Discovery of Sesamolin as a Potential Anti- <i>Helicobacter pylori</i> Agent by Virtual Screening against the Essential Response Regulator HsrA with <i>In Vitro</i> Evaluation

<i>Helicobacter pylori</i> infects nearly half of the world's population and contributes to chronic gastritis, gastric cancer, and other gastrointestinal diseases. Upon diagnosis, antibiotic-based regimens are typically used for eradication. However, the increasing antibiotic resistance of <i>H. pylori</i> and the side effects of these medications highlight the need for safer and more effective alternatives, particularly those derived from natural products. In this study, by using high-throughput molecular docking, 12 commercially available potential HsrA inhibitors were screened out from 13,142 natural compounds in the TCMSP database for the first time. After evaluation of their binding-mode stability to HsrA by using molecular dynamics (MD) simulations and their minimum inhibitory concentration (MIC), sesamolin (<b>3</b>) and coptisine (<b>6</b>), exhibiting stable binding modes and strong anti-<i>H. pylori</i> activity, were selected, and their inhibitory effects on the DNA-binding activity of HsrA were further confirmed using electrophoretic mobility shift assay (EMSA). However, compound <b>3</b> bound HsrA with high affinity (<i>K</i> _D = 17.08 nM), approximately 23-fold stronger than compound <b>6</b> (<i>K</i> _D = 399.60 nM). Further RT-qPCR analysis demonstrated that compound <b>3</b> exerted regulatory effects stronger than those of <b>6</b> on HsrA-linked genes (<i>tlpB</i>, <i>flhA</i>), urease genes (<i>ureA</i>, <i>ureB</i>), and the oxidative stress gene (<i>sodB</i>; reported to inversely correlate with HsrA levels). Consistently, <b>3</b> showed a greater suppression of urea chemotaxis and a larger increase in superoxide dismutase (SOD) activity than <b>6</b>. Our investigation uncovered sesamolin, a common lignan found in sesame, which could be a potential anti-<i>H. pylori</i> compound by binding with HsrA and regulating the related key genes of <i>H. pylori</i>.