Allosteric Coupling Between Drug Binding and the Aromatic Cassette in the Pore Domain of the hERG1 Channel: Implications for a State-Dependent Blockade.

Meruyert Kudaibergenova,James Lees-Miller,Sergei Yu Noskov,Hanif M Khan,Farhan Zahid,Jiqing Guo,Henry J Duff

doi:10.3389/fphar.2020.00914

Meruyert Kudaibergenova, James Lees-Miller + Show 5 more

Open Access

https://doi.org/10.3389/fphar.2020.00914

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Abstract

Human-ether-a-go-go-related channel (hERG1) is the pore-forming domain of the delayed rectifier K+ channel in the heart which underlies the IKr current. The channel has been extensively studied due to its propensity to bind chemically diverse group of drugs. The subsequent hERG1 block can lead to a prolongation of the QT interval potentially leading to an abnormal cardiac electrical activity. The recently solved cryo-EM structure featured a striking non-swapped topology of the Voltage-Sensor Domain (VSD) which is packed against the pore-domain as well as a small and hydrophobic intra-cavity space. The small size and hydrophobicity of the cavity was unexpected and challenges the already-established hypothesis of drugs binding to the wide cavity. Recently, we showed that an amphipathic drug, ivabradine, may favorably bind the channel from the lipid-facing surface and we discovered a mutant (M651T) on the lipid facing domain between the VSD and the PD which inhibited the blocking capacity of the drug. Using multi-microseconds Molecular Dynamics (MD) simulations of wild-type and M651T mutant hERG1, we suggested the block of the channel through the lipid mediated pathway, the opening of which is facilitated by the flexible phenylalanine ring (F656). In this study, we characterize the dynamic interaction of the methionine-aromatic cassette in the S5-S6 helices by combining data from electrophysiological experiments with MD simulations and molecular docking to elucidate the complex allosteric coupling between drug binding to lipid-facing and intra-cavity sites and aromatic cassette dynamics. We investigated two well-established hERG1 blockers (ivabradine and dofetilide) for M651 sensitivity through electrophysiology and mutagenesis techniques. Our electrophysiology data reveal insensitivity of dofetilide to the mutations at site M651 on the lipid facing side of the channel, mirroring our results obtained from docking experiments. Moreover, we show that the dofetilide-induced block of hERG1 occurs through the intracellular space, whereas little to no block of ivabradine is observed during the intracellular application of the drug. The dynamic conformational rearrangement of the F656 appears to regulate the translocation of ivabradine into the central cavity. M651T mutation appears to disrupt this entry pathway by altering the molecular conformation of F656.

Highlights

The human-ether-a-go-go-related gene encodes a homo-tetrameric potassium channel found in excitable cells such as neurons in the brain (Wymore et al, 1997; Papa et al, 2003), adrenal glands, heart and smooth muscle tissues throughout the human body (Warmke and Ganetzky, 1994; Wymore et al, 1997; Farrelly et al, 2003)
We explore in further detail the dynamics of the hydrophobic cassette (F656, F557, Y652, and M651) in WThERG1 and M651T-hERG1 channels
We investigated the binding routes of dofetilide and ivabradine by combining mutagenesis and electrophysiology invitro data with docking to the Molecular Dynamics (MD)-derived hERG1 structures (Figures 1 and 2)

Summary

Introduction

The human-ether-a-go-go-related gene (hERG1) encodes a homo-tetrameric potassium channel found in excitable cells such as neurons in the brain (Wymore et al, 1997; Papa et al, 2003), adrenal glands, heart and smooth muscle tissues throughout the human body (Warmke and Ganetzky, 1994; Wymore et al, 1997; Farrelly et al, 2003). The function of the channel is most studied in the cardiovascular system, where hERG1 encodes for the a-subunit of the rapid delayed rectifier K+ current (Ikr), contributing to phase 3 of the cardiac action potential and the QT interval observed in electrocardiograms (Trudeau et al, 1995). Most common congenital mutations in hERG1 result in reduced Ikr current, elongating the QT wave and potentially causing a Long QT Syndrome (Sanguinetti et al, 1995). Long QT syndrome is a serious condition related to torsade de pointes arrhythmias which may deteriorate into ventricular fibrillation and sudden cardiac death (Romano, 1965; Sanguinetti and Tristani-Firouzi, 2006). It was estimated that hundreds of patients suffered from sudden cardiac death and ventricular fibrillation due to the off-target block of hERG1, making the channel an object of intense pharmacological interest (Rampe et al, 1997). Elucidating the promiscuous block of the channel by drugs represents a major research question which may have a profound impact on human health and drug development

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