Binding Mode of Small Molecule Splice Modifiers to RNA

The Allain and Campagne labs previously elucidated the binding mode of the SMN-C5 splicing modifier molecule to its target RNA, a 5'-splice site in the SMN2 mRNA, and called its mode of action 5'-splice site bulge repair. They followed up this study by determining the structure of four additional splicing modifiers that either bind to the same 5' splice in the SMN2 mRNA or a 5'-splice site in the HTT mRNA. Despite being chemically different, the molecules bind their RNA target in a similar fashion. Their results have been published in the article "The diversity of splicing modifiers acting on A-1 bulged 5'-splice sites reveals rules for rational drug design" in Nucleic Acids Research.

Pharmacological modulation of RNA splicing by small molecules is an emerging facet of drug discovery. In this context, the SMN2 splicing modifier SMN-C5 was used as a prototype to understand the mode of action of small molecule splicing modifiers and propose the concept of 5'-splice site bulge repair. In this study, we combined in vitro binding assays and structure determination by NMR spectroscopy to identify the binding modes of four other small molecule splicing modifiers that switch the splicing of either the SMN2 or the HTT gene. Here, we determined the solution structures of risdiplam, branaplam, SMN-CX and SMN-CY bound to the intermolecular RNA helix epitope containing an unpaired adenine within the G-2A-1G+1U+2 motif of the 5'-splice site. Despite notable differences in their scaffolds, risdiplam, SMN-CX, SMN-CY and branaplam contact the RNA epitope similarly to SMN-C5, suggesting that the 5'-splice site bulge repair mechanism can be generalised. 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.

Read the Publication in Nucleic Acids Research (Open Access)

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Abstract, figure and title from Malard, Wolter et al (2024) Nucleic Acids Res published under a CC BY-NC 4.0 license.