A a new docking approach to find peptides renin inhibitors derived from food proteins

Autores
Nardo, Agustina Estefania; Añon, Maria Cristina; Quiroga, Alejandra Viviana
Año de publicación
2019
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
Structure-based computer modeling of peptide-protein interactions is a core component of modern bioinformatics approach to study bioactive peptide. Molecular docking is the most common technique used to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Most of docking programs, like AutoDock, are successful to work with small peptides but not with larger ones due to its high flexibility and freedom of movement. The objective of this work was to try out new free, friendly and rigorous servers developed specifically for peptides that act as ligands to predict with greater confidence the best peptides that could potentially act as inhibitors of an enzyme. For this purpose we use six peptides (SFNLPILR; FNLPILR; SFNLPIL; QAFEDGFEWVSFK; AFEDGFEWVSFK; VNVDDPSKA) identified in an amaranth alcalase hydrolyzate (HD 21±4 %) as renin (EC 3.4.23.15) inhibitors. As controls the renin substrate (angiotensinogen), a competitive inhibitor (IRLIIVLMPILMA, IC50=6.5 mM) and a tridecapeptide of alanines were used. In a first stage, CABS dock server (http://biocomp.chem.uw.edu.pl/CABSdock) was use to generate the peptide-renin (PDB 2V0Z chain C) complex and identify the most likely interaction sites. In the second stage, FlexPepDock server (http://flexpepdock.furmanlab.cs.huji.ac.il/) was used to refine the interaction energy of the complex and calculate a score that serves to select the best inhibitors from the set of peptides used. Comparing the obtained means of three independent replicates of the FlexPepDock score the peptides AFEDGFEWVSFK and SFNLPILR had a similar interaction energy to as control IRLIIVLMPILMA (Tukey test, p=0.05). Both peptides were synthesized to evaluate its inhibitory activity in vitro. The docking using peptide remains to be a challenge for the scientific community, the protocol used in this work use new servers specifically developed for this purpose with the additional advantage of being fast implementation and friendly with experimental scientists.
Fil: Nardo, Agustina Estefania. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; Argentina
Fil: Añon, Maria Cristina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; Argentina
Fil: Quiroga, Alejandra Viviana. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; Argentina
2nd International Symposium on Bioactive Peptides
Valencia
España
Consejo Superior de Investigaciones Científicas. Instituto de Agroquímica y Tecnología de Alimentos
University of Alberta.Department of Agricultural, Food and Nutritional Science
Materia
DOCKING APPROACH
RENIN INHIBITORS
PEPTIDES
AMARANTH
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/178799
Acceder
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network_name_str CONICET Digital (CONICET)
spelling A a new docking approach to find peptides renin inhibitors derived from food proteinsNardo, Agustina EstefaniaAñon, Maria CristinaQuiroga, Alejandra VivianaDOCKING APPROACHRENIN INHIBITORSPEPTIDESAMARANTHhttps://purl.org/becyt/ford/2.11https://purl.org/becyt/ford/2Structure-based computer modeling of peptide-protein interactions is a core component of modern bioinformatics approach to study bioactive peptide. Molecular docking is the most common technique used to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Most of docking programs, like AutoDock, are successful to work with small peptides but not with larger ones due to its high flexibility and freedom of movement. The objective of this work was to try out new free, friendly and rigorous servers developed specifically for peptides that act as ligands to predict with greater confidence the best peptides that could potentially act as inhibitors of an enzyme. For this purpose we use six peptides (SFNLPILR; FNLPILR; SFNLPIL; QAFEDGFEWVSFK; AFEDGFEWVSFK; VNVDDPSKA) identified in an amaranth alcalase hydrolyzate (HD 21±4 %) as renin (EC 3.4.23.15) inhibitors. As controls the renin substrate (angiotensinogen), a competitive inhibitor (IRLIIVLMPILMA, IC50=6.5 mM) and a tridecapeptide of alanines were used. In a first stage, CABS dock server (http://biocomp.chem.uw.edu.pl/CABSdock) was use to generate the peptide-renin (PDB 2V0Z chain C) complex and identify the most likely interaction sites. In the second stage, FlexPepDock server (http://flexpepdock.furmanlab.cs.huji.ac.il/) was used to refine the interaction energy of the complex and calculate a score that serves to select the best inhibitors from the set of peptides used. Comparing the obtained means of three independent replicates of the FlexPepDock score the peptides AFEDGFEWVSFK and SFNLPILR had a similar interaction energy to as control IRLIIVLMPILMA (Tukey test, p=0.05). Both peptides were synthesized to evaluate its inhibitory activity in vitro. The docking using peptide remains to be a challenge for the scientific community, the protocol used in this work use new servers specifically developed for this purpose with the additional advantage of being fast implementation and friendly with experimental scientists.Fil: Nardo, Agustina Estefania. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; ArgentinaFil: Añon, Maria Cristina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; ArgentinaFil: Quiroga, Alejandra Viviana. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; Argentina2nd International Symposium on Bioactive PeptidesValenciaEspañaConsejo Superior de Investigaciones Científicas. Instituto de Agroquímica y Tecnología de AlimentosUniversity of Alberta.Department of Agricultural, Food and Nutritional ScienceUniversitat de ValènciaToldrá, Fidel2019info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectSimposioBookhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/178799A a new docking approach to find peptides renin inhibitors derived from food proteins; 2nd International Symposium on Bioactive Peptides; Valencia; España; 2019; 70-70CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://congresos.adeituv.es/bioactivepeptides/ficha.en.htmlInternacionalinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:10:55Zoai:ri.conicet.gov.ar:11336/178799instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:10:55.558CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv A a new docking approach to find peptides renin inhibitors derived from food proteins
title A a new docking approach to find peptides renin inhibitors derived from food proteins
spellingShingle A a new docking approach to find peptides renin inhibitors derived from food proteins
Nardo, Agustina Estefania
DOCKING APPROACH
RENIN INHIBITORS
PEPTIDES
AMARANTH
title_short A a new docking approach to find peptides renin inhibitors derived from food proteins
title_full A a new docking approach to find peptides renin inhibitors derived from food proteins
title_fullStr A a new docking approach to find peptides renin inhibitors derived from food proteins
title_full_unstemmed A a new docking approach to find peptides renin inhibitors derived from food proteins
title_sort A a new docking approach to find peptides renin inhibitors derived from food proteins
dc.creator.none.fl_str_mv Nardo, Agustina Estefania
Añon, Maria Cristina
Quiroga, Alejandra Viviana
author Nardo, Agustina Estefania
author_facet Nardo, Agustina Estefania
Añon, Maria Cristina
Quiroga, Alejandra Viviana
author_role author
author2 Añon, Maria Cristina
Quiroga, Alejandra Viviana
author2_role author
author
dc.contributor.none.fl_str_mv Toldrá, Fidel
dc.subject.none.fl_str_mv DOCKING APPROACH
RENIN INHIBITORS
PEPTIDES
AMARANTH
topic DOCKING APPROACH
RENIN INHIBITORS
PEPTIDES
AMARANTH
purl_subject.fl_str_mv https://purl.org/becyt/ford/2.11
https://purl.org/becyt/ford/2
dc.description.none.fl_txt_mv Structure-based computer modeling of peptide-protein interactions is a core component of modern bioinformatics approach to study bioactive peptide. Molecular docking is the most common technique used to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Most of docking programs, like AutoDock, are successful to work with small peptides but not with larger ones due to its high flexibility and freedom of movement. The objective of this work was to try out new free, friendly and rigorous servers developed specifically for peptides that act as ligands to predict with greater confidence the best peptides that could potentially act as inhibitors of an enzyme. For this purpose we use six peptides (SFNLPILR; FNLPILR; SFNLPIL; QAFEDGFEWVSFK; AFEDGFEWVSFK; VNVDDPSKA) identified in an amaranth alcalase hydrolyzate (HD 21±4 %) as renin (EC 3.4.23.15) inhibitors. As controls the renin substrate (angiotensinogen), a competitive inhibitor (IRLIIVLMPILMA, IC50=6.5 mM) and a tridecapeptide of alanines were used. In a first stage, CABS dock server (http://biocomp.chem.uw.edu.pl/CABSdock) was use to generate the peptide-renin (PDB 2V0Z chain C) complex and identify the most likely interaction sites. In the second stage, FlexPepDock server (http://flexpepdock.furmanlab.cs.huji.ac.il/) was used to refine the interaction energy of the complex and calculate a score that serves to select the best inhibitors from the set of peptides used. Comparing the obtained means of three independent replicates of the FlexPepDock score the peptides AFEDGFEWVSFK and SFNLPILR had a similar interaction energy to as control IRLIIVLMPILMA (Tukey test, p=0.05). Both peptides were synthesized to evaluate its inhibitory activity in vitro. The docking using peptide remains to be a challenge for the scientific community, the protocol used in this work use new servers specifically developed for this purpose with the additional advantage of being fast implementation and friendly with experimental scientists.
