A systems biology approach reveals dual neurotherapeutic mechanisms of Dioscorea bulbifera in Alzheimer's disease via estrogen signaling and cholinergic modulation.

Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder marked by cognitive decline, cholinergic dysfunction, synaptic loss, and neuroinflammation. Existing therapies such as Donepezil and estrogen replacement offer only symptomatic relief, failing to address the complexity of the disease due to their reductionist, single-targeted approach. In this study, we employed an integrative systems biology framework to evaluate the neurotherapeutic potential of Dioscorea bulbifera (DB), a core component of the US-patented polyherbal formulation BHD (comprising Bacopa monnieri, Hippophae rhamnoides, and DB), which has shown promising neuroprotective properties in preclinical models. We identified active phytoconstituents of DB-including Emodin, Beta-sitosterol, Diosgenin, Stigmasterol, Diosbulbin B, Jarnol, and Myricetin-and systematically assessed their interaction with Alzheimer's-relevant hub-bottleneck (H-B) genes using molecular docking, gene expression integration, network pharmacology, and molecular dynamics simulations. Our findings delineate a dual mechanistic model of DB's action: (1) an Estrogen Signaling Module centered around ESR1 and its key signaling associates (MAPK1, MAPK8, AKT1, EGFR, PIK3CA, and MAP2K1), forming a tightly interconnected, feedback-regulated pathway modulating memory, synaptic plasticity, neuroprotection, and inflammation; and (2) a Cholinergic Module involving direct inhibition of ACHE, providing rapid symptomatic relief. Molecular docking and dynamic simulations confirmed the strong and stable interactions of DB bioactives with both ESR1 and ACHE, showing comparable or superior stability to reference drugs (Estradiol and Donepezil). Regulatory network analysis revealed that ESR1 is one of the most connected genes in hippocampal-specific PPI networks and is co-regulated by numerous miRNAs and transcription factors. Co-expression analysis identified additional AD-relevant genes (e.g., PIK3R1, MAPK14, PTEN, DHODH, CAV1) involved in synaptic signaling, oxidative stress, and neurogenesis, while TF-miRNA coregulatory nodes such as miR-199a-3p, miR-181a-5p, GATA2, CREB1, and HINFP added further mechanistic layers to DB's network modulation. KEGG and GO enrichment analyses mapped DB-targeted genes to critical AD pathways, including Estrogen signaling, MAPK, PI3K-AKT, TNF, FoxO, and the Alzheimer's disease pathway itself. This multi-targeted, systems-level modulation by DB underscores its potential not only as a neuroprotective nutraceutical-especially for postmenopausal women vulnerable to estrogen loss-but also as a promising adjuvant to standard AD therapies.