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Liu Y, Wang L, Zhao L, Zhang Y, Li ZT, Huang F. Multiple hydrogen bonding driven supramolecular architectures and their biomedical applications. Chem Soc Rev 2024; 53:1592-1623. [PMID: 38167687 DOI: 10.1039/d3cs00705g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Supramolecular chemistry combines the strength of molecular assembly via various molecular interactions. Hydrogen bonding facilitated self-assembly with the advantages of directionality, specificity, reversibility, and strength is a promising approach for constructing advanced supramolecules. There are still some challenges in hydrogen bonding based supramolecular polymers, such as complexity originating from tautomerism of the molecular building modules, the assembly process, and structure versatility of building blocks. In this review, examples are selected to give insights into multiple hydrogen bonding driven emerging supramolecular architectures. We focus on chiral supramolecular assemblies, multiple hydrogen bonding modules as stimuli responsive sources, interpenetrating polymer networks, multiple hydrogen bonding assisted organic frameworks, supramolecular adhesives, energy dissipators, and quantitative analysis of nano-adhesion. The applications in biomedical materials are focused with detailed examples including drug design evolution for myotonic dystrophy, molecular assembly for advanced drug delivery, an indicator displacement strategy for DNA detection, tissue engineering, and self-assembly complexes as gene delivery vectors for gene transfection. In addition, insights into the current challenges and future perspectives of this field to propel the development of multiple hydrogen bonding facilitated supramolecular materials are proposed.
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Affiliation(s)
- Yanxia Liu
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, Sichuan, China.
| | - Lulu Wang
- State Key Laboratory of Chemistry and Utilization of Carbon-based Energy Resource, Xinjiang University, Urumqi, Xinjiang 830046, China
| | - Lin Zhao
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, Sichuan, China.
| | - Yagang Zhang
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, Sichuan, China.
| | - Zhan-Ting Li
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules, Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of Sciences, Shanghai 200032, China
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, 2205 Songhu Road, Shanghai 200438, China.
| | - Feihe Huang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Center-Hangzhou Zhijiang Silicone Chemicals Co. Ltd. Joint Lab, Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
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2
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Gibaut QR, Bush JA, Tong Y, Baisden JT, Taghavi A, Olafson H, Yao X, Childs-Disney JL, Wang ET, Disney MD. Transcriptome-Wide Studies of RNA-Targeted Small Molecules Provide a Simple and Selective r(CUG) exp Degrader in Myotonic Dystrophy. ACS CENTRAL SCIENCE 2023; 9:1342-1353. [PMID: 37521782 PMCID: PMC10375898 DOI: 10.1021/acscentsci.2c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Indexed: 08/01/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is caused by a highly structured RNA repeat expansion, r(CUG)exp, harbored in the 3' untranslated region (3' UTR) of dystrophia myotonica protein kinase (DMPK) mRNA and drives disease through a gain-of-function mechanism. A panel of low-molecular-weight fragments capable of reacting with RNA upon UV irradiation was studied for cross-linking to r(CUG)expin vitro, affording perimidin-2-amine diazirine (1) that bound to r(CUG)exp. The interactions between the small molecule and RNA were further studied by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. Binding of 1 in DM1 myotubes was profiled transcriptome-wide, identifying 12 transcripts including DMPK that were bound by 1. Augmenting the functionality of 1 with cleaving capability created a chimeric degrader that specifically targets r(CUG)exp for elimination. The degrader broadly improved DM1-associated defects as assessed by RNA-seq, while having limited effects on healthy myotubes. This study (i) provides a platform to investigate molecular recognition of ligands directly in disease-affected cells; (ii) illustrates that RNA degraders can be more specific than the binders from which they are derived; and (iii) suggests that repeating transcripts can be selectively degraded due to the presence of multiple ligand binding sites.
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Affiliation(s)
- Quentin
M. R. Gibaut
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica A. Bush
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yuquan Tong
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jared T. Baisden
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Amirhossein Taghavi
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hailey Olafson
- Center
for NeuroGenetics, University of Florida, Gainesville, Florida 32610, United States
- Department
of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Xiyuan Yao
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Eric T. Wang
- Center
for NeuroGenetics, University of Florida, Gainesville, Florida 32610, United States
- Department
of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Matthew D. Disney
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
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3
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Morozov B, Oshchepkov AS, Klemt I, Agafontsev AM, Krishna S, Hampel F, Xu HG, Mokhir A, Guldi D, Kataev E. Supramolecular Recognition of Cytidine Phosphate in Nucleotides and RNA Sequences. JACS AU 2023; 3:964-977. [PMID: 37006770 PMCID: PMC10052242 DOI: 10.1021/jacsau.2c00658] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 06/19/2023]
Abstract
Supramolecular recognition of nucleotides would enable manipulating crucial biochemical pathways like transcription and translation directly and with high precision. Therefore, it offers great promise in medicinal applications, not least in treating cancer or viral infections. This work presents a universal supramolecular approach to target nucleoside phosphates in nucleotides and RNA. The artificial active site in new receptors simultaneously realizes several binding and sensing mechanisms: encapsulation of a nucleobase via dispersion and hydrogen bonding interactions, recognition of the phosphate residue, and a self-reporting feature-"turn-on" fluorescence. Key to the high selectivity is the conscious separation of phosphate- and nucleobase-binding sites by introducing specific spacers in the receptor structure. We have tuned the spacers to achieve high binding affinity and selectivity for cytidine 5' triphosphate coupled to a record 60-fold fluorescence enhancement. The resulting structures are also the first functional models of poly(rC)-binding protein coordinating specifically to C-rich RNA oligomers, e.g., the 5'-AUCCC(C/U) sequence present in poliovirus type 1 and the human transcriptome. The receptors bind to RNA in human ovarian cells A2780, causing strong cytotoxicity at 800 nM. The performance, self-reporting property, and tunability of our approach open up a promising and unique avenue for sequence-specific RNA binding in cells by using low-molecular-weight artificial receptors.
