1
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Guo P, Han D. Targeting Pathogenic DNA and RNA Repeats: A Conceptual Therapeutic Way for Repeat Expansion Diseases. Chemistry 2022; 28:e202201749. [PMID: 35727679 DOI: 10.1002/chem.202201749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 11/06/2022]
Abstract
Expansions of short tandem repeats (STRs) in the human genome cause nearly 50 neurodegenerative diseases, which are mostly inheritable, nonpreventable and incurable, posing as a huge threat to human health. Non-B DNAs formed by STRs are thought to be structural intermediates that can cause repeat expansions. The subsequent transcripts harboring expanded RNA repeats can further induce cellular toxicity through forming specific structures. Direct targeting of these pathogenic DNA and RNA repeats has emerged as a new potential therapeutic strategy to cure repeat expansion diseases. In this conceptual review, we first introduce the roles of DNA and RNA structures in the genetic instabilities and pathomechanisms of repeat expansion diseases, then describe structural features of DNA and RNA repeats with a focus on the tertiary structures determined by X-ray crystallography and solution nuclear magnetic resonance spectroscopy, and finally discuss recent progress and perspectives of developing chemical tools that target pathogenic DNA and RNA repeats for curing repeat expansion diseases.
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Affiliation(s)
- Pei Guo
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China
| | - Da Han
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China.,Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
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2
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Chang Z, Zheng YY, Mathivanan J, Valsangkar VA, Du J, Abou-Elkhair RAI, Hassan AEA, Sheng J. Fluorescence-Based Binding Characterization of Small Molecule Ligands Targeting CUG RNA Repeats. Int J Mol Sci 2022; 23:ijms23063321. [PMID: 35328743 PMCID: PMC8955525 DOI: 10.3390/ijms23063321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Pathogenic CUG and CCUG RNA repeats have been associated with myotonic dystrophy type 1 and 2 (DM1 and DM2), respectively. Identifying small molecules that can bind these RNA repeats is of great significance to develop potential therapeutics to treat these neurodegenerative diseases. Some studies have shown that aminoglycosides and their derivatives could work as potential lead compounds targeting these RNA repeats. In this work, sisomicin, previously known to bind HIV-1 TAR, is investigated as a possible ligand for CUG RNA repeats. We designed a novel fluorescence-labeled RNA sequence of r(CUG)10 to mimic cellular RNA repeats and improve the detecting sensitivity. The interaction of sisomicin with CUG RNA repeats is characterized by the change of fluorescent signal, which is initially minimized by covalently incorporating the fluorescein into the RNA bases and later increased upon ligand binding. The results show that sisomicin can bind and stabilize the folded RNA structure. We demonstrate that this new fluorescence-based binding characterization assay is consistent with the classic UV Tm technique, indicating its feasibility for high-throughput screening of ligand-RNA binding interactions and wide applications to measure the thermodynamic parameters in addition to binding constants and kinetics when probing such interactions.
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Affiliation(s)
- Zhihua Chang
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Ya Ying Zheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Johnsi Mathivanan
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Vibhav A. Valsangkar
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Jinxi Du
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Reham A. I. Abou-Elkhair
- Applied Nucleic Acids Research Center & Chemistry Department, Faculty of Science, Zagazig University, Zagazig 44523, Egypt;
| | - Abdalla E. A. Hassan
- Applied Nucleic Acids Research Center & Chemistry Department, Faculty of Science, Zagazig University, Zagazig 44523, Egypt;
- Correspondence: (A.E.A.H.); (J.S.)
| | - Jia Sheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
- Correspondence: (A.E.A.H.); (J.S.)
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3
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Haify SN, Buijsen RAM, Verwegen L, Severijnen LAWFM, de Boer H, Boumeester V, Monshouwer R, Yang WY, Cameron MD, Willemsen R, Disney MD, Hukema RK. Small molecule 1a reduces FMRpolyG-mediated toxicity in in vitro and in vivo models for FMR1 premutation. Hum Mol Genet 2021; 30:1632-1648. [PMID: 34077515 PMCID: PMC8369842 DOI: 10.1093/hmg/ddab143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 12/15/2022] Open
Abstract
Fragile X-associated tremor and ataxia syndrome (FXTAS) is a late-onset, progressive neurodegenerative disorder characterized by tremors, ataxia and neuropsychological problems. This disease is quite common in the general population with approximately 20 million carriers worldwide. The risk of developing FXTAS increases dramatically with age, with about 45% of male carriers over the age of 50 being affected. FXTAS is caused by a CGG-repeat expansion (CGGexp) in the fragile X mental retardation 1 (FMR1) gene. CGGexp RNA is translated into the FMRpolyG protein by a mechanism called RAN translation. Although both gene and pathogenic trigger are known, no therapeutic interventions are available at this moment. Here, we present, for the first time, primary hippocampal neurons derived from the ubiquitous inducible mouse model which is used as a screening tool for targeted interventions. A promising candidate is the repeat binding, RAN translation blocking, small molecule 1a. Small molecule 1a shields the disease-causing CGGexp from being translated into the toxic FMRpolyG protein. Primary hippocampal neurons formed FMRpolyG-positive inclusions, and upon treatment with 1a, the numbers of FMRpolyG-positive inclusions are reduced. We also describe for the first time the formation of FMRpolyG-positive inclusions in the liver of this mouse model. Treatment with 1a reduced the insoluble FMRpolyG protein fraction in the liver but not the number of inclusions. Moreover, 1a treatment had a reducing effect on the number of Rad23b-positive inclusions and insoluble Rad23b protein levels. These data suggest that targeted small molecule therapy is effective in an FXTAS mouse model and has the potential to treat CGGexp-mediated diseases, including FXTAS.
