Three-Dimensional Quantitative Structure-Activity Relationship for Inhibition of Human Ether-a-Go-Go-Related Gene Potassium Channel
Jun 08, 2002 • By SEAN EKINS, WILLIAM J. CRUMB, R. DUSTAN SARAZAN, JAMES H. WIKEL, and STEVEN A. WRIGHTON
Abstract
The protein product of the human ether-a-go-go gene (hERG) is a potassium channel that when inhibited by some drugs may lead to cardiac arrhythmia. Previously, a three-dimensional quantitative structure-activity relationship (3D-QSAR) pharmacophore model was constructed using Catalyst with in vitro inhibition data for antipsychotic agents. The rationale of the current study was to use a combination of in vitro and in silico technologies to further test the pharmacophore model and qualitatively predict whether molecules are likely to inhibit this potassium channel. These predictions were assessed with the experimental data using the Spearman’s rho rank correlation. The antipsychotic-based hERG inhibitor model produced a statistically significant Spearman’s rho of 0.71 for 11 molecules. In addition, 15 molecules from the literature were used as a further test set and were also well ranked by the same model with a statistically significant Spearman’s rho value of 0.76. A Catalyst General hERG pharmacophore model was generated with these literature molecules, which contained four hydrophobic features and one positive ionizable feature. Linear regression of log-transformed observed versus predicted IC50 values for this training set resulted in an r2 value of 0.90. The model based on literature data was evaluated with the in vitro data generated for the original 22 molecules (including the antipsychotics) and illustrated a significant Spearman’s rho of 0.77. Thus, the Catalyst 3D-QSAR approach provides useful qualitative predictions for test set molecules. The model based on literature data therefore provides a potentially valuable tool for discovery chemistry as future molecules may be synthesized that are less likely to inhibit hERG based on information provided by a pharmacophore for the inhibition of this potassium channel.
In recent years several drugs have been withdrawn from the market due to cardiovascular toxicity associated with QT interval prolongation. Considerable interest in predicting this effect by noncardiovascular drugs earlier in their development has occurred since the issuance by the European pharmaceutical regulatory authority, the Committee of Proprietary Medicinal Products, of a position on QT interval prolongation in 1997 (Committee of Proprietary Medicinal Products/986/96). The focus of many in vitro studies to date is the membrane-bound inward (rapid activating delayed) rectifier potassium channel (IKr) [also known as the product of the human ether-a-go-go-related gene (hERG)]. This channel contributes to phase 3 repolarization by opposing the depolarizing Ca2 influx during the plateau phase (Crumb and Cavero, 1999). Drugs or their metabolites may block this channel, thereby prolonging the QT interval and in some cases leading to the potentially life-threatening ventricular arrhythmia. QT prolongation may frequently result in torsades de pointes (twisting of the points), which refers to the sinusoidal variation in the QRS axis around the isoelectric line of the electrocardiogram. The end result of torsades de pointes is a ventricular tachyarrhythmia, with the prolongation of the QT interval of the last sinus beat that precedes the onset of arrhythmia. Possession of a mutation in hERG (Curran et al., 1995) or KCNE2 (Sesti et al., 2000) in the form of a single nucleotide polymorphism, may make carriers particularly sensitive to xenobiotics that in turn affect potassium currents and trigger arrhythmic events (Crumb and Cavero, 1999). It would be of considerable value in drug discovery to understand the structural requirements of inhibitors of this potassium channel before significant investment is made in a clinical candidate that may ultimately prove to be a potent hERG inhibitor. The understanding of important structural features of molecules (the pharmacophore) that inhibit hERG would enable the prediction of inhibition before molecule synthesis. Such information would reduce the likelihood of developing drugs that could lead to a life-threatening ventricular arrhythmia. At present, various in vivo and in vitro models for QT prolongation and subsequent arrhythmia exist but they may not be entirely predictive for humans. Perhaps the closest model to the human in vivo situation would be healthy human-derived cardiac tissue, but this is not readily available (Rees and Curtis, 1996). However, various cell systems expressing the hERG channel have been developed using Xenopus oocytes (Sanguinetti et al., 1995) and mammalian cell lines such as human embryonic kidney (HEK)-293 (Smith et al., 1996). The latter are perhaps more amenable to higher throughput testing but are themselves beset with limitations due to the level of expression of the channel.