Inhibition of Voltage-gated K channel Kv1.5 by Anti-arrhythmic drugs

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Inhibition of Voltage-gated K channel Kv1.5 by Anti-arrhythmic drugs Rong Chen, and Shin-Ho Chung Biochemistry, Just Accepted Manuscript • DOI: 10.1021/acs.biochem.8b00268 • Publication Date (Web): 13 Apr 2018 Downloaded from http://pubs.acs.org on April 13, 2018

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Biochemistry

Inhibition of Voltage-gated K+ channel Kv1.5 by Anti-arrhythmic drugs Rong Chen and Shin-Ho Chung* Research School of Biology, Australian National University, Canberra, Acton ACT 2601, Australia *Correspondence: [email protected]; Phone: +61-2-6125-2024; Fax: +61-2-6125-0739

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ABSTRACT 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 the 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 of 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. Keywords Kv1.5; potassium channels; vernakalant; flecainide; molecular dynamics; TOC Figure

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INTRODUCTION K+ channels are involved in the repolarization of the membrane potential in excitable cells and their malfunction is implicated in many human diseases 1. The voltage-gated K+ channel Kv1.5, primarily expressed in cardiac myocytes, is a potential target for combating cardiac arrhythmias 2, 3. Inhibitors of Kv1.5 are being developed for the treatment of atrial fibrillation 4. Kv1.5 is a prototype channel for the understanding of therapeutic and side effects of anti-arrhythmia drugs 5. Many small molecules such as 5-(4-phenoxybutoxy)psoralen (PAP-1), vernakalant (VER) and flecainide (FLE) are potent inhibitors of Kv1.5. Because the inner cavities of different cationic channels are highly similar, these molecules are likely to interact with many channels other than Kv1.5. The three drugs we have studied have diverse chemical properties, which may be related to their distinct mechanisms of action. For example, PAP-1 is neutral, while VER and FLE carry one positive charge at neutral pH (Fig. 1A). The binding of PAP-1 to Kv1.5 is characterized by a Hill coefficient of 2, indicating that multiple PAP-1 molecules may act cooperatively to block the channel 6. On the other hand, the Hill coefficient of both VER and FLE for Kv1.5 is close to unity, consistent with non-cooperative block 7, 8.

Figure 1. Structures of a Kv1.5 homology model and three ligands of Kv1.5. (A) Chemical structure of PAP-1, vernakalant (VER) and flecainide (FLE). (B) Structure of the Kv1.5 model. Two subunits of

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the homo-tetrameric protein are shown. Four of the residues proposed to be important for ligand binding are highlighted. The S5 (pink) and S6 (grey) trans-membrane helices of Kv1.5 are indicated.

The mechanisms by which PAP-1, VER and FLE block Kv1.5 and related channels have been examined extensively from both experimental 7-11 and computational perspectives

12-17

. The studies

revealed that the inner cavity is the primary binding site for these compounds. For example, PAP-1 competes with tetraethylammonium and verapamil that are known to bind to the inner cavity 9. The mutations of several residues, such as Thr479 and Thr480 from the selectivity filter, and Ile502, Val505, Ile508 and Val512 from the S6 helix, which are on the wall of the inner cavity (Fig. 1B), affect the binding of the three molecules significantly 7, 9, 11. Recent experimental and computational studies suggest that a secondary binding site at the backsides of the S5 and S6 helices and outside the channel could also be relevant 16, 18. The drug molecules may enter the inner cavity via three different pathways: (i) the selectivity filter from the extracellular side; (ii) the side fenestrations from within the membrane; and (iii) the inner gate from the intracellular side. The selectivity filter in a diameter of less than 3 Å only allows a single file of water molecules and ions to pass through, and thus would be too narrow for drug molecules to penetrate. The fenestrations in Kv1.5, with a maximum diameter of 3.5 Å

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, is also

too narrow for even a water molecule to move across. Thus, the drug molecules must first cross the cell membrane and then move into the inner cavity through the inner gate. Using all-atom molecular dynamics (MD) simulations, we examine the interactions of the three drug molecules, PAP-1, VER and FLE, with the inner cavity of Kv1.5. We demonstrate that PAP-1 forms stable dimers in water, and all the three molecules partition into the hydrophobic core of a lipid bilayer at a concentration of 13 mM. We then determine the binding modes of the three ligands in the inner cavity of Kv1.5 and the mechanisms of ion conduction block.

