cognitive decline. Front Aging Neurosci. 2017;9:1–10.

    Article  CAS  Google Scholar 

  32. le Sage C, Lawo S, Cross BCS. CRISPR: A screener’s guide. SLAS Discov. 2020;25(3):233–40.

    Article  PubMed  Google Scholar 

  33. Jansen R, Van Embden JDA, Gaastra W, et al. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol. 2002;43:1565–75.

    Article  CAS  PubMed  Google Scholar 

  34. Kurata M, Yamamoto K, Moriarity BS, et al. CRISPR/Cas9 library screening for drug target discovery. J Hum Genet. 2018;63:179–86.

    Article  CAS  PubMed  Google Scholar 

  35. Herrera-Carrillo E, Gao Z, Berkhout B. CRISPR therapy towards an HIV cure. Brief Funct Genomics. 2020;19(3):201–8.

    Article  CAS  PubMed  Google Scholar 

  36. Bartel DP. MicroRNAs: Target recognition and regulatory functions. Cell. 2009;136:215–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Wang Z. MicroRNA-Interference Technologies. Springer-Verlag, Heidelberg, Germany; New York, USA. 2009; ISBN-13: 978-3-642-00488-9.

    Google Scholar 

  38. Wang Z, Luo X, Lu Y, et al. miRNAs at the heart of the matter. J Mol Med. 2008;86:771–3.

    Article  CAS  PubMed  Google Scholar 

  39. Wang Z, Yang B. MicroRNA Expression Detection Methods. Springer-Verlag, Heidelberg, Germany; New York, USA. 2010; ISBN-13: 978-3-642-04927-9.

    Google Scholar 

  40. Friedman RC, Farh KK-H, Burge CB, et al. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009;19:92–105.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Bartel DP. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell. 2004;116:281–97.

    Article  CAS  PubMed  Google Scholar 

  42. Yang D, Wan X, Dennis AT, et al. MicroRNA biophysically modulates cardiac action potential by direct binding to ion channel. Circulation. 2021;143(16):1597–613.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Bonneau E, Neveu B, Kostantin E, et al. How close are miRNAs from clinical practice? A perspective on the diagnostic and therapeutic market. Ejifcc. 2019;30:114–27.

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Lim LP, Lau NC, Garrett-engele P, et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature. 2005;292:288–92.

    Google Scholar 

  45. Baek D, Villen J, Shin C, et al. The impact of microRNAs on protein output. Nature. 2008;455:64–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Selbach M, Schwanhausser B, Thierfelder N, et al. Widespread changes in protein synthesis induced by microRNAs. Nature. 2008;455:58–63.

    Article  CAS  PubMed  Google Scholar 

  47. Farh KK, Grimson A, Jan C, et al. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science. 2005;310:1817–21.

    Article  CAS  PubMed  Google Scholar 

  48. Satoh J, Tabunoki H. Comprehensive analysis of human microRNA target networks. BioData Mining. 2011;4:17.

    Article  PubMed  PubMed Central  Google Scholar 

  49. Li Z, Rana TM. Therapeutic targeting of microRNAs: Current status and future challenges. Nat Rev Drug Discov. 2014;13:622–38.

    Article  CAS  PubMed  Google Scholar 

  50. Alles J, Fehlmann T, Fischer U, et al. An estimate of the total number of true human miRNAs. Nucleic Acids Res. 2019;47(7):3353–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Plotnikova O, Baranova A, Skoblov M. Comprehensive analysis of human microRNA-mRNA interactome. Front Genet. 2019;10:933.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Brennecke J, Stark A, Russell RB, et al. Principles of microRNA-target recognition. PLoS Biol. 2005;3:e85.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  53. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005;120:15–20.

    Article  CAS  PubMed  Google Scholar 

  54. Lewis BP, Shih IH, Jones-Rhoades MW, et al. Prediction of mammalian microRNA targets. Cell. 2003;115:787–98.

    Article  CAS  PubMed  Google Scholar 

  55. Doench JG, Sharp PA. Specificity of microRNA target selection in translational repression. Genes Dev. 2004;18:504–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Schirle NT, MacRae IJ. The crystal structure of human Argonaute2. Science. 2012;336:1037–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Didiano D, Hobert O. Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat Struct Mol Biol. 2006;13:849–51.

    Article  CAS  PubMed  Google Scholar 

  58. Hausser J, Landthaler M, Jaskiewicz L, et al. Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets. Genome Res. 2009;19:2009–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Grimson A, Farh KK, Johnston WK, et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007;27:91–105.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Kertesz M, Iovino N, Unnerstall U, et al. The role of site accessibility in microRNA target recognition. Nat Genet. 2007;39:1278–84.

    Article  CAS  PubMed  Google Scholar 

  61. Saini HK, Griffiths-Jones S, Enright AJ. Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci U S A. 2007;104(45):17719–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Glaich O, Parikh S, Bell RE, et al. DNA methylation directs microRNA biogenesis in mammalian cells. Nat Commun. 2019;10(1):5657.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  63. Ivey KN, Muth A, Arnold J, et al. MicroRNA regulation of cell lineages in mouse and human embryonic stem cells. Cell Stem Cell. 2008;2:219–29.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Anokye-Danso F, Trivedi CM, Juhr D, et al. Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency. Cell Stem Cell. 2011;8:376–88.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Chi SW, Hannon GJ, Darnell RB. An alternative mode of microRNA target recognition. Nat. Struct. Mol. Biol. 2012;19:321–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Rupaimoole R, Calin GA, Lopez-Berestein G, et al. MiRNA deregulation in cancer cells and the tumor microenvironment. Cancer Discov. 2016;6:235–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Ha M, Kim VN. Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol. 2014;15:509–24.

    Article  CAS  PubMed  Google Scholar 

  68. Lin S, Gregory RI. MicroRNA biogenesis pathways in cancer. Nat Rev Cancer. 2015;15:321–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Wang Z. MicroRNAs and Cardiovascular Disease. Bentham Science Publishers, Potomac. 2010; eISBN: 978-1-60805-184-7.

    Google Scholar 

  70. Yang B, Lin H, **ao J, et al. The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2. Nat Med. 2007;13:486–91.

    Article  CAS  PubMed  Google Scholar 

  71. Lu Y, Zhang Y, Wang N, et al. Control of experimental atrial fibrillation by microRNA-328. Circulation. 2010;122:2378–87.

    Article  CAS  PubMed  Google Scholar 

  72. **ao J, Lin H, Luo X, et al. miRNA-605 joins the p53 network to form a p53:miRNA-605:Mdm2 positive feedback loop in response to cellular stress. EMBO J. 2011;30:524–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Luo X, Pan Z, Shan H, et al. MicroRNA-26 governs profibrillatory inward-rectifier potassium current changes in atrial fibrillation. J Clin Invest. 2013;123:1939–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Zhang S, Yue W, **e Y, et al. The four-microRNA signature identified by bioinformatics analysis predicts the prognosis of nasopharyngeal carcinoma patients. Oncol Rep. 2019;1767–80

    Google Scholar 

  75. Andersen GB, Tost J. Circulating miRNAs as biomarker in cancer. In: Schaffner F, Merlin JL, von Bubnoff N (eds). Tumor liquid biopsies. Volume 215. Springer, Cham. 2020. Recent Results in Cancer Research.

    Google Scholar 

  76. Rooij E, Kauppinen S. Development of micro RNA therapeutics is coming of age. EMBO Mol Med. 2014;6:851–64.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  77. Cavalcante P, Mizrachi T, Barzago C, et al. MicroRNA signature associated with treatment response in myasthenia gravis: A further step towards precision medicine. Pharmacol Res. 2019;148:104388.

    Article  CAS  PubMed  Google Scholar 

  78. Wang Y, Ru J, ** T, et al. An approach to identify individual functional single nucleotide polymorphisms and isoform microRNAs. Biomed Res Int. 2019;2019:6193673.

    PubMed  PubMed Central  Google Scholar 

  79. Johnson CD, Esquela-Kerscher A, Stefani G, et al. The let-7 microRNA represses cell proliferation pathways in human cells. Cancer Res. 2007;67:7713–22.

    Article  CAS  PubMed  Google Scholar 

  80. Yu F, Yao H, Zhu P, et al. let-7 Regulates self renewal and tumorigenicity of breast cancer cells. Cell. 2007;131:1109–23.

    Article  CAS  PubMed  Google Scholar 

  81. Bonci D, Coppola V, Musumeci M, et al. The miR-15a-miR-16-1 cluster controls prostate cancer by targeting multiple oncogenic activities. Nat Med. 2008;14:1271–7.

    Article  CAS  PubMed  Google Scholar 

  82. Metias SM, Lianidou E, Yousef GM. MicroRNAs in clinical oncology: At the crossroads between promises and problems. J Clin Pathol. 2009;62:771–6.

    Article  CAS  PubMed  Google Scholar 

  83. Farooqi AA, Fayyaz S, Shatynska-Mytsyk I, et al. Is miR-34a a well-equipped swordsman to conquer temple of molecular oncology? Chem Biol Drug Des. 2016;87:321–34.

    Article  CAS  PubMed  Google Scholar 

  84. Wang Z. The guideline of the design and validation of miRNA mimics. Methods Mol Biol. 2011;676:211–24.

    Article  CAS  PubMed  Google Scholar 

  85. Kumar MS, Erkeland SJ, Pester RE, et al. Suppression of non-small cell lung tumor development by the let-7 microRNA family. Proc Natl Acad Sci USA. 2008;105:3903–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Esquela-Kerscher A, Trang P, Wiggins JF, et al. The let-7 microRNA reduces tumor growth in mouse models of lung cancer. Cell Cycle. 2008;7:759–64.

    Article  CAS  PubMed  Google Scholar 

  87. Boudreau RL, Monteys AM, Davidson BL. Minimizing variables among hairpin-based RNAi vectors reveals the potency of shRNAs. RNA. 2008;14:1834–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Bauer M, Kinkl N, Meixner A, et al. Prevention of interferon-stimulated gene expression using microRNA-designed hairpins. Gene Ther. 2009;16:142–7.

    Article  CAS  PubMed  Google Scholar 

  89. Aagaard LA, Zhang J, von Eije KJ, et al. Engineering and optimization of the miR-106b cluster for ectopic expression of multiplexed anti-HIV RNAs. Gene Ther. 2008;15:1536–49.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Liu YP, Haasnoot J, ter Brake O, et al. Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron. Nucleic Acids Res. 2008;36:2811–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Seyhan AA. A multiplexed miRNA and transgene expression platform for simultaneous repression and expression of protein coding sequences. Mol Biosyst. 2016;12(1):295–312.

    Article  CAS  PubMed  Google Scholar 

  92. Rooij E, Kauppinen S. Development of microRNA therapeutics is coming of age. EMBO Mol Med. 2014;6:851–64.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  93. Mollaei H, Safaralizadeh R, Rostami Z. MicroRNA replacement therapy in cancer. J Cell Physiol. 2019;234(8):12369–84.

    Article  CAS  PubMed  Google Scholar 

  94. Simonson B, Das S. MicroRNA therapeutics: The next magic bullet? Mini Rev Med Chem. 2015;15(6):467–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Fiedler J, Batkai S, Thum T. MicroRNA-based therapy in cardiology. Herz. 2014;39(2):194–200.

    Article  CAS  PubMed  Google Scholar 

  96. Mellis D, Caporali A. MicroRNA-based therapeutics in cardiovascular disease: screening and delivery to the target. Biochem Soc Trans. 2018;46(1):11–21.

    Article  CAS  PubMed  Google Scholar 

  97. Bader AG, Brown D, Winkler M. The promise of microRNA replacement therapy. Cancer Res. 2010;70(18):7027–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Greenberg DS, Soreq H. MicroRNA therapeutics in neurological disease. Curr Pharm Des. 2014;20(38):6022–7.

    Article  CAS  PubMed  Google Scholar 

  99. Singh S, Narang AS, Mahato RI. Subcellular fate and off-target effects of siRNA, shRNA, and miRNA. Pharm Res. 2011;28:2996–3015.

    Article  CAS  PubMed  Google Scholar 

  100. Chen Y, Zhao H, Tan Z, et al. Bottleneck limitations for microRNA-based therapeutics from bench to the bedside. Pharmazie. 2015;70:147–54.

    CAS  PubMed  Google Scholar 

  101. Jackson AL, Burchard J, Schelter J, et al. Widespread siRNA “off-target” transcript silencing mediated by seed region sequence complementarity. RNA. 2006;12:1179–87.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Lal A, Navarro F, Maher CA, et al. miR-24 inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to “seedless” 3′UTR microRNA recognition elements. Mol Cell. 2009;35:610–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Seitz H. Redefining microRNA targets. Curr Biol. 2009;19:870–3.

    Article  CAS  PubMed  Google Scholar 

  104. Lee YJ, Kim V, Muth DC, et al. Validated microRNA target databases: An evaluation. Drug Dev Res. 2015;76:389–96.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  105. Leclercq M, Diallo AB, Blanchette M. Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences. Nucleic Acids Res. 2017;45:556–66.

    Article  CAS  PubMed  Google Scholar 

  106. Grimm D, Wang L, Lee JS, et al. Argonaute proteins are key determinants of RNAi efficacy, toxicity, and persistence in the adult mouse liver. J Clin Investig. 2010;20:3106–19.

    Article  CAS  Google Scholar 

  107. Diederichs S, Jung S, Rothenberg SM, et al. Coexpression of Argonaute-2 enhances RNA interference toward perfect match binding sites. Proc Natl Acad Sci USA. 2008;105:9284–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. McBride JL, Boudreau RL, Harper SQ, et al. Artificial miRNAs mitigate shRNA-mediated toxicity in the brain: Implications for the therapeutic development of RNAi. Proc Natl Acad Sci USA. 2008;105:5868–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Boudreau RL, Martins I, Davidson BL. Artificial MicroRNAs as siRNA shuttles: Improved safety as compared to shRNAs in vitro and In vivo. Mol Ther. 2009;17:169–75.

    Article  CAS  PubMed  Google Scholar 

  110. Beer S, Bellovin DI, Lee JS, et al. Low-level shRNA cytotoxicity can contribute to MYC-induced hepatocellular carcinoma in adult mice. Mol Ther. 2010;18:161–70.

    Article  CAS  PubMed  Google Scholar 

  111. Gallant-Behm CL, Piper J, Lynch JM, et al. A microRNA-29 mimic (Remlarsen) represses extracellular matrix expression and fibroplasia in the skin. J Investig Dermatol. 2019;139:1073–81.

    Article  CAS  PubMed  Google Scholar 

  112. Reid G, Pel ME, Kirschner MB, et al. Restoring expression of miR-16: A novel approach to therapy for malignant pleural mesothelioma. Ann Oncol. 2013;24:3128–35.

    Article  CAS  PubMed  Google Scholar 

  113. van Zandwijk N, Pavlakis N, Kao SC, et al. Safety and activity of microRNA-loaded minicells in patients with recurrent malignant pleural mesothelioma: A first-in-man, phase 1, open-label, dose-escalation study. Lancet Oncol. 2017;18:1386–96.

    Article  PubMed  Google Scholar 

  114. Bouchie A. First microRNA mimic enters clinic. Nat Biotechnol. 2013;31:577.

    Article  CAS  PubMed  Google Scholar 

  115. Adams BD, Parsons C, Slack FJ. The tumor-suppressive and potential therapeutic functions of miR-34a in epithelial carcinomas. Expert Opin Ther Targets. 2016;20:737–53.

    Article  CAS  PubMed  Google Scholar 

  116. Misso G, Di Martino MT, De Rosa G, et al. Mir-34: A new weapon against cancer? Mol Ther Nucleic Acids. 2014;3:e195.

    Article  PubMed Central  CAS  Google Scholar 

  117. Ling H, Girnita L, Buda O, et al. Non-coding RNAs: The cancer genome dark matter that matters! Clin Chem Lab Med. 2017;55:705–14.

    Article  CAS  PubMed  Google Scholar 

  118. Bhan A, Mandal SS. LncRNA HOTAIR: A master regulator of chromatin dynamics and cancer. Biochim Biophys Acta. 2015;1856:151–64.

    CAS  PubMed  PubMed Central  Google Scholar 

  119. Ma L, Bajic VB, Zhang Z. On the classification of long non-coding RNAs. RNA Biol. 2013;10:925–33.

    Article  PubMed  Google Scholar 

  120. Bhan A, Mandal SS. Long noncoding RNAs: emerging stars in gene regulation, epigenetics and human disease. ChemMedChem. 2014;9:1932–56.

    Article  CAS  PubMed  Google Scholar 

  121. Wang Kevin C, Chang HY. Molecular mechanisms of long noncoding RNAs. Molecular cell. 2011;43:904–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Sanfilippo PG, Hewitt AW. Translating the ENCyclopedia of DNA Elements Project findings to the clinic: ENCODE’s implications for eye disease. Clin Exp Ophthalmol. 2014;42:78–83.

    Article  PubMed  Google Scholar 

  123. Tragante V, Moore JH, Asselbergs FW. The ENCODE project and perspectives on pathways. Genet Epidemiol. 2014;38:275–80.

    Article  PubMed  Google Scholar 

  124. Statello L, Guo CJ, Chen LL, et al. Gene regulation by long non-coding RNAs and its biological functions Nat Rev Mol Cell Biol. 2021; 22(2): 96–118.

    Google Scholar 

  125. Dykes IM, Emanueli C. Transcriptional and post-transcriptional gene regulation by long non-coding RNA. Genom Proteom Bioinform. 2017;15(3):177–86.

    Article  Google Scholar 

  126. Gil N, Ulitsky I. Regulation of gene expression by cis-acting long non-coding RNAs Nat Rev Genet. 2020; 21(2): 102–117.

    Google Scholar 

  127. Zhang Y, Du W, Yang B. Long non-coding RNAs as new regulators of cardiac electrophysiology and arrhythmias: Molecular mechanisms, therapeutic implications and challenges. Pharmacol Ther. 2019;203:107389.

    Article  CAS  PubMed  Google Scholar 

  128. Kim TK, Shiekhattar R. Diverse regulatory interactions of long noncoding RNAs. Curr Opin Genet Dev. 2016;36:73–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Zhang Y, Jiao L, Sun L, et al. LncRNA ZFAS1 as a SERCA2a inhibitor to cause intracellular Ca2+ overload and contractile dysfunction in a mouse model of myocardial infarction. Circ Res. 2018;122(10):1354–68.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Ferrè F, Colantoni A, Helmer-Citterich M. Revealing protein-lncRNA interaction. Brief Bioinform. 2016;17(1):106–16.

    Article  PubMed  CAS  Google Scholar 

  131. Long Y, Wang X, Youmans DT, et al. How do lncRNAs regulate transcription? Sci Adv. 2017;3(9):eaao2110.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  132. Jonas K, Calin GA, Pichler M. RNA-binding proteins as important regulators of long non-coding RNAs in cancer. Int J Mol Sci. 2020;21(8):2969.

    Article  CAS  PubMed Central  Google Scholar 

  133. Prabhakar B, Zhong XB, Rasmussen TP. Exploiting long noncoding RNAs as pharmacological targets to modulate epigenetic diseases. Yale J Biol Med. 2017;90(1):73–86.

    CAS  PubMed  PubMed Central  Google Scholar 

  134. Wapinski O, Chang HY. Long noncoding RNAs and human disease. Trends Cell Biol. 2011;21(6):354–61.

    Article  CAS  PubMed  Google Scholar 

  135. Schmitz SU, Grote P, Herrmann BG. Mechanisms of long noncoding RNA function in development and disease. Cell Mol Life Sci. 2016;73(13):2491–509.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Uchida S, Dimmeler S. Long noncoding RNAs in cardiovascular diseases. Circ Res. 2015;116(4):737–50.

    Article  CAS  PubMed  Google Scholar 

  137. Yu B, Wang S. Angio-LncRs: LncRNAs that regulate angiogenesis and vascular disease. Theranostics. 2018;8(13):3654–75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Chi Y, Wang D, Wang J, et al. Long non-coding RNA in the pathogenesis of cancers. Cells. 2019;8(9):1015.

    Article  CAS  PubMed Central  Google Scholar 

  139. Song H, Sun W, Ye G, et al. Long non-coding RNA expression profile in human gastric cancer and its clinical significances. J Transl Med. 2013;11(225):5876.

    Google Scholar 

  140. Hajjari M, Salavaty A. HOTAIR: An oncogenic long non-coding RNA in different cancers. Cancer Biol Med. 2015;12(1):1–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  141. Gupta RA, Shah N, Wang KC, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010;464(7291):1071–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Yap KL, Li S, Munoz-Cabello AM, et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell. 2010;38(5):662–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Huarte M, Guttman M, Feldser D, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell. 2010;142(3):409–19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Tang SS, Zheng BY, **ong XD. LincRNA-p21: Implications in human diseases. Int J Mol Sci. 2015;16(8):18732–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Jiao L, Li M, Shao Y, Zhang Y, et al. lncRNA-ZFAS1 induces mitochondria-mediated apoptosis by causing cytosolic Ca2+ overload in myocardial infarction mice model. Cell Death Dis. 2019;10(12):942.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Hu F, Shao L, Zhang J, et al. Knockdown of ZFAS1 inhibits hippocampal neurons apoptosis and autophagy by activating the PI3K/AKT pathway via up-regulating miR-421 in epilepsy. Neurochem Res. 2020;45(10):2433–41.

    Article  CAS  PubMed  Google Scholar 

  147. Wu H, Qin W, Lu S, et al. Long noncoding RNA ZFAS1 promoting small nucleolar RNA-mediated 2′-O-methylation via NOP58 recruitment in colorectal cancer. Mol Cancer. 2020;19(1):95.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  148. Ishii N, Ozaki K, Sato H, et al. Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet. 2006;51(12):1087–99.

    Article  CAS  PubMed  Google Scholar 

  149. Vausort M, Wagner DR, Devaux Y. Long noncoding RNAs in patients with acute myocardial infarction. Circ Res. 2014;115:668–77.

    Article  CAS  PubMed  Google Scholar 

  150. Zhu XH, Yuan YX, Rao SL, et al. LncRNA MIAT enhances cardiac hypertrophy partly through sponging miR-150. Eur Rev Med Pharmacol Sci. 2016;20:3653–60.

    PubMed  Google Scholar 

  151. Qu X, Du Y, Shu Y, et al. MIAT is a pro-fibrotic long non-coding RNA governing cardiac fibrosis in post-infarct myocardium. Sci Rep. 2017;7:42657.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Zhou X, Zhang W, ** M, et al. lncRNA MIAT functions as a competing endogenous RNA to upregulate DAPK2 by sponging miR-22-3p in diabetic cardiomyopathy. Cell Death Dis. 2017;8:e2929.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Yan B, Yao J, Liu JY, et al. LncRNA-MIAT regulates microvascular dysfunction by functioning as a competing endogenous RNA. Circ Res. 2015;116:1143–56.

    Article  CAS  PubMed  Google Scholar 

  154. Sleutels F, Zwart R, Barlow DP. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature. 2002;415:810–3.

    Article  CAS  PubMed  Google Scholar 

  155. Pandey RR, Mondal T, Mohammad F, et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell. 2008;32:232–46.

    Article  CAS  PubMed  Google Scholar 

  156. Novikova IV, Hennelly SP, Sanbonmatsu KY. Sizing up long non-coding RNAs. Do lncRNAs have secondary and tertiary structure? Bioarchitecture. 2012;2(6):189–99.

    Article  PubMed  PubMed Central  Google Scholar 

  157. Sone M, Hayashi T, Tarui H, et al. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci. 2017;120:2498–506.

    Article  CAS  Google Scholar 

  158. Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature. 2012;482(7385):339–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Thorenoor N, Faltejskova-Vychytilova P, Hombach S, et al. Long non-coding RNA ZFAS1 interacts with CDK1 and is involved in p53-dependent cell cycle control and apoptosis in colorectal cancer. Oncotarget. 2016;7(1):622–37.

    Article  PubMed  Google Scholar 

  160. Liu G, Wang L, Han H, et al. LncRNA ZFAS1 promotes growth and metastasis by regulating BMI1 and ZEB2 in osteosarcoma. Am J Cancer Res. 2017;7(7):1450–62.

    CAS  PubMed  PubMed Central  Google Scholar 

  161. Quinn JJ, Ilik IA, Qu K, et al. Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nat Biotechnol. 2014;32(9):933–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Mercer TR, Mattick JS. Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol. 2013;20(3):300–7.

    Article  CAS  PubMed  Google Scholar 

  163. Zucchelli S, Cotella D, Takahashi H, et al. SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that activate translation. RNA Biol. 2015;12(8):771–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  164. Zucchelli S, Fasolo F, Russo R, et al. SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells. Front Cell Neurosci. 2015;9:174.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  165. Carrieri C, Cimatti L, Biagioli M, et al. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature. 2012;491(7424):454–7.

    Article  CAS  PubMed  Google Scholar 

  166. Indrieri A, Grimaldi C, Zucchelli S, et al. Synthetic long non-coding RNAs (SINEUPs) rescue defective gene expression in vivo. Sci Rep. 2016;6:27315.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Kristensen LS, Andersen MS, Stagsted LVW, et al. The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet. 2019;20(11):675–91.

    Article  CAS  PubMed  Google Scholar 

  168. Vicens Q, Westhof E. Biogenesis of circular RNAs. Cell. 2014;159:13–4.

    Article  CAS  PubMed  Google Scholar 

  169. Zhang XO, Dong R, Zhang Y, et al. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016;26:1277–87.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  170. Panda AC. Circular RNAs act as miRNA sponges. Adv Exp Med Biol. 2018;1087:67–79.

    Article  CAS  PubMed  Google Scholar 

  171. Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495:333–8.

    Article  CAS  PubMed  Google Scholar 

  172. Hansen TB, Jensen TI, Clausen BH, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495:384–8.

    Article  CAS  PubMed  Google Scholar 

  173. Salzman J. Circular RNA expression: Its potential regulation and function. Trends Genet. 2016;32:309–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  174. Jeck WR, Sharpless NE. Detecting and characterizing circular RNAs. Nat Biotechnol. 2014;32:453–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Rybak-Wolf A, Stottmeister C, Glazar P, et al. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol Cell. 2015;58:870–85.

    Article  CAS  PubMed  Google Scholar 

  176. Gruner H, Cortés-López M, Cooper DA, et al. CircRNA accumulation in the aging mouse brain. Sci Rep. 2016;6:38907.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Westholm JO, Miura P, Olson S, et al. Genome-wide analysis of Drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Rep. 2014;9:1966–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  178. Patop IL, Wüst S, Kadener S. Past, present, and future of circRNAs. EMBO J. 2019;38(16):e100836.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  179. Guo JU, Agarwal V, Guo H, et al. Expanded identification and characterization of mammalian circular RNAs. Genome Biol. 2014;15:409.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  180. Hanan M, Soreq H, Kadener S. CircRNAs in the brain. RNA Biol. 2017;14:1028–34.

    Article  PubMed  Google Scholar 

  181. Bachmayr-Heyda A, Reiner AT, Auer K, et al. Correlation of circular RNA abundance with proliferation–exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues. Sci Rep. 2015;5:8057.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. Werfel S, Nothjunge S, Schwarzmayr T, et al. Characterization of circular RNAs in human, mouse and rat hearts. J Mol Cell Cardiol. 2016;98:103–7.

    Article  CAS  PubMed  Google Scholar 

  183. Salzman J, Gawad C, Wang PL, et al. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One. 2012;7:e30733.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Denzler R, Agarwal V, Stefano J, et al. Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol Cell. 2014;54:766–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  185. Jens M, Rajewsky N, et al. Competition between target sites of regulators shapes post-transcriptional gene regulation. Nat Rev Genet. 2015;16:113–26.

    Article  CAS  PubMed  Google Scholar 

  186. Legnini I, Di Timoteo G, Rossi F, et al. Circ-ZNF609 is a circular RNA that can be translated and functions in myogenesis. Mol Cell. 2017;66:22–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Yang Y, Fan X, Mao M, et al. Extensive translation of circular RNAs driven by N6-methyladenosine. Cell Res. 2017;27:626–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  188. Pamudurti NR, Bartok O, Jens M, et al. Translation of circRNAs. Mol Cell. 2017;66:9–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Yang Y, Gao X, Zhang M, et al. Novel role of FBXW7 circular RNA in repressing glioma tumorigenesis. J Natl Cancer Inst. 2018;110:304–15.

    Article  CAS  Google Scholar 

  190. Holdt LM, Stahringer A, Sass K, et al. Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans. Nat Commun. 2016;7:12429.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Abdelmohsen K, Panda AC, Munk R, et al. Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1. RNA Biol. 2017;14:361–9.

