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

Liberty François-Moutal, Shahriyar Jahanbakhsh, Andrew D.L. Nelson, Debashish Ray, David D. Scott, Matthew R. Hennefarth, Aubin Moutal, Samantha Perez-Miller, Andrew J. Ambrose, Ahmed Al-Shamari, Philippe Coursodon, Bessie Meechoovet, Rebecca Reiman, Eric Lyons, Mark Beilstein, Eli Chapman, Quaid D. Morris, Kendall Van Keuren-Jensen, Timothy R. Hughes, Rajesh KhannaCarla Koehler, Joanna Jen, Vijay Gokhale, May Khanna

Research output: Contribution to journalArticlepeer-review


Mutations of EXOSC3 have been linked to the rare neurological disorder known as Pontocerebellar Hypoplasia type 1B (PCH1B). EXOSC3 is one of three putative RNA-binding structural cap proteins that guide RNA into the RNA exosome, the cellular machinery that degrades RNA. Using RNAcompete, we identified a G-rich RNA motif binding to EXOSC3. Surface plasmon resonance (SPR) and microscale thermophoresis (MST) indicated an affinity in the low micromolar range of EXOSC3 for long and short G-rich RNA sequences. Although several PCH1B-causing mutations in EXOSC3 did not engage a specific RNA motif as shown by RNAcompete, they exhibited lower binding affinity to G-rich RNA as demonstrated by MST. To test the hypothesis that modification of the RNA-protein interface in EXOSC3 mutants may be phenocopied by small molecules, we performed an in-silico screen of 50 000 small molecules and used enzyme-linked immunosorbant assays (ELISAs) and MST to assess the ability of the molecules to inhibit RNA-binding by EXOSC3. We identified a small molecule, EXOSC3-RNA disrupting (ERD) compound 3 (ERD03), which (i) bound specifically to EXOSC3 in saturation transfer difference nuclear magnetic resonance (STD-NMR), (ii) disrupted the EXOSC3-RNA interaction in a concentration-dependent manner, and (iii) produced a PCH1B-like phenotype with a 50% reduction in the cerebellum and an abnormally curved spine in zebrafish embryos. This compound also induced modification of zebrafish RNA expression levels similar to that observed with a morpholino against EXOSC3. To our knowledge, this is the first example of a small molecule obtained by rational design that models the abnormal developmental effects of a neurodegenerative disease in a whole organism.

Original languageEnglish (US)
Pages (from-to)3000-3010
Number of pages11
JournalACS Chemical Biology
Issue number10
StatePublished - Oct 19 2018

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine


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