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The resistance of cancer and <i>Helicobacter pylori</i> to several drugs reflects a worldwide problem, and it has been the intention of numerous researchers to overcome this problem. Thus, in this study, <i>Acacia nilotica</i> fruits were subjected to HPLC analysis to detect their phenolic compounds and flavonoids. Moreover, <i>A. nilotica</i>‘s anti-<i>H. pylori</i> activity and its inhibitory activity against human hepatocellular carcinoma (HepG-2 cells) were reported. Various compounds with different concentrations, such as ferulic acid (5451.04 µg/mL), chlorogenic acid (4572.26 µg/mL), quercetin (3733.37 µg/mL), rutin (2393.13 µg/mL), gallic acid (2116.77 µg/mL), cinnamic acid (69.72 µg/mL), hesperetin (121.39 µg/mL) and methyl gallate (140.45 µg/mL), were detected. Strong anti-<i>H. pylori</i> activity at 31 mm was reported, compared to the positive control of the 21.67 mm inhibition zone. Moreover, the MIC and MBC were 7.8 µg/mL and 15.62 µg/mL, respectively, while the MIC and MBC of the positive control were 31.25 µg/mL. The concentration of MBC at 25%, 50% and 75% reflected <i>H. pylori</i>’s anti-biofilm activity of 70.38%, 82.29% and 94.22%, respectively. Good antioxidant properties of the <i>A. nilotica</i> flower extract were documented at 15.63, 62.50, 250 and 1000 µg/mL, causing the DPPH scavenging percentages of 42.3%, 52.6%, 65.5% and 80.6%, respectively, with a IC₅₀ of 36.74 µg/mL. HepG-2 cell proliferation was inhibited (91.26%) using 500 µg/mL of flower extract with an IC₅₀ of 176.15 µg/mL, compared to an IC₅₀ of 395.30 µg/mL used against human normal melanocytes. Molecular docking was applied to investigate ferulic acid with the <i>H. pylori</i> (4HI0) crystal structure to determine the best binding mode that interacted most energetically with the binding sites. Molecular docking indicated that ferulic acid was a proper inhibitor for the 4HI0 protein enzyme of <i>H. pylori</i>. A low energy score (−5.58 Kcal/mol) was recorded as a result of the interaction of ferulic acid with the residue’s SER 139 active site caused by the O 29 atom, which was important for its antibacterial activity.