Molecular Mechanisms Of Herg Potassium Channel Interactions With Ivabradine: Importance Of The Lipophilic Route

Human-ether-a-go-go-related channel (hERG) is a voltage gated potassium channel expressed in heart and brain. hERG is notorious for its interaction with various medications blocking K+ transport, thereby prolonging action potentials and resulting in an arrhythmias. Even recently released antiarrhythmic agents such as ivabradine have been found to block hERG via unknown mechanisms. Common mechanisms of intracellular blockade of hERG imply access to major intra-cavitary binding site from the cytosol, while the second path involves the ligand passing through the membrane and interacting with the transmembrane channel via a lipophilic pathway. The recent solution of the high-resolution Cryo-EM structure for open-state of the hERG1 channel (PDB:5VA1) has provided an enhanced ability to resolve molecular details. Previous experimental and computational efforts conducted by our lab have demonstrated the feasibility of the lipophilic route for the ivabradine mediated block of hERG currents. This work used ivabradine as a molecular probe to map the lipophilic path of the drug binding to the open and closed states of hERG channel. We developed biomolecular CHARMM force field compatible parameters for a different ionization states of ivabradine and used all-atom molecular dynamics simulations to compute kinetics and thermodynamics of their partitioning through hydrated lipid membranes for different drug ionization states. The data combined from molecular docking and MD simulations of WT and mutated forms of hERG1 enabled mapping key residues interacting with ivabradine and drug localization in the membrane. The residues essential for lipophilic blockade were further tested by the combination of the site-directed mutagenesis and electrophysiological recordings. Our work established that ivabradine is interacting in the state-depending manner with the hydrophobic pocket formed by lipid-facing residues from S5-S6 helices of the channel, the feature that may explain blockers risk propensities for arrhythmogenesis.