Macrocyclic peptide inhibitors of protein-RNA interactions

Protein-RNA interactions are essential in the regulation and function of any given RNA. Aberrant formation of such interactions can therefore rapidly lead to disease making them attractive therapeutic targets. Targeting such interactions is challenging however since they involve large interfaces and typically lack well defined pockets. To overcome this challenge, we take inspiration from strategies originally developed to identify protein-protein interaction inhibitors and adapt them for protein-RNA interaction inhibitors. The first strategy we used is structure-based design of stapled peptides as inhibitors of the splicing factor polypyrimidine-tract binding protein 1 (PTBP1). By exploring various stapling strategies, an inhibitory peptide was identified that was stable against proteolysis as well as cell permeable and able to modulate splicing events regulated by PTBP1. When a given target lacks structural information a structure-based design approach can’t be used. To be able to identify inhibitors in this situation we use genetically encoded cyclic peptide libraries (i.e.: SICLOPPS) in combination with an in-house developed assay to screen for inhibitory peptides of the splicing factor hnRNP A2/B1. Preliminary data shows that hits can be found from a single screening round when combined with next generation sequencing and that structural optimization is feasible.