Abstract
In the Nav channel family the lipophilic drugs/toxins binding sites and the presence of fenestrations in the channel pore wall are well defined and categorized. No such classification exists in the much larger Kv channel family, although certain lipophilic compounds seem to deviate from binding to well-known hydrophilic binding sites. By mapping different compound binding sites onto 3D structures of Kv channels, there appear to be three distinct lipid-exposed binding sites preserved in Kv channels: the front and back side of the pore domain, and S2-S3/S3-S4 clefts. One or a combination of these sites is most likely the orthologous equivalent of neurotoxin site 5 in Nav channels. This review describes the different lipophilic binding sites and location of pore wall fenestrations within the Kv channel family and compares it to the knowledge of Nav channels.
Introduction
Voltage-gated ion channels are transmembrane proteins that are selectively permeable to physiological important ions such as Na+, K+, Ca2+, and Cl-. Under influence of the membrane potential (Vm) these channels change their conductance. In the conductive open (or activated) state, ions flow down their electrochemical gradient through the channel pore. The flux of these ions elicits an electrical current that directly influences the Vm. For voltage-gated sodium and potassium channels (Nav and Kv), the main focus of this review, the Vm will shift towards the ion's equilibrium potential, which under normal conditions is depolarizing and repolarizing, respectively (). Although Nav and Kv channels differ in selectivity from one another, their structure is quite similar. However, a main difference is that Nav channels are characterized by one large α-subunit containing four recognizable domains (DI–IV), whereas Kv channels are formed by tetramerization of four individual α-subunits. In both cases, these four entities comprise six transmembrane segments (S1–S6), which are divided into a voltage sensing domain (VSD, S1–S4) and a pore-forming domain (PD, S5–S6) that are connected by the S4–S5 linker. The four PDs assemble into the ion permeation pathway (or pore) that is surrounded by four VSDs. In the non-conductive closed (or deactivated) state, ion permeation is prevented by the intracellular activation gate, located at the point where the four S6 helices cross. The aperture-like opening and closure of this gate is controlled by the VSD (; ; ; ). The main component of the VSD is the S4 segment that physically moves in response to a change in Vm, due to the presence of positively charged residues (arginine and lysine) that detect changes in the membrane electric field (). The S4–S5 linker is a component of the electro-mechanical coupling that translates S4 movements into opening or closing of the activation gate (; ). After opening, fast inactivation occurs in Nav and in some Kv channels, which is caused by the physical occlusion of the pore by an inactivation particle. For Nav channels this inactivation particle is the linker between DIII and DIV, while in Kv channels it is located at the N-terminus of each subunit, hence termed N-type inactivation (; West et al., 1992; ). Alternatively, Kv channel inactivation can occur via the slower C- or U-type inactivation mechanism that makes the channels non or less conductive (; ; ).
Binding of drugs/toxins to Nav and Kv channels may alter the activation, deactivation, and/or inactivation process(es), which may cause or alleviate aberrant electrical excitability. Therefore, knowledge about the different binding sites is key for drug development and pharmacovigilance. The binding sites for these drugs/toxins are well defined and categorized within the Nav channel family, as opposed to the much larger Kv channel family. Most binding sites are enveloped by water, locating either inside or outside the channel's pore. However, some compounds bind to a site(s) that does not fit any of the hydrophilic binding sites. For instance, brevetoxins and ciguatoxins bind to a conserved hydrophobic site within the Nav channel family, termed neurotoxin site 5 (; ). For the Kv channel family no such site has been described, but certain compounds have been shown to deviate from binding to hydrophilic binding sites like; retigabine, gambierol, psora-4, polyunsaturated fatty acids (PUFAs), ICA-compounds (Vennekamp et al., 2004; ; ; ). It is notable that these are rather lipophilic compounds and there has been, and still is, a growing interest in such compounds for their use in treating neurological disorders (e.g., as anti-convulsant).
