Gastrodin alleviates mild cognitive impairment and Alzheimer’s disease via candidate targeting of ACHE, S1PR5, SERPINE1, and TOP2A: an integrative computational and cellular study

Abstract

Alzheimer’s disease (AD) and its prodromal mild cognitive impairment (MCI) lack effective disease-modifying therapeutic strategies. Gastrodin (GAS), the major bioactive compound of Gastrodia elata , exhibits pronounced neuroprotective effects. However, the precise candidate molecular targets and systematic mechanisms by which GAS protects against AD and MCI remain poorly clarified; target engagement is inferred from computational simulation rather than direct biochemical validation. This study adopted an integrated approach of network pharmacology, transcriptome-based machine learning, molecular simulation, and in vitro cellular validation to explore the therapeutic mechanisms of GAS against AD/MCI. A total of 127 overlapping therapeutic targets of GAS, AD, and MCI were identified, which were mainly enriched in synaptic transmission and calcium signaling pathways. Four core hub genes ( ACHE , S1PR5 , SERPINE1 , and TOP2A ) were further screened by intersecting candidate targets with AD differentially expressed genes from the GSE329677 dataset. The ensemble Logistic + SVM machine learning model exhibited optimal diagnostic efficiency with an AUC value of 0.897. Molecular docking and 50 ns molecular dynamics simulations confirmed that GAS stably bound to the four target proteins and maintained stable binding states under physiological conditions. In an Aβ 1-42 oligomer-injured N2a neuronal model, GAS showed no significant cytotoxicity at concentrations ranging from 0.1 to 100 μM. Notably, 25 μM GAS markedly reversed Aβ 1-42 -induced neuronal death and excessive intracellular ROS accumulation. This study identifies four novel candidate core therapeutic targets of GAS against AD/MCI and provides computational evidence for their stable atomic-level binding characteristics. GAS exerts prominent neuroprotective effects through anti-apoptotic and antioxidant mechanisms in Aβ-injured neurons. These findings provide a novel theoretical basis and preclinical evidence for the development of GAS as a natural candidate agent for AD intervention.