    Article  PubMed  PubMed Central  Google Scholar 

  192. Du WW, Yang W, Liu E, et al. Foxo3 circular RNA retards cell cycle progression via forming ternary complexes with p21 and CDK2. Nucleic Acids Res. 2016;6:2846–58.

    Article  Google Scholar 

  193. Kristensen LS, Hansen TB, Venø MT, et al. Circular RNAs in cancer: opportunities and challenges in the field. Oncogene. 2018;37(5):555–65.

    Article  CAS  PubMed  Google Scholar 

  194. Wang Y, Mo Y, Gong Z, et al. Circular RNAs in human cancer. Mol Cancer. 2017;16:25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Ng WL, Mohd Mohidin TB, Shukla K. Functional role of circular RNAs in cancer development and progression. RNA Biol. 2018;15(8):995–1005.

    PubMed  PubMed Central  Google Scholar 

  196. Floris G, Zhang L, Follesa P, et al. Regulatory role of circular RNAs and neurological disorders. Mol Neurobiol. 2017;54(7):5156–65.

    Article  CAS  PubMed  Google Scholar 

  197. Altesha MA, Ni T, Khan A, et al. Circular RNA in cardiovascular disease. J Cell Physiol. 2019;234(5):5588–600.

    Article  CAS  PubMed  Google Scholar 

  198. Wang T, Pan W, Hu J, et al. Circular RNAs in metabolic diseases. Adv Exp Med Biol. 2018;1087:275–85.

    Article  CAS  PubMed  Google Scholar 

  199. Zeng Y, Zheng Z, Liu F, et al. Circular RNAs in metabolism and metabolic disorders. Obes Rev. 2021;22(7):e13220.

    Article  CAS  PubMed  Google Scholar 

  200. Yang D, Yang K, Yang M. Circular RNA in aging and age-related diseases. Adv Exp Med Biol. 2018;1086:17–35.

    Article  CAS  PubMed  Google Scholar 

  201. Verduci L, Strano S, Yarden Y, et al. The circRNA-microRNA code: emerging implications for cancer diagnosis and treatment. Mol Oncol. 2019;13(4):669–80.

    Article  PubMed  PubMed Central  Google Scholar 

  202. Lasda E, Parker R. Circular RNAs: diversity of form and function. RNA. 2014;20:1829–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Li F, Zhang L, Li W, et al. Circular RNA ITCH has inhibitory effect on ESCC by suppressing the Wnt/β-catenin pathway. Oncotarget. 2015;6:6001–13.

    Article  PubMed  PubMed Central  Google Scholar 

  204. Du WW, Yang W, Liu E, et al. Foxo3 circular RNA retards cell cycle progression via forming ternary complexes with p21 and CDK2. Nucleic Acids Res. 2016;44:2846–58.

    Article  PubMed  PubMed Central  Google Scholar 

  205. Wang Z. Antisense RNA and cancer. In: Cancer and noncoding RNAs by Jaybokas Chakrabarti & Sanga Mitra (eds), Translational epigenetics series. Elsevier AP Academic Press, London. 2017; ISBN: 978-0-12-811022-5.

    Google Scholar 

  206. Katayama S, Tomaru Y, Kasukawa T, et al. Antisense transcript in the mammalian transcriptome. Science. 2005;309:1564–6.

    Article  PubMed  Google Scholar 

  207. Pelechano V, Steinmetz LM. Gene regulation by antisense transcription. Nat Rev Genet. 2013;14(12):880–93.

    Article  CAS  PubMed  Google Scholar 

  208. Faghihi MA, Wahlestedt C. Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol. 2009;10(9):637–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  209. Piatek MJ, Henderson V, Zynad HS, et al. Natural antisense transcription from a comparative perspective. Genomics. 2016;108(2):56–63.

    Article  CAS  PubMed  Google Scholar 

  210. Wight M, Werner A. The functions of natural antisense transcripts. Essays Biochem. 2013;54:91–101.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  211. Mahmoudi S, Henriksson S, Corcoran M, et al. Wrap53, a natural p53 antisense transcript required for p53 induction upon DNA damage. Mol Cell. 2009;33:462–71.

    Article  CAS  PubMed  Google Scholar 

  212. Su WY, Li JT, Cui Y, et al. Bidirectional regulation between WDR83 and its natural antisense transcript DHPS in gastric cancer. Cell Res. 2012;22(9):1374–89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  213. Galante PA, Vidal DO, de Souza JE, et al. Sense-antisense pairs in mammals: functional and evolutionary considerations. Genome Biol. 2007;8(3):R40.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  214. Bartonicek N, Maag JL, Dinger ME. Long noncoding RNAs in cancer: mechanisms of action and technological advancements. Mol Cancer. 2016;15(1):43.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  215. Berteaux N, Aptel N, Cathala G, et al. A novel H19 antisense RNA overexpressed in breast cancer contributes to paternal IGF2 expression. Mol Cell Biol. 2008;28(22):6731–45.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  216. Ling MHT, Ban Y, Wen H, et al. Conserved expression of natural antisense transcripts in mammals. BMC Genomics. 2013;14:243.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  217. Pestka S, Daugherty BL, Jung V, et al. Anti-mRNA: specific inhibition of translation of single mRNA molecules. Proc Natl Acad Sci U S A. 1984;81(23):7525–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  218. Munroe SH. Antisense RNA inhibits splicing of pre-mRNA in vitro. EMBO J. 1988;7:2523–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  219. Wang Z. The principle of miRNA-Masking antisense oligonucleotides technology. Methods Mol Biol. 2011;676:43–50.

    Article  CAS  PubMed  Google Scholar 

  220. Wang Z. The principle of miRNA-Masking antisense oligonucleotides technology. In MicroRNA and cancer: Methods and protocols by Wei Wu (ed), pp 43–50. Springer-Verlag/Humana Press, New York. 2011; ISBN: 978-1-60761-862-1.

    Google Scholar 

  221. Murakami K, Miyagishi M. Tiny masking locked nucleic acids effectively bind to mRNA and inhibit binding of microRNAs in relation to thermodynamic stability. Biomed Rep. 2014;2(4):509–12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  222. Ors-Kumoglu G, Gulce-Iz S, Biray-Avci C. Therapeutic microRNAs in human cancer. Cytotechnology. 2019;71(1):411–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  223. Gambari R, Brognara E, Spandidos DA, et al. Targeting oncomiRNAs and mimicking tumor suppressor miRNAs: nuew trends in the development of miRNA therapeutic strategies in oncology. Int J Oncol. 2016;49(1):5–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Zhang S, Yan ML, Yang L, et al. MicroRNA-153 impairs hippocampal synaptic vesicle trafficking via downregulation of synapsin I in rats following chronic cerebral hypoperfusion. Exp Neurol. 2020;332:113389.

    Article  CAS  PubMed  Google Scholar 

  225. Wang N, Sun LY, Zhang SC, et al. MicroRNA-23a participates in estrogen deficiency induced gap junction remodeling of rats by targeting GJA1. Int J Biol Sci. 2015;11(4):390–403.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  226. Duan MJ, Yan ML, Wang Q, et al. Overexpression of miR-1 in the heart attenuates hippocampal synaptic vesicle exocytosis by the posttranscriptional regulation of SNAP-25 through the transportation of exosomes. Cell Commun Signal. 2018;16(1):91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  227. Zhang T, Hu Y, Ju J, et al. Downregulation of miR-522 suppresses proliferation and metastasis of non-small cell lung cancer cells by directly targeting DENN/MADD domain containing 2D. Sci Rep. 2016;6:19346.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  228. Hong H, Tao T, Chen S, et al. MicroRNA-143 promotes cardiac ischemia-mediated mitochondrial impairment by the inhibition of protein kinase Cepsilon. Basic Res Cardiol. 2017;112(6):60.

    Article  PubMed  CAS  Google Scholar 

  229. Qiu Y, Cheng R, Liang C, et al. MicroRNA-20b promotes cardiac hypertrophy by the inhibition of mitofusin 2-mediated inter-organelle Ca2+ cross-talk. Mol Ther Nucleic Acids. 2020;19:1343–56.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  230. Haseloff J, Gerlach WL. Simple RNA enzymes with new and highly specific endoribonuclease activities. Biotechnology. 1992;24:264–9.

    CAS  PubMed  Google Scholar 

  231. Scott WG, Murray JB, Arnold JR, et al. Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme. Science. 1996;274(5295):2065–9.

    Article  CAS  PubMed  Google Scholar 

  232. Citti L, Rainaldi G. Synthetic hammerhead ribozymes as therapeutic tools to control disease genes. Curr Gene Ther. 2005;5(1):11–24.

    Article  CAS  PubMed  Google Scholar 

  233. Phylactou LA, Tsipouras P, Kilpatrick MW. Hammerhead ribozymes targeted to the FBN1 mRNA can discriminate a single base mismatch between ribozyme and target. Biochem Biophys Res Commun. 1998;249(3):804–10.

    Article  CAS  PubMed  Google Scholar 

  234. Beigelman L, McSwiggen JA, Draper KG, et al. Chemical modification of hammerhead ribozymes. Catalytic activity and nuclease resistance. J Biol Chem. 1995;270(43):25702–8.

    Article  CAS  PubMed  Google Scholar 

  235. Heidenreich O, Benseler F, Fahrenholz A, et al. High activity and stability of hammerhead ribozymes containing 2′-modified pyrimidine nucleosides and phosphorothioates. J Biol Chem. 1994;269(3):2131–8.

    Article  CAS  PubMed  Google Scholar 

  236. Serganov A, Patel DJ. Ribozymes, riboswitches and beyond: Regulation of gene expression without proteins. Nat Rev Genet. 2007;8(10):776–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  237. Pavco PA, Bouhana KS, Gallegos AM, et al. Antitumor and antimetastatic activity of ribozymes targeting the messenger RNA of vascular endothelial growth factor receptors. Clin Cancer Res. 2000;6(5):2094–103.

    CAS  PubMed  Google Scholar 

  238. Johnston WK, Unrau PJ, Lawrence MS, et al. RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science. 292(5520): 1319–25.

    Google Scholar 

  239. de Feyter R, Li P. Technology evaluation: HIV ribozyme gene therapy, Gene Shears Pty Ltd. Curr Opin Mol Therap. 2000;2(3):332–5.

    CAS  Google Scholar 

  240. Khan AU. Ribozyme: a clinical tool Clinica Chimica Acta/Intern J Clin Chem. 2006; 367(1–2): 20–27.

    Google Scholar 

  241. Asha K, Kumar P, Sanicas M, et al. Advancements in nucleic acid based therapeutics against respiratory viral infections. J Clin Med. 2018;8(1):6.

    Article  PubMed Central  CAS  Google Scholar 

  242. Khanna M, Saxena L, Rajput R, et al. Gene silencing: a therapeutic approach to combat influenza virus infections. Future Microbiol. 2015;10(1):131–40.

    Article  CAS  PubMed  Google Scholar 

  243. Kumar B, Khanna M, Kumar P, et al. Nucleic acid-mediated cleavage of M1 gene of influenza A virus is significantly augmented by antisense molecules targeted to hybridize close to the cleavage site. Mol Biotechnol. 2012;51(1):27–36.

    Article  CAS  PubMed  Google Scholar 

  244. Kumar B, Asha K, Khanna M, et al. The emerging influenza virus threat: status and new prospects for its therapy and control. Arch Virol. 2018;163(4):831–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  245. Lieber A, He CY, Polyak SJ, et al. Elimination of hepatitis C virus RNA in infected human hepatocytes by adenovirus-mediated expression of ribozymes. J Virol. 1996;70(12):8782–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  246. Marwick C. First “antisense” drug will treat CMV retinitis. JAMA. 1998; 280 (10): 871.

    Google Scholar 

  247. Hair P, Cameron F, McKeage K. Mipomersen sodium: First global approval. Drugs. 2013;73:487–93.

    Article  CAS  PubMed  Google Scholar 

  248. Suhr OB, Coelho T, Buades J, et al. Efficacy and safety of patisiran for familial amyloidotic polyneuropathy: A phase II multi-dose study. Orphanet J Rare Dis. 2015;10:109.

    Article  PubMed  PubMed Central  Google Scholar 

  249. Mendell JR, Rodino-Klapac LR, Sahenk Z, et al. Eteplirsen for the treatment of Duchenne muscular dystrophy. Ann Neurol. 2013;74:637–47.

    Article  CAS  PubMed  Google Scholar 

  250. Dias N, Stein CA. Antisense oligonucleotides: Basic concepts and mechanisms. Mol Cancer Ther. 2002;5:347–55.

    Google Scholar 

  251. Juliano RL. The delivery of therapeutic oligonucleotides. Nucleic Acids Res. 2016;44:6518–48.

    Article  PubMed  PubMed Central  Google Scholar 

  252. Tanaka M, Nyce JW. Respirable antisense oligonucleotides: A new drug class for respiratory disease. Respir Res. 2001;2:5–9.

    Article  CAS  PubMed  Google Scholar 

  253. Stephenson ML, Zamecnik PC. Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide. Proc Natl Acad Sci USA. 1978;75:285–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  254. Popescu FD. Antisense- and RNA interference-based therapeutic strategies in allergy. J Cell Mol Med. 2005;9:840–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  255. Arroyo JD, Gallichotte EN, Tewari M. Systematic design and functional analysis of artificial microRNAs. Nucleic Acids Res. 2014;42(9):6064–77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  256. Calloni R, Bonatto D. Scaffolds for artificial miRNA expression in animal cells. Hum Gene Ther Methods. 2015;26(5):162–74.

    Article  CAS  PubMed  Google Scholar 

  257. Fowler DK, Williams C, Gerritsen AT, et al. Improved knockdown from artificial microRNAs in an enhanced miR-155 backbone: a designer’s guide to potent multi-target RNAi. Nucleic Acids Res. 2016;44(5):e48.

    Article  PubMed  CAS  Google Scholar 

  258. Lebbink RJ, Lowe M, Chan T, et al. Polymerase II promoter strength determines efficacy of microRNA adapted shRNAs. PLoS One. 2011;6:e26213.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  259. Chung KH, Hart CC, Al-Bassam S, et al. Polycistronic RNA polymerase II expression vectors for RNA interference based on BIC/miR-155. Nucleic Acids Res. 2006;34:e53.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  260. Yang JS, Maurin T, Robine N, et al. Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis. Proc Natl Acad Sci USA. 2010;107:15163–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  261. Chen SC, Stern P, Guo Z, et al. Expression of multiple artificial microRNAs from a chicken miRNA126-based lentiviral vector. PLoS One. 2011;6:e22437.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  262. Zeng Y, Wagner EJ, Cullen BR. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol Cell. 2002;9:1327–33.

    Article  CAS  PubMed  Google Scholar 

  263. Grimm D, Wang L, Lee JS, et al. Argonaute proteins are key determinants of RNAi efficacy, toxicity, and persistence in the adult mouse liver. J Clin Invest. 2010;120:3106–19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  264. Snove O Jr, Rossi JJ. Toxicity in mice expressing short hairpin RNAs gives new insight into RNAi. Genome Biol. 2006;7:231.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  265. Grimm D, Streetz KL, Jopling CL, et al. Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature. 2006;441:537–41.

    Article  CAS  PubMed  Google Scholar 

  266. Amendola M, Passerini L, Pucci F, et al. Regulated and multiple miRNA and siRNA delivery into primary cells by a lentiviral platform. Mol Ther. 2009;17:1039–52.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  267. Giering JC, Grimm D, Storm TA, et al. Expression of shRNA from a tissue-specific pol II promoter is an effective and safe RNAi therapeutic. Mol Ther. 2008;16:1630–6.

    Article  CAS  PubMed  Google Scholar 

  268. Shin KJ, Wall EA, Zavzavadjian JR, et al. A single lentiviral vector platform for microRNA-based conditional RNA interference and coordinated transgene expression. Proc Natl Acad Sci USA. 2006;103:13759–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  269. Stegmeier F, Hu G, Rickles RJ, et al. A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. Proc Natl Acad Sci USA. 2005;102:13212–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  270. Du G, Yonekubo J, Zeng Y, et al. Design of expression vectors for RNA interference based on miRNAs and RNA splicing. FEBS J. 2006;273:5421–7.

    Article  CAS  PubMed  Google Scholar 

  271. Hu T, Fu Q, Chen P, et al. Construction of an artificial MicroRNA expression vector for simultaneous inhibition of multiple genes in mammalian cells. Int J Mol Sci. 2009;10:2158–68.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  272. Sun D, Melegari M, Sridhar S, et al. Multi-miRNA hairpin method that improves gene knockdown efficiency and provides linked multi-gene knockdown. Biotechniques. 2006;41:59–63.

    Article  CAS  PubMed  Google Scholar 

  273. Grimm D, Kay MA. Combinatorial RNAi: a winning strategy for the race against evolving targets. Mol Ther. 2007;15:878–88.

    Article  CAS  PubMed  Google Scholar 

  274. Herrera-Carrillo E, Berkhout B. The impact of HIV-1 genetic diversity on the efficacy of a combinatorial RNAi-based gene therapy. Gene Ther. 2015;22:485–95.

    Article  CAS  PubMed  Google Scholar 

  275. Aagaard L, Rossi JJ. RNAi therapeutics: principles, prospects and challenges. Adv Drug Deliv Rev. 2007;59:75–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  276. Wang SL, Yao HH, Qin ZH. Strategies for short hairpin RNA delivery in cancer gene therapy. Expert Opin Biol Ther. 2009;9:1357–68.

    Article  CAS  PubMed  Google Scholar 

  277. Amarzguioui M, Prydz H. An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun. 2004;316:1050–8.

    Article  CAS  PubMed  Google Scholar 

  278. Fellmann C, Zuber J, McJunkin K, et al. Functional identification of optimized RNAi triggers using a massively parallel sensor assay. Mol Cell. 2011;41:733–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  279. Pei Y, Tuschl T. On the art of identifying effective and specific siRNAs. Nat Methods. 2006;3:670–6.

    Article  CAS  PubMed  Google Scholar 

  280. Reynolds A, Leake D, Boese Q, et al. Rational siRNA design for RNA interference. Nat Biotechnol. 2004;22:326–30.

    Article  CAS  PubMed  Google Scholar 

  281. Ui-Tei K, Naito Y, Takahashi F, et al. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res. 2004;32:936–48.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  282. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31:3406–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  283. Kotowska-Zimmer A, Pewinska M, Olejniczak M. Artificial miRNAs as therapeutic tools: Challenges and opportunities. Wiley Interdiscip Rev RNA. 2021;12(4):e1640.

    Article  CAS  PubMed  Google Scholar 

  284. Elbashir SM, Harborth J, Lendeckel W, et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature. 2001;411:494–8.

    Article  CAS  PubMed  Google Scholar 

  285. Passioura T, Gozar MM, Goodchild A, et al. Interfering ribonucleic acids that suppress expression of multiple unrelated genes. BMC Biotechnol. 2009;9:57.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  286. Stegmeier F, Hu G, Rickles RJ, Hannon GJ, Elledge SJ. A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. Proc Natl Acad Sci U S A. 2005;102:13212–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  287. Wang J, Theunissen TW, Orkin SH. Site-directed, virus-free, and inducible RNAi in embryonic stem cells. Proc Natl Acad Sci U S A. 2007;104:20850–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  288. Zhou HX, **a XG, Xu ZS. An RNA polymerase II construct synthesizes short-hairpin RNA with a quantitative indicator and mediates highly efficient RNAi. Nucleic Acids Research. 2005;33:e62.

    Article  PubMed  PubMed Central  Google Scholar 

  289. **a XG, Zhou HX, Xu ZS. Multiple shRNAs expressed by an inducible pol II promoter can knock down the expression of multiple target genes. Biotechniques. 2006;41:64–8.

    Article  CAS  PubMed  Google Scholar 

  290. Zhu XC, Santa LA, Chang MS, et al. A versatile approach to multiple gene RNA interference using microRNA-based short hairpin RNAs. BMC Molecular Biology. 2007;8:98.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  291. Ebert MS, Neilson JR, Sharp PA. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods. 2007;4(9):721–6.

    Article  CAS  PubMed  Google Scholar 

  292. Lu Y, **ao J, Lin H, et al. A single anti-microRNA antisense oligodeoxyribonucleotide (AMO) targeting multiple microRNAs offers an improved approach for microRNA interference. Nucleic Acids Res. 2009;37:e24–33.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  293. Wang Z. New concepts of miRNAi technologies. In: MicroRNA interference technologies by Wang Z. Heidelberg: Springer-Verlag; 2009.

    Chapter  Google Scholar 

  294. Wang Z. The concept of multiple-target anti-miRNA antisense oligonucleotides technology. Methods Mol Biol. 2011;676:51–7.

    Article  CAS  PubMed  Google Scholar 

  295. Wang Z. The concept of multiple-target anti-miRNA antisense oligonucleotides technology. In: Wu W, editor. MicroRNA and cancer. Totowa: Humana Press; 2011.

    Google Scholar 

  296. Lindow M, Kauppinen S. Discovering the first microRNA-targeted drug. J Cell Biol. 2012;199:407–12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  297. Umbach JL, Cullen BR. The role of RNAi and microRNAs in animal virus replication and antiviral immunity. Genes Dev. 2009;23:1151–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  298. Gebert LFR, Rebhan MAE, Crivelli SEM, et al. Miravirsen (SPC3649) can inhibit the biogenesis of miR-122. Nucleic Acids Res. 2014;42:609–21.

    Article  CAS  PubMed  Google Scholar 

  299. Jopling C. Liver-specific microRNA-122. RNA Biol. 2012;9:137–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  300. Jopling CL, Schütz S, Sarnow P. Position-Dependent Function for a Tandem MicroRNA miR-122-Binding Site Located in the Hepatitis C Virus RNA Genome. Cell Host Microbe. 2008;4:77–85.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  301. Baek J, Kang S, Min H. MicroRNA-targeting therapeutics for hepatitis C. Arch Pharm Res. 2014;37:299–305.

    Article  CAS  PubMed  Google Scholar 

  302. Seto AG, Beatty X, Lynch JM, et al. Cobomarsen, an oligonucleotide inhibitor of miR-155, co-ordinately regulates multiple survival pathways to reduce cellular proliferation and survival in cutaneous T-cell lymphoma. Br J Haematol. 2018;183:428–44.

    Article  CAS  PubMed  Google Scholar 

  303. Xu L, Dai WQ, Xu XF, et al. Effects of multiple-target anti-microRNA antisense oligodeoxyribonucleotides on proliferation and migration of gastric cancer cells. Asian Pac J Cancer Prev. 2012;13(7):3203–7.

    Article  PubMed  Google Scholar 

  304. Subramanian RR, Wysk MA, Ogilvie KM, et al. Enhancing antisense efficacy with multimers and multi-targeting oligonucleotides (MTOs) using cleavable linkers. Nucleic Acids Res. 2015;43(19):9123–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  305. Zhou T, Meng X, Che H, et al. Regulation of insulin resistance by multiple miRNAs via targeting the GLUT4 signaling pathway. Cell Physiol Biochem. 2016;38(5):2063–78.

    Article  CAS  PubMed  Google Scholar 

  306. Zaman MS, Maher DM, Khan S, et al. Current status and implications of microRNAs in ovarian cancer diagnosis and therapy. J Ovarian Res. 2012;5(1):44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  307. Kolse R, Krainer AR, Altman S. RNA therapeutics: beyond RNA interference and antisense oligonucleotides. Nat Rev Drug Discov. 2012;11:125–40.

    Article  CAS  Google Scholar 

  308. Lennox KA, Behlke MA. Chemical modification and design of anti-miRNA oligonucleotides. Gene Therapy. 2011;18:1111–20.

    Article  CAS  PubMed  Google Scholar 

  309. Kurreck J, Wyszko E, Gillen C, et al. Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Res. 2002;30:1911–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  310. Seth PP, Siwkowski A, Allerson CR, et al. Short antisense oligonucleotides with novel 2′-4′ conformationaly restricted nucleoside analogues show improved potency without increased toxicity in animals. J Med Chem. 2009;52:10–3.

    Article  CAS  PubMed  Google Scholar 

  311. Stanton R, Sciabola S, Salatto C, et al. Chemical modification study of antisense gapmers. Nucleic Acid Ther. 2012;22:344–59.

    Article  CAS  PubMed  Google Scholar 

  312. Straarup EM, Fisker N, Hedtjärn M, et al. Short locked nucleic acid antisense oligonucleotides potently reduce apolipoprotein B mRNA and serum cholesterol in mice and non-human primates. Nucleic Acids Res. 2010;38:7100–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  313. Murray S, Ittig D, Koller E, et al. TricycloDNA-modified oligo-2′-deoxyribonucleotides reduce scavenger receptor B1 mRNA in hepatic and extra-hepatic tissues–a comparative study of oligonucleotide length, design and chemistry. Nucleic Acids Res. 2012;40:6135–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  314. Obad S, dos Santos CO, Petri A, et al. Silencing of microRNA families by seed-targeting tiny LNAs. Nature Genet. 2011;43:371–8.

    Article  CAS  PubMed  Google Scholar 

  315. Watanabe TA, Geary RS, Levin AA. Plasma protein binding of an antisense oligonucleotide targeting human ICAM-1 (ISIS 2302). Oligonucleotides. 2006;16:169–80.

    Article  CAS  PubMed  Google Scholar 

  316. Koller E, Vincent TM, Chappell A, et al. Mechanisms of single-stranded phosphorothioate modified antisense oligonucleotide accumulation in hepatocytes. Nucleic Acids Res. 2011;39:4795–807.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  317. Elmen J, Lindow M, Schütz S, et al. LNA-mediated microRNA silencing in non-human primates. Nature. 2008;452:896–9.

    Article  CAS  PubMed  Google Scholar 

  318. Rossor AM, Reilly MM, Sleigh JN. Antisense oligonucleotides and other genetic therapies made simple. Pract Neurol. 2018;18:126–31.

    Article  PubMed  Google Scholar 

  319. Crooke ST, editor. Antisense drug technology: principles, strategies, and applications. 1. New York: Marcel Dekker; 2001.

    Google Scholar 

  320. Bennett CF, Baker BF, Pham N, et al. Pharmacology of antisense drugs. Annu Rev Pharmacol Toxicol. 2017;57:81–105.

    Article  CAS  PubMed  Google Scholar 

  321. Bennett CF. Therapeutic antisense oligonucleotides are coming of age. Annu Rev Med. 2019;70:307–21.

    Article  CAS  PubMed  Google Scholar 

  322. Lee RG, Crosby J, Baker BF, et al. Antisense technology: an emerging platform for cardiovascular disease therapeutics. J Cardiovasc Transl Res. 2013;6(6):969–80.

    Article  PubMed  PubMed Central  Google Scholar 

  323. Stephenson ML, Zamecnik PC. Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide. Proc Nat Acad Sci U S A. 1978;75(1):285–8.

    Article  CAS  Google Scholar 

  324. Fortin M, D’Anjou H, Higgins ME, et al. A multi-target antisense approach against PDE4 and PDE7 reduces smoke-induced lung inflammation in mice. Respir Res. 2009;10(1):39.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  325. Burdick AD, Sciabola S, Mantena SR, et al. Sequence motifs associated with hepatotoxicity of locked nucleic acid–modified antisense oligonucleotides. Nucleic Acids Res. 2014;42:4882–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  326. Schuster S, Miesen P, van Rij RP. Antiviral RNAi in insects and mammals: Parallels and differences. Viruses. 2019;11:448.

    Article  CAS  PubMed Central  Google Scholar 

  327. Sharp PA. RNAi and double-strand RNA. Genes Dev. 1999:139–41.

    Google Scholar 

  328. Schwarz DS, Ding H, Kennington L, et al. Designing siRNA that distinguish between genes that differ by a single nucleotide. PLoS Genet. 2006;2:1307–18.

    Article  CAS  Google Scholar 

  329. Jackson AL, Linsley PS. Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nat Rev Drug Discov. 2010;9:57–67.

    Article  CAS  PubMed  Google Scholar 

  330. Grimm D. The dose can make the poison: Lessons learned from adverse in vivo toxicities caused by RNAi overexpression. Silence. 2011;2:8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  331. Chakraborty C, Sharma AR, Sharma G, et al. Therapeutic miRNA and siRNA: Moving from bench to clinic as next generation medicine. Mol Ther Nucl Acid. 2017;8:132–43.

    Article  CAS  Google Scholar 

  332. Liu YP, Haasnoot J, Berkhout B. Design of extended short hairpin RNAs for HIV-1 inhibition. Nucl Acid Res. 2007;35:5683–93.

    Article  CAS  Google Scholar 

  333. Liu YP, von Eije KJ, Schopman NCT, et al. Combinatorial RNAi against HIV-1 using extended short hairpin RNAs. Mol Ther. 2009;17:1712–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  334. Lam JK, Chow MY, Zhang Y, et al. siRNA versus miRNA as therapeutics for gene silencing. Mol Ther Nucleic Acids. 2015;4:e252.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  335. Ren S, Liu Y, Xu W, et al. Long noncoding RNA MALAT-1 is a new potential therapeutic target for castration resistant prostate cancer. J Urol. 2013;190(6):2278–87.

