Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel

Abstract

Voltage-gated sodium (Na v ) channels are important targets in the treatment of a range of pathologies. Bacterial channels, for which crystal structures have been solved, exhibit modulation by local anesthetic and anti-epileptic agents, allowing molecular-level investigations into sodium channel-drug interactions. These structures reveal no basis for the "hinged lid"-based fast inactivation, seen in eukaryotic Na v channels. Thus, they enable examination of potential mechanisms of use-or state-dependent drug action based on activation gating, or slower pore-based inactivation processes. Multimicrosecond simulations of Na v Ab reveal high-affinity binding of benzocaine to F203 that is a surrogate for FS6, conserved in helix S6 of Domain IV of mammalian sodium channels, as well as low-affinity sites suggested to stabilize different states of the channel. Phenytoin exhibits a different binding distribution owing to preferential interactions at the membrane and water-protein interfaces. Two drug-access pathways into the pore are observed: via lateral fenestrations connecting to the membrane lipid phase, as well as via an aqueous pathway through the intracellular activation gate, despite being closed. These observations provide insight into drug modulation that will guide further developments of Na v inhibitors.bacterial sodium channel | drug binding

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

“…(Jensen et al, 2012), have indeed revealed protein conformational changes relevant to activity, e.g. (Boiteux et al, 2014a; Boiteux et al, 2014b). …”

“…They have also uncovered the interplay between the protein and the lipid membrane via fenestrations in the pore domain. Importantly, they have revealed the distribution of lipids and lipophilic drugs around the channel pore domain and fenestrations, as well as key details of the interactions responsible for drug binding and pathways (Boiteux et al, 2014a; Boiteux et al, 2014b). The field of biomolecular simulation is therefore beginning to uncover the quantitative mechanisms of ion channel function and modulation, enabling future developments in drug discovery.…”

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

“…Nowadays, MD simulations are applied to many membrane proteins in realistic cellular membrane environments [33,34] to examine conformational dynamics on the time scale of microseconds [35,36]. Furthermore, MD-special supercomputers, Anton [37] or Anton2 [38], make it possible to reach even longer time scales up to milliseconds so that biologically relevant events can be sampled frequently in a single MD trajectory [39-42]. In spite of these advances, many phenomena in biomembranes are still difficult to be simulated by conventional all-atom MD simulations because of limited simulation time scales.…”

Structural Insights into the Atomistic Mechanisms of Action of Small Molecule Inhibitors Targeting the KCa3.1 Channel Pore

“…Rosetta has previously been successfully used to calculate gating charges (Khalili-Araghi et al, 2010), simulate voltagesensor movements (Decaen et al, 2008(Decaen et al, , 2009(Decaen et al, , 2011YarovYarovoy et al, 2012;Tuluc et al, 2016), construct open and closed state conformations of Kv channels (Yarov-Yarovoy et al, 2006a;Pathak et al, 2007), and model the interactions of scorpion toxins with voltage-gated Na 1 channels (Cestèle et al, 2006;Wang et al, 2011;Zhang et al, 2011Zhang et al, , 2012. More recently, Rosetta has been used to simulate the access and binding of local anesthetics and anticonvulsants to Na 1 channels (Boiteux et al, 2014), study the interaction of capsaicin with the TRPV1 channel (Yang et al, 2015), and rationally design a vanilloid-sensitive TRPV2 channel (Yang et al, 2016). Similarly, the KCa3.1 structural models we developed in our current study accurately identified key residues for binding of several small molecule probes and explain their atomistic mechanisms of action.…”