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Affiliation(s)
- Saif N Haify
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | - Ronald A M Buijsen
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands.,Department of Human Genetics, LUMC, Leiden, the Netherlands
| | - Lucas Verwegen
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands.,Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands
| | | | - Helen de Boer
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | | | - Roos Monshouwer
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | - Wong Y Yang
- Department of Chemistry, Scripps Research Institute, Florida, the United States
| | - Michael D Cameron
- Department of Chemistry, Scripps Research Institute, Florida, the United States
| | - Rob Willemsen
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | - Matthew D Disney
- Department of Chemistry, Scripps Research Institute, Florida, the United States
| | - Renate K Hukema
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands.,Department of Health Care Studies, Rotterdam University of Applied Sciences, Rotterdam, the Netherlands
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4
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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: 82] [Impact Index Per Article: 20.5] [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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5
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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 PMCID: PMC7081929 DOI: 10.1021/acschembio.9b00958] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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6
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Benhamou RI, Angelbello AJ, Wang ET, Disney MD. A Toxic RNA Catalyzes the Cellular Synthesis of Its Own Inhibitor, Shunting It to Endogenous Decay Pathways. Cell Chem Biol 2020; 27:223-231.e4. [PMID: 31981476 DOI: 10.1016/j.chembiol.2020.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/22/2019] [Accepted: 01/03/2020] [Indexed: 12/12/2022]
Abstract
Myotonic dystrophy type 2 (DM2) is a genetically defined disease caused by a toxic expanded repeat of r(CCUG) [r(CCUG)exp], harbored in intron 1 of CCHC-type zinc-finger nucleic acid binding protein (CNBP) pre-mRNA. This r(CCUG)exp causes toxicity via a gain-of-function mechanism, resulting in three pathological hallmarks: aggregation into nuclear foci; sequestration of muscleblind-like-1 (MBNL1) protein, leading to splicing defects; and retention of CNBP intron 1. We studied two types of small molecules with different modes of action, ones that simply bind and ones that are templated by r(CCUG)exp in cells, i.e., the RNA synthesizes its own drug. Indeed, our studies completed in DM2 patient-derived fibroblasts showed that the compounds disrupt the r(CCUG)exp-MBNL1 complex, reduce intron retention, subjecting the liberated intronic r(CCUG)exp to native decay pathways, and rescue other DM2-associated cellular defects. Importantly, this study shows that small molecules can modulate RNA biology by shunting toxic transcripts toward native decay pathways.
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Affiliation(s)
- Raphael I Benhamou
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Alicia J Angelbello
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Eric T Wang
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, UF Genetics Institute, University of Florida, 2033 Mowry Road, Gainesville, FL 32610, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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7
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Reddy K, Jenquin JR, Cleary JD, Berglund JA. Mitigating RNA Toxicity in Myotonic Dystrophy using Small Molecules. Int J Mol Sci 2019; 20:E4017. [PMID: 31426500 PMCID: PMC6720693 DOI: 10.3390/ijms20164017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 12/26/2022] Open
Abstract
This review, one in a series on myotonic dystrophy (DM), is focused on the development and potential use of small molecules as therapeutics for DM. The complex mechanisms and pathogenesis of DM are covered in the associated reviews. Here, we examine the various small molecule approaches taken to target the DNA, RNA, and proteins that contribute to disease onset and progression in myotonic dystrophy type 1 (DM1) and 2 (DM2).
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Affiliation(s)
- Kaalak Reddy
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA.
| | - Jana R Jenquin
- Center for NeuroGenetics and Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32608, USA
| | - John D Cleary
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - J Andrew Berglund
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA.
- Center for NeuroGenetics and Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32608, USA.
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8
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Di Giorgio A, Duca M. Synthetic small-molecule RNA ligands: future prospects as therapeutic agents. MEDCHEMCOMM 2019; 10:1242-1255. [PMID: 31534649 PMCID: PMC6748380 DOI: 10.1039/c9md00195f] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2022]
Abstract
RNA is one of the most intriguing and promising biological targets for the discovery of innovative drugs in many pathologies and various biologically relevant RNAs that could serve as drug targets have already been identified. Among the most important ones, one can mention prokaryotic ribosomal RNA which is the target of several marketed antibiotics, viral RNAs or oncogenic microRNAs that are tightly involved in the development and progression of various cancers. Oligonucleotides are efficient and specific RNA targeting agents but suffer from poor pharmacodynamic and pharmacokinetic properties. For this reason, a number of synthetic small-molecule ligands have been identified and studied upon screening of chemical libraries or focused design of RNA binders. In this review, we report the most relevant examples of synthetic compounds bearing sufficient selectivity to envisage clinical studies and future therapeutic applications with a particular attention for the main strategies that can be undertaken toward the improvement of selectivity and biological activity.
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Affiliation(s)
- A Di Giorgio
- Université Côte d'Azur , CNRS , Institute of Chemistry of Nice (ICN) , Nice , France .
| | - M Duca
- Université Côte d'Azur , CNRS , Institute of Chemistry of Nice (ICN) , Nice , France .
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9
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Costales MG, Hoch DG, Abegg D, Childs-Disney JL, Velagapudi SP, Adibekian A, Disney MD. A Designed Small Molecule Inhibitor of a Non-Coding RNA Sensitizes HER2 Negative Cancers to Herceptin. J Am Chem Soc 2019; 141:2960-2974. [PMID: 30726072 DOI: 10.1021/jacs.8b10558] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A small molecule (1) with overlapping affinity for two microRNA (miRNA) precursors was used to inform design of a dimeric compound (2) selective for one of the miRNAs. In particular, 2 selectively targets the microRNA(miR)-515 hairpin precursor to inhibit production of miR-515 that represses sphingosine kinase 1 (SK1), a key enzyme in the biosynthesis of sphingosine 1-phosphate (S1P). Application of 2 to breast cancer cells enhanced SK1 and S1P levels, triggering a migratory phenotype. Knockout of SK1, forced overexpression of miR-515, and application of a small molecule SK1 inhibitor all ablated 2's effect on phenotype, consistent with its designed mode of action. Target profiling studies via Chem-CLIP showed that 2 bound selectively to the miR-515 hairpin precursor in cells. Global neoprotein synthesis upon addition of 2 to MCF-7 breast cancer cells demonstrated 2's selectivity and upregulation of cancer-associated proteins regulated by S1P. The most upregulated protein was human epidermal growth factor receptor 2 (ERBB2/HER2), which is regulated by the SK1/S1P pathway and is normally not expressed in MCF-7 cells. Like triple negative breast cancer (TNBC) cells, the lack of HER2 renders them insusceptible to Herceptin and its antibody-drug conjugate Kadcyla. In addition to proteomics, an RNA-seq study supports that 2 has limited off target effects and other studies support that 2 is more selective than an oligonucleotide. We therefore hypothesized that 2 could sensitize MCF-7 cells to anti-HER2 therapies. Indeed, application of 2 sensitized cells to Herceptin. These results were confirmed in two other cell lines that express miR-515 and are HER2-, the hepatocellular carcinoma cell line HepG2 and the TNBC line MDA-MB-231. Importantly, normal breast epithelial cells (MCF-10A) that do not express miR-515 are not affected by 2. These observations suggest a precision medicine approach to sensitize HER2- cancers to approved anticancer medicines. This study has implications for broadening the therapeutic utility of known targeted cancer therapeutics by using a secondary targeted approach to render otherwise insensitive cells, sensitive to a targeted therapeutic.