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METHODS Molecular dynamics The homology model of Kv1.5 is constructed with the crystal structure of the Kv1.2 channel in the activated state

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as the template, using the homology modeling server SWISS-MODEL

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. The

primary structure of the region most relevant for drug binding, namely, the S6 helix, is identical between Kv1.2 and Kv1.5, and the sequence identify between the two channel in the pore domain (residues 415 to 527 in Kv1.5) is 89%, indicating that Kv1.2 is a reasonable template for Kv1.5 14. The pore domain of Kv1.5 is embedded in a POPC (1-palmitoyl-2-oleoyl-sn-glycero-3phosphocholine) bilayer and a box of explicit water. The simulation box, comprising the channel protein, 157 POPC molecules and ~15500 water molecules, is approximately 85×85×105 Å3 in size. A total of 58 K+ and 62 Cl- ions are added into the system to maintain charge neutrality and a salt concentration of approximately 0.2 M. The drug molecule is added to the cytoplasmic side of the channel and allowed to bind into the inner cavity in the presence of a flat-bottom distance restraint. The distance restraint is applied between the inner end of the selectivity filter and the drug molecule over the first 16 ns, during which the upper bound of the restraint is progressively reduced from 20 to 10 Å, such that the ligand is drawn into the inner cavity gradually. Afterwards the distance restraint is completely removed. All MD simulations are performed under periodic boundary conditions using NAMD 2.10

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. The

CHARMM36 force fields and the TIP3P model for water are used to describe the interatomic

interactions in the system 23-25. The topology of each of the three drug molecules is generated using the ParamChem server 26, 27. The penalty scores for atomic charges are less than 10 for over 85% of atoms, and the maximum penalty score is 21 for VER and 19 for FLE, indicating that the analogy between the drugs and existing molecules in the force field is reasonable. The CHARMM general force field is used to describe the drug molecules 28. The switch and cutoff distances for short-range interactions are set to 8.0 Å and 12.0 Å, respectively. The long-range electrostatic interactions are 5 ACS Paragon Plus Environment

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accounted for using the particle mesh Ewald method, with a maximum grid spacing of 1.0 Å. Bond lengths are maintained rigid with the SHAKE and SETTLE algorithms 29, 30, allowing a time step of 2 fs to be used. The average temperature and pressure are maintained constant at 300 K and 1 atm by using Langevin dynamics and the Nosé-Hoover Langevin Piston method

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, respectively. The

pressure coupling is isotropic when no lipids are present in the system, and semi-isotropic when the system contains a lipid bilayer. Trajectories are saved every 20 ps for analysis. PMF calculations Potential of mean force (PMF) for the binding of the drug to the lipid bilayer and the permeation of a K+ ion along the channel pore are constructed. The reaction coordinates are the center of mass (COM) distance between the drug and the lipid bilayer, and between the ion and the channel backbone along the bilayer normal (z), respectively. For the drug binding to the lipid bilayer, the starting structures of umbrella windows spaced at 0.5 Å intervals are generated by pulling the drug from its bound position to the bulk over a simulation period of 2 ns using constant speed steered molecular dynamics. The profiles of PMF encountered by a permeating ion are similarly constructed. Umbrella sampling windows, spaced at 0.5 Å intervals, are generated by moving a K+ ion along the channel central axis (z). The biasing harmonic potential of umbrella window is 30 kcal/mol/Å2 in all cases. The COM of the lipid bilayer and the channel backbone is at z=0 Å. A flat-bottom harmonic restraint is applied to maintain the COM of the ion within a cylinder of 5 Å in radius centered on the channel axis. The diameter of the cylinder is comparable to that of the widest section of the inner cavity. Each umbrella window is simulated for at least 8 ns until the depth of the PMF profiles evolve by less than 0.5 kT over the last 1 ns, at which convergence is assumed. The first 1 ns of each window is considered as equilibration and removed from data analysis. The z coordinate is saved every 1 ps for analysis. The dissociation constant Kd of drug binding to the lipid bilayer is estimated from the PMF, W(z), using the following equation 32, 33: 6 ACS Paragon Plus Environment

