Precise Small-molecule Recognition of a Toxic CUG RNA Repeat Expansion

Overview

Journal Nat Chem Biol

Specialties Biochemistry
Biology
Chemistry

Date 2016 Dec 13

PMID 27941760

Citations 103

Authors

Suzanne G Rzuczek

Lesley A Colgan

Yoshio Nakai

Michael D Cameron

Denis Furling

Ryohei Yasuda

Matthew D Disney

Affiliations

Soon will be listed here.

Abstract

Excluding the ribosome and riboswitches, developing small molecules that selectively target RNA is a longstanding problem in chemical biology. A typical cellular RNA is difficult to target because it has little tertiary, but abundant secondary structure. We designed allele-selective compounds that target such an RNA, the toxic noncoding repeat expansion (r(CUG)) that causes myotonic dystrophy type 1 (DM1). We developed several strategies to generate allele-selective small molecules, including non-covalent binding, covalent binding, cleavage and on-site probe synthesis. Covalent binding and cleavage enabled target profiling in cells derived from individuals with DM1, showing precise recognition of r(CUG). In the on-site probe synthesis approach, small molecules bound adjacent sites in r(CUG) and reacted to afford picomolar inhibitors via a proximity-based click reaction only in DM1-affected cells. We expanded this approach to image r(CUG) in its natural context.

Citing Articles

Functions of the Muscleblind-like protein family and their role in disease.

Zhou H, Xu J, Pan L Cell Commun Signal. 2025; 23(1):97.

PMID: 39966885 PMC: 11837677. DOI: 10.1186/s12964-025-02102-5.

The evolution and application of RNA-focused small molecule libraries.

Taghavi A, Springer N, Zanon P, Li Y, Li C, Childs-Disney J RSC Chem Biol. 2025; .

PMID: 39957993 PMC: 11824871. DOI: 10.1039/d4cb00272e.

RNA gain-of-function mechanisms in short tandem repeat diseases.

Davenport M, Swanson M RNA. 2024; 31(3):349-358.

PMID: 39725460 PMC: 11874975. DOI: 10.1261/rna.080277.124.

Technologies for Targeted RNA Degradation and Induced RNA Decay.

Mikutis S, Bernardes G Chem Rev. 2024; 124(23):13301-13330.

PMID: 39499674 PMC: 11638902. DOI: 10.1021/acs.chemrev.4c00472.

NMR structures of small molecules bound to a model of a CUG RNA repeat expansion.

Chen J, Taghavi A, Frank A, Fountain M, Choudhary S, Roy S Bioorg Med Chem Lett. 2024; 111:129888.

PMID: 39002937 PMC: 11702287. DOI: 10.1016/j.bmcl.2024.129888.

References

TANEJA K, McCurrach M, Schalling M, Housman D, Singer R . Foci of trinucleotide repeat transcripts in nuclei of myotonic dystrophy cells and tissues. J Cell Biol. 1995; 128(6):995-1002. PMC: 2120416. DOI: 10.1083/jcb.128.6.995. View

Pradeep Velagapudi S, Gallo S, Disney M . Sequence-based design of bioactive small molecules that target precursor microRNAs. Nat Chem Biol. 2014; 10(4):291-7. PMC: 3962094. DOI: 10.1038/nchembio.1452. View

Wang E, Cody N, Jog S, Biancolella M, Wang T, Treacy D . Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell. 2012; 150(4):710-24. PMC: 3428802. DOI: 10.1016/j.cell.2012.06.041. View

Shapiro I, Cheng A, Flytzanis N, Balsamo M, Condeelis J, Oktay M . An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. PLoS Genet. 2011; 7(8):e1002218. PMC: 3158048. DOI: 10.1371/journal.pgen.1002218. View

Warf M, Nakamori M, Matthys C, Thornton C, Berglund J . Pentamidine reverses the splicing defects associated with myotonic dystrophy. Proc Natl Acad Sci U S A. 2009; 106(44):18551-6. PMC: 2774031. DOI: 10.1073/pnas.0903234106. View

Chen C, Sobczak K, Hoskins J, Southall N, Marugan J, Zheng W . Two high-throughput screening assays for aberrant RNA-protein interactions in myotonic dystrophy type 1. Anal Bioanal Chem. 2012; 402(5):1889-98. PMC: 3280409. DOI: 10.1007/s00216-011-5604-0. View

