Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets

Detalhes bibliográficos
Autor(a) principal: Dias, Tiago Gonçalves
Data de Publicação: 2023
Tipo de documento: Dissertação
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10451/63291
Resumo: Tese de mestrado, Bioquímica e Biomedicina, 2023, Universidade de Lisboa, Faculdade de Ciências
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spelling Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targetsligação de hidrogénioligação de halogéneoσ-holeTeses de mestrado - 2023Departamento de Química e BioquímicaTese de mestrado, Bioquímica e Biomedicina, 2023, Universidade de Lisboa, Faculdade de CiênciasThe characterization of protein-ligand complexes is essential for research in structural biochemistry, drug discovery, and biology. These protein–ligand interactions comprise hydrophobic interactions, hydrogen bonds, aromatic stacking, salt bridges, and even halogen bonds. There are several tools that automatically assign the presence of noncovalent protein–ligand interactions in PDB structures. This is extremely useful in drug design since in the initial stages, prior to library screening or molecule design, a comparative analysis of binding patterns in a target is often performed, thus helping to identify key residues. To assign the existence of a bond (such as hydrogen or a halogen bonds), these tools verify if certain geometric requirements are fulfilled, i.e., they use angle and distance thresholds. This might be problematic since the thresholds are empiric and might be excluding (or erroneously including) interactions. Therefore, the use of an energy-based criterion is a great advantage, as previously shown with the Define Secondary Structure of Proteins (DSSP) algorithm, which is a popular standard method for assigning the secondary structure to the amino acids of a protein. Based on previous work by our group which showed the existence of energy thresholds for the identification of these interactions, in this project, by using computational and modeling tools such as force field methods, a robust energy-based criterion to assign noncovalent interactions involving protein-ligand complexes was tested. The method was also tested in membrane-ligand systems thus hopefully contributing to the improvement of computational drug discovery tools.Costa, Paulo Jorge Ferreira de Matos, 1980-Victor, Bruno Lourenço da SilvaRepositório da Universidade de LisboaDias, Tiago Gonçalves2024-03-08T09:44:48Z202320232023-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttp://hdl.handle.net/10451/63291engmetadata only accessinfo: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:RCAAP2024-03-11T01:20:23Zoai:repositorio.ul.pt:10451/63291Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:14:32.183457Repositório 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 Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets
title Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets
spellingShingle Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets
Dias, Tiago Gonçalves
ligação de hidrogénio
ligação de halogéneo
σ-hole
Teses de mestrado - 2023
Departamento de Química e Bioquímica
title_short Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets
title_full Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets
title_fullStr Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets
title_full_unstemmed Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets
title_sort Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets
author Dias, Tiago Gonçalves
author_facet Dias, Tiago Gonçalves
author_role author
dc.contributor.none.fl_str_mv Costa, Paulo Jorge Ferreira de Matos, 1980-
Victor, Bruno Lourenço da Silva
Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Dias, Tiago Gonçalves
dc.subject.por.fl_str_mv ligação de hidrogénio
ligação de halogéneo
σ-hole
Teses de mestrado - 2023
Departamento de Química e Bioquímica
topic ligação de hidrogénio
ligação de halogéneo
σ-hole
Teses de mestrado - 2023
Departamento de Química e Bioquímica
description Tese de mestrado, Bioquímica e Biomedicina, 2023, Universidade de Lisboa, Faculdade de Ciências
publishDate 2023
dc.date.none.fl_str_mv 2023
2023
2023-01-01T00:00:00Z
2024-03-08T09:44:48Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10451/63291
url http://hdl.handle.net/10451/63291
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv metadata only access
info:eu-repo/semantics/openAccess
rights_invalid_str_mv metadata only access
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
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
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
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reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection 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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