So, is there a unifying picture of the lipid exposed/accessible drug/toxin binding sites within the large Kv channel family and even between Kv and Nav channels? Several lipophilic binding sites have been described in different Kv channels, while in fact some may converge to just one binding region preserved between Kv channel (sub)families. In this review, the well-documented Nav lipophilic binding sites, neurotoxin site 2, site 5, and the access to the local anaesthetic (LA) binding site within the pore through fenestrations is compared to what has been reported for Kv channels.
Voltage-Gated Sodium Channels
The Nav channel family contains nine isoforms (Nav1.1 to Nav1.9) that display a high sequence homology, especially within the transmembrane segments (; ). This facilitated the categorization of drug/toxin binding sites within the Nav channel family. Over the past decades a detailed picture emerged on where compounds bind within these channels and resulted in a well-documented classification of seven different sites (site 1 to 7) and a LA binding site (Stevens et al., 2011; ). As the focus of this review is on the binding sites that involve lipid soluble and/or transmembrane binding compounds only binding site 5 and site 2 will be briefly discussed. The LA binding site is also mentioned as some compounds can reach their binding site via hydrophobic fenestrations in the pore wall of the channel protein. To maintain an orderly overview, all Nav residues are numbered according to the Nav1.4 channel when possible. In case the sequence could not be aligned, as for bacterial Nav structures, it will be noted and the original numbering is maintained.
The Closed State Accessible LA Binding Site: Pore-Accessibility Through Channel Fenestrations
LA compounds and anti-arrhythmic drugs inhibit Nav channels by occlusion of the pore. Most LA compounds have a similar structure consisting of a tertiary hydrophilic amine domain (head) linked with an aromatic hydrophobic ring domain, with a total length of 10–15Å (). Three types of block can be observed. First type is the use dependent open state block, or high affinity block, which occurs after channel opening and LA compounds enter the pore via the intracellular side (; ; ). The second type is flicker block, or fast block, which is only observed when the channel's inactivation process is modulated. For example, by other compounds such as batrachotoxin (BTX) (CAS No.:23509-16-2) that binds at site 2 (; Uehara and Moczydlowski, 1986; Zamponi et al., 1993). The third and least common type is the resting or hydrophilic block that establishes when the channel is closed. LA compounds are thought to enter the ion conductive pore and find their binding site trough fenestrations in the lipid exposed part of the PD (). LA compounds are protonated but for crossing the cell membrane they need to be deprotonated. This is possible when their pKA value is close to the physiological pH values in the extracellular environment. After traversing the cell membrane the compounds are protonated again to exert their pharmacological effect (). As the binding site is located within the pore, block occurs with the highest affinity when the channel is opened or used, while applying frequent channel activating stimuli. Two residues within the S6 of domain four (DIV-S6) have been identified to be important for LA binding/modulation, namely, F1586 and Y1593, (Nav1.4 numbering). F1586 probably binds to the alkylamino head, while Y1593 interacts with the aromatic ring structure (Ragsdale et al., 1994; Yarov-Yarovoy et al., 2002) (Figures 1A, B). As these residues reside within the pore and certain compounds display closed state block, this requires a hydrophobic pathway to the binding site when the channel gate is closed ().
