MINERVA: a public XAI-powered platform advancing multi-target discovery in Alzheimer's disease

Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder involving a complex interplay of interconnected pharmacological targets, a feature that limits the success of traditional single-target medicinal chemistry approaches. Here, we present MINERVA (Multi-target Interactive Network for Explainable Research and Visualization in Alzheimer's disease), a public web-based platform designed to support multi-target drug discovery assisted by eXplainable Artificial Intelligence (XAI) strategies. MINERVA integrates large-scale disease-focused high-quality data comprising as many as 70,960 small molecules annotated across 33 AD relevant targets, taken from ChEMBL and CADRO databases. To capture different levels of pharmacological relevance, four distinct pharmacological thresholds (i.e., 10 μM, 1 μM, 100 nM, and 10 nM) were set to enable the parallel exploration of weak to high-affinity ligand spaces. Independent Balanced Random Forest (BRF) classifiers were trained for each AD target threshold combination using an extended core-substituent fingerprint, which ensures robustness against class imbalance and chemical heterogeneity. MINERVA incorporates a probability binning based domain of applicability (DoA) to quantify prediction reliability and a SHAP-based explainability framework to fairly map fragment-level contributions directly onto chemical structures. MINERVA is freely accessible at https://prometheus.farmacia.uniba.it/minerva/.Scientific contributionHerein we introduce MINERVA, the first freely accessible platform that combines large-scale AD-related data curation, multi-target prediction, and multi-threshold bioactivity modeling within a fully explainable and user-friendly environment. By enabling transparent, ligand-based exploration of chemical space across multiple AD pathways, MINERVA provides a unique and practical resource for accelerating multi-target drug discovery in the neurodegenerative research area.