Johnson L, Abelson H, Penman S, Green H . The relative amounts of the cytoplasmic RNA species in normal, transformed and senescent cultured cell lines. J Cell Physiol. 1977; 90(3):465-70. DOI: 10.1002/jcp.1040900310. View

Yang W, Wilson H, Pradeep Velagapudi S, Disney M . Inhibition of Non-ATG Translational Events in Cells via Covalent Small Molecules Targeting RNA. J Am Chem Soc. 2015; 137(16):5336-45. PMC: 4856029. DOI: 10.1021/ja507448y. View

Brook J, McCurrach M, Harley H, Buckler A, Church D, Aburatani H . Molecular basis of myotonic dystrophy: expansion of a trinucleotide (CTG) repeat at the 3' end of a transcript encoding a protein kinase family member. Cell. 1992; 68(4):799-808. DOI: 10.1016/0092-8674(92)90154-5. View

10.

Childs-Disney J, Stepniak-Konieczna E, Tran T, Yildirim I, Park H, Chen C . Induction and reversal of myotonic dystrophy type 1 pre-mRNA splicing defects by small molecules. Nat Commun. 2013; 4:2044. PMC: 3710115. DOI: 10.1038/ncomms3044. View

11.

Pushechnikov A, Lee M, Childs-Disney J, Sobczak K, French J, Thornton C . Rational design of ligands targeting triplet repeating transcripts that cause RNA dominant disease: application to myotonic muscular dystrophy type 1 and spinocerebellar ataxia type 3. J Am Chem Soc. 2009; 131(28):9767-79. PMC: 2731475. DOI: 10.1021/ja9020149. View

12.

Wheeler T, Sobczak K, Lueck J, Osborne R, Lin X, Dirksen R . Reversal of RNA dominance by displacement of protein sequestered on triplet repeat RNA. Science. 2009; 325(5938):336-9. PMC: 4109973. DOI: 10.1126/science.1173110. View

13.

Strack R, Disney M, Jaffrey S . A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. Nat Methods. 2013; 10(12):1219-24. PMC: 3852148. DOI: 10.1038/nmeth.2701. View

14.

Francois V, Klein A, Beley C, Jollet A, Lemercier C, Garcia L . Selective silencing of mutated mRNAs in DM1 by using modified hU7-snRNAs. Nat Struct Mol Biol. 2010; 18(1):85-7. DOI: 10.1038/nsmb.1958. View

15.

Lima W, Monia B, Ecker D, Freier S . Implication of RNA structure on antisense oligonucleotide hybridization kinetics. Biochemistry. 1992; 31(48):12055-61. DOI: 10.1021/bi00163a013. View

16.

Guan L, Disney M . Covalent small-molecule-RNA complex formation enables cellular profiling of small-molecule-RNA interactions. Angew Chem Int Ed Engl. 2013; 52(38):10010-3. PMC: 3876275. DOI: 10.1002/anie.201301639. View

17.

Paige J, Wu K, Jaffrey S . RNA mimics of green fluorescent protein. Science. 2011; 333(6042):642-6. PMC: 3314379. DOI: 10.1126/science.1207339. View

18.

Blount K, Megyola C, Plummer M, Osterman D, OConnell T, Aristoff P . Novel riboswitch-binding flavin analog that protects mice against Clostridium difficile infection without inhibiting cecal flora. Antimicrob Agents Chemother. 2015; 59(9):5736-46. PMC: 4538501. DOI: 10.1128/AAC.01282-15. View

19.

Hampf M, Gossen M . A protocol for combined Photinus and Renilla luciferase quantification compatible with protein assays. Anal Biochem. 2006; 356(1):94-9. DOI: 10.1016/j.ab.2006.04.046. View

20.

Carter B, de Vroom E, Long E, van der Marel G, VAN Boom J, Hecht S . Site-specific cleavage of RNA by Fe(II).bleomycin. Proc Natl Acad Sci U S A. 1990; 87(23):9373-7. PMC: 55167. DOI: 10.1073/pnas.87.23.9373. View