    Article  CAS  PubMed  Google Scholar 

  336. Davis S, Lollo B, Freier S, et al. Improved targeting of miRNA with antisense oligonucleotides. Nucleic Acids Res. 2006;34:2294–304.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  337. Esau C, Davis S, Murray SF, et al. miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell Metab. 2006;3:87–98.

    Article  CAS  PubMed  Google Scholar 

  338. Ørom UA, Kauppinen S, Lund AH. LNA-modified oligonucleotides mediate specific inhibition of microRNA function. Gene. 2006;372:137–41.

    Article  PubMed  CAS  Google Scholar 

  339. Lennox KA, Behlke MA. A direct comparison of anti-microRNA oligonucleotide potency. Pharm Res. 2010;27:1788–99.

    Article  CAS  PubMed  Google Scholar 

  340. Elmén J, Lindow M, Schütz S, et al. LNA-mediated microRNA silencing in non-human primates. Nature. 2008;452:896–9.

    Article  PubMed  CAS  Google Scholar 

  341. Lanford RE, Hildebrandt-Eriksen ES, Petri A, et al. Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science. 2010;327:198–201.

    Article  CAS  PubMed  Google Scholar 

  342. Soutschek J, Akinc A, Bramlage B, et al. Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs. Nature. 2004;432:173–8.

    Article  CAS  PubMed  Google Scholar 

  343. Wolfrum C, Shi S, Jayaprakash KN, et al. Mechanisms and optimization of in vivo delivery of lipophilic siRNAs. Nat Biotechnol. 2007;25:1149–57.

    Article  CAS  PubMed  Google Scholar 

  344. Petrova NS, Chernikov IV, Meschaninova MI, et al. Carrier-free cellular uptake and the gene-silencing activity of the lipophilic siRNAs is strongly affected by the length of the linker between siRNA and lipophilic group. Nucleic Acids Res. 2012;40:2330–44.

    Article  CAS  PubMed  Google Scholar 

  345. Letsinger RL, Zhang G, Sun DK, et al. Cholesteryl-conjugated oligonucleotides: Synthesis, properties, and activity as inhibitors of replication of human immunodeficiency virus in cell culture. Proc Natl Acad Sci USA. 1989;86:6553–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  346. Ligtenberg MA, Pico de Coaña Y, Shmushkovich T, et al. Self-Delivering RNAi Targeting PD-1 Improves Tumor-Specific T Cell Functionality for Adoptive Cell Therapy of Malignant Melanoma. Mol Ther. 2018;26:1482–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  347. McNamara JO, Andrechek ER, Wang Y, et al. Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras. Nat. Biotechnol. 2006;24:1005–15.

    Article  CAS  PubMed  Google Scholar 

  348. Dassie JP, Liu XY, Thomas GS, et al. Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors. Nat Biotechnol. 2009;27:839–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  349. Zhou J, Swiderski P, Li H, et al. Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of Dicer substrate siRNAs into HIV infected cells. Nucleic Acids Res. 2009;37:3094–109.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  350. Morrissey DV, Lockridge JA, Shaw L, et al. Potent and persistent in vivo anti-HBV activity of chemically modified siRNAs. Nat Biotechnol. 2005;23(8):1002–7.

    Article  CAS  PubMed  Google Scholar 

  351. Kumar P, Ban HS, Kim SS, et al. T Cell-Specific siRNA Delivery Suppresses HIV-1 Infection in Humanized Mice. Cell. 2008;134:577–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  352. Song E, Zhu P, Lee SK, et al. Antibody mediated in vivo delivery of small interfering RNAs via cell-surface receptors. Nat Biotechnol. 2005;23:709–17.

    Article  CAS  PubMed  Google Scholar 

  353. Wagner RW. Gene inhibition using antisense oligodeoxynucleotides. Nature. 1994;372(6504):3339–5.

    Article  Google Scholar 

  354. Stein CA, Narayanan R. Antisense oligodeoxynucleotides. Curr Opin Oncol. 1994;6(6):587–94.

    Article  CAS  PubMed  Google Scholar 

  355. Mahato RI, Cheng K, Guntaka RV. Modulation of gene expression by antisense and antigene oligodeoxynucleotides and small interfering RNA. Expert Opin Drug Deliv. 2005;2(1):3–28.

    Article  CAS  PubMed  Google Scholar 

  356. Ghosh MK, Cohen JS. Oligodeoxynucleotides as antisense inhibitors of gene expression. Prog Nucleic Acid Res Mol Biol. 1992;42:79–126.

    Article  CAS  PubMed  Google Scholar 

  357. Feng J, Wible B, Li GR, et al. Antisense oligodeoxynucleotides directed against Kv1.5 mRNA specifically inhibit ultrarapid delayed rectifier K+ current in cultured adult human atrial myocytes. Circ Res. 1997;80(4):572–9.

    Article  CAS  PubMed  Google Scholar 

  358. Aboul-Fadl T. Antisense oligonucleotides: the state of the art. Curr Med Chem. 2005;12(19):2193–214.

    Article  CAS  PubMed  Google Scholar 

  359. Pirollo KF, Rait A, Sleer LS, Chang EH. Antisense therapeutics: from theory to clinical practice. Pharmacol Ther. 2003;99(1):55–77.

    Article  CAS  PubMed  Google Scholar 

  360. Agrawal S, Kandimalla ER. Antisense and/or immunostimulatory oligonucleotide therapeutics. Curr Cancer Drug Targets. 2001;1(3):197–209.

    Article  CAS  PubMed  Google Scholar 

  361. Bajan S, Hutvagner G. RNA-based therapeutics: From antisense oligonucleotides to miRNAs. Cells. 2020;9(1):137.

    Article  CAS  PubMed Central  Google Scholar 

  362. Allakhverdi Z, Allam M, Guimond A, et al. Multitargeted approach using antisense oligonucleotides for the treatment of asthma. Ann N Y Acad Sci. 2006;1082:62–73.

    Article  CAS  PubMed  Google Scholar 

  363. Zhang Y, **e X, Ma W, et al. Multi-targeted antisense oligonucleotide delivery by a framework nucleic acid for inhibiting biofilm formation and virulence. Nanomicro Lett. 2020;12(1):74.

    CAS  PubMed  PubMed Central  Google Scholar 

  364. Lewis K. Persister cells, dormancy and infectious disease. Nat Rev Microbiol. 2007;5(1):48–56.

    Article  CAS  PubMed  Google Scholar 

  365. Hall-Stoodley L, Costerton JW, et al. Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol. 2004;2(2):95–108.

    Article  CAS  PubMed  Google Scholar 

  366. Senadheera DB, Cordova M, Ayala EA, et al. Regulation of bacteriocin production and cell death by the VicRK signaling system in Streptococcus mutans. J Bacteriol. 2012;194(6):1307–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  367. Dubrac S, Msadek T. Identification of genes controlled by the essential YycG/YycF two-component system of Staphylococcus aureus. J Bacteriol. 2004;186(4):1175–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  368. Senadheera MD, Guggenheim B, Spatafora GA, et al. A VicRK signal transduction system in Streptococcus mutans affects gtfBCD, gbpB, and ftf expression, biofilm formation, and genetic competence development. J Bacteriol. 2005;187(12):4064–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  369. Bielinska A, Shivdasani RA, Zhang L, et al. Regulation of gene expression with double-stranded phosphorothioate oligonucleotides. Science. 1990;250:997–1000.

    Article  CAS  PubMed  Google Scholar 

  370. Morishita R, Gibbons GH, Horiuchi M, et al. A gene therapy strategy using a transcription factor decoy of the E2F binding site inhibits smooth muscle proliferation in vivo. Proc Natl Acad Sci USA. 1995;92:5855–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  371. Morishita R, Sugimoto T, Aoki M, et al. In vivo transfection of cis element “decoy” against nuclear factor-kappaB binding site prevents myocardial infarction. Nat Med. 1997;13:894–9.

    Article  Google Scholar 

  372. Gao H, **ao J, Yang B, et al. A single decoy oligodeoxynucleotides targeting multiple oncoproteins produces strong anti-cancer effects. Mol Pharmacol. 2006;70:1621–9.

    Article  CAS  PubMed  Google Scholar 

  373. Wang X, Liu Q, Hou B, et al. Concomitant targeting of multiple key transcription factors effectively disrupts cancer stem cells enriched in side population of human pancreatic cancer cells. PLoS One. 2013;8(9):e73942.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  374. Rad SM, Bamdad T, Sadeghizadeh M, et al. Transcription factor decoy against stem cells master regulators, Nanog and Oct-4: a possible approach for differentiation therapy. Tumour Biol. 2015;36(4):2621–9.

    Article  CAS  PubMed  Google Scholar 

  375. Swindell WR, Sarkar MK, Stuart PE, et al. Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites. Clin Transl Med. 2015;4:13.

    Article  PubMed  PubMed Central  Google Scholar 

  376. Johari B, Zargan J. Simultaneous targeted inhibition of Sox2-Oct4 transcription factors using decoy oligodeoxynucleotides to repress stemness properties in mouse embryonic stem cells. Cell Biol Int. 2017;41(12):1335–44.

    Article  CAS  PubMed  Google Scholar 

  377. Johari B, Rezaeejam H, Moradi M, et al. Increasing the colon cancer cells sensitivity toward radiation therapy via application of Oct4-Sox2 complex decoy oligodeoxynucleotides. Mol Biol Rep. 2020;47(9):6793–805.

    Article  CAS  PubMed  Google Scholar 

  378. Bigdelou Z, Mortazavi Y, Saltanatpour Z, et al. Role of Oct4-Sox2 complex decoy oligodeoxynucleotides strategy on reverse epithelial to mesenchymal transition (EMT) induction in HT29-ShE encompassing enriched cancer stem-like cells. Mol Biol Rep. 2020;47(3):1859–69.

    Article  CAS  PubMed  Google Scholar 

  379. Tehran MM, Rezaei S, Jalili A, et al. Decoy oligodeoxynucleotide technology: an emerging paradigm for breast cancer treatment. Drug Discov Today. 2020;25(1):195–200.

    Article  CAS  PubMed  Google Scholar 

  380. Osako MK, Nakagami H, Morishita R. Modification of decoy oligodeoxynucleotides to achieve the stability and therapeutic efficacy. Curr Top Med Chem. 2012;12(15):1603–7.

    Article  CAS  PubMed  Google Scholar 

  381. Morishita R, Aoki M, Kaneda Y. Decoy oligodeoxynucleotides as novel cardiovascular drugs for cardiovascular disease. Ann N Y Acad Sci. 2001;947:294–301.

    Article  CAS  PubMed  Google Scholar 

  382. Roth M. Transcription factors: Are they a real target for future therapeutic strategies? Pharmacologyonline. 2005;1:45–66.

    Google Scholar 

  383. Morishita R, Aoki M, KanedaY. Decoy oligodeoxynucleotides as novel cardiovascular drugs for cardiovascular disease. Ann NY Acad Sci. 2001;947:294–301.

    Article  CAS  PubMed  Google Scholar 

  384. Mann MJ, Dzau VJ. Therapeutic applications of transcription factor decoy oligonucleotides. J Clin Invest. 2000;106:1071–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  385. Martin TA, Goyal A, Watkins G, et al. Expression of the transcription factors snail, slug, and twist and their clinical significance in human breast cancer. Ann Surg Oncol. 2005;12:488–96.

    Article  PubMed  Google Scholar 

  386. Wang LH, Yang XY, Zhang X, et al. The cis decoy against the estrogen response element suppresses breast cancer cells via target disrupting c-fos not mitogen-activated protein kinase activity. Cancer Res. 2003;63:2046–51.

    CAS  PubMed  Google Scholar 

  387. Budhram-Mahadeo V, Ndisang D, Ward T, et al. The Brn-3b POU family transcription factor represses expression of the BRCA-1 antioncogene in breast cancer cells. Oncogene. 1999;18:6684–91.

    Article  CAS  PubMed  Google Scholar 

  388. Tripathi MK. Regulation of BRCA2 gene expression by the SLUG repressor protein in human breast cells. J Biol Chem. 2005;280:17163–71.

    Article  CAS  PubMed  Google Scholar 

  389. Suzuki YJ, Evans T. Regulation of cardiac myocyte apoptosis by the GATA-4 transcription factor. Life Sci. 2004;74:1829–38.

    Article  CAS  PubMed  Google Scholar 

  390. Kassiri Z, Oudit GY, Sanchez O, et al. Combination of tumor necrosis factor-alpha ablation and matrix metalloproteinase inhibition prevents heart failure after pressure overload in tissue inhibitor of metalloproteinase-3 knock-out mice. Circ Res. 2005;97:380–90.

    Article  CAS  PubMed  Google Scholar 

  391. Rosati B, Grau F, McKinnon D. Regional variation in mRNA transcript abundance within the ventricular wall. J Mol Cell Cardiol. 2006;40:295–302.

    Article  CAS  PubMed  Google Scholar 

  392. Costantini DL, Arruda EP, Agarwal P, et al. The homeodomain transcription factor Irx5 establishes the mouse cardiac ventricular repolarization gradient. Cell. 2006;23:347–58.

    Google Scholar 

  393. Mohibi S, Chen X, Zhang J. Cancer the ‘RBP’eutics-RNA-binding proteins as therapeutic targets for cancer. Pharmacol Ther. 2019;203:107390.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  394. DeJong ES, Luy B, Marino JP. RNA and RNA-protein complexes as targets for therapeutic intervention. Curr Top Med Chem. 2002;2(3):289–302.

    Article  CAS  PubMed  Google Scholar 

  395. Cheng MS, Su MX, Wang MX, et al. Probes and drugs that interfere with protein translation via targeting to the RNAs or RNA-protein interactions. Methods. 2019;167:124–33.

    Article  CAS  PubMed  Google Scholar 

  396. Baker JD, Uhrich RL, Strovas TJ, et al. Targeting pathological tau by Small molecule inhibition of the Poly(A):MSUT2 RNA-protein interaction. ACS Chem Neurosci. 2020;11(15):2277–85.

    Article  CAS  PubMed  Google Scholar 

  397. Hermann T. Strategies for the design of drugs targeting RNA and RNA-protein complexes. Angew Chem Int Ed Engl. 2000;39(11):1890–904.

    Article  CAS  PubMed  Google Scholar 

  398. Baudin F, Bach C, Cusack S, et al. Structure of influenza virus RNP. I. Influenza virus nucleoprotein melts secondary structure in panhandle RNA and exposes the bases to the solvent. EMBO J. 1994;13(13):3158–65.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  399. Lukong KE, Chang K-W, Khandjian EW, et al. RNA-binding proteins in human genetic disease. Trends Genet. 2008;24(8):416–25.

    Article  CAS  PubMed  Google Scholar 

  400. Keene JD. RNA regulons: coordination of post-transcriptional events. Nat Rev Genet. 2007;8(7):533–43.

    Article  CAS  PubMed  Google Scholar 

  401. Zhang J, Chen X. Posttranscriptional regulation of p53 and its targets by RNA-binding proteins. Curr Mol Med. 2008;8(8):845–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  402. Kechavarzi B, Janga SC. Dissecting the expression landscape of RNA-binding proteins in human cancers. Genome Biol. 2014;15(1):R14.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  403. Neelamraju Y, Gonzalez-Perez A, Bhat-Nakshatri P, et al. Mutational landscape of RNA-binding proteins in human cancers. RNA Biol. 2018;15(1):115–29.

    Article  PubMed  Google Scholar 

  404. Pereira B, Billaud M, Almeida R. RNA-binding proteins in cancer: Old players and new actors. Trends Cancer. 2017;3(7):506–28.

    Article  CAS  PubMed  Google Scholar 

  405. Lunde BM, Moore C, Varani G. RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol. 2007;8(6):479–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  406. Baltz AG, Munschauer M, Schwanhäusser B, et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell. 2012;46(5):674–90.

    Article  CAS  PubMed  Google Scholar 

  407. Castello A, Fischer B, Eichelbaum K, et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell. 2012;149(6):1393–406.

    Article  CAS  PubMed  Google Scholar 

  408. Gerstberger S, Hafner M, Tuschl T. A census of human RNA-binding proteins. Nat Rev Genet. 2014;15(12):829–45.

    Article  CAS  PubMed  Google Scholar 

  409. Wang ZL, Li B, Luo YX, et al. Comprehensive genomic characterization of RNA-binding proteins across human cancers. Cell Rep. 2018;22(1):286–98.

    Article  CAS  PubMed  Google Scholar 

  410. Hentze MW, Castello A, Schwarzl T, et al. A brave new world of RNA-binding proteins. Nat Rev Mol Cell Biol. 2018;19(5):327–41.

    Article  CAS  PubMed  Google Scholar 

  411. Moore S, Järvelin AI, Davis I, et al. Expanding horizons: new roles for non-canonical RNA-binding proteins in cancer. Curr Opin Genet Dev. 2018;48:112–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  412. Bank, RCSB Protein data. RCSB Protein Data Bank-RCSB PDB. Retrieved 2021-08-28.

    Google Scholar 

  413. Lewis BA, Walia RR, Terribilini M, et al. PRIDB: a protein–RNA interface database. Nucleic Acids Res. 2016;39:D277–82.

    Article  CAS  Google Scholar 

  414. Stein CA, Castanotto D. FDA-approved oligonucleotide therapies in 2017. Mol Ther. 2017;25(5):1069–75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  415. Hua Y, Sahashi K, Hung G, et al. Antisense correction of SMN2 splicing in the CNS rescues necrosis in a type III SMA mouse model. Genes Dev. 2010;24(15):1634–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  416. Rigo F, Hua Y, Krainer AR, et al. Antisense-based therapy for the treatment of spinal muscular atrophy. J Cell Biol. 2012;199(1):21–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  417. Chiriboga CA, Swoboda KJ, Darras BT, et al. Results from a phase 1 study of nusinersen (ISIS-SMN(Rx)) in children with spinal muscular atrophy. Neurology. 2016;86(10):890–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  418. Mercuri E, Darras BT, Chiriboga CA, et al. CHERISH Study Group. Nusinersen versus sham control in later-onset spinal muscular atrophy. N Engl J Med. 2018;378(7):625–35.

    Article  CAS  PubMed  Google Scholar 

  419. Nussbacher JK, Tabet R, Yeo GW, et al. Disruption of RNA metabolism in neurological diseases and emerging therapeutic interventions. Neuron. 2019;102(2):294–320.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  420. Hong DS, Kurzrock R, Oh Y, et al. A phase 1 dose escalation, pharmacokinetic, and pharmacodynamic evaluation of eIF-4E antisense oligonucleotide LY2275796 in patients with advanced cancer. Clin Cancer Res. 2011;17(20):6582–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  421. Duffy AG, Makarova-Rusher OV, Ulahannan SV, et al. Modulation of tumor eIF4E by antisense inhibition: A phase I/II translational clinical trial of ISIS 183750-an antisense oligonucleotide against eIF4E-in combination with irinotecan in solid tumors and irinotecan-refractory colorectal cancer. Int J Cancer. 2016;139(7):1648–57.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  422. Fox RG, Lytle NK, Jaquish DV, et al. Image-based detection and targeting of therapy resistance in pancreatic adenocarcinoma. Nature. 2016;534(7607):407–11.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  423. Muralidharan R, Babu A, Amreddy N, et al. Tumor-targeted nanoparticle delivery of HuR siRNA inhibits lung tumor growth in vitro and in vivo by disrupting the oncogenic activity of the RNA-binding protein HuR. Mol Can Therapeut. 2017;16(8):1470–86.

    Article  CAS  Google Scholar 

  424. Jimbo M, Blanco FF, Huang YH, et al. Targeting the mRNA-binding protein HuR impairs malignant characteristics of pancreatic ductal adenocarcinoma cells. Oncotarget. 2015;6(29):27312–31.

    Article  PubMed  PubMed Central  Google Scholar 

  425. Mehta M, Basalingappa K, Griffith JN, et al. HuR silencing elicits oxidative stress and DNA damage and sensitizes human triple-negative breast cancer cells to radiotherapy. Oncotarget. 2016;7(40):64820–35.

    Article  PubMed  PubMed Central  Google Scholar 

  426. Huang YH, Peng W, Furuuchi N, et al. Delivery of therapeutics targeting the mRNA-binding protein HuR using 3DNA nanocarriers suppresses ovarian tumor growth. Cancer Res. 2016;76(6):1549–59.

    Article  CAS  PubMed  Google Scholar 

  427. Dong K, Wang R, Wang X, et al. Tumor-specific RNAi targeting eIF4E suppresses tumor growth, induces apoptosis and enhances cisplatin cytotoxicity in human breast carcinoma cells. Breast Cancer Res Treat. 2009;113(3):443–56.

    Article  CAS  PubMed  Google Scholar 

  428. Chen H, Liu J, Wang H, et al. Inhibition of RNA-binding protein musashi-1 suppresses malignant properties and reverses paclitaxel resistance in ovarian carcinoma. J Cancer. 2019;10(6):1580–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  429. Sheng W, Dong M, Chen C, et al. Musashi2 promotes the development and progression of pancreatic cancer by down-regulating Numb protein. Oncotarget. 2017;8(9):14359–73.

    Article  PubMed  Google Scholar 

  430. Sureban SM, May R, George RJ, et al. Knockdown of RNA binding protein musashi-1 leads to tumor regression in vivo. Gastroenterology. 2008;134(5):1448–58.

    Article  CAS  PubMed  Google Scholar 

  431. Bai X, Yang C, Jiao L, et al. LncRNA MIAT impairs cardiac contractile function by acting on mitochondrial translocator protein TSPO in a mouse model of myocardial infarction. Signal Transduct Target Ther. 2021;6(1):172.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  432. Mercer JR. Mitochondrial bioenergetics and therapeutic intervention in cardiovascular disease. Pharmacol Ther. 2014;141:13–20.

    Article  CAS  PubMed  Google Scholar 

  433. Morin D, Musman J, Pons S, et al. Mitochondrial translocator protein (TSPO): From physiology to cardioprotection. Biochem Pharmacol. 2016;105:1–13.

    Article  CAS  PubMed  Google Scholar 

  434. Ashwal-Fluss R, Meyer M, Pamudurti NR, et al. Circ RNA Biogenesis competes with Pre-mRNA splicing. Molecular Cell. 2014;56(1):55–66.

    Article  CAS  PubMed  Google Scholar 

  435. Abdelmohsen K, Panda AC, Munk R, et al. Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1. RNA Biology. 2017;14(3):361–9.

    Article  PubMed  PubMed Central  Google Scholar 

  436. Mascini M, Palchetti I, Tombelli S. Nucleic acid and peptide aptamers: Fundamentals and bioanalytical aspects. Angewandte Chemie International Edition. 2012;51(6):1316–32.

    Article  CAS  PubMed  Google Scholar 

  437. Zhou J, Rossi J. Aptamers as targeted therapeutics: Current potential and challenges. Nat Rev Drug Discov. 2017;16(3):181–202.

    Article  CAS  PubMed  Google Scholar 

  438. Nimjee SM, White RR, Becker RC, et al. Aptamers as therapeutics. Annu Rev Pharmacol Toxicol. 2017;57:61–79.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  439. Wu YX, Kwon YJ. Aptamers: The “evolution” of SELEX. Methods. 2016;106:21–8.

    Article  CAS  PubMed  Google Scholar 

  440. Reverdatto S, Burz DS, Shekhtman A. Peptide aptamers: development and applications. Curr Top Med Chem. 2015;15(12):1082–101.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  441. New RRC, Bui TTT, Bogus M. Binding interactions of peptide aptamers. Molecules. 2020;25(24):6055.

    Article  CAS  PubMed Central  Google Scholar 

  442. Li J, Tan S, Chen X, et al. Peptide aptamers with biological and therapeutic applications. Curr Med Chem. 2011;18(27):4215–22.

    Article  CAS  PubMed  Google Scholar 

  443. Baines IC, Colas P. Peptide aptamers as guides for small-molecule drug discovery. Drug Discov Today. 2006;11(7-8):334–41.

    Article  CAS  PubMed  Google Scholar 

  444. Hoppe-Seyler F, Crnkovic-Mertens I, Tomai E, et al. Peptide aptamers: specific inhibitors of protein function. Curr Mol Med. 2004;4(5):529–38.

    Article  CAS  PubMed  Google Scholar 

  445. Crawford M, Woodman R, Ko FP. Peptide aptamers: tools for biology and drug discovery. Brief Funct Genomic Proteomic. 2003;2(1):72–9.

    Article  CAS  PubMed  Google Scholar 

  446. Morita Y, Leslie M, Kameyama H, et al. Aptamer therapeutics in cancer: Current and future. Cancers (Basel). 2018;10(3):80.

    Article  PubMed Central  CAS  Google Scholar 

  447. Berger CM, Gaume X, Bouvet P. The roles of nucleolin subcellular localization in cancer. Biochimie. 2015;113:78–85.

    Article  CAS  PubMed  Google Scholar 

  448. Ireson CR, Kelland LR. Discovery and development of anticancer aptamers. Mol Can Therapeut. 2006;5(12):2957–62.

    Article  CAS  Google Scholar 

  449. Marqus S, Pirogova E, Piva TJ. Evaluation of the use of therapeutic peptides for cancer treatment. J Biomed Sci. 2017;24(1):21.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  450. Song YK, Guo H, Barengo N, et al. Inhibition of ovarian cancer growth by a tumor-targeting peptide that binds eukaryotic translation initiation factor 4E. Clin Can Res. 2009;15(13):4336–47.

    Article  CAS  Google Scholar 

  451. Lucchesi CA, Zhang J, Ma B, et al. Disruption of the RBM38-eIF4E complex with a synthetic peptide PEP8 increases p53 expression. Can Res. 2019;79(4):807–18.

    Article  CAS  Google Scholar 

  452. Zhang J, Cho SJ, Shu L, et al. Translational repression of p53 by RNPC1, a p53 target overexpressed in lymphomas. Genes Dev. 2011;25(14):1528–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  453. Ebner S, Trieb M, Schönfeld M, et al. Decoy peptides derived from the extracellular domain of toll-like receptor 2 (TLR2) show anti-inflammatory properties. Bioorg Med Chem. 2018;26(16):4615–23.

    Article  CAS  PubMed  Google Scholar 

  454. Piao W, Vogel SN, Toshchakov VY. Inhibition of TLR4 signaling by TRAM-derived decoy peptides in vitro and in vivo. J Immunol. 2013;190(5):2263–72.

    Article  CAS  PubMed  Google Scholar 

  455. Allette Y, Kim Y, Randolph A, et al. Decoy peptide targeted to the Toll-IL-1R domain inhibits LPS and TLR4-active metabolite morphine-3 glucuronide sensitization of sensory neurons. Sci Rep.;7(1): 3741.

    Google Scholar 

  456. Mantovani A, Locati M, Vecchi A, et al. Decoy receptors: a strategy to regulate inflammatory cytokines and chemokines. Trends Immunol. 2001;22(6):328–36.

    Article  CAS  PubMed  Google Scholar 

  457. Husain M, Becker EJ Jr, Bone NB, et al. NOX2 decoy peptides disrupt trauma-mediated neutrophil immunosuppression and protect against lethal peritonitis. Redox Biol. 2020;36:101651.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  458. Mahjoubin-Tehran M, Rezaei S, Jalili A, et al. Peptide decoys: a new technology offering therapeutic opportunities for breast cancer. Drug Discov Today. 2020;25(3):593–8.

    Article  CAS  PubMed  Google Scholar 

  459. Wu FY, Ou ZL, Feng LY, et al. Chemokine decoy receptor d6 plays a negative role in human breast cancer. Mol Cancer Res. 2008;6(8):1276–88.

    Article  CAS  PubMed  Google Scholar 

  460. Kwon YJ, Leibovitch BA, Bansal N, et al. Targeted interference of SIN3A-TGIF1 function by SID decoy treatment inhibits Wnt signaling and invasion in triple negative breast cancer cells. Oncotarget. 2016;8(51):88421–36.

    Article  PubMed  PubMed Central  Google Scholar 

  461. Zhang Y, Li D, Zhao X, et al. Decoy receptor 3 suppresses FasL-induced apoptosis via ERK1/2 activation in pancreatic cancer cells. Biochem Biophys Res Commun. 2015;463(4):1144–51.

    Article  CAS  PubMed  Google Scholar 

  462. Oh JG, Kim J, Jang SP, et al. Decoy peptides targeted to protein phosphatase 1 inhibit dephosphorylation of phospholamban in cardiomyocytes. J Mol Cell Cardiol. 2013;56:63–71.

