1
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Marzullo M, Coni S, De Simone A, Canettieri G, Ciapponi L. Modeling Myotonic Dystrophy Type 2 Using Drosophila melanogaster. Int J Mol Sci 2023; 24:14182. [PMID: 37762484 PMCID: PMC10532015 DOI: 10.3390/ijms241814182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/04/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Myotonic dystrophy 2 (DM2) is a genetic multi-systemic disease primarily affecting skeletal muscle. It is caused by CCTGn expansion in intron 1 of the CNBP gene, which encodes a zinc finger protein. DM2 disease has been successfully modeled in Drosophila melanogaster, allowing the identification and validation of new pathogenic mechanisms and potential therapeutic strategies. Here, we describe the principal tools used in Drosophila to study and dissect molecular pathways related to muscular dystrophies and summarize the main findings in DM2 pathogenesis based on DM2 Drosophila models. We also illustrate how Drosophila may be successfully used to generate a tractable animal model to identify novel genes able to affect and/or modify the pathogenic pathway and to discover new potential drugs.
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Affiliation(s)
- Marta Marzullo
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (M.M.)
| | - Sonia Coni
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Assia De Simone
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (M.M.)
| | - Gianluca Canettieri
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
- Istituto Pasteur Italia, Fondazione Cenci Bolognetti, 00161 Rome, Italy
| | - Laura Ciapponi
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (M.M.)
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2
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Bush JA, Meyer SM, Fuerst R, Tong Y, Li Y, Benhamou RI, Aikawa H, Zanon PRA, Gibaut QMR, Angelbello AJ, Gendron TF, Zhang YJ, Petrucelli L, Heick Jensen T, Childs-Disney JL, Disney MD. A blood-brain penetrant RNA-targeted small molecule triggers elimination of r(G 4C 2) exp in c9ALS/FTD via the nuclear RNA exosome. Proc Natl Acad Sci U S A 2022; 119:e2210532119. [PMID: 36409902 PMCID: PMC9860304 DOI: 10.1073/pnas.2210532119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/17/2022] [Indexed: 11/22/2022] Open
Abstract
A hexanucleotide repeat expansion in intron 1 of the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia, or c9ALS/FTD. The RNA transcribed from the expansion, r(G4C2)exp, causes various pathologies, including intron retention, aberrant translation that produces toxic dipeptide repeat proteins (DPRs), and sequestration of RNA-binding proteins (RBPs) in RNA foci. Here, we describe a small molecule that potently and selectively interacts with r(G4C2)exp and mitigates disease pathologies in spinal neurons differentiated from c9ALS patient-derived induced pluripotent stem cells (iPSCs) and in two c9ALS/FTD mouse models. These studies reveal a mode of action whereby a small molecule diminishes intron retention caused by the r(G4C2)exp and allows the liberated intron to be eliminated by the nuclear RNA exosome, a multi-subunit degradation complex. Our findings highlight the complexity of mechanisms available to RNA-binding small molecules to alleviate disease pathologies and establishes a pipeline for the design of brain penetrant small molecules targeting RNA with novel modes of action in vivo.
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Affiliation(s)
- Jessica A. Bush
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Samantha M. Meyer
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Rita Fuerst
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Yuquan Tong
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Yue Li
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Raphael I. Benhamou
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Haruo Aikawa
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Patrick R. A. Zanon
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Quentin M. R. Gibaut
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Alicia J. Angelbello
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | | | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL32224
| | | | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus CDK-8000, Denmark
| | - Jessica L. Childs-Disney
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
- Department of Neuroscience, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
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3
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Development of Therapeutic Approaches for Myotonic Dystrophies Type 1 and Type 2. Int J Mol Sci 2022; 23:ijms231810491. [PMID: 36142405 PMCID: PMC9499601 DOI: 10.3390/ijms231810491] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Myotonic Dystrophies type 1 (DM1) and type 2 (DM2) are complex multisystem diseases without disease-based therapies. These disorders are caused by the expansions of unstable CTG (DM1) and CCTG (DM2) repeats outside of the coding regions of the disease genes: DMPK in DM1 and CNBP in DM2. Multiple clinical and molecular studies provided a consensus for DM1 pathogenesis, showing that the molecular pathophysiology of DM1 is associated with the toxicity of RNA CUG repeats, which cause multiple disturbances in RNA metabolism in patients' cells. As a result, splicing, translation, RNA stability and transcription of multiple genes are misregulated in DM1 cells. While mutant CCUG repeats are the main cause of DM2, additional factors might play a role in DM2 pathogenesis. This review describes current progress in the translation of mechanistic knowledge in DM1 and DM2 to clinical trials, with a focus on the development of disease-specific therapies for patients with adult forms of DM1 and congenital DM1 (CDM1).
