Discovery of new selective antagonists of G-protein coupled receptors of therapeutic interest
GPCR are integral membrane receptor proteins that are characterized by heptahelical transmembrane domains connected by intracellular and extracellular loops. GPCRs are an attractive class of proteins for drug discovery, with more than 50% of all drugs regulating GPCR function, and some 30% of these...
| Autor: | |
|---|---|
| Tipo de documento: | tese |
| Data de publicação: | 2016 |
| País: | España |
| Recursos: | Universitat Politècnica de Catalunya (UPC) |
| Repositório: | UPCommons. Portal del coneixement obert de la UPC |
| Idioma: | inglês |
| OAI Identifier: | oai:upcommons.upc.edu:2117/109356 |
| Acesso em linha: | https://hdl.handle.net/2117/109356 https://dx.doi.org/10.5821/dissertation-2117-109356 |
| Access Level: | Acceso aberto |
| Palavra-chave: | Àrees temàtiques de la UPC::Enginyeria agroalimentària |
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Discovery of new selective antagonists of G-protein coupled receptors of therapeutic interest |
| title |
Discovery of new selective antagonists of G-protein coupled receptors of therapeutic interest |
| spellingShingle |
Discovery of new selective antagonists of G-protein coupled receptors of therapeutic interest Lupala, Cecylia Severin Àrees temàtiques de la UPC::Enginyeria agroalimentària |
| title_short |
Discovery of new selective antagonists of G-protein coupled receptors of therapeutic interest |
| title_full |
Discovery of new selective antagonists of G-protein coupled receptors of therapeutic interest |
| title_fullStr |
Discovery of new selective antagonists of G-protein coupled receptors of therapeutic interest |
| title_full_unstemmed |
Discovery of new selective antagonists of G-protein coupled receptors of therapeutic interest |
| title_sort |
Discovery of new selective antagonists of G-protein coupled receptors of therapeutic interest |
| dc.creator.none.fl_str_mv |
Lupala, Cecylia Severin |
| author |
Lupala, Cecylia Severin |
| author_facet |
Lupala, Cecylia Severin |
| author_role |
author |
| dc.contributor.none.fl_str_mv |
Pérez González, Juan Jesús |
| dc.subject.none.fl_str_mv |
Àrees temàtiques de la UPC::Enginyeria agroalimentària |
| topic |
Àrees temàtiques de la UPC::Enginyeria agroalimentària |
| description |
GPCR are integral membrane receptor proteins that are characterized by heptahelical transmembrane domains connected by intracellular and extracellular loops. GPCRs are an attractive class of proteins for drug discovery, with more than 50% of all drugs regulating GPCR function, and some 30% of these drugs directly target GPCRs. Despite the number of GPCR crystal structures determined recently, they only represent a small fraction of total number of GPCRs known. Homology modelling has been the methodology used to fill the gap. However, the low sequence similarity between targets and templates hampers these studies. Aimed at overcoming these drawbacks template selection and the refinement process were studied in this work. Thus, several atomistic models of rat M3 muscarinic receptor were constructed from human M2 muscarinic receptor, human histamine 1 receptor and bovine rhodopsin receptor as templates. Moreover, in order to determine the effect of ligand in the simulation system, an extra model of M2 receptor was refined with NMS bound inside and an extra model refined without ligand. Results show the sampling time 500ns is adequate simulation time and molecular dynamics simulation of the protein embedded in a lipid bilayer as a refinement process improves on the homology models. Specifically, the refinement process can correct the length of the TM segment of the target receptor; the accuracy of the model greatly depends on the proximity of the template and the target in the phylogenetic tree and finally, the presence of a ligand produces a faster equilibration of the system. This methodology was used to study the pharmacological profile of bradykinin receptors B1 and B2. The B1 receptor was constructed using the chemokine CXC4 and bovine rhodopsin receptors as templates. Antagonists selected for the docking studies include Compound 11, Compound 12, Chroman28, SSR240612, NPV-SAA164 and PS020990. Analysis of the ligand-receptor complexes permitted the definition of a pharmacophore that describes the stereochemical requirements of antagonist binding. For the B2 receptor, a similar procedure was followed using the same template. In this case, the set of compounds used were Fasitibant, FR173657, Anatibant, WIN64338, Bradyzide, CHEMBL442294, and JSM10292. The outcome of this study is summarized in a 3D pharmacophore that explains the observed structure-activity results and provides insight into the design of novel molecules with antagonistic profile. To prove the validity of the pharmacophoric hypotheses, a virtual screening process was carried out. The results of the binding studies show about a 33% success rate with a correlation between the number of pharmacophore points fulfilled and their antagonistic potency. Some of these structures are disclosed in this thesis. Moreover, the B1R and B2R pharmacophores developed were compared and the observed differences permitted to explain the stereochemical requirements for receptor-selective ligands. The final study of this study was to establish a rational explanation for the role of zinc in preventing the dimerization of the serotonin 5-Hydroxytryptamine 1A receptor (5-HT1A) and Galanin receptor 1 (GALR1) involved in depression. Homology modeling was used to build atomistic models of these receptors using the crystallographic structures of 5-HT1B and κ– opioid receptor, respectively. First, prospective zinc binding sites were identified for the 5-HT1A using a molecular probe. Second, heterodimers of the two receptors were constructed with different interfaces: TM4 and TM5; TM6 and TM7; TM1 and TM2. Analysis of the 12 zinc-binding sites and the heterodimer interfaces suggests that there is a coincidence between zinc binding sites and heterodimerization interfaces providing a rational explanation for the role of zinc in the molecular processes associated with heterodimer prevention |
