Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes

Nat Commun. 2018 May 23;9(1):2032. doi: 10.1038/s41467-018-04110-1.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing
  • Animals
  • Animals, Genetically Modified
  • Drosophila
  • Drug Evaluation, Preclinical
  • Exons / genetics
  • HeLa Cells
  • Humans
  • Imidazoles / chemistry
  • Imidazoles / pharmacology*
  • Imidazoles / therapeutic use
  • Indoles / chemistry
  • Indoles / pharmacology*
  • Indoles / therapeutic use
  • Molecular Targeted Therapy / methods
  • Muscular Atrophy, Spinal / drug therapy*
  • Muscular Atrophy, Spinal / genetics
  • Phenotype
  • RNA Splice Sites
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Regulatory Elements, Transcriptional / drug effects
  • Survival of Motor Neuron 2 Protein / genetics

Substances

  • Imidazoles
  • Indoles
  • RNA Splice Sites
  • RNA, Messenger
  • SMN2 protein, human
  • Survival of Motor Neuron 2 Protein
  • topsentin