ArticleACS chemical biology2013
Small molecule regulation of protein conformation by binding in the Flap of HIV protease.
Article in ACS chemical biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 35 citations in OpenAlex.
- Conformational asymmetry of human immunodeficiency virus-1 protease flaps increases along the darunavir drug resistance pathway.Protein science : a publication of the Protein Society · 2026Article
- Subtype-Specific HIV-1 Protease and the Role of Hinge and Flap Dynamics in Drug Resistance: A Subtype C Narrative.Viruses · 2025Review
- Theoretical Basis for Refractive Index Changes Resulting from Solution Phase Molecular Interaction.The journal of physical chemistry. B · 2025Article
- Elasticity-Associated Functionality and Inhibition of the HIV Protease.Advances in experimental medicine and biology · 2022Article
- Molecular Docking-Based Screening for Novel Inhibitors of the Human Immunodeficiency Virus Type 1 Protease that Effectively Reduce the Viral Replication in Human Cells.Journal of AIDS & clinical research · 2021Article
- The AutoDock suite at 30.Protein science : a publication of the Protein Society · 2021Article
- Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling.International journal of molecular sciences · 2020Article
- Rapid quantification of two chemical nerve agent metabolites in serum.Biosensors & bioelectronics · 2019Article
- Flap-site Fragment Restores Back Wild-type Behaviour in Resistant Form of HIV Protease.Molecular informatics · 2018Article
- An experimental check of backscattering interferometry.Sensors and actuators. B, Chemical · 2017Article
- Reply to Varma: Elucidation of the signal origin for label-free, free-solution interactions.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors.Journal of medicinal chemistry · 2016Article
- Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case.Biopolymers · 2016Article
- Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.Journal of molecular recognition : JMR · 2016Article
- Charting a Path to Success in Virtual Screening.Molecules (Basel, Switzerland) · 2015Review
- Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease.The journal of physical chemistry. B · 2015Article
- Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge.Journal of computer-aided molecular design · 2014Article
- Crystallographic fragment-based drug discovery: use of a brominated fragment library targeting HIV protease.Chemical biology & drug design · 2014Article
Corrections and comments
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Authors and funding
13 authors at 1 institution in 1 country.
Funding
Abstract
The fragment indole-6-carboxylic acid (1F1), previously identified as a flap site binder in a fragment-based screen against HIV protease (PR), has been cocrystallized with pepstatin-inhibited PR and with apo-PR. Another fragment, 3-indolepropionic acid (1F1-N), predicted by AutoDock calculations and confirmed in a novel inhibition of nucleation crystallization assay, exploits the same interactions in the flap site in two crystal structures. Both 1F1 and 1F1-N bind to the closed form of apo-PR and to pepstatin:PR. In solution, 1F1 and 1F1-N raise the Tm of apo-PR by 3.5-5 °C as assayed by differential scanning fluorimetry (DSF) and show equivalent low-micromolar binding constants to both apo-PR and pepstatin:PR, assayed by backscattering interferometry (BSI). The observed signal intensities in BSI are greater for each fragment upon binding to apo-PR than to pepstatin-bound PR, consistent with greater conformational change in the former binding event. Together, these data indicate that fragment binding in the flap site favors a closed conformation of HIV PR.
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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.