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Affiliation(s)
- Boris
S. Morozov
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
| | | | - Insa Klemt
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
| | - Aleksandr M. Agafontsev
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
| | - Swathi Krishna
- Department
of Chemistry and Pharmacy, Interdisciplinary Center for Molecular
Materials (ICMM), Friedrich-Alexander-Universität
Erlangen-Nürnberg, Egerlandstr. 3, Erlangen 91058, Germany
| | - Frank Hampel
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
| | - Hong-Gui Xu
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
| | - Andriy Mokhir
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
| | - Dirk Guldi
- Department
of Chemistry and Pharmacy, Interdisciplinary Center for Molecular
Materials (ICMM), Friedrich-Alexander-Universität
Erlangen-Nürnberg, Egerlandstr. 3, Erlangen 91058, Germany
| | - Evgeny Kataev
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
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4
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NAKATANI K. Possibilities and challenges of small molecule organic compounds for the treatment of repeat diseases. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:30-48. [PMID: 35013029 PMCID: PMC8795530 DOI: 10.2183/pjab.98.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
The instability of repeat sequences in the human genome results in the onset of many neurological diseases if the repeats expand above a certain threshold. The transcripts containing long repeats sequester RNA binding proteins. The mechanism of repeat instability involves metastable slip-out hairpin DNA structures. Synthetic organic chemists have focused on the development of small organic molecules targeting repeat DNA and RNA sequences to treat neurological diseases with repeat-binding molecules. Our laboratory has studied a series of small molecules binding to mismatched base pairs and found molecules capable of binding CAG repeat DNA, which causes Huntington's disease upon expansion, CUG repeat RNA, a typical toxic RNA causing myotonic dystrophy type 1, and UGGAA repeat RNA causing spinocerebellar ataxia type 31. These molecules exhibited significant beneficial effects on disease models in vivo, suggesting the possibilities for small molecules as drugs for treating these neurological diseases.
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Affiliation(s)
- Kazuhiko NAKATANI
- SANKEN, The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
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5
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Quemener AM, Bachelot L, Forestier A, Donnou-Fournet E, Gilot D, Galibert MD. The powerful world of antisense oligonucleotides: From bench to bedside. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1594. [PMID: 32233021 PMCID: PMC9285911 DOI: 10.1002/wrna.1594] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 02/12/2020] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
Abstract
Antisense oligonucleotides (ASOs) represent a new and highly promising class of drugs for personalized medicine. In the last decade, major chemical developments and improvements of the backbone structure of ASOs have transformed them into true approved and commercialized drugs. ASOs target both DNA and RNA, including pre‐mRNA, mRNA, and ncRDA, based on sequence complementary. They are designed to be specific for each identified molecular and genetic alteration to restore a normal, physiological situation. Thus, the characterization of the underpinning mechanisms and alterations that sustain pathology is critical for accurate ASO‐design. ASOs can be used to cure both rare and common diseases, such as orphan genetic alterations and cancer. Through pioneering examples, this review shows the versatility of the mechanisms of action that provide ASOs with the potential capacity to achieve custom treatment, revolutionizing personalized medicine. This article is categorized under:RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions
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Affiliation(s)
- Anaïs M Quemener
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR6290, ARC Foundation Labellized Team, Rennes, France
| | - Laura Bachelot
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR6290, ARC Foundation Labellized Team, Rennes, France
| | - Anne Forestier
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR6290, ARC Foundation Labellized Team, Rennes, France
| | - Emmanuelle Donnou-Fournet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR6290, ARC Foundation Labellized Team, Rennes, France
| | - David Gilot
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR6290, ARC Foundation Labellized Team, Rennes, France
| | - Marie-Dominique Galibert
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR6290, ARC Foundation Labellized Team, Rennes, France.,Department of Molecular Genetics and Genomic, CHU Rennes, Hospital-University of Rennes, Rennes, France
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6
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Rong Z, Hu J, Corey DR, Mootha VV. Quantitative Studies of Muscleblind Proteins and Their Interaction With TCF4 RNA Foci Support Involvement in the Mechanism of Fuchs' Dystrophy. Invest Ophthalmol Vis Sci 2019; 60:3980-3991. [PMID: 31560764 PMCID: PMC6779288 DOI: 10.1167/iovs.19-27641] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023] Open
Abstract
Purpose Fuchs' endothelial corneal dystrophy (FECD) is a major cause of vision loss and the most common nucleotide repeat disorder, affecting 4% of United States population greater than 40 years of age. Seventy percent of FECD cases are due to an intronic CTG expansion within the TCF4 gene, resulting in accumulation of CUG repeat RNA nuclear foci in corneal endothelium. Each endothelial cell has approximately two sense foci, and each focus is a single RNA molecule. This study aimed to obtain a better understanding of how rare repeat RNA species lead to disease. Methods We quantitatively examined muscleblind-like (MBNL) proteins and their interaction with foci in both patient-derived corneal endothelial cell lines and human corneal endothelial tissue. Results Using fluorescent in situ hybridization and immunofluorescence, we found that depletion of both MBNL1 and MBNL2 reduces nuclear RNA foci formed by the repeat, suggesting that both are necessary for foci. Quantitative studies of RNA and protein copy number revealed MBNLs to be abundant in the total cellular pool in endothelial cell lines but are much lower in human corneal endothelial tissue. Studies using human tissue nuclear and cytoplasmic fractions indicate that most MBNL proteins are localized to the cytoplasm. Conclusions The low levels of MBNL1/2 in corneal tissue, in combination with the small fraction of protein in the nucleus, may make corneal endothelial cells especially susceptible to sequestration of MBNL1/2 by CUG repeat RNA. These observations may explain how a limited number of RNA molecules can cause widespread alteration of splicing and late-onset degenerative FECD.
