Computational investigations of hERG channel blockers: New insights and current predictive models

Identification of potential human Ether-a-go-go Related-Gene (hERG) potassium channel blockers is an essential part of the drug development and drug safety process in pharmaceutical industries or academic drug discovery centers, as they may lead to drug-induced QT prolongation, arrhythmia and Torsade de Pointes. Recent reports also suggest starting to address such issues at the hit selection stage.In order to prioritize molecules during the early drug discovery phase and to reduce the risk of drug attrition due to cardiotoxicity during pre-clinical and clinical stages, computational approaches have been developed to predict the potential hERG blockage of new drug candidates.In this review, we will describe the current in silico methods developed and applied to predict and to understand the mechanism of actions of hERG blockers, including ligand-based and structure-based approaches. We then discuss ongoing research on other ion channels and hERG polymorphism susceptible to be involved in LQTS and how systemic approaches can help in the drug safety decision.     

Towards automation of a valuable preclinical cardiac safety pharmacology assay: Evaluation of the effects of cardiac ion channel blockers on cardiac repolarisation in vitro

INTRODUCTION: Purkinje fibre repolarisation assays are valuable tools for identifying compounds which affect cardiac ion channels. The throughput of compound testing in this assay is low therefore we designed a novel recording system to improve screening and animal tissue usage efficiencies. METHODS: The system was used to evaluate compounds using standard sharp microelectrode techniques. Animal tissue usage efficiencies were quantified by adding up the total number of Purkinje fibres from which recordings were attempted and dividing this by the number of experimental data sets generated, to arrive at a 'fibres per data set' ratio. Test compounds were dofetilide (3 x 10(-10) to 10(-8) M), cisapride (10(-8) to 3 x 10(-7) M), terodiline (10(-6) to 3 x 10(-5) M) and verapamil (3 x 10(-7) to 10(-5) M). RESULTS: Using the novel modified system, 21 data sets were generated from 29 fibres, compared to 24 data sets from 41 fibres using the conventional manual recording system, demonstrating a 24% improvement in the efficiency of animal tissue usage. Comparing data from the manual and modified systems revealed differences in absolute values for all parameters including APD90 (308.73 +/- 9.97 ms, n = 24, compared to 275.27 +/- 8.25 ms, n = 21, respectively; P < 0.05). Differences in the magnitude of changes in action potential parameters between the systems were also evident for all compounds including terodiline (1 x 10(-5) M) which caused a -27.1 +/- 16.5% reduction in APD50 in the manual system, compared to a - 55.2 +/- 2.2% reduction in the modified system. DISCUSSION: Although the value of the present study is limited by the small sample sizes, it has demonstrated utility of the modified system in improving efficiency of animal tissue usage. It offers potential utility in a higher throughput screening environment for examining the electrophysiological properties of novel compounds in native cardiac tissues, particularly where functional patch clamp data are limited.     

Effects of estradiol on cardiac ion channel currents

Steroids are known to exert direct and indirect effects on cardiovascular functions, and women have been found to be more susceptible to QT prolongation than men. Although many clinical studies have been performed, the effects of steroids on cardiac repolarization are not yet fully understood. We examined the effects of 17-beta-estradiol (estradiol) on the major cardiac currents that are correlated to clinical observations of arrhythmias. Effects on the two major currents responsible for repolarization of the cardiac action potential (mediated by the human ether-à-gogo related gene (HERG) product), and by the potassium channel Q1 (KCNQ1) co-expressed with the potassium channel accessory subunit E1 (KCNE1) were examined, as well as effects on the sodium inward current (mediated by the sodium channel 5A (SCN5A) and generating the rapid upstroke of the action potential). A concentration-dependent effect of estradiol on the KCNQ1/KCNE1-mediated potassium current was observed. The half-maximal inhibition concentration (IC(50)) of estradiol on the KCNQ1/KCNE1 ion channel was calculated to 1.13+/-0.23 microM. The HERG-mediated potassium and the SCN5A-mediated sodium currents, however, were only slightly reduced by estradiol at concentrations of up to 30 microM. This suggests that alterations of the cardiac action potentials by steroids may be mediated by interaction with the KCNQ1/KCNE1 ion channel.     