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4
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Krueger SB, Lanzendorf AN, Jeon HH, Zimmerman SC. Selective and Reversible Ligand Assembly on the DNA and RNA Repeat Sequences in Myotonic Dystrophy. Chembiochem 2022; 23:e202200260. [PMID: 35790065 PMCID: PMC9733911 DOI: 10.1002/cbic.202200260] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/03/2022] [Indexed: 02/06/2023]
Abstract
Small molecule targeting of DNA and RNA sequences has come into focus as a therapeutic strategy for diseases such as myotonic dystrophy type 1 (DM1), a trinucleotide repeat disease characterized by RNA gain-of-function. Herein, we report a novel template-selected, reversible assembly of therapeutic agents in situ via aldehyde-amine condensation. Rationally designed small molecule targeting agents functionalized with either an aldehyde or an amine were synthesized and screened against the target nucleic acid sequence. The assembly of fragments was confirmed by MALDI-MS in the presence of DM1-relevant nucleic acid sequences. The resulting hit combinations of aldehyde and amine inhibited the formation of r(CUG)exp in vitro in a cooperative manner at low micromolar levels and rescued mis-splicing defects in DM1 model cells. This reversible template-selected assembly is a promising approach to achieve cell permeable and multivalent targeting via in situ synthesis and could be applied to other nucleic acid targets.
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Affiliation(s)
- Sarah B Krueger
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Amie N Lanzendorf
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Hyoeun Heather Jeon
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
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5
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Wang W, He S, Dong G, Sheng C. Nucleic-Acid-Based Targeted Degradation in Drug Discovery. J Med Chem 2022; 65:10217-10232. [PMID: 35916496 DOI: 10.1021/acs.jmedchem.2c00875] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Targeted protein degradation (TPD), represented by proteolysis-targeting chimera (PROTAC), has emerged as a novel therapeutic modality in drug discovery. However, the application of conventional PROTACs is limited to protein targets containing cytosolic domains with ligandable sites. Recently, nucleic-acid-based modalities, such as modified oligonucleotide mimics and aptamers, opened new avenues to degrade protein targets and greatly expanded the scope of TPD. Beyond constructing protein-degrading chimeras, nucleic acid motifs can also serve as substrates for targeted degradation. Particularly, the new type of chimeric RNA degrader termed ribonuclease-targeting chimera (RIBOTAC) has shown promising features in drug discovery. Here, we provide an overview of the newly emerging TPD strategies based on nucleic acids as well as new strategies for targeted degradation of nucleic acid (RNA) targets. The design strategies, case studies, potential applications, and challenges are focused on.
