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Abstract:

Drug development for neglected diseases has been historically hampered due to lack of market incentives. The advent of public domain resources containing chemical information from high throughput screenings is changing the landscape of drug discovery for these diseases. In this work we took advantage of data from extensively studied organisms like human, mouse, E. coli and yeast, among others, to develop a novel integrative network model to prioritize and identify candidate drug targets in neglected pathogen proteomes, and bioactive drug-like molecules. We modeled genomic (proteins) and chemical (bioactive compounds) data as a multilayer weighted network graph that takes advantage of bioactivity data across 221 species, chemical similarities between 1.7 105compounds and several functional relations among 1.67 105proteins. These relations comprised orthology, sharing of protein domains, and shared participation in defined biochemical pathways. We showcase the application of this network graph to the problem of prioritization of new candidate targets, based on the information available in the graph for known compound-target associations. We validated this strategy by performing a cross validation procedure for known mouse and Trypanosoma cruzi targets and showed that our approach outperforms classic alignment-based approaches. Moreover, our model provides additional flexibility as two different network definitions could be considered, finding in both cases qualitatively different but sensible candidate targets. We also showcase the application of the network to suggest targets for orphan compounds that are active against Plasmodium falciparum in high-throughput screens. In this case our approach provided a reduced prioritization list of target proteins for the query molecules and showed the ability to propose new testable hypotheses for each compound. Moreover, we found that some predictions highlighted by our network model were supported by independent experimental validations as found post-facto in the literature. © 2016 Berenstein et al.

Registro:

Documento: Artículo
Título:A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases
Autor:Berenstein, A.J.; Magariños, M.P.; Chernomoretz, A.; Agüero, F.
Filiación:Laboratorio de Bioinformática, Fundación Instituto Leloir, Buenos Aires, Argentina
Departamento de Física, Universidad de Buenos Aires, Buenos Aires, Argentina
Laboratorio de Genómica y Bioinformática, Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico de Chascomús, Universidad de San Martín–CONICET, Sede San Martín, San Martín, Buenos Aires, Argentina
ChEMBL Group, European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom
Palabras clave:chemical compound; peptide deformylase; antiparasitic agent; Article; biological activity; drug repositioning; genome; high throughput screening; Kinetoplastida; mathematical computing; neglected disease; nonhuman; Plasmodium falciparum; protein analysis; protein domain; sequence analysis; Trypanosoma cruzi; animal; biology; drug development; drug repositioning; human; isolation and purification; mouse; Neglected Diseases; procedures; Animals; Antiparasitic Agents; Computational Biology; Drug Discovery; Drug Repositioning; Humans; Mice; Neglected Diseases
Año:2016
Volumen:10
Número:1
DOI: http://dx.doi.org/10.1371/journal.pntd.0004300
Título revista:PLoS Neglected Tropical Diseases
Título revista abreviado:PLoS. Negl. Trop. Dis.
ISSN:19352727
CAS:peptide deformylase; Antiparasitic Agents
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_19352727_v10_n1_p_Berenstein

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Citas:

---------- APA ----------
Berenstein, A.J., Magariños, M.P., Chernomoretz, A. & Agüero, F. (2016) . A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases. PLoS Neglected Tropical Diseases, 10(1).
http://dx.doi.org/10.1371/journal.pntd.0004300
---------- CHICAGO ----------
Berenstein, A.J., Magariños, M.P., Chernomoretz, A., Agüero, F. "A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases" . PLoS Neglected Tropical Diseases 10, no. 1 (2016).
http://dx.doi.org/10.1371/journal.pntd.0004300
---------- MLA ----------
Berenstein, A.J., Magariños, M.P., Chernomoretz, A., Agüero, F. "A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases" . PLoS Neglected Tropical Diseases, vol. 10, no. 1, 2016.
http://dx.doi.org/10.1371/journal.pntd.0004300
---------- VANCOUVER ----------
Berenstein, A.J., Magariños, M.P., Chernomoretz, A., Agüero, F. A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases. PLoS. Negl. Trop. Dis. 2016;10(1).
http://dx.doi.org/10.1371/journal.pntd.0004300