Molecular determinants of pro-arrhythmia proclivity of d- and l-sotalol via a multi-scale modeling pipeline

Figures

• 

  Fig. 1.. Distribution of cationic(+) or neutral(0) d- or l-sotalol around the hERG channel from multi-μs long unbiased MD simulations. (A) Chemical structures of neutral(0) and cationic(+) forms of d- and l-sotalol (B) Snapshots of the molecular systems consisting of the hERG channel embedded in the POPC bilayer, solvated with aqueous 150 mM KCl and initial 50 mM sotalol solution, at the end of 8.1 μs MD simulations. For sotalol molecules within 3.5 Å of hERG protein residues non‑hydrogen atoms are shown in the colored space filling representation, non-interacting sotalol molecules are shown as gray sticks. The hERG channel is shown as green ribbons, POPC lipid tails as thin gray sticks, water as aquamarine surface, K+ and Cl− ions are not shown for clarity. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

• 

  Fig. 2.. Binding sites of neutral(0) or cationic(+) d- or l-sotalol around the hERG channel from 8.1 μs long unbiased MD simulations. (A) d-sotalol(0); (B) l-sotalol(0); (C) d-sotalol(+); (D) l-sotalol(+). Left panels: Time-series rendering for binding of one or two sotalol molecules (labeled M1 and M2) within the hERG pore. Sotalol molecules in the frames are shown by colored sticks from the beginning (red) to the end (blue) of each representative binding event. The hERG channel is shown in the initial (transparent green ribbons) and the final (solid green ribbons) conformations. Canonical drug interacting residues Phe656 and Tyr652 as well as selectivity filter (SF) residues are shown as solid or transparent atom-colored ribbons (C – gray, O – red, N – blue). Right panels: Representative binding poses adopted by sotalol molecules (thick atom-colored sticks with C – cyan, S – yellow, others as above) in the hERG channel pore. Interacting hERG residues (within 3.5 Å of any non-H atoms of the drug) are shown as thick atom-colored sticks (C – gray, others are as above). Non-interacting hERG residues Phe656, Tyr652 as well as its SF residues are shown as thin pink, blue and yellow sticks.…

• 

  Fig. 3.. Representative binding poses of neutral(0) and cationic(+) d- and l-sotalol to open hERG channel obtained from US-MD simulations. (A) hERG channel – bound sotalol structures from four US-MD runs corresponding to free energy minima for each simulation are superimposed and represented by different shades. Two opposite chains of the open-state hERG channel structures are shown as green ribbons. Bound sotalol molecules are shown as thick colored sticks: d-sotalol(0) – blue, d-sotalol(+) – purple, l-sotalol(0) – orange, and l-sotalol(+) – red. hERG SF residues are shown as yellow thin sticks, and canonical binding residues F656 and Y652 as thin pink and ice-blue sticks. (B) Close-up views of sotalol hERG binding poses corresponding to a dotted black box location in panel A. Sotalol molecules are shown as thick atom-colored sticks (C – cyan, N – blue, O – red, S – yellow). hERG channel is shown by transparent green ribbons with residues within 3.5 Å of sotalol non‑hydrogen atoms shown by thin atom-colored sticks (C – gray, N – blue, O – red). Non-interacting SF, F656 and Y652 residues are shown by thin colored sticks as in panel A. Hydrogen atoms are not shown for clarity. Box border…

