ArticleScientific reports2015
HIV-1 Protease Dimerization Dynamics Reveals a Transient Druggable Binding Pocket at the Interface.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
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Who cites it
11 citing papers in PubMed.
- Identification of Protein Cryptic Sites via Conformational Dynamics Capturing and Water-Based Pocket Characterization in Molecular Dynamics Simulations.Journal of chemical theory and computation · 2025Article
- Selection of Nucleotide-Encoded Mass Libraries of Macrocyclic Peptides for Inaccessible Drug Targets.Chemical reviews · 2024Review
- Evolution of drug resistance drives destabilization of flap region dynamics in HIV-1 protease.Biophysical reports · 2023Article
- Pharmacological Chaperones and Protein Conformational Diseases: Approaches of Computational Structural Biology.International journal of molecular sciences · 2023Review
- Precursors of Viral Proteases as Distinct Drug Targets.Viruses · 2021Review
- Predicted antiviral drugs Darunavir, Amprenavir, Rimantadine and Saquinavir can potentially bind to neutralize SARS-CoV-2 conserved proteins.Journal of biological research (Thessalonike, Greece) · 2021Article
- Inhibition of HIV-1 Protease byEvidence-based complementary and alternative medicine : eCAM · 2020Article
- Inhibition of the precursor and mature forms of HIV-1 protease as a tool for drug evaluation.Scientific reports · 2018Article
- TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets.Nucleic acids research · 2017Article
- Investigational protease inhibitors as antiretroviral therapies.Expert opinion on investigational drugs · 2016Review
- Glutamine Synthetase Drugability beyond Its Active Site: Exploring Oligomerization Interfaces and Pockets.Molecules (Basel, Switzerland) · 2016Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The binding mechanism of HIV-1 protease monomers leading to the catalytically competent dimeric enzyme has been investigated by means of state-of-the-art atomistic simulations. The emerging picture allows a deeper understanding of experimental observations and reveals that water molecules trapped at the interface have an important role in slowing down the kinetics of the association process. Unexpectedly, a cryptic binding pocket is identified at the interface of the complex, corresponding to a partially bound dimer that lacks enzymatic function. The pocket has a transient nature with a lifetime longer than 1 μs, and it displays very favorable druggability features. Docking as well as MM-GBSA free-energy calculations further support the possibility to target the new binding site by means of inhibitors able to prevent the complete dimerization by capturing the inactive conformation. This discovery could open the way to the rational design of a new class of anti-HIV drugs.
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Registered trials
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