Eradication of Helicobacter pylori through the inhibition of urease and peptide deformylase: Computational and biological studies.

This work tested anti- Helicobacter pylori, free radicals scavenging and toxicity property as well as chemical constituents in the extract of chloroform (CE) and ethyl acetate (EAE) from the pedicel of Diospyros kaki L. (PDK-CE and PDK-EAE). There were 33 and 36 chemical constituents respectively in the extracts of PDK-CE and PDK-EAE, belonging to the fatty acids methyl ester, fatty acids, and stearic acids, as revealed by Gas Chromatography-Mass Spectrometry (GC-MS). The extracts did not exhibit any toxicity on NIH3T3 cells, but they significantly showed scavenging of NO, DPPH, and H2O2 free radicals. The extracts displayed in vitro anti-H. pylori activity. PDK-CE had the maximum inhibitory zone at a minimal inhibitory concentration (MIC) of 10 μg. ml-1 and the extract also triggered the cellular damage in the bacteria. PDK-CE extract had a high urease inhibitory activity (IC50 value of 8.5 μg). Further, in silico studies was performed by using 41 compounds against H. pylori urease (HPU) and H. pylori peptide deformylase (HPPD). The score value was the maximum (-19.58 kcal/mol) against HPU with 17-(5-ethyl-6-methylheptan-2-yl)-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol, while the score value was the maximum (-14.51 kcal/mol) against HPPD with hexadecanoic acid. The results demonstrated the importance of the pedicel extracts in future pharmaceutical drug development against H. pylori infections.