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zmax

Kd −1 = 1000π R 2 N A

∫ exp[−W ( z) / kT ] dz

(1)

zmin

where πR2 is the area of the bilayer plane, NA is Avogadro's number, zmin and zmax are the z positions of the drug COM when deep inside the bilayer and in the bulk, respectively. RESULTS AND DISCUSSION PAP-1 dimerization in water The Hill coefficient of 2 observed experimentally suggests that multiple PAP-1 molecules may bind corporately to the same or different binding sites in Kv1.3, a channel that shares the identical sequence with Kv1.5 in the inner cavity region 6. Zimin et al. 9, based on Monte Carlo calculations, proposed that two PAP-1 molecules bind to the inner cavity of Kv1.3, and entrap a K+ ion through electrostatic interactions between the ion and the carbonyl group of PAP-1. Here we examine whether PAP-1 forms stable dimers in water and how a K+ ion would interact with the dimer. The dimerization of VER and FLE in water is also examined for comparison. We place two drug molecules and one K+ ion in a cubic box of water (70 Å in each dimension) containing a pair of K+ and Cl- ions. The two drug molecules are restraint to a sphere of 15 Å in radius centered on the K+ ion (Fig. 2A), and the concentration of the drug in the sphere is about 0.2 M. The system is then simulated for 50 ns twice. The COM distance between the three-ring heads, as defined in Fig. 2B, of the two PAP-1 molecules is used as a measure of dimerization. The COM distance is less than 5 Å approximately 60% of times and less than 10 Å about 95% of times (Fig. 2C), indicating that a PAP-1 dimer is formed through the hydrophobic interactions between the two heads. The head-head dimerization is reasonably stable, as the average RMSD with reference to the average structure is only 1.5 Å over the last 30 ns. However, the K+ ion does not interact favorably with the PAP-1 dimer. The K+ ion is more than 7 Å from the carbonyl oxygen of PAP-1 85% of times (Fig. 2D), suggesting that PAP-1

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can form stable dimers but the interactions between the K+ ion and the carbonyl group of PAP-1 are rather weak. These results are expected because the K+ ion can form similar interactions with the oxygen atoms of water molecules.

Figure 2. Dimerization of PAP-1 in water. (A) Two PAP-1 are restrained to a sphere of 15 Å in radius centered on a K+ ion in water. (B) Definition of the head and tail of PAP-1. (C) The cumulative probability, Pc(x), of the distance between the centers of mass of the heads of two PAP-1 molecules. Data obtained from the last 40 ns of two independent simulations of 50 ns each are shown. A typical snapshot of a head-to-head dimer of PAP-1 (red and blue) is shown in the inset. (D) Pc(x) of the distance between the K+ ion and the carbonyl oxygen of PAP-1 over the last 40 ns of two simulations.

In contrast, the same simulations performed on VER demonstrate that it does not form stable dimers in water. We use the COM distance between the benzene ring as an indicator of dimer formation. 8 ACS Paragon Plus Environment

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The other end of VER carrying a tertiary amine group is less likely to contact due to electrostatic repulsion from the positive charge it carries. Fig. 3 shows that more than 60% of times the COM distance between the benzene rings of the two VER molecules is larger than 10 Å, indicating that no stable dimerization is evident. Similarly, the simulations of two FLE molecules in water also show that no formation of dimer is evident. These results are consistent with the fact that VER and FLE are charged and less hydrophobic than PAP-1, indicating that the force field is able to discriminate the different physical properties of PAP-1, VER and FLE.

Fig. 3. The cumulative probability, Pc(x), of the distance between the COM of the benzene rings of the two copies of VER. The last 40 ns of two simulations of 50 ns each are used for analysis.

