Computational assay of hERG ion permeation and its modulation by small-molecule compounds

Abstract

The human ether-a-go-go-related gene (hERG) potassium channel is an important off-target in drug discovery, as its inhibition can disrupt cardiac repolarisation and cause potentially fatal arrhythmias. Despite its importance, the molecular mechanisms underlying hERG ion permeation and its modulation by small molecules remain elusive. Here, we use molecular dynamics simulations to reproduce sustained K+ permeation and single-channel conductance comparable to experimental measurements. Our simulations reproduce the characteristic asymmetry in hERG single-channel conductance and reveal a structural mechanism underlying this behaviour. We identify the conformational dynamics of S624, located at the innermost ion-binding site of the selectivity filter, as a determinant of this conductance asymmetry. Substitution of S624 with the canonical threonine abolishes conductance asymmetry by facilitating K+ entry into the S4 binding site. Simulations of classical hERG inhibitors from cryo-EM-derived binding poses show that bound inhibitors sterically occlude K+ access to the selectivity filter, with binding stabilised by interactions with hydrophobic residues lining the central cavity. In contrast, simulations of hERG activators support a fenestration binding mode consistent with mutagenesis data, in which PD-118057 and PD-307243 increase cavity K+ occupancy and enhance conductance by two- to threefold relative to the apo channel. Together, these results establish a molecular framework connecting hERG structure, ion permeation, and small-molecule modulation, providing a basis for directly assessing the functional consequences of compound binding.