    Article  CAS  PubMed  Google Scholar 

  463. Nabi AN, Biswas KB, Arai Y, et al. Functional characterization of the decoy peptide, [R10P]IFLKRMPSI[19P]. Front Biosci (Elite Ed). 2010;2:1211–7.

    Article  PubMed  Google Scholar 

  464. Mahjoubin-Tehran M, Rezaei S, Atkin SL, et al. Decoys as potential therapeutic tools for diabetes. Drug Discov Today. 2021;26(7):1669–79.

    Article  CAS  PubMed  Google Scholar 

  465. Ichihara A, Sakoda M, Kurauchi-Mito A, et al. Drug discovery for overcoming chronic kidney disease (CKD): new therapy for CKD by a (pro)renin-receptor-blocking decoy peptide. J Pharmacol Sci. 2009;109(1):20–3.

    Article  CAS  PubMed  Google Scholar 

  466. Chan KK, Tan TJC, Narayanan KK, et al. An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. Sci Adv. 2021;7(8):eabf1738.

    Article  PubMed  PubMed Central  Google Scholar 

  467. **g W, Procko E. ACE2-based decoy receptors for SARS coronavirus 2. Proteins. 2021;89(9):1065–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  468. Villard S, Piquer D, Raut S, et al. Low molecular weight peptides restore the procoagulant activity of factor VIII in the presence of the potent inhibitor antibody ESH8. J Biol Chem. 2002;277(30):27232–9.

    Article  CAS  PubMed  Google Scholar 

  469. Ananyeva NM, Lacroix-Desmazes S, Hauser CA, et al. Inhibitors in hemophilia A: mechanisms of inhibition, management and perspectives. Blood Coagul Fibrinolysis. 2004;15(2):109–24.

    Article  CAS  PubMed  Google Scholar 

  470. Schlesinger N. Anti-interleukin-1 therapy in the management of gout. Curr Rheumatol Rep. 2014;16(2):398.

    Article  PubMed  CAS  Google Scholar 

  471. Woods AS, Kaminski R, Oz M, et al. Decoy peptides that bind dynorphin noncovalently prevent NMDA receptor-mediated neurotoxicity. J Proteome Res. 2006;5(4):1017–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  472. Bechara C, Sagan S. Cell-penetrating peptides: 20 years later, where do we stand? FEBS letters. 2013;587:1693–702.

    Article  CAS  PubMed  Google Scholar 

  473. Guo Z, Peng H, Kang J, et al. Cell-penetrating peptides: Possible transduction mechanisms and therapeutic applications. Biomedical reports. 2016;4:528–34.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  474. Toshchakov VY, Javmen A. Targeting the TLR signalosome with TIR domain-derived cell-permeable decoy peptides: the current state and perspectives. Innate Immun. 2020;26(1):35–47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  475. Copolovici DM, Langel K, Eriste E, et al. Cell-penetrating peptides: design, synthesis, and applications. ACS Nano. 2014;8:1972–94.

    Article  CAS  PubMed  Google Scholar 

  476. Kauffman WB, Fuselier T, He J, et al. Mechanism matters: A taxonomy of cell penetrating peptides. Trends Biochem Sci. 2015;40:749–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  477. Heitz F, Morris MC, Divita G. Twenty years of cell-penetrating peptides: from molecular mechanisms to therapeutics. Br J Pharmacol. 2009;157:195–206.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  478. Milletti F. Cell-penetrating peptides: classes, origin, and current landscape. Drug discovery today. 2012;17:850–60.

    Article  CAS  PubMed  Google Scholar 

  479. Järver P, Langel K, El-Andaloussi S, et al. Applications of cell-penetrating peptides in regulation of gene expression. Biochem Soc Trans. 2007;35(Pt 4):770–4.

    Article  PubMed  Google Scholar 

  480. Toshchakov VY, Vogel SN. Cell-penetrating TIR BB loop decoy peptides a novel class of TLR signaling inhibitors and a tool to study topology of TIR-TIR interactions. Expert Opinion Biol Therapy. 2007;7:1035–50.

    Article  CAS  Google Scholar 

  481. Wirth T, Parker N, Ylä-Herttuala S. History of gene therapy. Gene. 2013;525(2):162–9.

    Article  CAS  PubMed  Google Scholar 

  482. Brody H. Gene therapy. Nature. 2018;564(7735):S5.

    Article  CAS  PubMed  Google Scholar 

  483. Ylä-Herttuala S. The pharmacology of gene therapy. Mol Ther. 2017;25(8):1731–2.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  484. Tang R, Xu Z. Gene therapy: a double-edged sword with great powers. Mol Cell Biochem. 2020;474(1-2):73–81.

    Article  CAS  PubMed  Google Scholar 

  485. Mullard A. Gene therapy boom continues. Nat Rev Drug Discov. 2019;18(10):737.

    PubMed  Google Scholar 

  486. Bak RO, Gomez-Ospina N, Porteus MH. Gene editing on center stage. Trends in Genetics. 2018;34(8):600–11.

    Article  CAS  PubMed  Google Scholar 

  487. Memi F, Ntokou A, Papangeli I. CRISPR/Cas9 gene-editing: Research technologies, clinical applications and ethical considerations. Semin Perinatol. 2018;42(8):487–500.

    Article  PubMed  Google Scholar 

  488. Sanches-da-Silva GN, Medeiros LF, Lima FM. The potential use of the CRISPR-Cas system for HIV-1 gene therapy. Intl J Genom. 2019;2019:8458263.

    Google Scholar 

  489. Cavazzana-Calvo M, Thrasher A, Mavilio F. The future of gene therapy. Nature. 2004;427:779–81.

    Article  CAS  PubMed  Google Scholar 

  490. Kotani H, Kmiec EB. A role for RNA synthesis in homologous pairing events. Mol Cell Biol. 1994;14:6097–106.

    CAS  PubMed  PubMed Central  Google Scholar 

  491. Yoon K, Cole-Strauss A, Kmiec EB. Targeted gene correction of episomal DNA in mammalian cells mediated by a chimeric RNA/DNA oligonucleotide. Proc Natl Acad Sci USA. 1996;93:2071–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  492. Andersen MS, Sorensen CB, Bolund L, et al. Mechanisms underlying targeted gene correction using chimeric RNA/DNA and single-stranded DNA oligonucleotides. J Mol Med. 2002;80:770–81.

    Article  CAS  PubMed  Google Scholar 

  493. Leclerc X, Danos O, Scherman D, et al. A comparison of synthetic oligodeoxynucleotides, DNA fragments and AAV-1 for targeted episomal and chromosomal gene repair. BMC Biotechnol. 2009;9:35.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  494. Liu X, Yan Z, Luo M, et al. Targeted correction of single-base-pair mutations with adeno-associated virus vectors under nonselective conditions. J Virol. 2004;78:4165–75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  495. Urnov FD, Miller JC, Lee YL, et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature. 2005;435:646–51.

    Article  CAS  PubMed  Google Scholar 

  496. Gruenert DC, Bruscia E, Novelli G, et al. Sequence-specific modification of genomic DNA by small DNA fragments. J Clin Invest. 2003;112:637–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  497. Nickerson HD, Colledge WH. A comparison of gene repair strategies in cell culture using a lacZ reporter system. Gene Ther. 2003;10:1584–91.

    Article  CAS  PubMed  Google Scholar 

  498. Bertoni C, Morris GE, Rando TA. Strand bias in oligonucleotide-mediated dystrophin gene editing. Hum Mol Genet. 2005;14:221–33.

    Article  CAS  PubMed  Google Scholar 

  499. Katada H, Komiyama M. Artificial restriction DNA cutters as new tools for gene manipulation. Chembiochem. 2009;10:1279–88.

    Article  CAS  PubMed  Google Scholar 

  500. Miller DG, Wang PR, Petek LM, et al. Gene targeting in vivo by adeno-associated virus vectors. Nat Biotechnol. 2006;24:1022–6.

    Article  CAS  PubMed  Google Scholar 

  501. Olsen PA, Solhaug A, Booth JA, et al. Cellular responses to targeted genomic sequence modification using single-stranded oligonucleotides and zinc-finger nucleases. DNA Repair (Amst). 2009;8:298–308.

    Article  CAS  Google Scholar 

  502. Engstrom JU, Suzuki T, Kmiec EB. Regulation of targeted gene repair by intrinsic cellular processes. Bioessays. 2009;31:159–68.

    Article  CAS  PubMed  Google Scholar 

  503. Igoucheva O, Peritz AE, Levy D, et al. A sequence-specific gene correction by an RNA-DNA oligonucleotide in mammalian cells characterized by transfection and nuclear extract using a lacZ shuttle system. Gene Ther. 1999;6:1960–71.

    Article  CAS  PubMed  Google Scholar 

  504. Radecke S, Radecke F, Peter I, et al. Physical incorporation of a single-stranded oligodeoxynucleotide during targeted repair of a human chromosomal locus. J Gene Med. 2006;8:217–28.

    Article  CAS  PubMed  Google Scholar 

  505. Parekh-Olmedo H, Ferrara L, Brachman E, et al. Gene therapy progress and prospects: targeted gene repair. Gene Ther. 2005;12:639–46.

    Article  CAS  PubMed  Google Scholar 

  506. Maguire KK, Kmiec EB. Multiple roles for MSH2 in the repair of a deletion mutation directed by modified single-stranded oligonucleotides. Gene. 2007;386:107–14.

    Article  CAS  PubMed  Google Scholar 

  507. Pierce EA, Liu Q, Igoucheva O, et al. Oligonucleotide-directed single-base DNA alterations in mouse embryonic stem cells. Gene Ther. 2003;10:24–33.

    Article  CAS  PubMed  Google Scholar 

  508. Dekker M, Brouwers C, te Riele H. Targeted gene modification in mismatch-repair-deficient embryonic stem cells by single-stranded DNA oligonucleotides. Nucleic Acids Res. 2003;31:e27.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  509. Parekh-Olmedo H, Kmiec EB. Progress and prospects: targeted gene alteration (TGA). Gene Ther. 2007;14:1675–80.

    Article  CAS  PubMed  Google Scholar 

  510. Bonner M, Kmiec EB. DNA breakage associated with targeted gene alteration directed by DNA oligonucleotides. Mutat Res. 2009;669:85–94.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  511. Gamper HB Jr, Cole-Strauss A, Metz R, et al. A plausible mechanism for gene correction by chimeric oligonucleotides. Biochemistry. 2000;39:5808–16.

    Article  CAS  PubMed  Google Scholar 

  512. Cole-Strauss A, Gamper H, Holloman WK, et al. Targeted gene repair directed by the chimeric RNA/DNA oligonucleotide in a mammalian cell-free extract. Nucleic Acids Res. 1999;27:1323–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  513. Zayed H, McIvor RS, Wiest DL, et al. In vitro functional correction of the mutation responsible for murine severe combined immune deficiency by small fragment homologous replacement. Hum Gene Ther. 2006;17:158–66.

    Article  CAS  PubMed  Google Scholar 

  514. Sangiuolo F, Scaldaferri ML, Filareto A, et al. Cftr gene targeting in mouse embryonic stem cells mediated by Small Fragment Homologous Replacement (SFHR). Front Biosci. 2008;13:2989–99.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  515. Bedayat B, Abdolmohamadi A, Ye L, et al. Sequence-specific correction of genomic hypoxanthine-guanine phosphoribosyl transferase mutations in lymphoblasts by small fragment homologous replacement. Oligonucleotides. 2010;20:7–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  516. Gatz SA, Wiesmuller L. p53 in recombination and repair. Cell Death Differ. 2006;13:1003–16.

    Article  CAS  PubMed  Google Scholar 

  517. Tsuchiya H, Harashima H, Kamiya H. Increased SFHR gene correction efficiency with sense single-stranded DNA. J Gene Med. 2005;7:486–93.

    Article  CAS  PubMed  Google Scholar 

  518. Goncz KK, Prokopishyn NL, Abdolmohammadi A, et al. Small fragment homologous replacement-mediated modification of genomic beta-globin sequences in human hematopoietic stem/progenitor cells. Oligonucleotides. 2006;16:213–24.

    Article  CAS  PubMed  Google Scholar 

  519. Gruenert DC. Gene correction with small DNA fragments. Curr Res Mol Ther. 1998;1:607–13.

    CAS  Google Scholar 

  520. Colosimo A, Guida V, Antonucci I, et al. Sequence-specific modification of a beta-thalassemia locus by small DNA fragments in human erythroid progenitor cells. Haematologica. 2007;92:129–30.

    Article  CAS  PubMed  Google Scholar 

  521. Todaro M, Quigley A, Kita M, et al. Effective detection of corrected dystrophin loci in mdx mouse myogenic precursors. Hum Mutat. 2007;28:816–23.

    Article  CAS  PubMed  Google Scholar 

  522. Mcnab GL, Ahmad A, Mistry D, et al. Modification of gene expression and increase in alpha1-antitrypsin (alpha1-AT) secretion after homologous recombination in alpha1-AT-deficient monocytes. Hum Gene Ther. 2007;18:1171–7.

    Article  CAS  PubMed  Google Scholar 

  523. Sangiuolo F, Filareto A, Spitalieri P, et al. In vitro restoration of functional SMN protein in human trophoblast cells affected by spinal muscular atrophy by small fragment homologous replacement. Hum Gene Ther. 2005;16:869–80.

    Article  CAS  PubMed  Google Scholar 

  524. Consortium TCFGA. World-wide survey of ΔF508 mutation—report from Cystic Fibrosis Genetic Analysis Consortium. Am J Hum Genet. 1990;47:354–7.

    Google Scholar 

  525. Bruscia E, Sangiuolo F, Sinibaldi P, et al. Isolation of CF cell lines corrected at DeltaF508-CFTR locus by SFHR-mediated targeting. Gene Ther. 2002;9:683–5.

    Article  CAS  PubMed  Google Scholar 

  526. Kunzelmann K, Legendre JY, Knoell DL, et al. Gene targeting of CFTR DNA in CF epithelial cells. Gene Ther. 1996;3:859–67.

    CAS  PubMed  Google Scholar 

  527. Sangiuolo F, Bruscia E, Serafino A, et al. In vitro correction of cystic fibrosis epithelial cell lines by small fragment homologous replacement (SFHR) technique. BMC Med Genet. 2002;3:8.

    Article  PubMed  PubMed Central  Google Scholar 

  528. Knauert MP, Glazer PM. Triplex forming oligonucleotides: sequence-specific tools for gene targeting. Hum Mol Genet. 2001;10(20):2243–51.

    Article  CAS  PubMed  Google Scholar 

  529. Kuan JY, Glazer PM. Targeted gene modification using triplex-forming oligonucleotides. Methods Mol Biol. 2004;262:173–94.

    CAS  PubMed  Google Scholar 

  530. Hélène C. The anti-gene strategy: control of gene expression by triplex-forming-oligonucleotides. Anticancer Drug Des. 1991;6(6):569–84.

    PubMed  Google Scholar 

  531. Hansen ME, Bentin T, Nielsen PE. High-affinity triplex targeting of double stranded DNA using chemically modified peptide nucleic acid oligomers. Nucleic Acids Res. 2009;37:4498–507.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  532. Chin JY, Glazer PM. Repair of DNA lesions associated with triplex-forming oligonucleotides. Mol Carcinog. 2009;48:389–99.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  533. Lonkar P, Kim KH, Kuan JY, et al. Targeted correction of a thalassemia-associated beta-globin mutation induced by pseudo-complementary peptide nucleic acids. Nucleic Acids Res. 2009;37:3635–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  534. Wang G, Seidman MM, Glazer PM. Mutagenesis in mammalian cells induced by triple helix formation and transcription-coupled repair. Science. 1996;271:802–5.

    Article  CAS  PubMed  Google Scholar 

  535. Felsenfeld G, Rich A. Studies on the formation of two- and three-stranded polyribonucleotides. Biochim Biophys Acta. 1957;26:457–68.

    Article  CAS  PubMed  Google Scholar 

  536. Kallenbach NR, Daniel WE Jr, Kaminker MA. Nuclear magnetic resonance study of hydrogen-bonded ring protons in oligonucleotide helices involving classical and nonclassical base pairs. Biochemistry. 1976;15:1218–24.

    Article  CAS  PubMed  Google Scholar 

  537. Wang G, Glazer PM. Altered repair of targeted psoralen photo-adducts in the context of an oligonucleotide-mediated triple helix. J Biol Chem. 1995;270:22595–601.

    Article  CAS  PubMed  Google Scholar 

  538. Vasquez KM, Dagle JM, Weeks DL, et al. Chromosome targeting at short polypurine sites by cationic triplex-forming oligonucleotides. J Biol Chem. 2001;276:38536–41.

    Article  CAS  PubMed  Google Scholar 

  539. Luo Z, Macris MA, Faruqi AF, et al. High-frequency intrachromosomal gene conversion induced by triplex-forming oligonucleotides microinjected into mouse cells. Proc Natl Acad Sci U S A. 2000;97:9003–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  540. Datta HJ, Glazer PM. Intracellular generation of single-stranded DNA for chromosomal triplex formation and induced recombination. Nucleic Acids Res. 2001;29:5140–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  541. Chan PP, Lin M, Faruqi AF, et al. Targeted correction of an episomal gene in mammalian cells by a short DNA fragment tethered to a triplex-forming oligonucleotide. J Biol Chem. 1999;274:11541–8.

    Article  CAS  PubMed  Google Scholar 

  542. Maurisse R, Feugeas JP, Biet E, et al. A new method (GOREC) for directed mutagenesis and gene repair by homologous recombination. Gene Ther. 2002;9:703–7.

    Article  CAS  PubMed  Google Scholar 

  543. Culver KW, Hsieh WT, Huyen Y, et al. Correction of chromosomal point mutations in human cells with bifunctional oligonucleotides. Nat Biotechnol. 1999;17:989–93.

    Article  CAS  PubMed  Google Scholar 

  544. Datta HJ, Chan PP, Vasquez KM, et al. Triplex-induced recombination in human cell-free extracts. Dependence on XPA and HsRad51. J Biol Chem. 2001;276:18018–23.

    Article  CAS  PubMed  Google Scholar 

  545. Goni JR, De La Cruz X, Orozco M. Triplex-forming oligonucleotide target sequences in the human genome. Nucleic Acids Res. 2004;32:354–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  546. Simon P, Cannata F, Concordet JP, et al. Targeting DNA with triplex-forming oligonucleotides to modify gene sequence. Biochimie. 2008;90:1109–16.

    Article  CAS  PubMed  Google Scholar 

  547. Chin JY, Kuan JY, Lonkar PS, et al. Correction of a splice-site mutation in the beta-globin gene stimulated by triplex-forming peptide nucleic acids. Proc Natl Acad Sci USA. 2008;105:13514–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  548. Nielsen PE. PNA Technology. Mol Biotechnol. 2004;26:233–48.

    Article  CAS  PubMed  Google Scholar 

  549. Bentin T, Nielsen PE. Superior duplex DNA strand invasion by acridine conjugated peptide nucleic acids. J Am Chem Soc. 2003;125:6378–9.

    Article  CAS  PubMed  Google Scholar 

  550. Kim KH, Nielsen PE, Glazer PM. Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids. Nucleic Acids Res. 2007;35:7604–13.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  551. Nielsen PE, Egholm M, Buchardt O. Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement. J Mol Recognit. 1994;7:165–70.

    Article  CAS  PubMed  Google Scholar 

  552. Yamamoto Y, Yoshida J, Tedeschi T, et al. Highly efficient strand invasion by peptide nucleic acid bearing optically pure lysine residues in its backbone. Nucleic Acids Symp Ser (Oxf). 2006; pp109–10.

    Google Scholar 

  553. Coura RS, Nardi NB. The state of the art of adeno-associated virus-based vectors in gene therapy. Virol J. 2007;4:99.

    Article  PubMed Central  CAS  Google Scholar 

  554. Vasileva A, Linden RM, Jessberger R. Homologous recombination is required for AAV-mediated gene targeting. Nucleic Acids Res. 2006;34:3345–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  555. Gellhaus K, Cornu TI, Heilbronn R, et al. Fate of recombinant adeno-associated viral vector genomes during DNA double-strand break-induced gene targeting in human cells. Hum Gene Ther. 2010;21:543–53.

    Article  CAS  PubMed  Google Scholar 

  556. Chamberlain JR, Deyle DR, Schwarze U, et al. Gene targeting of mutant COL1A2 alleles in mesenchymal stem cells from individuals with osteogenesis imperfecta. Mol Ther. 2008;16:187–93.

    Article  CAS  PubMed  Google Scholar 

  557. Khan IF, Hirata RK, Wang PR, et al. Engineering of human pluripotent stem cells by AAV-mediated gene targeting. Mol Ther. 2010;18:1192–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  558. Paiboonsukwong K, Ohbayashi F, Shiiba H, et al. Correction of mutant Fanconi anemia gene by homologous recombination in human hematopoietic cells using adeno-associated virus vector. J Gene Med. 2009;11:1012–9.

    Article  CAS  PubMed  Google Scholar 

  559. Mitsui K, Suzuki K, Aizawa E, et al. Gene targeting in human pluripotent stem cells with adeno-associated virus vectors. Biochem Biophys Res Commun. 2009;388:711–7.

    Article  CAS  PubMed  Google Scholar 

  560. Macielag MJ. Chemical properties of antibacterials and their uniqueness. In: Dougherty TJ, Pucci MJ (eds). Antibiotic Discovery and Development. 2012; pp. 801–2.

    Google Scholar 

  561. Ngo HX, Garneau-Tsodikova S. What are the drugs of the future? MedChemComm. 2018;9(5):757–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  562. Arkin MR, Wells JA. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov. 2004;3(4):301–17.

    Article  CAS  PubMed  Google Scholar 

  563. Veber DF, Johnson SR, Cheng HY, et al. Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem. 2002;45(12):2615–23.

    Article  CAS  PubMed  Google Scholar 

  564. Lipinski CA. Lead-and drug-like compounds: the rule-of-five revolution. Drug Discov Today: Technol. 2004;1(4):337–41.

    Article  CAS  Google Scholar 

  565. Leeson PD, Springthorpe B. The influence of drug-like concepts on decision-making in medicinal chemistry. Nat Rev Drug Discov. 2007;6(11):881–90.

    Article  CAS  PubMed  Google Scholar 

  566. Samanen J. Chapter 5.2 How do SMDs differ from biomolecular drugs? In Ganellin CR, Jefferis R, Roberts SM (eds.). Introduction to Biological and Small Molecule Drug Research and Development: theory and case studies (Kindle ed.). New York: Academic Press. 2013; pp161–203.

    Google Scholar 

  567. Santos R, Ursu O, Gaulton A, et al. A comprehensive map of molecular drug targets. Nat Rev Drug Discov. 2017;16(1):19–34.

    Article  CAS  PubMed  Google Scholar 

  568. Usmani SS, Bedi G, Samuel JS, et al. THPdb: Database of FDA-approved peptide and protein therapeutics. PLoS One. 2017;12(7):e0181748.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  569. Yin W, Rogge M. Targeting RNA: A transformative therapeutic strategy. Clin Transl Sci. 2019;12(2):98–112.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  570. Warner KD, Hajdin CE, Weeks KM. Principles for targeting RNA with drug-like small molecules. Nat Rev Drug Discov. 2018;17(8):547–58.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  571. Yu AM, Choi YH, Tu MJ. RNA drugs and RNA targets for small molecules: principles, progress, and challenges. Pharmacol Rev. 2020;72(4):862–98.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  572. Clamp M. Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA. 2007;104:19428–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  573. Ezkurdia I. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Hum Mol Genet. 2014;23:5866–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  574. Hopkins AL, Groom CR. The druggable genome. Nat Rev Drug Discov. 2002;1:727–30.

    Article  CAS  PubMed  Google Scholar 

  575. Overington JP, Al-Lazikani B, Hopkins AL. How many drug targets are there? Nat Rev Drug Discov. 2006;5:993–6.

    Article  CAS  PubMed  Google Scholar 

  576. Dixon SJ, Stockwell BR. Identifying druggable disease-modifying gene products. Curr Opin Chem Biol. 2009;13:549–55.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  577. Santos R. A comprehensive map of molecular drug targets. Nat Rev Drug Discov. 2017;16:19–34.

    Article  CAS  PubMed  Google Scholar 

  578. Sharp PA. The centrality of RNA. Cell. 2009;136:577–80.

    Article  CAS  PubMed  Google Scholar 

  579. Cech TR, Steitz JA. The noncoding RNA revolution-trashing old rules to forge new ones. Cell. 2014;157:77–94.

    Article  CAS  PubMed  Google Scholar 

  580. Djebali S. Landscape of transcription in human cells. Nature. 2012;489:101–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  581. Adams BD, Parsons C, Walker L, et al. Targeting noncoding RNAs in disease. J Clin Invest. 2017;127:761–71.

    Article  PubMed  PubMed Central  Google Scholar 

  582. Harrow J. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012;22:1760–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  583. Wilson DN. The A-Z of bacterial translation inhibitors. Crit Rev Biochem Mol Biol. 2009;44:393–33.

    Article  CAS  PubMed  Google Scholar 

  584. Lin J, Zhou D, Steitz TA, et al. Ribosome-targeting antibiotics: modes of action, mechanisms of resistance, and implications for drug design. Annu Rev Biochem. 2018;87:451–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  585. Donlic A, Hargrove AE. Targeting RNA in mammalian systems with small molecules. Wiley Interdiscip Rev RNA. 2018;9:e1477.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  586. Hermann T. Small molecules targeting viral RNA. Wiley Interdiscip Rev RNA. 2016;7:726–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  587. McCown PJ, Corbino KA, Stav S, et al. Riboswitch diversity and distribution. RNA. 2017;23:995–1011.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  588. Cruz JA, Westhof E. The dynamic landscapes of RNA architecture. Cell. 2009;136:604–9.

    Article  CAS  PubMed  Google Scholar 

  589. Butcher SE, Pyle AM. The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Acc Chem Res. 2011;44:1302–11.

    Article  CAS  PubMed  Google Scholar 

  590. Jones CP, Ferré-D’Amaré AR. RNA quaternary structure and global symmetry. Trends Biochem Sci. 2015;40:211–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  591. Schlick T. Adventures with RNA graphs. Methods. 2018;143:16–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  592. Mustoe AM, Busan S, Rice GM, et al. Pervasive regulatory functions of mRNA structure revealed by high-resolution SHAPE probing. Cell. 2018;173:181–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  593. Morgan BS, Forte JE, Culver RN, et al. Discovery of key physicochemical, structural, and spatial properties of RNA-targeted bioactive ligands. Angew Chem Int Ed Engl. 2017;56:13498–502.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  594. Morgan BS, Forte JE, Hargrove AE. Insights into the development of chemical probes for RNA. Nucleic Acids Res. 2018;46:8025–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  595. Wilson DN. Ribosome-targeting antibiotics and mechanisms of bacterial resistance. Nat Rev Microbiol. 2014;12:35–48.

    Article  CAS  PubMed  Google Scholar 

  596. Steitz TA. A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol. 2008;9:242–53.

    Article  CAS  PubMed  Google Scholar 

  597. Lynch SR, Gonzalez RL, Puglisi JD. Comparison of X-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex. Structure. 2003;11:43–53.

    Article  CAS  PubMed  Google Scholar 

  598. Fourmy D, Recht MI, Blanchard SC, et al. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science. 1996;274:1367–71.

    Article  CAS  PubMed  Google Scholar 

  599. Demirci H, Murphy F IV, Murphy E, et al. A structural basis for streptomycin-induced misreading of the genetic code. Nat Commun. 2013;4:1355.

    Article  PubMed  CAS  Google Scholar 

  600. Kanazawa H, Baba F, Koganei M, et al. A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA. Nucleic Acids Res. 2017;45:12529–35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  601. Kondo J. A structural basis for the antibiotic resistance conferred by an A1408G mutation in 16S rRNA and for the antiprotozoal activity of aminoglycosides. Angew Chem Int Ed Engl. 2012;51:465–8.

    Article  CAS  PubMed  Google Scholar 

  602. Zhang X, Lai M, Chang W, et al. Structures and stabilization of kinetoplastid-specific split rRNAs revealed by comparing leishmanial and human ribosomes. Nat Commun. 2016;7:13223.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  603. Myasnikov AG, Kundhavai Natchiar S, et al. Structure-function insights reveal the human ribosome as a cancer target for antibiotics. Nat Commun. 2016;7:12856.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  604. Di Giorgio A, Duca M. Synthetic small-molecule RNA ligands: future prospects as therapeutic agents. MedChemComm. 2019;10:1242–55.

    Article  PubMed  PubMed Central  Google Scholar 

  605. Stevens M, De Clercq E, Balzarini J. The regulation of HIV-1 transcription: molecular targets for chemotherapeutic intervention. Med Res Rev. 2006;26:595–625.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  606. Kulinski T, Olejniczak M, Huthoff H, et al. The apical loop of the HIV-1 TAR RNA hairpin is stabilized by a cross-loop base pair. J Biol Chem. 2003;278:38892–901.

