Multi-output model with box-jenkins operators of quadratic indices for prediction of malaria and cancer inhibitors targeting ubiquitin-proteasome pathway (UPP) proteins

The ubiquitin-proteasome pathway (UPP) is the primary degradation system of short-lived regulatory proteins. Cellular processes such as the cell cycle, signal transduction, gene expression, DNA repair and apoptosis are regulated by this UPP and dysfunctions in this system have important implications...

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Fecha de publicación:: 2016

Institución:: Universidad Tecnológica de Bolívar

Repositorio:: Repositorio Institucional UTB

Idioma:: eng

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network_acronym_str	UTB2
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dc.title.none.fl_str_mv	Multi-output model with box-jenkins operators of quadratic indices for prediction of malaria and cancer inhibitors targeting ubiquitin-proteasome pathway (UPP) proteins
title	Multi-output model with box-jenkins operators of quadratic indices for prediction of malaria and cancer inhibitors targeting ubiquitin-proteasome pathway (UPP) proteins
spellingShingle	Multi-output model with box-jenkins operators of quadratic indices for prediction of malaria and cancer inhibitors targeting ubiquitin-proteasome pathway (UPP) proteins Atom-based quadratic indices Cancer CHEMBL Malaria Moving average Multi-scale and multi-output model Multi-target QSAR UPP inhibitor Antineoplastic agent Proteasome Ubiquitin Antimalarial agent Antineoplastic agent Proteasome Ubiquitin ALMA model Apoptosis Article Bob Jenkins operator Cell cycle Computer program Diagnostic accuracy DNA repair Gene expression Malaria Model Mus musculus Oryctolagus cuniculus Plasmodium falciparum Quantitative structure activity relation Rattus norvegicus Sensitivity and specificity Signal transduction Biology Drug database Drug development Drug effects Human Malaria Metabolism Molecularly targeted therapy Neoplasms Protein degradation Antimalarials Antineoplastic agents Computational Biology Databases, Pharmaceutical Drug Discovery Humans Malaria Molecular Targeted Therapy Neoplasms Proteasome Endopeptidase Complex Proteolysis Ubiquitin
title_short	Multi-output model with box-jenkins operators of quadratic indices for prediction of malaria and cancer inhibitors targeting ubiquitin-proteasome pathway (UPP) proteins
title_full	Multi-output model with box-jenkins operators of quadratic indices for prediction of malaria and cancer inhibitors targeting ubiquitin-proteasome pathway (UPP) proteins
title_fullStr	Multi-output model with box-jenkins operators of quadratic indices for prediction of malaria and cancer inhibitors targeting ubiquitin-proteasome pathway (UPP) proteins
title_full_unstemmed	Multi-output model with box-jenkins operators of quadratic indices for prediction of malaria and cancer inhibitors targeting ubiquitin-proteasome pathway (UPP) proteins
title_sort	Multi-output model with box-jenkins operators of quadratic indices for prediction of malaria and cancer inhibitors targeting ubiquitin-proteasome pathway (UPP) proteins
dc.subject.keywords.none.fl_str_mv	Atom-based quadratic indices Cancer CHEMBL Malaria Moving average Multi-scale and multi-output model Multi-target QSAR UPP inhibitor Antineoplastic agent Proteasome Ubiquitin Antimalarial agent Antineoplastic agent Proteasome Ubiquitin ALMA model Apoptosis Article Bob Jenkins operator Cell cycle Computer program Diagnostic accuracy DNA repair Gene expression Malaria Model Mus musculus Oryctolagus cuniculus Plasmodium falciparum Quantitative structure activity relation Rattus norvegicus Sensitivity and specificity Signal transduction Biology Drug database Drug development Drug effects Human Malaria Metabolism Molecularly targeted therapy Neoplasms Protein degradation Antimalarials Antineoplastic agents Computational Biology Databases, Pharmaceutical Drug Discovery Humans Malaria Molecular Targeted Therapy Neoplasms Proteasome Endopeptidase Complex Proteolysis Ubiquitin
topic	Atom-based quadratic indices Cancer CHEMBL Malaria Moving average Multi-scale and multi-output model Multi-target QSAR UPP inhibitor Antineoplastic agent Proteasome Ubiquitin Antimalarial agent Antineoplastic agent Proteasome Ubiquitin ALMA model Apoptosis Article Bob Jenkins operator Cell cycle Computer program Diagnostic accuracy DNA repair Gene expression Malaria Model Mus musculus Oryctolagus cuniculus Plasmodium falciparum Quantitative structure activity relation Rattus norvegicus Sensitivity and specificity Signal transduction Biology Drug database Drug development Drug effects Human Malaria Metabolism Molecularly targeted therapy Neoplasms Protein degradation Antimalarials Antineoplastic agents Computational Biology Databases, Pharmaceutical Drug Discovery Humans Malaria Molecular Targeted Therapy Neoplasms Proteasome Endopeptidase Complex Proteolysis Ubiquitin