Figure 1
These pathways, or fenestrations, in the lipid exposed part of the PD were first observed in the crystal structure of bacterial Nav channels such as NavAb (Payandeh et al., 2011; Payandeh et al., 2012), NavMs () and NavRh (Zhang et al., 2012). It should be noted that bacterial Nav channels are constructed out of four separate α-subunits instead of one large subunit. For the bacterial Nav channels, four fenestrations are observed between the different domains where the radius of the fenestration varies from 0.8Å minimally to 2.59-2.83Å (). Nonetheless, these fenestrations are wide enough for small LA compounds and anti-arrhythmic drugs to pass. The narrowest point in the fenestration, termed “bottleneck”, is created by the amino acid residues M174, T175, F203, T206, and M209 (NavAb numbering), with F203 being the most important residue (Figure 1C). These amino acids will sterically hinder the passage of compounds through the fenestration. Mutation of F203 to an alanine increased the size of the fenestration allowing easier access of flecainide (CAS No.:54143-55-4, polar surface area=59.6Å) to its binding site within the pore, with as result an increased tonic, closed state, block (). The mutation did not affect lidocaine block as this compound is smaller (polar surface area=32.3Å) and can easily traverse the wild type fenestration (). The F203W mutation on the other hand reduces fenestration size and consequently the access of both lidocaine and flecainide is reduced, decreasing tonic block (). Computational modelling using the Nav1.4 3D structure resulted in the observation of four fenestrations just as in bacterial Nav channels, with the exception that the size of two out of the four fenestrations seemed inadequate for compound access, namely the fenestration constructed by DII–DIII and DIV–DI (). Fenestrations in between DI-DII and DIII-DIV seemed sufficiently wide for compounds to cross (Figure 1C). The bottleneck of these fenestrations is formed by residues N790, L438, and M786 for the fenestration between DI-DII and by I1582, I1583, and F1586 (if rotated) for the fenestration between DIII-DIV. These fenestrations lining residues, are well conserved in the different Nav channel isoforms. Mutating DIV-S6 residue I1582 appeared to create an extra pore access pathway (Ragsdale et al., 1994) and allowed the external blocker QX314 (CAS No.:24003-58-5, polar surface area: 29.1Å), which is a charged LA compound at physiological pH and therefore not able to traverse the membrane, to access the LA binding site when added in the extracellular environment (Sunami et al., 2001).
Apart from LAs that have a distinct binding site, sevoflurane (CAS No.: 28523-86-6), an inhalational anaesthetic, has a more complex binding profile. Sevoflurane binding results in a decrease of the peak sodium current, a hyperpolarised shift in the voltage dependence of inactivation and a slowing of the recovery from inactivation (; Ouyang et al., 2009). Within the bacterial sodium channel NaChBac, binding regions have been located at the pore region, selectivity filter, and the S4–S5 linker/S6 interface (Ouyang et al., 2007; Raju et al., 2013). MD simulations suggested that the binding of sevoflurane to the selectivity filter and the S4–S5 linker occurs mainly when the channel is in the activated/open state, while in the closed state the channel gate and the VSD are targeted (). A state independent binding site is possibly the central cavity that is accessed by the fenestrations. Residues T220 and F227 (NavChBac numbering) are proposed to be responsible for sevoflurane binding in the central cavity, which are the homologue residues for LA binding in Nav1.4 (F1764, Y1771).
Binding Site 2 Compounds, Though Being Lipophilic, Bind to the Inner Pore
Compounds binding at site 2 of the Nav channel include batrachotoxin (; ), grayanotoxin (Yuki et al., 2001; ), CAS No.: 54781-61-2), and alkaloids from plant such as veratridine (Ulbricht, 1969; Sutro, 1986), CAS No.:71-62-5), aconitine and mesaconitine (; ) (CAS No.: 302-27-2). All these compounds are lipid soluble and need to traverse the cell membrane before influencing the channel in a use-dependent manner, comparable to the action of LA compounds (; ; ; ; Sutro, 1986; ; ; Yuki et al., 2001; Wang and Wang, 2003). Their effects can be a combination of: (1) a hyperpolarised shift of the voltage dependence of activation, (2) inhibition of the fast inactivation process, leading to persistent sodium currents, (3) decrease in ion conductance, and/or (4) decrease of the Na+ selectivity. The location of binding site 2 is thought to be at the S6 of all four domains and to overlap with the LA binding site or at least allosterically hinder LA binding.