    Article  CAS  PubMed  Google Scholar 

  607. Le Grice SF. Targeting the HIV RNA genome: high-hanging fruit only needs a longer ladder. Curr Top Microbiol Immunol. 2015;389:147–69.

    PubMed  PubMed Central  Google Scholar 

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

    Google Scholar 

  609. Stelzer AC, Frank AT, Kratz JD, et al. Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. Nat Chem Biol. 2011;7:553–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  610. Dibrov SM, Parsons J, Carnevali M, et al. Hepatitis C virus translation inhibitors targeting the internal ribosomal entry site. J Med Chem. 2014;57:1694–707.

    Article  CAS  PubMed  Google Scholar 

  611. Plant EP, Pérez-Alvarado GC, Jacobs JL, et al. A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal. PLoS Biol. 2005;3:e172.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  612. Su MC, Chang CT, Chu CH, et al. An atypical RNA pseudoknot stimulator and an upstream attenuation signal for -1 ribosomal frameshifting of SARS coronavirus. Nucleic Acids Res. 2005;33:4265–75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  613. Park SJ, Kim YG, Park HJ. Identification of RNA pseudoknot-binding ligand that inhibits the -1 ribosomal frameshifting of SARS-coronavirus by structure-based virtual screening. J Am Chem Soc. 2011;133:10094–100.

    Article  CAS  PubMed  Google Scholar 

  614. Ritchie DB, Soong J, Sikkema WK, et al. Anti-frameshifting ligand reduces the conformational plasticity of the SARS virus pseudoknot. J Am Chem Soc. 2005;136:2196–9.

    Article  CAS  Google Scholar 

  615. Tucker BJ, Breaker RR. Riboswitches as versatile gene control elements. Curr Opin Struct Biol. 2005;15:342–8.

    Article  CAS  PubMed  Google Scholar 

  616. Hallberg ZF, Su Y, Kitto RZ, et al. Engineering and in vivo applications of riboswitches. Annu Rev Biochem. 2017;86:515–39.

    Article  CAS  PubMed  Google Scholar 

  617. Chauvier A, Picard-Jean F, Berger-Dancause JC, et al. Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation. Nat Commun. 2017;8:13892.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  618. Lee ER, Blount KF, Breaker RR. Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression. RNA Biol. 2009;6:187–94.

    Article  CAS  PubMed  Google Scholar 

  619. Winkler WC, Cohen-Chalamish S, Breaker RR. An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci USA. 2002;99:15908–13.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  620. Serganov A, Nudler E. A decade of riboswitches. Cell. 2013;152:17–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  621. Zhang R, Ou HY, Zhang CT. DEG: a database of essential genes. Nucleic Acids Res. 2004;32:D271–2.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  622. Serganov A, Huang L, Patel DJ. Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature. 2009;458:233–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  623. Howe JA, Wang H, Fischmann TO, et al. Selective small-molecule inhibition of an RNA structural element. Nature. 2015;526:672–7.

    Article  CAS  PubMed  Google Scholar 

  624. Ottesen EW. ISS-N1 makes the first FDA-approved drug for spinal muscular atrophy. Transl Neurosci. 2017;8:1–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  625. Aartsma-Rus A, Krieg AM. FDA approves eteplirsen for Duchenne muscular dystrophy: the next chapter in the eteplirsen saga. Nucleic Acid Ther. 2017;27:1–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  626. Naryshkin NA, Weetall M, Dakka A, et al. Motor neuron disease. SMN2 splicing modifiers improve motor function and longevity in mice with spinal muscular atrophy. Science. 2014;345:688–93.

    Article  CAS  PubMed  Google Scholar 

  627. Ratni H, Ebeling M, Baird J, et al. Discovery of risdiplam, a selective survival of motor neuron-2 (SMN2) gene splicing modifier for the treatment of spinal muscular atrophy (SMA). J Med Chem. 2018;61:6501–17.

    Article  CAS  PubMed  Google Scholar 

  628. Sturm S, Günther A, Jaber B, et al. A phase 1 healthy male volunteer single escalating dose study of the pharmacokinetics and pharmacodynamics of risdiplam (RG7916, RO7034067), a SMN2 splicing modifier. Br J Clin Pharmacol. 2019;85:181–93.

    Article  CAS  PubMed  Google Scholar 

  629. Palacino J, Swalley SE, Song C, et al. SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice. Nat Chem Biol. 2015;11:511–7.

    Article  CAS  PubMed  Google Scholar 

  630. Cheung AK, Hurley B, Kerrigan R, et al. Discovery of small molecule splicing modulators of survival motor neuron-2 (SMN2) for the treatment of spinal muscular atrophy (SMA). J Med Chem. 2018;61:11021–36.

    Article  CAS  PubMed  Google Scholar 

  631. Velagapudi SP, Gallo SM, Disney MD. Sequence-based design of bioactive small molecules that target precursor microRNAs. Nat Chem Biol. 2014;10:291–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  632. Velagapudi SP, Cameron MD, Haga CL, et al. Design of a small molecule against an oncogenic noncoding RNA. Proc Natl Acad Sci USA. 2016;113:5898–903.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  633. Li Y, Disney MD. Precise small molecule degradation of a noncoding RNA identifies cellular binding sites and modulates an oncogenic phenotype. ACS Chem Biol. 2018;13:3065–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  634. Costales MG, Hoch DG, Abegg D, Childs-Disney JL, Velagapudi SP, Adibekian A, Disney MD. (2019a) A designed small molecule inhibitor of a non-coding RNA sensitizes HER2 negative cancers to herceptin. J Am Chem Soc. 2019;141:2960–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  635. Costales MG, Haga CL, Velagapudi SP, et al. Small molecule inhibition of microRNA-210 reprograms an oncogenic hypoxic circuit. J Am Chem Soc. 2017;139:3446–55.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  636. Costales MG, Suresh B, Vishnu K, et al. Targeted degradation of a hypoxia-associated non-coding RNA enhances the selectivity of a small molecule interacting with RNA. Cell Chem Biol. 2019;26:1180–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  637. Velagapudi SP, Costales MG, Vummidi BR, et al. Approved anti-cancer drugs target oncogenic non-coding RNAs. Cell Chem Biol. 2018;25:1086–94.e7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  638. Brown JA, Bulkley D, Wang J, et al. Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. Nat Struct Mol Biol. 2014;21(7):633–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  639. Pedram Fatemi R, Salah-Uddin S, Modarresi F, et al. Screening for small-molecule modulators of long noncoding RNA-protein interactions using AlphaScreen. J Biomol Screen. 2015;20(9):1132–41.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  640. Fatemi RP, Velmeshev D, Faghihi MA. De-repressing LncRNA-targeted genes to upregulate gene expression: Focus on small molecule therapeutics. Mol Ther Nucleic Acids. 2014;3:e196.

    Article  PubMed  PubMed Central  Google Scholar 

  641. Bennett CF, Swayze EE. RNA targeting therapeutics: Molecular mechanisms of antisense oligonucleotides as a therapeutic platform. Annu Rev Pharmacol Toxicol. 2010;50(1):259–93.

    Article  CAS  PubMed  Google Scholar 

  642. Simone R, Balendra R, Moens TG, et al. G-quadruplex-binding small molecules ameliorate C9orf72 FTD/ALS pathology in vitro and in vivo. EMBO Mol Med. 2018;10:22–31.

    Article  CAS  PubMed  Google Scholar 

  643. Su Z, Zhang Y, Gendron TF, et al. Discovery of a biomarker and lead small molecules to target r(GGGGCC)-associated defects in c9FTD/ALS. Neuron. 2014;83:1043–50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  644. Disney MD, Liu B, Yang WY, et al. A small molecule that targets r(CGG)(exp) and improves defects in fragile X-associated tremor ataxia syndrome. ACS Chem Biol. 2012;7:1711–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  645. Qurashi A, Liu H, Ray L, et al. Chemical screen reveals small molecules suppressing fragile X premutation rCGG repeat-mediated neurodegeneration in Drosophila. Hum Mol Genet. 2012;21:2068–75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  646. Green KM, Sheth UJ, Flores BN, et al. High-throughput screening yields several small-molecule inhibitors of repeat-associated non-AUG translation. J Biol Chem. 2019;294:18624–38.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  647. Parkesh R, Childs-Disney JL, Nakamori M, et al. Design of a bioactive small molecule that targets the myotonic dystrophy type 1 RNA via an RNA motif-ligand database and chemical similarity searching. J Am Chem Soc. 2012;134:4731–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  648. Angelbello AJ, Rzuczek SG, Mckee KK, et al. Precise small-molecule cleavage of an r(CUG) repeat expansion in a myotonic dystrophy mouse model. Proc Natl Acad Sci USA. 2019;116:7799–804.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  649. Rzuczek SG, Colgan LA, Nakai Y, et al. Precise small-molecule recognition of a toxic CUG RNA repeat expansion. Nat Chem Biol. 2017;13:188–93.

    Article  CAS  PubMed  Google Scholar 

  650. Miglietta G, Cogoi S, Marinello J, et al. RNA G-quadruplexes in Kirsten Ras (KRAS) oncogene as targets for small molecules inhibiting translation. J Med Chem. 2017;60:9448–61.

    Article  CAS  PubMed  Google Scholar 

  651. Katsuda Y, Sato S, Asano L, et al. A small molecule that represses translation of G-quadruplex-containing mRNA. J Am Chem Soc. 2016;138:9037–40.

    Article  CAS  PubMed  Google Scholar 

  652. Zhang P, Park HJ, Zhang J, et al. Translation of the intrinsically disordered protein α-synuclein is inhibited by a small molecule targeting its structured mRNA. Proc Natl Acad Sci USA. 2020;117:1457–67.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  653. Liang X-H. Translation efficiency of mRNAs is increased by antisense oligonucleotides targeting upstream open reading frames. Nat Biotechnol. 2016;34:875–80.

    Article  CAS  PubMed  Google Scholar 

  654. Liang X-H. Antisense oligonucleotides targeting translation inhibitory elements in 5′ UTRs can selectively increase protein levels. Nucleic Acids Res. 2017;45:9528–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  655. Fellmann C, Gowen BG, Lin P-C, et al. Cornerstones of CRISPR-Cas in drug discovery and therapy. Nat Rev Drug Discov. 2017;16:89–100.

    Article  CAS  PubMed  Google Scholar 

  656. Childs-Disney JL, Disney MD. Approaches to validate and manipulate RNA targets with small molecules in cells. Annu Rev Pharmacol Toxicol. 2016;56:123–40.

    Article  CAS  PubMed  Google Scholar 

  657. Wakelin LP. Polyfunctional DNA intercalating agents. Med Res Rev. 1986;6:275–340.

    Article  CAS  PubMed  Google Scholar 

  658. Costales MG, Childs-Disney JL, Haniff HS, et al. How we think about targeting RNA with small molecules. J Med Chem. 2020;63(17):8880–900.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  659. Chaires JB. Drug-DNA interactions. Curr Opin Struc Biol. 1998;8:314–20.

    Article  CAS  Google Scholar 

  660. Graves DE. Targeting DNA through-covalent interactions of reversible binding drugs. Methods Enzymol. 2001;340:377–95.

    Article  CAS  PubMed  Google Scholar 

  661. Rehman SU, Sarwar T, Husain MA, et al. Studying non-covalent drug-DNA interactions. Arch Biochem Biophys. 2015;576:49–60.

    Article  PubMed  CAS  Google Scholar 

  662. Strekowski L, Wilson B. Noncovalent interactions with DNA: an overview. Mutat Res. 2007;623(1-2):3–13.

    Article  CAS  PubMed  Google Scholar 

  663. Turner PR, Denny WA. The genome as a drug target: sequence specific minor groove binding ligands. Curr Drug Targ. 2000;1:1–14.

    Article  CAS  Google Scholar 

  664. Geierstanger BH, Wemmer DE. Complexes of the minor groove of DNA. Annu Rev Biophys Biomol Struct. 1995;24:463–93.

    Article  CAS  PubMed  Google Scholar 

  665. Reddy BS, Sondhi SM, Lown JW. Synthetic DNA minor groove-binding drugs. Pharmacol Ther. 1999;84:1–111.

    Article  CAS  PubMed  Google Scholar 

  666. Dervan PB, Edelson BS. Recognition of the DNA minor groove by pyrrole-imidazole polyamides. Curr Opin Struct Biol. 2003;13:284–99.

    Article  CAS  PubMed  Google Scholar 

  667. Neidle S. Structural aspects of drug-DNA complexes: molecular modelling of intercalative interactions. Drugs Exp Clin Res. 1986;12(6-7):455–62.

    CAS  PubMed  Google Scholar 

  668. Trotta E, D’Ambrosio E, Ravagnan G, et al. Evidence for DAPI intercalation in CG sites of DNA oligomer [d(CGACGTCG)]2: a 1H NMR study. Nucleic Acids Res. 1995;23(8):1333–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  669. Dziegielewski J, Slusarski B, Konitz A, et al. Intercalation of imidazoacridinones to DNA and its relevance to cytotoxic and antitumor activity. Biochem Pharmacol. 2002;63(9):1653–62.

    Article  CAS  PubMed  Google Scholar 

  670. Misra VK, Honig B. On the magnitude of the electrostatic contribution to ligand-DNA interactions. Proc Nat Acad Sci USA. 1995;92:4691–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  671. Manning GS. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys. 1978;11:179–246.

    Article  CAS  PubMed  Google Scholar 

  672. Dogra S, Awasthi P, Tripathi S, et al. NMR-based structure of anticancer drug mitoxantrone stacked with terminal base pair of DNA hexamer sequence d-(ATCGAT)2. J Biomol Struct Dyn. 2014;32(7):1164–83.

    Article  CAS  PubMed  Google Scholar 

  673. Egger G, Liang G, Aparicio A, et al. Epigenetics in human disease and prospects for epigenetic therapy. Nature. 2004;429:457–63.

    Article  CAS  PubMed  Google Scholar 

  674. Holliday R. Epigenetics: A historical overview. Epigenetics. 2006;1(2):76–80.

    Article  PubMed  Google Scholar 

  675. Lorch Y, Maier-Davis B, Kornberg RD. Mechanism of chromatin remodeling. PNAS. 2010;107(8):3458–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  676. Lorch Y, Kornberg RD. Chromatin-remodeling for transcription. Q Rev Biophys. 2017;50:e5.

    Article  PubMed  Google Scholar 

  677. Kaur J, Daoud A, Eblen ST. Targeting chromatin remodeling for cancer therapy. Curr Mol Pharmacol. 2019;12(3):215–29.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  678. Lyko F. The DNA methyltransferase family: a versatile toolkit for epigenetic regulation. Nat Rev Genet. 2018;19(2):81–92.

    Article  CAS  PubMed  Google Scholar 

  679. Wu X, Zhang Y. TET-mediated active DNA demethylation: mechanism, function and beyond. Nat Rev Genet. 2017;18(9):517–34.

    Article  CAS  PubMed  Google Scholar 

  680. Mirfattah B, Herring J, Tang H, et al. Probes and targets of DNA methylation and demethylation in drug development. Curr Top Med Chem. 2017;17(15):1727–40.

    Article  CAS  PubMed  Google Scholar 

  681. Kohli RM, Zhang Y. TET enzymes, TDG and the dynamics of DNA demethylation. Nature. 2013;502(7472):472–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  682. Pastor WA, Aravind L, Rao A. TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol. 2013;14(6):341–56.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  683. Lu X, Zhao BS, He C. TET family proteins: oxidation activity, interacting molecules, and functions in diseases. Chem Rev. 2015;115(6):2225–39.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  684. Bannister AJ, Zegerman P, Partridge JF, et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature. 2001;410(6824):120–4.

    Article  CAS  PubMed  Google Scholar 

  685. Strahl BD, Allis CD. The language of covalent histone modifications. Nature. 2000;403(6765):41–5.

    Article  CAS  PubMed  Google Scholar 

  686. Grunstein M. Histone acetylation in chromatin structure and transcription. Nature. 1997;389(6649):349–52.

    Article  CAS  PubMed  Google Scholar 

  687. Roth SY, Denu JM, Allis CD. Histone acetyltransferases. Annu Rev Biochem. 2001;70:81–120.

    Article  CAS  PubMed  Google Scholar 

  688. Schneider A, Chatterjee S, Bousiges O, et al. Acetyltransferases (HATs) as targets for neurological therapeutics. Neurotherapeutics. 2013;10(4):568–88.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  689. Wang Y, Miao X, Liu Y, et al. Dysregulation of histone acetyltransferases and deacetylases in cardiovascular diseases. Oxid Med Cell Longev. 2014;2014:641979.

    Article  PubMed  PubMed Central  Google Scholar 

  690. Falkenberg KJ, Johnstone RW. Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders. Nat Rev Drug Discov. 2014;13(9):673–91.

    Article  CAS  PubMed  Google Scholar 

  691. Ropero S, Esteller M. The role of histone deacetylases (HDACs) in human cancer. Mol Oncol. 2007;1(1):19–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  692. Benedetti R, Conte M, Altucci L. Targeting Histone deacetylases in diseases: Where are we? Antioxid Redox Signal. 2015;23(1):99–126.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  693. Husmann D, Gozani O. Histone lysine methyltransferases in biology and disease. Nat Struct Mol Biol. 2019;26(10):880–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  694. McCabe MT, Mohammad HP, Barbash O, et al. Targeting Histone methylation in cancer. Cancer J. 2017;23(5):292–301.

    Article  CAS  PubMed  Google Scholar 

  695. Yi X, Jiang X, Li X, et al. Histone lysine methylation and congenital heart disease: From bench to bedside. Int J Mol Med. 2017;40(4):953–64.

    Article  CAS  PubMed  Google Scholar 

  696. Hashimoto H, Vertino PM, Cheng X. Molecular coupling of DNA methylation and histone methylation. Epigenomics. 2010;2(5):657–6.

    Article  CAS  PubMed  Google Scholar 

  697. Du J, Johnson LM, Jacobsen SE, et al. DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol. 2015;16(9):519–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  698. Michalak EM, Burr ML, Bannister AJ, et al. The roles of DNA, RNA and histone methylation in ageing and cancer. Nat Rev Mol Cell Biol. 2019;20(10):573–89.

    Article  CAS  PubMed  Google Scholar 

  699. Richart L, Margueron R. Drugging histone methyltransferases in cancer. Curr Opin Chem Biol. 2020;56:51–62.

    Article  CAS  PubMed  Google Scholar 

  700. Liu Q, Wang MW. Histone lysine methyltransferases as anti-cancer targets for drug discovery. Acta Pharmacol Sin. 2016;37(10):1273–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  701. Blanc RS, Richard S. Arginine methylation: The coming of age. Mol Cell. 2017;65(1):8–24.

    Article  CAS  PubMed  Google Scholar 

  702. Guccione E, Richard S. The regulation, functions and clinical relevance of arginine methylation. Nat Rev Mol Cell Biol. 2019;20(10):642–57.

    Article  CAS  PubMed  Google Scholar 

  703. Cha B, Jho EH. Protein arginine methyltransferases (PRMTs) as therapeutic targets. Expert Opin Ther Targets. 2012;16(7):651–64.

    Article  CAS  PubMed  Google Scholar 

  704. Zhang J, **g L, Li M, et al. Regulation of histone arginine methylation/demethylation by methylase and demethylase. Mol Med Rep. 2019;19(5):3963–71.

    CAS  PubMed  PubMed Central  Google Scholar 

  705. Hashizume R, Andor N, Ihara Y, et al. Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma. Nat Med. 2014;20(12):1394–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  706. Berry WL, Janknecht R. KDM4/JMJD2 histone demethylases: epigenetic regulators in cancer cells. Cancer Res. 2013;73(10):2936–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  707. Maiques-Diaz A, Somervaille TC. LSD1: biologic roles and therapeutic targeting. Epigenomics. 2016;8(8):1103–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  708. Harmeyer KM, Facompre ND, Herlyn M, et al. JARID1 histone demethylases: Emerging targets in cancer. Trends Cancer. 2017;3(10):713–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  709. Niu Y, Zhao X, Wu YS, et al. N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. Genomics Proteom Bioinform. 2013;11(1):8–17.

    Article  CAS  Google Scholar 

  710. Frye M, Harada BT, Behm M, et al. RNA modifications modulate gene expression during development. Science. 2018;361(6409):1346–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  711. Cantara WA, Crain PF, Rozenski J, et al. The RNA modification database, RNAMDB: 2011 update. Nucleic Acids Res. 2011;39:D195–201.

    Article  CAS  PubMed  Google Scholar 

  712. Czerwoniec A, Dunin-Horkawicz S, Purta E, et al. MODOMICS: a database of RNA modification pathways 2008 update. Nucleic Acids Res. 2009;37:D118–21.

    Article  CAS  PubMed  Google Scholar 

  713. Narayan P, Rottman FM. Methylation of mRNA. Adv Enzymol Relat Areas Mol Biol. 1992;65:255–85.

    CAS  PubMed  Google Scholar 

  714. Adams JM, Cory S. Modified nucleosides and bizarre 5′-termini in mouse myeloma mRNA. Nature. 1975;255:28–33.

    Article  CAS  PubMed  Google Scholar 

  715. Desrosiers RC, Friderici KH, Rottman FM. Characterization of Novikoff hepatoma mRNA methylation and heterogeneity in the methylated 5′ terminus. Biochemistry. 1975;14:4367–74.

    Article  CAS  PubMed  Google Scholar 

  716. Canaani D, Kahana C, Lavi S, et al. Identification and map** of N6-methyladenosine containing sequences in simian virus 40 RNA. Nucleic Acids Res. 1979;6:2879–99.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  717. Chen-Kiang S, Nevins JR, Darnell JE Jr. N-6-methyl-adenosine in adenovirus type 2 nuclear RNA is conserved in the formation of messenger RNA. J Mol Biol. 1979;135:733–52.

    Article  CAS  PubMed  Google Scholar 

  718. Traube FR, Carell T. The chemistries and consequences of DNA and RNA methylation and demethylation. RNA Biol. 2017;14(9):1099–107.

    Article  PubMed  PubMed Central  Google Scholar 

  719. Chen X, Sun YZ, Liu H, et al. RNA methylation and diseases: experimental results, databases, Web servers and computational models. Brief Bioinform. 2019;20(3):896–917.

    Article  CAS  PubMed  Google Scholar 

  720. Meyer KD, Saletore Y, Zumbo P, et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell. 2012;149:1635–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  721. Dominissini D, Moshitch-Moshkovitz S, Schwartz S, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 2012;485:201–6.

    Article  CAS  PubMed  Google Scholar 

  722. Chen XY, Zhang J, Zhu JS. The role of m6A RNA methylation in human cancer. Mol Cancer. 2019;18(1):103.

    Article  PubMed  PubMed Central  Google Scholar 

  723. Zhao W, Qi X, Liu L, et al. Epigenetic regulation of m6A modifications in human cancer. Mol Ther Nucleic Acids. 2020;19:405–12.

    Article  CAS  PubMed  Google Scholar 

  724. Qin Y, Li L, Luo E, et al. Role of m6A RNA methylation in cardiovascular disease. Int J Mol Med. 2020;46(6):1958–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  725. Zeng C, Huang W, Li Y, et al. Roles of METTL3 in cancer: mechanisms and therapeutic targeting. J Hematol Oncol. 2020;13(1):117.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  726. Ma S, Chen C, Ji X, et al. The interplay between m6A RNA methylation and noncoding RNA in cancer. J Hematol Oncol. 2019;12(1):121.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  727. Yue Y, Liu J, Cui X, et al. VIRMA mediates preferential m6a mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation. Cell Discov. 2018;4:10.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  728. Wen J, Lv R, Ma H, et al. Zc3h13 regulates nuclear RNA m6A methylation and mouse embryonic stem cell self-renewal. Mol Cell. 2018;69(6):1028–38.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  729. Patil DP, Chen CK, Pickering BF, et al. m6A RNA methylation promotes XIST-mediated transcriptional repression. Nature. 2016;537(7620):369–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  730. Liu J, Yue Y, Han D, et al. A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol. 2014;10(2):93–5.

    Article  CAS  PubMed  Google Scholar 

  731. Mendel M, Chen KM, Homolka D, et al. Methylation of structured RNA by the m6A writer METTL16 is essential for mouse embryonic development. Mol Cell. 2018;71(6):986–1000.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  732. Warda AS, Kretschmer J, Hackert P, et al. Human METTL16 is a N6-methyladenosine (m6A) methyltransferase that targets pre-mRNAs and various non-coding RNAs. EMBO Rep. 2017;18(11):2004–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  733. Pendleton KE, Chen B, Liu K, et al. The U6 snRNA m6A methyltransferase METTL16 regulates SAM synthetase intron retention. Cell. 2017;169(5):824–35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  734. Ignatova VV, Stolz P, Kaiser S, et al. The rRNA m6A methyltransferase METTL5 is involved in pluripotency and developmental programs. Genes Dev. 2020;34(9-10):715–29.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  735. van Tran N, Ernst FGM, Hawley BR, et al. The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112. Nucleic Acids Res. 2019;47(15):7719–33.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  736. Pinto R, Vagbo CB, Jakobsson ME, et al. The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA. Nucleic Acids Res. 2020;48(2):830–46.

    Article  CAS  PubMed  Google Scholar 

  737. Ren W, Lu J, Huang M, et al. Structure and regulation of ZCCHC4 in m6A-methylation of 28S rRNA. Nat Commun. 2019;10(1):5042.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  738. Ma H, Wang X, Cai J, et al. N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol. 2019;15(1):88–94.

    Article  CAS  PubMed  Google Scholar 

  739. Blanquart C, Linot C, Cartron PF, et al. Epigenetic metalloenzymes. Curr Med Chem. 2019;26(15):2748–85.

    Article  CAS  PubMed  Google Scholar 

  740. Zwergel C, Valente S, Jacob C, et al. Emerging approaches for histone deacetylase inhibitor drug discovery. Expert Opin Drug Discov. 2015;10(6):599–613.

    Article  CAS  PubMed  Google Scholar 

  741. Faria Freitas M, Cuendet M, Bertrand P. HDAC inhibitors: A 2013–2017 patent survey. Expert Opin Ther Pat. 2018;1–17

    Google Scholar 

  742. Yang XF, Zhao ZJ, Liu JJ, et al. SAHA and/or MG132 reverse the aggressive phenotypes of glioma cells: An in vitro and vivo study. Oncotarget. 2017;8(2):3156–69.

    Article  PubMed  Google Scholar 

  743. Glaser KB. HDAC inhibitors: clinical update and mechanism-based potential. Biochem Pharmacol. 2007;74(5):659–71.

    Article  CAS  PubMed  Google Scholar 

  744. Munster PN, Thurn KT, Thomas S, et al. A phase II study of the histone deacetylase inhibitor vorinostat combined with tamoxifen for the treatment of patients with hormone therapy-resistant breast cancer. Br J Cancer. 2011;104(12):1828–35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  745. Gore SD. Combination therapy with DNA methyltransferase inhibitors in hematologic malignancies. Nat Clin Pract Oncol. 2005; 2 Suppl1: S30–S35.

    Google Scholar 

  746. Berry DH, Fernbach DJ, Herson J, et al. Comparison of prednisolone, vincristine, methotrexate and 6-mercaptopurine vs. 6-mercaptopurine and prednisone maintenance therapy in childhood acute leukemia: A Southwest Oncology Group Study. Cancer. 1980;46(5):1098–103.

    Article  CAS  PubMed  Google Scholar 

  747. Hollenbach PW, Nguyen AN, Brady H, et al. A comparison of azacitidine and decitabine activities in acute myeloid leukemia cell lines. PLoS One. 2010;5(2):e9001.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  748. Han T, Zhuo M, Hu H, et al. Synergistic effects of the combination of 5-Aza-CdR and suberoylanilide hydroxamic acid on the anticancer property of pancreatic cancer. Oncol Rep. 2018;39(1):264–70.

    CAS  PubMed  Google Scholar 

  749. Meeran SM, Patel SN, Tollefsbol TO. Sulforaphane causes epigenetic repression of hTERT expression in human breast cancer cell lines. PLoS One. 2010;5(7):e11457.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  750. Paul B, Li Y, Tollefsbol TO. The Effects of combinatorial genistein and sulforaphane in breast tumor inhibition: Role in epigenetic regulation. Int J Mol Sci. 2018;19(6):1754.

