Inhibitior Discovery Of Helicobacter Pylori Peptide Deformylase And Crystal Structure Determination And Function Study For PDF-ligand Complex

Helicobacter pylori (Hp), a gram-negative bacterium, is associated with numerous human diseases, such as chronic gastritis, peptic ulcer, mucosa-associated lymphoid tissue lymphoma, and gastric cancer. The primary factor interfering with the efficacy of current therapeutic regimens for H. pylori infection is the increasing prevalence of H. pylori antibiotic resisitence. Therefore, developing novel antibiotics that acting at new targets or via distinct modes is most likely to overcome the obstacle. Peptide deformylase (PDF), a member of a unique subclass of metalloenzymes, catalyzes the hydrolytic removal of the N-terminal formyl group from methionine residues following protein synthesis. PDF is essential for bacterial growth but not required by eukaryotes, which imply an attractive target for developing new antibacterial agents. Natural products have been considered as crucial sources for lead compounds in discovering new drugs due to their chemical diversity and ability to act on various biological targets. The enzymatic activity of HpPDF was evaluated using a FDH-coupled assay. We evaluated a collection of compounds derived from our natural product library for enzyme inhibition against HpPDF. Caffeic acid phenethyl ester (CAPE), one of the main medicinal components of propolis, was found as a competitive inhibitor against HpPDF. Furthermore, the UV-visible absorption spectroscopy of the CAPE-PDF complex is very different from the actinonin-PDF complex. Crystal structural characterization revealed that the main reason for the inhibition on HpPDF is that CAPE blocks the substrate entrance, preventing substrate from approaching the active site. Our study provides valuable information for understanding the potential anti-H. pylori mechanism of propolis, and CAPE could be served as a lead compound for further anti-bacterical drug discovery.