The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets

Autores
Hassan, Syed S.; Jamal, Syed B.; Radusky, Leandro Gabriel; Tiwari, Sandeep; Ullah, Asad; Ali, Javed; Behramand, null; de Carvalho, Paulo V. S. D.; Shams, Rida; Khan, Sabir; Figueiredo, Henrique C. P.; Barh, Debmalya; Ghosh, Preetam; Silva, Artur; Baumbach, Jan; Röttger, Richard; Turjanski, Adrian; Azevedo, Vasco A. C.
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Diphtheria is an acute and highly infectious disease, previously regarded as endemic in nature but vaccine-preventable, is caused by Corynebacterium diphtheriae (Cd). In this work, we used an in silico approach along the 13 complete genome sequences of C. diphtheriae followed by a computational assessment of structural information of the binding sites to characterize the "pocketome druggability." To this end, we first computed the "modelome" (3D structures of a complete genome) of a randomly selected reference strain Cd NCTC13129; that had 13,763 open reading frames (ORFs) and resulted in 1,253 (~9%) structure models. The amino acid sequences of these modeled structures were compared with the remaining 12 genomes and consequently, 438 conserved protein sequences were obtained. The RCSB-PDB database was consulted to check the template structures for these conserved proteins and as a result, 401 adequate 3D models were obtained. We subsequently predicted the protein pockets for the obtained set of models and kept only the conserved pockets that had highly druggable (HD) values (137 across all strains). Later, an off-target host homology analyses was performed considering the human proteome using NCBI database. Furthermore, the gene essentiality analysis was carried out that gave a final set of 10-conserved targets possessing highly druggable protein pockets. To check the target identification robustness of the pipeline used in this work, we crosschecked the final target list with another in-house target identification approach for C. diphtheriae thereby obtaining three common targets, these were; hisE-phosphoribosyl-ATP pyrophosphatase, glpX-fructose 1,6-bisphosphatase II, and rpsH-30S ribosomal protein S8. Our predicted results suggest that the in silico approach used could potentially aid in experimental polypharmacological target determination in C. diphtheriae and other pathogens, thereby, might complement the existing and new drug-discovery pipelines.
Fil: Hassan, Syed S.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Jamal, Syed B.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Radusky, Leandro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Tiwari, Sandeep. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Ullah, Asad. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Ali, Javed. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Behramand, null. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: de Carvalho, Paulo V. S. D.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Shams, Rida. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Khan, Sabir. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Figueiredo, Henrique C. P.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Barh, Debmalya. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Ghosh, Preetam. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Silva, Artur. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Baumbach, Jan. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Röttger, Richard. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Turjanski, Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Azevedo, Vasco A. C.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Materia
CORYNEBACTERIUM DIPHTHERIA
DRUGGABLE GENOME
GLOBAL DRUGGABLE (GD)
HIGHLY DRUGGABLE (HD)
POCKETOME
PUTATIVE THERAPEUTIC TARGETS
STRUCTURAL PROTEOMICS
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/93934

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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targetsHassan, Syed S.Jamal, Syed B.Radusky, Leandro GabrielTiwari, SandeepUllah, AsadAli, JavedBehramand, nullde Carvalho, Paulo V. S. D.Shams, RidaKhan, SabirFigueiredo, Henrique C. P.Barh, DebmalyaGhosh, PreetamSilva, ArturBaumbach, JanRöttger, RichardTurjanski, AdrianAzevedo, Vasco A. C.CORYNEBACTERIUM DIPHTHERIADRUGGABLE GENOMEGLOBAL DRUGGABLE (GD)HIGHLY DRUGGABLE (HD)POCKETOMEPUTATIVE THERAPEUTIC TARGETSSTRUCTURAL PROTEOMICShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Diphtheria is an acute and highly infectious disease, previously regarded as endemic in nature but vaccine-preventable, is caused by Corynebacterium diphtheriae (Cd). In this work, we used an in silico approach along the 13 complete genome sequences of C. diphtheriae followed by a computational assessment of structural information of the binding sites to characterize the "pocketome druggability." To this end, we first computed the "modelome" (3D structures of a complete genome) of a randomly selected reference strain Cd