Peptic ulcer disease, affecting up to 20% of the global population, poses a significant health challenge with limited treatment options due to side effects and inefficiency of existing drugs. Helicobacter pylori is a common gastric pathogen associated with multiple clinical syndromes, including cancer. Eradication rates of H. pylori remain suboptimal despite the progress made in the past few decades in improving treatment strategies. The low eradication rates are mainly driven by antibiotic resistance of H. pylori. Non-invasive molecular testing to identify patients with antibiotic-resistant H. pylori represents a promising therapeutic avenue, however, this technology currently remains limited by availability, costs, and lack of robust validation. This study explores the potential of penicillin-binding proteins (PBPs) as targets for peptic ulcer treatment. PBPs, critical for bacterial cell wall integrity, are inhibited by beta-lactam antibiotics, leading to bacterial vulnerability. Flavonoids, prominent in plants, exhibit antimicrobial and gastroprotective properties against peptic ulcers. Docking analysis of 35 phytochemicals from the Artocarpus plant against PBP (PDB code: 1QMF) revealed Artocarpin as a promising candidate (docking score: -148.24 Kcal/mol). Artocarpin exhibited interactions with key amino acids and demonstrated favorable in-silico pharmacokinetics, including high absorption and good drug-likeness. Additionally, Engeletin 5 and Rutin showed significant docking scores (−134.89 and −148.07 kcal/mol, respectively). Artocarpin, identified as a potential H. pylori inhibitor, presents a promising avenue for peptic ulcer treatment, warranting further exploration of its therapeutic application. This study contributes valuable insights into the molecular interactions of phytochemicals with PBPs, paving the way for novel and effective approaches in peptic ulcer therapy.