Partition in a lipid bilayer In order to move into the inner cavity of the channel, the drug molecule must first cross the membrane and then enter into the intracellular side of the cell. Therefore, membrane partition properties are important for understanding the pharmacological profile of inner cavity blockers. To examine whether PAP-1, VER and FLE would partition into the membrane, we place two copies of each molecule approximately 10 Å above a POPC bilayer of 74 lipids in each leaflet, allowing the molecule to bind the bilayer spontaneously. The bilayer is fully hydrated with approximately 60 9 ACS Paragon Plus Environment

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water molecules per lipid, thus making the concentration of each drug to 13 mM. Note that this concentration is about three orders of magnitude higher than the maximum therapeutic plasma concentrations of VER and FLE, which are in the order of 1 µg/ml and 3 µM 34, 35.

Figure 4. Binding of PAP-1, VER and FLE to the POPC bilayer. The position of the three molecules relative to the bilayer viewed approximately perpendicular to the bilayer normal is shown. The dashed lines indicate the approximate average position of the lipid phosphorus atoms.

At the start of the simulation, which is continued for 100 ns, the drug molecule is placed appximately 10 Å away from the surface of the bilayer. In the case of PAP-1, the two copies form a dimer in water and then bind into the bilayer. The position of the two PAP-1 molecules relative to the bilayer is similar, with an average COM distance of 10.2±1.3 Å from the bilayer center. However, the dimer is no longer intact (Fig. 4). One VER molecule partitions into the bilayer after approximately 20 ns (Fig. 4), and its average COM distance from the bilayer center is 16.0±2.2 Å. Both copies of FLE are partitioned into the bilayer after 20 ns and remain bound afterwards (Fig. 4). Once inside the bilayer, the position of the drug molecule relative to the bilayer center remains stable, with COM distance fluctuating on an average of approximately 12.8±1.4 Å in all cases. The simulations demonstrate that all the three drugs can partition into the bilayer. Energetics of binding to the lipid bilayer To determine how strongly PAP-1, VER and FLE bind to the POPC bilayer, we construct the PMF profile of the binding along the bilayer normal. The COM distance between the drug molecule and the bilayer center is used as the reaction coordinate. Each profile is replicated a second time to 10 ACS Paragon Plus Environment

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verify the convergence. The PMF profiles we constructed confirm that all the three molecules bind to a similar depth in the bilayer. When PAP-1 is at its most favorable position, it is approximately 11 Å from the bilayer center, where the average well depth of the two PMF profiles is -9 kT (Fig. 5A). The average depth of the PMF profiles for VER is about -6 kT (Fig. 5B), which is shallower than that of PAP-1 (-9 kT, Fig. 5A) and FLE (-11 kT, Fig. 5C). Therefore, VER binds the bilayer less strongly than PAP-1 and FLE. The surface area of the bilayer is approximately 50 nm2, and the Kd values derived from the PMF profiles are 0.5 µM, 52 µM and 0.14 µM for PAP-1, VER and FLE, respectively. The Kd values for a real cell membrane would be much lower, because the surface area of a cell membrane would be much larger than the bilayer patch used in our calculations. The Kd values derived from our bilayer patch are comparable to the therapeutic plasma concentration of the drugs, which is in the order of 3 µM 34, suggesting that membrane partitioning may be relevant for drug action.

Fig. 5. The potential of mean force (PMF) profile of PAP-1 (A), VER (B) and FLE (C) binding to the POPC bilayer. For each molecule, two profiles, shown in red and blue, are constructed from two independent series of umbrella sampling simulations. The reaction coordinate is the COM distance between the molecule and the bilayer along the bilayer normal.

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Binding of PAP-1 to Kv1.5 Experimental data suggest that the inner cavity is the primary binding site for PAP-1 9. To understand the critical interactions between PAP-1 and Kv1.5, we determine the binding modes of a monomer as well as a dimer of PAP-1 to the inner cavity of Kv1.5 using MD with distance restraint. A distance restraint is applied to the COM of the PAP-1 monomer and dimer, respectively. The upper bound of the flat-bottom distance restraint between the COM of PAP-1 and the backbone of the inner end of the channel filter is reduced from 20 Å to 10 Å over the first 10 ns and then maintained constant at 10 Å for another 6 ns, after which the restraint is removed. Since the COM distance is approximately 10 Å when the drug is fully bound to the inner cavity of the channel, the restraining potential is zero once PAP-1 binds to the inner cavity. The simulation is continued until 100 ns, allowing PAP-1 to evolve to a favorable binding mode.

