8R62

Solution structure of Risdiplam bound to the RNA duplex formed upon 5'-splice site recognition

Summary for 8R62

• Entry DOI: 10.2210/pdb8r62/pdb
• NMR Information: BMRB: 34878
• Descriptor: RNA (5'-R(*AP*UP*AP*CP*(PSU)P*(PSU)P*AP*CP*CP*UP*G)-3'), RNA (5'-R(P*GP*GP*AP*GP*UP*AP*AP*GP*UP*CP*U)-3'), 7-(4,7-diazaspiro[2.5]octan-7-yl)-2-(2,8-dimethylimidazo[1,2-b]pyridazin-6-yl)-1~{H}-pyrido[1,2-a]pyrimidin-4-one (3 entities in total)
• Functional Keywords: rna splicing correction, small molecule splicing modifier, molecular glue, rna
• Biological source: Homo sapiens; More
• Total number of polymer chains: 2
• Total formula weight: 7377.71

Authors

Malard, F.,Campagne, S. (deposition date: 2023-11-20, release date: 2024-03-06, Last modification date: 2024-05-22)

Primary citation

Malard, F.,Wolter, A.C.,Marquevielle, J.,Morvan, E.,Ecoutin, A.,Rudisser, S.H.,Allain, F.H.T.,Campagne, S.
The diversity of splicing modifiers acting on A-1 bulged 5'-splice sites reveals rules for rational drug design.
Nucleic Acids Res., 52:4124-4136, 2024

PubMed Abstract: 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.

PubMed: 38554107
DOI: 10.1093/nar/gkae201

Experimental method

SOLUTION NMR