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Affiliation(s)
- Matthew G Costales
- Department of Chemistry , The Scripps Research Institute , 130 Scripps Way , Jupiter , Florida 33458 , United States
| | - Dominic G Hoch
- Department of Chemistry , The Scripps Research Institute , 130 Scripps Way , Jupiter , Florida 33458 , United States
| | - Daniel Abegg
- 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
| | - Sai Pradeep Velagapudi
- Department of Chemistry , The Scripps Research Institute , 130 Scripps Way , Jupiter , Florida 33458 , United States
| | - Alexander Adibekian
- 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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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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11
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Gorske BC, Mumford EM, Gerrity CG, Ko I. A Peptoid Square Helix via Synergistic Control of Backbone Dihedral Angles. J Am Chem Soc 2017; 139:8070-8073. [DOI: 10.1021/jacs.7b02319] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Benjamin C. Gorske
- Department of Chemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011-8466, United States
| | - Emily M. Mumford
- Department of Chemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011-8466, United States
| | - Charles G. Gerrity
- Department of Chemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011-8466, United States
| | - Imelda Ko
- Department of Chemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011-8466, United States
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12
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Velagapudi SP, Luo Y, Tran T, Haniff HS, Nakai Y, Fallahi M, Martinez GJ, Childs-Disney JL, Disney MD. Defining RNA-Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA. ACS CENTRAL SCIENCE 2017; 3:205-216. [PMID: 28386598 PMCID: PMC5364451 DOI: 10.1021/acscentsci.7b00009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Indexed: 05/03/2023]
Abstract
RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif-small molecule interactions identified via selection. Named High Throughput Structure-Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif-small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule-RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs.
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Affiliation(s)
- Sai Pradeep Velagapudi
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Yiling Luo
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Tuan Tran
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Hafeez S. Haniff
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Yoshio Nakai
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Mohammad Fallahi
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Gustavo J. Martinez
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Jessica L. Childs-Disney
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Matthew D. Disney
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
- E-mail:
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13
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Precise small-molecule recognition of a toxic CUG RNA repeat expansion. Nat Chem Biol 2016; 13:188-193. [PMID: 27941760 DOI: 10.1038/nchembio.2251] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 10/03/2016] [Indexed: 01/10/2023]
Abstract
Excluding the ribosome and riboswitches, developing small molecules that selectively target RNA is a longstanding problem in chemical biology. A typical cellular RNA is difficult to target because it has little tertiary, but abundant secondary structure. We designed allele-selective compounds that target such an RNA, the toxic noncoding repeat expansion (r(CUG)exp) that causes myotonic dystrophy type 1 (DM1). We developed several strategies to generate allele-selective small molecules, including non-covalent binding, covalent binding, cleavage and on-site probe synthesis. Covalent binding and cleavage enabled target profiling in cells derived from individuals with DM1, showing precise recognition of r(CUG)exp. In the on-site probe synthesis approach, small molecules bound adjacent sites in r(CUG)exp and reacted to afford picomolar inhibitors via a proximity-based click reaction only in DM1-affected cells. We expanded this approach to image r(CUG)exp in its natural context.
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14
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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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15
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Abulwerdi FA, Schneekloth JS. Microarray-based technologies for the discovery of selective, RNA-binding molecules. Methods 2016; 103:188-95. [PMID: 27109057 PMCID: PMC6314024 DOI: 10.1016/j.ymeth.2016.04.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/18/2016] [Accepted: 04/18/2016] [Indexed: 11/20/2022] Open
Abstract
The identification of small molecules that bind specifically to RNA is a challenge. However, the recent explosion in knowledge about the role RNA plays in a number of physiological processes apart from coding for protein sequences makes it a highly interesting target for chemical probes and therapeutics. One technology that has played an important role in the discovery of RNA-binding molecules is microarrays. Microarrays have been broadly employed to screen, profile, and quantify RNA interactions, and will likely play an important role in the discovery of new classes of ligands going forward. Here, we discuss the development of microarray technologies, including aminoglycoside, peptide, peptoid, and small molecule microarrays, and their use in studying RNA-interacting molecules.
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Affiliation(s)
- Fardokht A Abulwerdi
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States; Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States.
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16
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Yang WY, Gao R, Southern M, Sarkar PS, Disney MD. Design of a bioactive small molecule that targets r(AUUCU) repeats in spinocerebellar ataxia 10. Nat Commun 2016; 7:11647. [PMID: 27248057 PMCID: PMC4895354 DOI: 10.1038/ncomms11647] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 04/18/2016] [Indexed: 12/22/2022] Open
Abstract
RNA is an important target for chemical probes of function and lead therapeutics; however, it is difficult to target with small molecules. One approach to tackle this problem is to identify compounds that target RNA structures and utilize them to multivalently target RNA. Here we show that small molecules can be identified to selectively bind RNA base pairs by probing a library of RNA-focused small molecules. A small molecule that selectively binds AU base pairs informed design of a dimeric compound (2AU-2) that targets the pathogenic RNA, expanded r(AUUCU) repeats, that causes spinocerebellar ataxia type 10 (SCA10) in patient-derived cells. Indeed, 2AU-2 (50 nM) ameliorates various aspects of SCA10 pathology including improvement of mitochondrial dysfunction, reduced activation of caspase 3, and reduction of nuclear foci. These studies provide a first-in-class chemical probe to study SCA10 RNA toxicity and potentially define broadly applicable compounds targeting RNA AU base pairs in cells. Expanded RNA repeats in non-coding region of a gene represent a hallmark of several diseases. Here, the authors identify two small molecules that selectively bind AU repeats and use them to design a compound that targets the pathogenic RNA associated with spinocerebellar ataxia type 10.
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Affiliation(s)
- Wang-Yong Yang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, USA
| | - Rui Gao
- Mitchell Center for Neurodegenerative Disorders, Department of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Mark Southern
- Informatics Core, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, USA
| | - Partha S Sarkar
- Mitchell Center for Neurodegenerative Disorders, Department of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Matthew D Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, USA
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17
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Gorske BC, Mumford EM, Conry RR. Tandem Incorporation of Enantiomeric Residues Engenders Discrete Peptoid Structures. Org Lett 2016; 18:2780-3. [DOI: 10.1021/acs.orglett.6b01283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Benjamin C. Gorske
- Department
of Chemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011-8466, United States
| | - Emily M. Mumford
- Department
of Chemistry, Bowdoin College, 6600 College Station, Brunswick, Maine 04011-8466, United States
| | - Rebecca R. Conry
- Department
of Chemistry, Colby College, 5750 Mayflower Hill, Waterville, Maine 04901, United States
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18
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Wynn JE, Zhang W, Tebit DM, Gray LR, Hammarskjold ML, Rekosh D, Santos WL. Characterization and in vitro activity of a branched peptide boronic acid that interacts with HIV-1 RRE RNA. Bioorg Med Chem 2016; 24:3947-3952. [PMID: 27091070 DOI: 10.1016/j.bmc.2016.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
A branched peptide containing multiple boronic acids was found to bind RRE IIB selectively and inhibit HIV-1 p24 capsid production in a dose-dependent manner. Structure-activity relationship studies revealed that branching in the peptide is crucial for the low micromolar binding towards RRE IIB, and the peptide demonstrates selectivity towards RRE IIB in the presence of tRNA. Footprinting studies suggest a binding site on the upper stem and internal loop regions of the RNA, which induces enzymatic cleavage of the internal loops of RRE IIB upon binding.