Fig. 6. Binding of PAP-1 to Kv1.5. (A) Snapshot of a PAP-1 monomer in the inner cavity of Kv1.5 after 100 ns of simulation. Two K+ ions in the S2 and S4 ion binding sites of the selectivity filter are shown as green spheres. The side chains of three residues on the inner wall of Kv1.5 are highlighted. (B) Water molecules within 4 Å of a PAP-1 monomer. The view is from the extracellular side along the channel axis. (C) Position of a PAP-1 dimer relative to the inner cavity of Kv1.5 after 100 ns of simulation.

The PAP-1 monomer binds to the cage between the two rings of Ile508 and Val512 from the four channel subunits, just below the ring of Thr480, which is at the inner end of the filter (Fig. 6A). The presence of PAP-1 causes the inner cavity of the channel to dehydrate, and only a single file of

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water molecules around PAP-1 is evident (Fig. 6B). The PAP-1 monomer is highly mobile when bound to the channel. For example, the average root mean square fluctuation (RMSF) of the heavy atoms of PAP-1 is 2.8 Å, which is even larger than the radius of gyration of tryptophan (2.2 Å). The PAP-1 dimer readily occupies the inner cavity just below the filter (Fig. 6C), indicating that two PAP-1 molecules can bind to the channel concurrently. Binding of VER and FLE to Kv1.5 Following the same approach to that of PAP-1, we predict the binding modes of VER and FLE monomers to the inner cavity of Kv1.5 using MD. Both drugs bind to inner cavity and interact intimately with Thr480, Ile508 and Val512 (Fig. 7 A and B), consistent with the predicted binding mode of PAP-1 (Fig. 6A).

Figure 7. Binding modes of VER and FLE to Kv1.5. In (A) and (B), the position of VER and FLE with respect to the inner cavity of Kv1.5 is shown, respectively. Two channel subunits are shown as white ribbons. In (C) and (D), water molecules within 4 Å of VER and FLE are shown, respectively. The view is from the extracellular side along the channel axis.

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In the case of VER, the ligand is closely coupled with Val505, Ile508 and Val512 from multiple subunits, with the distance between the drug and those residues being less than 3 Å. FLE is also in close proximity to these three hydrophobic residues from multiple subunits. Both drugs tumble significantly within the inner cavity (average RMSF of 2.4 Å for VER and 2.1 Å for FLE), but their binding to the inner cavity remains intact. Thus, the same key residues in Kv1.5 are responsible for VER and FLE binding. However, in contrast to PAP-1, which is significantly dehydrated once inside the channel (Fig. 5B), both VER and FLE remain hydrated by a large number of water molecules (Fig. 7 C and D). PAP-1 effect on permeation To examine how the presence of a PAP-1 monomer would affect ion permeation through Kv1.5, we construct the PMF profile of a K+ ion as it moves through the channel from the intracellular side. The PMF profile, as shown in Fig. 8A, is constructed in the presence of a PAP-1 monomer in the inner cavity. The profile of K+ moving through Kv1.2 in the absence of any drug we derived previously

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is also shown in the figure for comparison. As Kv1.2 and Kv1.5 are highly relevant

and their conductance are within 2-fold 1, the profiles for the two channels in the absence of ligands are expected to be comparable. In the absence of any drug, the maximum energy barrier for a K+ ion to move through the inner cavity is only about 2 kT (Fig. 8A) 36. However, in the presence of a PAP-1 monomer, this barrier increases to 13 kT, indicating that PAP-1 causes a barrier of 11 kT for the permeating ion (Fig. 8A).

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Figure 8. PMF profiles of a K+ ion moving through the cytoplasmic gate of Kv1.2 and Kv1.5 along the channel axis (z). The COM of the channel backbone is at z=0 Å. (A) The profiles are constructed in the absence of any ligand in Kv1.2 and in the presence of PAP-1 in the inner cavity of Kv1.5. The position of the permeating K+ at z=5 Å and z=10 Å relative to PAP-1 and two K+ ions in the S2 and S4 ion binding sites of the filter are indicated in the insets. The random error of the profile for PAP-1 as estimated from the bootstrap analysis 37 is 0.4 kT. (B) The profiles are constructed in the presence of a protonated and deprotonated VER in the inner cavity of Kv1.5, respectively. The random errors of the profiles for the protonated and deprotonated VER are 0.6 and 0.3 kT, respectively. The inset shows the position of the potassium ion (green sphere) relative to VER at z=12.5 Å.

