Integration of network pharmacology, structure-based pharmacophore modeling, DFT, molecular docking, and molecular dynamics simulations to identify multi-target small molecule inhibitors against Alzheimer's disease.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder associated with cognitive impairment, synaptic malfunction, oxidative stress, cholinergic deficits, and a lack of effective disease-modifying therapeutics. In this study, we integrated in silico approaches with network pharmacology to identify novel multi-target ligands against three key AD-associated proteins: acetylcholinesterase (AChE), protein kinase B (AKT1), and monoamine oxidase B (MAO-B). Structure-based e-pharmacophore modeling and virtual screening were conducted using Pharmit, a large compound library from the ZINC and COCONUT databases, followed by stringent ADMET filtering to obtain drug-like candidates. Network pharmacology analysis identified AKT1 as the best hub gene between predicted hit compounds and AD-associated gene-enriched pathways, such as PI3K-Akt, FoxO, calcium, and cAMP signaling pathways. Four hits (1-4) were screened for binding affinity evaluation using molecular docking, followed by MM-GBSA, and molecular dynamics (MD) simulations. Hit1 (N-(2-(1H-indol-3-yl)ethyl)-7-hydroxy-5,6-dimethoxy-[1,2,4]triazolo[4,3-a]quinazoline-3-carboxamide) (ZINC000033435965) demonstrated the strongest binding affinities across all complexes, with docking scores of - 11.4, - 11.8, and - 12.1 kcal/mol for hAChE, AKT1, and MAO-B, respectively. MD simulations over 100 ns for Hit1 revealed stable interaction as described by RMSD, RMSF, Rg, SASA, and HB profiles. E-pharmacophore and validation demonstrated strong predictive performance across the complexes, especially for AKT1 and MAO-B with high enrichment factors and ROC-AUC values (0.95 and 0.94). Additionally, DFT analysis of Hit1 revealed a favorable electronic stability energy (- 1479.283992 Eh). ADMET profiling predicted favorable oral bioavailability, BBB permeability, drug-likeness, and low predicted toxicity. The findings of this study suggest that Hit1 could be a promising multi-target molecule capable of modulating cholinergic transmission, neuronal survival pathways, and oxidative stress in AD. Experimental validation, including in vitro enzymatic assays and in vivo evaluations, is essential to further establish the therapeutic potential of Hit1.