Revealing that quercetin targets RPA3 to alleviate chondrocyte injury in knee osteoarthritis based on bioinformatics analysis and molecular docking

Background Knee osteoarthritis (OA) is a prevalent degenerative joint disease characterized by cartilage degradation and inflammation. Quercetin has shown chondroprotective potential, but its mechanism of action remains unclear. Objective This study aims to investigate the molecular mechanism by which quercetin may alleviate knee OA progression by targeting replication protein A3 (RPA3). Methods Differentially expressed genes (DEGs) related to OA were identified from the GEO database (GSE55457) and analyzed using weighted gene co-expression network analysis (WGCNA). Functional enrichment and protein-protein interaction network analyses were performed to identify key targets. Molecular docking was conducted to predict the interaction between quercetin and RPA3. In vitro validation was performed using IL-1β-induced human chondrocytes (CHON-001). The effects of quercetin, RPA3 overexpression (OE-RPA3), and a PI3K pathway agonist (740Y-P) were evaluated by examining inflammatory cytokines (IL-6, TNF-α), extracellular matrix (ECM) degradation markers (MMP-3, MMP-13), oxidative stress indicators (ROS, MDA), and PI3K-AKT pathway using western blot, ELISA, and biochemical assays. Results Bioinformatics analysis identified RPA3 as a key target among 15 intersection genes from DEGs and WGCNA. Molecular docking confirmed a strong binding affinity between quercetin and RPA3 with a binding energy of −8.5 kcal/mol. In IL-1β-induced CHON-001 cells, quercetin significantly suppressed RPA3 expression and inhibited inflammation, ECM degradation, and oxidative stress. However, OE-RPA3 promoted IL-1β-induced CHON-001 cell inflammation, ECM degradation, and oxidative stress, as well as reversed the protective effects of quercetin. Furthermore, quercetin repressed the activity of PI3K-AKT pathway, while 740Y-P counteracted quercetin’s inhibitory effects on IL-1β-induced CHON-001 cell injury. Conclusion Quercetin alleviates IL-1β-induced chondrocyte inflammation, ECM degradation, and oxidative stress by downregulating RPA3 and inhibiting PI3K-AKT pathway, providing novel insights into the mechanism of quercetin as a potential therapeutic agent for knee OA.