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Affiliation(s)
- Wei Wang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Shipeng He
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Guoqiang Dong
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
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6
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Jenquin JR, O’Brien AP, Poukalov K, Lu Y, Frias JA, Shorrock HK, Richardson JI, Mazdiyasni H, Yang H, Huigens RW, Boykin D, Ranum LP, Cleary JD, Wang ET, Berglund JA. Molecular characterization of myotonic dystrophy fibroblast cell lines for use in small molecule screening. iScience 2022; 25:104198. [PMID: 35479399 PMCID: PMC9035709 DOI: 10.1016/j.isci.2022.104198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/30/2021] [Accepted: 04/01/2022] [Indexed: 01/05/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are common forms of adult onset muscular dystrophy. Pathogenesis in both diseases is largely driven by production of toxic-expanded repeat RNAs that sequester MBNL RNA-binding proteins, causing mis-splicing. Given this shared pathogenesis, we hypothesized that diamidines, small molecules that rescue mis-splicing in DM1 models, could also rescue mis-splicing in DM2 models. While several DM1 cell models exist, few are available for DM2 limiting research and therapeutic development. Here, we characterize DM1 and DM2 patient-derived fibroblasts for use in small molecule screens and therapeutic studies. We identify mis-splicing events unique to DM2 fibroblasts and common events shared with DM1 fibroblasts. We show that diamidines can partially rescue molecular phenotypes in both DM1 and DM2 fibroblasts. This study demonstrates the potential of fibroblasts as models for DM1 and DM2, which will help meet an important need for well-characterized DM2 cell models.
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Affiliation(s)
- Jana R. Jenquin
- Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Alana P. O’Brien
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Kiril Poukalov
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Yidan Lu
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jesus A. Frias
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Hannah K. Shorrock
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Jared I. Richardson
- Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Hormoz Mazdiyasni
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Hongfen Yang
- Department of Medicinal Chemistry, Center for Natural Products Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Robert W. Huigens
- Department of Medicinal Chemistry, Center for Natural Products Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - David Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Laura P.W. Ranum
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - John Douglas Cleary
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Eric T. Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - J. Andrew Berglund
- Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
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7
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Bush JA, Williams CC, Meyer SM, Tong Y, Haniff HS, Childs-Disney JL, Disney MD. Systematically Studying the Effect of Small Molecules Interacting with RNA in Cellular and Preclinical Models. ACS Chem Biol 2021; 16:1111-1127. [PMID: 34166593 PMCID: PMC8867596 DOI: 10.1021/acschembio.1c00014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The interrogation and manipulation of biological systems by small molecules is a powerful approach in chemical biology. Ideal compounds selectively engage a target and mediate a downstream phenotypic response. Although historically small molecule drug discovery has focused on proteins and enzymes, targeting RNA is an attractive therapeutic alternative, as many disease-causing or -associated RNAs have been identified through genome-wide association studies. As the field of RNA chemical biology emerges, the systematic evaluation of target validation and modulation of target-associated pathways is of paramount importance. In this Review, through an examination of case studies, we outline the experimental characterization, including methods and tools, to evaluate comprehensively the impact of small molecules that target RNA on cellular phenotype.
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Affiliation(s)
- Jessica A Bush
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Christopher C Williams
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Samantha M Meyer
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Yuquan Tong
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hafeez S Haniff
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
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8
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Zhang N, Bewick B, Schultz J, Tiwari A, Krencik R, Zhang A, Adachi K, Xia G, Yun K, Sarkar P, Ashizawa T. DNAzyme Cleavage of CAG Repeat RNA in Polyglutamine Diseases. Neurotherapeutics 2021; 18:1710-1728. [PMID: 34160773 PMCID: PMC8609077 DOI: 10.1007/s13311-021-01075-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 02/05/2023] Open
Abstract
CAG repeat expansion is the genetic cause of nine incurable polyglutamine (polyQ) diseases with neurodegenerative features. Silencing repeat RNA holds great therapeutic value. Here, we developed a repeat-based RNA-cleaving DNAzyme that catalyzes the destruction of expanded CAG repeat RNA of six polyQ diseases with high potency. DNAzyme preferentially cleaved the expanded allele in spinocerebellar ataxia type 1 (SCA1) cells. While cleavage was non-allele-specific for spinocerebellar ataxia type 3 (SCA3) cells, treatment of DNAzyme leads to improved cell viability without affecting mitochondrial metabolism or p62-dependent aggresome formation. DNAzyme appears to be stable in mouse brain for at least 1 month, and an intermediate dosage of DNAzyme in a SCA3 mouse model leads to a significant reduction of high molecular weight ATXN3 proteins. Our data suggest that DNAzyme is an effective RNA silencing molecule for potential treatment of multiple polyQ diseases.
