Abstract
Helicobacter pylori (H. pylori) is associated with gastrointestinal diseases including duodenal ulcers and gastric adenocarcinoma. Over 80% of the population is infected with H. pylori. Traditional triple therapy has become less effective because of drug resistance. Mycobacterium tuberculosis (M. tuberculosis) causes over 1.4 million deaths per year estimating from The World Health Organization (WHO) and is difficult to treat which leads to multi-drug resistance. In order to develop new antimicrobial agents against H. pylori and M. tuberculosis, we target the shikimate biosynthesis pathway that consists of seven-step enzymatic processes in microbial and parasites but absent in mammals. In this study, we focus on the fourth enzyme, shikimate dehydrogenase (SDH), uses NADPH as a cofactor to catalyze 3-dehydroshikimate into shikimate. Dr. Wang’s prior works have identified a potent SDH inhibitor (7a) that blocked the growth of H. pylori. In this work, we have screened for new inhibitors based on the 7a skeleton using a structure-guided approach. Of 7a similar compounds (n =78), 7m was identified to block both HpSDH and MtSDH (IC50: 11.7 µM for HpSDH and 32.2 µM for MtSDH). Kinetic analysis revealed that 7m displays uncompetitive and competitive inhibition pattern toward shikimate and NADP+, respectively. Moreover, 7m reduced H. pylori growth (MBC value: 25 µM). The HpSDH-7m complex model is built by Discovery Studio 3.0, which reveals that Lys69, Glu70 and Ser129 are crucial binding residues. Site-directed mutagenesis analysis revealed that S129A and E70D were less sensitive to 7m (IC50 = 17.8 for S129A and 22.89 µM for E70D). Together, our results suggest that the SDH inhibitor 7m is a new inhibitor for antibiotics development and provides a new skeleton for further antibiotic development.