Exploring the Anti-Inflammatory Potential of Saudi Propolis Through Phytochemical Characterization, Molecular Docking, and Dynamic Simulation

Background/Objectives: Propolis is a resinous natural product rich in phenolic acids and flavonoids, recognized in ethnopharmacology for its antioxidant and anti-inflammatory properties. This study aimed to identify the most bioactive Saudi propolis extract using a bioassay-guided strategy and investigate its chemical profile and mechanistic anti-inflammatory potential. Methods: Four propolis extracts (P1–P4) collected from different regions of Saudi Arabia were evaluated for their antioxidant (DPPH and ABTS) and anti-inflammatory (COX-1 and COX-2) activities. The most active extract was profiled using liquid chromatography–mass spectrometry (LC–MS), followed by molecular docking and molecular dynamics simulations. Results: Among all samples, P3 demonstrated the strongest antioxidant activity, with IC50 values of 25.84 ± 0.96 µg/mL (DPPH) and 32.30 ± 1.20 µg/mL (ABTS), comparable to ascorbic acid (27.45 ± 1.42 and 21.22 ± 0.79, respectively). P3 also exhibited potent and selective COX-2 inhibition with an IC50 of 6.19 ± 0.21 µg/mL (relative to celecoxib, IC50 0.681 ± 0.02 as positive control). LC–MS analysis identified 26 secondary metabolites. Computational studies ranked kaempferol as forming the most conformationally stable COX-2 complex among the ligands examined, including the reference inhibitor, on the basis of molecular dynamics descriptors of pose persistence and conformational confinement. Conclusions: Saudi propolis P3 is a potent source of bioactive compounds with strong antioxidant and selective COX-2 inhibitory activity. These findings highlight its anti-inflammatory potential and suggest its value as a natural lead for developing safer therapeutics targeting inflammation-related chronic diseases.