ArticleACS chemical biology2011
Paramagnetic relaxation assisted docking of a small indole compound in the HIV-1 gp41 hydrophobic pocket.
Article in ACS chemical biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Investigating the role of a conserved hydrophobic pocket of gp41 in the anti-HIV activity of fusion inhibitors.Protein science : a publication of the Protein Society · 2026Article
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling.Frontiers in molecular biosciences · 2021Article
- Paramagnetic NMR in drug discovery.Journal of biomolecular NMR · 2020Review
- Allosteres to regulate neurotransmitter sulfonation.The Journal of biological chemistry · 2019Article
- Tetrahydrobiopterin regulates monoamine neurotransmitter sulfonation.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Evaluation of ligand-based NMR screening methods to characterize small molecule binding to HIV-1 glycoprotein-41.Organic & biomolecular chemistry · 2017Article
- The structure of the catechin-binding site of human sulfotransferase 1A1.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Process of Fragment-Based Lead Discovery-A Perspective from NMR.Molecules (Basel, Switzerland) · 2016Review
- Anti-HIV drug development through computational methods.The AAPS journal · 2014Review
- Identification of fragments targeting an alternative pocket on HIV-1 gp41 by NMR screening and similarity searching.Bioorganic & medicinal chemistry letters · 2013Article
- NMR-assisted computational studies of peptidomimetic inhibitors bound in the hydrophobic pocket of HIV-1 glycoprotein 41.Journal of computer-aided molecular design · 2013Article
- Computer-Aided Approaches for Targeting HIVgp41.Biology · 2012Article
- Virtual interactomics of proteins from biochemical standpoint.Molecular biology international · 2012Article
- Amphipathic properties of HIV-1 gp41 fusion inhibitors.Current topics in medicinal chemistry · 2011Review
- Development of indole compounds as small molecule fusion inhibitors targeting HIV-1 glycoprotein-41.Journal of medicinal chemistry · 2011Article
- The molecular basis of OH-PCB estrogen receptor activation.The Journal of biological chemistryArticle
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Authors and funding
3 authors.
Funding
Abstract
The hydrophobic pocket contained within the gp41 coiled coil is an important target for small molecules designed to inhibit HIV-1 fusion. While various screening experiments have identified molecules purported to bind in this pocket, few have confirmed details of the interaction, instead relying on computational docking to predict the binding mode. This is made more challenging by the fact that residues lining the hydrophobic pocket are highly flexible, as is typical for a protein-protein interaction site, limiting the predictive power of computational tools. In this study, we report on an NMR method to define the binding mode of 1-5i, a compound in a series of newly developed indole inhibitors. We show that paramagnetic relaxation enhancement of ligand protons due to an MTSL group positioned close to the binding pocket could be applied quantitatively to distinguish between more than 30 different computational poses, selecting a single pose that agreed with the NMR data. In this pose, important hydrophobic and polar contacts occur with pocket lysine, tryptophan, and glutamine residues, including putative hydrogen bonds between the ligand carboxylate and the lysine ε-amino group. A study of the ligand orientation suggests directions for optimization.
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