Characterizing RNA-Small Molecule Interactions for the Design of Selective, Bioactive Small Molecules Targeting RNA from Sequence
Velagapudi, Sai Pradeep
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There are many potential RNA drug targets in bacterial, viral, and human transcriptomes. However, there are few small molecules that modulate RNA function. This is due, in part, to a lack of fundamental understanding about RNA-ligand interactions including the types of small molecules that bind to RNA structural elements and the RNA structural elements that bind to small molecules. If such information were known, it could allow for small molecules to be exploited to target RNAs implicated in pathological or disease condition. We utilized Two-Dimensional Combinatorial Screening (2DCS), a library-versus-library screening approach, to select the motifs displayed in a RNA library displaying either an internal loop or a hairpin loop library. The results from 2DCS were used to identify statistically significant trends. RNA-Privileged Space Predictor (RNA-PSP) was created to automate statistical analysis of the selected RNA motifs to determine features (for example, 5'GC steps) in the selected sequences that occur with ≥95% confidence. These motifs were then analyzed using Structure-Activity Relationships Through Sequencing (StARTS), a statistical approach that defines the privileged RNA motif space that binds a small molecule. StARTS allowed for the facile annotation of the selected RNA motif-small molecule interactions in terms of affinity and selectivity. Thus 2DCS and StARTS allowed us to establish and annotate a database of RNA-small molecule interactions. In order to utilize the information in the RNA motif-small molecule database a computational algorithm was developed to parse RNA secondary structures into motifs. These motifs were then compared to our database of RNA motif-small molecule interactions to identify overlap. The output of which is the targetable motifs and the corresponding lead small molecules for an RNA of interest. This approach termed "inforna" was developed to design small molecule effectors of RNA in a transcriptome-wide manner from solely sequence. Inforna was applied towards the entire composite of human microRNA precursors and identified multiple bioactive small molecules that inhibit biogenesis by binding to Dicer or Drosha processing sites. Amongst 26 lead interactions, the most avid interaction is between a benzimidazole ( 14 ) and precursor microRNA-96. Compound 14 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by a siRNA, validating compound selectivity for the microRNA-96- FOXO1 pathway. Importantly, microRNA profiling shows that 14 only significantly effects microRNA-96 biogenesis and that 14 is a more selective modulator of microRNA-96 than an oligonucleotide. Since a myriad of genomic and functional studies are rapidly providing information about disease-associated genes, our approach could provide an expedited route to small molecules that target the RNA product of those genes and potentially transform the manner in which RNA-directed chemical probes or therapeutics are identified.