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Affiliation(s)
- Ziye Rong
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Jiaxin Hu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - David R. Corey
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - V. Vinod Mootha
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States
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7
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Oshchepkov AS, Shumilova TA, Zerson M, Magerle R, Khrustalev VN, Kataev EA. Conformational Selection in Anion Recognition: cGMP-Selective Binding by a Naphthalimide-Functionalized Amido-Amine Macrocycle. J Org Chem 2019; 84:9034-9043. [PMID: 31117577 DOI: 10.1021/acs.joc.9b00947] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Amido-amine macrocycles with two and four naphthalimide dyes were designed to bind nucleoside monophosphates and oligonucleotides in an aqueous buffered solution. Anion-templated synthesis was used to direct the macrocyclization reaction to the [2+2] product, while high dilution conditions favored the formation of the [4+4] macrocycle with an unprecedented geometry, as revealed from the X-ray analysis. The [2+2] product was found to exhibit a remarkable binding strength and fluorescence response for cyclic guanosine monophosphate (cGMP) in an aqueous solution. To our knowledge, this is the first synthetic receptor for cGMP, which also demonstrates a high preference to bind guanine-rich sequences accomplished by a strong fluorescence quenching. The receptor conformation is very sensitive to the guest structure in an aqueous solution, thus modeling the adaptive behavior of proteins. The study of synthetic systems with a detectable conformational equilibrium represents a great potential for understanding highly specific and tightly regulated interactions in biological systems.
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Affiliation(s)
- Aleksandr S Oshchepkov
- Faculty of Natural Sciences , Technische Universität Chemnitz , Chemnitz 09107 , Germany.,Peoples' Friendship University of Russia (RUDN University) , Moscow 117198 , Russia
| | - Tatiana A Shumilova
- Faculty of Natural Sciences , Technische Universität Chemnitz , Chemnitz 09107 , Germany
| | - Mario Zerson
- Faculty of Natural Sciences , Technische Universität Chemnitz , Chemnitz 09107 , Germany
| | - Robert Magerle
- Faculty of Natural Sciences , Technische Universität Chemnitz , Chemnitz 09107 , Germany
| | - Victor N Khrustalev
- Peoples' Friendship University of Russia (RUDN University) , Moscow 117198 , Russia.,National Research Center (Kurchatov Institute) , Moscow 123098 , Russia
| | - Evgeny A Kataev
- Faculty of Natural Sciences , Technische Universität Chemnitz , Chemnitz 09107 , Germany
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8
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Affinity capillary electrophoresis for identification of active drug candidates in myotonic dystrophy type 1. Anal Bioanal Chem 2018; 410:4495-4507. [DOI: 10.1007/s00216-018-1107-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 03/16/2018] [Accepted: 04/24/2018] [Indexed: 12/31/2022]
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9
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Thomas JD, Oliveira R, Sznajder ŁJ, Swanson MS. Myotonic Dystrophy and Developmental Regulation of RNA Processing. Compr Physiol 2018; 8:509-553. [PMID: 29687899 DOI: 10.1002/cphy.c170002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Myotonic dystrophy (DM) is a multisystemic disorder caused by microsatellite expansion mutations in two unrelated genes leading to similar, yet distinct, diseases. DM disease presentation is highly variable and distinguished by differences in age-of-onset and symptom severity. In the most severe form, DM presents with congenital onset and profound developmental defects. At the molecular level, DM pathogenesis is characterized by a toxic RNA gain-of-function mechanism that involves the transcription of noncoding microsatellite expansions. These mutant RNAs disrupt key cellular pathways, including RNA processing, localization, and translation. In DM, these toxic RNA effects are predominantly mediated through the modulation of the muscleblind-like and CUGBP and ETR-3-like factor families of RNA binding proteins (RBPs). Dysfunction of these RBPs results in widespread RNA processing defects culminating in the expression of developmentally inappropriate protein isoforms in adult tissues. The tissue that is the focus of this review, skeletal muscle, is particularly sensitive to mutant RNA-responsive perturbations, as patients display a variety of developmental, structural, and functional defects in muscle. Here, we provide a comprehensive overview of DM1 and DM2 clinical presentation and pathology as well as the underlying cellular and molecular defects associated with DM disease onset and progression. Additionally, fundamental aspects of skeletal muscle development altered in DM are highlighted together with ongoing and potential therapeutic avenues to treat this muscular dystrophy. © 2018 American Physiological Society. Compr Physiol 8:509-553, 2018.