Fil: Nardo, Agustina Estefania. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; Argentina
Fil: Añon, Maria Cristina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; Argentina
Fil: Quiroga, Alejandra Viviana. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; Argentina
2nd International Symposium on Bioactive Peptides
Valencia
España
Consejo Superior de Investigaciones Científicas. Instituto de Agroquímica y Tecnología de Alimentos
University of Alberta.Department of Agricultural, Food and Nutritional Science
description Structure-based computer modeling of peptide-protein interactions is a core component of modern bioinformatics approach to study bioactive peptide. Molecular docking is the most common technique used to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Most of docking programs, like AutoDock, are successful to work with small peptides but not with larger ones due to its high flexibility and freedom of movement. The objective of this work was to try out new free, friendly and rigorous servers developed specifically for peptides that act as ligands to predict with greater confidence the best peptides that could potentially act as inhibitors of an enzyme. For this purpose we use six peptides (SFNLPILR; FNLPILR; SFNLPIL; QAFEDGFEWVSFK; AFEDGFEWVSFK; VNVDDPSKA) identified in an amaranth alcalase hydrolyzate (HD 21±4 %) as renin (EC 3.4.23.15) inhibitors. As controls the renin substrate (angiotensinogen), a competitive inhibitor (IRLIIVLMPILMA, IC50=6.5 mM) and a tridecapeptide of alanines were used. In a first stage, CABS dock server (http://biocomp.chem.uw.edu.pl/CABSdock) was use to generate the peptide-renin (PDB 2V0Z chain C) complex and identify the most likely interaction sites. In the second stage, FlexPepDock server (http://flexpepdock.furmanlab.cs.huji.ac.il/) was used to refine the interaction energy of the complex and calculate a score that serves to select the best inhibitors from the set of peptides used. Comparing the obtained means of three independent replicates of the FlexPepDock score the peptides AFEDGFEWVSFK and SFNLPILR had a similar interaction energy to as control IRLIIVLMPILMA (Tukey test, p=0.05). Both peptides were synthesized to evaluate its inhibitory activity in vitro. The docking using peptide remains to be a challenge for the scientific community, the protocol used in this work use new servers specifically developed for this purpose with the additional advantage of being fast implementation and friendly with experimental scientists.
publishDate 2019
dc.date.none.fl_str_mv 2019
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info:eu-repo/semantics/conferenceObject
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http://purl.org/coar/resource_type/c_5794
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status_str publishedVersion
format conferenceObject
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/178799
A a new docking approach to find peptides renin inhibitors derived from food proteins; 2nd International Symposium on Bioactive Peptides; Valencia; España; 2019; 70-70
CONICET Digital
CONICET
url http://hdl.handle.net/11336/178799
identifier_str_mv A a new docking approach to find peptides renin inhibitors derived from food proteins; 2nd International Symposium on Bioactive Peptides; Valencia; España; 2019; 70-70
CONICET Digital
CONICET
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language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://congresos.adeituv.es/bioactivepeptides/ficha.en.html
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eu_rights_str_mv openAccess
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application/pdf
application/pdf
application/pdf
dc.coverage.none.fl_str_mv Internacional
dc.publisher.none.fl_str_mv Universitat de València
publisher.none.fl_str_mv Universitat de València
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
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repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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