To describe neurotoxin site 2 in more detail, we focus on the most potent site 2 toxin reported to date, batrachotoxin (BTX) a steroidal alkaloid indirectly produced by the South-American poison dart frogs of the genus Phyllobates (). Binding of BTX is highly irreversible and only possible when the channel is in its activated open state (; ). BTX shifts the voltage dependence of channel activation by approximately −40 mV toward more hyperpolarized potentials (), reducing the channel's ion conductance and selectivity. BTX also reduces the affinity for LA, which is thought to be caused by non-competitive antagonism (i.e., allosteric effect) because of overlapping binding sites as BTX and LA share the binding residue F1586 (). Residue mutations affecting BTX in Nav1.4 were first described in DI-S6 and DIV-S6: I439K, N440K, L443K, F1586K, and N1591K, respectively (Wang and Wang, 1998; Wang and Wang, 1999). Afterwards the DIII-S6 residues Ser1283 and leu1287 were identified (Wang et al., 2000) and finally DII-S6 residues N790 and L794 (Wang et al., 2001). All these residues line the inside of the pore (Figure 2). Non-pore lining residues involved in BTX sensitivity locate at the putative hinge region of the channel gate, Gly1282 and Phe1284, respectively (). While Phe1284 is important for the stabilisation of the ammonium group of BTX, Gly1282 is not a direct binding receptor for BTX and mutations of this residue affect binding allosterically by changing the channels gating properties. Modeling studies suggest that BTX binds to the pore but does not completely prevent ion conduction because of its “horseshoe-like” structure (). Only upon mutation of DII-S6 N790 BTX becomes a full blocker (Wang et al., 2007).
Figure 2
Binding Site 5 Locates Between DIS6 and DIVS5
Some of the toxins that bind to site 5 of Nav channels are brevetoxins (; Poli et al., 1986) and ciguatoxins (; ), both originate from marine dinoflagellates (Gambierdiscus toxicus) and are structurally comparable. Brevetoxins are produced by unarmoured marine dinoflagellates (e.g., Karenia brevis, Gymnodinium breve, or Ptychodiscus brevis). Ingestion of these toxins can lead to poisoning and death of marine animals and cause the disease neurotoxic shellfish poisoning in humans (; ). Eleven different brevetoxins have been discovered today with brevetoxin A (PbTX1, CAS No.:98112-41-5) and brevetoxin B (PbTX2 and 3, CAS No.:79580-28-2 and 85079-48-7) being the most investigated ones. These toxins are about 30Å in length, 6Å in width, and 6Å high. They are composed of four recognizable parts: a lactone ring (the head) linked with a linker to a multiple carbon ring (the tail) ending in a rest-group (). While the head is responsible for the effect, without the linker and the tail the toxin cannot modulate the channel as it allows the head region to reach its binding site (Rein et al., 1994). PbTX binds to the Nav channel at the DI-S6, DIV-S5, and DIV-S6 segments (Trainer et al., 1991; Trainer et al., 1994; ). The region spans within DI-S6 from Ala418/Thr422 to Lys465/Lys477 and within DIV-S5 from Glu1510 to lys1557 with possible extension to Lys1565 (Figure 3). The tail of the molecule will be situated at the S5–S6 extracellular loop while the head is able to reach, due to the long linker and tail region, the inactivation gate at the intracellular side of the channel (Trainer et al., 1991; Trainer et al., 1994). Interaction of the head with the inactivation gate reduces channel inactivation, leading to a persistent sodium current (Sheridan and Adler, 1989; Schreibmayer and Jeglitsch, 1992).
