Deciphering and Leveraging Prominent Features of RNA-Targeting Small Molecules

Amanda Hargrove, Ph.D., Advisor

Abstract

Non-coding RNAs (ncRNAs) are a newly discovered class of biomolecules implicated in biological processes and disease pathogenesis. Small molecules have been proven to be a viable avenue to study biologically relevant ncRNAs; however, the development of RNA-targeting chemical probes has been hindered due in part to a lack of guiding principles for achieving selective RNA:small molecule interactions. Therefore, there is a need to extensively evaluate interactions between chemically diverse small molecules and structurally distinct RNAs in order to comprehensively understand the properties that lead to selective recognition.

Recent studies from our laboratory and others have analyzed features of selective RNA-binding compounds and suggested the existence of a privileged chemical space for RNA-targeting small molecules. Consequently, this work aims to examine the potential existence and boundaries of RNA-privileged chemical space. Towards these goals, we have taken three different approaches that generally involve the evaluation of small molecule binding to various RNA targets using indicator displacement assays and computational analysis of molecular features. In the first approach, we explicitly tested and leveraged properties of bioactive, RNA-targeting small molecules through the curation and evaluation of an RNA-biased library. In the second approach, we utilized and evaluated an unbiased library to generally probe and decipher small molecule features that are relevant for targeting RNA. Lastly, in the third approach, we developed and synthesized RNA libraries that consisted of a single secondary structure motif in order to identify favorable features of both RNA and small molecules.

Collectively, our efforts have afforded a large dataset profiling ~180,000 RNA:small molecule interactions. We successfully identified multiple RNA-binding small molecules, several of which bind with high affinity and are comprised of novel scaffolds. By analyzing our dataset, we have obtained insights into chemical space that is favorable for targeting RNA. Furthermore, we have learned valuable lessons and considerations for approaches used to discover RNA:small molecule interactions. Altogether, these efforts contribute to furthering a fundamental understanding of small molecule recognition of RNA, which in turn, will facilitate the development of RNA-targeting small molecule probes and therapeutics.