ArticleNucleic acids research2011
Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
43 citing papers in PubMed.
- Detecting and quantifying overparametrization in RNA language models with REDIAL.bioRxiv : the preprint server for biology · 2026Article
- The kinase inhibitor palbociclib binds to HIV TAR RNA with very low nanomolar affinity and exquisite specificity.Nucleic acids research · 2026Article
- Three-dimensional structure of the palbociclib-HIV TAR complex.Nucleic acids research · 2026Article
- Decoding RNA Structural Ensembles: Energy Landscape Exploration of the TAR Stemloop.Journal of chemical theory and computation · 2026Article
- Tackling Undruggable Targets with Designer Peptidomimetics and Synthetic Biologics.Chemical reviews · 2024Review
- Structure of Essential RNA Regulatory Elements in the West Nile Virus 3'-Terminal Stem Loop.Journal of molecular biology · 2024Article
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules.Journal of chemical theory and computation · 2022Article
- Deep structural insights into RNA-binding disordered protein regions.Wiley interdisciplinary reviews. RNA · 2022Review
- A Slow Dynamic RNA Switch Regulates Processing of microRNA-21.Journal of molecular biology · 2022Article
- A Modular Synthesis of Teraryl-Based α-Helix Mimetics, Part 3: Iodophenyltriflate Core Fragments Featuring Side Chains of Proteinogenic Amino Acids.European journal of organic chemistry · 2022Article
- RNA-Binding Macrocyclic Peptides.Frontiers in molecular biosciences · 2022Review
- Structure-based deep learning for binding site detection in nucleic acid macromolecules.NAR genomics and bioinformatics · 2021Article
- Role and Perspective of Molecular Simulation-Based Investigation of RNA-Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding.Molecules (Basel, Switzerland) · 2021Review
- Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.The Journal of biological chemistry · 2020Article
- Exposing Hidden High-Affinity RNA Conformational States.Journal of the American Chemical Society · 2020Article
- Face-time with TAR: Portraits of an HIV-1 RNA with diverse modes of effector recognition relevant for drug discovery.The Journal of biological chemistry · 2019Review
- An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb.Nucleic acids research · 2019Article
- Design of RNA-targeting macrocyclic peptides.Methods in enzymology · 2019Article
- Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The pharmacological disruption of the interaction between the HIV Tat protein and its cognate transactivation response RNA (TAR) would generate novel anti-viral drugs with a low susceptibility to drug resistance, but efforts to discover ligands with sufficient potency to warrant pharmaceutical development have been unsuccessful. We have previously described a family of structurally constrained β-hairpin peptides that potently inhibits viral growth in HIV-infected cells. The nuclear magnetic resonance (NMR) structure of an inhibitory complex revealed that the peptide makes intimate contacts with the 3-nt bulge and the upper helix of the RNA hairpin, but that a single residue contacts the apical loop where recruitment of the essential cellular co-factor cyclin T₁ occurs. Attempting to extend the peptide to form more interactions with the RNA loop, we examined a library of longer peptides and achieved > 6-fold improvement in affinity. The structure of TAR bound to one of the extended peptides reveals that the peptide slides down the major groove of the RNA, relative to our design, in order to maintain critical interactions with TAR. These conserved contacts involve three amino acid side chains and identify critical interaction points required for potent and specific binding to TAR RNA. They constitute a template of essential interactions required for inhibition of this RNA.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.