Our analysis reveals that PAP-1 causes the permeating ion to dehydrate, thereby creating the energy barrier. The radial distribution function, g(r), of water oxygen atom around the ion is significantly different between the two umbrella windows, z=5 Å and z=25 Å. As the ion moves across the drug (from z=25 Å to z=5 Å), the g(r) peak values are significantly reduced (Fig. 9A), indicating that the ion is less dehydrated when it moves closer to the drug. This mechanism is similar to that of TRAM-34 36, which is also a neutral molecule that binds to the inner cavity of the channel. In the presence of TRAM-34, the permeating ion has to shed more than one water molecule from its first 15 ACS Paragon Plus Environment

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hydration shell 36. The dehydration mechanism by PAP-1 and TRAM-34 may be common to other neutral inner cavity blockers. In contrast, the g(r) peak remains largely unchanged when the ion crosses over the neutral VER (Fig. 9B).

Figure 9. The radial distribution function, g(r), of water oxygen atoms around the permeating K+ ion in two umbrella windows, z=5 Å and z=25 Å, in the presence of PAP-1 (A) and deprotonated VER (B) in the inner cavity.

VER effect on permeation To examine the role of the positive charge in VER and FLE in their mechanism of channel inhibition, we construct the PMF profiles of a K+ ion moving through the inner cavity of the channel in the presence of a charged and neutral (deprotonated) VER, respectively (Fig. 8B). The PMF profiles show that VER in the charged form creates a significant energy barrier for the ion, while the neutral form is unable to create an energy barrier. The profile has a local well at z=12.5 Å, because the ion forms favorable interactions with the two oxygen atoms on the benzene ring of VER (see inset of Fig. 8B). In contrast to PAP-1, the neutral form of VER does not induce ion dehydration. For example, the peak g(r) values does not change significantly when the ion is 16 ACS Paragon Plus Environment

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Biochemistry

moving across VER (Fig. 9B). These results suggest that the presence of VER in the inner cavity inhibits ion conduction via an electrostatic mechanism, which is similar to that of lidocaine

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Lidocaine in its neutral form does not cause the ion to dehydrate either 36. Therefore, both VER and lidocaine must be in their charged form to inhibit ion conduction. CONCLUSIONS MD simulations are used to elucidate the mechanisms by which three drug molecules, PAP-1, VER and FLE, block the voltage-gated K+ channel Kv1.5, a target for the treatment of heart arrhythmia. We only consider the primary binding site, which is the inner cavity. The drug molecules may be able to access the secondary binding site located at the backsides of the S5 and S6 helices within the membrane, because all the molecules readily partition into the membrane as we demonstrated here. This secondary site was suggested for PAP-1 and Psora-4, both of which are uncharged at neutral pH 16, 18. Future experimental studies are required to ascertain whether the secondary site is relevant for VER and FLE that carry a positive charge. The binding modes between the drugs and Kv1.5 show that all the three molecules interact intimately with Ile508 and Val512 when bound to the inner cavity of Kv1.5, suggesting that they share a common binding mode. Once a monomeric PAP-1 is present in the inner cavity, the cavity is dehydrated and only a single file of water is around PAP-1, thereby creating a large energy barrier of at least 11 kT for the permeating K+ ion to move across. On the other hand, VER does not cause ion dehydration and must be in its charged form to inhibit ion permeation. ACKNOWLEDGEMENTS Supported by the National Health and Medical Research Council of Australia and the Medical Advances Without Animals (MAWA) Trust. All the calculations were undertaken on the National Computational Infrastructure in Canberra, Australia, which is supported by the Australian Commonwealth Government.