NCTC13129; that had 13,763 open reading frames (ORFs) and resulted in 1,253 (~9%) structure models. The amino acid sequences of these modeled structures were compared with the remaining 12 genomes and consequently, 438 conserved protein sequences were obtained. The RCSB-PDB database was consulted to check the template structures for these conserved proteins and as a result, 401 adequate 3D models were obtained. We subsequently predicted the protein pockets for the obtained set of models and kept only the conserved pockets that had highly druggable (HD) values (137 across all strains). Later, an off-target host homology analyses was performed considering the human proteome using NCBI database. Furthermore, the gene essentiality analysis was carried out that gave a final set of 10-conserved targets possessing highly druggable protein pockets. To check the target identification robustness of the pipeline used in this work, we crosschecked the final target list with another in-house target identification approach for C. diphtheriae thereby obtaining three common targets, these were; hisE-phosphoribosyl-ATP pyrophosphatase, glpX-fructose 1,6-bisphosphatase II, and rpsH-30S ribosomal protein S8. Our predicted results suggest that the in silico approach used could potentially aid in experimental polypharmacological target determination in C. diphtheriae and other pathogens, thereby, might complement the existing and new drug-discovery pipelines.Fil: Hassan, Syed S.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Jamal, Syed B.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Radusky, Leandro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Tiwari, Sandeep. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Ullah, Asad. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Ali, Javed. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Behramand, null. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: de Carvalho, Paulo V. S. D.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Shams, Rida. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Khan, Sabir. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Figueiredo, Henrique C. P.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Barh, Debmalya. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Ghosh, Preetam. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Silva, Artur. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Baumbach, Jan. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Röttger, Richard. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFil: Turjanski, Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Azevedo, Vasco A. C.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; ArgentinaFrontiers Research Foundation2018-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/93934Hassan, Syed S.; Jamal, Syed B.; Radusky, Leandro Gabriel; Tiwari, Sandeep; Ullah, Asad; et al.; The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets; Frontiers Research Foundation; Frontiers in Genetics; 9; 44; 2-2018; 1-91664-8021CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://journal.frontiersin.org/article/10.3389/fgene.2018.00044/fullinfo:eu-repo/semantics/altIdentifier/doi/10.3389/fgene.2018.00044info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:59:38Zoai:ri.conicet.gov.ar:11336/93934instacron: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 09:59:38.843CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets
title The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets
spellingShingle The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets
Hassan, Syed S.
CORYNEBACTERIUM DIPHTHERIA
DRUGGABLE GENOME
GLOBAL DRUGGABLE (GD)
HIGHLY DRUGGABLE (HD)
POCKETOME
PUTATIVE THERAPEUTIC TARGETS
STRUCTURAL PROTEOMICS
title_short The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets
title_full The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets
title_fullStr The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets
title_full_unstemmed The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets
title_sort The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets
dc.creator.none.fl_str_mv Hassan, Syed S.
Jamal, Syed B.
Radusky, Leandro Gabriel
Tiwari, Sandeep
Ullah, Asad
Ali, Javed
Behramand, null
de Carvalho, Paulo V. S. D.
Shams, Rida
Khan, Sabir
Figueiredo, Henrique C. P.
Barh, Debmalya
Ghosh, Preetam
Silva, Artur
Baumbach, Jan
Röttger, Richard
Turjanski, Adrian
Azevedo, Vasco A. C.
author Hassan, Syed S.
author_facet Hassan, Syed S.
Jamal, Syed B.
Radusky, Leandro Gabriel
Tiwari, Sandeep
Ullah, Asad
Ali, Javed
Behramand, null
de Carvalho, Paulo V. S. D.
Shams, Rida
Khan, Sabir
Figueiredo, Henrique C. P.
Barh, Debmalya
Ghosh, Preetam
Silva, Artur
Baumbach, Jan
Röttger, Richard
Turjanski, Adrian
Azevedo, Vasco A. C.
author_role author
author2 Jamal, Syed B.
Radusky, Leandro Gabriel
Tiwari, Sandeep
Ullah, Asad
Ali, Javed
Behramand, null
de Carvalho, Paulo V. S. D.
Shams, Rida
Khan, Sabir
Figueiredo, Henrique C. P.