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Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Denis M Tebit
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Laurie R Gray
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - David Rekosh
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States.
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19
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Childs-Disney JL, Disney MD. Approaches to Validate and Manipulate RNA Targets with Small Molecules in Cells. Annu Rev Pharmacol Toxicol 2015; 56:123-40. [PMID: 26514201 DOI: 10.1146/annurev-pharmtox-010715-103910] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA has become an increasingly important target for therapeutic interventions and for chemical probes that dissect and manipulate its cellular function. Emerging targets include human RNAs that have been shown to directly cause cancer, metabolic disorders, and genetic disease. In this review, we describe various routes to obtain bioactive compounds that target RNA, with a particular emphasis on the development of small molecules. We use these cases to describe approaches that are being developed for target validation, which include target-directed cleavage, classic pull-down experiments, and covalent cross-linking. Thus, tools are available to design small molecules to target RNA and to identify the cellular RNAs that are their targets.
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Affiliation(s)
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458; ,
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20
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Abstract
RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics.
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Affiliation(s)
- Viachaslau Bernat
- 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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21
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Wynn JE, Santos WL. HIV-1 drug discovery: targeting folded RNA structures with branched peptides. Org Biomol Chem 2015; 13:5848-58. [PMID: 25958855 PMCID: PMC4511164 DOI: 10.1039/c5ob00589b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) is an RNA virus that is prone to high rates of mutation. While the disease is managed with current antiretroviral therapies, drugs with a new mode of action are needed. A strategy towards this goal is aimed at targeting the native three-dimensional fold of conserved RNA structures. This perspective highlights medium-sized peptides and peptidomimetics used to target two conserved RNA structures of HIV-1. In particular, branched peptides have the capacity to bind in a multivalent fashion, utilizing a large surface area to achieve the necessary affinity and selectivity toward the target RNA.
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Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, USA.
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22
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Park S, Kim GH, Park SH, Pai J, Rathwell D, Park JY, Kang YS, Shin I. Probing cell-surface carbohydrate binding proteins with dual-modal glycan-conjugated nanoparticles. J Am Chem Soc 2015; 137:5961-8. [PMID: 25939670 DOI: 10.1021/jacs.5b00592] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Dual-modal fluorescent magnetic glyconanoparticles have been prepared and shown to be powerful in probing lectins displayed on pathogenic and mammalian cell surfaces. Blood group H1- and Le(b)-conjugated nanoparticles were found to bind to BabA displaying Helicobacter pylori, and Le(a)- and Le(b)-modified nanoparticles are both recognized by and internalized into DC-SIGN and SIGN-R1 expressing mammalian cells via lectin-mediated endocytosis. In addition, glyconanoparticles block adhesion of H. pylori to mammalian cells, suggesting that they can serve as inhibitors of infection of host cells by this pathogen. It has been also shown that owing to their magnetic properties, glyconanoparticles are useful tools to enrich lectin expressing cells. The combined results indicate that dual-modal glyconanoparticles are biocompatible and that they can be employed in lectin-associated biological studies and biomedical applications.
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Affiliation(s)
- Sungjin Park
- †Department of Chemistry, Yonsei University, Seoul 120-749 Korea
| | - Gun-Hee Kim
- †Department of Chemistry, Yonsei University, Seoul 120-749 Korea
| | - Seong-Hyun Park
- †Department of Chemistry, Yonsei University, Seoul 120-749 Korea
| | - Jaeyoung Pai
- †Department of Chemistry, Yonsei University, Seoul 120-749 Korea
| | - Dominea Rathwell
- †Department of Chemistry, Yonsei University, Seoul 120-749 Korea
| | - Jin-Yeon Park
- ‡Department of Veterinary Medicine, Department of Biomedical Science and Technology, Konkuk University, Seoul 143-701 Korea
| | - Young-Sun Kang
- ‡Department of Veterinary Medicine, Department of Biomedical Science and Technology, Konkuk University, Seoul 143-701 Korea
| | - Injae Shin
- †Department of Chemistry, Yonsei University, Seoul 120-749 Korea
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23
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Paolantoni D, Cantel S, Dumy P, Ulrich S. A dynamic combinatorial approach for identifying side groups that stabilize DNA-templated supramolecular self-assemblies. Int J Mol Sci 2015; 16:3609-25. [PMID: 25667976 PMCID: PMC4346916 DOI: 10.3390/ijms16023609] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 12/16/2022] Open
Abstract
DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.
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Affiliation(s)
- Delphine Paolantoni
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Sonia Cantel
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
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24
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Shortridge MD, Varani G. Structure based approaches for targeting non-coding RNAs with small molecules. Curr Opin Struct Biol 2015; 30:79-88. [PMID: 25687935 PMCID: PMC4416997 DOI: 10.1016/j.sbi.2015.01.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/19/2015] [Accepted: 01/28/2015] [Indexed: 12/22/2022]
Abstract
The increasing appreciation of the central role of non-coding RNAs (miRNAs and long non-coding RNAs) in chronic and degenerative human disease makes them attractive therapeutic targets. This would not be unprecedented: the bacterial ribosomal RNA is a mainstay for antibacterial treatment, while the conservation and functional importance of viral RNA regulatory elements has long suggested they would constitute attractive targets for new antivirals. Oligonucleotide-based chemistry has obvious appeals but also considerable pharmacological limitations that are yet to be addressed satisfactorily. Recent studies identifying small molecules targeting non-coding RNAs may provide an alternative approach to oligonucleotide methods. Here we review recent work investigating new structural and chemical principles for targeting RNA with small molecules.
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Affiliation(s)
- Matthew D Shortridge
- Department of Chemistry, University of Washington, Seattle, Box 351700, Seattle 98195, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Box 351700, Seattle 98195, USA.
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25
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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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26
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Fosso MY, Li Y, Garneau-Tsodikova S. New trends in aminoglycosides use. MEDCHEMCOMM 2014; 5:1075-1091. [PMID: 25071928 PMCID: PMC4111210 DOI: 10.1039/c4md00163j] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Despite their inherent toxicity and the acquired bacterial resistance that continuously threaten their long-term clinical use, aminoglycosides (AGs) still remain valuable components of the antibiotic armamentarium. Recent literature shows that the AGs' role has been further expanded as multi-tasking players in different areas of study. This review aims at presenting some of the new trends observed in the use of AGs in the past decade, along with the current understanding of their mechanisms of action in various bacterial and eukaryotic cellular processes.
