<p>The group of inhibitors known as Potassium Competitive Acid Blockers (PCABs) has become one of the main topics of current research into reducing gastric H,K-ATPase activity. The design of novel PCABs relies on structure-based drug design strategies that integrate structural data with molecular dynamics simulations. A key aspect in conventional molecular dynamics simulations is the assignment of residue charge states, since the local physicochemical environment influences the pKa of amino acids. This computational work investigates the impact of the protonation state of key residues on the interactions between PCABs and the gastric H,K-ATPase. The study focusses on Glu343, Glu795, and Glu820, from the cation binding cavity, and vonoprazan and tegoprazan; two chemically unrelated PCABs. The results show how protonation states generate changes in interactions, especially with the charged group of inhibitors. Simulations in which Glu343 or Glu795 were protonated showed that the charged secondary amine of vonoprazan could rotate freely, favoring hydrogen bonding with some of the glutamic residues deep within the pocket. In contrast, the positive charge of tegoprazan is located in the benzimidazole ring, a rigid and bulky structure, which moves away from the center of the cavity when Glu343 or Glu795 are protonated. The inspection of the ionization states of amino acids reveals the conformational flexibility of the protonated group of PCABs as pivotal for binding affinity and highlights the importance of considering the protonation state of protein residues before performing any conventional molecular dynamics simulations for drug design.</p> Graphical Abstract <p></p>