Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein−Protein Interactions?
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10316/25236 https://doi.org/10.1021/ml400296c |
Resumo: | 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. |
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Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein−Protein Interactions?NMR fragment screeningprotein−protein interactionsbinding affinitydruggabilityModulation 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.This work was supported by the Fundação para a Ciência e a Tecnologia (FCT, SFRH/BD/81735/2011 Studentship to D.M.D.), the U.K. BBSRC (BB/G023123/1, David Phillips Fellowship to A.C.), the European Research Council ERC-2012- StG-311460 DrugE3CRLs (Starting Grant to A.C.), the EC PIEF-GA-2010-275683 (Marie-Curie Intra European Fellowship to I.V.M.), and the EMBO ASTF 165-2012 (Short-Term Fellowship to C.G.).American Chemical Society2014info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://hdl.handle.net/10316/25236http://hdl.handle.net/10316/25236https://doi.org/10.1021/ml400296ceng1948-5875http://pubs.acs.org/doi/abs/10.1021/ml400296cDias, David M.Van Molle, IngeBaud, Matthias G. J.Galdeano, CarlesGeraldes, Carlos F. G. C.Ciulli, Alessioinfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2020-11-06T17:00:00Zoai:estudogeral.uc.pt:10316/25236Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T20:56:00.223769Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
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? |
spellingShingle |
Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein−Protein Interactions? Dias, David M. NMR fragment screening protein−protein interactions binding affinity druggability |
title_short |
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_sort |
Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein−Protein Interactions? |
author |
Dias, David M. |
author_facet |
Dias, David M. Van Molle, Inge Baud, Matthias G. J. Galdeano, Carles Geraldes, Carlos F. G. C. Ciulli, Alessio |
author_role |
author |
author2 |
Van Molle, Inge Baud, Matthias G. J. Galdeano, Carles Geraldes, Carlos F. G. C. Ciulli, Alessio |
author2_role |
author author author author author |
dc.contributor.author.fl_str_mv |
Dias, David M. Van Molle, Inge Baud, Matthias G. J. Galdeano, Carles Geraldes, Carlos F. G. C. Ciulli, Alessio |
dc.subject.por.fl_str_mv |
NMR fragment screening protein−protein interactions binding affinity druggability |
topic |
NMR fragment screening protein−protein interactions binding affinity druggability |
description |
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. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10316/25236 http://hdl.handle.net/10316/25236 https://doi.org/10.1021/ml400296c |
url |
http://hdl.handle.net/10316/25236 https://doi.org/10.1021/ml400296c |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
1948-5875 http://pubs.acs.org/doi/abs/10.1021/ml400296c |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
American Chemical Society |
publisher.none.fl_str_mv |
American Chemical Society |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799133845497315328 |