Molecular Docking Calculations of Helicobacter Pylori and Its Inhibitors

Abstract

H. pylori is a bacterium usually found in the stomach. H. pylori infection sometimes causes gastritis or ulcers of the stomach and has been link to a wide range of other diseases. Purine nucleoside phosphorylase (PNP) is an essential enzyme in the purine salvage pathway of H. pylori. It is thought that binding of phosphate, one of the substrates, induces a conformational change in the active site of the enzyme. It is thus interesting to investigate whether the presence of phosphate in the active site will affect the binding mode of inhibitors. Totally 20 inhibitors were computationally docked into the H. pylori PNP structures (HpPNP) with and without phosphate and the docked configuration of each ligand to the two HpPNP structures were comparatively analyzed. The results showed that most ligands bind to HpPNP differently when there is phosphate in the active site.