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Affiliation(s)
- Nan Zhang
- Department of Neurology, Neuroscience Program, Houston Methodist Research Institute, Houston, TX USA
| | - Brittani Bewick
- Department of Neurology, Neuroscience Program, Houston Methodist Research Institute, Houston, TX USA
| | - Jason Schultz
- Department of Neurology, Neuroscience Program, Houston Methodist Research Institute, Houston, TX USA
| | - Anjana Tiwari
- Department of Neurology, Neuroscience Program, Houston Methodist Research Institute, Houston, TX USA
| | - Robert Krencik
- Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX USA
| | - Aijun Zhang
- Center for Bioenergetics, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX USA
| | - Kaho Adachi
- Department of Molecular and Cell Biology, UC-Berkeley, Berkeley, CA USA
| | - Guangbin Xia
- Indiana University School of Medicine-Fort Wayne, Fort Wayne, IN USA
| | - Kyuson Yun
- Department of Neurology, Neuroscience Program, Houston Methodist Research Institute, Houston, TX USA
| | - Partha Sarkar
- Department of Neurology and Department of Neuroscience, Cell Biology and Anatomy, UTMB Health, Galveston, TX USA
| | - Tetsuo Ashizawa
- Department of Neurology, Neuroscience Program, Houston Methodist Research Institute, Houston, TX USA
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9
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Wagner-Griffin S, Abe M, Benhamou RI, Angelbello AJ, Vishnu K, Chen JL, Childs-Disney JL, Disney MD. A Druglike Small Molecule that Targets r(CCUG) Repeats in Myotonic Dystrophy Type 2 Facilitates Degradation by RNA Quality Control Pathways. J Med Chem 2021; 64:8474-8485. [PMID: 34101465 DOI: 10.1021/acs.jmedchem.1c00414] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myotonic dystrophy type 2 (DM2) is one of >40 microsatellite disorders caused by RNA repeat expansions. The DM2 repeat expansion, r(CCUG)exp (where "exp" denotes expanded repeating nucleotides), is harbored in intron 1 of the CCHC-type zinc finger nucleic acid binding protein (CNBP). The expanded RNA repeat causes disease by a gain-of-function mechanism, sequestering various RNA-binding proteins including the pre-mRNA splicing regulator MBNL1. Sequestration of MBNL1 results in its loss-of-function and concomitant deregulation of the alternative splicing of its native substrates. Notably, this r(CCUG)exp causes retention of intron 1 in the mature CNBP mRNA. Herein, we report druglike small molecules that bind the structure adopted by r(CCUG)exp and improve DM2-associated defects. These small molecules were optimized from screening hits from an RNA-focused small-molecule library to afford a compound that binds r(CCUG)exp specifically and with nanomolar affinity, facilitates endogenous degradation of the aberrantly retained intron in which it is harbored, and rescues alternative splicing defects.
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Affiliation(s)
- Sarah Wagner-Griffin
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Masahito Abe
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Raphael I Benhamou
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Alicia J Angelbello
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Kamalakannan Vishnu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jonathan L Chen
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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10
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Angelbello AJ, Benhamou RI, Rzuczek SG, Choudhary S, Tang Z, Chen JL, Roy M, Wang KW, Yildirim I, Jun AS, Thornton CA, Disney MD. A Small Molecule that Binds an RNA Repeat Expansion Stimulates Its Decay via the Exosome Complex. Cell Chem Biol 2020; 28:34-45.e6. [PMID: 33157036 DOI: 10.1016/j.chembiol.2020.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/08/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022]
Abstract
Many diseases are caused by toxic RNA repeats. Herein, we designed a lead small molecule that binds the structure of the r(CUG) repeat expansion [r(CUG)exp] that causes myotonic dystrophy type 1 (DM1) and Fuchs endothelial corneal dystrophy (FECD) and rescues disease biology in patient-derived cells and in vivo. Interestingly, the compound's downstream effects are different in the two diseases, owing to the location of the repeat expansion. In DM1, r(CUG)exp is harbored in the 3' untranslated region, and the compound has no effect on the mRNA's abundance. In FECD, however, r(CUG)exp is located in an intron, and the small molecule facilitates excision of the intron, which is then degraded by the RNA exosome complex. Thus, structure-specific, RNA-targeting small molecules can act disease specifically to affect biology, either by disabling the gain-of-function mechanism (DM1) or by stimulating quality control pathways to rid a disease-affected cell of a toxic RNA (FECD).
