The Sodium Ion Binding Region at the Focus of P1 Helices Attracts both Charged and Electroneutral Ligands of Sodium Channels

Abstract

The inner pore of eukaryotic voltage-gated sodium channels is targeted by ligands of dramatically different chemical structures. These include organic cations such as a local anesthetic lidocaine and electroneutral drugs such as an anticonvulsant carbamazepine. Mutations of the critical phenylalanine residue in helix IVS6 and some other inner pore-facing residues are known to affect action of both charged and neutral ligands. The structural cause of this ligand-binding promiscuity of sodium channels is unclear. Here we used the X-ray structure of a prokaryotic sodium channel NavMs to model the pore domain of the Nav1.x channels. We further employed the Monte Carlo energy-minimization method to perform intensive docking of lidocaine and carbamazepine from thousands starting points in the inner-pore region. The sodium ion NaIII, which is located between the four backbone carbonyls at the C-ends of P1 helices and does not make direct contacts with the channel protein, attracted carbamazepine, but repelled lidocaine. Therefore we further docked electroneutral ligands (lamotrigine, carbamazepine, phenytoin, lacosamide and bisphenol A) and cationic ligands (lidocaine, QX-314, cocaine, quinidine, and sipatrigine) in the channel models, respectively, with and without NaIII. In our models all the ligands interacted with the phenylalanine residue in IVS6 and most of the ligands also interacted with the tyrosine residue in IVS6. Some ligands extended their moieties in the III/IV sidewalk (fenestration). The electroneutral ligands bound the sodium ion with their electronegative groups and lacosamide chelated this ion. The ligand-bound ion remained close to the NaIII position due to attraction to the pore-facing backbone carbonyls. The same region attracted the charged group of the cationic ligands. In the predicted binding modes even small-size ligands would block the ion permeation by the electrostatic and steric mechanisms. Our study proposes a common pharmacophore for the diverse ligands. It includes a cation (the ligand's ammonium group or the ligand-bound sodium ion) and an aromatic moiety, which are usually linked by four bonds. Supported by NSERC and RFBR.