Chemical Biology Approaches for Investigating RNA-Protein Interactions

Recent studies have shown that RNAs are invariably bound to and often modified by RNA-binding proteins (RBPs). Thus, it is no surprise that RBPs have been found to play key roles in regulating many aspects of coding and non-coding RNA biology, including RNA processing, nuclear export, cellular transport, function, localization, and stability. These efforts are carried out by >1,500 unique RBPs that utilize a variety of RNA-binding domains to achieve oftentimes specific and high affinity interactions with target transcripts; however, non-canonical RBPs have also been identified. Disruption of this complex network of RNA-protein interactions (RPIs) has been implicated in a number of human diseases. Thus, the targeting of RBPs and RPIs has arisen as a new frontier in RNA-targeted drug discovery. Recent work from our laboratory has resulted in the development of tools and technologies applicable to the study of RPIs, including biochemical and cellular assays for the detection, validation, and screening of RPIs; the discovery of small molecule, peptide, and natural product inhibitors of RPIs and RBPs; and the discovery of new biological insights into the regulation of RPIs and RBPs. Building upon our recent progress, the research proposed in this project is focused on three major research directions. For the first project, we will continue our efforts to develop our laboratory’s live-cell RPI assay technology, RNA interaction with Protein-mediated Complementation Assay (RiPCA), as a scalable and robust platform for validating and manipulating cellular RPIs. For the second project, we will utilize RiPCA to expand our access to high-quality chemical probes for targeting cellular RPIs. For the third project, we will use mechanistically distinct chemical probes targeting eIF4E to explore the context-dependence of RBP regulation and activity. Through these combined research efforts, we will enable the study of RBPs and RPIs in living cells to promote our understanding of this new frontier of cellular biology with great potential for the development of new medicines.