Integrated computational screening and biochemical validation identify natural small molecules targeting Aβ aggregation and dissociation

Alzheimer's disease (AD) is characterized by the accumulation of amyloid-β (Aβ), a pathological hallmark implicated in disease onset and progression. Aβ undergoes self-assembly from monomers into soluble oligomers, protofibrils, insoluble fibrils, and extracellular plaques. Our previous studies have shown that Jowiseungchungtang, which consists of 14 medicinal herbs, inhibits Aβ aggregation and ameliorates Aβ-mediated pathology in AD models. However, the active small molecules underlying these effects remain unidentified. To identify small molecules from these 14 medicinal herbs, we constructed a library of 1,751 compounds and applied an integrated in silico and in vitro workflow. First, these 1,751 compounds were filtered based on drug-likeness and predicted blood-brain barrier permeability, yielding 566 candidates. Second, molecular docking of 566 selected compounds against Aβ conformers identified five candidates predicted to interact with aggregation-prone residues critical for Aβ aggregation and fibril stabilization. Third, Thioflavin T assays demonstrated that four compounds-1-monopalmitin, isobutyl octyl oxalate, pentadecanoic acid, and dimethyl azelate-significantly inhibited Aβ₄₂ aggregation. Additionally, isobutyl octyl oxalate and pentadecanoic acid disaggregated preformed Aβ₄₂ aggregates. Fourth, molecular dynamics simulations were performed to examine the short-timescale behavior of the candidate compounds with the Aβ_17-42 dimer, showing transient ligand-Aβ interactions associated with structural rearrangements at the dimer interface. Pharmacokinetic predictions supported drug-likeness, showing blood-brain barrier permeability and systemic clearance. Collectively, these findings identify four Jowiseungchungtang (JWS)-derived candidate compounds with Aβ aggregation-inhibitory activity and provide a mechanistic and pharmacokinetic basis for further development of these compounds as potential therapeutic agents in AD.