Figure 3
Like brevetoxins, ciguatoxins (CTX) bind at site 5 and their effects are consequently similar. Ciguatoxins are classified based on their geographic origin, with P-CTX (
Voltage-Gated Potassium Channels
The Kv channel family is impressively large compared to this of Nav channels, due to an extensive library of genes encoding different α-subunits that in some subfamilies can “mix-and-match” to form functional Kv channels. Additionally, alternative splicing, RNA editing, and post-translational modification further expand on the Kv channel family (
Extracellular and Intracellular Exposed “Hydrophilic” Binding Sites
The well-documented Kv channel binding sites can be topologically located on the intracellular or extracellular side of the channels. Extracellularly the most well-known conserved binding sites are those of the pore blockers and VSD targeting gating modifiers, while intracellularly the inner pore block is the most notable one (Wulff et al., 2009). Certain toxins from a variety of venomous animals target the extracellular binding sites. For example, scorpion toxins like charybdotoxin (CTX, CAS No.: 95751-30-7) and agitoxin (AgTx, CAS No.: 168147-41-9) target the water enveloped extracellular mouth of Kv channels, thereby physically occluding the permeation pore (
Lipid Embedded “Hydrophobic” Binding Site(s) and Pore Wall Fenestrations in the Shaker-Type Kv Family, Kv7 Family, and Kv10.1/Kv11.1 Channel
The next part reviews the potential lipophilic binding sites and pore wall fenestrations in different Kv channel types. To define the binding site(s) of certain compounds, the PD is divided into a “front side” and “back side”. Residues of the front side point towards the VSD of the same α-subunit, while residues of the “back side” point in the opposite direction, thus towards the VSD of a neighboring α-subunit (Figures 4D, 5D and 6C).
Figure 4

Lipid-exposed binding sites within the crystal structure of a Kv1.2–Kv2.1 paddle chimera channel (PDB: 2R9R). (A) Sequence alignment of part of the PD (S5-S6 segment) of Kv1.2-2.1, Kv1.2, Kv1.5, and Kv3.1, with Kv1.2-2.1 as reference. Residues important for gambierol and psora-4 action are highlighted in blue and yellow respectively. (B) Sequence alignment of the S3–S4 segments of Kv1.2–2.1 and shaker, with Kv1.2–2.1 as reference. Highlighted in green are the residues important for PUFA action. (C) Schematic visualization of one Kv channel α-subunit consisting out of six transmembrane segments (1–6) and a pore helix (PH). In blue the residues important for gambierol binding (L327, F330, and T397 according to Kv1.2–2.1 numbering) and in yellow those for psora-4 binding (L327, F329, F330, I333, L337, F338, I392, T397, and L400). Residues important for PUFA interaction are shown in green (V268, R287, V288, and L272). (D) Schematic visualization of the pore domain of the Kv1.2–Kv2.1 channel. Four pore-forming domains tetramerize to form the channel pore. The blue and yellow circle highlights the proposed gambierol/psora-4 binding site regions on the front- and/or backside of the pore-forming domain, respectively. (E) Side view of the Kv1.2–Kv2.1 channel with the front and back subunit omitted for clarity. Residues involved in gambierol and psora-4 interaction are shown in blue (L327, F330, and T397) and yellow (I392, T397, and L400), respectively. The PUFA action site is visualized in green (V268, R287, V288, and L272). (F) Top view of the Kv1.2–Kv2.1 channel, with each α subunit named α1–α4. Residues involved in gambierol and psora-4 interaction are shown in blue (L327, F330, and T397) and yellow (I392, T397, and L400), respectively. In green the PUFA action site comprising residuesV268, R287, V288, and L272. Kv1.2–Kv2.1 crystal structure (PDB: 2R9R) (
Figure 5

