A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B)

Mutations mapping to the RNA-binding interface of EXOSC3 have been linked to the rare neurological disorder known as Pontocerebellar Hypoplasia type1B (PCH1B). EXOSC3 is part of three putative RNA-binding structural cap proteinsthat guideRNA intothe RNA exosome, thecellular machinery that2degrades RNA. Here, using RNAcompete, we identifieda G-rich RNA motifthat requirestheK homology and ribosomal protein S1domains of EXOSC3. Interestingly, several PCH1B-causing mutations in EXOSC3do not engage this RNA motif. To test the hypothesis thatmodificationof the RNA-protein interface in EXOSC3 mutants may be phenocopied by small molecules, we performedan in silicoscreen of 50,000 small molecules and used enzyme-linked immunosorbant assays(ELISAs)to assess the ability ofthe molecules to inhibit RNA-bindingbyEXOSC3. We identified asmall molecule, EXOSC3-RNA disrupting (ERD) compound 3 (ERD03), which: (i) bound specifically to EXOSC3in saturation transfer difference nuclear magnetic resonance (STD NMR); (ii)disruptedthe EXOSC3-RNAinteraction in a concentration-dependent manner; (iii) induced an abnormal curved spine PCH1B-like phenotype in zebrafish embryos.This compound induced a comparable modification of RNA expression levels coupled with an atrophy of the cerebellum in the zebrafish. To our knowledge, this is the first example of a small molecule obtained by rational design thatmodelsthe abnormal developmental effectsof a neurodegenerative diseasein a whole organism.