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Affiliation(s)
- James D Thomas
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Ruan Oliveira
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Łukasz J Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
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10
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Pramanik A, Abbasi M, Maji K, Nandi SK, Datta R, Haldar D. Selective Sensing of Ammonium Ion Over Other Biologically Important Ammonia Derivatives by a Coumarin-Based ϵ-Amino Ester. ChemistrySelect 2018. [DOI: 10.1002/slct.201702068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Apurba Pramanik
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 West Bengal India
| | - Mazharul Abbasi
- Department of Biological Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 West Bengal India
| | - Krishnendu Maji
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 West Bengal India
| | - Sujay Kumar Nandi
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 West Bengal India
| | - Rupak Datta
- Department of Biological Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 West Bengal India
| | - Debasish Haldar
- Department of Chemical Sciences; Indian Institute of Science Education and Research Kolkata; Mohanpur 741246 West Bengal India
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11
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Konieczny P, Selma-Soriano E, Rapisarda AS, Fernandez-Costa JM, Perez-Alonso M, Artero R. Myotonic dystrophy: candidate small molecule therapeutics. Drug Discov Today 2017; 22:1740-1748. [PMID: 28780071 DOI: 10.1016/j.drudis.2017.07.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/14/2017] [Accepted: 07/25/2017] [Indexed: 01/01/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a rare multisystemic neuromuscular disorder caused by expansion of CTG trinucleotide repeats in the noncoding region of the DMPK gene. Mutant DMPK transcripts are toxic and alter gene expression at several levels. Chiefly, the secondary structure formed by CUGs has a strong propensity to capture and retain proteins, like those of the muscleblind-like (MBNL) family. Sequestered MBNL proteins cannot then fulfill their normal functions. Many therapeutic approaches have been explored to reverse these pathological consequences. Here, we review the myriad of small molecules that have been proposed for DM1, including examples obtained from computational rational design, HTS, drug repurposing, and therapeutic gene modulation.
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Affiliation(s)
- Piotr Konieczny
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Estela Selma-Soriano
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Anna S Rapisarda
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Juan M Fernandez-Costa
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Manuel Perez-Alonso
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Ruben Artero
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain.
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12
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Thornton CA, Wang E, Carrell EM. Myotonic dystrophy: approach to therapy. Curr Opin Genet Dev 2017; 44:135-140. [PMID: 28376341 PMCID: PMC5447481 DOI: 10.1016/j.gde.2017.03.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/25/2017] [Accepted: 03/13/2017] [Indexed: 01/16/2023]
Abstract
Myotonic dystrophy (DM) is a dominantly-inherited genetic disorder affecting skeletal muscle, heart, brain, and other organs. DM type 1 is caused by expansion of a CTG triplet repeat in DMPK, whereas DM type 2 is caused by expansion of a CCTG tetramer repeat in CNBP. In both cases the DM mutations lead to expression of dominant-acting RNAs. Studies of RNA toxicity have now revealed novel mechanisms and new therapeutic targets. Preclinical data have suggested that RNA dominance is responsive to therapeutic intervention and that DM therapy can be approached at several different levels. Here we review recent efforts to alleviate RNA toxicity in DM.
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Affiliation(s)
- Charles A Thornton
- Department of Neurology, University of Rochester, Rochester 14642, NY, United States.
| | - Eric Wang
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, University of Florida, Gainesville, FL, United States
| | - Ellie M Carrell
- Department of Neurology, University of Rochester, Rochester 14642, NY, United States
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13
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Bai Y, Nguyen L, Song Z, Peng S, Lee J, Zheng N, Kapoor I, Hagler LD, Cai K, Cheng J, Chan HYE, Zimmerman SC. Integrating Display and Delivery Functionality with a Cell Penetrating Peptide Mimic as a Scaffold for Intracellular Multivalent Multitargeting. J Am Chem Soc 2016; 138:9498-507. [DOI: 10.1021/jacs.6b03697] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | | | | | - Shaohong Peng
- Laboratory
of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong SAR, China
| | | | | | | | | | | | | | - H. Y. Edwin Chan
- Laboratory
of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong SAR, China
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14
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Boehm EM, Spies M, Washington MT. PCNA tool belts and polymerase bridges form during translesion synthesis. Nucleic Acids Res 2016; 44:8250-60. [PMID: 27325737 PMCID: PMC5041468 DOI: 10.1093/nar/gkw563] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/10/2016] [Indexed: 12/12/2022] Open
Abstract
Large multi-protein complexes play important roles in many biological processes, including DNA replication and repair, transcription, and signal transduction. One of the challenges in studying such complexes is to understand their mechanisms of assembly and disassembly and their architectures. Using single-molecule total internal reflection (TIRF) microscopy, we have examined the assembly and disassembly of the multi-protein complex that carries out translesion synthesis, the error-prone replication of damaged DNA. We show that the ternary complexes containing proliferating cell nuclear antigen (PCNA) and two non-classical DNA polymerases, Rev1 and DNA polymerase η, have two architectures: PCNA tool belts and Rev1 bridges. Moreover, these complexes are dynamic and their architectures can interconvert without dissociation. The formation of PCNA tool belts and Rev1 bridges and the ability of these complexes to change architectures are likely means of facilitating selection of the appropriate non-classical polymerase and polymerase-switching events.
