Protein conformational flexibility modulates kinetics and thermodynamics of drug binding
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | https://doi.org/10.1038/s41467-017-02258-w |
Resumo: | Structure-based drug design has often been restricted by the rather static picture of protein-ligand complexes presented by crystal structures, despite the widely accepted importance of protein flexibility in biomolecular recognition. Here we report a detailed experimental and computational study of the drug target, human heat shock protein 90, to explore the contribution of protein dynamics to the binding thermodynamics and kinetics of drug-like compounds. We observe that their binding properties depend on whether the protein has a loop or a helical conformation in the binding site of the ligand-bound state. Compounds bound to the helical conformation display slow association and dissociation rates, high-affinity and high cellular efficacy, and predominantly entropically driven binding. An important entropic contribution comes from the greater flexibility of the helical relative to the loop conformation in the ligand-bound state. This unusual mechanism suggests increasing target flexibility in the bound state by ligand design as a new strategy for drug discovery. |
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Protein conformational flexibility modulates kinetics and thermodynamics of drug bindingChemistry(all)Biochemistry, Genetics and Molecular Biology(all)Physics and Astronomy(all)Structure-based drug design has often been restricted by the rather static picture of protein-ligand complexes presented by crystal structures, despite the widely accepted importance of protein flexibility in biomolecular recognition. Here we report a detailed experimental and computational study of the drug target, human heat shock protein 90, to explore the contribution of protein dynamics to the binding thermodynamics and kinetics of drug-like compounds. We observe that their binding properties depend on whether the protein has a loop or a helical conformation in the binding site of the ligand-bound state. Compounds bound to the helical conformation display slow association and dissociation rates, high-affinity and high cellular efficacy, and predominantly entropically driven binding. An important entropic contribution comes from the greater flexibility of the helical relative to the loop conformation in the ligand-bound state. This unusual mechanism suggests increasing target flexibility in the bound state by ligand design as a new strategy for drug discovery.Molecular, Structural and Cellular Microbiology (MOSTMICRO)Instituto de Tecnologia Química e Biológica António Xavier (ITQB)RUNAmaral, MartaKokh, D. B.Bomke, J.Wegener, A.Buchstaller, H. P.Eggenweiler, H. M.Matias, P.Sirrenberg, C.Wade, R. C.Frech, M.2019-10-24T22:35:34Z2017-12-012017-12-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://doi.org/10.1038/s41467-017-02258-weng2041-1723PURE: 4080850http://www.scopus.com/inward/record.url?scp=85039455347&partnerID=8YFLogxKhttps://doi.org/10.1038/s41467-017-02258-winfo: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:RCAAP2024-03-11T04:38:21Zoai:run.unl.pt:10362/85347Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:36:36.256756Repositório 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 |
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding |
title |
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding |
spellingShingle |
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding Amaral, Marta Chemistry(all) Biochemistry, Genetics and Molecular Biology(all) Physics and Astronomy(all) |
title_short |
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding |
title_full |
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding |
title_fullStr |
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding |
title_full_unstemmed |
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding |
title_sort |
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding |
author |
Amaral, Marta |
author_facet |
Amaral, Marta Kokh, D. B. Bomke, J. Wegener, A. Buchstaller, H. P. Eggenweiler, H. M. Matias, P. Sirrenberg, C. Wade, R. C. Frech, M. |
author_role |
author |
author2 |
Kokh, D. B. Bomke, J. Wegener, A. Buchstaller, H. P. Eggenweiler, H. M. Matias, P. Sirrenberg, C. Wade, R. C. Frech, M. |
author2_role |
author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Molecular, Structural and Cellular Microbiology (MOSTMICRO) Instituto de Tecnologia Química e Biológica António Xavier (ITQB) RUN |
dc.contributor.author.fl_str_mv |
Amaral, Marta Kokh, D. B. Bomke, J. Wegener, A. Buchstaller, H. P. Eggenweiler, H. M. Matias, P. Sirrenberg, C. Wade, R. C. Frech, M. |
dc.subject.por.fl_str_mv |
Chemistry(all) Biochemistry, Genetics and Molecular Biology(all) Physics and Astronomy(all) |
topic |
Chemistry(all) Biochemistry, Genetics and Molecular Biology(all) Physics and Astronomy(all) |
description |
Structure-based drug design has often been restricted by the rather static picture of protein-ligand complexes presented by crystal structures, despite the widely accepted importance of protein flexibility in biomolecular recognition. Here we report a detailed experimental and computational study of the drug target, human heat shock protein 90, to explore the contribution of protein dynamics to the binding thermodynamics and kinetics of drug-like compounds. We observe that their binding properties depend on whether the protein has a loop or a helical conformation in the binding site of the ligand-bound state. Compounds bound to the helical conformation display slow association and dissociation rates, high-affinity and high cellular efficacy, and predominantly entropically driven binding. An important entropic contribution comes from the greater flexibility of the helical relative to the loop conformation in the ligand-bound state. This unusual mechanism suggests increasing target flexibility in the bound state by ligand design as a new strategy for drug discovery. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017-12-01 2017-12-01T00:00:00Z 2019-10-24T22:35:34Z |
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 |
https://doi.org/10.1038/s41467-017-02258-w |
url |
https://doi.org/10.1038/s41467-017-02258-w |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
2041-1723 PURE: 4080850 http://www.scopus.com/inward/record.url?scp=85039455347&partnerID=8YFLogxK https://doi.org/10.1038/s41467-017-02258-w |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
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application/pdf |
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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 |
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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) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799137983957303296 |