Helicobacter pylori (H. pylori) secretes the chaperone and serine protease high temperature requirement A (HtrA) that cleaves gastric epithelial cell surface proteins to disrupt the epithelial integrity and barrier function. First inhibitory lead structures have demonstrated the essential role of HtrA in H. pylori physiology and pathogenesis. Comprehensive drug discovery techniques allowing high-throughput screening are now required to develop effective compounds. Here, we designed a novel fluorescence resonance energy transfer (FRET) peptide derived from a gel-based label-free proteomic approach (direct in-gel profiling of protease specificity) as a valuable substrate for H. pylori HtrA. Since serine proteases are often sensitive to metal ions, we investigated the influence of different divalent ions on the activity of HtrA. We identified Zn ++ and cu ++ ions as inhibitors of H. pylori HtrA activity, as monitored by in vitro cleavage experiments using casein or E-cadherin as substrates and in the FRET peptide assay. Putative binding sites for Zn ++ and cu ++ were then analyzed in thermal shift and microscale thermophoresis assays. The findings of this study will contribute to the development of novel metal ion-dependent protease inhibitors, which might help to fight bacterial infections. Gastric cancer is associated with one of the highest mortality rates among all cancerous diseases in humans since efficient treatment options are still not available 1. Persistent infections with the gastric pathogen Helicobacter pylori (H. pylori) are a significant risk factor for the induction and progression of stomach cancer. Approximately 50% of the human population is infected with H. pylori, which can induce chronic gastritis, duodenal, and gastric ulcers and finally gastric adenocarcinoma or MALT (mucosa-associated lymphoid tissue) lymphoma 2,3. Accordingly, the complex network of cellular and molecular mechanisms of H. pylori-host interactions has been intensively investigated. The finding that the serine protease high temperature requirement A (HtrA) expressed by H. pylori targets cell surface proteins of infected host cells added an important aspect to the model of H. pylori pathogenesis. During infection, H. pylori secretes HtrA and cleaves off the ectodomain of the cell adhesion protein and tumor