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Affiliation(s)
- Marina Y. Fosso
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, BioPharm Complex, Room 423, 789 South Limestone Street, Lexington, KY, 40536-0596, U.S.A
| | - Yijia Li
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, BioPharm Complex, Room 423, 789 South Limestone Street, Lexington, KY, 40536-0596, U.S.A
| | - Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, BioPharm Complex, Room 423, 789 South Limestone Street, Lexington, KY, 40536-0596, U.S.A
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27
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Levine PM, Garabedian MJ, Kirshenbaum K. Targeting the androgen receptor with steroid conjugates. J Med Chem 2014; 57:8224-37. [PMID: 24936953 PMCID: PMC4207530 DOI: 10.1021/jm500101h] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The androgen receptor (AR) is a major therapeutic target in prostate cancer pharmacology. Progression of prostate cancer has been linked to elevated expression of AR in malignant tissue, suggesting that AR plays a central role in prostate cancer cell biology. Potent therapeutic agents can be precisely crafted to specifically target AR, potentially averting systemic toxicities associated with nonspecific chemotherapies. In this review, we describe various strategies to generate steroid conjugates that can selectively engage AR with high potency. Analogies to recent developments in nonsteroidal conjugates targeting AR are also evaluated. Particular focus is placed on potential applications in AR pharmacology. The review culminates with a description of future prospects for targeting AR.
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Affiliation(s)
- Paul M Levine
- Department of Chemistry, New York University , New York, New York 10003, United States
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28
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29
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Blakeley BD, McNaughton BR. Synthetic RNA recognition motifs that selectively recognize HIV-1 trans-activation response element hairpin RNA. ACS Chem Biol 2014; 9:1320-9. [PMID: 24635165 DOI: 10.1021/cb500138h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A multitude of RNA hairpins are directly implicated in human disease. Many of these RNAs are potentially valuable targets for drug discovery and basic research. However, very little is known about the molecular requirements for achieving sequence-selective recognition of a particular RNA sequence and structure. Although a relatively modest number of synthetic small to medium-sized RNA-binding molecules have been reported, rapid identification of sequence-selective RNA-binding molecules remains a daunting challenge. RNA recognition motif (RRM) domains may represent unique privileged scaffolds for the generation of synthetic proteins that selectively recognize structured disease-relevant RNAs, including RNA hairpins. As a demonstration of this potential, we mutated putative RNA-binding regions within the U1A RRM and a variant thereof and screened these synthetic proteins for affinity to HIV-1 trans-activation response (TAR) element hairpin RNA. Some of these U1A-derived proteins bind TAR with single-digit micromolar dissociation constants, and they do so preferentially over the native protein's original target RNA (U1hpII) and a DNA TAR variant. Binding affinity is not appreciably diminished by addition of 10 molar equivalents of cellular tRNAs from Escherichia coli. Taken together, our findings represent the first synthetic RRMs that selectively bind a disease-relevant RNA hairpin and may represent a general approach for achieving sequence-selective recognition of RNA hairpins, which are the focus of therapeutic discovery and basic research.
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Affiliation(s)
- Brett D. Blakeley
- Department of Chemistry, and ‡Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Brian R. McNaughton
- Department of Chemistry, and ‡Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
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30
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Nguyen L, Lee J, Wong CH, Zimmerman SC. Small molecules that target the toxic RNA in myotonic dystrophy type 2. ChemMedChem 2014; 9:2455-62. [PMID: 24938413 DOI: 10.1002/cmdc.201402095] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Indexed: 12/19/2022]
Abstract
Myotonic dystrophy type 2 (DM2) is caused by an expansion of CCTG repeats in the zinc-finger protein gene (ZNF9). Transcribed CCUG repeats sequester muscleblind-like protein 1 (MBNL1), an important alternative splicing regulator, preventing its normal function, leading to the disease phenotype. We describe a series of ligands that disrupt the MBNL1-r(CCUG)n interaction as potential lead agents for developing DM2 therapeutics. A previously reported triaminopyrimidine-acridine conjugate was a moderate inhibitor in vitro, however it proved to be poorly water-soluble and not cell-permeable. To improve its therapeutic potential, the new set of ligands maintained the key triaminopyrimidine recognition unit but replaced the acridine intercalator with a bisamidinium groove binder. The optimized ligands exhibit low micromolar inhibition potency to MBNL1-r(CCUG)8. Importantly, the ligands are the first to show the ability to disrupt the MBNL1-r(CCUG)n foci in DM2 model cell culture and exhibit low cytotoxicity.
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Affiliation(s)
- Lien Nguyen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 (USA)
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31
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Fiszer A, Krzyzosiak WJ. Oligonucleotide-based strategies to combat polyglutamine diseases. Nucleic Acids Res 2014; 42:6787-810. [PMID: 24848018 PMCID: PMC4066792 DOI: 10.1093/nar/gku385] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Considerable advances have been recently made in understanding the molecular aspects of pathogenesis and in developing therapeutic approaches for polyglutamine (polyQ) diseases. Studies on pathogenic mechanisms have extended our knowledge of mutant protein toxicity, confirmed the toxicity of mutant transcript and identified other toxic RNA and protein entities. One very promising therapeutic strategy is targeting the causative gene expression with oligonucleotide (ON) based tools. This straightforward approach aimed at halting the early steps in the cascade of pathogenic events has been widely tested for Huntington's disease and spinocerebellar ataxia type 3. In this review, we gather information on the use of antisense oligonucleotides and RNA interference triggers for the experimental treatment of polyQ diseases in cellular and animal models. We present studies testing non-allele-selective and allele-selective gene silencing strategies. The latter include targeting SNP variants associated with mutations or targeting the pathologically expanded CAG repeat directly. We compare gene silencing effectors of various types in a number of aspects, including their design, efficiency in cell culture experiments and pre-clinical testing. We discuss advantages, current limitations and perspectives of various ON-based strategies used to treat polyQ diseases.
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Affiliation(s)
- Agnieszka Fiszer
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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32
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Zhang W, Bryson DI, Crumpton JB, Wynn J, Santos WL. Targeting folded RNA: a branched peptide boronic acid that binds to a large surface area of HIV-1 RRE RNA. Org Biomol Chem 2014; 11:6263-71. [PMID: 23925474 DOI: 10.1039/c3ob41053f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
On-bead high-throughput screening of a medium-sized (1000-2000 Da) branched peptide boronic acid (BPBA) library consisting of 46,656 unique sequences against HIV-1 RRE RNA generated peptides with binding affinities in the low micromolar range. In particular, BPBA1 had a K(d) of 1.4 μM with RRE IIB, preference for RNA over DNA (27 fold), and selectivity of up to >75 fold against a panel of RRE IIB variants. Structure-activity studies suggest that the boronic acid moiety and "branching" in peptides are key structural features for efficient binding and selectivity for the folded RNA target. BPBA1 was efficiently taken up by HeLa and A2780 cells. RNA-footprinting studies revealed that the BPBA1 binding site encompasses a large surface area that spans both the upper stem as well as the internal loop regions of RRE IIB.
