The diversity of splicing modifiers acting on A-1 bulged 5'-splice sites reveals rules to guide rational design

Non-physiological alternative splicing patterns are associated with numerous human diseases. Among the strategies developed to treat these diseases, small molecule splicing modifiers are emerging as a new class of RNA therapeutics. The SMN2 splicing modifier SMN-C5 was used as a prototype to understand their mode of action and discover the concept of 5-splice site bulge repair. However, different small molecules harbouring a similar activity were also identified. In this study, we combined NMR spectroscopy and computational approaches to determine the binding modes of other SMN2 and HTT splicing modifiers at the interface between U1 snRNP and an A-1 bulged 5-splice site. Our results show that the other splicing modifiers interact with the intermolecular RNA helix epitope containing an unpaired adenine within a G-2A-1G+1U+2 motif, which is essential for their biological activity. We also determined structural models of risdiplam, SMN-CX, and branaplam bound to RNA, and solved the solution structure of the most divergent SMN2 splicing modifier, SMN-CY, in complex with the RNA helix. These findings not only deepen our understanding of the chemical diversity of splicing modifiers that target A-1 bulged 5-splice sites, but also identify common pharmacophores required for modulating 5-splice site selection with small molecules.