    Article  PubMed Central  CAS  Google Scholar 

  751. Easwaran H, Tsai HC, Baylin SB. Cancer epigenetics: tumor heterogeneity, plasticity of stem-like states, and drug resistance. Mol Cell. 2014;54(5):716–27.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  752. Miller KM, Tjeertes JV, Coates J, et al. Human HDAC1 and HDAC2 function in the DNA-damage response to promote DNA nonhomologous end-joining. Nat Struct Mol Biol. 2010;17(9):1144–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  753. Lee JH, Choy ML, Ngo L, et al. Histone deacetylase inhibitor induces DNA damage, which normal but not transformed cells can repair. Proc Natl Acad Sci U S A. 2010;107(33):14639–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  754. Schiller JH, Harrington D, Belani CP, et al. Comparison of four chemotherapy regimens for advanced non-small-cell lung cancer. N Engl J Med. 2002;346(2):92–8.

    Article  CAS  PubMed  Google Scholar 

  755. Group NM-AC. Chemotherapy in addition to supportive care improves survival in advanced non-small-cell lung cancer: a systematic review and meta-analysis of individual patient data from 16 randomized controlled trials. J Clin Oncol. 2008;26(28):4617–25.

    Article  Google Scholar 

  756. D’Addario G, Pintilie M, Leighl NB, et al. Platinum-based versus non-platinum-based chemotherapy in advanced non-small-cell lung cancer: a meta-analysis of the published literature. J Clin Oncol. 2005;23(13):2926–36.

    Article  PubMed  CAS  Google Scholar 

  757. Mroz EA, Rocco JW. The challenges of tumor genetic diversity. Cancer. 2017;123(6):917–27.

    Article  PubMed  Google Scholar 

  758. Dumbrava EI, Meric-Bernstam F. Personalized cancer therapy-leveraging a knowledge base for clinical decision-making. Cold Spring Harb Mol Case Stud. 2018;4(2):a001578.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  759. Morphy R, Rankovic Z. Designed multiple ligands. An emerging drug discovery paradigm. J Med Chem. 2005;48(21):6523–43.

    Article  CAS  PubMed  Google Scholar 

  760. Chou TC. Theoretical basis, experimental design, and computerized simulation of synergism and antagonism in drug combination studies. Pharmacol Rev. 2006;58(3):621–81.

    Article  CAS  PubMed  Google Scholar 

  761. Wang DF, Helquist P, Wiech NL, et al. Toward selective histone deacetylase inhibitor design: homology modeling, docking studies, and molecular dynamics simulations of human class I histone deacetylases. J Med Chem. 2005;48(22):6936–47.

    Article  CAS  PubMed  Google Scholar 

  762. Butler KV, Kozikowski AP. Chemical origins of isoform selectivity in histone deacetylase inhibitors. Curr Pharm Des. 2008;14(6):505–28.

    Article  CAS  PubMed  Google Scholar 

  763. Rotili D, Tomassi S, Conte M, et al. Pan-histone demethylase inhibitors simultaneously targeting Jumonji C and lysine-specific demethylases display high anticancer activities. J Med Chem. 2014;57(1):42–55.

    Article  CAS  PubMed  Google Scholar 

  764. Dokmanovic M, Clarke C, Marks PA. Histone deacetylase inhibitors: overview and perspectives. Mol Cancer Res. 2007;5(10):981–9.

    Article  CAS  PubMed  Google Scholar 

  765. Inoue S, Riley J, Gant TW, et al. Apoptosis induced by histone deacetylase inhibitors in leukemic cells is mediated by Bim and Noxa. Leukemia. 2007;21(8):1773–82.

    Article  CAS  PubMed  Google Scholar 

  766. Zang L, Kondengaden SM, Zhang Q, et al. Structure based design, synthesis and activity studies of small hybrid molecules as HDAC and G9a dual inhibitors. Oncotarget. 2017;8(38):63187–207.

    Article  PubMed  PubMed Central  Google Scholar 

  767. Kargbo RB. Histone deacetylase inhibitors as treatment for targeting multiple components in cancer therapy. ACS Med Chem Lett. 2018;9(3):167–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  768. Wishart DS, Feunang YD, Guo AC, et al. DrugBank 5.0: A major update to the DrugBank database for 2018. Nucleic Acids Res. 2018;46:D1074–82.

    Article  CAS  PubMed  Google Scholar 

  769. Li YH, Yu CY, Li XX, et al. Therapeutic target database update 2018: Enriched resource for facilitating bench-to-clinic research of targeted therapeutics. Nucleic Acids Res. 2018;46:D1121–7.

    Article  CAS  PubMed  Google Scholar 

  770. Gaulton A, Hersey A, Nowotka M, et al. The ChEMBL database in 2017. Nucleic Acids Res. 2017;45:D945–54.

    Article  CAS  PubMed  Google Scholar 

  771. Kim S, Thiessen PA, Bolton EE, et al. PubChem substance and compound databases. Nucleic Acids Res. 2016;44:D1202–13.

    Article  CAS  PubMed  Google Scholar 

  772. Gilson MK, Liu T, Baitaluk M, et al. BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res. 2016;44:D1045–53.

    Article  CAS  PubMed  Google Scholar 

  773. Günther S, Kuhn M, Dunkel M, et al. SuperTarget and matador: Resources for exploring drug-target relationships. Nucleic Acids Res. 2008;36:D919–22.

    Article  PubMed  CAS  Google Scholar 

  774. Yıldırım MA, Goh K-I, Cusick ME, et al. Drug—target network. Nat Biotechnol. 2007;25:1119–26.

    Article  PubMed  CAS  Google Scholar 

  775. Cheng F, Liu C, Jiang J, et al. Prediction of drug-target interactions and drug repositioning via network-based inference. PLoS Comput Biol. 2012;8:e1002503.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  776. Lu J-J, Pan W, Hu Y-J, et al. Multi-target drugs: The trend of drug research and development. PLoS One. 2012;7:e40262.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  777. Santos R, Ursu O, Gaulton A, et al. A comprehensive map of molecular drug targets. Nat Rev Drug Discovery. 2016;16:19–34.

    Article  PubMed  CAS  Google Scholar 

  778. Hert KMJ, Irwin JJ, et al. Quantifying the Relationships among Drug Classes. J Chem Inf Model. 2008;48:755–65.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  779. Shi D, Khan F, Abagyan R. Extended multitarget pharmacology of anticancer drugs. J Chem Inf Model. 2019;59(6):3006–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  780. He S, Dong G, Wu S, et al. Small molecules simultaneously inhibiting p53-murine double minute 2 (MDM2) interaction and histone deacetylases (HDACs): Discovery of novel multitargeting antitumor agents. J Med Chem. 2018;61(16):7245–60.

    Article  CAS  PubMed  Google Scholar 

  781. Evans BE, Rittle KE, Bock MG, et al. Methods for drug discovery: development of potent, selective, orally effective cholecystokinin antagonists. J Med Chem. 1988;31(12):2235–46.

    Article  CAS  PubMed  Google Scholar 

  782. Zhao H, Dietrich J. Privileged scaffolds in lead generation. Expert Opin Drug Discov. 2015;10(7):781–90.

    Article  CAS  PubMed  Google Scholar 

  783. Silva CFM, Pinto DCGA, Silva AMS. Chromones: privileged scaffolds for the production of multi-target-directed-ligand agents for the treatment of Alzheimer’s disease. Expert Opin Drug Discov. 2018;13(12):1141–51.

    Article  CAS  PubMed  Google Scholar 

  784. Faheem, Karan Kumar B, Venkata Gowri Chandra Sekhar K, et al. 1,2,3,4-Tetrahydroisoquinoline (THIQ) as privileged scaffold for anticancer de novo drug design Expert Opin Drug Discov. 2021: 16(10): 1119–1147.

    Google Scholar 

  785. Liargkova T, Eleftheriadis N, Dekker F, et al. Small multitarget molecules incorporating the enone moiety. Molecules. 2019;24(1):199.

    Article  PubMed Central  CAS  Google Scholar 

  786. Gupta D, Jaina DK, Trivedi P. Recent advances in chalcones as antiinfective agents. Int J Chem Sci. 2010;8:649–54.

    CAS  Google Scholar 

  787. Sinha S, Medhi B, Sehga R. Chalcones as an emerging lead molecule for antimalarial therapy: A review. J Mod Med Chem. 2013;1:64–77.

    Google Scholar 

  788. Yadav VR, Prasad S, Sung B, et al. The role of chalcones in suppression of NF-κB-mediated inflammation and cancer. Int Immunopharmacol. 2011;11:295–309.

    Article  CAS  PubMed  Google Scholar 

  789. Nowakowska Z. A review of anti-infective and anti-inflammatory chalcones. Eur J Med Chem. 2007;42:125–37.

    Article  CAS  PubMed  Google Scholar 

  790. Katsori AM, Hadjipavlou-Litina D. Recent progress in therapeutic applications of chalcones. Expert Opin Ther Pat. 2011;21:1575–96.

    Article  CAS  PubMed  Google Scholar 

  791. Rahman MA. Chalcone: A valuable insight into the recent advances and potential pharmacological activities. Chem Sci J. 2011;29:1–16.

    Google Scholar 

  792. Di Carlo G, Mascolo N, Izzo AA, et al. Flavonoids: Old and new aspects of a class of natural therapeutic drugs. Life Sci. 1999;65:337–53.

    Article  PubMed  Google Scholar 

  793. Nasir S, Bukhari A, Jasamai M, et al. Synthesis and biological evaluation of chalcone derivatives (mini review). Med Chem. 2012;12:1394–403.

    Google Scholar 

  794. Eddarir S, Cotelle N, Bakkour Y, et al. An efficient synthesis of chalcones based on the Suzuki reaction. Tetrahedron Lett. 2003;44:5359–63.

    Article  CAS  Google Scholar 

  795. Dhar DN. Chemistry of chalcones and related compounds. John Wiley & Sons, Inc.; New York, NY, USA: 1981; pp213.

    Google Scholar 

  796. Guida A, Lhouty MH, Tichit D, et al. Hydrotalcites as base catalysts. Kinetics of Claisen-Schmidt condensation, intramolecular condensation of acetonylacetone and synthesis of chalcone. Appl Catal A. 1997;164:251–64.

    Article  CAS  Google Scholar 

  797. Romanelli G, Pasquale G, Sathicq A, et al. Synthesis of chalcones catalyzed by aminopropylated silica sol–gel under solvent-free conditions. J Mol Catal A Chem. 2011;340:24–32.

    Article  CAS  Google Scholar 

  798. Kamboj S, Singh R. Chromanone-A prerogative therapeutic scaffold: An overview. Arab J Sci Eng. 2021: 1–37.

    Google Scholar 

  799. Emami S, Ghanbarimasir Z. Recent advances of chroman-4-one derivatives: synthetic approaches and bioactivities. Eur J Med Chem. 2015;93:539–63.

    Article  CAS  PubMed  Google Scholar 

  800. Panche AN, Diwan AD, Chandra R. Flavonoids: an overview. J Nutr Sci. 2016;5(47):1–15.

    Google Scholar 

  801. Christophe Carola H, Ralf Rosskopf M. Use of chroman-4-one derivatives. United States Patent application publication. US 2010/0028278 A1,1, 1–24 (2010).

    Google Scholar 

  802. Cotelle N. Role of flavonoids in oxidative stress. Curr Top Med Chem. 2001;I(2001):569–90.

    Article  Google Scholar 

  803. Park JH, Lee SU, Kim SH, et al. Chromone and chromanone derivatives as strand transfer inhibitors of HIV-1 integrase. Arch Pharm Res. 2008;31(1):1–5.

    Article  CAS  PubMed  Google Scholar 

  804. Jalili-Baleh L, Babaei E, Abdpour S, et al. A review on flavonoid-based scaffolds as multi-target-directed ligands (MTDLs) for Alzheimer’s disease. Eur J Med Chem. 2018;152:570–89.

    Article  CAS  PubMed  Google Scholar 

  805. Stefanachi A, Leonetti F, Pisani L. Coumarin: A natural, privileged and versatile scaffold for bioactive compounds. Molecules. 2018;23(2):250.

    Article  PubMed Central  CAS  Google Scholar 

  806. Vogel A. Darstellung von Benzoesaure aus der Tonka-Boline und aus den MeliIoten-oder Steinklee-Blumen. Ann Phys. 1820;64:161–6.

    Article  Google Scholar 

  807. Dean FM. Naturally occurring coumarins. Fortschr Chem Org Naturst IX. 1952;9:225–91.

    CAS  Google Scholar 

  808. Murray RDH, Mendez J, Brown SA. The Natural coumarins: Occurrence, chemistry and biochemistry. New York, NY, USA: John Wiley & Sons; 1982.

    Google Scholar 

  809. Murray RDH. Naturally occurring plant coumarins. Fortschr Chem Org Naturst. 1991;58:84–322.

    Google Scholar 

  810. O’Kennedy R. Thornes RD (eds). Biology, applications, and mode of action. John Wiley & Sons, New York, NY, USA: Coumarins; 1997.

    Google Scholar 

  811. Mzezewa SC, Omoruyi SI, Zondagh LS, et al. Design, synthesis, and evaluation of 3,7-substituted coumarin derivatives as multifunctional Alzheimer’s disease agents. J Enzyme Inhib Med Chem. 2021;36(1):1607–21.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  812. Jameel E, Umar T, Kumar J, et al. Coumarin: A privileged scaffold for the design and development of antineurodegenerative agents. Chem Biol Drug Des. 2016;87(1):21–38.

    Article  CAS  PubMed  Google Scholar 

  813. Detsi A, Kontogiorgis C, Hadjipavlou-Litina D. Coumarin derivatives: An updated patent review (2015–2016). Expert Opin Ther Pat. 2017;27:1201–27.

    Article  CAS  PubMed  Google Scholar 

  814. Barot KP, Jain SV, Kremer L, et al. Recent advances and therapeutic journey of coumarins: Current status and perspectives. Med Chem Res. 2015;24:2771–98.

    Article  CAS  Google Scholar 

  815. Uto Y. 1, 2-Benzisoxazole: A privileged structure with a potential for polypharmacology. Curr Pharm Des. 2016;22(21):3201–11.

    Article  CAS  PubMed  Google Scholar 

  816. Rakesh KP, Shantharam CS, Sridhara MB. Benzisoxazole: a privileged scaffold for medicinal chemistry. Medchemcomm. 2017;8(11):2023–39.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  817. Kirk KL, Filler R. In Biomedical frontiers of fluorine chemistry, symposium series. American Chemical Society, Washington, DC. 1996; vol. 639: pp 1–24.

    Google Scholar 

  818. Gelders YG, Heylen SLE, Vander BG, et al. Pilot clinical investigation of risperidone in the treatment of psychotic patients. J Pharmacopsychiatry. 1990;23:206–11.

    Article  CAS  Google Scholar 

  819. Dollery C. Therapeutic drugs. Edinburgh, UK: Churchill Livingstone; 1999.

    Google Scholar 

  820. Park BK, Kitteringham NR. Effects of fluorine substitution on drug metabolism: pharmacological and toxicological implications. Drug Metab Rev. 1994;26:605–43.

    Article  CAS  PubMed  Google Scholar 

  821. Deng BL, Cullen MD, Zhou Z, et al. Synthesis and anti-HIV activity of new alkenyldiarylmethane (ADAM) non-nucleoside reverse transcriptase inhibitors (NNRTIs) incorporating benzoxazolone and benzisoxazole rings. Bioorg Med Chem. 2006;14:2366–74.

    Article  CAS  PubMed  Google Scholar 

  822. Chaker A, Najahi E, Chatriant O, et al. New 3-substituted-2,1-benzisoxazoles: synthesis and antimicrobial activities. Arab J Chem. 2017;10:S2464–70.

    Article  CAS  Google Scholar 

  823. Sivala MR, Chintha V, Potla KM, et al. In silico docking studies and synthesis of new phosphoramidate derivatives of 6-fluoro-3-(piperidin-4-yl)benzo[d]isoxazole as potential antimicrobial agents. J Recept Signal Transduct. 2020;40:1–7.

    Article  CAS  Google Scholar 

  824. Shivaprasad CM, Jagadish S, Swaroop TR, et al. Synthesis of new benzisoxazole derivatives and their antimicrobial, antioxidant and anti-inflammatory activities. Eur J Chem. 2014;5:91–5.

    Article  CAS  Google Scholar 

  825. Wierenga W, Evans BR, Zurenko GE. Benzisoxazolones: antimicrobial and antileukemic activity. J Med Chem. 1984;27:1212–5.

    Article  CAS  PubMed  Google Scholar 

  826. Hrib NJ, Jurcak JG, Burgher KL, et al. Benzisoxazole- and benzisothiazole-3-carboxamides as potential atypical antipsychotic agents. J Med Chem. 1994;37:2308–14.

    Article  CAS  PubMed  Google Scholar 

  827. Davis L, Effland RC, Klein JT, et al. 3-substituted-1,2-benzisoxazoles: Novel antipsychotic agents. Drug Des Disco. 1992;8:225–40.

    CAS  Google Scholar 

  828. Saunders JC, Williamson WRN. Potential antiinflammatory compounds. 2. Acidic antiinflammatory 1,2-benzisoxazoles. J Med Chem. 1979;22:1554–8.

    Article  CAS  PubMed  Google Scholar 

  829. Khedekar P, Bahekar R, Chopadec R, et al. Synthesis and anti-inflammatory activity of alkyl/arylidene-2-aminobenzothiazoles and 1-benzothiazol-2-yl-3-chloro-4-substituted-azetidin-2-ones. Arzneimittelforschung. 2011;53:640–7.

    Article  Google Scholar 

  830. Anand M, Selvaraj V, Alagar M. Synthesis, characterization and evaluation of antioxidant and anticancer activities of novel benzisoxazole-substituted-allyl derivatives. Korean J Chem Eng. 2014;31:659–63.

    Article  CAS  Google Scholar 

  831. Chandra S, Mahadimane V. Effect of novel benzisoxazole derivatives against ehrlich ascites carcinoma cells in swiss albino mice: cytotoxic and haematalogical studies. Int J Pharma Sci Res. 2015;6:3606–11.

    Google Scholar 

  832. Jain M, Kwon CH. 1,2-Benzisoxazole phosphorodiamidates as novel anticancer prodrugs requiring bioreductive activation. J Med Chem. 2003;46:5428–36.

    Article  CAS  PubMed  Google Scholar 

  833. Ashwini N, Garg M, Mohan CD, et al. Synthesis of 1,2-benzisoxazole tethered 1,2,3-triazoles that exhibit anticancer activity in acute myeloid leukemia cell lines by inhibiting histone deacetylases, and inducing p21 and tubulin acetylation. Bioorg Med Chem. 2015;23:6157–65.

    Article  CAS  PubMed  Google Scholar 

  834. Aiello S, Wells G, Stone EL, et al. Synthesis and biological properties of benzothiazole, benzoxazole, and chromen-4-one analogues of the potent antitumor agent 2-(3,4-dimethoxyphenyl)-5- fluorobenzothiazole (PMX 610, NSC 721648). J Med Chem. 2008;51:5135–9.

    Article  CAS  PubMed  Google Scholar 

  835. Rakesh KP, Shantharam CS, Sridhara MB, et al. Benzisoxazole: a privileged scaffold for medicinal chemistry. Med Chem Commun. 2017;8:2023–39.

    Article  CAS  Google Scholar 

  836. Purohit SS, VeerapurV P. Benzisoxazole containing thiazolidinediones as peroxisome proliferator activated receptor-γ agonists: design, molecular docking, synthesis & antidiabetic studies. Sch Acad J Pharm. 2014;3:26–37.

    Google Scholar 

  837. Sills GJ. Zonisamide. In: Enna SJ, Bylund DB, editors. xPharm: the comprehensive pharmacology reference. University of Liverpool, Liverpool, United Kingdom, Elsevier. 2009; p1–6.

    Google Scholar 

  838. Vasquez AR, Bobo WV. Mood stabilizers: risperidone for treating bipolar disorders in adults. In: Riederer P, Laux G, Mulsant B, Le W, Nagatsu T, editors. NeuroPsychopharmacotherapy. Cham: Springer; 2020; pp1–32.

    Google Scholar 

  839. Green B. Paliperidone: a clinical review. Curr Drug Ther. 2009;4:7–11.

    Article  CAS  Google Scholar 

  840. Weiden P. Iloperidone for the treatment of schizophrenia: an updated clinical review. Clin Schizophr Relat Psychoses. 2012;6:34–44.

    Article  PubMed  Google Scholar 

  841. Uto Y. 1,2-Benzisoxazole compounds: a patent review (2009 - 2014). Expert Opin Ther Pat. 2015; 25(6): 643–662.

    Google Scholar 

  842. Deering RW, Whalen KE, Alvarez I, et al. Identification of a bacteria-produced benzisoxazole with antibiotic activity against multi-drug resistant Acinetobacter baumannii. J Antibiot (Tokyo). 2021;74(6):370–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  843. Giacomini E, Rupiani S, Guidotti L, et al. The use of stilbene scaffold in medicinal chemistry and multi- target drug design. Curr Med Chem. 2016;23(23):2439–89.

    Article  CAS  PubMed  Google Scholar 

  844. De Filippis B, Ammazzalorso A, Fantacuzzi M, et al. Anticancer activity of stilbene-based derivatives. ChemMedChem. 2017;12(8):558–70.

    Article  PubMed  CAS  Google Scholar 

  845. Rauf A, Imran M, Butt MS, et al. Resveratrol as an anti-cancer agent: A review. Crit Rev Food Sci Nutr. 2018;58(9):1428–47.

    Article  PubMed  Google Scholar 

  846. Dyck GJB, Raj P, Zieroth S, et al. The effects of resveratrol in patients with cardiovascular disease and heart failure: A narrative review. Int J Mol Sci. 2019;20(4):904.

    Article  CAS  PubMed Central  Google Scholar 

  847. Bonnefont-Rousselot D. Resveratrol and cardiovascular diseases. Nutrients. 2016;8(5):250.

    Article  PubMed Central  CAS  Google Scholar 

  848. Komorowska J, Wątroba M, Szukiewicz D. Review of beneficial effects of resveratrol in neurodegenerative diseases such as Alzheimer’s disease. Adv Med Sci. 2020;65(2):415–23.

    Article  PubMed  Google Scholar 

  849. De Filippis B, Ammazzalorso A, Amoroso R, et al. Stilbene derivatives as new perspective in antifungal medicinal chemistry. Drug Dev Res. 2019;80(3):285–93.

    Article  PubMed  CAS  Google Scholar 

  850. Chaudhary A, Pandeya SN, Kumar P, et al. Combretastatin a-4 analogs as anticancer agents. Mini Rev Med Chem. 2007;7(12):1186–205.

    Article  CAS  PubMed  Google Scholar 

  851. McCormack D, McFadden D. A review of pterostilbene antioxidant activity and disease modification. Oxid Med Cell Longev. 2013;2013:575482.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  852. McCormack D, McFadden D. Pterostilbene and cancer: current review. J Surg Res. 2012;173(2):e53–61.

    Article  CAS  PubMed  Google Scholar 

  853. Kershaw J, Kim KH. The therapeutic potential of piceatannol, a Natural stilbene, in metabolic diseases: A review. J Med Food. 2017;20(5):427–38.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  854. Banik K, Ranaware AM, Harsha C, et al. Piceatannol: A natural stilbene for the prevention and treatment of cancer. Pharmacol Res. 2020;153:104635.

    Article  CAS  PubMed  Google Scholar 

  855. Morphy R, Rankovic Z. Design of multitarget ligands. In: Rankovic Z, Morphy R, editors. Lead generation approaches in drug discovery. Hoboken: Wiley; 2010. p. 141–64.

    Chapter  Google Scholar 

  856. Morphy R, Rankovic Z. Designing multiple ligands—medicinal chemistry strategies and challenges. Curr Pharm Des. 2009;15(6):587–600.

    Article  CAS  PubMed  Google Scholar 

  857. Bérubé G. An overview of molecular hybrids in drug discovery. Expert Opin Drug Discov. 2016;11(3):281–305.

    Article  PubMed  CAS  Google Scholar 

  858. Morphy R, Rankovic Z. The physicochemical challenges of designing multiple ligands. J Med Chem. 2006;49(16):4961–70.

    Article  CAS  PubMed  Google Scholar 

  859. Decker M. Design of hybrid molecules for drug development. Amsterdam: Elsevier; 2017.

    Google Scholar 

  860. Das N, Dhanawat M, Dash B, et al. Codrug: an efficient approach for drug optimization. Eur J Pharm Sci. 2010;41(5):571–88.

    Article  CAS  PubMed  Google Scholar 

  861. Vu CB, Bemis JE, Benson E, et al. Synthesis and characterization of fatty acid conjugates of niacin and salicylic acid. J Med Chem. 2016;5(3):1217–31.

    Article  CAS  Google Scholar 

  862. Fornasari E, Di Stefano A, Cacciatore I. Direct-and spacer-coupled codrug strategies for the treatment of Alzheimer’s disease. Austin Alzheimers J Parkinsons Dis. 2014;1(2):9.

    Google Scholar 

  863. Poudel YB, Chowdari NS, Cheng H, et al. Chemical modification of linkers provides stable linker-payloads for the generation of antibody-drug conjugates. ACS Med Chem Lett. 2020;11(11):2190–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  864. Talevi A. Multi-target pharmacology: possibilities and limitations of the “skeleton key approach” from a medicinal chemist perspective. Front Pharmacol. 2015;6:205.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  865. Hopkins AL, Keserü GM, Leeson PD, et al. The role of ligand efficiency metrics in drug discovery. Nat Rev Drug Discov. 2014;13:105–21.

    Article  CAS  PubMed  Google Scholar 

  866. Meunier B. Hybrid molecules with a dual mode of action: dream or reality? Acc Chem Res. 2008;41(1):69–77.

    Article  CAS  PubMed  Google Scholar 

  867. Zimmermann GR, Lehar J, Keith CT. Multi-target therapeutics: when the whole is greater than the sum of the parts. Drug Discovery Today. 2007;12(1-2):34–42.

    Article  CAS  PubMed  Google Scholar 

  868. Kabir MT, Uddin MS, Mamun AA, et al. Combination drug therapy for the management of Alzheimer’s disease. Int J Mol Sci. 2020;21(9):3272.

    Article  CAS  PubMed Central  Google Scholar 

  869. Cummings JL, Morstorf T, Zhong K. Alzheimer’s disease drug-development pipeline: Few candidates, frequent failures. Alzheimers Res Ther. 2014;6:37.

    Article  PubMed  PubMed Central  Google Scholar 

  870. Kabir MT, Abu Sufian M, Uddin MS, et al. NMDA receptor antagonists: Repositioning of memantine as multitargeting agent for Alzheimer’s therapy. Curr Pharm Des. 2019;25:3506–18.

    Article  CAS  PubMed  Google Scholar 

  871. Uddin MS, Kabir MT, Tewari D, et al. Emerging signal regulating potential of small molecule biflavonoids to combat neuropathological insults of Alzheimer’s disease. Sci Total Environ. 2020;700:1–11.

    Article  CAS  Google Scholar 

  872. Kabir MT, Uddin MS, Begum MM, et al. Cholinesterase inhibitors for Alzheimer’s disease: Multitargeting strategy based on anti-Alzheimer’s drugs repositioning. Curr Pharm Des. 2019;25:3519–35.

    Article  CAS  PubMed  Google Scholar 

  873. Deardorff WJ, Grossberg GT. A fixed-dose combination of memantine extended-release and donepezil in the treatment of moderate-to-severe Alzheimer’s disease. Drug Des Devel Ther. 2016;10:3267–79.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  874. Agatonovic-Kustrin S, Kettle C, Morton DW. A molecular approach in drug development for Alzheimer’s disease. Biomed Pharmacother. 2018;106:553–65.

    Article  CAS  PubMed  Google Scholar 

  875. Capurro V, Busquet P, Lopes JP, et al. Pharmacological characterization of memoquin, a multi-target compound for the treatment of Alzheimer’s disease. PLoS ONE. 2013;8:e56870.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  876. Parsons CG, Danysz W, Dekundy A, et al. Memantine and cholinesterase inhibitors: Complementary mechanisms in the treatment of Alzheimer’s disease. Neurotox Res. 2013;24:358–69.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  877. Patel L, Grossberg GT. Combination therapy for Alzheimer’s disease. Drugs Aging. 2011;28:539–46.

    Article  CAS  PubMed  Google Scholar 

  878. Posadas I, Lopez-Hernandez B, Cena V. Nicotinic receptors in neurodegeneration. Curr Neuropharmacol. 2013;11:298–314.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  879. Jun Kawamata J, Syuuichirou SS, Shun SS. α7 nicotinic acetylcholine receptor mediated neuroprotection in Parkinson’s disease. Curr Drug Targets. 2012;13:623–30.

    Article  PubMed  Google Scholar 

  880. Takada-Takatori Y, Kume T, Sugimoto M, et al. Acetylcholinesterase inhibitors used in treatment of Alzheimer’s disease prevent glutamate neurotoxicity via nicotinic acetylcholine receptors and phosphatidylinositol 3-kinase cascade. Neuropharmacology. 2006;51:474–86.