Lipid-exposed binding sites within a homology model of the Kv7.2 channel based on the 3D structure of Kv7.1 (PDB: 5VMS). (A) Sequence alignment of part of the PD of Kv7.1–Kv7.5, with Kv7.2 residue numbering. Highlighted in red and purple are the residues important for RTG and zinc pyrithione action, respectively. (B) Sequence alignment of the S3-S4 segment of Kv7.2, Kv7.4, and Kv7.5, with Kv7.2 as reference. Highlighted in green is the residue important for ICA73 action. (C) Schematic visualization of one Kv7 channel α-subunit consisting out of 6 transmembrane segments (1–6) and a pore helix (PH). Location of the residues involved in the interaction of Kv7.2 with retigabine are represented in red. Represented in purple are residues important for zinc pyrithione action). The residue important for ICA73 interaction is shown in green. (D) Schematic visualization of the PD of Kv7.2. The red and purple circle highlight the proposed retigabine/zinc pyrithione binding site on either the front- or back-side of the PD pore-forming domain, respectively. (E) Side view of Kv7.2 with the front and back subunit omitted for clarity. Residues involved in retigabine and zinc pyrithione interaction are shown in red (W236, L243, L299, and G301) and purple (L249 and L275), respectively. In green the ICA73 action site is visualized (A181). (F) Top view of Kv7.2, with each α subunit named α1–α4. Residues important for retigabine, zinc pyrithione, and ICA73 action are shown in red (W236, L243, L299, and G301), purple (L249 and L275), and green (A181), respectively. Shown Kv7.2 structure is a homology model of the 3D structure of Kv7.1 (PDB: 5VMS) (Sun and Mackinnon, 2017), generated with SWISS-MODEL (Waterhouse et al., 2018) and visualized using chimera software (Pettersen et al., 2004). The amino acid sequences are aligned using Jalview (Waterhouse et al., 2009).
The Shaker-Type Kv Channel Family
Whereas gambierol does not modulate Nav channels, it is capable of inhibiting Kv1 and Kv3 channels (
On the other hand, psora-4 (CAS No.: 724709-68-6), a potent inhibitor of Kv1.3, has been shown to predominantly bind to the back side of the PD (Figure 4) (Vennekamp et al., 2004;
The inhalation anaesthetic, sevoflurane, seems to bind within the central cavity and to a similar hydrophobic pocket as psora-4 (Stock et al., 2018). Apart from these binding regions, the polar lipophilic molecule has been shown to interact with the S4–S5 linker, pore helix, segment S6, and even the VSD, likewise to the many binding regions of sevoflurane on the Nav channel (
PUFAs are charged lipophilic compounds that position at the lipid membrane interface, although in small quantities (Yazdi et al., 2016). Nonetheless, PUFAs may play an important role in the treatment of arrhythmias and epilepsy, due to their modulating effect on, but not limited to, voltage-gated ion channels (
The Kv7 Family
The well characterized retigabine (RTG, CAS No.: 150812-12-7) binding site is localized between the front side of one PD and the back side of an adjacent PD of Kv7.2–Kv7.5 (KCNQ2-5) channels (Figure 5) (Schenzer et al., 2005;
The hydrophobic pocket of the RTG binding site also seems to be able to accommodate endogenous hydrophilic neurotransmitters like γ-aminobutyric acid (GABA), which directly activates Kv7.3 and Kv7.5 via W236. In contrast to RTG, GABA does not readily cross the plasma membrane to reach its site of action. Based on the Kv1.2–Kv2.1 paddle chimera structure the tryptophan also seems to be accessible from the extracellular side (
ICA-compounds (ICAgen, Durham, NC, US), which are benzanilide Kv7 channel openers, were developed as RTG alternatives (
PUFAs have also been described to electrostatically affect Kv7.1 channels, resulting in a negative shift of the conductance-voltage curve. This modulation of Kv7.1 channels by PUFAs is similar to what has been described for shaker Kv channels (
The hERG (Kv11.1) and EAG (Kv10.1) Channel
The human ether-a-go-go related gene (hERG) type 1 encodes for the Kv11.1 channel, which functions as the rapid component of the delayed rectifier K+ current contributing to the repolarization of cardiac action potentials (Vandenberg et al., 2012). Alteration of the native functioning of Kv11.1 channels, either genetically or pharmacologically, can disrupt this repolarization, leading to various cardiac rhythm disorders (Thomas et al., 2006). Furthermore, the role of Kv11.1 is not limited to the heart, as it also seems to play a role in the central nervous system, digestive, secretory, and reproductive system, and even cancer (
Figure 6

