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AlzyFinder: A Machine-Learning-Driven Platform for Ligand-Based Virtual Screening and Network Pharmacology
Indexado
WoS WOS:001382182800001
Scopus SCOPUS_ID:85208101621
DOI 10.1021/ACS.JCIM.4C01481
Año 2024
Tipo artículo de investigación

Citas Totales

Autores Afiliación Chile

Instituciones Chile

% Participación
Internacional

Autores
Afiliación Extranjera

Instituciones
Extranjeras


Abstract



Alzheimer's disease (AD), a prevalent neurodegenerative disorder, presents significant challenges in drug development due to its multifactorial nature and complex pathophysiology. The AlzyFinder Platform, introduced in this study, addresses these challenges by providing a comprehensive, free web-based tool for parallel ligand-based virtual screening and network pharmacology, specifically targeting over 85 key proteins implicated in AD. This innovative approach is designed to enhance the identification and analysis of potential multitarget ligands, thereby accelerating the development of effective therapeutic strategies against AD. AlzyFinder Platform incorporates machine learning models to facilitate the ligand-based virtual screening process. These models, built with the XGBoost algorithm and optimized through Optuna, were meticulously trained and validated using robust methodologies to ensure high predictive accuracy. Validation included extensive testing with active, inactive, and decoy molecules, demonstrating the platform's efficacy in distinguishing active compounds. The models are evaluated based on balanced accuracy, precision, and F1 score metrics. A unique soft-voting ensemble approach is utilized to refine the classification process, integrating the strengths of individual models. This methodological framework enables a comprehensive analysis of interaction data, which is presented in multiple formats such as tables, heat maps, and interactive Ligand-Protein Interaction networks, thus enhancing the visualization and analysis of drug-protein interactions. AlzyFinder was applied to screen five molecules recently reported (and not used to train or validate the ML models) as active compounds against five key AD targets. The platform demonstrated its efficacy by accurately predicting all five molecules as true positives with a probability greater than 0.70. This result underscores the platform's capability in identifying potential therapeutic compounds with high precision. In conclusion, AlzyFinder's innovative approach extends beyond traditional virtual screening by incorporating network pharmacology analysis, thus providing insights into the systemic actions of drug candidates. This feature allows for the exploration of ligand-protein and protein-protein interactions and their extensions, offering a comprehensive view of potential therapeutic impacts. As the first open-access platform of its kind, AlzyFinder stands as a valuable resource for the AD research community, available at http://www.alzyfinder-platform.udec.cl with supporting data and scripts accessible via GitHub https://github.com/ramirezlab/AlzyFinder.

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Disciplinas de Investigación



WOS
Chemistry, Multidisciplinary
Computer Science, Interdisciplinary Applications
Computer Science, Information Systems
Chemistry, Medicinal
Scopus
Library And Information Sciences
Computer Science Applications
Chemistry (All)
Chemical Engineering (All)
SciELO
Sin Disciplinas

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Publicaciones WoS (Ediciones: ISSHP, ISTP, AHCI, SSCI, SCI), Scopus, SciELO Chile.

Colaboración Institucional



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Autores - Afiliación



Ord. Autor Género Institución - País
1 Valero-Rojas, Jessica - Universidad de Concepción - Chile
2 Ramirez-Sanchez, Camilo - Inst Univ Politecn Gran Colombiano - Colombia
Institution Universitaria Politecnico Grancolombiano - Colombia
3 Pacheco-Paternina, Laura - Universidad de Concepción - Chile
4 Valenzuela-Hormazabal, Paulina - Universidad de Concepción - Chile
5 Saldivar-Gonzalez, Fernanda I. - Univ Nacl Autonoma Mexico - México
Universidad Nacional Autónoma de México - México
6 Santana, Paula - Universidad Autónoma de Chile - Chile
7 Gonzalez, Janneth - Pontificia Univ Javeriana - Colombia
Pontificia Universidad Javeriana - Colombia
8 Gutierrez-Bunster, Tatiana - Universidad del Bío Bío - Chile
9 Valdes-Jimenez, Alejandro Hombre Universidad del Bío Bío - Chile
10 RAMIREZ-SANCHEZ, DAVID MAURICIO Hombre Universidad de Concepción - Chile

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Financiamiento



Fuente
Fondo Nacional de Desarrollo Científico y Tecnológico
Agencia Nacional de Investigación y Desarrollo
Agencia Nacional de Investigacion y Desarrollo (ANID) - Fondo Nacional de Desarrollo Cientifico y Tecnologico (FONDECYT)

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Agradecimientos



Agradecimiento
This work was supported by the Agencia Nacional de Investigacion y Desarrollo (ANID) - Fondo Nacional de Desarrollo Cientifico y Tecnologico (FONDECYT) grant no. 1220656 to DR.
This work was supported by the Agencia Nacional de Investigacio\u0301n y Desarrollo (ANID) \u2013 Fondo Nacional de Desarrollo Cienti\u0301fico y Tecnolo\u0301gico (FONDECYT) grant no. 1220656 to DR.

Muestra la fuente de financiamiento declarada en la publicación.