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Affiliation(s)
- Alicia J Angelbello
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Raphael I Benhamou
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Suzanne G Rzuczek
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Shruti Choudhary
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Zhenzhi Tang
- Department of Neurology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Jonathan L Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Madhuparna Roy
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Kye Won Wang
- Department of Chemistry, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Ilyas Yildirim
- Department of Chemistry, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Albert S Jun
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Charles A Thornton
- Department of Neurology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
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11
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Meyer SM, Williams CC, Akahori Y, Tanaka T, Aikawa H, Tong Y, Childs-Disney JL, Disney MD. Small molecule recognition of disease-relevant RNA structures. Chem Soc Rev 2020; 49:7167-7199. [PMID: 32975549 PMCID: PMC7717589 DOI: 10.1039/d0cs00560f] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Targeting RNAs with small molecules represents a new frontier in drug discovery and development. The rich structural diversity of folded RNAs offers a nearly unlimited reservoir of targets for small molecules to bind, similar to small molecule occupancy of protein binding pockets, thus creating the potential to modulate human biology. Although the bacterial ribosome has historically been the most well exploited RNA target, advances in RNA sequencing technologies and a growing understanding of RNA structure have led to an explosion of interest in the direct targeting of human pathological RNAs. This review highlights recent advances in this area, with a focus on the design of small molecule probes that selectively engage structures within disease-causing RNAs, with micromolar to nanomolar affinity. Additionally, we explore emerging RNA-target strategies, such as bleomycin A5 conjugates and ribonuclease targeting chimeras (RIBOTACs), that allow for the targeted degradation of RNAs with impressive potency and selectivity. The compounds discussed in this review have proven efficacious in human cell lines, patient-derived cells, and pre-clinical animal models, with one compound currently undergoing a Phase II clinical trial and another that recently garnerd FDA-approval, indicating a bright future for targeted small molecule therapeutics that affect RNA function.
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Affiliation(s)
- Samantha M Meyer
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Christopher C Williams
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Yoshihiro Akahori
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Toru Tanaka
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Haruo Aikawa
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Yuquan Tong
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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Disney MD, Suresh BM, Benhamou RI, Childs-Disney JL. Progress toward the development of the small molecule equivalent of small interfering RNA. Curr Opin Chem Biol 2020; 56:63-71. [PMID: 32036231 PMCID: PMC7311281 DOI: 10.1016/j.cbpa.2020.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 12/26/2022]
Abstract
Given that many small molecules could bind to structured regions at sites that will not affect function, approaches that trigger degradation of RNA could provide a general way to affect biology. Indeed, targeted RNA degradation is an effective strategy to selectively and potently modulate biology. We describe several approaches to endow small molecules with the power to cleave RNAs. Central to these strategies is Inforna, which designs small molecules targeting RNA from human genome sequence. Inforna deduces the uniqueness of a druggable pocket, enables generation of hypotheses about functionality of the pocket, and defines on- and off-targets to drive compound optimization. RNA-binding compounds are then converted into cleavers that degrade the target directly or recruit an endogenous nuclease to do so. Cleaving compounds have significantly contributed to understanding and manipulating biological functions. Yet, there is much to be learned about how to affect human RNA biology with small molecules.
