Metformin-Mediated Modulation of the AMPK/mTOR Axis in Hashimoto’s Thyroiditis: A Network Pharmacology and Molecular Docking Investigation

Introduction: Hashimoto’s thyroiditis (HT) is the most prevalent organ-specific autoimmune disorder worldwide, characterized by lymphocytic thyroid infiltration and the presence of circulating anti-thyroid autoantibodies. Conventional levothyroxine replacement normalizes circulating thyroid hormone levels but is fundamentally incapable of interrupting the underlying autoimmune cascade, leaving a critical therapeutic gap. Metformin, a biguanide with well-established antidiabetic properties, has emerged as a promising immunomodulatory candidate through its activation of AMP-activated protein kinase (AMPK) and consequent suppression of the mechanistic target of rapamycin (mTOR). Objective: To delineate the molecular mechanisms through which metformin engages immunological circuits in HT by integrating bulk transcriptomic profiling, network pharmacology, and molecular docking simulations targeting the AMPK/mTOR signaling axis. Methods: Four GEO datasets (n = 76 HT cases, n = 51 euthyroid controls) were integrated after ComBat batch-effect correction. Differential expression analysis, weighted gene co-expression network analysis (WGCNA), and multi-database metformin target curation identified 47 pharmacological intersection genes. Protein-protein interaction networks were constructed via STRING/Cytoscape, and KEGG/GO enrichment performed with clusterProfiler. Molecular docking of metformin was executed against AMPK α1β1γ1 (PDB: 4CFE) and mTOR kinase domain (PDB: 4JSP) using AutoDock Vina, with interaction profiling via PLIP. Results: WGCNA identified 94 immune-metabolic hub genes co-dysregulated in HT, with nine network hubs (including MTOR, AKT1, PIK3CA, STAT1, and PRKAA1) significantly enriched in AMPK/mTOR, T cell receptor, and JAK-STAT pathways. Molecular docking demonstrated thermodynamically favorable binding of metformin to AMPKγ1 (ΔG = −7.4 kcal/mol; 4 hydrogen bonds) and mTOR (ΔG = −6.1 kcal/mol; 3 hydrogen bonds), compared with re-docked native ligands AICAR (RMSD = 1.13 Å) and Torin2 (RMSD = 0.97 Å). Conclusion: This integrated in silico framework establishes a mechanistic basis for metformin’s immunomodulatory activity in HT through preferential AMPK engagement and secondary mTOR suppression, providing mechanistic grounds to support experimental and clinical evaluation of metformin as an adjuvant disease-modifying therapy.