Lipid-exposed binding site(s) within the cryo-EM structure of the Kv11.1 (hERG) channel (PDB: 5VA1). (A) Sequence alignment of part of the PD of Kv11.1 and Kv10.1, with Kv11.1 residue numbering. Highlighted in pink and blue are the residues important for ICA74 and PD57 action, respectively. (B) Schematic visualization of one Kv channel α-subunit consisting out of six transmembrane segments (1–6) and a pore helix (PH). In blue the critical residues of PD57 (F619 and L646 according to Kv11.1 numbering) and in pink the residues lining the proposed hydrophobic ICA74 binding pocket (F619, F557, L622, T623, M645, L646, M651, Y652, and F656). (C) Schematic visualization of the pore domain of the Kv11.1 channel. Four pore-forming domains tetramerize to form the channel pore. The blue and pink circle highlights the proposed PD57 and ICA74 binding site regions on the front- and/or backside of the pore-forming domain. (D) Side view of the Kv11.1 channel with the front and back subunit omitted for clarity. Residues involved in PD57 and ICA74 interaction are shown in blue (F619 and L646) and pink (F619, F557, L622, T623, M645, L646, M651, Y652, and F656), respectively. The residues F619 and L646 are both critical residues for PD57 and ICA74, but are shown in blue. (E) Top view of the Kv11.1 channel, with each α subunit named α1–α4. Residues involved in PD57 and ICA74 interaction are shown in blue (F619 and L646) and pink (F619, F557, L622, T623, M645, L646 M651, Y652, and F656), respectively. Kv11.1 cryo-EM structure (PDB: 5VA1) (Wang and Mackinnon, 2017) was visualized with chimera software (Pettersen et al., 2004) and amino acid sequence alignment with Jalview (Waterhouse et al., 2009).
Interestingly, ICA74 binds to a similar hydrophobic pocket in the related ether-a-go-go (EAG) type 1 channel (Kv10.1), although eliciting an opposite effect as in Kv11.1. ICA74 inhibits Kv10.1 currents by enhancing channel inactivation (
Lateral Pore Wall Fenestrations
The reports of compounds that can access the inner cavity from lipid exposed side-pocket through lateral pore wall fenestrations in Kv channels is still very limited. In Kv7.1 a pore wall fenestration is formed upon interaction with the β-subunit KCNE1 such that adamantane compounds, AC-1 (CAS No.: 878489-28-2) and its analogs (ACs), can reach their binding site (
In Kv11.1, a lateral pore wall fenestration is possibly formed upon mutation of residue F557 to leucine (F557L), explaining the decrease in current inhibition of six known hERG blockers (dofetilide, haloperidol, terfenadine, astemizole, cisapride, and amiodarone) (Saxena et al., 2016). For Kv1.5 it has been proposed that psora-4 molecules can move in the I502A mutant between the central cavity and the lipophilic side-pockets through fenestration between segments S5–S6 (
Unifying the Lipid Exposed/Accessible Drug/Toxin Binding Sites of Kv and Nav Channels
Whereas a classification exists for the different drug/toxin binding sites in Nav channels, such a categorization is currently lacking for the Kv channel family. In this review we take a first step and describe the hydrophobic binding sites reported in different Kv channel families. A compound like gambierol (Figures 4 and 7) has been shown to mostly bind to the front side of the PD, while RTG (Figures 5 and 7) PD57, and ICA74 (Figure 6) also interact with the back side of the PD of an adjacent α-subunit. When mapping all the sites it appears that gambierol, ICA74, RTG, and PD57 bind to an analogues binding site present in different Kv channel types (Figure 7) (Schenzer et al., 2005;
Figure 7

Superposition of the lipid-exposed binding sites within the Kv1.2–2.1 paddle chimera channel (PDB: 2R9R) and Kv7.2. (A) Side view of one α-subunit of the Kv1.2–2.1 channel with the residues important for gambierol, psora-4, and PUFA action represented by spheres and highlighted in blue, yellow, and green, respectively. The VSD, PD, and S4–S5 linker are also indicated. (B) Side view of one Kv7.2 α-subunit with the residues important for retigabine, zinc pyrithione, and ICA73 action represented by red, purple, and green spheres, respectively. (C) Superposition of the structures shown in panel (A, B). (D) Superposition of the Kv1.2–2.1 and Kv7.2 channel structure shown as top view. The red and blue circle highlight the proposed retigabine/gambierol binding site on the “front side” of the PD, while the binding sites for zinc pyrithione and psora-4 on the “back side” of the PD are highlighted with the purple and yellow circles, respectively. Structures are visualized using chimera software (Pettersen et al., 2004).
