Modeling the pore structure of voltage-gated sodium channels in closed, open, and fast-inactivated conformation reveals details of site 1 toxin and local anesthetic binding

In this work molecular modeling was applied to generate homology models of the pore region of the Nav1.2 and Nav1.8 isoforms of human voltage-gated sodium channels. The models represent the channels in the resting, open, and fast-inactivated states. The transmembrane portions of the channels were based on the equivalent domains of the closed and open conformation potassium channels KcsA and MthK, respectively. The critical selectivity loops were modeled using a structural template identified by a novel 3D-search technique and subsequently merged with the transmembrane portions. The resulting draft models were used to study the differences of tetrodotoxin binding to the tetrodotoxin-sensitive Nav1.2 (EC50: 0.012 μM) and -insensitive Nav1.8 (EC50: 60 μM) isoforms, respectively. Furthermore, we investigated binding of the local anesthetic tetracaine to Nav1.8 (EC50: 12.5 μM) in resting, conducting, and fast-inactivated state. In accordance with experimental mutagenesis studies, computational docking of tetrodotoxin and tetracaine provided (1) a description of site 1 toxin and local anesthetic binding sites in voltage-gated sodium channels. (2) A rationale for site 1 toxin-sensitivity versus -insensitivity in atomic detail involving interactions of the Nav1.2 residues F385-I and W943-II. (3) A working hypothesis of interactions between Nav1.8 in different conformational states and the local anesthetic tetracaine.