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Affiliation(s)
- Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, USA
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33
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Childs-Disney JL, Yildirim I, Park H, Lohman JR, Guan L, Tran T, Sarkar P, Schatz GC, Disney MD. Structure of the myotonic dystrophy type 2 RNA and designed small molecules that reduce toxicity. ACS Chem Biol 2014; 9:538-550. [PMID: 24341895 DOI: 10.1021/cb4007387] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Myotonic dystrophy type 2 (DM2) is an incurable neuromuscular disorder caused by a r(CCUG) expansion (r(CCUG)(exp)) that folds into an extended hairpin with periodically repeating 2×2 nucleotide internal loops (5'CCUG/3'GUCC). We designed multivalent compounds that improve DM2-associated defects using information about RNA-small molecule interactions. We also report the first crystal structure of r(CCUG) repeats refined to 2.35 Å. Structural analysis of the three 5'CCUG/3'GUCC repeat internal loops (L) reveals that the CU pairs in L1 are each stabilized by one hydrogen bond and a water-mediated hydrogen bond, while CU pairs in L2 and L3 are stabilized by two hydrogen bonds. Molecular dynamics (MD) simulations reveal that the CU pairs are dynamic and stabilized by Na(+) and water molecules. MD simulations of the binding of the small molecule to r(CCUG) repeats reveal that the lowest free energy binding mode occurs via the major groove, in which one C residue is unstacked and the cross-strand nucleotides are displaced. Moreover, we modeled the binding of our dimeric compound to two 5'CCUG/3'GUCC motifs, which shows that the scaffold on which the RNA-binding modules are displayed provides an optimal distance to span two adjacent loops.
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Affiliation(s)
| | - Ilyas Yildirim
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | | | | | | | | | - Partha Sarkar
- Department
of Neurology, University of Texas Medical Branch, 301 University
Boulevard, Galveston, Texas 77555-0539, United States
| | - George C. Schatz
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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Disney MD, Yildirim I, Childs-Disney JL. Methods to enable the design of bioactive small molecules targeting RNA. Org Biomol Chem 2014; 12:1029-39. [PMID: 24357181 PMCID: PMC4020623 DOI: 10.1039/c3ob42023j] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
RNA is an immensely important target for small molecule therapeutics or chemical probes of function. However, methods that identify, annotate, and optimize RNA-small molecule interactions that could enable the design of compounds that modulate RNA function are in their infancies. This review describes recent approaches that have been developed to understand and optimize RNA motif-small molecule interactions, including structure-activity relationships through sequencing (StARTS), quantitative structure-activity relationships (QSAR), chemical similarity searching, structure-based design and docking, and molecular dynamics (MD) simulations. Case studies described include the design of small molecules targeting RNA expansions, the bacterial A-site, viral RNAs, and telomerase RNA. These approaches can be combined to afford a synergistic method to exploit the myriad of RNA targets in the transcriptome.
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Affiliation(s)
- Matthew D Disney
- The Department of Chemistry, The Scripps Research Institute, 130 Scripps Way #3A1, Jupiter, FL 33458, USA.
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35
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Yadav AR, Mace CR, Miller BL. Examining the interactions of the splicing factor MBNL1 with target RNA sequences via a label-free, multiplex method. Anal Chem 2014; 86:1067-75. [PMID: 24377303 DOI: 10.1021/ac402603j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The near-ubiquity of the involvement of RNA in crucial biological processes is accepted. It is important, therefore, to study and understand the biophysical principles that regulate the function of RNA and its interactions with other molecules (e.g., proteins and antibiotics). Methods enabling the high-throughput determination of RNA-protein binding kinetics and thermodynamics would greatly accelerate understanding of these interactions. To that end, we describe the development of a real-time biomolecular interaction analysis platform based on arrayed imaging reflectometry (AIR) for multiplex analysis of RNA-protein interactions. We demonstrate the use of aqueous AIR by measuring the binding kinetics between muscleblind-like 1 (MBNL1), a splicing regulator protein that plays a pivotal role in the Myotonic Dystrophies and Huntington's Disease, and several of its RNA targets simultaneously on a microarrayed chip. Using this approach, we observe that the kinetics of MBNL1 binding isolated CUG and repeat CUG RNA sequences (as models for "normal" and "pathogenic" RNA, respectively) are different even though their steady state binding constants are similar. The ability to compare binding kinetics between RNA sequences rapidly and easily may provide insight into the molecular basis of MBNL1-RNA binding, and more generally suggests that AIR can be a powerful tool to enable the label-free, real-time analysis of biomolecular interactions in a high-throughput format.
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Affiliation(s)
- Amrita R Yadav
- Department of Physics and Astronomy, University of Rochester , Rochester, NY 14627, United States
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36
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Induction and reversal of myotonic dystrophy type 1 pre-mRNA splicing defects by small molecules. Nat Commun 2013; 4:2044. [PMID: 23806903 PMCID: PMC3710115 DOI: 10.1038/ncomms3044] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/23/2013] [Indexed: 02/06/2023] Open
Abstract
The ability to control pre-mRNA splicing with small molecules could facilitate the development of therapeutics or cell-based circuits that control gene function. Myotonic dystrophy type 1 (DM1) is caused by the dysregulation of alternative pre-mRNA splicing due to sequestration of muscleblind-like 1 protein (MBNL1) by expanded, non-coding r(CUG) repeats (r(CUG)exp). Here we report two small molecules that induce or ameliorate alternative splicing dysregulation. The thiophene-containing small molecule (1) inhibits the interaction of MBNL1 with its natural pre-mRNA substrates. Compound (2), a substituted naphthyridine, binds r(CUG)exp and displaces MBNL1. Structural models show that 1 binds MBNL1 in the Zn-finger domain and that 2 interacts with UU loops in r(CUG)exp. This study provides a structural framework for small molecules that target MBNL1 by mimicking r(CUG)exp and shows that targeting MBNL1 causes dysregulation of alternative splicing, suggesting that MBNL1 is thus not a suitable therapeutic target for the treatment of DM1.
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37
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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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38
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Coonrod LA, Nakamori M, Wang W, Carrell S, Hilton CL, Bodner MJ, Siboni RB, Docter AG, Haley MM, Thornton CA, Berglund JA. Reducing levels of toxic RNA with small molecules. ACS Chem Biol 2013; 8:2528-37. [PMID: 24028068 DOI: 10.1021/cb400431f] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Myotonic dystrophy (DM) is one of the most common forms of muscular dystrophy. DM is an autosomal dominant disease caused by a toxic gain of function RNA. The toxic RNA is produced from expanded noncoding CTG/CCTG repeats, and these CUG/CCUG repeats sequester the Muscleblind-like (MBNL) family of RNA binding proteins. The MBNL proteins are regulators of alternative splicing, and their sequestration has been linked with mis-splicing events in DM. A previously reported screen for small molecules found that pentamidine was able to improve splicing defects associated with DM. Biochemical experiments and cell and mouse model studies of the disease indicate that pentamidine and related compounds may work through binding the CTG*CAG repeat DNA to inhibit transcription. Analysis of a series of methylene linker analogues of pentamidine revealed that heptamidine reverses splicing defects and rescues myotonia in a DM1 mouse model.