Computational models for cytochrome P450: a predictive electronic model for aromatic oxidation and hydrogen atom abstraction.

Experimental observations suggest that electronic characteristics play a role in the rates of substrate oxidation for cytochrome P450 enzymes. For example, the tendency for oxidation of a certain functional group generally follows the relative stability of the radicals that are formed (e.g., N-dealkylation > O-dealkylation > 2 degrees carbon oxidation > 1 degree carbon oxidation). In addition, results show that useful correlations between the rates of product formation can be developed using electronic models. In this article, we attempt to determine whether a combined computational model for aromatic and aliphatic hydroxylation can be developed. Toward this goal, we used a combination of experimental data and semiempirical molecular orbital calculations to predicted activation energies for aromatic and aliphatic hydroxylation. The resulting model extends the predictive capacity of our previous aliphatic hydroxylation model to include the second most important group of oxidations, aromatic hydroxylation. The combined model can account for about 83% of the variance in the data for the 20 compounds in the training set and has an error of about 0.7 kcal/mol.     

Measurements of cardiac ion channel subunits in the chronic atrioventricular block dog

The chronic atrioventricular block (CAVB) dog has been widely used as an in vivo proarrhythmia model. mRNA levels of K(+) and Ca(2+) channels in the isolated ventricular tissues from normal and CAVB dogs were assayed using a real-time PCR. The mRNA levels of KvLQT1 and MiRP1 were significantly less in the CAVB heart compared with those in the intact heart, whereas no significant difference was detected in the mRNA levels of other K(+)- or Ca(2+)-channel subunits. Adaptation against chronic bradycardia-related pathophysiology may have decreased the mRNA levels of cardiac K(+) channels, which may partly explain the arrhythmogenic property of this model.     

GBR12909 possesses anticonvulsant activity in zebrafish and rodent models of generalized epilepsy but cardiac ion channel effects limit its clinical utility

BACKGROUND/AIMS: GBR12909 has been reported to possess anticonvulsant activity with focal brain perfusion to the hippocampus of pilocarpine, although an earlier publication suggested any anticonvulsant effects were only mild. Here we further explored the anticonvulsant potential of GBR12909 with a suite of anticonvulsant assays in both zebrafish and mammals and then explored whether it possessed any QT effects which might limit clinical utility. METHODS: We assessed the anticonvulsant effects of GBR12909 in zebrafish pentylenetetrazole (PTZ), mammalian maximal electroshock and PTZ models of generalized epilepsy and a rodent hippocampal kindling model. Cardiac effects were assessed in zebrafish and man. RESULTS: GBR12909 possesses anticonvulsant activity in zebrafish and rodent models of generalized epilepsy. However, phase 1 human data indicated potential QT effects. Subsequent testing in a zebrafish QT assay confirmed marked arrhythmogenic potential. CONCLUSION: Further clinical development of GBR12909 in epilepsy was considered inappropriate because of insufficient window between the therapeutic effects and the cardiac arrhythmia problems identified in zebrafish assays. Any further development based on this mechanism of action should avoid the GBR12909 chemical scaffold, or involve structure-activity dissociation of its neurological and cardiac effects.     

Computational assessment of drug-induced effects on the electrocardiogram: from ion channel to body surface potentials

Background and Purpose

Understanding drug effects on the heart is key to safety pharmacology assessment and anti-arrhythmic therapy development. Here our goal is to demonstrate the ability of computational models to simulate the effect of drug action on the electrical activity of the heart, at the level of the ion-channel, cell, heart and ECG body surface potential.

Experimental Approach

We use the state-of-the-art mathematical models governing the electrical activity of the heart. A drug model is introduced using an ion channel conductance block for the hERG and fast sodium channels, depending on the IC₅₀ value and the drug dose. We simulate the ECG measurements at the body surface and compare biomarkers under different drug actions.

