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AlzyFinder: A Machine-Learning-Driven Platform for Ligand-Based Virtual Screening and Network Pharmacology.

Jessica Valero-Rojas1,2, Camilo Ramírez-Sánchez3, Laura Pacheco-Paternina1

  • 1Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4070386, Chile.

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The AlzyFinder Platform accelerates Alzheimer's disease (AD) drug discovery using AI-driven virtual screening and network pharmacology. This free tool identifies potential multitarget ligands, aiding in the development of novel AD therapeutics.

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Area of Science:

  • Computational chemistry and pharmacology
  • Bioinformatics and cheminformatics
  • Neuroscience and drug discovery

Background:

  • Alzheimer's disease (AD) drug development faces challenges due to its complex nature.
  • Identifying effective multitarget ligands is crucial for AD therapeutics.
  • Existing tools lack integrated virtual screening and network pharmacology for AD.

Purpose of the Study:

  • To introduce AlzyFinder, a free, web-based platform for Alzheimer's disease research.
  • To enable parallel ligand-based virtual screening and network pharmacology analysis.
  • To accelerate the identification and analysis of potential multitarget ligands for AD.

Main Methods:

  • Development of machine learning models (XGBoost, Optuna) for ligand-based virtual screening.
  • Validation of models using active, inactive, and decoy molecules with metrics like balanced accuracy, precision, and F1 score.
  • Integration of a soft-voting ensemble approach for refined classification and comprehensive analysis of interaction data.

Main Results:

  • AlzyFinder successfully screened five known active compounds against key AD targets, predicting them as true positives (>0.70 probability).
  • The platform demonstrated high precision in identifying potential therapeutic compounds.
  • Network pharmacology analysis provided insights into systemic drug actions and interactions.

Conclusions:

  • AlzyFinder is the first open-access platform combining virtual screening and network pharmacology for AD.
  • The platform enhances visualization and analysis of drug-protein and protein-protein interactions.
  • AlzyFinder serves as a valuable resource for accelerating Alzheimer's disease therapeutic development.