Homology modeling of Kv1.5 channel block by cationic and electroneutral ligands

Structural modeling of peptide toxin-ion channel interactions using RosettaDock

Voltage-gated ion channels play essential physiological roles in action potential generation and propagation. Peptidic toxins from animal venoms target ion channels and provide useful scaffolds for the rational design of novel channel modulators with enhanced potency and subtype selectivity. Despite recent progress in obtaining experimental structures of peptide toxin-ion channel complexes, structural determination of peptide toxins bound to ion channels in physiologically important states remains challenging. Here we describe an application of RosettaDock approach to the structural modeling of peptide toxins interactions with ion channels. We tested this approach on 10 structures of peptide toxin-ion channel complexes and demonstrated that it can sample near-native structures in all tested cases. Our approach will be useful for improving the understanding of the molecular mechanism of natural peptide toxin modulation of ion channel gating and for the structural modeling of novel peptide-based ion channel modulators.

Open channel block of Kv1.5 channels by HMQ1611

Kv1.5 channels conduct the ultra-rapid delayed rectifier potassium current (I_Kur). Pharmacological blockade of human Kv1.5 (hKv1.5) has been regarded as an effective treatment of re-entrant based atrial fibrillation, because Kv1.5 is highly expressed in human cardiac atria but scarcely in ventricles. The Kv1.5 blockade is also expected to be used in cancer therapeutics since Kv1.5 is overexpressed in some types of human tumors. Here, we investigated the blockade of hKv1.5 channels by HMQ1611, a symmetrical biphenyl derivative. hKv1.5 channels were heterologously expressed in Chinese hamster ovary cells. The effects of HMQ1611 on wild-type and 13 hKv1.5 mutant channels were examined using the whole-cell patch-clamp method, and molecular docking simulation was conducted to predict the docking position of HMQ1611 within Kv1.5 channels. We showed that HMQ1611 reversibly inhibited the hKv1.5 current in a concentration-dependent manner (IC₅₀ = 2.07 μM). HMQ1611 blockade of hKv1.5 current developed with time during depolarizing voltage-clamp steps, and this blockade was also voltage-dependent with a steep increase over the voltage range for channel openings. HMQ1611 inhibition was significantly reduced in the T479A, T480A, V505A, I508A, L510A, V512A, and V516A hKv1.5 mutant channels. Molecular docking analysis predicted that V505, V512, and T480 were involved in the blocking action of HMQ1611 on hKv1.5 channels. These results suggest that HMQ1611 inhibits hKv1.5 currents as an open channel blocker. Amino acid residues located at the base of the selectivity filter (T479 and T480) and in the S6 segment (V505, I508, L510, V512, and V516) of hKv1.5 appear to constitute potential binding sites for HMQ1611.

Common Structural Pattern for Flecainide Binding in Atrial-Selective Kv1.5 and Nav1.5 Channels: A Computational Approach

Atrial fibrillation (AF) is the most common cardiac arrhythmia. Its treatment includes antiarrhythmic drugs (AADs) to modulate the function of cardiac ion channels. However, AADs have been limited by proarrhythmic effects, non-cardiovascular toxicities as well as often modest antiarrhythmic efficacy. Theoretical models showed that a combined blockade of Na_v1.5 (and its current, I_Na) and K_v1.5 (and its current, I_Kur) ion channels yield a synergistic anti-arrhythmic effect without alterations in ventricles. We focused on K_v1.5 and Na_v1.5 to search for structural similarities in their binding site (BS) for flecainide (a common blocker and widely prescribed AAD) as a first step for prospective rational multi-target directed ligand (MTDL) design strategies. We present a computational workflow for a flecainide BS comparison in a flecainide-K_v1.5 docking model and a solved structure of the flecainide-Na_v1.5 complex. The workflow includes docking, molecular dynamics, BS characterization and pattern matching. We identified a common structural pattern in flecainide BS for these channels. The latter belongs to the central cavity and consists of a hydrophobic patch and a polar region, involving residues from the S6 helix and P-loop. Since the rational MTDL design for AF is still incipient, our findings could advance multi-target atrial-selective strategies for AF treatment.

Identification of a critical binding site for local anaesthetics in the side pockets of Kv 1 channels

BACKGROUND AND PURPOSE

Local anaesthetics block sodium and a variety of potassium channels. Although previous studies identified a residue in the pore signature sequence together with three residues in the S6 segment as a putative binding site, the precise molecular basis of inhibition of K_v channels by local anaesthetics remained unknown. Crystal structures of K_v channels predict that some of these residues point away from the central cavity and face into a drug binding site called side pockets. Thus, the question arises whether the binding site of local anaesthetics is exclusively located in the central cavity or also involves the side pockets.

