Drug Binding Interactions in the Inner Cavity of hERG Channels: Molecular Insights from Structure-Activity Relationships of Clofilium and Ibutilide Analogs

Abstract

Block of human ether-a-go-go related gene (hERG) Kϩ channels by otherwise useful drugs is the most common cause of long QT syndrome, a disorder of cardiac repolarization that predisposes patients to potentially fatal arrhythmias. This undesirable long QT side effect has been a major reason for the withdrawal of medications from the pharmaceutical market. Understanding the molecular basis of hERG block is therefore essential to facilitate the design of safe drugs. Binding sites for hERG blockers have been mapped within the inner cavity of the channel and include aromatic residues in the S6 helix (Tyr-652, Phe-656) and residues in the pore helix (Thr-623, Ser-624, Val-625). We used mutagenesis of these residues, combined with an investigation of hERG block by close analogs of clofilium and ibutilide, to assess how specific alterations in drug structure affected potency and binding interactions. Although changing the basic nitrogen from quaternary to tertiary accelerated the onset of block, the IC 50 and kinetics for recovery from block were similar. In contrast, analogs with different para-substituents on the phenyl ring had significantly different potencies for wild-type hERG block. The highest potency was achieved with polar or electronegative para-substituents, whereas neutral para-substituents had potencies more than 100-fold lower. Results from mutagenesis and molecular modeling studies suggest that phenyl ring para-substituents influence drug interactions with Thr-623, Ser-624, and Tyr-652 and strongly affect binding affinity. Together, these findings suggest that modifying the para-substituent could be a useful strategy for reducing hERG potency and increasing the safety margin of compounds in development.

Integrating cardiomyocytes from human pluripotent stem cells in safety pharmacology: has the time come?

“…It is a recurring condition for the K v 11.1 channel [encoded by the human ether‐à‐go‐go‐related gene (hERG) also called KCNH2 ], which, together with its β‐subunit MinK‐related peptide 1, is responsible for I Kr . Key aromatic residues in the S6 helix (Tyr 652 , Phe 656 ) and the pore helix (Thr 623 , Ser 624 , Val 625 ) of the K v 11.1 channel have been identified as the detrimental target of a broad spectrum of compounds (Perry, 2005) that impair K + ion flux through the pore and therefore reduce I Kr . This generates a prolongation of the QT interval of the electrocardiogram (ECG), with the potential occurrence of a polymorphic form of ventricular tachycardia known as torsades de pointes (TdP), which can cause sudden death (Sanguinetti and Tristani‐Firouzi, 2006).…”

In Silico Prediction of the Chemical Block of Human Ether-a-Go-Go-Related Gene (hERG) K+ Current

“…A closed conformation state model of hERG has been also used as a template for docking studies [45,99]. By rotating the S6 helix of the closed conformation model, Perry et al (2006) [45] suggested that most compounds position along the ion conduction pathway and that the geometrical arrangement of features are in good agreement with pharmacophore distribution predicted by a ligand-based approach [17].…”

“…By rotating the S6 helix of the closed conformation model, Perry et al (2006) [45] suggested that most compounds position along the ion conduction pathway and that the geometrical arrangement of features are in good agreement with pharmacophore distribution predicted by a ligand-based approach [17]. MK-499 was reported to be retained in the central cavity, and hERG was in the closed state [100].…”

“…Phe656 on the same helix is involved in the association with blockers through hydrophobic/π-stacking interaction [42][43][44]. Furthermore, hydroxyl groups of Thr623 and Ser624 in a loop between the pore helix and the selectivity filter are thought to be involved in blocker-hERG association through hydrogen bonding [45]. These experimentally identifi ed elements of interaction between compounds and hERG do not match with the features identified by in silico analysis, and the orientation of the pharmacophore within the central cavity of the hERG pore is also ambiguous.…”

Procaine, a State-Dependent Blocker, Inhibits HERG Channels by Helix Residue Y652 and F656 in the S6 Transmembrane Domain

“…Most HERG-blocking drugs that have been examined for their molecular determinants of blockade have been shown to be dependent on a variety of amino-acid residues in the pore-S6 region (the inner lining of the pore). Alanine-scanning mutagenesis has previously been used to determine residues important for block of the HERG channel (5,26), which showed that drug-induced blockade was dependent on a variety of amino-acid residues in the S6 helices. Presumably, the residues of S6 that face into the vestibule and those residues deep in the selectivity filter might trap drugs within the vestibule and contribute to their efficacy of block.…”