Ligand Docking to the Acidic Pocket of the Proton-Gated Ion Channel Asic1A

Abstract

In this study, we performed the docking of ligands of the ASIC1a ion channel, which exert potentiating or inhibitory effects by stabilizing the open and closed states, respectively. It is shown for the first time that the direction of effect may depend on the three-dimensional structure of the ligand. Potentiators and inhibitors differently interact with the amino acid residues of the so-called “acidic pocket,” where the binding of protons takes place. These results open up an opportunity for theoretical design of new pharmaceuticals.