description	The ubiquitin-proteasome pathway (UPP) is the primary degradation system of short-lived regulatory proteins. Cellular processes such as the cell cycle, signal transduction, gene expression, DNA repair and apoptosis are regulated by this UPP and dysfunctions in this system have important implications in the development of cancer, neurodegenerative, cardiac and other human pathologies. UPP seems also to be very important in the function of eukaryote cells of the human parasites like Plasmodium falciparum, the causal agent of the neglected disease Malaria. Hence, the UPP could be considered as an attractive target for the development of compounds with Anti-Malarial or Anti-cancer properties. Recent online databases like ChEMBL contains a larger quantity of information in terms of pharmacological assay protocols and compounds tested as UPP inhibitors under many different conditions. This large amount of data give new openings for the computer-aided identification of UPP inhibitors, but the intrinsic data diversity is an obstacle for the development of successful classifiers. To solve this problem here we used the Bob-Jenkins moving average operators and the atom-based quadratic molecular indices calculated with the software TOMOCOMD-CARDD (TC) to develop a quantitative model for the prediction of the multiple outputs in this complex dataset. Our multi-target model can predict results for drugs against 22 molecular or cellular targets of different organisms with accuracies above 70% in both training and validation sets. © 2016 Bentham Science Publishers.
publishDate	2016
dc.date.issued.none.fl_str_mv	2016
dc.date.accessioned.none.fl_str_mv	2020-03-26T16:32:43Z
dc.date.available.none.fl_str_mv	2020-03-26T16:32:43Z
dc.type.coarversion.fl_str_mv	http://purl.org/coar/version/c_970fb48d4fbd8a85
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dc.type.driver.none.fl_str_mv	info:eu-repo/semantics/article
dc.type.hasversion.none.fl_str_mv	info:eu-repo/semantics/publishedVersion
dc.type.spa.none.fl_str_mv	Artículo
status_str	publishedVersion
dc.identifier.citation.none.fl_str_mv	Current Protein and Peptide Science; Vol. 17, Núm. 3; pp. 220-227
dc.identifier.issn.none.fl_str_mv	13892037
dc.identifier.uri.none.fl_str_mv	https://hdl.handle.net/20.500.12585/8989
dc.identifier.instname.none.fl_str_mv	Universidad Tecnológica de Bolívar
dc.identifier.reponame.none.fl_str_mv	Repositorio UTB
dc.identifier.orcid.none.fl_str_mv	9434652400 36454896800 6701762262 55665599200 6602955498 7103043662 6603767394
identifier_str_mv	Current Protein and Peptide Science; Vol. 17, Núm. 3; pp. 220-227 13892037 Universidad Tecnológica de Bolívar Repositorio UTB 9434652400 36454896800 6701762262 55665599200 6602955498 7103043662 6603767394
url	https://hdl.handle.net/20.500.12585/8989
dc.language.iso.none.fl_str_mv	eng
language	eng
dc.rights.coar.fl_str_mv	http://purl.org/coar/access_right/c_16ec
dc.rights.uri.none.fl_str_mv	http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.accessrights.none.fl_str_mv	info:eu-repo/semantics/restrictedAccess
dc.rights.cc.none.fl_str_mv	Atribución-NoComercial 4.0 Internacional
rights_invalid_str_mv	http://creativecommons.org/licenses/by-nc-nd/4.0/ Atribución-NoComercial 4.0 Internacional http://purl.org/coar/access_right/c_16ec
eu_rights_str_mv	restrictedAccess
dc.format.medium.none.fl_str_mv	Recurso electrónico
dc.format.mimetype.none.fl_str_mv	application/pdf
dc.publisher.none.fl_str_mv	Bentham Science Publishers B.V.
publisher.none.fl_str_mv	Bentham Science Publishers B.V.
dc.source.none.fl_str_mv	https://www.scopus.com/inward/record.uri?eid=2-s2.0-84961704457&partnerID=40&md5=7b0b58b4cfd95174bb7c8a0deac6d6ba
institution	Universidad Tecnológica de Bolívar
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spelling	2020-03-26T16:32:43Z2020-03-26T16:32:43Z2016Current Protein and Peptide Science; Vol. 17, Núm. 3; pp. 220-22713892037https://hdl.handle.net/20.500.12585/8989Universidad Tecnológica de BolívarRepositorio UTB943465240036454896800670176226255665599200660295549871030436626603767394The ubiquitin-proteasome pathway (UPP) is the primary degradation system of short-lived regulatory proteins. Cellular processes such as the cell cycle, signal transduction, gene expression, DNA repair and apoptosis are regulated by this UPP and dysfunctions in this system have important implications in the development of cancer, neurodegenerative, cardiac and other human pathologies. UPP seems also to be very important in the function of eukaryote cells of the human parasites like Plasmodium falciparum, the causal agent of the neglected disease Malaria. Hence, the UPP could be considered as an attractive target for the development of compounds with Anti-Malarial or Anti-cancer properties. Recent online databases like ChEMBL