    Article  CAS  PubMed  Google Scholar 

  881. Lopes JP, Tarozzo G, Reggiani A, et al. Galantamine potentiates the neuroprotective effect of memantine against NMDA-induced excitotoxicity. Brain Behav. 2013;3:67–74.

    Article  PubMed  PubMed Central  Google Scholar 

  882. Rosini M, Simoni E, Bartolini M, et al. Inhibition of acetylcholinesterase, β-amyloid aggregation, and NMDA receptors in Alzheimer’s disease: A promising direction for the multi-target-directed ligands gold rush. J Med Chem. 2008;51:4381–4.

    Article  CAS  PubMed  Google Scholar 

  883. Simoni E, Daniele S, Bottegoni G, et al. Combining galantamine and memantine in multitargeted, new chemical entities potentially useful in Alzheimer’s disease. J Med Chem. 2012;55:9708–21.

    Article  CAS  PubMed  Google Scholar 

  884. Lipton SA. Paradigm shift in neuroprotection by NMDA receptor blockade: Memantine and beyond. Nat Rev Drug Discov. 2006;5:160–70.

    Article  CAS  PubMed  Google Scholar 

  885. Lipton SA, Choi YB, Pan ZH, et al. A redox-based mechanism for the neuroprotective and neurodestructive effects of nitric oxide and related nitroso-compounds. Nature. 1993;364:626–32.

    Article  CAS  PubMed  Google Scholar 

  886. Tsiailanis A, Tsoumani M, Stylos EK, et al. Designing natural product hybrids bearing triple antiplatelet profile and evaluating their human plasma stability. Methods Mol Biol. 2018;1824:371–85.

    Article  CAS  PubMed  Google Scholar 

  887. Alam MM, Hassan AHE, Kwon YH, et al. Design, synthesis and evaluation of alkylphosphocholine-gefitinib conjugates as multitarget anticancer agents. Arch Pharm Res. 2018;41(1):35–45.

    Article  CAS  PubMed  Google Scholar 

  888. Price AJ, Howard S, Cons BD. Fragment-based drug discovery and its application to challenging drug targets. Essays in Biochem. 2017;61(5):475–84.

    Article  Google Scholar 

  889. Tounge BA, Parker MH. Designing a diverse high-quality library for crystallography-based FBDD screening. Fragment-based drug design—Tools, practical approaches, and examples. Methods in Enzymol. 2011;493:3–20.

    Article  CAS  Google Scholar 

  890. Li Q. Application of fragment-based drug discovery to versatile targets. Front Mol Biosci. 2020;7:180.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  891. Doak BC, Norton RS, Scanlon MJ. The ways and means of fragment-based drug design. Pharmacol Therapeut. 2016;167:28–37.

    Article  CAS  Google Scholar 

  892. Murray CW, Rees DC. The rise of fragment-based drug discovery. Nat Chem. 2009;1:187–92.

    Article  CAS  PubMed  Google Scholar 

  893. Erlanson DA, Fesik SW, Hubbard RE, et al. Twenty years on: the impact of fragments on drug discovery. Nat Rev Drug Discov. 2016;15:605–19.

    Article  CAS  PubMed  Google Scholar 

  894. Bollag G, Hirth P, Tsai J, et al. Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma. Nature. 2010;467:596.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  895. Bollag G, Tsai J, Zhang J, et al. Vemurafenib: the first drug approved for BRAF-mutant cancer. Nat Rev Drug Discovery. 2012;11:873.

    Article  CAS  PubMed  Google Scholar 

  896. Erlanson DA. Introduction to fragment-based drug discovery. In Fragment-Based Drug Discovery and X-Ray Crystallography. Davies TG, Hyvönen M (eds). Springer-Verlag, Berlin. 2012; pp1–32.

    Google Scholar 

  897. Jacquemard C, Kellenberger E. A bright future for fragment-based drug discovery: What does it hold? Exp Opin Drug Discov. 2019;14:413–6.

    Article  Google Scholar 

  898. Whittaker M, Law RJ, Ichihara O, et al. Fragments: past, present and future. Drug Discov Today. 2010;7:e163–71.

    Article  CAS  Google Scholar 

  899. Aretz J, Kondoh Y, Honda K, et al. Chemical fragment arrays for rapid druggability assessment. Chem Commun. 2016;52:9067–70.

    Article  CAS  Google Scholar 

  900. Gee CT, Arntson KE, Urick AK, et al. Protein-observed 19F-NMR for fragment screening, affinity quantification and druggability assessment. Nat Protoc. 2016;11:1414.

    Article  PubMed  PubMed Central  Google Scholar 

  901. Dang CV, Reddy EP, Shokat KM, et al. Drugging the ‘undruggable’ cancer targets. Nat Rev Cancer. 2017;17:502–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  902. Owens J. Determining druggability. Nat Rev Drug Discov. 2007;6:187.

    Article  CAS  Google Scholar 

  903. Cheng AC, Coleman RG, Smyth KT, et al. Structure-based maximal affinity model predicts small-molecule druggability. Nat Biotechnol. 2007;25:71–5.

    Article  PubMed  CAS  Google Scholar 

  904. Arkin MR, Tang Y, Wells JA. Small-molecule inhibitors of protein-protein interactions: progressing toward the reality. Chem Biol. 2014;21:1102–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  905. Erlanson DA. Fragment-based lead discovery: a chemical update. Curr Opin Biotechnol. 2006;17:643–52.

    Article  CAS  PubMed  Google Scholar 

  906. Lamoree B, Hubbard RE. Current perspectives in fragment-based lead discovery (FBLD). Essays Biochem. 2017;61:453–64.

    Article  PubMed  PubMed Central  Google Scholar 

  907. Brunst S, Kramer JS, Kilu W, et al. Systematic assessment of fragment identification for multitarget drug design. ChemMedChem. 2021;16(7):1088–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  908. Morphy R, Rankovic Z. Fragments, network biology and designing multiple ligands. Drug Discovery Today. 2007;12:156–60.

    Article  CAS  PubMed  Google Scholar 

  909. Bottegoni G, Favia AD, Recanatini M, et al. The role of fragment-based and computational methods in polypharmacology. Drug Discovery Today. 2012;17:23–34.

    Article  CAS  PubMed  Google Scholar 

  910. Howard S, Berdini V, Boulstridge JA, et al. Fragment-based discovery of the pyrazol-4-yl urea (AT9283), a multitargeted kinase inhibitor with potent aurora kinase activity. J Med Chem. 2009;52(2):379–88.

    Article  CAS  PubMed  Google Scholar 

  911. Speck-Planche A, Kleandrova VV, Luan F, et al. Multi-target inhibitors for proteins associated with Alzheimer: in silico discovery using fragment-based descriptors. Curr Alzheimer Res. 2013;10(2):117–24.

    Article  CAS  PubMed  Google Scholar 

  912. Speck-Planche A, Cordeiro MNDS. Fragment-based in silico modeling of multi-target inhibitors against breast cancer-related proteins. Mol Divers. 2017;21(3):511–23.

    Article  CAS  PubMed  Google Scholar 

  913. Moroz E, Matoori S, Leroux JC. Oral delivery of macromolecular drugs: Where we are after almost 100 years of attempts. Adv Drug Deliv Rev. 2016;101:108–21.

    Article  CAS  PubMed  Google Scholar 

  914. Yang J, Kopeček J. Macromolecular therapeutics. J Control Release. 2014; 0: 288–303.

    Google Scholar 

  915. Rütter M, Milošević N, David A. Say no to drugs: Bioactive macromolecular therapeutics without conventional drugs. J Control Release. 2021;330:1191–207.

    Article  PubMed  CAS  Google Scholar 

  916. Ramsay RR, Popovic-Nikolic MR, Nikolic K, et al. A perspective on multi-target drug discovery and design for complex diseases. Clin Transl Med. 2018;7:3.

    Article  PubMed  PubMed Central  Google Scholar 

  917. Dimitrov DS. Therapeutic proteins. Methods Mol Biol. 2012;899:1–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  918. Raju TS, Strohl WR. Potential therapeutic roles for antibody mixtures. Expert Opin Biol Ther. 2013;13(10):1347–52.

    Article  CAS  PubMed  Google Scholar 

  919. Jakob CG, Edalji R, Judge RA, et al. Structure reveals function of the dual variable domain immunoglobulin (DVD-Ig™) molecule. MAbs. 2013;5:358–63.

    Article  PubMed  PubMed Central  Google Scholar 

  920. Günther G, Dreger B. Post-marketing observational study on 5% intravenous immunoglobulin therapy (Alphaglobin®/Flebogamma®) in secondary immunodeficiency with recurrent serious bacterial infections. Microbiol Immunol. 2013;57(7):527–35.

    PubMed  Google Scholar 

  921. Meng Q, Garcia-Rodriguez C, Manzanarez G, et al. Engineered domain-based assays to identify individual antibodies in oligoclonal combinations targeting the same protein. Anal Biochem. 2012;430:141–50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  922. Haurum JS. Recombinant polyclonal antibodies: the next generation of antibody therapeutics? Drug Discov Today. 2006;11:655–60.

    Article  CAS  PubMed  Google Scholar 

  923. Strohl WR, Strohl LM. Therapeutic antibody engineering: current and future advances driving the strongest growth area in the pharma industry. Woodhead Publishing Series in Biomedicine No. 11 Woodhead Publishing; Cambridge. 2012.

    Google Scholar 

  924. Skartved NJ, Jacobsen HJ, Pedersen MW, et al. Preclinical pharmacokinetics and safety of Sym004: a synergistic antibody mixture directed against epidermal growth factor receptor. Clin Cancer Res. 2011;17:5962–72.

    Article  CAS  PubMed  Google Scholar 

  925. Labrijn AF, Meesters JI, de Goeij BE, et al. Efficient generation of stable bispecific IgG1 by controlled Fab-arm exchange. Proc Natl Acad Sci USA. 2013;110:5145–50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  926. Labrijn AF, Janmaat ML, Reichert JM, et al. Bispecific antibodies: a mechanistic review of the pipeline. Nat Rev Drug Discov. 2019;18(8):585–608.

    Article  CAS  PubMed  Google Scholar 

  927. Shin SU. Chimeric antibody: potential applications for drug delivery and immunotherapy. Biotherapy. 1991;3(1):43–53.

    Article  CAS  PubMed  Google Scholar 

  928. Wright A, Shin SU, Morrison SL. Genetically engineered antibodies: progress and prospects. Crit Rev Immunol. 1992;12(3-4):125–68.

    CAS  PubMed  Google Scholar 

  929. Panowski S, Bhakta S, Raab H, et al. Site-specific antibody drug conjugates for cancer therapy. MAbs. 2014;6(1):34–45.

    Article  PubMed  Google Scholar 

  930. Khongorzul P, Ling CJ, Khan FU, et al. Antibody-drug conjugates: A comprehensive review. Mol Cancer Res. 2020;18(1):3–19.

    Article  CAS  PubMed  Google Scholar 

  931. Hamilton GS. Antibody-drug conjugates for cancer therapy: The technological and regulatory challenges of develo** drug-biologic hybrids. Biologicals. 2015;43(5):318–32.

    Article  CAS  PubMed  Google Scholar 

  932. Fitzpatrick-Dimond PF. Antibody-drug conjugates stage a comeback. GEN: Genetic Engineering and Biotechnology News. 2010.

    Google Scholar 

  933. DiJoseph JF, Armellino DC, Boghaert ER, et al. Antibody-targeted chemotherapy with CMC-544: a CD22-targeted immunoconjugate of calicheamicin for the treatment of B-lymphoid malignancies. Blood. 2004;103(5):1807–14.

    Article  CAS  PubMed  Google Scholar 

  934. Mullard A. Maturing antibody-drug conjugate pipeline hits 30. Nat Rev Drug Discov. 2013;12(5):329–32.

    Article  CAS  PubMed  Google Scholar 

  935. Chari RV, Martell BA, Gross JL, et al. Immunoconjugates containing novel maytansinoids: promising anticancer drugs. Can Res. 1992;52(1):127–31.

    CAS  Google Scholar 

  936. Beck A, Goetsch L, Dumontet C, et al. Strategies and challenges for the next generation of antibody-drug conjugates. Nat Rev Drug Discov. 2017;16(5):315–37.

    Article  CAS  PubMed  Google Scholar 

  937. Damelin M, Zhong W, Myers J, et al. Evolving strategies for target selection for antibody-drug conjugates. Pharm Res. 2015;32:3494–507.

    Article  CAS  PubMed  Google Scholar 

  938. Diamantis N, Banerji U. Antibody-drug conjugates–an emerging class of cancer treatment. Br J Can. 2016;114:362–7.

    Article  CAS  Google Scholar 

  939. Tipton TR, Roghanian A, Oldham RJ, et al. Antigenic modulation limits the effector cell mechanisms employed by type I anti-CD20 monoclonal antibodies. Blood. 2015;125:1901–9.

    Article  CAS  PubMed  Google Scholar 

  940. Donaghy H. Effects of antibody, drug and linker on the preclinical and clinical toxicities of antibody-drug conjugates. mAbs. 2016;8:659–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  941. Casi G, Neri D. Noninternalizing targeted cytotoxics for cancer therapy. Mol Pharm. 2015;12:1880–4.

    Article  CAS  PubMed  Google Scholar 

  942. Kovtun YV, Goldmacher VS. Cell killing by antibody-drug conjugates. Can Lett. 2007;255(2):232–40.

    Article  CAS  Google Scholar 

  943. Bąchor R, Kluczyk A, Stefanowicz P, et al. New method of peptide cleavage based on Edman degradation. Mol Divers. 2013;17(3):605–11.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  944. Axup JY, Bajjuri KM, Ritland M, et al. (October 2012). Synthesis of site-specific antibody-drug conjugates using unnatural amino acids. Proc Nat Acad Sci U S A. 109 (40): 16101–16106.

    Google Scholar 

  945. Lyon RP, Setter JR, Bovee TD, et al. Self-hydrolyzing maleimides improve the stability and pharmacological properties of antibody-drug conjugates. Nat Biotechnol. 2014;32(10):1059–62.

    Article  CAS  PubMed  Google Scholar 

  946. Kolodych S, Koniev O, Baatarkhuu Z, et al. CBTF: new amine-to-thiol coupling reagent for preparation of antibody conjugates with increased plasma stability. Bioconjugate Chem. 2015;26(2):197–200.

    Article  CAS  Google Scholar 

  947. Wulbrand C, Seidl C, Gaertner FC, et al. Alpha-particle emitting 213Bi-anti-EGFR immunoconjugates eradicate tumor cells independent of oxygenation. PLOS ONE. 2013;8(5):e64730.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  948. Cardoso MM, Peça IN, Roque AC. Antibody-conjugated nanoparticles for therapeutic applications. Curr Medicinal Chem. 2012;19(19):3103–27.

    Article  CAS  Google Scholar 

  949. Dovgan I, Koniev O, Kolodych S, et al. Antibody-oligonucleotide conjugates as therapeutic, imaging, and detection agents. Bioconjugate Chem. 2019;30(10):2483–501.

    Article  CAS  Google Scholar 

  950. Walsh SJ, Bargh JD, Dannheim FM, et al. Site-selective modification strategies in antibody-drug conjugates. Chem Soc Rev. 2021;50(2):1305–53.

    Article  CAS  PubMed  Google Scholar 

  951. Axup JY, Bajjuri KM, Ritland M, et al. Synthesis of site-specific antibody-drug conjugates using unnatural amino acids. Proc Natl Acad Sci U S A. 2012;109(40):16101–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  952. Schumacher D, Hackenberger CP, Leonhardt H, et al. Current status: Site-specific antibody drug conjugates. J Clin Immunol. 2016;36(Suppl 1):100–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  953. Sochaj AM, Świderska KW, Otlewski J. Current methods for the synthesis of homogeneous antibody-drug conjugates. Biotechnol Adv. 2015;33(6 Pt 1):775–84.

    Article  CAS  PubMed  Google Scholar 

  954. Hussain AF, Grimm A, Sheng W, et al. Toward homogenous antibody drug conjugates using enzyme-based conjugation approaches. Pharmaceuticals (Basel). 2021;14(4):343.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  955. Chernikov IV, Vlassov VV, Chernolovskaya EL. Current development of siRNA bioconjugates: From research to the clinic. Front Pharmacol. 2019;10:444.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  956. **a CF, Boado RJ, Pardridge WM. Antibody-mediated targeting of siRNA via the human insulin receptor using avidin-biotin technology. Mol Pharm. 2009;6:747–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  957. Ma Y, Kowolik CM, Swiderski PM, et al. Humanized Lewis-Y specific antibody-based delivery of STAT3 siRNA. ACS Chem Biol. 2011;6:962–70.

    Article  CAS  PubMed  Google Scholar 

  958. Sugo T, Terada M, Oikawa T, et al. Development of antibody-siRNA conjugate targeted to cardiac and skeletal muscles. J Control Release. 2016;237:1–13.

    Article  CAS  PubMed  Google Scholar 

  959. Ibtehaj N, Huda R. High-dose BAFF receptor specific mAb-siRNA conjugate generates Fas-expressing B cells in lymph nodes and high-affinity serum autoantibody in a myasthenia mouse model. Clin Immunol. 2017;176:122–30.

    Article  CAS  PubMed  Google Scholar 

  960. Cuellar TL, Barnes D, Nelson C, et al. Systematic evaluation of antibody-mediated siRNA delivery using an industrial platform of THIOMAB-siRNA conjugates. Nucleic Acids Res. 2014;43:1189–203.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  961. Inumaru S. Introduction to advanced biologics. Vet Immunol Immunopathol. 2012;148(1-2):126–8.

    Article  PubMed  Google Scholar 

  962. Lacaná E, Amur S, Mummanneni P, et al. The emerging role of pharmacogenomics in biologics. Clin Pharmacol Ther. 2007;82(4):466–71.

    Article  PubMed  CAS  Google Scholar 

  963. O’Neill ID, Scully C. Biologics in oral medicine: principles of use and practical considerations. Oral Dis. 2012;18(6):525–36.

    Article  PubMed  Google Scholar 

  964. Greish K, Fang J, Inutsuka T, et al. Macromolecular therapeutics. Clin Pharmacokinet. 2003;42:1089–105.

    Article  CAS  PubMed  Google Scholar 

  965. Matsumura Y, Maeda H. A new concept for macromolecular therapeutics in cancer chemotherapy: mechanism of tumoritropic accumulation of proteins and the antitumor agent SMANCS. Cancer Res. 1986;46:6387–92.

    CAS  PubMed  Google Scholar 

  966. Kopeček J. Polymer-drug conjugates: origins, progress to date and future directions. Adv Drug Deliv Rev. 2013;65:49–59.

    Article  PubMed  CAS  Google Scholar 

  967. Seymour LW, et al. Phase II studies of polymer-doxorubicin (PK1, FCE28068) in the treatment of breast, lung and colorectal cancer. Int J Oncol. 2009;34:1629–36.

    Article  CAS  PubMed  Google Scholar 

  968. Chipman SD, Oldham FB, Pezzoni G, Singer JW. Biological and clinical characterization of paclitaxel poliglumex (PPX, CT-2103), a macromolecular polymer-drug conjugate. Int J Nanomedicine. 2006;1:375–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  969. Weiss GJ, et al. First-in-human phase 1/2a trial of CRLX101, a cyclodextrin-containing polymer-camptothecin nanopharmaceutical in patients with advanced solid tumor malignancies. Invest New Drugs. 2013;31:986–1000.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  970. Yurkovetskiy AV, Fram RJ. XMT-1001, a novel polymeric camptothecin pro-drug in clinical development for patients with advanced cancer. Adv Drug Deliv Rev. 2009;61:1193–202.

    Article  CAS  PubMed  Google Scholar 

  971. Couvreur P, Vauthier C. Nanotechnology: Intelligent design to treat complex disease. Pharm Res. 2006;23:1417–50.

    Article  CAS  PubMed  Google Scholar 

  972. Vicent MJ, Ringsdorf H, Duncan R. Polymer therapeutics: clinical applications and challenges for development. Adv Drug Deliv Rev. 2009;61:1117–20.

    Article  CAS  PubMed  Google Scholar 

  973. Destouches D, Page N, Hamma-Kourbali Y, et al. A simple approach to cancer therapy afforded by multivalent pseudopeptides that target cell-surface nucleoproteins. Cancer Res. 2011;71:3296–305.

    Article  CAS  PubMed  Google Scholar 

  974. Zhang Z, et al. DNA-scaffolded multivalent ligands to modulate cell function. Chembiochem. 2014;15:1268–73.

    Article  CAS  PubMed  Google Scholar 

  975. Kiessling LL, Gestwicki JE, Strong LE. Synthetic multivalent ligands in the exploration of cell-surface interactions. Curr Opin Chem Biol. 2000;4:696–703.

    Article  CAS  PubMed  Google Scholar 

  976. Stephens B, Handel TM. Chemokine receptor oligomerization and allostery. Prog Mol Biol Transl Sci. 2013;115:375–420.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  977. Ljubimova JY, Fujita M, Ljubimov AV, et al. Poly(malic acid) nanoconjugates containing various antibodies and oligonucleotides for multitargeting drug delivery. Nanomedicine (Lond). 2008;3(2):247–65.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  978. Maeda H, Wu J, Sawa T, et al. Tumor vascular permeability and the EPR effect in macromolecular therapeutics: a review. J Control Release. 2000;65:271–84.

    Article  CAS  PubMed  Google Scholar 

  979. Li L, Yang J, Wang J, et al. Drug-free macromolecular therapeutics exhibit amplified apoptosis in G2/M phase arrested cells J Drug Target. 2019; 27(5-6): 566–72.

    Google Scholar 

  980. Chu TW, Kopeček J. drug-free macromolecular therapeutics--a new paradigm in polymeric nanomedicines. Biomater Sci. 2015; 3(7): 908–922.

    Google Scholar 

  981. Tavares MR, Pechar M, Chytil P, et al. Polymer-based drug-free therapeutics for anticancer, anti-inflammatory, and antibacterial treatment. Macromol Biosci. 2021;21(8):e2100135.

    Article  PubMed  CAS  Google Scholar 

  982. Wu K, Liu J, Johnson RN, et al. Drug-free macromolecular therapeutics: induction of apoptosis by coiled-coil-mediated cross-linking of antigens on the cell surface. Angew Chem Int Ed. 2010;49:1451–5.

    Article  CAS  Google Scholar 

  983. Ho TT, Tran QT, Chai CL. The polypharmacology of natural products. Future Med Chem. 2018;10(11):1361–8.

    Article  CAS  PubMed  Google Scholar 

  984. Fang J, Liu C, Wang Q, et al. In silico polypharmacology of natural products. Brief Bioinform. 2018;19(6):1153–71.

    CAS  PubMed  Google Scholar 

  985. Kibble M, Saarinen N, Tang J, et al. Network pharmacology applications to map the unexplored target space and therapeutic potential of natural products. Nat Prod Rep. 2015;32(8):1249–66.

    Article  CAS  PubMed  Google Scholar 

  986. Butler MS, Robertson AA, Cooper MA. Natural product and natural product derived drugs in clinical trials. Nat Prod Rep. 2014;31:1612–61.

    Article  CAS  PubMed  Google Scholar 

  987. Shen B. A new golden age of natural products drug discovery. Cell. 2015;163:1297–300.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  988. Lee KW, Bode AM, Dong Z. Molecular targets of phytochemicals for cancer prevention. Nat Rev Cancer. 2011;11:211–8.

    Article  CAS  PubMed  Google Scholar 

  989. Fang J, Cai C, Wang Q, et al. Systems pharmacology-based discovery of natural products for precision oncology through targeting cancer mutated genes. CPT Pharmacometrics Syst Pharmacol. 2017;6:177–87.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  990. Gu J, Gui Y, Chen L, et al. Use of natural products as chemical library for drug discovery and network pharmacology. PLoS One. 2013;8(4):e62839.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  991. Yildirim MA, Goh KI, Cusick ME, et al. Drug-target network. Nat Biotechnol. 2007;25:1119–26.

    Article  CAS  PubMed  Google Scholar 

  992. Barneh F, Jafari M, Mirzaie M. Updates on drug-target network; facilitating polypharmacology and data integration by growth of DrugBank database. Brief Bioinform. 2016;17:1070–80.

    CAS  PubMed  Google Scholar 

  993. Bento AP, Gaulton A, Hersey A, et al. The ChEMBL bioactivity database: an update. Nucleic Acids Res. 2014;42:D1083–90.

    Article  CAS  PubMed  Google Scholar 

  994. Wang Y, Bolton E, Dracheva S, et al. An overview of the PubChem BioAssay resource. Nucleic Acids Res. 2010;38:D255–66.

    Article  CAS  PubMed  Google Scholar 

  995. Law V, Knox C, Djoumbou Y, et al. DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. 2014;42:D1091–7.

    Article  CAS  PubMed  Google Scholar 

  996. Yang H, Qin C, Li YH, et al. Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. Nucleic Acids Res. 2016;44:D1069–74.

    Article  CAS  PubMed  Google Scholar 

  997. Wagner AH, Coffman AC, Ainscough BJ, et al. DGIdb 2.0: mining clinically relevant drug-gene interactions. Nucleic Acids Res. 2016;44:D1036–44.

    Article  CAS  PubMed  Google Scholar 

  998. Kuhn M, Szklarczyk D, Pletscher-Frankild S, et al. STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res. 2014;42:D401–7.

    Article  CAS  PubMed  Google Scholar 

  999. Nickel J, Gohlke BO, Erehman J, et al. SuperPred: update on drug classification and target prediction. Nucleic Acids Res. 2014;42:W26–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1000. Ye H, Ye L, Kang H, et al. HIT: linking herbal active ingredients to targets. Nucleic Acids Res. 2011;39:D1055–9.

    Article  CAS  PubMed  Google Scholar 

  1001. Xue R, Fang Z, Zhang M, et al. TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Res. 2013;41:D1089–95.

    Article  CAS  PubMed  Google Scholar 

  1002. Ru J, Li P, Wang J, et al. TCMSP: a database of systems pharmacology for drug discovery from herbal medicines. J Cheminform. 2014;6:13.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  1003. Mangal M, Sagar P, Singh H, et al. NPACT: naturally occurring plant-based anti-cancer compound-activity-target database. Nucleic Acids Res. 2013;41:D1124–9.

    Article  CAS  PubMed  Google Scholar 

  1004. Tao W, Li B, Gao S, et al. CancerHSP: anticancer herbs database of systems pharmacology. Sci Rep. 2015;5:11481.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1005. Bredel M, Jacoby E. Chemogenomics: an emerging strategy for rapid target and drug discovery. Nat Rev Genet. 2004;5:262–75.

    Article  CAS  PubMed  Google Scholar 

  1006. 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 

  1007. Duan Q, Flynn C, Niepel M, et al. LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Res. 2014;42:W449–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1008. Igarashi Y, Nakatsu N, Yamashita T, et al. Open TG-GATEs: a large-scale toxicogenomics database. Nucleic Acids Res. 2015;43:D921–7.

    Article  CAS  PubMed  Google Scholar 

  1009. Ganter B, Snyder RD, Halbert DN, et al. Toxicogenomics in drug discovery and development: mechanistic analysis of compound/class-dependent effects using the DrugMatrix database. Pharmacogenomics. 2006;7:1025–44.

    Article  CAS  PubMed  Google Scholar 

  1010. Lamb J. The connectivity map: a new tool for biomedical research. Nat Rev Can. 2007;7:54–60.

    Article  CAS  Google Scholar 

  1011. Adams JU. Genetics: big hopes for big data. Nature. 2015;527:S108–9.

    Article  CAS  PubMed  Google Scholar 

  1012. Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, et al. The BioGRID interaction database: 2015 update. Nucleic Acids Res. 2015;43:D470–8.

    Article  CAS  PubMed  Google Scholar 

  1013. Keshava Prasad TS, Goel R, Kandasamy K, et al. Human protein reference database–2009 update. Nucleic Acids Res. 2009;37:D767–72.

    Article  CAS  PubMed  Google Scholar 

  1014. Mosca R, Ceol A, Aloy P. Interactome3D: adding structural details to protein networks. Nat Methods. 2013;10:47–53.

    Article  CAS  PubMed  Google Scholar 

  1015. Szklarczyk D, Morris JH, Cook H, et al. The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2017;45:D362–8.

    Article  CAS  PubMed  Google Scholar 

  1016. Licata L, Briganti L, Peluso D, et al. MINT, themolecular interaction database: 2012 update. Nucleic Acids Res. 2012;40:D857–61.

    Article  CAS  PubMed  Google Scholar 

  1017. Cheng F, Jia P, Wang Q, et al. Quantitative network map** of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy. Oncotarget. 2014;5:3697–710.

