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 H Lyons, Mark A 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 journalArticle

2 Citations (Scopus)

Abstract

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)
JournalACS Chemical Biology
DOIs
StateAccepted/In press - Jan 1 2018

Fingerprint

RNA
Thermophoresis
Zebrafish
Molecules
Exosome Multienzyme Ribonuclease Complex
RNA Cap-Binding Proteins
Guide RNA
Morpholinos
Mutation
Nucleotide Motifs
Surface Plasmon Resonance
Pontocerebellar Hypoplasia
Nervous System Diseases
Neurodegenerative Diseases
Computer Simulation
Cerebellum
Neurodegenerative diseases
Spine
Magnetic Resonance Spectroscopy
Embryonic Structures

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine

Cite this

François-Moutal, L., Jahanbakhsh, S., Nelson, A. D. L., Ray, D., Scott, D. D., Hennefarth, M. R., ... Khanna, M. (Accepted/In press). A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B). ACS Chemical Biology. https://doi.org/10.1021/acschembio.8b00745

A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B). / François-Moutal, Liberty; Jahanbakhsh, Shahriyar; Nelson, Andrew D.L.; Ray, Debashish; Scott, David D.; Hennefarth, Matthew R.; Moutal, Aubin; Perez-Miller, Samantha; Ambrose, Andrew J.; Al-Shamari, Ahmed; Coursodon, Philippe; Meechoovet, Bessie; Reiman, Rebecca; Lyons, Eric H; Beilstein, Mark A; Chapman, Eli; Morris, Quaid D.; Van Keuren-Jensen, Kendall; Hughes, Timothy R.; Khanna, Rajesh; Koehler, Carla; Jen, Joanna; Gokhale, Vijay; Khanna, May.

In: ACS Chemical Biology, 01.01.2018.

Research output: Contribution to journalArticle

François-Moutal, L, Jahanbakhsh, S, Nelson, ADL, Ray, D, Scott, DD, Hennefarth, MR, Moutal, A, Perez-Miller, S, Ambrose, AJ, Al-Shamari, A, Coursodon, P, Meechoovet, B, Reiman, R, Lyons, EH, Beilstein, MA, Chapman, E, Morris, QD, Van Keuren-Jensen, K, Hughes, TR, Khanna, R, Koehler, C, Jen, J, Gokhale, V & Khanna, M 2018, 'A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B)', ACS Chemical Biology. https://doi.org/10.1021/acschembio.8b00745
François-Moutal L, Jahanbakhsh S, Nelson ADL, Ray D, Scott DD, Hennefarth MR et al. A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B). ACS Chemical Biology. 2018 Jan 1. https://doi.org/10.1021/acschembio.8b00745
François-Moutal, Liberty ; Jahanbakhsh, Shahriyar ; Nelson, Andrew D.L. ; Ray, Debashish ; Scott, David D. ; Hennefarth, Matthew R. ; Moutal, Aubin ; Perez-Miller, Samantha ; Ambrose, Andrew J. ; Al-Shamari, Ahmed ; Coursodon, Philippe ; Meechoovet, Bessie ; Reiman, Rebecca ; Lyons, Eric H ; Beilstein, Mark A ; Chapman, Eli ; Morris, Quaid D. ; Van Keuren-Jensen, Kendall ; Hughes, Timothy R. ; Khanna, Rajesh ; Koehler, Carla ; Jen, Joanna ; Gokhale, Vijay ; Khanna, May. / A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B). In: ACS Chemical Biology. 2018.
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AU - Ray, Debashish

AU - Scott, David D.

AU - Hennefarth, Matthew R.

AU - Moutal, Aubin

AU - Perez-Miller, Samantha

AU - Ambrose, Andrew J.

AU - Al-Shamari, Ahmed

AU - Coursodon, Philippe

AU - Meechoovet, Bessie

AU - Reiman, Rebecca

AU - Lyons, Eric H

AU - Beilstein, Mark A

AU - Chapman, Eli

AU - Morris, Quaid D.

AU - Van Keuren-Jensen, Kendall

AU - Hughes, Timothy R.

AU - Khanna, Rajesh

AU - Koehler, Carla

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