contains a larger quantity of information in terms of pharmacological assay protocols and compounds tested as UPP inhibitors under many different conditions. This large amount of data give new openings for the computer-aided identification of UPP inhibitors, but the intrinsic data diversity is an obstacle for the development of successful classifiers. To solve this problem here we used the Bob-Jenkins moving average operators and the atom-based quadratic molecular indices calculated with the software TOMOCOMD-CARDD (TC) to develop a quantitative model for the prediction of the multiple outputs in this complex dataset. Our multi-target model can predict results for drugs against 22 molecular or cellular targets of different organisms with accuracies above 70% in both training and validation sets. © 2016 Bentham Science Publishers.Ministerio de Economía y Competitividad: CTQ2013-41229-Pproteasome, 140879-24-9; ubiquitin, 60267-61-0; Antimalarials; Antineoplastic Agents; Proteasome Endopeptidase Complex; UbiquitinGonzalez-Diaz H. acknowledges financial support from the grant MINECO (CTQ2013-41229-P), Spain.Recurso electrónicoapplication/pdfengBentham Science Publishers B.V.http://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/restrictedAccessAtribución-NoComercial 4.0 Internacionalhttp://purl.org/coar/access_right/c_16echttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84961704457&partnerID=40&md5=7b0b58b4cfd95174bb7c8a0deac6d6baMulti-output model with box-jenkins operators of quadratic indices for prediction of malaria and cancer inhibitors targeting ubiquitin-proteasome pathway (UPP) proteinsinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArtículohttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_2df8fbb1Atom-based quadratic indicesCancerCHEMBLMalariaMoving averageMulti-scale and multi-output modelMulti-targetQSARUPP inhibitorAntineoplastic agentProteasomeUbiquitinAntimalarial agentAntineoplastic agentProteasomeUbiquitinALMA modelApoptosisArticleBob Jenkins operatorCell cycleComputer programDiagnostic accuracyDNA repairGene expressionMalariaModelMus musculusOryctolagus cuniculusPlasmodium falciparumQuantitative structure activity relationRattus norvegicusSensitivity and specificitySignal transductionBiologyDrug databaseDrug developmentDrug effectsHumanMalariaMetabolismMolecularly targeted therapyNeoplasmsProtein degradationAntimalarialsAntineoplastic agentsComputational BiologyDatabases, PharmaceuticalDrug DiscoveryHumansMalariaMolecular Targeted TherapyNeoplasmsProteasome Endopeptidase ComplexProteolysisUbiquitinCasañola-Martín G.M.Le-Thi-Thu H.Pérez-Giménez F.Marrero-Ponce Y.Merino-Sanjuán M.Abad C.González-Díaz H.Tu, Y., Chen, C., Pan, J., Xu, J., Zhou, Z.G., Wang, C.Y., The ubiquitin proteasome pathway (UPP) in the regulation of cell cycle control and DNA damage repair and its implication in tumorigenesis (2012) Int. J. Clin. Exp. Pathol., 5 (8), pp. 726-738Driscoll, J.J., Dechowdhury, R., Therapeutically targeting the SUMOylation, ubiquitination and proteasome pathways as a novel anticancer strategy (2010) Targ. Oncol., 5 (4), pp. 281-289Stein, M.L., Groll, M., Applied techniques for mining natural proteasome inhibitors. BBA-Mol (2014) Cell. Res., 1843 (1), pp. 26-38Aminake, M.N., Arndt, H.D., Pradel, G., The proteasome of malaria parasites: A multi-stage drug target for chemotherapeutic intervention (2012) Int. J. Parasitol. Drugs Drug Resist., 2, pp. 1-10Casañola-Martin, G.M., Le-Thi-Thu, H., Marrero-Ponce, Y., Castillo- Garit, J.A., Torrens, F., Perez-Gimenez, F., Abad, C., Analysis of Proteasome Inhibition Prediction Using Atom-Based Quadratic Indices Enhanced by Machine Learning Classification Techniques (2014) Lett. Drug Des. Discov., 11 (6), pp. 705-711Gaulton, A., Bellis, L.J., Bento, A.P., Chambers, J., Davies, M., Hersey, A., Light, Y., Overington, J.P., ChEMBL: A large-scale bioactivity database for drug discovery (2012) Nucleic Acids Res., 40 (Database issue), pp. D1100-1107Heikamp, K., Bajorath, J., Large-scale similarity search profiling of ChEMBL compound data sets (2011) J. Chem. Inf. Model, 51 (8), pp. 1831-1839Mok, N.Y., Brenk, R., Mining the ChEMBL database: An efficient chemoinformatics workflow for assembling an ion channel-focused screening library (2011) J. Chem. Inf. Model, 51 (10), pp. 2449-2454Hu, Y., Bajorath, J., Molecular scaffolds with high propensity to form multi-target activity cliffs (2010) J. Chem. Inf. Model, 50 (4), pp. 500-510Erhan, D., L'heureux, P.J., Yue, S.Y., Bengio, Y., Collaborative filtering on a family of biological targets (2006) J. Chem. Inf. 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Multi-output model with box-jenkins operators of quadratic indices for prediction of malaria and cancer inhibitors targeting ubiquitin-proteasome pathway (UPP) proteins

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