Literature DB >> 26514201

Approaches to Validate and Manipulate RNA Targets with Small Molecules in Cells.

Jessica L Childs-Disney1, Matthew D Disney1.   

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.

Entities:  

Keywords:  Inforna; RNA; antibacterials; antisense oligonucleotides; genetic disease; nucleic acids; orphan disease; rational design; target identification

Mesh:

Substances:

Year:  2015        PMID: 26514201      PMCID: PMC4876813          DOI: 10.1146/annurev-pharmtox-010715-103910

Source DB:  PubMed          Journal:  Annu Rev Pharmacol Toxicol        ISSN: 0362-1642            Impact factor:   13.820


  94 in total

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2.  Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein.

Authors:  Amy Davidson; Thomas C Leeper; Zafiria Athanassiou; Krystyna Patora-Komisarska; Jonathan Karn; John A Robinson; Gabriele Varani
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-07       Impact factor: 11.205

3.  Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration.

Authors:  Clotilde Lagier-Tourenne; Michael Baughn; Frank Rigo; Shuying Sun; Patrick Liu; Hai-Ri Li; Jie Jiang; Andrew T Watt; Seung Chun; Melanie Katz; Jinsong Qiu; Ying Sun; Shuo-Chien Ling; Qiang Zhu; Magdalini Polymenidou; Kevin Drenner; Jonathan W Artates; Melissa McAlonis-Downes; Sebastian Markmiller; Kasey R Hutt; Donald P Pizzo; Janet Cady; Matthew B Harms; Robert H Baloh; Scott R Vandenberg; Gene W Yeo; Xiang-Dong Fu; C Frank Bennett; Don W Cleveland; John Ravits
Journal:  Proc Natl Acad Sci U S A       Date:  2013-10-29       Impact factor: 11.205

4.  Myotonic dystrophy in transgenic mice expressing an expanded CUG repeat.

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Review 5.  MiRNAs and cancer.

Authors:  Rosa Visone; Carlo M Croce
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6.  Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.

Authors:  Maria A Borovinskaya; Raj D Pai; Wen Zhang; Barbara S Schuwirth; James M Holton; Go Hirokawa; Hideko Kaji; Akira Kaji; Jamie H Doudna Cate
Journal:  Nat Struct Mol Biol       Date:  2007-07-29       Impact factor: 15.369

7.  Inhibition of both HIV-1 reverse transcription and gene expression by a cyclic peptide that binds the Tat-transactivating response element (TAR) RNA.

Authors:  Matthew S Lalonde; Michael A Lobritz; Annette Ratcliff; Mastooreh Chamanian; Zafiria Athanassiou; Mudit Tyagi; Julian Wong; John A Robinson; Jonathan Karn; Gabriele Varani; Eric J Arts
Journal:  PLoS Pathog       Date:  2011-05-19       Impact factor: 6.823

8.  Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein.

Authors:  Amy Davidson; Krystyna Patora-Komisarska; John A Robinson; Gabriele Varani
Journal:  Nucleic Acids Res       Date:  2010-08-19       Impact factor: 16.971

9.  Targeting the r(CGG) repeats that cause FXTAS with modularly assembled small molecules and oligonucleotides.

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Journal:  ACS Chem Biol       Date:  2014-02-19       Impact factor: 5.100

10.  C9orf72 FTLD/ALS-associated Gly-Ala dipeptide repeat proteins cause neuronal toxicity and Unc119 sequestration.

Authors:  Stephanie May; Daniel Hornburg; Martin H Schludi; Thomas Arzberger; Kristin Rentzsch; Benjamin M Schwenk; Friedrich A Grässer; Kohji Mori; Elisabeth Kremmer; Julia Banzhaf-Strathmann; Matthias Mann; Felix Meissner; Dieter Edbauer
Journal:  Acta Neuropathol       Date:  2014-08-14       Impact factor: 17.088

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  30 in total

Review 1.  Small molecule targeting of RNA structures in neurological disorders.

Authors:  Alicia J Angelbello; Jonathan L Chen; Matthew D Disney
Journal:  Ann N Y Acad Sci       Date:  2019-04-09       Impact factor: 5.691

2.  Identifying and validating small molecules interacting with RNA (SMIRNAs).

Authors:  Matthew D Disney; Sai Pradeep Velagapudi; Yue Li; Matthew G Costales; Jessica L Childs-Disney
Journal:  Methods Enzymol       Date:  2019-05-15       Impact factor: 1.600

3.  Design, Optimization, and Study of Small Molecules That Target Tau Pre-mRNA and Affect Splicing.

Authors:  Jonathan L Chen; Peiyuan Zhang; Masahito Abe; Haruo Aikawa; Liying Zhang; Alexander J Frank; Timothy Zembryski; Christopher Hubbs; HaJeung Park; Jane Withka; Claire Steppan; Lucy Rogers; Shawn Cabral; Martin Pettersson; Travis T Wager; Matthew A Fountain; Gavin Rumbaugh; Jessica L Childs-Disney; Matthew D Disney
Journal:  J Am Chem Soc       Date:  2020-05-04       Impact factor: 15.419

Review 4.  Long Noncoding RNA in Cancer: Wiring Signaling Circuitry.

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Journal:  Trends Cell Biol       Date:  2017-12-20       Impact factor: 20.808

5.  Macrocyclization of a Ligand Targeting a Toxic RNA Dramatically Improves Potency.

Authors:  Raphael I Benhamou; Simon Vezina-Dawod; Shruti Choudhary; Kye Won Wang; Samantha M Meyer; Ilyas Yildirim; Matthew D Disney
Journal:  Chembiochem       Date:  2020-08-26       Impact factor: 3.164

Review 6.  The roles of structural dynamics in the cellular functions of RNAs.

Authors:  Laura R Ganser; Megan L Kelly; Daniel Herschlag; Hashim M Al-Hashimi
Journal:  Nat Rev Mol Cell Biol       Date:  2019-08       Impact factor: 94.444

Review 7.  Physics-based all-atom modeling of RNA energetics and structure.

Authors:  Louis G Smith; Jianbo Zhao; David H Mathews; Douglas H Turner
Journal:  Wiley Interdiscip Rev RNA       Date:  2017-09       Impact factor: 9.957

8.  Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site.

Authors:  Chia-Chieh Chu; Raphael Plangger; Christoph Kreutz; Hashim M Al-Hashimi
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Review 9.  Targeting RNA in mammalian systems with small molecules.

Authors:  Anita Donlic; Amanda E Hargrove
Journal:  Wiley Interdiscip Rev RNA       Date:  2018-05-03       Impact factor: 9.957

Review 10.  Non-coding RNAs as drug targets.

Authors:  Masayuki Matsui; David R Corey
Journal:  Nat Rev Drug Discov       Date:  2016-07-22       Impact factor: 84.694

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