Structural Basis for Pharmacology of Voltage-Gated Sodium and Calcium Channels

Abstract

Voltage-gated sodium channels initiate action potentials in nerve, muscle, and other electrically excitable cells. Voltage-gated calcium channels are activated by depolarization during action potentials, and calcium influx through them is the key second messenger of electrical signaling, initiating secretion, contraction, neurotransmission, gene transcription, and many other intracellular processes. Drugs that block sodium channels are used in local anesthesia and the treatment of epilepsy, bipolar disorder, chronic pain, and cardiac arrhythmia. Drugs that block calcium channels are used in the treatment of epilepsy, chronic pain, and cardiovascular disorders, including hypertension, angina pectoris, and cardiac arrhythmia. The principal pore-forming subunits of voltage-gated sodium and calcium channels are structurally related and likely to have evolved from ancestral voltage-gated sodium channels that are widely expressed in prokaryotes. Determination of the structure of a bacterial ancestor of voltage-gated sodium and calcium channels at high resolution now provides a three-dimensional view of the binding sites for drugs acting on sodium and calcium channels. In this minireview, we outline the different classes of sodium and calcium channel drugs, review studies that have identified amino acid residues that are required for their binding and therapeutic actions, and illustrate how the analogs of those key amino acid residues may form drug-binding sites in three-dimensional models derived from bacterial channels.

Graphical abstract

Fig. 1.

Structure of voltage-gated sodium channels. (A) A transmembrane folding diagram of the Na_V1.2 channel. Cylinders represent α-helical segments. Bold lines represent the polypeptide chains of each subunit, with a length approximately proportional to the number of amino acid residues in the brain sodium channel subtypes. The extracellular domains of the β1 and β2 subunits are shown as immunoglobulin-like folds. Ψ, sites of probable N-linked glycosylation; P in red, sites of demonstrated protein phosphorylation by protein kinase A (circles) and protein kinase C (diamonds); blue, pore-lining segments; yellow circles, the outer (EEEE) and inner (DEKA) rings of amino residues that form the tetrodotoxin-binding site and ion selectivity filter; green, S1–S4 voltage sensors; h in blue circle, inactivation particle in the inactivation gate loop; blue circles, sites implicated in forming the inactivation gate receptor. ScTx, scorpion toxin. (B) Model of the local anesthetic receptor site in mammalian Na_V1.2 channels. (C) Side view of Na_VAb channels colored according to (A): voltage-sensing module (green); pore module (blue); S4-S5 linker (red). (D) Side view of the ion selectivity filter. Glu177 (purple) interactions with Gln172, Ser178, and the backbone of Ser180 are shown in the far subunit. F_o-F_c omit map, 4.75 σ (blue); putative cations or water molecules (red spheres, ion_EX). Electron-density around Leu176 (gray; F_o-F_c omit map at 1.75 σ) and a putative water molecule is shown (gray sphere). Na⁺-coordination sites: site_HFS, site_CEN, and site_IN. (E) Architecture of the Na_VAb pore: Glu177 side chains (purple) and pore volume (gray). The S5 and S6 segments and P loop from two lateral subunits are shown.

Fig. 2.

Drug-binding sites and fenestrations in NavAb. (A) Side view through the pore module illustrating fenestrations (portals) and hydrophobic access to central cavity. Phe203 side chains are yellow sticks. Surface representations of Na_VAb residues aligning with those implicated in drug binding and block: Thr206 (blue), Met209 (green), and Val213 (orange). Membrane boundaries are gray lines. Electron-density from an F_o-F_c omit map is contoured at 2.0 σ. (B) Top view sectioned below the selectivity filter colored as in (A). (C) Structure of the drug-binding site in the slow-inactivated state in Na_VAb.

Fig. 3.

Amino acid side chains in the local anesthetic–binding site of NavAb. (A) Amino acid residues identified by mutagenesis of mammalian sodium channels and shown to be important in the drug block are illustrated as orange spheres. Helices S5 and S6 and the pore domain are depicted in a side view of the preopen state of NavAb. (B) Similar view to (A) showing the slow-inactivated state of NavAb. (C) NavAb is shown from the extracellular side. The S5 and S6 segments are shown as cylinders. Amino acid residues identified by mutagenesis of mammalian sodium channels and shown to be important in the drug block are illustrated as orange spheres. (D) Similar view to (C) showing the inactivated state of NavAb.

Fig. 4.

Amino acid side chains in the phenylalkylamine-binding site. (A) Top view of the pore module of CavAb in the preopen state, with amino acid side chains analogous to those implicated in phenylalkylamine binding illustrated in green and amino acid side chains specific for dihydropyridine illustrated in blue. (B) Side view of CavAb in the slow-inactivated state, with amino acid side chains analogous to those implicated in phenylalkylamine binding illustrated in green. (C) Top view of CavAb pore module in the preopen state, with the S5 and S6 segments illustrated as cylinders and amino acid side chains analogous to those implicated in phenylalkylamine binding illustrated in dark green for Ca_V1.2-specific residues and in light green for Ca_V-conserved residues. (D) Similar view to (C) of the inactivated state.

Fig. 5.

Amino acid side chains in the dihydropyridine-binding site. (A) Side view of intact CavAb in the preopen state with the two voltage-sensing domains illustrated in dark gray and the intervening pore domain illustrated in light gray. Amino acid side chains analogous to those implicated in dihydropyridine binding are illustrated in dark blue for Ca_V1.2-specific residues and in light blue for Ca_V-conserved residues. (B) Side view of CavAb in the slow-inactivated state, with amino acid side chains analogous to those implicated in dihydropyridine binding illustrated in blue. (C) Top view of the pore domain of CavAb in the preopen state, with amino acid side chains analogous to those implicated in dihydropyridine binding illustrated in blue. (D) Top view of the pore domain of CavAb in the slow inactivated state, with amino acid side chains analogous to those implicated in dihydropyridine binding illustrated in blue.