Protonation state of inhibitors determines interaction sites within voltage-gated sodium channels

Abstract

Voltage-gated sodium channels are essential for carrying electrical signals throughout the body, and mutations in these proteins are responsible for a variety of disorders, including epilepsy and pain syndromes. As such, they are the target of a number of drugs used for reducing pain or combatting arrhythmias and seizures. However, these drugs affect all sodium channel subtypes found in the body. Designing compounds to target select sodium channel subtypes will provide a new therapeutic pathway and would maximize treatment efficacy while minimizing side effects. Here, we examine the binding preferences of nine compounds known to be sodium channel pore blockers in molecular dynamics simulations. We use the approach of replica exchange solute tempering (REST) to gain a more complete understanding of the inhibitors' behavior inside the pore of NavMs, a bacterial sodium channel, and NavPas, a eukaryotic sodium channel. Using these simulations, we are able to show that both charged and neutral compounds partition into the bilayer, but neutral forms more readily cross it. We show that there are two possible binding sites for the compounds: () a site on helix 6, which has been previously determined by many experimental and computational studies, and () an additional site, occupied by protonated compounds in which the positively charged part of the drug is attracted into the selectivity filter. Distinguishing distinct binding poses for neutral and charged compounds is essential for understanding the nature of pore block and will aid the design of subtype-selective sodium channel inhibitors.

Protonation underlies tonic vs. use-dependent block

“…Overall, the results by Buyan et al (17) provide accurate predictions about the binding mode of pore blockers and, for the first time, mechanistic insight about the differences between tonic and use-dependent blockers. Taken together, these predictions will help to design novel pore binders and to predict their behavior in future experiments.…”

“…Buyan et al (17) show that the results are robust with respect to the choice of the molecule (they consider three perpetually neutral and three titrable molecules) and are consistent for two VGSCs: one prokaryotic (NavMs) and the other eukaryotic (NavPas). Importantly, the novel binding site can explain the halogen electronic density measured by Bagnéris et al (18) by cocrystallizing NavMs with PF-5215786.…”

“…In PNAS, Buyan et al (17) provide a rigorous and systematic exploration of the binding of six molecules known to act as sodium channel pore blockers. The authors use molecular dynamics simulations in connection with an enhanced sampling technique to exhaustively explore the conformational space of the drug molecule.…”

Mechanism of non-blocking inhibition of sodium channels revealed by conformation-selective photolabeling

“…As for the location, in silico docking revealed that unlike other sodium channel inhibitor molecules, riluzole was preferentially located within the fenestrations, and tended to avoid the central part of the pore or the vicinity of the selectivity filter, where it could interfere with conduction. Localization within the fenestration has been previously observed in molecular dynamics simulations investigating the general anesthetic isoflurane 24 and propofol 25 , as well as the local anesthetic benzocaine [26][27][28] and lidocaine (neutral form) 29 , but it has never been found to be the dominant position. The unusual location predicted by in silico docking is supported by the way riluzole acted in experiments.…”

Molecular charge associated with antiarrhythmic actions in a series of amino-2-cyclohexyl ester derivatives

“…Sodium channel pores are small in diameter (~4.1 Å), water-filled (Courtney, 1987;Payandeh et al, 2011) and narrow toward the selectivity filter (Heinemann et al, 1992;Favre et al, 1996) suggesting sodium channel pores "restrict" drug blockerbinding interactions. Recently, Buyan et al (2018) conducted a molecular dynamics examination of the binding of six compounds (three electrically neutral and three existing in neutral and positively charged forms at pH 7.0) that block sodium channels. While both forms partition into the lipid bilayer, findings suggest the existence of two possible binding sites.…”