Barh, Debmalya
Ghosh, Preetam
Silva, Artur
Baumbach, Jan
Röttger, Richard
Turjanski, Adrian
Azevedo, Vasco A. C.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv CORYNEBACTERIUM DIPHTHERIA
DRUGGABLE GENOME
GLOBAL DRUGGABLE (GD)
HIGHLY DRUGGABLE (HD)
POCKETOME
PUTATIVE THERAPEUTIC TARGETS
STRUCTURAL PROTEOMICS
topic CORYNEBACTERIUM DIPHTHERIA
DRUGGABLE GENOME
GLOBAL DRUGGABLE (GD)
HIGHLY DRUGGABLE (HD)
POCKETOME
PUTATIVE THERAPEUTIC TARGETS
STRUCTURAL PROTEOMICS
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Diphtheria is an acute and highly infectious disease, previously regarded as endemic in nature but vaccine-preventable, is caused by Corynebacterium diphtheriae (Cd). In this work, we used an in silico approach along the 13 complete genome sequences of C. diphtheriae followed by a computational assessment of structural information of the binding sites to characterize the "pocketome druggability." To this end, we first computed the "modelome" (3D structures of a complete genome) of a randomly selected reference strain Cd NCTC13129; that had 13,763 open reading frames (ORFs) and resulted in 1,253 (~9%) structure models. The amino acid sequences of these modeled structures were compared with the remaining 12 genomes and consequently, 438 conserved protein sequences were obtained. The RCSB-PDB database was consulted to check the template structures for these conserved proteins and as a result, 401 adequate 3D models were obtained. We subsequently predicted the protein pockets for the obtained set of models and kept only the conserved pockets that had highly druggable (HD) values (137 across all strains). Later, an off-target host homology analyses was performed considering the human proteome using NCBI database. Furthermore, the gene essentiality analysis was carried out that gave a final set of 10-conserved targets possessing highly druggable protein pockets. To check the target identification robustness of the pipeline used in this work, we crosschecked the final target list with another in-house target identification approach for C. diphtheriae thereby obtaining three common targets, these were; hisE-phosphoribosyl-ATP pyrophosphatase, glpX-fructose 1,6-bisphosphatase II, and rpsH-30S ribosomal protein S8. Our predicted results suggest that the in silico approach used could potentially aid in experimental polypharmacological target determination in C. diphtheriae and other pathogens, thereby, might complement the existing and new drug-discovery pipelines.
Fil: Hassan, Syed S.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Jamal, Syed B.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Radusky, Leandro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Tiwari, Sandeep. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Ullah, Asad. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Ali, Javed. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Behramand, null. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: de Carvalho, Paulo V. S. D.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Shams, Rida. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Khan, Sabir. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Figueiredo, Henrique C. P.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Barh, Debmalya. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Ghosh, Preetam. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Silva, Artur. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Baumbach, Jan. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Röttger, Richard. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
Fil: Turjanski, Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Azevedo, Vasco A. C.. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad de Buenos Aires; Argentina
description Diphtheria is an acute and highly infectious disease, previously regarded as endemic in nature but vaccine-preventable, is caused by Corynebacterium diphtheriae (Cd). In this work, we used an in silico approach along the 13 complete genome sequences of C. diphtheriae followed by a computational assessment of structural information of the binding sites to characterize the "pocketome druggability." To this end, we first computed the "modelome" (3D structures of a complete genome) of a randomly selected reference strain Cd NCTC13129; that had 13,763 open reading frames (ORFs) and resulted in 1,253 (~9%) structure models. The amino acid sequences of these modeled structures were compared with the remaining 12 genomes and consequently, 438 conserved protein sequences were obtained. The RCSB-PDB database was consulted to check the template structures for these conserved proteins and as a result, 401 adequate 3D models were obtained. We subsequently predicted the protein pockets for the obtained set of models and kept only the conserved pockets that had highly druggable (HD) values (137 across all strains). Later, an off-target host homology analyses was performed considering the human proteome using NCBI database. Furthermore, the gene essentiality analysis was carried out that gave a final set of 10-conserved targets possessing highly druggable protein pockets. To check the target identification robustness of the pipeline used in this work, we crosschecked the final target list with another in-house target identification approach for C. diphtheriae thereby obtaining three common targets, these were; hisE-phosphoribosyl-ATP pyrophosphatase, glpX-fructose 1,6-bisphosphatase II, and rpsH-30S ribosomal protein S8. Our predicted results suggest that the in silico approach used could potentially aid in experimental polypharmacological target determination in C. diphtheriae and other pathogens, thereby, might complement the existing and new drug-discovery pipelines.
publishDate 2018
dc.date.none.fl_str_mv 2018-02
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/93934
Hassan, Syed S.; Jamal, Syed B.; Radusky, Leandro Gabriel; Tiwari, Sandeep; Ullah, Asad; et al.; The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets; Frontiers Research Foundation; Frontiers in Genetics; 9; 44; 2-2018; 1-9
1664-8021
CONICET Digital
CONICET
url http://hdl.handle.net/11336/93934
identifier_str_mv Hassan, Syed S.; Jamal, Syed B.; Radusky, Leandro Gabriel; Tiwari, Sandeep; Ullah, Asad; et al.; The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets; Frontiers Research Foundation; Frontiers in Genetics; 9; 44; 2-2018; 1-9
1664-8021
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
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info:eu-repo/semantics/altIdentifier/doi/10.3389/fgene.2018.00044
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
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application/pdf
dc.publisher.none.fl_str_mv Frontiers Research Foundation
publisher.none.fl_str_mv Frontiers Research Foundation
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repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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