Literature DB >> 25687935

Structure based approaches for targeting non-coding RNAs with small molecules.

Matthew D Shortridge1, Gabriele Varani2.   

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.
Copyright © 2015 Elsevier Ltd. All rights reserved.

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Year:  2015        PMID: 25687935      PMCID: PMC4416997          DOI: 10.1016/j.sbi.2015.01.008

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  78 in total

1.  Targeting microRNAs with small molecules: from dream to reality.

Authors:  S Zhang; L Chen; E J Jung; G A Calin
Journal:  Clin Pharmacol Ther       Date:  2010-04-28       Impact factor: 6.875

Review 2.  Regulation of mRNA translation and stability by microRNAs.

Authors:  Marc Robert Fabian; Nahum Sonenberg; Witold Filipowicz
Journal:  Annu Rev Biochem       Date:  2010       Impact factor: 23.643

3.  Small-molecule inhibitors of microrna miR-21 function.

Authors:  Kiranmai Gumireddy; Douglas D Young; Xin Xiong; John B Hogenesch; Qihong Huang; Alexander Deiters
Journal:  Angew Chem Int Ed Engl       Date:  2008       Impact factor: 15.336

4.  A fragment-based approach to identifying ligands for riboswitches.

Authors:  Liuhong Chen; Elena Cressina; Finian J Leeper; Alison G Smith; Chris Abell
Journal:  ACS Chem Biol       Date:  2010-04-16       Impact factor: 5.100

5.  New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays.

Authors:  Jonathan B Baell; Georgina A Holloway
Journal:  J Med Chem       Date:  2010-04-08       Impact factor: 7.446

6.  Small molecule modifiers of microRNA miR-122 function for the treatment of hepatitis C virus infection and hepatocellular carcinoma.

Authors:  Douglas D Young; Colleen M Connelly; Christoph Grohmann; Alexander Deiters
Journal:  J Am Chem Soc       Date:  2010-06-16       Impact factor: 15.419

7.  Structure-activity relationships through sequencing (StARTS) defines optimal and suboptimal RNA motif targets for small molecules.

Authors:  Sai Pradeep Velagapudi; Steven J Seedhouse; Matthew D Disney
Journal:  Angew Chem Int Ed Engl       Date:  2010-05-17       Impact factor: 15.336

8.  Controlling the specificity of modularly assembled small molecules for RNA via ligand module spacing: targeting the RNAs that cause myotonic muscular dystrophy.

Authors:  Melissa M Lee; Jessica L Childs-Disney; Alexei Pushechnikov; Jonathan M French; Krzysztof Sobczak; Charles A Thornton; Matthew D Disney
Journal:  J Am Chem Soc       Date:  2009-12-02       Impact factor: 15.419

9.  The role of flexibility in the rational design of modularly assembled ligands targeting the RNAs that cause the myotonic dystrophies.

Authors:  Matthew D Disney; Melissa M Lee; Alexei Pushechnikov; Jessica L Childs-Disney
Journal:  Chembiochem       Date:  2010-02-15       Impact factor: 3.164

10.  Pentamidine reverses the splicing defects associated with myotonic dystrophy.

Authors:  M Bryan Warf; Masayuki Nakamori; Catherine M Matthys; Charles A Thornton; J Andrew Berglund
Journal:  Proc Natl Acad Sci U S A       Date:  2009-10-12       Impact factor: 11.205

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  28 in total

Review 1.  RNA Structural Differentiation: Opportunities with Pattern Recognition.

Authors:  Christopher S Eubanks; Amanda E Hargrove
Journal:  Biochemistry       Date:  2018-12-18       Impact factor: 3.162

2.  NMR probing of invisible excited states using selectively labeled RNAs.

Authors:  Regan M LeBlanc; Andrew P Longhini; Vitali Tugarinov; T Kwaku Dayie
Journal:  J Biomol NMR       Date:  2018-06-01       Impact factor: 2.835

Review 3.  Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions.

Authors:  Aline Umuhire Juru; Neeraj N Patwardhan; Amanda E Hargrove
Journal:  ACS Chem Biol       Date:  2019-05-01       Impact factor: 5.100

4.  Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA.

Authors:  Fardokht A Abulwerdi; Matthew D Shortridge; Joanna Sztuba-Solinska; Robert Wilson; Stuart F J Le Grice; Gabriele Varani; John S Schneekloth
Journal:  J Med Chem       Date:  2016-12-02       Impact factor: 7.446

5.  Small Molecule-Based Pattern Recognition To Classify RNA Structure.

Authors:  Christopher S Eubanks; Jordan E Forte; Gary J Kapral; Amanda E Hargrove
Journal:  J Am Chem Soc       Date:  2016-12-22       Impact factor: 15.419

6.  Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

Authors:  Kyle D Berger; Scott D Kennedy; Susan J Schroeder; Brent M Znosko; Hongying Sun; David H Mathews; Douglas H Turner
Journal:  Biochemistry       Date:  2018-03-23       Impact factor: 3.162

Review 7.  Synthetic small-molecule RNA ligands: future prospects as therapeutic agents.

Authors:  A Di Giorgio; M Duca
Journal:  Medchemcomm       Date:  2019-04-30       Impact factor: 3.597

Review 8.  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

9.  A Macrocyclic Peptide Ligand Binds the Oncogenic MicroRNA-21 Precursor and Suppresses Dicer Processing.

Authors:  Matthew D Shortridge; Matthew J Walker; Tom Pavelitz; Yu Chen; Wen Yang; Gabriele Varani
Journal:  ACS Chem Biol       Date:  2017-05-02       Impact factor: 5.100

10.  RLDOCK: A New Method for Predicting RNA-Ligand Interactions.

Authors:  Li-Zhen Sun; Yangwei Jiang; Yuanzhe Zhou; Shi-Jie Chen
Journal:  J Chem Theory Comput       Date:  2020-10-23       Impact factor: 6.006

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