    Article  PubMed  PubMed Central  Google Scholar 

  1018. Cheng F, Murray JL, Zhao J, et al. Systems biology-based investigation of cellular antiviral drug targets identified by gene-trap insertional mutagenesis. PLoS Comput Biol. 2016;12:e1005074.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  1019. Cheng F, Liu C, Shen B, et al. Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach. BMC Syst Biol. 2016;10(Suppl 3):65.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  1020. Cheng F, Jia P, Wang Q, et al. Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome. Mol Biol Evol. 2014;31:2156–69.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1021. Chen X, Yan CC, Zhang X, et al. Drug-target interaction prediction: databases, web servers and computational models. Brief Bioinform. 2016;17:696–712.

    Article  CAS  PubMed  Google Scholar 

  1022. Koutsoukas A, Simms B, Kirchmair J, et al. From in silico target prediction to multi-target drug design: current databases, methods and applications. J Proteomics. 2011;74:2554–74.

    Article  CAS  PubMed  Google Scholar 

  1023. Yue R, Shan L, Yang X, et al. Approaches to target profiling of natural products. Curr Med Chem. 2012;19:3841–55.

    Article  CAS  PubMed  Google Scholar 

  1024. Jenkins JL, Bender A, Davies JW. In silico target fishing: predicting biological targets from chemical structure. Drug Discov Today Technol. 2007;3:413–21.

    Article  Google Scholar 

  1025. Harren J, Andrew RL. Structure-based Drug Discovery. Dordrecht: Netherlands, Springer; 2007.

    Google Scholar 

  1026. Taboureau O, Baell JB, Fernandez-Recio J, et al. Established and emerging trends in computational drug discovery in the structural genomics era. Chem Biol. 2012;19:29–41.

    Article  CAS  PubMed  Google Scholar 

  1027. Luo H, Mattes W, Mendrick DL, et al. Molecular docking for identification of potential targets for drug repurposing. Curr Top Med Chem. 2016;16:3636–45.

    Article  CAS  PubMed  Google Scholar 

  1028. Ye H, Wei J, Tang K, et al. Drug repositioning through network pharmacology. Curr Top Med Chem. 2016;16:3646–56.

    Article  CAS  PubMed  Google Scholar 

  1029. Sakkiah S, Ng HW, Tong W, et al. Structures of androgen receptor bound with ligands: advancing understanding of biological functions and drug discovery. Expert Opin Ther Targets. 2016;20:1267–82.

    Article  CAS  PubMed  Google Scholar 

  1030. Liu LJ, Leung KH, Chan DS, et al. Identification of a natural product-like STAT3 dimerization inhibitor by structure-based virtual screening. Cell Death Dis. 2014;5:e1293.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1031. Zhong HJ, Lee BR, Boyle JW, et al. Structure-based screening and optimization of cytisine derivatives as inhibitors of the menin-MLL interaction. Chem Commun. 2016;52:5788–91.

    Article  CAS  Google Scholar 

  1032. Singh T, Gupta NA, Xu S, et al. Honokiol inhibits the growth of head and neck squamous cell carcinoma by targeting epidermal growth factor receptor. Oncotarget. 2015;6:21268–82.

    Article  PubMed  PubMed Central  Google Scholar 

  1033. Zhong HJ, Ma VP, Cheng Z, et al. Discovery of a natural product inhibitor targeting protein neddylation by structure-based virtual screening. Biochimie. 2012;94:2457–60.

    Article  CAS  PubMed  Google Scholar 

  1034. Lee HM, Chan DS, Yang F, et al. Identification of natural product fonsecin B as a stabilizing ligand of c-myc G-quadruplex DNA by high-throughput virtual screening. Chem Commun. 2010;46:4680–2.

    Article  CAS  Google Scholar 

  1035. Ma D-L, Chan DS-H, Leung C-H. Molecular docking for virtual screening of natural product databases. ChemSci. 2011;2:1656–65.

    CAS  Google Scholar 

  1036. Cierpicki T, Grembecka J. Challenges and opportunities in targeting the menin-MLL interaction. Future Med Chem. 2014;6:447–62.

    Article  CAS  PubMed  Google Scholar 

  1037. Chen YZ, Zhi DG. Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins. 2001;43:217–26.

    Article  CAS  PubMed  Google Scholar 

  1038. Wang JC, Chu PY, Chen CM, et al. 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 

  1039. Lauro G, Romano A, Riccio R, et al. Inverse virtual screening of antitumor targets: pilot study on a small database of natural bioactive compounds. J Nat Prod. 2011;74:1401–7.

    Article  CAS  PubMed  Google Scholar 

  1040. Lauro G, Masullo M, Piacente S, et al. Inverse virtual screening allows the discovery of the biological activity of natural compounds. Bioorg Med Chem. 2012;20:3596–602.

    Article  CAS  PubMed  Google Scholar 

  1041. Vuong H, Cheng F, Lin CC, et al. Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach. Genome Med. 2014;6:81.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  1042. Zhao J, Cheng F, Wang Y, et al. Systematic prioritization of druggable mutations in approximately 5000 genomes across 16 cancer types using a structural genomics-based approach. Mol Cell Proteomics. 2016;15:642–56.

    Article  CAS  PubMed  Google Scholar 

  1043. Lu W, Cheng F, Jiang J, et al. FXR antagonism of NSAIDs contributes to drug-induced liver injury identified by systems pharmacology approach. Sci Rep. 2015;5:8114.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1044. Sliwoski G, Kothiwale S, Meiler J, et al. Computational methods in drug discovery. Pharmacol Rev. 2014;66:334–95.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  1045. Lavecchia A. Machine-learning approaches in drug discovery: methods and applications. Drug Discov Today. 2015;20:318–31.

    Article  PubMed  Google Scholar 

  1046. Yan X, Liao C, Liu Z, et al. Chemical structure similarity search for ligand-based virtual screening: methods and computational resources. Curr Drug Targets. 2016;17:1580–5.

    Article  CAS  PubMed  Google Scholar 

  1047. Liu X, Ouyang S, Yu B, et al. PharmMapper server: a web server for potential drug target identification using pharmacophore map** approach. Nucleic Acids Res. 2010;38:W609–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1048. Yan X, Li J, Liu Z, et al. Enhancing molecular shape comparison by weighted Gaussian functions. J Chem Inf Model. 2013;53:1967–78.

    Article  CAS  PubMed  Google Scholar 

  1049. Fang J, Yang R, Gao L, et al. Predictions of BuChE inhibitors using support vector machine and naive Bayesian classification techniques in drug discovery. J Chem Inf Model. 2013;53:3009–20.

    Article  CAS  PubMed  Google Scholar 

  1050. Fang J, Yang R, Gao L, et al. Consensus models for CDK5 inhibitors in silico and their application to inhibitor discovery. Mol Divers. 2015;19:149–62.

    Article  CAS  PubMed  Google Scholar 

  1051. Fang J, Li Y, Liu R, et al. Discovery of multitarget-directed ligands against Alzheimer’s disease through systematic prediction of chemical-protein interactions. J Chem Inf Model. 2015;55:149–64.

    Article  CAS  PubMed  Google Scholar 

  1052. Fang J, Pang X, Wu P, et al. Discovery of neuroprotective compounds by machine learning approaches. RSC Adv. 2016;6:9857.

    Article  CAS  Google Scholar 

  1053. Cheng F, Li W, Liu G, et al. In silico ADMET prediction: recent advances, current challenges and future trends. Curr Top Med Chem. 2013;13:1273–89.

    Article  CAS  PubMed  Google Scholar 

  1054. Sprague B, Shi Q, Kim MT, et al. Design, synthesis and experimental validation of novel potential chemopreventive agents using random forest and support vector machine binary classifiers. J Comput Aided Mol Des. 2014;28:631–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1055. Bilsland AE, Pugliese A, Liu Y, et al. Identification of a selective G1-phase benzimidazolone inhibitor by a senescence-targeted virtual screen using artificial neural networks. Neoplasia. 2015;17:704–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1056. Liu H, Sun J, Guan J, et al. Improving compound-protein interaction prediction by building up highly credible negative samples. Bioinformatics. 2015;31:i221–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1057. Mousavian Z, Masoudi-Nejad A. Drug-target interaction prediction via chemogenomic space: learning-based methods. Expert Opin Drug Metab Toxicol. 2014;10:1273–87.

    Article  PubMed  Google Scholar 

  1058. Yamanishi Y. Chemogenomic approaches to infer drug-target interaction networks. Methods Mol Biol. 2013;939:97–113.

    Article  CAS  PubMed  Google Scholar 

  1059. Zhao S, Li S. Network-based relating pharmacological and genomic spaces for drug target identification. PLoS One. 2010;5:e11764.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  1060. Yamanishi Y, Araki M, Gutteridge A, et al. Prediction of drug target interaction networks from the integration of chemical and genomic spaces. Bioinformatics. 2008;24:i232–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1061. Bleakley K, Yamanishi Y. Supervised prediction of drug target interactions using bipartite local models. Bioinformatics. 2009;25:2397–403.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1062. Keum J, Yoo S, Lee D, et al. Prediction of compound-target interactions of natural products using large-scale drug and protein information. BMC Bioinformatics. 2016;17(Suppl 6):219.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  1063. Yu H, Chen J, Xu X, et al. A systematic prediction of multiple drug-target interactions from chemical, genomic, and pharmacological data. PLoS One. 2012;7:e37608.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1064. Huang C, Zheng C, Li Y, et al. Systems pharmacology in drug discovery and therapeutic insight for herbal medicines. Brief Bioinform. 2014;15:710–33.

    Article  PubMed  Google Scholar 

  1065. Sawada R, Kotera M, Yamanishi Y. Benchmarking a wide range of chemical descriptors for drug-target interaction prediction using a chemogenomic approach. Mol Inform. 2014;33:719–31.

    Article  CAS  PubMed  Google Scholar 

  1066. Cheng F, Zhou Y, Li J, et al. Prediction of chemical-protein interactions: multitarget-QSAR versus computational chemogenomic methods. Mol Biosyst. 2012;8:2373–84.

    Article  CAS  PubMed  Google Scholar 

  1067. Cheng F, Zhou Y, Li W, et al. Prediction of chemical-protein interactions network with weighted network-based inference method. PLoS One. 2012;7:e41064.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1068. Wu Z, Cheng F, Li J, et al. SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioning. Brief Bioinform. 2017;18:333–47.

    CAS  PubMed  Google Scholar 

  1069. Wu Z, Lu W, Wu D, et al. In silico prediction of chemical mechanism of action via an improved network-based inference method. Br J Pharmacol. 2016;173:3372–85.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1070. Cheng F, LiW ZY, et al. Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic derived models (PTDMs). Mol Biosyst. 2013;9:1316–25.

    Article  CAS  PubMed  Google Scholar 

  1071. Li J, Wu Z, Cheng F, et al. Computational prediction of microRNA networks incorporating environmental toxicity and disease etiology. Sci Rep. 2014;4:5576.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1072. Li J, Lei K, Wu Z, et al. Network-based identification of microRNAs as potential pharmacogenomic biomarkers for anticancer drugs. Oncotarget. 2016;7:45584–96.

    Article  PubMed  PubMed Central  Google Scholar 

  1073. Kitano H. Systems biology: a brief overview. Science. 2002;295:1662–4.

    Article  CAS  PubMed  Google Scholar 

  1074. Kitano H. Computational systems biology. Nature. 2002;420:206–10.

    Article  CAS  PubMed  Google Scholar 

  1075. Berg EL. Systems biology in drug discovery and development. Drug Discov Today. 2014;19:113–25.

    Article  CAS  PubMed  Google Scholar 

  1076. Cheng F, Murray JL, Rubin DH. Drug repurposing: new treatments for Zika virus infection? Trends Mol Med. 2016;22:919–21.

    Article  PubMed  Google Scholar 

  1077. Qu XA, Rajpal DK. Applications of connectivity map in drug discovery and development. Drug Discov Today. 2012;17:1289–98.

    Article  CAS  PubMed  Google Scholar 

  1078. Hieronymus H, Lamb J, Ross KN, et al. Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. Cancer Cell. 2006;10:321–30.

    Article  CAS  PubMed  Google Scholar 

  1079. Wei G, Twomey D, Lamb J, et al. Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance. Cancer Cell. 2006;10:331–42.

    Article  CAS  PubMed  Google Scholar 

  1080. Langley SR, Dwyer J, Drozdov I, et al. Proteomics: from single molecules to biological pathways. Cardiovasc Res. 2013;97:612–22.

    Article  CAS  PubMed  Google Scholar 

  1081. Bensimon A, Heck AJ, Aebersold R. Mass spectrometry-based proteomics and network biology. Annu Rev Biochem. 2012;81:379–405.

    Article  CAS  PubMed  Google Scholar 

  1082. Savitski MM, Reinhard FB, Franken H, et al. Tracking cancer drugs in living cells by thermal profiling of the proteome. Science. 2014;346:1255784.

    Article  PubMed  CAS  Google Scholar 

  1083. Franken H, Mathieson T, Childs D, et al. Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry. Nat Protoc. 2015;10:1567–93.

    Article  CAS  PubMed  Google Scholar 

  1084. Reinhard FB, Eberhard D. Thermal proteome profiling monitors ligand interactions with cellular membrane proteins. Nat Methods. 2015;12:1129–31.

    Article  CAS  PubMed  Google Scholar 

  1085. Sacco F, Silvestri A, Posca D, et al. Deep proteomics of breast cancer cells reveals that metformin rewires signaling networks away from a pro-growth state. Cell Syst. 2016;2:159–71.

    Article  CAS  PubMed  Google Scholar 

  1086. Harvey AL, Edrada-Ebel R, Quinn RJ. The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov. 2015;14:111–29.

    Article  CAS  PubMed  Google Scholar 

  1087. Kaddurah-Daouk R, Kristal BS, Weinshilboum RM. Metabolomics: a global biochemical approach to drug response and disease. Annu Rev Pharmacol Toxicol. 2008;48:653–83.

    Article  CAS  PubMed  Google Scholar 

  1088. Birkenstock T, Liebeke M, Winstel V, et al. Exometabolome analysis identifies pyruvate dehydrogenase as a target for the antibiotic triphenylbismuthdichloride in multiresistant bacterial pathogens. J Biol Chem. 2012;287:2887–95.

    Article  CAS  PubMed  Google Scholar 

  1089. Zhang B, Watts KM, Hodge D, et al. A second target of the antimalarial and antibacterial agent fosmidomycin revealed by cellular metabolic profiling. Biochemistry. 2011;50:3570–7.

    Article  CAS  PubMed  Google Scholar 

  1090. Bayet-Robert M, Lim S, Barthomeuf C, et al. Biochemical disorders induced by cytotoxic marine natural products in breast cancer cells as revealed by proton NMR spectroscopy-based metabolomics. Biochem Pharmacol. 2010;80:1170–9.

    Article  CAS  PubMed  Google Scholar 

  1091. Pulido MR, Garcia-Quintanilla M, Gil-Marques ML, et al. Identifying targets for antibiotic development using omics technologies. Drug Discov Today. 2016;21:465–72.

    Article  CAS  PubMed  Google Scholar 

  1092. Zhao Y, Hu Q, Cheng F, et al. SoNar, a highly responsive NADþ/NADH sensor, allows high-throughput metabolic screening of anti-tumor agents. Cell Metab. 2015;21:777–89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1093. Kim HK, Wilson EG, Choi YH, et al. Metabolomics: a tool for anticancer lead-finding from natural products. Planta Med. 2010;76:1094–102.

    Article  CAS  PubMed  Google Scholar 

  1094. Collins GS, de Groot JA, Dutton S, et al. External validation of multivariable prediction models: a systematic review of methodological conduct and reporting. BMC Med Res Methodol. 2014;14:40.

    Article  PubMed  PubMed Central  Google Scholar 

  1095. Reker D, Perna AM, Rodrigues T, et al. Revealing the macromolecular targets of complex natural products. Nat Chem. 2014;6(12):1072–8.

    Article  CAS  PubMed  Google Scholar 

  1096. Ashburn TT, Thor KB. Drug repositioning: identifying and develo** new uses for existing drugs. Nat Rev Drug Discov. 2004;3(8):673–83.

    Article  CAS  PubMed  Google Scholar 

  1097. Pushpakom S, Iorio F, Eyers PA, et al. Drug repurposing: progress, challenges and recommendations. Nat Rev Drug Discov. 2019;18(1):41–58.

    Article  CAS  PubMed  Google Scholar 

  1098. Schcolnik-Cabrera A, Juárez-López D, Duenas-Gonzalez A. Perspectives on drug repurposing. Curr Med Chem. 2021;28(11):2085–99.

    Article  CAS  PubMed  Google Scholar 

  1099. Sleigh SH, Barton CL. Repurposing strategies for therapeutics. Pharmaceutical Med. 2012;24(3):151–9.

    Article  Google Scholar 

  1100. Cha Y, Erez T, Reynolds IJ, et al. Drug repurposing from the perspective of pharmaceutical companies. Br J Pharmacol. 2018;175(2):168–80.

    Article  CAS  PubMed  Google Scholar 

  1101. Sam E, Athri P. Web-based drug repurposing tools: a survey. Brief Bioinform. 2019;20(1):299–316.

    Article  PubMed  CAS  Google Scholar 

  1102. Masoudi-Sobhanzadeh Y, Omidi Y, Amanlou M, et al. Drug databases and their contributions to drug repurposing Genomics. 2020; 112(2): 1087–1095.

    Google Scholar 

  1103. Karaman B, Sippl W. Computational drug repurposing: Current trends. Curr Med Chem. 2019;26(28):5389–409.

    Article  CAS  PubMed  Google Scholar 

  1104. Oprea TI, Bauman JE, Bologa CG, et al. Drug repurposing from an academic perspective. Drug Discov Today. 2011;8(3-4):61–9.

    Google Scholar 

  1105. Haupt VJ, Daminelli S, Schroeder M. Drug promiscuity in PDB: Protein binding site similarity is key. PLoS One. 2013;8(6):e65894.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1106. Feldmann C, Miljković F, Yonchev D, et al. Identifying promiscuous compounds with activity against different target classes. Molecules. 2019;24(22):4185.

    Article  CAS  PubMed Central  Google Scholar 

  1107. Gupta MN, Alam A, Hasnain SE. Protein promiscuity in drug discovery, drug-repurposing and antibiotic resistance. Biochimie. 2020;175:50–7.

    Article  CAS  PubMed  Google Scholar 

  1108. Gilberg E, Gütschow M, Bajorath J. Promiscuous ligands from experimentally determined structures, binding conformations, and protein family-dependent interaction hotspots. ACS Omega. 2019;4(1):1729–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1109. Irwin JJ, Duan D, Torosyan H, et al. An aggregation advisor for ligand discovery. J Med Chem. 2015;58:7076–87.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1110. Baell JB, Walters MA. Chemistry: Chemical con artists foil drug discovery. Nature. 2014;513:481–3.

    Article  CAS  PubMed  Google Scholar 

  1111. Aldrich C, Bertozzi C, Georg GI, et al. The ecstasy and agony of assay interference compounds. J Chem Inf Model. 2017;57:387–90.

    Article  CAS  PubMed  Google Scholar 

  1112. Stumpfe D, Tinivella A, Rastelli G, et al. Promiscuity of inhibitors of human protein kinases at varying data confidence levels and test frequencies. RSC Adv. 2017;7:41265–71.

    Article  CAS  Google Scholar 

  1113. Hu Y, Bajorath J. Entering the ‘big data’ era in medicinal chemistry: Molecular promiscuity analysis revisited. Future Sci OA. 2017;3:FSO179.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1114. Woolf SH. The meaning of translational research and why it matters. JAMA. 2008;299:211–3.

    Article  CAS  PubMed  Google Scholar 

  1115. Schuster D, Laggner C, Langer T. Why drugs fail—a study on side effects in new chemical entities. Curr Pharm Des. 2005;11:3545–59.

    Article  CAS  PubMed  Google Scholar 

  1116. Morgan P, Van Der Graaf PH, Arrowsmith J, et al. Can the flow of medicines be improved? Fundamental pharmacokinetic and pharmacological principles toward improving phase II survival. Drug Discov Today. 2012;17:419–24.

    Article  CAS  PubMed  Google Scholar 

  1117. Oprea TI, Bauman JE, Bologa CG, et al. Drug repurposing from an academic perspective. Drug Discov Today Ther Strateg. 2011;8:61–9.

    Article  PubMed  PubMed Central  Google Scholar 

  1118. Oprea TI, Mestres J. Drug repurposing: far beyond new targets for old drugs. AAPS J. 2012;14:759–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1119. Gallo K, Goede A, Eckert A, et al. PROMISCUOUS 2.0: a resource for drug-repositioning. Nucleic Acids Res. 2021;49(D1):D1373–80.

    Article  CAS  PubMed  Google Scholar 

  1120. Xue H, Li J, **e H, et al. Review of drug repositioning approaches and resources. Int J Biol Sci. 2018;14:1232–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1121. Swinney DC, Anthony J. How were new medicines discovered? Nat Rev Drug Discov. 2011;10:507–19.

    Article  CAS  PubMed  Google Scholar 

  1122. Eder J, Sedrani R, Wiesmann C. The discovery of first-in class drugs: origins and evolution. Nat Rev Drug Discov. 2014;13:577–87.

    Article  CAS  PubMed  Google Scholar 

  1123. Horvath P, Aulner N, Bickle M, et al. Screening out irrelevant cell-based models of disease. Nat Rev Drug Discov. 2016;15:715–69.

    Article  CAS  Google Scholar 

  1124. Pandey UB, Nichols CD. Human disease models in Drosophila melanogaster and the role of the fly in therapeutic drug discovery. Pharmacol Rev. 2011;63:411–36.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1125. Sanseau P, Agarwal P, Barnes MR, et al. Use of genome-wide association studies. Nat Biotechnol. 2012;30:317–20.

    Article  CAS  PubMed  Google Scholar 

  1126. Rastegar-Mojarad M, Zhan Y, Kolesar JM, et al. Opportunities for drug repositioning from phenome-wide association studies. Nat Biotechnol. 2015;33:342–5.

    Article  CAS  PubMed  Google Scholar 

  1127. Iorio F, Rittman T, Ge H, et al. Transcriptional data: a new gateway to drug repositioning? Drug Discov Today. 2013;18:350–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1128. Sirota M, Dudley JT, Kim J, et al. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med. 2011;3:96ra77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1129. Teachey DT, Sheen C, Hall J, et al. mTOR inhibitors are synergistic with methotrexate: an effective combination to treat acute lymphoblastic leukemia. Blood. 2008;112:2020–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1130. Fransecky L, Mochmann LH, Baldus CD. Outlook on PI3K/AKT/mTOR inhibition in acute leukemia. Mol Cell Ther. 2015;3:2–19.

    Article  PubMed  PubMed Central  Google Scholar 

  1131. Geva M, Kusko R, Soares H, et al. Pridopidine activates neuroprotective pathways impaired in Huntington disease. Hum Mol Genet. 2016;25(18):3975–87.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1132. Nelson MR, Tipney H, Painter JL, et al. The support of human genetic evidence for approved drug indications. Nat Genet. 2015;47:856–60.

    Article  CAS  PubMed  Google Scholar 

  1133. Fowler KD, Funt JM, Artyomov MN, et al. Leveraging existing data sets to generate new insights into Alzheimer’s disease biology in specific patient subsets. Sci Rep. 2015;5:14324–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1134. Xu H, Aldrich MC, Chen Q, et al. Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. J Am Med Inform Assoc. 2014;22:179–91.

    Article  PubMed  PubMed Central  Google Scholar 

  1135. Yang L, Agarwal P. Systematic drug repositioning based on clinical side-effects. PLoS One. 2011;6:e28025.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1136. Kuhn M. The SIDER database of drugs and side effects. Nucleic Acids Res. 2016;44:D1075–9.

    Article  CAS  PubMed  Google Scholar 

  1137. Gottlieb A, Stein GY, Ruppin ER, et al. PREDICT: a method for inferring novel drug indications with application to personalized medicine. Mol Syst Biol. 2011;7:496–505.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  1138. Yu L, Ma X, Zhang L, et al. Prediction of new drug indications based on clinical data and network modularity. Sci Rep. 2016;6:32530.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1139. Tan F, Yang R, Xu X, et al. Drug repositioning by applying ‘expression profiles’ generated by integrating chemical structure similarity and gene semantic similarity. Mol Biosyst. 2014;10:1126–38.

    Article  CAS  PubMed  Google Scholar 

  1140. Paik H, Chung AY, Park HC, et al. Repurpose terbutaline sulfate for amyotrophic lateral sclerosis using electronic medical records. Sci Rep. 2015;5:8580–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1141. Shameer K, Glicksberg BS, Hodos R, et al. Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. Brief Bioinform. 2018;19:656–78.

    Article  CAS  PubMed  Google Scholar 

  1142. Brown AS, Patel CJ. A standard database for drug repositioning. Sci Data. 2017;4:170029.

    Article  PubMed  PubMed Central  Google Scholar 

  1143. Zhao C, Dai X, Li Y, et al. EK-DRD: a comprehensive database for drug repositioning inspired by experimental knowledge. J Chem Inf Model. 2019;59:3619–24.

    Article  CAS  PubMed  Google Scholar 

  1144. Wu H, Huang J, Zhong Y, et al. DrugSig: A resource for computational drug repositioning utilizing gene expression signatures. PLoS One. 2017;12:e0177743.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  1145. Avram S, Bologa CG, Holmes J, et al. DrugCentral 2021 supports drug discovery and repositioning. Nucleic Acids Res. 2021;49(D1):D1160–9.

    Article  CAS  PubMed  Google Scholar 

  1146. Ursu O, Holmes J, Knockel J, et al. DrugCentral: Online drug compendium. Nucleic Acids Res. 2017;45:D932–9.

    Article  CAS  PubMed  Google Scholar 

  1147. UniProtConsortium UniProt. a worldwide hub of protein knowledge. Nucleic Acids Res. 2019;47:D506–15.

    Article  CAS  Google Scholar 

  1148. Hastings J, Owen G, Dekker A, et al. ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res. 2016;44:D1214–9.

    Article  CAS  PubMed  Google Scholar 

  1149. Himmelstein DS, Lizee A, Hessler C, et al. Systematic integration of biomedical knowledge prioritizes drugs for repurposing. Elife. 2017;6:e26726.

    Article  PubMed  PubMed Central  Google Scholar 

  1150. Aguirre-Plans J, Piñero J, Sanz F, et al. GUILDify v2.0: A tool to identify molecular networks underlying human diseases, their comorbidities and their druggable targets. J Mol Biol. 2019;431:2477–84.

    Article  CAS  PubMed  Google Scholar 

  1151. Chambers J, Davies M, Gaulton A, et al. UniChem: a unified chemical structure cross-referencing and identifier tracking system. J Cheminform. 2013;5:3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  1152. Alexander SPH, Kelly E, Mathie A, et al. The concise guide to pharmacology 2019/20: Introduction and other protein targets. Br J Pharmacol. 2019;176:S1–20.

    PubMed  PubMed Central  Google Scholar 

  1153. Brown AS, Patel CJ. A standard database for drug repositioning. Scientific Data. 2017;4:170029.

    Article  PubMed  PubMed Central  Google Scholar 

  1154. Mayers M, Li TS, Queralt-Rosinach N, et al. Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network. BMC Bioinformatics. 2019;20:653.

    Article  PubMed  PubMed Central  Google Scholar 

  1155. Wu Q, Taboureau O, Audouze K. Development of an adverse drug event network to predict drug toxicity. Curr Res Toxicol. 2020;1:48–55.

    Article  PubMed  PubMed Central  Google Scholar 

  1156. Ursu O, Holmes J, Bologa CG, et al. DrugCentral 2018: an update. Nucleic Acids Res. 2019;47:D963–70.

    Article  CAS  PubMed  Google Scholar 

  1157. Levin JM, Oprea TI, Davidovich S, et al. Artificial intelligence, drug repurposing and peer review. Nat Biotechnol. 2020;38:1127–31.

    Article  CAS  PubMed  Google Scholar 

  1158. Avram S, Curpan R, Halip L, et al. Off-patent drug repositioning. J Chem Inf Model. 2020;60(12):5746–53.

    Article  CAS  PubMed  Google Scholar 

  1159. KC G, Bocci G, Verma S, et al. REDIAL-2020: A suite of machine learning models to estimate anti-SARS-CoV-2 activities. ChemRxiv. 2020.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Wang, Z., Yang, B. (2022). Polypharmacology in Drug Design and Discovery—Basis for Rational Design of Multitarget Drugs. In: Polypharmacology. Springer, Cham. https://doi.org/10.1007/978-3-031-04998-9_12

Download citation

Publish with us

Policies and ethics

Navigation