In Silico exploration for potent phytochemicals targeting Helicobacter pylori: assessment of ADMET profiles and molecular docking analysis

Treatment of Helicobacter pylori (H. pylori) infections faces challenges such as drug adherence, drug resistance, and re-infection. Surface antigens like BabA and SabA cause the disease, while phytochemicals like glycyrrhizin and cinnamaldehyde in liquorice and cinnamon are highly absorbed by H. pylori. Other molecules like coumarin can disrupt H. pylori adherence. Optimizing pharmacokinetics of certain drugs remain a challenge. Plant-derived chemical compounds can overcome treatment restrictions using molecular docking research, drug compatibility, and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) examinations. These tools help to determine the appropriate usage of phytochemicals in bacteria. Our work aims to explore the potential of phytochemicals (glycyrrhizin, cinnamaldehyde, coumarin) as a treatment for H. pylori disease using molecular docking (BabA, SabA, CagA, VacA and urease) and ADMET analysis by in silico approaches. Glycyrrhizin has the most favorable binding energies with both CagA (− 8.9 kcal/mol) and VacA (− 8.4 kcal/mol), indicating stable interactions. Cinnamaldehyde and coumarin show weaker binding energies, suggesting less stability. Amoxicillin and clarithromycin showed moderate binding energy. Glycyrrhizin, cinnamaldehyde, and coumarin showed non-toxicity in assays, while amoxicillin and clarithromycin displayed toxicity, underscoring the importance of thorough safety assessments in drug development by ADMET study. Compounds meeting Lipinski's Rule of Five criteria, including cinnamaldehyde and coumarin, demonstrate potential for good oral bioavailability. Despite these difficulties, substances like coumarin, glycyrrhizin, and cinnamondehyde can be useful in the treatment of H. pylori. In-depth safety evaluations and continuous research are essential for improving medication development and promoting more effective H. pylori treatment.