EXPERIMENTAL APPROACH

A systematic functional alanine mutagenesis approach, scanning 58 mutants, together with in silico docking experiments and molecular dynamics simulations was utilized to elucidate the binding site of bupivacaine and ropivacaine.

KEY RESULTS

Inhibition of K_v 1.5 channels by local anaesthetics requires binding to the central cavity and the side pockets, and the latter requires interactions with residues of the S5 and the back of the S6 segments. Mutations in the side pockets remove stereoselectivity of inhibition of K_v 1.5 channels by bupivacaine. Although binding to the side pockets is conserved for different local anaesthetics, the binding mode in the central cavity and the side pockets shows considerable variations.

CONCLUSION AND IMPLICATIONS

Local anaesthetics bind to the central cavity and the side pockets, which provide a crucial key to the molecular understanding of their K_v channel affinity and stereoselectivity, as well as their spectrum of side effects.

Challenges Faced with Small Molecular Modulators of Potassium Current Channel Isoform Kv1.5

The voltage-gated potassium channel Kv1.5, which mediates the cardiac ultra-rapid delayed-rectifier (IKur) current in human cells, has a crucial role in atrial fibrillation. Therefore, the design of selective Kv1.5 modulators is essential for the treatment of pathophysiological conditions involving Kv1.5 activity. This review summarizes the progress of molecular structures and the functionality of different types of Kv1.5 modulators, with a focus on clinical cardiovascular drugs and a number of active natural products, through a summarization of 96 compounds currently widely used. Furthermore, we also discuss the contributions of Kv1.5 and the regulation of the structure-activity relationship (SAR) of synthetic Kv1.5 inhibitors in human pathophysiology. SAR analysis is regarded as a useful strategy in structural elucidation, as it relates to the characteristics that improve compounds targeting Kv1.5. Herein, we present previous studies regarding the structural, pharmacological, and SAR information of the Kv1.5 modulator, through which we can assist in identifying and designing potent and specific Kv1.5 inhibitors in the treatment of diseases involving Kv1.5 activity.

Inhibition of Voltage-Gated K+ Channel Kv1.5 by Antiarrhythmic Drugs

Molecular dynamics simulations are employed to determine the inhibitory mechanisms of three drugs, 5-(4-phenoxybutoxy)psoralen (PAP-1), vernakalant, and flecainide, on the voltage-gated K⁺ channel Kv1.5, a target for the treatment of cardiac arrhythmia. At neutral pH, PAP-1 is neutral, whereas the other two molecules carry one positive charge. We show that PAP-1 forms stable dimers in water, primarily through hydrophobic interactions between aromatic rings. All three molecules bind to the cavity between the Ile508 and Val512 residues from the four subunits of the channel. Once bound, the drug molecules are flexible, with the average root-mean-square fluctuation being between 2 and 3 Å, which is larger than the radius of gyration of a bulky amino acid. The presence of a monomeric PAP-1 causes the permeating K⁺ ion to dehydrate, thereby creating a significant energy barrier. In contrast, vernakalant blocks the ion permeation primarily via an electrostatic mechanism and, therefore, must be in the protonated and charged form to be effective.

Sodium ion unlocks understanding of channel blockade

New simulations explain how several types of drugs block sodium channels.

New simulations explain how several types of drugs block sodium channels.

Modeling interactions between blocking and permeant cations in the NavMs channel

Mechanisms of sodium channel block by local anesthetics (LAs) are still a matter of intensive studies. In the absence of high-resolution structures of eukaryotic channels, atomic details of LA-channel interactions are analyzed using homology modeling. LAs are predicted to access the closed channel through a sidewalk (fenestration) between the channel repeats, bind in a horizontal orientation, and leave its aromatic moiety in the interface. Recent X-ray structure of a bacterial sodium channel NavMs with a cationic molecule Pl1, which is structurally similar to LAs, has confirmed this theoretical prediction and demonstrated a reduced selectivity filter occupancy by the permeant ions in the Pl1-bound channel. However, the nature of the antagonism between LAs and permeant ions is still unclear. Here we used the NavMs structure and Monte Carlo energy minimizations to model Pl1 binding. Our computations predict that Pl1 can displace permeant ion(s) from the selectivity filter by both steric and electrostatic mechanisms. We hypothesize that the electrostatic mechanism is more general, because it is applicable to many LAs and related drugs, which lack a moiety capable to enter the selectivity filter and sterically displace the permeant ion. The electrostatic mechanism is also consistent with the data that various cationic blockers of potassium channels bind in the inner pore without entering the selectivity filter.