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Affiliation(s)
| | - Masayuki Nakamori
- Department
of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Wenli Wang
- Department
of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Samuel Carrell
- Department
of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | | | | | | | | | | | - Charles A. Thornton
- Department
of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
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39
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Gorske BC, Nelson RC, Bowden ZS, Kufe TA, Childs AM. “Bridged” n→π* Interactions Can Stabilize Peptoid Helices. J Org Chem 2013; 78:11172-83. [DOI: 10.1021/jo4014113] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Benjamin C. Gorske
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
| | - Ryan C. Nelson
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
| | - Zara S. Bowden
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
| | - Turner A. Kufe
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
| | - Adam M. Childs
- Department of Chemistry, Bowdoin College, 6600 College
Station, Brunswick, Maine 04011-8466, United States
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40
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Rzuczek SG, Gao Y, Tang ZZ, Thornton CA, Kodadek T, Disney MD. Features of modularly assembled compounds that impart bioactivity against an RNA target. ACS Chem Biol 2013; 8:2312-21. [PMID: 24032410 DOI: 10.1021/cb400265y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Transcriptomes provide a myriad of potential RNAs that could be the targets of therapeutics or chemical genetic probes of function. Cell-permeable small molecules, however, generally do not exploit these targets, owing to the difficulty in the design of high affinity, specific small molecules targeting RNA. As part of a general program to study RNA function using small molecules, we designed bioactive, modularly assembled small molecules that target the noncoding expanded RNA repeat that causes myotonic dystrophy type 1 (DM1), r(CUG)(exp). Herein, we present a rigorous study to elucidate features in modularly assembled compounds that afford bioactivity. Different modular assembly scaffolds were investigated, including polyamines, α-peptides, β-peptides, and peptide tertiary amides (PTAs). On the basis of activity as assessed by improvement of DM1-associated defects, stability against proteases, cellular permeability, and toxicity, we discovered that constrained backbones, namely, PTAs, are optimal. Notably, we determined that r(CUG)(exp) is the target of the optimal PTA in cellular models and that the optimal PTA improves DM1-associated defects in a mouse model. Biophysical analyses were employed to investigate potential sources of bioactivity. These investigations show that modularly assembled compounds have increased residence times on their targets and faster on rates than the RNA-binding modules from which they were derived. Moreover, they have faster on rates than the protein that binds r(CUG)(exp), the inactivation of which gives rise to DM1-associated defects. These studies provide information about features of small molecules that are programmable for targeting RNA, allowing for the facile optimization of therapeutics or chemical probes against other cellular RNA targets.
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Affiliation(s)
- Suzanne G. Rzuczek
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Yu Gao
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Zhen-Zhi Tang
- Department
of Neurology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Charles A. Thornton
- Department
of Neurology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Thomas Kodadek
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
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41
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Disney MD. Rational design of chemical genetic probes of RNA function and lead therapeutics targeting repeating transcripts. Drug Discov Today 2013; 18:1228-36. [PMID: 23939337 DOI: 10.1016/j.drudis.2013.07.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 07/26/2013] [Accepted: 07/31/2013] [Indexed: 02/06/2023]
Abstract
RNA is an important yet vastly underexploited target for small molecule chemical probes or lead therapeutics. Small molecules have been used successfully to modulate the function of the bacterial ribosome, viral RNAs and riboswitches. These RNAs are either highly expressed or can be targeted using substrate mimicry, a mainstay in the design of enzyme inhibitors. However, most cellular RNAs are neither highly expressed nor have a lead small molecule inhibitor, a significant challenge for drug discovery efforts. Herein, I describe the design of small molecules targeting expanded repeating transcripts that cause myotonic muscular dystrophy (DM). These test cases illustrate the challenges of designing small molecules that target RNA and the advantages of targeting repeating transcripts. Lastly, I discuss how small molecules might be more advantageous than oligonucleotides for targeting RNA.
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Affiliation(s)
- Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way #3A1, Jupiter, FL 33458, USA.
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42
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Guan L, Disney MD. Covalent Small-Molecule-RNA Complex Formation Enables Cellular Profiling of Small-Molecule-RNA Interactions. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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43
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Guan L, Disney MD. Covalent small-molecule-RNA complex formation enables cellular profiling of small-molecule-RNA interactions. Angew Chem Int Ed Engl 2013; 52:10010-3. [PMID: 23913698 DOI: 10.1002/anie.201301639] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 05/02/2013] [Indexed: 01/13/2023]
Abstract
Won't let you go! A strategy is described to design small molecules that react with their cellular RNA targets. This approach not only improves the activity of compounds targeting RNA in cell culture by a factor of about 2500 but also enables cell-wide profiling of its RNA targets.
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Affiliation(s)
- Lirui Guan
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, 3A1, Jupiter, FL 33458 (USA)
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44
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Velagapudi SP, Disney MD. Defining RNA motif-aminoglycoside interactions via two-dimensional combinatorial screening and structure-activity relationships through sequencing. Bioorg Med Chem 2013; 21:6132-8. [PMID: 23719281 DOI: 10.1016/j.bmc.2013.04.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 04/12/2013] [Accepted: 04/19/2013] [Indexed: 10/26/2022]
Abstract
RNA is an extremely important target for the development of chemical probes of function or small molecule therapeutics. Aminoglycosides are the most well studied class of small molecules to target RNA. However, the RNA motifs outside of the bacterial rRNA A-site that are likely to be bound by these compounds in biological systems is largely unknown. If such information were known, it could allow for aminoglycosides to be exploited to target other RNAs and, in addition, could provide invaluable insights into potential bystander targets of these clinically used drugs. We utilized two-dimensional combinatorial screening (2DCS), a library-versus-library screening approach, to select the motifs displayed in a 3×3 nucleotide internal loop library and in a 6-nucleotide hairpin library that bind with high affinity and selectivity to six aminoglycoside derivatives. The selected RNA motifs were then analyzed using structure-activity relationships through sequencing (StARTS), a statistical approach that defines the privileged RNA motif space that binds a small molecule. StARTS allowed for the facile annotation of the selected RNA motif-aminoglycoside interactions in terms of affinity and selectivity. The interactions selected by 2DCS generally have nanomolar affinities, which is higher affinity than the binding of aminoglycosides to a mimic of their therapeutic target, the bacterial rRNA A-site.