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Affiliation(s)
- Elizabeth M Boehm
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - M Todd Washington
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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15
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Luu LM, Nguyen L, Peng S, Lee J, Lee HY, Wong CH, Hergenrother PJ, Chan HYE, Zimmerman SC. A Potent Inhibitor of Protein Sequestration by Expanded Triplet (CUG) Repeats that Shows Phenotypic Improvements in a Drosophila Model of Myotonic Dystrophy. ChemMedChem 2016; 11:1428-35. [PMID: 27245480 DOI: 10.1002/cmdc.201600081] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/29/2016] [Indexed: 11/09/2022]
Abstract
Myotonic dystrophy is the most common form of adult-onset muscular dystrophy, originating in a CTG repeat expansion in the DMPK gene. The expanded CUG transcript sequesters MBNL1, a key regulator of alternative splicing, leading to the misregulation of numerous pre-mRNAs. We report an RNA-targeted agent as a possible lead compound for the treatment of myotonic dystrophy type 1 (DM1) that reveals both the promise and challenges for this type of small-molecule approach. The agent is a potent inhibitor of the MBNL1-rCUG complex with an inhibition constant (Ki ) of 25±8 nm, and is also relatively nontoxic to HeLa cells, able to dissolve nuclear foci, and correct the insulin receptor splicing defect in DM1 model cells. Moreover, treatment with this compound improves two separate disease phenotypes in a Drosophila model of DM1: adult external eye degeneration and larval crawling defect. However, the compound has a relatively low maximum tolerated dose in mice, and its cell uptake may be limited, providing insight into directions for future development.
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Affiliation(s)
- Long M Luu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA
| | - Lien Nguyen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA
| | - Shaohong Peng
- Laboratory of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - JuYeon Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA
| | - Hyang Yeon Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA
| | - Chun-Ho Wong
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA
| | - H Y Edwin Chan
- Laboratory of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China.
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA.
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16
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Boehm EM, Powers KT, Kondratick CM, Spies M, Houtman JCD, Washington MT. The Proliferating Cell Nuclear Antigen (PCNA)-interacting Protein (PIP) Motif of DNA Polymerase η Mediates Its Interaction with the C-terminal Domain of Rev1. J Biol Chem 2016; 291:8735-44. [PMID: 26903512 DOI: 10.1074/jbc.m115.697938] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Indexed: 11/06/2022] Open
Abstract
Y-family DNA polymerases, such as polymerase η, polymerase ι, and polymerase κ, catalyze the bypass of DNA damage during translesion synthesis. These enzymes are recruited to sites of DNA damage by interacting with the essential replication accessory protein proliferating cell nuclear antigen (PCNA) and the scaffold protein Rev1. In most Y-family polymerases, these interactions are mediated by one or more conserved PCNA-interacting protein (PIP) motifs that bind in a hydrophobic pocket on the front side of PCNA as well as by conserved Rev1-interacting region (RIR) motifs that bind in a hydrophobic pocket on the C-terminal domain of Rev1. Yeast polymerase η, a prototypical translesion synthesis polymerase, binds both PCNA and Rev1. It possesses a single PIP motif but not an RIR motif. Here we show that the PIP motif of yeast polymerase η mediates its interactions both with PCNA and with Rev1. Moreover, the PIP motif of polymerase η binds in the hydrophobic pocket on the Rev1 C-terminal domain. We also show that the RIR motif of human polymerase κ and the PIP motif of yeast Msh6 bind both PCNA and Rev1. Overall, these findings demonstrate that PIP motifs and RIR motifs have overlapping specificities and can interact with both PCNA and Rev1 in structurally similar ways. These findings also suggest that PIP motifs are a more versatile protein interaction motif than previously believed.
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Affiliation(s)
| | | | | | | | - Jon C D Houtman
- Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
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17
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Zimmerman SC. A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy. Beilstein J Org Chem 2016; 12:125-38. [PMID: 26877815 PMCID: PMC4734311 DOI: 10.3762/bjoc.12.14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/06/2016] [Indexed: 12/02/2022] Open
Abstract
This review summarizes part of the author’s research in the area of supramolecular chemistry, beginning with his early life influences and early career efforts in molecular recognition, especially molecular tweezers. Although designed to complex DNA, these hosts proved more applicable to the field of host–guest chemistry. This early experience and interest in intercalation ultimately led to the current efforts to develop small molecule therapeutic agents for myotonic dystrophy using a rational design approach that heavily relies on principles of supramolecular chemistry. How this work was influenced by that of others in the field and the evolution of each area of research is highlighted with selected examples.
