Dynamic Combinatorial Selection of Molecules Capable of Inhibiting the (CUG) Repeat RNA−MBNL1 Interaction In Vitro: Discovery of Lead Compounds Targeting Myotonic Dystrophy (DM1)

Gareiss, Peter C.; Sobczak, Krzysztof; McNaughton, Brian R.; Palde, Prakash B.; Thornton, Charles A.; Miller, Benjamin L.

doi:10.1021/ja804398y

Cited by 177 publications

(164 citation statements)

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“…8). [10,35,42] The 22 nucleotide hairpin sequence in the HIV-1 frameshift stem-loop RNA was targeted . Structures of (a) oxazole-based peptide macrocycle 7, (b) cationic benzylic thiols, and (c) neutral carboydrate benzylic thiols used to generate a dynamic combinatorial library for recognition of quadruplex DNA targets.…”

Section: Rnamentioning

confidence: 99%

“…In an independent study, the same library was screened for target compounds able to inhibit muscular dystrophy type 1 (MBNL1) binding to (CUG) repeat RNA. [42] Four lead compounds were identified and inhibited the interaction of GGG(CUG) 109 GGG RNA with MBNL1 in vitro with K i values in the low micromolar range. In a very recent study, the olefin and hydrocarbon isosteres of 14, compounds 15 and 16 respectively (Fig.…”

Section: Rnamentioning

confidence: 99%

“…[46] TFO designed to bind to a DNA target and stabilize triple-helix formation were selected from a DCL of amines and polyamines. [42] and (b) the lead compound 14 detected using this assay for HIV-1 frameshift stem loop RNA, [35] and hydrocarbon isosteres 15 and 16. [10] …”

Section: Stabilized Oligonucleotide Conjugatesmentioning

confidence: 99%

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Targeting Nucleic Acids using Dynamic Combinatorial Chemistry

Durai

Harding

2011

Aust. J. Chem.

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Dynamic combinatorial chemistry (DCC) is a powerful method for the identification of novel ligands for the molecular recognition of receptor molecules. The method relies on self-assembly processes to generate libraries of compounds under reversible conditions, allowing a receptor molecule to select the optimal binding ligand from the mixture. However, while DCC is now an established field of chemistry, there are limited examples of the application of DCC to nucleic acids. The requirement to conduct experiments under physiologically relevant conditions, and avoid reaction with, or denaturation of, the target nucleic acid secondary structure, limits the choice of the reversible chemistry, and presents restrictions on the building block design. This review will summarize recent examples of applications of DCC to the recognition of nucleic acids. Studies with duplex DNA, quadruplex DNA, and RNA have utilized mainly thiol disulfide libraries, although applications of imine libraries, in combination with metal coordination, have been reported. The use of thiol disulfide libraries produces lead compounds with limited biostability, and hence design of stable analogues or mimics is required for many applications.

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Section: Rnamentioning

confidence: 99%

Section: Rnamentioning

confidence: 99%

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Targeting Nucleic Acids using Dynamic Combinatorial Chemistry

Durai

Harding

2011

Aust. J. Chem.

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“…They demonstrated that expanded CTG-induced effects could be reverted if CTG-repeat transgene expression was interrupted in a DM1 mouse model. Several other groups developed synthetic molecules and (CAG)n oligonucleotides that disrupted MBNL1 interaction with expanded CUG repeats (17)(18)(19)(20)(21)(22). However, those approaches may not address all the pathological consequences of expanded CUG RNAs.…”

mentioning

confidence: 99%

In vivo discovery of a peptide that prevents CUG–RNA hairpin formation and reverses RNA toxicity in myotonic dystrophy models

Garcia-Lopez

Llamusí

Orzáez

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Myotonic dystrophy type 1 (DM1) is caused by the expansion of noncoding CTG repeats in the dystrophia myotonica-protein kinase gene. Mutant transcripts form CUG hairpins that sequester RNAbinding factors into nuclear foci, including Muscleblind-like-1 protein (MBNL1), which regulate alternative splicing and gene expression. To identify molecules that target toxic CUG transcripts in vivo, we performed a positional scanning combinatorial peptide library screen using a Drosophila model of DM1. The screen identified a D-amino acid hexapeptide (ABP1) that reduced CUG foci formation and suppressed CUG-induced lethality and muscle degeneration when administered orally. Transgenic expression of natural, L-amino acid ABP1 analogues reduced CUG-induced toxicity in fly eyes and muscles. Furthermore, ABP1 reversed muscle histopathology and splicing misregulation of MBNL1 targets in DM1 model mice. In vitro, ABP1 bound to CUG hairpins and induced a switch to a single-stranded conformation. Our findings demonstrate that ABP1 shows antimyotonic dystrophy activity by targeting the core of CUG toxicity.disease model | drug discovery | non-coding RNA disease | medicinal chemistry | RNA secondary structure M yotonic dystrophy type 1 (DM1, OMIM #160900) is an autosomal dominant disease caused by the expansion of a CTG trinucleotide repeat in the 3′ untranslated region (UTR) of the dystrophia myotonica-protein kinase (DMPK) gene. Characteristic symptoms include myotonia, progressive muscle wasting, and cardiac conduction defects, among other systemic manifestations. The molecular mechanisms underlying DM1 pathogenesis are complex and affect a large number of cellular processes (1). However, most data suggest that the main triggering event is a toxic gain-of-function of the expanded CUG RNA. CUG-repeat expansions form double-stranded hairpins that are retained as inclusions within the nucleus. These hairpins recruit a number of transcription and splicing factors, including Muscleblind-like 1 (MBNL1) (2-6). Sequestration of MBNL1 originates a loss of function, which plays a key role in the development of DM1 symptoms. Mbnl1 knockout mice reproduced typical features of DM1, and overexpression of Mbnl1 in a mouse model that expressed CTG repeats reversed these phenotypes (7,8). CTGrepeat expression in mice caused misregulation of at least 156 alternative splicing events. Of these, 128 also occurred in Mbnl1 knockout animals (9-12). The splicing factor CUG-binding protein 1 (CUGBP1) is another key component in the development of DM1 phenotypes. CUGBP1 antagonizes MBNL1 activity in the regulated use of alternative exons in a number of transcripts and is abnormally upregulated in patients with DM1, further contributing to splicing misregulation (13-15).Mahadevan et al. provided the first in vivo proof-of-principle for a therapeutic strategy based on ablating toxic RNA molecules in DM1 (16). They demonstrated that expanded CTG-induced effects could be reverted if CTG-repeat transgene expression was interrupted in a DM1 mouse model. Several ...