| publishDate |
2016 |
| dc.date.none.fl_str_mv |
2016 2016-01-28 2017 2017-10-30 |
| dc.type.none.fl_str_mv |
doctoral thesis http://purl.org/coar/resource_type/c_db06 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/doctoralThesis |
| format |
doctoralThesis |
| dc.identifier.none.fl_str_mv |
https://hdl.handle.net/2117/109356 https://dx.doi.org/10.5821/dissertation-2117-109356 |
| url |
https://hdl.handle.net/2117/109356 https://dx.doi.org/10.5821/dissertation-2117-109356 |
| dc.language.none.fl_str_mv |
Inglés eng |
| language_invalid_str_mv |
Inglés |
| language |
eng |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 |
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info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 |
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openAccess |
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application/pdf |
| dc.publisher.none.fl_str_mv |
Universitat Politècnica de Catalunya |
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Universitat Politècnica de Catalunya |
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reponame:UPCommons. Portal del coneixement obert de la UPC instname:Universitat Politècnica de Catalunya (UPC) |
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Universitat Politècnica de Catalunya (UPC) |
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UPCommons. Portal del coneixement obert de la UPC |
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UPCommons. Portal del coneixement obert de la UPC |
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1869415501008994304 |
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Discovery of new selective antagonists of G-protein coupled receptors of therapeutic interestLupala, Cecylia SeverinÀrees temàtiques de la UPC::Enginyeria agroalimentàriaGPCR are integral membrane receptor proteins that are characterized by heptahelical transmembrane domains connected by intracellular and extracellular loops. GPCRs are an attractive class of proteins for drug discovery, with more than 50% of all drugs regulating GPCR function, and some 30% of these drugs directly target GPCRs. Despite the number of GPCR crystal structures determined recently, they only represent a small fraction of total number of GPCRs known. Homology modelling has been the methodology used to fill the gap. However, the low sequence similarity between targets and templates hampers these studies. Aimed at overcoming these drawbacks template selection and the refinement process were studied in this work. Thus, several atomistic models of rat M3 muscarinic receptor were constructed from human M2 muscarinic receptor, human histamine 1 receptor and bovine rhodopsin receptor as templates. Moreover, in order to determine the effect of ligand in the simulation system, an extra model of M2 receptor was refined with NMS bound inside and an extra model refined without ligand. Results show the sampling time 500ns is adequate simulation time and molecular dynamics simulation of the protein embedded in a lipid bilayer as a refinement process improves on the homology models. Specifically, the refinement process can correct the length of the TM segment of the target receptor; the accuracy of the model greatly depends on the proximity of the template and the target in the phylogenetic tree and finally, the presence of a ligand produces a faster equilibration of the system. This methodology was used to study the pharmacological profile of bradykinin receptors B1 and B2. The B1 receptor was constructed using the chemokine CXC4 and bovine rhodopsin receptors as templates. Antagonists selected for the docking studies include Compound 11, Compound 12, Chroman28, SSR240612, NPV-SAA164 and PS020990. Analysis of the ligand-receptor complexes permitted the definition of a pharmacophore that describes the stereochemical requirements of antagonist binding. For the B2 receptor, a similar procedure was followed using the same template. In this case, the set of compounds used were Fasitibant, FR173657, Anatibant, WIN64338, Bradyzide, CHEMBL442294, and JSM10292. The outcome of this study is summarized in a 3D pharmacophore that explains the observed structure-activity results and provides insight into the design of novel molecules with antagonistic profile. To prove the validity of the pharmacophoric hypotheses, a virtual screening process was carried out. The results of the binding studies show about a 33% success rate with a correlation between the number of pharmacophore points fulfilled and their antagonistic potency. Some of these structures are disclosed in this thesis. Moreover, the