Exploring the mechanisms and targets of proton pump inhibitors-induced osteoporosis through network toxicology, molecular docking, and molecular dynamics simulations

Proton pump inhibitors (PPIs) are widely used for the treatment of acid-related disorders, but long-term use has been increasingly associated with an elevated risk of osteoporosis. However, the underlying molecular mechanisms and specific targets of PPIs-induced bone loss remain poorly understood. This study aimed to explore the molecular mechanisms and key genes of PPIs-induced osteoporosis using network toxicology, molecular docking, and molecular dynamics simulations. We identified common targets of four widely used PPIs (omeprazole, lansoprazole, pantoprazole, and rabeprazole) and osteoporosis by screening large-scale biological databases. A protein-protein interaction network was constructed, and key hub genes were determined based on topological parameters such as degree, betweenness centrality, and closeness centrality. Enrichment analysis was performed to explore the biological processes, cellular components, molecular functions, and KEGG pathways associated with the overlapping targets. Molecular docking was conducted to evaluate the binding affinities between PPIs and their potential targets, and molecular dynamics simulations were employed to assess the stability of these interactions over time. We identified 35 potential targets for omeprazole-induced osteoporosis, 39 for lansoprazole, 29 for pantoprazole, and 29 for rabeprazole. Topological analysis of the protein-protein interaction networks revealed the hub genes for each PPI: epidermal growth factor receptor (EGFR) for omeprazole, estrogen receptor 1 (ESR1) for lansoprazole, EGFR for pantoprazole, and Proto-oncogene tyrosine-protein kinase SRC for rabeprazole. Molecular docking demonstrated strong and stable binding affinities between PPIs and their respective targets, with binding energies all below -5 kcal/mol. Molecular dynamics simulations confirmed the structural stability of these complexes, characterized by low root mean square deviation and root mean square fluctuation values and consistent hydrogen bond formation. This study identified EGFR, ESR1, and SRC as key regulatory genes in PPIs-induced osteoporosis, highlighting their roles in bone metabolism. The stable interactions between PPIs and these targets suggest their involvement in bone loss, providing a foundation for future experimental validation.