Molecular simulations reveal a mechanism for enhanced allosteric coupling between voltage-sensor and pore domains in KCNQ1 explaining its activation by ML277

The voltage-gated potassium channel KCNQ1 (KV7.1) is important for the repolarizing phase of the cardiac action potential. Activators of KCNQ1 may provide a strategy for the pharmacological treatment of congenital long QT syndrome, a genetic disorder caused by pathogenic variants in KCNQ1 that promote arrhythmia susceptibility and elevate risk for sudden cardiac death. The small-molecule agonist ML277 recovers function of mutant KCNQ1 channels in human induced pluripotent stem cell-derived cardiomyocytes and could represent a starting point for drug development. Here we investigated ML277 mode of action by developing a molecular model of the KCNQ1-ML277 interaction corroborated by experimental and computational analyses. Ligand docking and molecular dynamics simulation demonstrated that ML277 binds to the interface between the voltage sensor and pore domains in KCNQ1. Model predicted binding energies for ML277 and 62 chemical analogs of ML277 correlated with EC50 data available for these compounds. We identified novel ML277-interacting residues on the S5 and S6 segments of KCNQ1 by performing MM/PBSA energy calculations and site-directed mutagenesis of KCNQ1 coupled to electrophysiological characterization of the generated channel mutants. Network analysis of the molecular dynamics simulations further showed that ML277 increases the allosteric coupling efficiency between residues in the voltage sensor domain and residues in the pore domain. Derivatives of ML277 that are not active on KCNQ1 fail to increase allosteric coupling efficiency in the computational simulations. Our results reveal atomic details of the ML277 modulation of KCNQ1 activation. These findings may be useful for the design of allosteric modulators of KCNQ1 and other KCNQ channels that bind at the membrane-accessible protein surface. Statement of SignificanceThe potassium ion channel KCNQ1 contributes to the generation of electrical impulses in the heart. Heritable mutations in KCNQ1 can cause channel loss-of-function and predispose to a life-threatening cardiac arrhythmia. Small molecules that bind KCNQ1 and enhance channel function could establish a novel anti-arrhythmic drug paradigm. We used molecular simulations to investigate how a small agonist of KCNQ1 (ML277) binds to the KCNQ1 channel and increases its function. We identified amino acids that are responsible for ML277 binding and show how ML277 promotes signaling in KCNQ1 and channel opening. This work advances our understanding how KCNQ1 and possibly other potassium channels can be activated with small molecules. These data provide a framework for drug development studies.