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Affiliation(s)
- Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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18
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Quantifying the Assembly of Multicomponent Molecular Machines by Single-Molecule Total Internal Reflection Fluorescence Microscopy. Methods Enzymol 2016; 581:105-145. [PMID: 27793278 PMCID: PMC5403009 DOI: 10.1016/bs.mie.2016.08.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Large, dynamic macromolecular complexes play essential roles in many cellular processes. Knowing how the components of these complexes associate with one another and undergo structural rearrangements is critical to understanding how they function. Single-molecule total internal reflection fluorescence (TIRF) microscopy is a powerful approach for addressing these fundamental issues. In this article, we first discuss single-molecule TIRF microscopes and strategies to immobilize and fluorescently label macromolecules. We then review the use of single-molecule TIRF microscopy to study the formation of binary macromolecular complexes using one-color imaging and inhibitors. We conclude with a discussion of the use of TIRF microscopy to examine the formation of higher-order (i.e., ternary) complexes using multicolor setups. The focus throughout this article is on experimental design, controls, data acquisition, and data analysis. We hope that single-molecule TIRF microscopy, which has largely been the province of specialists, will soon become as common in the tool box of biophysicists and biochemists as structural approaches have become today.
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19
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Nguyen L, Luu LM, Peng S, Serrano JF, Chan HYE, Zimmerman SC. Rationally designed small molecules that target both the DNA and RNA causing myotonic dystrophy type 1. J Am Chem Soc 2015; 137:14180-9. [PMID: 26473464 DOI: 10.1021/jacs.5b09266] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Single-agent, single-target therapeutic approaches are often limited by a complex disease pathobiology. We report rationally designed, multi-target agents for myotonic dystrophy type 1 (DM1). DM1 originates in an abnormal expansion of CTG repeats (CTG(exp)) in the DMPK gene. The resultant expanded CUG transcript (CUG(exp)) identified as a toxic agent sequesters important proteins, such as muscleblind-like proteins (MBNL), undergoes repeat-associated non-ATG (RAN) translation, and potentially causes microRNA dysregulation. We report rationally designed small molecules that target the DM1 pathobiology in vitro in three distinct ways by acting simultaneously as transcription inhibitors, by inhibiting aberrant protein binding to the toxic RNA, and by acting as RNase mimics to degrade the toxic RNA. In vitro, the agents are shown to (1) bind CTG(exp) and inhibit formation of the CUG(exp) transcript, (2) bind CUG(exp) and inhibit sequestration of MBNL1, and (3) cleave CUG(exp) in an RNase-like manner. The most potent compounds are capable of reducing the levels of CUG(exp) in DM1 model cells, and one reverses two separate CUG(exp)-induced phenotypes in a DM1 Drosophila model.
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Affiliation(s)
- Lien Nguyen
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Long M Luu
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Shaohong Peng
- Laboratory of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong , Shatin N.T., Hong Kong, SAR
| | - Julio F Serrano
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - H Y Edwin Chan
- Laboratory of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong , Shatin N.T., Hong Kong, SAR
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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20
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Ghoneim M, Spies M. Direct correlation of DNA binding and single protein domain motion via dual illumination fluorescence microscopy. NANO LETTERS 2014; 14:5920-31. [PMID: 25204359 PMCID: PMC4189620 DOI: 10.1021/nl502890g] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We report a dual illumination, single-molecule imaging strategy to dissect directly and in real-time the correlation between nanometer-scale domain motion of a DNA repair protein and its interaction with individual DNA substrates. The strategy was applied to XPD, an FeS cluster-containing DNA repair helicase. Conformational dynamics was assessed via FeS-mediated quenching of a fluorophore site-specifically incorporated into XPD. Simultaneously, binding of DNA molecules labeled with a spectrally distinct fluorophore was detected by colocalization of the DNA- and protein-derived signals. We show that XPD undergoes thermally driven conformational transitions that manifest in spatial separation of its two auxiliary domains. DNA binding does not strictly enforce a specific conformation. Interaction with a cognate DNA damage, however, stabilizes the compact conformation of XPD by increasing the weighted average lifetime of this state by 140% relative to an undamaged DNA. Our imaging strategy will be a valuable tool to study other FeS-containing nucleic acid processing enzymes.
