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Antioxidant is the important agent to inhibit free radical reaction. One of the enzymes that trigger the formation of superoxide anion radicals is xanthine oxidase enzyme (XO). Excessive total of free radicals formed by the XO enzyme can cause oxidative stress which would influence the human body health. It is needed natural antioxidant agent that is safe for consumption. In this study focus on the prediction of antioxidant activity through ligand-protein interaction by molecular docking with test ligands which were compounds isolated from Allium sativum (garlic) and Allium cepa (onion) leaves. This study uses method by in silico (molecular docking) in prediction of antioxidant activity. The result of molecular docking presents that compound 2 has the best inhibition to protein XO activity with resulting the lowest binding energy -8.64 kcal/mol, ΔG of -9.75 kcal/mol and Ki of 0.70 μM when compared with allopurinol as a positive control. Based on in silico, compound that results the lowest binding energy means having the good affinity and stable conformation.