PTGS2-Based Network Pharmacology and Molecular Modeling Investigation of the Antioxidant Potential of Ethanolic Allium atroviolaceum Boiss. Extracts Across Plant Parts: Compositional Diversity, UHPLC-QTOF-IMS, and Experimental Validation

Background/Objectives: Allium atroviolaceum Boiss. is a functional food rich in phenolic compounds; however, the contribution of different plant organs to its bioactivity remains insufficiently understood. Methods: An integrated approach combining UHPLC-QTOF-IMS based metabolite profiling, network pharmacology, molecular docking, and experimental antioxidant assays was employed. Results: Metabolite profiling revealed that the flowers were rich in anthocyanins and flavonoids; leaves in flavonol glycosides; bulbs in flavonoids, phenolics, and lipids; and flower stalks in flavonoid glycosides and sterols. Interestingly, flowers exhibited the strongest antioxidant scavenging activity, with the lowest IC₅₀ values of 3.08 ± 0.21 µg/mL and 89 ± 2.8 µg/mL in the DPPH and ABTS assays, respectively. They also showed the highest FRAP response at 2 mg/mL (1.367 ± 0.010 at 2 mg/mL). Moreover, flower stalks were particularly effective in limiting lipid oxidation, displaying the greatest activity in the β-carotene bleaching assay, with an IC₅₀ value of 14.75 ± 0.29 µg/mL. Network-based target prioritization highlighted several oxidative stress/inflammation-associated proteins, including EGFR, HRAS, TGFB1, BCL2, JUN, TNF, TP53, MAPK1, and PTGS2. Additionally, Caffeoyl pinoresinol showed the strongest predicted interaction with PTGS2 and was therefore selected as a candidate ligand for further computational evaluation. Conclusions: A. atroviolaceum exhibits organ-specific phytochemical diversity and potent antioxidant activity mediated through multiple molecular targets. The in silico analyses identified candidate compound-target associations related to oxidative stress and inflammatory pathways, but these findings remain predictive and require biochemical and cell-based validation.