ArticleBiophysical journal2010
Discovery of entry inhibitors for HIV-1 via a new de novo protein design framework.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed.
- Tailored structured peptide design with a key-cutting machine approach.Nature machine intelligence · 2025Article
- Intelligent Protein Design and Molecular Characterization Techniques: A Comprehensive Review.Molecules (Basel, Switzerland) · 2023Review
- Review
- Rigorous Computational and Experimental Investigations on MDM2/MDMX-Targeted Linear and Macrocyclic Peptides.Molecules (Basel, Switzerland) · 2019Article
- Development of peptide inhibitors of HIV transmission.Bioactive materials · 2016Review
- Drug delivery strategies and systems for HIV/AIDS pre-exposure prophylaxis and treatment.Journal of controlled release : official journal of the Controlled Release Society · 2015Review
- New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics.Journal of medicinal chemistry · 2015Article
- Computational Design of Hypothetical New Peptides Based on a Cyclotide Scaffold as HIV gp120 Inhibitor.PloS one · 2015Article
- Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family.ACS synthetic biology · 2014Article
- Derivation of ligands for the complement C3a receptor from the C-terminus of C5a.European journal of pharmacology · 2014Article
- De novo design and experimental characterization of ultrashort self-associating peptides.PLoS computational biology · 2014Article
- Elucidating a key anti-HIV-1 and cancer-associated axis: the structure of CCL5 (Rantes) in complex with CCR5.Scientific reports · 2014Article
- Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4.Journal of chemical information and modeling · 2014Article
- Protein folding and de novo protein design for biotechnological applications.Trends in biotechnology · 2014Review
- Molecular recognition of CCR5 by an HIV-1 gp120 V3 loop.PloS one · 2014Article
- De novo peptide design and experimental validation of histone methyltransferase inhibitors.PloS one · 2014Article
- Forcefield_PTM:Journal of chemical theory and computation · 2013Article
- Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures.Experimental eye research · 2013Article
- An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis.PLoS computational biology · 2013Article
- Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop.Biophysical journal · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
A new (to our knowledge) de novo design framework with a ranking metric based on approximate binding affinity calculations is introduced and applied to the discovery of what we believe are novel HIV-1 entry inhibitors. The framework consists of two stages: a sequence selection stage and a validation stage. The sequence selection stage produces a rank-ordered list of amino-acid sequences by solving an integer programming sequence selection model. The validation stage consists of fold specificity and approximate binding affinity calculations. The designed peptidic inhibitors are 12-amino-acids-long and target the hydrophobic core of gp41. A number of the best-predicted sequences were synthesized and their inhibition of HIV-1 was tested in cell culture. All peptides examined showed inhibitory activity when compared with no drug present, and the novel peptide sequences outperformed the native template sequence used for the design. The best sequence showed micromolar inhibition, which is a 3-15-fold improvement over the native sequence, depending on the donor. In addition, the best sequence equally inhibited wild-type and Enfuvirtide-resistant virus strains.
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.