Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble (Q39517694)

12 September 2017

Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble (English)

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12 September 2017

Andrew C Stelzer

1

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12 September 2017

Aaron T Frank

2

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12 September 2017

Jeremy D Kratz

3

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12 September 2017

Michael D Swanson

4

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12 September 2017

Marta J Gonzalez-Hernandez

5

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12 September 2017

Janghyun Lee

6

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12 September 2017

Ioan Andricioaei

7

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12 September 2017

David M Markovitz

8

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12 September 2017

Hashim M Al-Hashimi

9

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12 September 2017

26 June 2011

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12 September 2017

Nature Chemical Biology

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12 September 2017

7

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12 September 2017

8

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12 September 2017

553-559

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https://scigraph.springernature.com/pub.10.1038/nchembio.596

12 September 2017

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cites work

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

1 reference

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RNA dynamics by design: biasing ensembles towards the ligand-bound state.

12 September 2017

1 reference

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Molecular recognition of RNA: challenges for modelling interactions and plasticity

12 September 2017

1 reference

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The role of dynamic conformational ensembles in biomolecular recognition

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Conformational inhibition of the hepatitis C virus internal ribosome entry site RNA

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

DOCK 6: combining techniques to model RNA-small molecule complexes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

12 September 2017

1 reference

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Insight into the mechanisms of aminoglycoside derivatives interaction with HIV-1 entry steps and viral gene transcription

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Deciphering protein dynamics from NMR data using explicit structure sampling and selection

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Riboswitches as antibacterial drug targets

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Discoveries of Tat-TAR interaction inhibitors for HIV-1.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Ligand-induced changes in 2-aminopurine fluorescence as a probe for small molecule binding to HIV-1 TAR RNA

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Fluorescence-based approach for detecting and characterizing antibiotic-induced conformational changes in ribosomal RNA: comparing aminoglycoside binding to prokaryotic and eukaryotic ribosomal RNA sequences.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Using pyrene-labeled HIV-1 TAR to measure RNA-small molecule binding

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Proflavine acts as a Rev inhibitor by targeting the high-affinity Rev binding site of the Rev responsive element of HIV-1.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Rational ligand design for RNA: the role of static structure and conformational flexibility in target recognition

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Induced fit in RNA-protein recognition

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

NMRPipe: a multidimensional spectral processing system based on UNIX pipes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Structure-based strategies for drug design and discovery

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

New anti-human immunodeficiency virus type 1 6-aminoquinolones: mechanism of action

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Conformational constraint as a means for understanding RNA-aminoglycoside specificity.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Anti-HIV activity of a novel aminoglycoside-arginine conjugate

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Development of mitoxantrone

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Comparative assessment of scoring functions on a diverse test set.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Stochastic gating and drug-ribosome interactions.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Resolving the motional modes that code for RNA adaptation

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

Structure-activity relationships of aminoglycoside-arginine conjugates that bind HIV-1 RNAs as determined by fluorescence and NMR spectroscopy

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319144

ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

21 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNCHEMBIO.596

a high-throughput screening utilizing intramolecular fluorescence resonance energy transfer for the discovery of the molecules that bind hiv-1 tar rna specifically

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNCHEMBIO.596

Visualizing spatially correlated dynamics that directs RNA conformational transitions

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNCHEMBIO.596

Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements

21 January 2018

1 reference

12 December 2020

Conformation of the TAR RNA-Arginine Complex by NMR Spectroscopy

1 reference

12 December 2020

Targeting RNA with small molecules

1 reference

12 December 2020

The dynamic landscapes of RNA architecture

1 reference

12 December 2020

Identifiers

DOI

10.1038/NCHEMBIO.596

1 reference

Dimensions Publication ID

12 September 2017

1047767261

0 references

Fatcat ID

release_fullmu2zuzfztktt4wqrd6rapa

0 references

1 reference

12 September 2017

1 reference