Putative binding sites for arachidonic acid on the human cardiac Kv 1.5 channel

BACKGROUND AND PURPOSE

In human heart, the Kv 1.5 channel contributes to repolarization of atrial action potentials. This study examined the electrophysiological and molecular mechanisms underlying arachidonic acid (AA)-induced inhibition of the human Kv 1.5 (hKv 1.5) channel.

EXPERIMENTAL APPROACH

Site-directed mutagenesis was conducted to mutate amino acids that reside within the pore domain of the hKv 1.5 channel. Whole-cell patch-clamp method was used to record membrane currents through wild type and mutant hKv 1.5 channels heterologously expressed in CHO cells. Computer docking simulation was conducted to predict the putative binding site(s) of AA in an open-state model of the Kv 1.5 channel.

KEY RESULTS

The hKv 1.5 current was minimally affected at the onset of depolarization but was progressively reduced during depolarization by the presence of AA, suggesting that AA acts as an open-channel blocker. AA itself affected the channel at extracellular sites independently of its metabolites and signalling pathways. The blocking effect of AA was attenuated at pH 8.0 but not at pH 6.4. The blocking action of AA developed rather rapidly by co-expression of Kv β1.3. The AA-induced block was significantly attenuated in H463C, T480A, R487V, I502A, I508A, V512A and V516A, but not in T462C, A501V and L510A mutants of the hKv 1.5 channel. Docking simulation predicted that H463, T480, R487, I508, V512 and V516 are potentially accessible for interaction with AA.

CONCLUSIONS AND IMPLICATIONS

AA itself interacts with multiple amino acids located in the pore domain of the hKv 1.5 channel. These findings may provide useful information for future development of selective blockers of hKv 1.5 channels.

Interaction of propofol with voltage-gated human Kv1.5 channel through specific amino acids within the pore region

The intravenous anesthetic propofol affects the function of a diversity of ligand-gated and voltage-gated ion channels. However, there is little information as to whether propofol directly interacts with voltage-gated ion channel proteins to modulate their functions. The Kv1.5 channel is activated by membrane depolarization during action potentials and contributes to atrial repolarization in the human heart. This study was undertaken to examine the effect of propofol on voltage-gated human Kv1.5 (hKv1.5) channel and to elucidate the underlying molecular determinants. Site-directed mutagenesis was carried out through six amino acids that reside within the pore domain of hKv1.5 channel. Whole-cell patch-clamp technique was used to record membrane currents through the wild type and mutant hKv1.5 channels heterologously expressed in Chinese hamster ovary cells. Propofol (≥5 μM) reversibly and concentration-dependently (IC50 of 49.3±9.4 μM; n=6) blocked hKv1.5 current. Propofol-induced block of hKv1.5 current gradually progressed during depolarizing voltage-clamp steps and was enhanced by higher frequency of activation, consistent with a preferential block of the channels in their open state. The degree of current block by propofol was significantly attenuated in T480A, I502A, I508A and V516A, but not in H463C and L510A mutants of hKv1.5 channel. Thus, several amino acids near the selectivity filter (Thr480) or within S6 (Ile502, Ile508 and Val516) are found to be critically involved in the blocking action of propofol. This study provides the first evidence suggesting that direct interaction with specific amino acids underlies the blocking action of propofol on voltage-gated hKv1.5 channel.

Molecular basis of hERG potassium channel blockade by the class Ic antiarrhythmic flecainide

The class Ic antiarrhythmic drug flecainide inhibits KCNH2-encoded "hERG" potassium channels at clinically relevant concentrations. The aim of this study was to elucidate the underlying molecular basis of this action. Patch clamp recordings of hERG current (IhERG) were made from hERG expressing cells at 37°C. Wild-type (WT) IhERG was inhibited with an IC50 of 1.49μM and this was not significantly altered by reversing the direction of K(+) flux or raising external [K(+)]. The use of charged and uncharged flecainide analogues showed that the charged form of the drug accesses the channel from the cell interior to produce block. Promotion of WT IhERG inactivation slowed recovery from inhibition, whilst the N588K and S631A attenuated-inactivation mutants exhibited IC50 values 4-5 fold that of WT IhERG. The use of pore-helix/selectivity filter (T623A, S624A V625A) and S6 helix (G648A, Y652A, F656A) mutations showed <10-fold shifts in IC50 for all but V625A and F656A, which respectively exhibited IC50s 27-fold and 142-fold their WT controls. Docking simulations using a MthK-based homology model suggested an allosteric effect of V625A, since in low energy conformations flecainide lay too low in the pore to interact directly with that residue. On the other hand, the molecule could readily form π-π stacking interactions with aromatic residues and particularly with F656. We conclude that flecainide accesses the hERG channel from the cell interior on channel gating, binding low in the inner cavity, with the S6 F656 residue acting as a principal binding determinant.