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Affiliation(s)
- Mohamed Ghoneim
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Maria Spies
- Department
of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
- E-mail: . Phone +1-319-335-3221
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21
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Konieczny P, Stepniak-Konieczna E, Sobczak K. MBNL proteins and their target RNAs, interaction and splicing regulation. Nucleic Acids Res 2014; 42:10873-87. [PMID: 25183524 PMCID: PMC4176163 DOI: 10.1093/nar/gku767] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Muscleblind-like (MBNL) proteins are key regulators of precursor and mature mRNA metabolism in mammals. Based on published and novel data, we explore models of tissue-specific MBNL interaction with RNA. We portray MBNL domains critical for RNA binding and splicing regulation, and the structure of MBNL's normal and pathogenic RNA targets, particularly in the context of myotonic dystrophy (DM), in which expanded CUG or CCUG repeat transcripts sequester several nuclear proteins including MBNLs. We also review the properties of MBNL/RNA complex, including recent data obtained from UV cross-linking and immunoprecipitation (CLIP-Seq), and discuss how this interaction shapes normal MBNL-dependent alternative splicing regulation. Finally, we review how this acquired knowledge about the pathogenic RNA structure and nature of MBNL sequestration can be translated into the design of therapeutic strategies against DM.
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Affiliation(s)
- Patryk Konieczny
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Ewa Stepniak-Konieczna
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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22
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Hoskins JW, Ofori LO, Chen CZ, Kumar A, Sobczak K, Nakamori M, Southall N, Patnaik S, Marugan JJ, Zheng W, Austin CP, Disney MD, Miller BL, Thornton CA. Lomofungin and dilomofungin: inhibitors of MBNL1-CUG RNA binding with distinct cellular effects. Nucleic Acids Res 2014; 42:6591-602. [PMID: 24799433 PMCID: PMC4041448 DOI: 10.1093/nar/gku275] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a dominantly inherited neuromuscular disorder resulting from expression of RNA containing an expanded CUG repeat (CUGexp). The pathogenic RNA is retained in nuclear foci. Poly-(CUG) binding proteins in the Muscleblind-like (MBNL) family are sequestered in foci, causing misregulated alternative splicing of specific pre-mRNAs. Inhibitors of MBNL1-CUGexp binding have been shown to restore splicing regulation and correct phenotypes in DM1 models. We therefore conducted a high-throughput screen to identify novel inhibitors of MBNL1-(CUG)12 binding. The most active compound was lomofungin, a natural antimicrobial agent. We found that lomofungin undergoes spontaneous dimerization in DMSO, producing dilomofungin, whose inhibition of MBNL1–(CUG)12 binding was 17-fold more potent than lomofungin itself. However, while dilomofungin displayed the desired binding characteristics in vitro, when applied to cells it produced a large increase of CUGexp RNA in nuclear foci, owing to reduced turnover of the CUGexp transcript. By comparison, the monomer did not induce CUGexp accumulation in cells and was more effective at rescuing a CUGexp-induced splicing defect. These results support the feasibility of high-throughput screens to identify compounds targeting toxic RNA, but also demonstrate that ligands for repetitive sequences may have unexpected effects on RNA decay.
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Affiliation(s)
- Jason W Hoskins
- Department of Neurology, University of Rochester, Rochester, NY 14642, USA
| | - Leslie O Ofori
- Department of Chemistry, University of Rochester, Rochester, NY 14642, USA
| | - Catherine Z Chen
- Department of Chemistry, Scripps Florida, Jupiter, FL 33458, USA
| | - Amit Kumar
- Department of Dermatology, University of Rochester, Rochester, NY 14642, USA
| | - Krzysztof Sobczak
- Department of Neurology, University of Rochester, Rochester, NY 14642, USA
| | - Masayuki Nakamori
- Department of Neurology, University of Rochester, Rochester, NY 14642, USA
| | - Noel Southall
- Department of Chemistry, Scripps Florida, Jupiter, FL 33458, USA
| | - Samarjit Patnaik
- Department of Chemistry, Scripps Florida, Jupiter, FL 33458, USA
| | - Juan J Marugan
- Department of Chemistry, Scripps Florida, Jupiter, FL 33458, USA
| | - Wei Zheng
- Department of Chemistry, Scripps Florida, Jupiter, FL 33458, USA
| | | | - Matthew D Disney
- Department of Dermatology, University of Rochester, Rochester, NY 14642, USA
| | - Benjamin L Miller
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles A Thornton
- Department of Neurology, University of Rochester, Rochester, NY 14642, USA
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23
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Wojciechowska M, Taylor K, Sobczak K, Napierala M, Krzyzosiak WJ. Small molecule kinase inhibitors alleviate different molecular features of myotonic dystrophy type 1. RNA Biol 2014; 11:742-54. [PMID: 24824895 PMCID: PMC4156505 DOI: 10.4161/rna.28799] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Expandable (CTG)n repeats in the 3′ UTR of the DMPK gene are a cause of myotonic dystrophy type 1 (DM1), which leads to a toxic RNA gain-of-function disease. Mutant RNAs with expanded CUG repeats are retained in the nucleus and aggregate in discrete inclusions. These foci sequester splicing factors of the MBNL family and trigger upregulation of the CUGBP family of proteins resulting in the mis-splicing of their target transcripts. To date, many efforts to develop novel therapeutic strategies have been focused on disrupting the toxic nuclear foci and correcting aberrant alternative splicing via targeting mutant CUG repeats RNA; however, no effective treatment for DM1 is currently available. Herein, we present results of culturing of human DM1 myoblasts and fibroblasts with two small-molecule ATP-binding site-specific kinase inhibitors, C16 and C51, which resulted in the alleviation of the dominant-negative effects of CUG repeat expansion. Reversal of the DM1 molecular phenotype includes a reduction of the size and number of foci containing expanded CUG repeat transcripts, decreased steady-state levels of CUGBP1 protein, and consequent improvement of the aberrant alternative splicing of several pre-mRNAs misregulated in DM1.