Zinc pyrithione, on the other hand, seems to solely bind to the back side of the PD, implying that the front and back side of the PD could serve as distinct binding sites (Figures 5 and 7) (Xiong et al., 2007). Psora-4 and sevoflurane are less specific regarding their binding site, as they both bind to the front and back side of the PD, among others (
Another lipid facing binding site is located on the VSD, in particular the cleft between segments S2–S3 and S3–S4. PUFAs, DHAA and its derivatives, and ICA-compounds allegedly bind to these clefts in Shaker and Kv7 channels, respectively (Figures 4D, 5D, and 7) (Padilla et al., 2009;
Of note, the residues reported to affect drug/toxin affinity were in this review mapped on available 3D structures that are snapshots of the channel in a certain state, which should not be the high affinity state for the respective drug/toxin. As mentioned, several drugs/toxins are state dependent and bind with highest affinity to a certain conformation of the channel (e.g., the closed or open channel configuration). Consequently, the residues reported to be important for drug/toxin effect might orient differently when the conformation of the channel changes. Thus, when the channel is in its high affinity drug/toxin state, the orientation of the residues might be slightly different resulting in possibly broader binding regions than highlighted in the figures. Furthermore, several of the residues reported to be important for drug/toxin effect are likely not the binding partners of the drugs/toxins but alter affinity in an allosteric way. Nonetheless, there seem to be three distinct lipid-exposed binding sites preserved in Kv channels: the front and back side of the PD, and S2–S3/S3–S4 clefts. Future experiments will determine if the front and back PD binding sites are two distinct entities or if they converge to just one larger lipophilic binding site region.
Funding
This review was supported by a grant of the FWO (Fonds voor Wetenschappelijk onderzoek) G0C6220N (DJS) and by a GOA grant of the University of Antwerp.
Statements
Author contributions
All authors contributed in writing this review.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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Summary
Keywords
hydrophobic binding sites, voltage-gated potassium channels, voltage-gated sodium channels, channel fenestrations, lipophilic compounds
Citation
Van Theemsche KM, Van de Sande DV, Snyders DJ and Labro AJ (2020) Hydrophobic Drug/Toxin Binding Sites in Voltage-Dependent K+ and Na+ Channels. Front. Pharmacol. 11:735. doi: 10.3389/fphar.2020.00735
Received
31 January 2020
Accepted
04 May 2020
Published
15 May 2020
Volume
11 - 2020
Edited by
Mounir Tarek, Centre National de la Recherche Scientifique (CNRS), France
Reviewed by
Michael E. O'Leary, Cooper Medical School of Rowan University, United States; Roope Mannikko, University College London, United Kingdom
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© 2020 Van Theemsche, Van de Sande, Snyders and Labro.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Alain J. Labro, alain.labro@uantwerpen.be
†These authors share first authorship
This article was submitted to Pharmacology of Ion Channels and Channelopathies, a section of the journal Frontiers in Pharmacology
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