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Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein–Protein Interactions?
[Image: see text] Modulation of protein–protein interactions (PPIs) with small molecules has been hampered by a lack of lucid methods capable of reliably identifying high-quality hits. In fragment screening, the low ligand efficiencies associated with PPI target sites pose significant challenges to...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical
Society
2013
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891296/ https://www.ncbi.nlm.nih.gov/pubmed/24436777 http://dx.doi.org/10.1021/ml400296c |
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author | Dias, David M. Van Molle, Inge Baud, Matthias G. J. Galdeano, Carles Geraldes, Carlos F. G. C. Ciulli, Alessio |
author_facet | Dias, David M. Van Molle, Inge Baud, Matthias G. J. Galdeano, Carles Geraldes, Carlos F. G. C. Ciulli, Alessio |
author_sort | Dias, David M. |
collection | PubMed |
description | [Image: see text] Modulation of protein–protein interactions (PPIs) with small molecules has been hampered by a lack of lucid methods capable of reliably identifying high-quality hits. In fragment screening, the low ligand efficiencies associated with PPI target sites pose significant challenges to fragment binding detection. Here, we investigate the requirements for ligand-based NMR techniques to detect rule-of-three compliant fragments that form part of known high-affinity inhibitors of the PPI between the von Hippel–Lindau protein and the alpha subunit of hypoxia-inducible factor 1 (pVHL:HIF-1α). Careful triaging allowed rescuing weak but specific binding of fragments that would otherwise escape detection at this PPI. Further structural information provided by saturation transfer difference (STD) group epitope mapping, protein-based NMR, competitive isothermal titration calorimetry (ITC), and X-ray crystallography confirmed the binding mode of the rescued fragments. Our findings have important implications for PPI druggability assessment by fragment screening as they reveal an accessible threshold for fragment detection and validation. |
format | Online Article Text |
id | pubmed-3891296 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | American Chemical
Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-38912962014-01-14 Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein–Protein Interactions? Dias, David M. Van Molle, Inge Baud, Matthias G. J. Galdeano, Carles Geraldes, Carlos F. G. C. Ciulli, Alessio ACS Med Chem Lett [Image: see text] Modulation of protein–protein interactions (PPIs) with small molecules has been hampered by a lack of lucid methods capable of reliably identifying high-quality hits. In fragment screening, the low ligand efficiencies associated with PPI target sites pose significant challenges to fragment binding detection. Here, we investigate the requirements for ligand-based NMR techniques to detect rule-of-three compliant fragments that form part of known high-affinity inhibitors of the PPI between the von Hippel–Lindau protein and the alpha subunit of hypoxia-inducible factor 1 (pVHL:HIF-1α). Careful triaging allowed rescuing weak but specific binding of fragments that would otherwise escape detection at this PPI. Further structural information provided by saturation transfer difference (STD) group epitope mapping, protein-based NMR, competitive isothermal titration calorimetry (ITC), and X-ray crystallography confirmed the binding mode of the rescued fragments. Our findings have important implications for PPI druggability assessment by fragment screening as they reveal an accessible threshold for fragment detection and validation. American Chemical Society 2013-11-03 /pmc/articles/PMC3891296/ /pubmed/24436777 http://dx.doi.org/10.1021/ml400296c Text en Copyright © 2013 American Chemical Society Terms of Use CC-BY (http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html) |
spellingShingle | Dias, David M. Van Molle, Inge Baud, Matthias G. J. Galdeano, Carles Geraldes, Carlos F. G. C. Ciulli, Alessio Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein–Protein Interactions? |
title | Is NMR Fragment Screening Fine-Tuned to Assess Druggability
of Protein–Protein Interactions? |
title_full | Is NMR Fragment Screening Fine-Tuned to Assess Druggability
of Protein–Protein Interactions? |
title_fullStr | Is NMR Fragment Screening Fine-Tuned to Assess Druggability
of Protein–Protein Interactions? |
title_full_unstemmed | Is NMR Fragment Screening Fine-Tuned to Assess Druggability
of Protein–Protein Interactions? |
title_short | Is NMR Fragment Screening Fine-Tuned to Assess Druggability
of Protein–Protein Interactions? |
title_sort | is nmr fragment screening fine-tuned to assess druggability
of protein–protein interactions? |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891296/ https://www.ncbi.nlm.nih.gov/pubmed/24436777 http://dx.doi.org/10.1021/ml400296c |
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