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Affiliation(s)
- Marzena Wojciechowska
- Department of Molecular Biomedicine; Institute of Bioorganic Chemistry; Polish Academy of Sciences; Noskowskiego; Poznan, Poland
| | - Katarzyna Taylor
- Department of Gene Expression; Institute of Molecular Biology and Biotechnology; Adam Mickiewicz University; Umultowska 89; Poznan, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression; Institute of Molecular Biology and Biotechnology; Adam Mickiewicz University; Umultowska 89; Poznan, Poland
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics and UAB Stem Cell Institute; University of Alabama at Birmingham; Birmingham, AL USA
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine; Institute of Bioorganic Chemistry; Polish Academy of Sciences; Noskowskiego; Poznan, Poland
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24
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Honda M, Okuno Y, Hengel SR, Martín-López JV, Cook CP, Amunugama R, Soukup RJ, Subramanyam S, Fishel R, Spies M. Mismatch repair protein hMSH2-hMSH6 recognizes mismatches and forms sliding clamps within a D-loop recombination intermediate. Proc Natl Acad Sci U S A 2014; 111:E316-25. [PMID: 24395779 PMCID: PMC3903253 DOI: 10.1073/pnas.1312988111] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High fidelity homologous DNA recombination depends on mismatch repair (MMR), which antagonizes recombination between divergent sequences by rejecting heteroduplex DNA containing excessive nucleotide mismatches. The hMSH2-hMSH6 heterodimer is the first responder in postreplicative MMR and also plays a prominent role in heteroduplex rejection. Whether a similar molecular mechanism underlies its function in these two processes remains enigmatic. We have determined that hMSH2-hMSH6 efficiently recognizes mismatches within a D-loop recombination initiation intermediate. Mismatch recognition by hMSH2-hMSH6 is not abrogated by human replication protein A (HsRPA) bound to the displaced single-stranded DNA (ssDNA) or by HsRAD51. In addition, ATP-bound hMSH2-hMSH6 sliding clamps that are essential for downstream MMR processes are formed and constrained within the heteroduplex region of the D-loop. Moreover, the hMSH2-hMSH6 sliding clamps are stabilized on the D-loop by HsRPA bound to the displaced ssDNA. Our findings reveal similarities and differences in hMSH2-hMSH6 mismatch recognition and sliding-clamp formation between a D-loop recombination intermediate and linear duplex DNA.
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Affiliation(s)
- Masayoshi Honda
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | - Yusuke Okuno
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Sarah R. Hengel
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | - Juana V. Martín-López
- Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, OH 43210
| | - Christopher P. Cook
- Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, OH 43210
| | - Ravindra Amunugama
- Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, OH 43210
| | - Randal J. Soukup
- Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, OH 43210
| | - Shyamal Subramanyam
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Richard Fishel
- Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, OH 43210
- Human Genetics Institute, Ohio State University Medical Center, Columbus, OH 43210; and
- Physics Department, Ohio State University, Columbus, OH 43210
| | - Maria Spies
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
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25
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Granzhan A, Kotera N, Teulade-Fichou MP. Finding needles in a basestack: recognition of mismatched base pairs in DNA by small molecules. Chem Soc Rev 2014; 43:3630-65. [DOI: 10.1039/c3cs60455a] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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26
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Jahromi AH, Fu Y, Miller KA, Nguyen L, Luu LM, Baranger AM, Zimmerman SC. Developing bivalent ligands to target CUG triplet repeats, the causative agent of myotonic dystrophy type 1. J Med Chem 2013; 56:9471-9481. [PMID: 24188018 DOI: 10.1021/jm400794z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An expanded CUG repeat transcript (CUG(exp)) is the causative agent of myotonic dystrophy type 1 (DM1) by sequestering muscleblind-like 1 protein (MBNL1), a regulator of alternative splicing. On the basis of a ligand (1) that was previously reported to be active in an in vitro assay, we present the synthesis of a small library containing 10 dimeric ligands (4-13) that differ in length, composition, and attachment point of the linking chain. The oligoamino linkers gave a greater gain in affinity for CUG RNA and were more effective when compared to oligoether linkers. The most potent in vitro ligand (9) was shown to be aqueous-soluble and both cell- and nucleus-permeable, displaying almost complete dispersion of MBNL1 ribonuclear foci in a DM1 cell model. Direct evidence for the bioactivity of 9 was observed in its ability to disperse ribonuclear foci in individual live DM1 model cells using time-lapse confocal fluorescence microscopy.
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Affiliation(s)
- Amin Haghighat Jahromi
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA.,Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Yuan Fu
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Kali A Miller
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Lien Nguyen
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Long M Luu
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Anne M Baranger
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Steven C Zimmerman
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA.,Department of Chemistry, University of Illinois, Urbana, IL, USA
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