Life science
Healthcare, Drug discovery

Alleviation of RNA toxicity by small molecules targeting repeat
RNAs responsible for neurological diseases
Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN)
Assistant Professor Tomonori Shibata

Researchmap https://researchmap.jp/7000010597

Professor Kazuhiko Nakatani

Researchmap https://researchmap.jp/read0042668

主要図１
Life science

Abstract

Aberrant expansion of repeat sequences causes hereditary neuromuscular diseases called repeat expansion diseases. Transcription of the expanded repeats produces repeat RNAs termed as
toxic RNAs, which is thought to be associated with a pathogenetic
mechanism of repeat expansion diseases. Small molecules modulating structure and function of the toxic repeat RNAs have therapeutic potential for repeat expansion diseases. We have discovered a small molecule that binds to the UGGAA repeat responsiblefor spinocerebellar ataxia type 31 (SCA31) by screening using inhouse chemical library containing nucleic acid-targeting smallmolecules. The UGGAA repeat-binding small molecule showed inhibitory effect on RNA-protein interaction and the formation of RNA
aggregates consisting of UGGAA repeats in the nucleus, alleviating the RNA toxicity caused by UGGAA repeats in the Drosophilamodel of SCA31.

new therapeutic strategies for intractable diseases that have notbeen targeted by conventional protein-targeted drug discovery.
The discovery of small molecules targeting repeat RNAs and theelucidation of their mechanisms of action are expected to develop
therapies of incurable repeat expansion diseases.

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HOOONHNNNCD▍ Background & Results
Spinocerebellar ataxia type 31 (SCA31) is an inherited autosomal dominant spinocerebellar degeneration caused by theinsertion of TGGAA repeats into the intron region shared by theBEAN1 and TK2 genes in chromosome 16. The UGGAA repeatstranscribed from the inserted TGGAA repeats主要図２
are thought to exhibit
RNA toxicity by sequestration of RNA-binding proteins followed by
the formation of RNA aggregates in the nucleus. Previous studies
have reported that TDP-43, which has been identified as a UGGAA
repeat-binding protein, alleviates the RNA toxicity of SCA31. Basedon these reports, we performed the exploratory study on UGGAA
repeat-binding small molecules to alleviate the RNA toxicity ofSCA31 by small molecules. We found naphthyridine carbamate dimer (NCD) as UGGAA repeat-binding small molecules by screening using in-house chemical library containing nucleic acid-binding
small molecules. The structural analysis of the NCD-RNA complex
by NMR clarified that two molecules of NCD bound to the 5’-GGA3’/3’-AGG-5’ internal loop in UGGAA/UGGAA pentad via hydrogenbonding with guanine. In vitro pulldown assay revealed that NCD
interfered with the binding of RNA-binding proteins to UGGAArepeats. The inhibitory effect of NCD on the formation of RNA aggregates containing UGGAA repeats in the nucleus was examinedby RNA fluorescence in situ hybridization, demonstrating that NCD
disrupts RNA aggregates. Feeding NCD to larvae of the Drosophilamodel of SCA31 suppressed the degeneration of compound eyesin the adults. These results demonstrate the alleviation of the RNA
toxicity in SCA31 by a small molecule binding to UGGAA repeats.

NH90°

Structure of NCD–RNA complex
Pulldown: (UGGAA)20NCD‒UGGAA repeat-expressing cells+NCD+
TDP-43RNA foci

Disruption of RNA foci

HNRNPM

Drosophila model of SCA31+NCD

SRSF9Inhibition of RNA–protein interaction

Alleviation of compoundeye degeneration▍ Significance of the research and Future perspective
Although RNA has been thought to be undruggable, it has recently been attracting attention as a drug target. Small moleculesthat target disease-causing RNAs have the potential to open up

P a t e n t Japanese Patent Application No. 2019-182767
Shibata, T et al. Small molecule targeting r(UGGAA)n disrupts RNA foci and alleviates disease phenotype in Drosophila model. Nat. Commun. 2021; (12):Tr e a t i s e
236. doi: 10.1038/s41467-020-20487-4.
https://www.sanken.osaka-u.ac.jp/labs/rbc/index.html
URL
https://www.sanken.osaka-u.ac.jp/hot_topics/topics_20210108/
K e y w o r d RNA, repeat expansion diseases, RNA-targeting small molecules, spinocerebellar degeneration, drug discovery