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Affiliation(s)
- Sai Pradeep Velagapudi
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States; Department of Chemistry, University at Buffalo, Buffalo, NY 14620, United States
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45
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Tran T, Disney MD. Identifying the preferred RNA motifs and chemotypes that interact by probing millions of combinations. Nat Commun 2013; 3:1125. [PMID: 23047683 PMCID: PMC3533436 DOI: 10.1038/ncomms2119] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/05/2012] [Indexed: 12/16/2022] Open
Abstract
RNA is an important therapeutic target but information about RNA-ligand interactions is limited. Here, we report a screening method that probes over 3,000,000 combinations of RNA motif-small molecule interactions to identify the privileged RNA structures and chemical spaces that interact. Specifically, a small molecule library biased for binding RNA was probed for binding to over 70,000 unique RNA motifs in a high throughput solution-based screen. The RNA motifs that specifically bind each small molecule were identified by microarray-based selection. In this library-versus-library or multidimensional combinatorial screening approach, hairpin loops (among a variety of RNA motifs) were the preferred RNA motif space that binds small molecules. Furthermore, it was shown that indole, 2-phenyl indole, 2-phenyl benzimidazole and pyridinium chemotypes allow for specific recognition of RNA motifs. As targeting RNA with small molecules is an extremely challenging area, these studies provide new information on RNA-ligand interactions that has many potential uses.
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Affiliation(s)
- Tuan Tran
- The Department of Chemistry, University at Buffalo, Buffalo, New York 14260, USA
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46
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Tian X, Baek KH, Shin I. Dual-labeled glycoclusters: synthesis and their application in monitoring lectin-mediated endocytosis. MOLECULAR BIOSYSTEMS 2013; 9:978-86. [DOI: 10.1039/c3mb25491g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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47
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Levine PM, Carberry TP, Holub JM, Kirshenbaum K. Crafting precise multivalent architectures. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20338c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Development of elaborate three-dimensional multivalent displays appended on natural or synthetic molecular scaffolds.
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48
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Childs-Disney JL, Parkesh R, Nakamori M, Thornton CA, Disney MD. Rational design of bioactive, modularly assembled aminoglycosides targeting the RNA that causes myotonic dystrophy type 1. ACS Chem Biol 2012; 7:1984-93. [PMID: 23130637 DOI: 10.1021/cb3001606] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is caused when an expanded r(CUG) repeat (r(CUG)(exp)) binds the RNA splicing regulator muscleblind-like 1 protein (MBNL1) as well as other proteins. Previously, we reported that modularly assembled small molecules displaying a 6'-N-5-hexynoate kanamycin A RNA-binding module (K) on a peptoid backbone potently inhibit the binding of MBNL1 to r(CUG)(exp). However, these parent compounds are not appreciably active in cell-based models of DM1. The lack of potency was traced to suboptimal cellular permeability and localization. To improve these properties, second-generation compounds that are conjugated to a d-Arg(9) molecular transporter were synthesized. These modified compounds enter cells in higher concentrations than the parent compounds and are efficacious in cell-based DM1 model systems at low micromolar concentrations. In particular, they improve three defects that are the hallmarks of DM1: a translational defect due to nuclear retention of transcripts containing r(CUG)(exp); pre-mRNA splicing defects due to inactivation of MBNL1; and the formation of nuclear foci. The best compound in cell-based studies was tested in a mouse model of DM1. Modest improvement of pre-mRNA splicing defects was observed. These studies suggest that a modular assembly approach can afford bioactive compounds that target RNA.
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Affiliation(s)
- Jessica L. Childs-Disney
- Department
of Chemistry, Scripps Florida, 130 Scripps
Way, Jupiter, Florida
33458, United States
| | - Raman Parkesh
- Department
of Chemistry, Scripps Florida, 130 Scripps
Way, Jupiter, Florida
33458, United States
| | - Masayuki Nakamori
- Department
of Neurology, University of Rochester,
Rochester, New York 14642,
United States
| | - Charles A. Thornton
- Department
of Neurology, University of Rochester,
Rochester, New York 14642,
United States
| | - Matthew D. Disney
- Department
of Chemistry, Scripps Florida, 130 Scripps
Way, Jupiter, Florida
33458, United States
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49
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Velagapudi SP, Pushechnikov A, Labuda LP, French JM, Disney MD. Probing a 2-aminobenzimidazole library for binding to RNA internal loops via two-dimensional combinatorial screening. ACS Chem Biol 2012; 7:1902-9. [PMID: 22958065 DOI: 10.1021/cb300213g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
There are many potential RNA drug targets in bacterial, viral, and human transcriptomes. However, there are few small molecules that modulate RNA function. This is due, in part, to a lack of fundamental understanding about RNA-ligand interactions including the types of small molecules that bind to RNA structural elements and the RNA structural elements that bind to small molecules. In an effort to better understand RNA-ligand interactions, we diversified the 2-aminobenzimidazole core (2AB) and probed the resulting library for binding to a library of RNA internal loops. We chose the 2AB core for these studies because it is a privileged scaffold for binding RNA based on previous reports. These studies identified that N-methyl pyrrolidine, imidazole, and propylamine diversity elements at the R1 position increase binding to internal loops; variability at the R2 position is well tolerated. The preferred RNA loop space was also determined for five ligands using a statistical approach and identified trends that lead to selective recognition.
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Affiliation(s)
- Sai Pradeep Velagapudi
- Department
of Chemistry and
the Center of Excellence in Bioinformatics and Life Sciences, The
University at Buffalo, The State University of New York, 657 Natural Sciences Complex, Buffalo, New York 14260, United States
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Alexei Pushechnikov
- Department
of Chemistry and
the Center of Excellence in Bioinformatics and Life Sciences, The
University at Buffalo, The State University of New York, 657 Natural Sciences Complex, Buffalo, New York 14260, United States
| | - Lucas P. Labuda
- Department
of Chemistry and
the Center of Excellence in Bioinformatics and Life Sciences, The
University at Buffalo, The State University of New York, 657 Natural Sciences Complex, Buffalo, New York 14260, United States
| | - Jonathan M. French
- Department
of Chemistry and
the Center of Excellence in Bioinformatics and Life Sciences, The
University at Buffalo, The State University of New York, 657 Natural Sciences Complex, Buffalo, New York 14260, United States
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
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Wong CH, Richardson SL, Ho YJ, Lucas AMH, Tuccinardi T, Baranger AM, Zimmerman SC. Investigating the binding mode of an inhibitor of the MBNL1·RNA complex in myotonic dystrophy type 1 (DM1) leads to the unexpected discovery of a DNA-selective binder. Chembiochem 2012; 13:2505-9. [PMID: 23097190 DOI: 10.1002/cbic.201200602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Indexed: 01/12/2023]
Affiliation(s)
- Chun-Ho Wong
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
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