[show abstract][hide abstract] ABSTRACT: APA (aminopeptidase A; EC 220.127.116.11) is a membrane-bound zinc metallopeptidase, also activated by Ca2+, involved in the formation of brain angiotensin III, which exerts a tonic stimulatory action on the central control of blood pressure in hypertensive animals. In the present study, in the three-dimensional model of the ectodomain of mouse APA, we docked the specific APA inhibitor glutamate phosphonate, in the presence of Ca2+. The model showed the presence of one Ca2+ atom in an hydrophilic pocket corresponding to the S1 subsite in which the lateral chain of the inhibitor is pointing. In this pocket, the Ca2+ atom was hexaco-ordinated with the acidic side chains of Asp213 and Asp218, the carbonyl group of Glu215 and three water molecules, one of them being engaged in a hydrogen bond with the negatively charged carboxylate side chain of the inhibitor. Mutagenic replacement of Asp213 and Asp218 with a conservative residue maintained the ability of mutated APAs to be activated by Ca2+. However, the replacement by a non-conservative residue abolished this property, demonstrating the crucial role of these residues in Ca2+ binding. We also showed the involvement of these residues in the strict specificity of APA in the presence of Ca2+ for N-terminal acidic residues from substrates or inhibitors, since mutagenic replacement of Asp213 and Asp218 induced a decrease of the inhibitory potencies of inhibitors homologous with acidic residues. Finally, this led to the rational design of a new potent APA inhibitor, NI926 (Ki=70 nM), which allowed us to precisely localize Asp213 at the entrance and Asp218 at the bottom of the S1 subsite. Taken together, these data provide new insight into the organization and functional role of the APA S1 subsite and will allow the design of pharmacophore of the inhibitor, helpful for the development of a new generation of APA inhibitors as central-acting antihypertensive agents.