Experimentally Validated Novel Inhibitors of <i>Helicobacter pylori</i> Phosphopantetheine Adenylyltransferase Discovered by Virtual High-Throughput Screening

<div><p><i>Helicobacter pylori</i> is a major etiologic agent associated with the development and maintenance of human gastritis. The goal of this study was to develop novel antibiotics against <i>H. pylori</i>, and we thus targeted <i>H. pylori</i> phosphopantetheine adenylyltransferase (<i>Hp</i>PPAT). PPAT catalyzes the penultimate step in coenzyme A biosynthesis. Its inactivation effectively prevents bacterial viability, making it an attractive target for antibacterial drug discovery. We employed virtual high-throughput screening and the <i>Hp</i>PPAT crystal structure to identify compounds in the PubChem database that might act as inhibitors of <i>Hp</i>PPAT. d-amethopterin is a potential inhibitor for blocking <i>Hp</i>PPAT activity and suppressing <i>H. pylori</i> viability. Following treatment with d-amethopterin, <i>H. pylori</i> exhibited morphological characteristics associated with cell death. d-amethopterin is a mixed inhibitor of <i>Hp</i>PPAT activity; it simultaneously occupies the <i>Hp</i>PPAT 4'-phosphopantetheine- and ATP-binding sites. Its binding affinity is in the micromolar range, implying that it is sufficiently potent to serve as a lead compound in subsequent drug development. Characterization of the d-amethopterin and <i>Hp</i>PPAT interaction network in a docked model will allow us to initiate rational drug optimization to improve the inhibitory efficacy of d-amethopterin. We anticipate that novel, potent, and selective <i>Hp</i>PPAT inhibitors will emerge for the treatment of <i>H. pylori</i> infection.</p>