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REFERENCES [1] Gutman, G. A., Chandy, K. G., Grissmer, S., Lazdunski, M., McKinnon, D., Pardo, L. A., Robertson, G. A., Rudy, B., Sanguinetti, M. C., Stuhmer, W., and Wang, X. (2005) International Union of Pharmacology. LIII. Nomenclature and molecular relationships of voltage-gated potassium channels, Pharmacol. Rev. 57, 473-508. [2] van Wagoner, D. R., Pond, A. L., McCarthy, P. M., Trimmer, J. S., and Nerbonne, J. M. (1997) Outward K+ current densities and Kv1.5 expression are reduced in chronic human atrial fibrillation, Circ. Res. 80, 772-781. [3] Brendel, J., and Peukert, S. (2003) Blockers of the Kv1.5 channel for the treatment of atrial arrhythmias, Curr. Med. Chem. Cardiovasc. Hematol. Agents 1, 273-287. [4] Bilodeau, M. T., and Trotter, B. W. (2009) Kv1.5 blockers for the treatment of atrial fibrillation: approaches to optimization of potency and selectivity and translation to in vivo pharmacology, Curr. Top. Med. Chem. 9, 436-451. [5] Yang, P. C., Moreno, J. D., Miyake, C. Y., Vaughn-Behrens, S. B., Jeng, M. T., Grandi, E., Wehrens, X. H., Noskov, S. Y., and Clancy, C. E. (2016) In silico prediction of drug therapy in catecholaminergic polymorphic ventricular tachycardia, J. Physiol. 594, 567-593. [6] Schmitz, A., Sankaranarayanan, A., Azam, P., Schmidt-Lassen, K., Homerick, D., Hänsel, W., and Wulff, H. (2005) Design of PAP-1, a selective small molecule Kv1.3 blocker, for the suppression of effector memory T cells in autoimmune diseases, Mol. Pharmacol. 68, 12541270. [7] Eldstrom, J., Wang, Z., Xu, H., Pourrier, M., Ezrin, A., Gibson, K., and Fedida, D. (2007) The molecular basis of high-affinity binding of the antiarrhythmic compound vernakalant (RSD1235) to Kv1.5 channels, Mol. pharmacol. 72, 1522-1534. [8] Herrera, D., Mamarbachi, A., Simoes, M., Parent, L., Sauve, R., Wang, Z., and Nattel, S. (2005) A single residue in the S6 transmembrane domain governs the differential flecainide sensitivity of voltage-gated potassium channels, Mol. Pharmacol. 68, 305-316. [9] Zimin, P. I., Garic, B., Bodendiek, S. B., Mahieux, C., Wulff, H., and Zhorov, B. S. (2010) Potassium channel block by a tripartite complex of two cationophilic ligands and a potassium ion, Mol. Pharmacol. 78, 588-599.

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Page 18 of 21

Page 19 of 21 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Biochemistry

[10] Strutz-Seebohm, N., Gutcher, I., Decher, N., Steinmeyer, K., Lang, F., and Seebohm, G. (2007) Comparison of potent Kv1.5 potassium channel inhibitors reveals the molecular basis for blocking kinetics and binding mode, Cell. Physiol. Biochem. 20, 791-800. [11] Decher, N., Pirard, B., Bundis, F., Peukert, S., Baringhaus, K. H., Busch, A. E., Steinmeyer, K., and Sanguinetti, M. C. (2004) Molecular basis for Kv1.5 channel block. Conservation of drug binding sites among voltage-gated K+ channels, J. Biol. Chem. 279, 394-400. [12] Zhorov, B. S., and Tikhonov, D. B. (2013) Ligand action on sodium, potassium, and calcium channels: role of permeant ions, Trends Pharmacol. Sci. 34, 154-161. [13] Tikhonov, D. B., and Zhorov, B. S. (2014) Homology modeling of Kv1.5 channel block by cationic and electroneutral ligands, Biochim. Biophys. Acta 1838, 978-987. [14] Eldstrom, J., and Fedida, D. (2009) Modeling of high-affinity binding of the novel atrial antiarrhythmic agent, vernakalant, to Kv1.5 channels, J. Mol. Graph. Model. 28, 226-235. [15] Yang, Q., Du, L. P., Wang, X. J., Li, M. Y., and You, Q. D. (2008) Modeling the binding modes of Kv1.5 potassium channel and blockers, J. Mol. Graph. Model. 27, 178-187. [16] Jorgensen, C., Darre, L., Vanommeslaeghe, K., Omoto, K., Pryde, D., and Domene, C. (2015) In silico identification of PAP-1 binding sites in the Kv1.2 potassium channel, Mol. Pharm. 12, 1299-1307. [17] Wang, Y., Guo, J., Perissinotti, L. L., Lees-Miller, J., Teng, G., Durdagi, S., Duff, H. J., and Noskov, S. Y. (2016) Role of the pH in state-dependent blockade of hERG currents, Sci. Rep. 6, 32536. [18] Marzian, S., Stansfeld, P. J., Rapedius, M., Rinne, S., Nematian-Ardestani, E., Abbruzzese, J. L., Steinmeyer, K., Sansom, M. S., Sanguinetti, M. C., Baukrowitz, T., and Decher, N. (2013) Side pockets provide the basis for a new mechanism of Kv channel-specific inhibition, Nat. Chem. Biol., 507-513. [19] Jorgensen, C., Darré, L., Oakes, V., Torella, R., Pryde, D., and Domene, C. (2016) Lateral fenestrations in K+ channels explored using molecular dynamics simulations, Mol. Pharm. 13, 2263-2273. [20] Chen, X., Wang, Q., Ni, F., and Ma, J. (2010) Structure of the full-length Shaker potassium channel Kv1.2 by normal-mode-based X-ray crystallographic refinement, Proc. Natl. Acad. Sci. U. S. A. 107, 11352-11357.