Key Results

Introducing a 50% hERG-channel current block results in 8% prolongation of the APD₉₀ and 6% QT interval prolongation, hERG block does not affect the QRS interval. Introducing 50% fast sodium current block prolongs the QRS and the QT intervals by 12% and 5% respectively, and delays activation times, whereas APD₉₀ is not affected.

Conclusions and Implications

Both potassium and sodium blocks prolong the QT interval, but the underlying mechanism is different: for potassium it is due to APD prolongation; while for sodium it is due to a reduction of electrical wave velocity. This study shows the applicability of in silico models for the investigation of drug effects on the heart, from the ion channel to the ECG-based biomarkers.     

The effects of jaspamide on human cardiomyocyte function and cardiac ion channel activity

Jaspamide (jasplakinolide; NSC-613009) is a cyclodepsipeptide that has antitumor activity. A narrow margin of safety was observed between doses required for efficacy in mouse tumor models and doses that caused severe acute toxicity in rats and dogs. We explored the hypothesis that the observed toxicity was due to cardiotoxicity. Jaspamide was tested in a patch clamp assay to determine its effect on selected cardiac ion channels. Jaspamide (10 μM) inhibited Kv1.5 activity by 98.5%. Jaspamide also inhibited other channels including Cav1.2, Cav3.2, and HCN2; however, the Kv11.1 (hERG) channel was minimally affected. Using spontaneously contracting human cardiomyocytes derived from induced pluripotent stem cells, effects on cardiomyocyte contraction and viability were also examined. Jaspamide (30 nM to 30 μM) decreased cardiomyocyte cell indices and beat amplitude, putative measurements of cell viability and cardiac contractility, respectively. Concentration-dependent increases in rhythmic beating rate were noted at ?6 h of treatment, followed by dose-dependent decreases after 6 and 72 h exposure. The toxic effects of jaspamide were compared with that of the known cardiotoxicant mitoxantrone, and confirmed by multiparameter fluorescence imaging analysis. These results support the hypothesis that the toxicity observed in rats and dogs is due to toxic effects of jaspamide on cardiomyocytes.     

Computational models for prediction of interactions with ABC-transporters

The polyspecific ligand recognition pattern of ATB-binding cassette (ABC)-transporters, combined with the limited knowledge on the molecular basis of their multispecificity, makes it difficult to apply traditional molecular modelling and quantitative structure-activity relationships (QSAR) methods for identification of new ligands. Recent advances relied mainly on pharmacophore modelling and machine learning methods. Structure-based design studies suffer from the lack of available protein structures at atomic resolution. The recently published protein homology models of P-glycoprotein structure, based on the high-resolution structure of the bacterial ABC-transporter of Sav1866, may open a new chapter for structure-based studies. Last, but not least, molecular dynamics simulations have already proved their high potential for structure-function modelling of ABC-transporter. Because of the recognition of several ABC-transporters as antitargets, algorithms for predicting substrate properties are of increasing interest.     

Structural identifiability for mathematical pharmacology: models of myelosuppression

Structural identifiability is an often overlooked, but essential, prerequisite to the experiment design stage. The application of structural identifiability analysis to models of myelosuppression is used to demonstrate the importance of its considerations. It is shown that, under certain assumptions, these models are structurally identifiable and so drug and system specific parameters can truly be separated. Further it is shown via a meta-analysis of the literature that because of this the reported system parameter estimates for the “Friberg” or “Uppsala” model are consistent in the literature.     