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“…Diseases in which RNA repeats are found within a specific gene include spinocerebellar ataxia type 3 (sCA3) and Huntington's disease (HD). 3 "In theory, inhibiting the interaction of proteins with toxic RNA could be useful for any RNA-dominant disease caused by expanded repeats," Thornton told SciBX. "Other diseases caused by expanded repeats within untranslated regions are rare, but myotonic dystrophy type 2 (DM2) might be a logical disease to target, " he added.…”

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confidence: 99%

Targeting toxic RNA

Baas¹

2009

Science-Business eXchange

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Researchers at the University of Rochester have used an antisense molecule to reverse muscular defects in mice with myotonic dystrophy type 1. 1 The approach represents a new way to attack the most common form of adult muscular dystrophy and may be applicable to other diseases that are also characterized by expanded RNA repeats.Myotonic dystrophy type 1 (DM1) is an RNA-mediated, dominantly inherited disease caused by long triplet repeat regions of CUG in the noncoding region of the RNA that is translated into dystrophia myotonica protein kinase (DMPK). Whereas healthy people have about 5-30 copies of the triplet repeat, DM1 patients have hundreds to thousands of copies.The repeat regions produce problems because they have a high affinity for muscleblind-like 1 (MBNL1), a splicing regulator involved in the expression of several muscle proteins including muscle-specific chloride channel (ClC-1). The regions essentially sequester MBNL1, which results in low intracellular levels of MBNL1 and incorrect splicing of CIC-1. This, in turn, leads to the formation of aberrant chloride channels and muscular dysfunction.Previous strategies for treating DM1 have sought to cause overexpression of MBNL1, 2 but the Rochester group took a different tack: stop MBNL1 from binding to the RNA repeats. The hypothesis was that molecules that bind to expanded RNA in an untranslated region would inhibit the RNA-protein interaction and alleviate disease pathology (see Figure 1, "Effect of RNA expansion on disease pathology and therapeutic intervention").A team led by Charles Thornton, associate professor of neurology at the university's medical center, injected DM1 mice with a 25-nucleotidelong antisense morpholino, dubbed CAG25, which targeted the CUG repeats. The treatment resulted in Mbnl1 redistribution in muscle fibers and correction of aberrant splicing of ClC-1 and three other musclerelated proteins.CAG25 also restored chloride channel activity and reduced myotonia in the mice. Data were published in Science.Morpholinos are DNA analogs that have standard nucleic acid bases but are bound to morpholine rings instead of deoxyribose rings and are linked through phosphorodiamidate groups instead of phosphates. The result is that morpholinos are more resistant to degradation than DNA."The new study shows tremendous promise for treating triplet-expansion diseases and may have applications beyond the precise CUGrepeat RNA target to which it was applied, " said Benjamin Miller, an associate professor of biochemistry and biophysics at Rochester. Miller has collaborated with Thornton to identify small molecules that inhibit the CUG-repeat RNA of DM1 from interacting Figure . Effect of RNA expansion on disease pathology and therapeutic intervention. Molecules targeting RNA repeats could be useful for treating diseases in which expansion of these repeats within noncoding or coding regions of specific genes results in a high level of detrimental RNA-protein interactions.[a] Researchers at the University of Rochester showed that using an antisens...

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Dynamic Combinatorial Selection of Molecules Capable of Inhibiting the (CUG) Repeat RNA−MBNL1 Interaction In Vitro: Discovery of Lead Compounds Targeting Myotonic Dystrophy (DM1)

Cited by 177 publications

References 49 publications

Targeting Nucleic Acids using Dynamic Combinatorial Chemistry

Targeting Nucleic Acids using Dynamic Combinatorial Chemistry

In vivo discovery of a peptide that prevents CUG–RNA hairpin formation and reverses RNA toxicity in myotonic dystrophy models

Targeting toxic RNA

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