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Affiliation(s)
- Matthew D Disney
- Scripps Research, Department of Chemistry, 110 Scripps Way, Jupiter, FL, 33458, USA.
| | - Blessy M Suresh
- Scripps Research, Department of Chemistry, 110 Scripps Way, Jupiter, FL, 33458, USA
| | - Raphael I Benhamou
- Scripps Research, Department of Chemistry, 110 Scripps Way, Jupiter, FL, 33458, USA
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Angelbello AJ, DeFeo ME, Glinkerman CM, Boger DL, Disney MD. Precise Targeted Cleavage of a r(CUG) Repeat Expansion in Cells by Using a Small-Molecule-Deglycobleomycin Conjugate. ACS Chem Biol 2020; 15:849-855. [PMID: 32186845 DOI: 10.1021/acschembio.0c00036] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
RNA repeat expansions cause more than 30 neurological and neuromuscular diseases with no known cures. Since repeat expansions operate via diverse pathomechanisms, one potential therapeutic strategy is to rid them from disease-affected cells, using bifunctional small molecules that cleave the aberrant RNA. Such an approach has been previously implemented for the RNA repeat that causes myotonic dystrophy type 1 [DM1, r(CUG)exp] with Cugamycin, which is a small molecule that selectively binds r(CUG)exp conjugated to a bleomycin A5 cleaving module. Herein, we demonstrate that, by replacing bleomycin A5 with deglycobleomycin, an analogue in which the carbohydrate domain of bleomycin A5 is removed, the selectivity of the resulting small-molecule conjugate (DeglycoCugamycin) was enhanced, while maintaining potent and allele-selective cleavage of r(CUG)exp and rescue of DM1-associated defects. In particular, DeglycoCugamycin did not induce the DNA damage that is observed with high concentrations (25 μM) of Cugamycin, while selectively cleaving the disease-causing allele and improving DM1 defects at 1 μM.
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Affiliation(s)
- Alicia J. Angelbello
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Mary E. DeFeo
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Christopher M. Glinkerman
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dale L. Boger
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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Benhamou RI, Angelbello AJ, Andrews RJ, Wang ET, Moss WN, Disney MD. Structure-Specific Cleavage of an RNA Repeat Expansion with a Dimeric Small Molecule Is Advantageous over Sequence-Specific Recognition by an Oligonucleotide. ACS Chem Biol 2020; 15:485-493. [PMID: 31927948 DOI: 10.1021/acschembio.9b00958] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Myotonic dystrophy type 2 (DM2) is a genetically defined muscular dystrophy that is caused by an expanded repeat of r(CCUG) [r(CCUG)exp] in intron 1 of a CHC-type zinc finger nucleic acid binding protein (CNBP) pre-mRNA. Various mechanisms contribute to DM2 pathology including pre-mRNA splicing defects caused by sequestration of the RNA splicing regulator muscleblind-like-1 (MBNL1) by r(CCUG)exp. Herein, we study the biological impacts of the molecular recognition of r(CCUG)exp's structure by a designer dimeric small molecule that directly cleaves the RNA in patient-derived cells. The compound is comprised of two RNA-binding modules conjugated to a derivative of the natural product bleomycin. Careful design of the chimera affords RNA-specific cleavage, as attachment of the bleomycin cleaving module was done in a manner that disables DNA cleavage. The chimeric cleaver is more potent than the parent binding compound for alleviating DM2-associated defects. Importantly, oligonucleotides targeting the r(CCUG)exp sequence for cleavage exacerbate DM2 defects due to recognition of a short r(CCUG) sequence that is embedded in CNBP, argonaute-1 (AGO1), and MBNL1, reducing their levels. The latter event causes a greater depletion of functional MBNL1 than the amount already sequestered by r(CCUG)exp. Thus, compounds targeting RNA structures can have functional advantages over oligonucleotides that target the sequence in some disease settings, particularly in DM2.
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Affiliation(s)
- Raphael I. Benhamou
- Department of Chemistry, The Scripps Research Institute, 110 Scripps Way, Jupiter, Florida 33458, United States
| | - Alicia J. Angelbello
- Department of Chemistry, The Scripps Research Institute, 110 Scripps Way, Jupiter, Florida 33458, United States
| | - Ryan J. Andrews
- Roy J. Carver Department of Biophysics, Biochemistry, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Eric T. Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, UF Genetics Institute, University of Florida, 2033 Mowry Road, Gainesville, Florida 32610, United States
| | - Walter N. Moss
- Roy J. Carver Department of Biophysics, Biochemistry, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, 110 Scripps Way, Jupiter, Florida 33458, United States
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