B1R and B2R pharmacophores developed were compared and the observed differences permitted to explain the stereochemical requirements for receptor-selective ligands. The final study of this study was to establish a rational explanation for the role of zinc in preventing the dimerization of the serotonin 5-Hydroxytryptamine 1A receptor (5-HT1A) and Galanin receptor 1 (GALR1) involved in depression. Homology modeling was used to build atomistic models of these receptors using the crystallographic structures of 5-HT1B and κ– opioid receptor, respectively. First, prospective zinc binding sites were identified for the 5-HT1A using a molecular probe. Second, heterodimers of the two receptors were constructed with different interfaces: TM4 and TM5; TM6 and TM7; TM1 and TM2. Analysis of the 12 zinc-binding sites and the heterodimer interfaces suggests that there is a coincidence between zinc binding sites and heterodimerization interfaces providing a rational explanation for the role of zinc in the molecular processes associated with heterodimer preventionLos receptores acoplados a proteínas G (GPCRs) son proteínas de membrana que se caracterizan por dominios transmembrana heptahelicoidales conectados por lazos intracelulares y extracelulares. GPCRs son un atractivo grupo de proteínas para el descubrimiento de nuevos fármacos puesto que más del 50% de los medicamentos en el mercado que regulan su función y alrededor del 30% que tienen un GPCR como diana. A pesar del gran número de estructuras cristalográficas de GPCRs que se han determinado recientemente, estas solamente representan una pequeña fracción del número total de GPCRs. La homología de secuencia se utiliza de forma rutinaria para llenar el vacío, sin embargo, la baja identidad de secuencia entre miembros de esta familia obstaculiza estos estudios. Con el objetivo de superar estos inconvenientes, tanto el proceso de selección de la plantilla, como el proceso de refinamiento del modelo han sido estudiados en este trabajo. Se construyeron modelos atómicos del receptor muscarínico M3 de rata a partir del receptor humano M2 muscarínico, del de histamina humano 1 y de la rodopsina bovina como plantilla. Por otra parte, con el fin de determinar el efecto del ligando en el proceso de refinamiento, el receptor M2 fue refinado con el ligando NMS y además se construyó un modelo sin ligando. Los resultados muestran que un tiempo de muestreo 500ns es adecuado y que la dinámica molecular representa un proceso de refinamiento adecuado. Esta metodología se utilizó para estudiar el perfil farmacológico de los receptores de bradiquinina B1 y B2. El receptor B1 se construyó usando los receptores CXC4 de quimoquina y rodopsina bovina como plantillas. Los antagonistas seleccionados para los estudios de anclaje incluyen el Compuesto 11, el Compuesto 12, Chroman28, SSR240612, NVP-SAA164 y PS020990. El análisis de los complejos ligando-receptor permite la definición de un farmacóforo que describe los requisitos estereoquímicos de unión de antagonistas. Para el receptor B2, se siguió un procedimiento similar utilizando las mismas plantillas. En este caso, el conjunto de los compuestos utilizados fueron Fasitibant, FR173657, Anatibant, WIN64338, Bradyzide, CHEMBL442294 y JSM10292. El resultado de este estudio se resume en un farmacóforo 3D que explica los resultados estructura-actividad observados y ofrece información sobre el diseño de nuevas moléculas con el perfil antagonista. Para probar la validez de las hipótesis farmacofóricas, se llevó a cabo un proceso de cribado virtual. Los resultados de los estudios de unión muestran sobre una tasa de éxito del 33% con una correlación entre el número de puntos farmacóforicos cumplido y su potencia antagonista. Algunas de estas estructuras se describen en esta tesis. Por otra parte, los farmacóforos de B1R y B2R desarrollados se compararon y a través de las diferencias observadas explicar los requisitos estereoquımicos para que los ligandos sean selectivos. El estudio final de este trabajo fue el establecer una explicación racional para el papel del zinc en la prevención de la dimerización del receptor de serotonina 5-hidroxitriptamina 1A (5-HT1A) y el receptor galanina 1 (GALR1) que participan en la depresión. Homología de secuencia se utilizó para construir modelos atómicos de estos receptores utilizando las estructuras cristalográficas de los receptores 5-HT 1B y κ de opiáceos, respectivamente. En primer lugar, se identificaron los posibles sitios de unión de zinc para el 5-HT1A usando una sonda molecular. En segundo lugar, los heterodímeros de los dos receptores fueron construidos con diferentes interfaces: TM4 y TM5; TM6 y TM7; TM1 y TM2. El análisis de los 12 sitios de unión de zinc y las interfaces heterodímero sugiere que existe una coincidencia entre los sitios de unión de zinc y las interfaces de heterodimerización que proporcionan una explicación racional para el papel del zinc en los procesos moleculares asociados con la prevención heterodímero.Universitat Politècnica de CatalunyaPérez González, Juan Jesús20162016-01-2820172017-10-30doctoral thesishttp://purl.org/coar/resource_type/c_db06VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/doctoralThesisapplication/pdfhttps://hdl.handle.net/2117/109356https://dx.doi.org/10.5821/dissertation-2117-109356reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/1093562026-05-27T15:37:01Z |
| score |
15,301603 |