Background: Helicobacter pylori, a gram-negative bacterium, is a notorious human pathogen responsible for chronic gastritis, peptic ulcers, and gastric cancer. Given its prevalence worldwide and the serious health implications associated with its infection, there is a crucial need for effective therapeutic strategies. This study focused on the physicochemical properties analysis of ligands using Lipinski rules of five, essential in drug development. Additionally, the examination of protein-ligand interactions with virtual screening and molecular docking provides insights into potential antibacterial agents. The inclusion of bioactive compounds derived from marine sponges, have potentials for its broad-spectrum antibacterial activities, highlights its potential against thymidylate synthase, a crucial enzyme for bacterial DNA replication. Methods: The physicochemical properties analysis involves Lipinski's criteria and utilizes the PubChem database. The preparation of the receptor for molecular docking includes crucial steps to ensure the appropriateness of the protein structure. Virtual screening and molecular docking are conducted using PyRx Tools software, offering a comprehensive understanding of the interactions between ligands and the thymidylate synthase receptor. Results: Physicochemical properties analysis revealed adherence to Lipinski rules for a majority of ligands. The examination of protein ligand interactions, especially with norlichexanthone, demonstrated promising antibacterial activity. The study contributed valuable insights into potential alternative treatments for Helicobacter pylori infections. Conclusion: Norlichexanthone's favorable binding affinity to thymidylate synthase, its broad-spectrum antibacterial activity, and potential for reduced side effects position it as a compelling candidate for further development as an alternative treatment option against H. pylori. The study emphasizes the urgency of finding effective therapeutic interventions and encourages future research for in-depth validation in vivo and clinical settings.