Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes

• Published in: Nature communications Vol. 9; no. 1; pp. 2032 - 12
• Main Authors: Garcia-Lopez, Amparo, Tessaro, Francesca, Jonker, Hendrik R. A., Wacker, Anna, Richter, Christian, Comte, Arnaud, Berntenis, Nikolaos, Schmucki, Roland, Hatje, Klas, Petermann, Olivier, Chiriano, Gianpaolo, Perozzo, Remo, Sciarra, Daniel, Konieczny, Piotr, Faustino, Ignacio, Fournet, Guy, Orozco, Modesto, Artero, Ruben, Metzger, Friedrich, Ebeling, Martin, Goekjian, Peter, Joseph, Benoît, Schwalbe, Harald, Scapozza, Leonardo
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 23.05.2018; Nature Publishing Group; Macmillan; Nature Portfolio
• Subjects: 101/6; 13; 14; 38; 38/77; 38/91; 49; 631/154/1435/2163; 631/154/556; 631/45/500; 631/45/535/1267; 631/45/535/878/1263; Alternative Splicing; Animals; Animals, Genetically Modified; Atrophy; Atròfia muscular; Chemical Sciences; Cribratge; Drosophila; Drug discovery; Drug Evaluation, Preclinical; Exons - genetics; HeLa Cells; Humanities and Social Sciences; Humans; Imidazoles - chemistry; Imidazoles - pharmacology; Imidazoles - therapeutic use; Indoles - chemistry; Indoles - pharmacology; Indoles - therapeutic use; Infant mortality; Medical screening; Molecular chains; Molecular modelling; Molecular Targeted Therapy - methods; multidisciplinary; Muscular atrophy; Muscular Atrophy, Spinal - drug therapy; Muscular Atrophy, Spinal - genetics; Mutation; Neuromuscular diseases; NMR; Nuclear magnetic resonance; Organic chemistry; Pharmaceuticals; Phenotype; Phenotypes; Proteins; R&D; Regulatory Elements, Transcriptional - drug effects; Research & development; Ribonucleic acid; RNA; RNA Splice Sites; RNA, Messenger - chemistry; RNA, Messenger - genetics; RNA, Messenger - metabolism; Science; Science (multidisciplinary); SMN protein; Spectrum analysis; Spinal muscular atrophy; Splicing; Survival of Motor Neuron 2 Protein - genetics; Target recognition
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-04110-1

Modification of SMN2 exon 7 (E7) splicing is a validated therapeutic strategy against spinal muscular atrophy (SMA). However, a target-based approach to identify small-molecule E7 splicing modifiers has not been attempted, which could reveal novel therapies with improved mechanistic insight. Here, we chose as a target the stem-loop RNA structure TSL2, which overlaps with the 5′ splicing site of E7. A small-molecule TSL2-binding compound, homocarbonyltopsentin (PK4C9), was identified that increases E7 splicing to therapeutic levels and rescues downstream molecular alterations in SMA cells. High-resolution NMR combined with molecular modelling revealed that PK4C9 binds to pentaloop conformations of TSL2 and promotes a shift to triloop conformations that display enhanced E7 splicing. Collectively, our study validates TSL2 as a target for small-molecule drug discovery in SMA, identifies a novel mechanism of action for an E7 splicing modifier, and sets a precedent for other splicing-mediated diseases where RNA structure could be similarly targeted. Spinal muscular atrophy (SMA) is an autosomal recessive disorder with no present cure. Here the authors perform an in vitro screening leading to the identification of a small molecule that alters the conformational dynamics of the TSL2 RNA structure and acts as a modulator of SMN exon 7 splicing.