Structural basis for antiarrhythmic drug interactions with the human cardiac sodium channel

Figures

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  Fig. 1.. Rosetta model of the hNaV1.5 channel. (A) (Left) Extracellular and (Right) transmembrane views of the hNaV1.5 model shown in ribbon representation. (Insets) Zoom-in views of putative drug binding residues within hNaV1.5 pore lumen. Each domain is colored individually and labeled. In Insets, DIII residues are labeled orange, whereas DIV residues are labeled red. (B) (Left) Extracellular and (Center and Right) transmembrane views of all four hNaV1.5 fenestrations using molecular surface representation (shown in purple in Left and Center). In Right, fenestration-facing residue sidechains are labeled and shown in space-filling representations using corresponding domain colors, with O atoms shown in red. (C) (Left) The hNaV1.5 pore lumen radius (R) profile changes during molecular dynamic simulation at time 0 (colored red), at 0.5 μs (colored cyan), and at 1 μs (colored orange). A pore lumen R profile for a cryoEM eeNaV1.4 structure is also shown in gray for comparison. (Right) Sodium ion trajectories within the PD during a 1-μs molecular dynamic simulation of hNaV1.5.

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  Fig. 2.. Rosetta models of hNaV1.5 channel interaction with antiarrhythmic and local anesthetic drugs. Close-up (Left) transmembrane and (Right) extracellular views of hNaV1.5 interactions with (A) neutral lidocaine, (B) charged lidocaine, (C) QX-314, and (D) charged etidocaine. Drug molecules are shown in the wireframe representations, with basic N atoms depicted as purple balls. The hNaV1.5 DI is colored in blue, DII is colored in green, DIII is colored in gray, and DIV is colored in yellow. Sidechains of key residues forming the receptor site in DIIIS6 and DIVS6 segments are shown in stick representation and labeled in orange and red, respectively.

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  Fig. 3.. Rosetta models of hNaV1.5 channel interaction with antiarrhythmic and local anesthetic drugs. Close-up (Left) transmembrane and (Right) extracellular view of hNaV1.5 interactions with (A) flecainide and (B) ranolazine. Drug molecules are shown in the wireframe representations, with flecainide F atoms colored in green and basic N atoms of both drugs depicted as purple balls. The hNaV1.5 DI is colored in blue, DII is colored in green, DIII is colored in gray, and DIV is colored in yellow. Sidechains of key residues forming the receptor site in DIIIS6 and DIVS6 are shown in stick representation and labeled in orange and red, respectively.

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  Fig. 4.. MD simulation of the hNaV1.5 channel interaction with neutral lidocaine reveals two drug access pathways. (A) Free energy surface of neutral lidocaine binding projected on the y−z plane (with z corresponding to a transmembrane axis). Binding sites for neutral lidocaine, identified from free energy minima, are labeled as intracellular I1-5, channel pore C1-2, and extracellular E1-6. (B) Transmembrane view of the channel, with neutral lidocaine binding sites represented as colored surfaces. Colors and sizes are for clarity, not actual binding properties. (C) Close-up view of binding sites forming the hydrophobic (orange arrows) and hydrophilic (gray arrows) binding pathways. Lidocaine molecules (orange) and interacting residues on the channel (cyan for C, red for O, and blue for N) are shown using stick representation.

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  Fig. 5.. MD simulation of the hNaV1.5 channel interaction with neutral lidocaine reveal two binding poses: (A) states NA1 and NA2 for one lidocaine bound in the pore lumen and (B) NB1 and NB2 for two lidocaine molecules binding in the pore lumen at the same time. (Left) Free energy surfaces projected on the y−z plane, with binding sites identified from free energy minima and labeled. (Center and Right) Close-up transmembrane views of molecular models of charged lidocaine binding. In the close-up views, lidocaine molecules (orange and dark gray) and interacting residues on the channel (red) as well as SF DEKA motif (cyan for C, blue for N, and red for O) are shown using stick representation. Lidocaine basic N atoms are shown as small purple spheres, and an SF bound Na+ atom is shown as a yellow sphere.

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  Fig. 6.. MD simulation of hNaV1.5 channel interaction with charged lidocaine reveal two binding poses: (A) states CA1 and CA2 for one lidocaine bound in the pore lumen and (B) CB1 and CB2 for two lidocaine molecules binding in the pore lumen at the same time. (Left) Free energy surface projected on the y−z plane, with binding sites identified from free energy minima and labeled. (Middle and Right) Close-up transmembrane views of molecular models of charged lidocaine binding. SF DEKA motif residues are shown in stick representation and colored in cyan for C, blue for N, and red for O. Sodium ions are shown as spheres and colored in yellow. Lidocaine molecules are shown in stick representation and colored in gray or orange. The nitrogen atoms of the tertiary ammonium groups on charged lidocaine molecules are shown as small spheres and colored in purple. The F1760 sidechain is shown in stick representation and colored in red.

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  Fig. 7.. MD simulations reveal the free energy surfaces and binding sites for sodium ion within hNaV1.5 pore. (A) Transmembrane view projection of the free energy surface for sodium ion without lidocaine and in the presence of one or two neutral or charged lidocaine molecules. Specific Na+ binding sites are labeled S0, S1, S2, and S3 in the molecular representation of the channel SF on the right. (B) Representative transmembrane views of sodium ion binding sites within the SF region of the channel observed without lidocaine and in the presence of one or two neutral or charged lidocaine molecules. Sodium ions are shown as yellow spheres. The SF region residues are shown in stick representation and labeled.