Solving the Problem of Sequence Selective RNA Recognition by Small Molecules with Application to Myotonic Dystrophy and HIV

Synthetic small molecules that bind specific RNA sequences with high affinity are essential biochemical probes for understanding cellular process and as therapeutic agents for treatment of diseases. This is in part because ribonucleic acid (RNA) is not simply an intermediary between DNA and protein biosynthesis. Rather, RNA plays a central role in biochemical processes including enzyme catalysis, protein translation, transcription or posttranscriptional regulation of gene expression and in many disease states. However the ability to design small molecules to selectively bind RNA sequences and elicit RNA-dependent biological responses is still an unsolved topic in bioorganic chemistry.;This thesis describes a strategy to transform small molecules identified from a Resin Bound Dynamic Chemistry (RBDCC) library into high affinity and sequence selective RNA-ligands with in vitro and in vivo activities. This strategy was tested using a CUG trinucleotide repeat (implicated in Myotonic Dystrophy type 1) and an HIV-1 frameshift inducing RNA (relevant for effective translation of gag and pol gene during HIV replication) as models.;Introduction of a benzo[g]quinoline substructure previously unknown in the context of RNA recognition, as well as other modifications, provided several molecules with enhanced binding properties, including compounds with strong selectivity for CUG repeats over CAG repeats or CAG-CUG duplex RNA. Compounds readily penetrate cells, and improve luciferase activity in a mouse myoblast assay in which enzyme function is coupled to a release of nuclear CUG-RNA retention. Most importantly, two compounds are able to partially restore splicing in a mouse model of DM1. In a parallel effort, the natural product lomofungin was identified in a high throughput screen as potent inhibitor of the MBNL-CUG repeat RNA interaction. Analysis of lomofungin showed that it degraded in DMSO to form a dimer that was 17-fold more active than lomofungin. In the context of HIV-1, the transformed compounds stimulated frameshifting in HIV-1 by > 50 % as measured by a dual luciferase frameshift assay in transiently transfected HEK 293 FT cells. Importantly, this increased frameshifting translated into a significant inhibition of viral infectivity in pseudotyped HIV.