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[21] Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J., and Schwede, T. (2009) Protein structure homology modeling using SWISS-MODEL workspace, Nat. Protoc. 4, 1-13. [22] Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., and Schulten, K. (2005) Scalable molecular dynamics with NAMD, J. Comput. Chem. 26, 1781-1802. [23] Klauda, J. B., Venable, R. M., Freites, J. A., O'Connor, J. W., Tobias, D. J., MondragonRamirez, C., Vorobyov, I., MacKerell, A. D., Jr., and Pastor, R. W. (2010) Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types, J. Phys. Chem. B 114, 7830-7843. [24] MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiórkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem. B 102, 3586-3616. [25] Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1982) Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79, 926-935. [26] Vanommeslaeghe, K., and MacKerell, A. D., Jr. (2012) Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing, J. Chem. Inf. Model. 52, 31443154. [27] Vanommeslaeghe, K., Raman, E. P., and MacKerell, A. D., Jr. (2012) Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges, J. Chem. Inf. Model. 52, 3155-3168. [28] Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., and Mackerell, A. D., Jr. (2010) CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields, J. Comput. Chem. 31, 671-690. [29] Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, J. Comput. Phys. 23, 327-341.

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Page 20 of 21

Page 21 of 21 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Biochemistry

[30] Miyamoto, S., and Kollman, P. A. (1992) SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models, J. Comput. Chem. 13, 952-962. [31] Martyna, G. J., Tobias, D. J., and Klein, M. L. (1994) Constant pressure molecular dynamics algorithms, J. Chem. Phys. 101, 4177-4189. [32] Allen, T. W., Andersen, O. S., and Roux, B. (2004) Energetics of ion conduction through the gramicidin channel, Proc. Natl. Acad. Sci. U. S. A. 101, 117-122. [33] Gordon, D., Chen, R., and Chung, S. H. (2013) Computational methods of studying the binding of toxins from venomous animals to biological ion channels: theory and applications, Physiol. Rev. 93, 767-802. [34] Finnin, M. (2010) Vernakalant: A novel agent for the termination of atrial fibrillation, Am. J. Health Syst. Pharm. 67, 1157-1164. [35] Aliot, E., Capucci, A., Crijns, H. J., Goette, A., and Tamargo, J. (2011) Twenty-five years in the making: flecainide is safe and effective for the management of atrial fibrillation, Europace 13, 161-173. [36] Chen, R., Gryn'ova, G., Wu, Y., Coote, M. L., and Chung, S. H. (2014) Mechanisms and energetics of potassium channel block by local anesthetics and antifungal agents, Biochemistry 53, 6786-6792. [37] Grossfield, A. (2013) "WHAM: the weighted histogram analysis method", version 2.0.9, http://membrane.urmc.rochester.edu/content/wham.

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