Small conductance Ca 2+ -activated K + channels (SK or K Ca 2) couple beat-to-beat intracellular Ca 2+ rises to membrane potential in atria. In atrial fibrillation (AF), increased SK channel activity shortens atrial action potential duration and promotes reentrant arrhythmia. Since SK channels are more abundant in atria compared to ventricles, they represent promising AF targets. However, no SK-selective drug has been approved to-date. Moreover, how distinct SK2 channel modulators alter channel conformations and function remains unclear. Here, we compare four small molecules with distinct SK2 binding sites. NS309 binds at the calmodulin (CaM)-channel interface and acts as a positive modulator. AP14145 binds the inner cavity to inhibit SK2 channel. UCL1684 engages the external canopy motif above the selectivity filter and blocks the pore. AP30663 is an SK2 inhibitor with an unknown binding site. We used recent cryogenic-electron microscopy structures of the SK2 channel. Ligand docking with Rosetta GALigandDock was performed to estimate relative binding free energies and to propose a potential binding site for AP30663. Drug-flooding molecular dynamics (MD) simulations map drug binding pathways and conformational state preferences. All-atom MD simulations were performed in multiple SK2 conformational states with and without each modulator. Conformational changes were quantified by analyzing the hydrophobic gate radius of the pore, relative drug binding free energies, and relative Ca 2+ affinities. Membrane curvature was also analyzed across MD simulations. This is motivated by the observation that unlike a homologous SK4 channel, SK2 channel induces local bending of the membrane in MD simulations. We tested how these properties correlate with modulator-induced protein structural changes. This work provides new insights into how SK2 channel modulators work at the molecular level, paving the way for rational design of novel atrial-selective therapeutics for AF to improve their efficacy and decrease proarrhythmic risk.
Choi et al. (Sun,) studied this question.