Integrated In Silico Analysis Reveals ABC Transporter ATP-Binding Protein as a Therapeutic Target in Helicobacter pylori

AlphaFold2 modeling produced a high-confidence structure containing a conserved nucleotide-binding pocket. Molecular docking identified 5′-fluorosulfonylbenzoyl-5′-adenosine (FSBA) as the highest-affinity ligand (−7.3 kcal mol^–1), outperforming ATP and verapamil. Triplicate 1 μs molecular dynamics simulations of apo and halo AAD06727.1 demonstrated stable rmsd, RMSF, radius of gyration, solvent-accessible surface area, hydrogen-bond occupancy, and principal component profiles, indicating preservation of structural integrity following ATP binding.

Comparative simulations with the human ABCA12 nucleotide-binding domain showed conserved global architecture while revealing distinct ligand-recognition characteristics. Together, these findings identify AAD06727.1 as a structurally stable, pathogen-specific ATP-binding protein that represents a promising candidate for future structure-guided anti-H. pylori drug development.