• 

  Fig. 4.. Thermodynamics and kinetics of d- and l-sotalol binding to the open hERG pore from US-MD simulations. Free energy, ΔG, profiles (A) and corresponding diffusion coefficient, D, profiles (C) computed from US-MD simulations, and (B) free energy, ΔG, profiles alternatively computed from HREUS-MD simulations for d-sotalol(0) (blue), d-sotalol(+) (purple), l-sotalol(0) orange, and l-sotalol(+) (red). Error bars are computed from block averaging and represent standard errors of mean. (D) Molecular snapshots of d-sotalol(0) simulated systems with two opposite chains of the open hERG channel shown as green ribbons, selectivity filter residues shown as yellow sticks, and sotalol molecule shown in blue space-filling representation at the pore binding site (opaque) or in the bulk aqueous solution (transparent). The reaction coordinate for these simulations is the z-coordinate with respect to the SF backbone Cα center of mass, leading from the intracellular bulk aqueous solution (z = −50 Å) to the bottom of the selectivity filter (z = −5.5 Å), shown as an arrow and a bounding box with a 20 Å width corresponding to a diameter of the flat-bottom restraint in the xy-plane. (For interpretation of…

• 

  Fig. 5.. d- and l-Sotalol concentration-response data from patch clamp electrophysiology experiments. (Upper panels) Whole-cell currents from HEK-293 cells expressing hERG channels in response to voltage-clamp pulses from −80 mV to +20 mV and then to −60 mV to record pulse-current and tail currents, respectively. Black lines indicate the control currents and blue as well as red lines indicate the decreased currents in the presence of 300 μM of d- or l-sotalol, respectively. (Bottom panel) Concentration-response for block of hERG channels by d- (blue) or l-sotalol (red). Drug effects on tail current peak amplitude are plotted. Data are means ± standard error of means (SEM) from 3 cells each for d- or l-sotalol. Blue and red curves represent the fitted Hill equation.

• 

  Fig. 6.. Concentration dependent block of hERG and QT prolongation by sotalol. (A) Experimentally measured dose dependent inhibition of hERG channel by sotalol (colored symbols) and model 1 optimization based on experiments by us and others from expressed channels in mammalian cell lines for d-sotalol (solid light-blue line) and for l-sotalol (dashed black line). Black box indicates therapeutic plasma concentrations. Experimental data are from: Kramer et. al, 2013 – ref. [117]; Duff et. al., 1995 – ref. [80]; Perrin et. al., 2008 – ref. [79]; and this work – see Fig. 5. (B) Concentration dependent increase in QT intervals by d,l-sotalol with hERG channel block alone (blue circles) compared to clinical data (black diamonds) from ref. [82]. (C) During sympathetic stimulation via concurrent ISO 1 μM application, simulations showed a concentration dependent increase in QT interval by d,l-sotalol dependent hERG block and βAR blockade (blue asterisks) compared to clinical data from ref. [82] (black diamonds). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

• 

  Fig. 7.. Validation of computational drug screening with human clinical data. (A) Experimentally measured dose dependent inhibition of hERG by sotalol (colored symbols) and model 2 optimization for d-sotalol (solid red line) and for l-sotalol (dashed black line) using data from ref. [80]. See Fig. 6 caption for sources of experimental data. (B) Concentration dependent increase in QT intervals by d,l-sotalol with hERG channel block alone (red circles) compared to clinical data (black diamonds) from ref. [82]. (C) During concurrent ISO 1 μM application to model sympathetic stimulation, model 2 simulations showed a concentration dependent increase in QT interval by d,l-sotalol dependent hERG block and βAR blockade (red asterisks), which compared well to clinical data from ref. [82] (black diamonds).

• 

  Fig. 8.. Model prediction of sotalol effects on hERG block and βAR blockade during ISO 1 μM application. The timecourse of pseudo ECGs of model 2 between 820 and 830 s (red bars) at three sotalol plasma concentrations are shown in the left columns of every panel. The peaks of R and T waves are plotted during a 1000 s long simulation timecourse as summary data shown in the right columns of every panel. (A) The predicted additive effect of d-sotalol to block hERG and βAR did not abolish EADs at any tested concentrations. (B) l-sotalol with both hERG and βAR blockade abolished EADs at 1200 ng/ml and higher concentrations. (C) Similar to l-sotalol, racemic d,l-sotalol 1200 ng/ml removed EADs. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)