Rational design of modularly assembled small molecules to target the myotonic dystrophy RNAs
Lee, Melissa Mayyen
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The ubiquitous role of r ibo n ucleic a cids (RNA) in gene regulation coupled with the unique secondary and tertiary structures that they form make RNA a suitable candidate for drug targeting and design. A quintessential example would be the m yotonic d ystrophy RNAs (DM RNAs). M yotonic d ystrophy type 1 (DM1) and type 2 (DM2) are caused by a gain-of-function of the RNA transcripts resulting from a microsatellite expansion in the human genome. Although stemming from different genetic loci, the clinical presentations of these two diseases are similar, suggesting a common pathogenic mechanism. Indeed, both RNA transcripts form similar secondary structures that sequester m uscle b li n d- l ike- 1 protein (MBNL1), a splicing regulator protein. As a result, abnormal protein isoforms are translated from the misspliced mRNAs causing the symptoms observed in DM. A possible form of treatment for the disease would be to displace the sequestration of MBNL1 from the RNAs with a small molecule allowing the protein to regain its role as a splicing regulator. A previous two-dimensional screen of a small library of aminoglycosides to an RNA library established kanamycin A as a high-affinity, high-specificity binder of pyrimidine-rich RNA internal loops, not unlike those observed in DM RNAs. Additionally, Hoechst 33258 has been established as a lead molecule for binding to the DM1 repeat motifs. Herein, efforts to develop these two lead molecules into high-affinity and high-specificity inhibitors of the DM RNA-MBNL1 interaction are discussed. Employment of modular assembly in targeting several RNA motifs simultaneously was essential in establishing potent ligands. Spacing density and flexibility within the modularly assembled scaffold was essential in increasing affinity and specificity to targets. The most potent inhibitors of the DM RNA-MBNL1 interaction had higher affinity and specificity to their target molecules than that of its natural ligand, MBNL1. Finally, the inhibitors are assessed for cellular viability in live murine myoblast cells. The ligands developed were non-toxic and cell permeable. Cellular localization of the ligands was manipulated by attachment of nuclear localization signals on the pharmacophore. The utility of the peptoid scaffold in targeting different cell lines were also investigated.