Gastrointestinal-tract models and techniques for use in safety pharmacology

Introduction: The human ether-a-go-go-related gene (hERG) encodes a potassium channel responsible for the cardiac delayed rectifier current (I_Kr) involved in ventricular repolarization. Drugs that block hERG have been associated with QT interval prolongation and serious, sometimes fatal, cardiac arrhythmias (including torsade de pointes). While displacement of [³H]dofetilide, a potent methanesulfonanilide hERG blocker, from cells heterologously expressing hERG has been suggested as a screening assay, questions have been raised about its predictive value.Methods: To validate the utility of this assay as a screening tool, we performed a series of saturation and competition binding studies using [³H]dofetilide as ligand and either intact cells or membrane preparations from HEK 293 cells stably transfected with hERG K⁺ channels. The object of these experiments was to (1) compare binding K_i values for 22 hERG blockers using intact cells or membrane homogenates to determine whether maintaining cell integrity enhanced assay reliability; (2) evaluate the ability of different K⁺ concentrations (2, 5, 10, 20, and 60 mM) to modulate hERG binding; and (3) to establish the predictive value of the assay by comparing K_i values from binding studies at 5 and 60 mM [K⁺]_o to functional IC₅₀ values for hERG current block using 56 structurally diverse drugs.Results: We found (a) comparable K_i values in the intact cell and isolated membrane binding assays, although there were some differences in rank order; (b) increasing [K⁺]_o lowered the K_d and increased the B_max for [³H]dofetilide, particularly in the membrane assay; and (c) good correlation between binding K_i values and functional IC₅₀ values for hERG current block.Discussion: In conclusion, increasing K⁺ concentrations results in an increase in both [³H]dofetilide affinity for hERG and available binding sites, particularly when using membrane homogenates. There are no meaningful differences between K_i values when comparing intact cell versus membrane assay, neither are there meaningful trends with increasing [K⁺]_o within assays. There is good correlation between binding K_i values and functional (whole-cell patch clamp) IC₅₀ values at both 5 and 60 mM K⁺ concentrations (R² values of .824 and .863, respectively). The simplicity, predictability, and adaptability to high-throughput platforms make the [³H]dofetilide membrane binding assay a useful tool for screening and ranking compounds for their potential to block the hERG K⁺ channel.     

Computational models of antiviral toxicity

The high incidence of toxicity of antiviral drugs is a common complication in the long-term use of antiviral drugs to treat chronic viral infections, including HIV. This review describes the use of computational models to explore antiviral toxicity, concentrating on three series of recent papers that have used a combination of experimental and computational techniques to address the issue of antiviral toxicity from different viewpoints. The limitations of these studies are discussed and likely directions for future research are suggested.     

GABA(A) receptor channel pharmacology

GABA(A) receptor channels are ubiquitous in the mammalian central nervous system mediating fast inhibitory neurotransmission by becoming permeant to chloride ions in response to GABA. The emphasis of this review is on the rich chemical diversity of ligands that influence GABA(A) receptor function. Such diversity provides many avenues for the design and development of new chemical entities acting on GABA(A) receptors. There is also a significant diversity of GABA(A) receptor subtypes composed of different protein subunits. The discovery of subtype specific agents is a major challenge in the continuing development of GABA(A) receptor pharmacology. Leads for the discovery of new chemical entities that influence GABA(A) receptors come from using recombinant GABA(A) receptors of known subunit composition as has been elegantly demonstrated by the refining of benzodiazepine actions with alpha1 subunit preferring agents showing sedative properties but not anxiolytic properties. The most recent advances in the therapeutic use of agents acting on GABA(A) receptors concern the promotion of sound sleep. Many herbal medicines are used to promote sleep and many of their active ingredients include flavonoids and terpenoids known to modulate GABA(A) receptor function.     

Clinical pharmacology of potassium channel openers.

Opening of K+ channels in cell membranes with resulting increase in K+ conductance, shifts the membrane potential in a hyperpolarizing direction towards the K+ equilibrium potential. Hyperpolarization reduces the opening probability of ion channels involved in membrane depolarization and excitation is reduced. K+ channel openers are believed to hyperpolarize smooth muscle cells by a direct action on the cell membrane. The best known members of the group are cromakalim, nicorandil and pinacidil, but several new compounds are being evaluated. In addition, it has recently been shown that also clinically well-known drugs like, e.g. diazoxide and minoxidil exhibit K+ channel opening properties. Nicorandil and new compounds containing nitro groups have a dual mechanism of action, also activating guanylate cyclase, an effect that contributes to their cardiovascular effect profile. K+ channel openers have a wide range of effects. Some of their properties and actions are summarized, and their present applications and/or potential for future application, in e.g. hypertension, angina pectoris, asthma, bladder instability, and several other disorders are discussed. It is concluded that K+ channel openning represents an interesting pharmacological principle with many potential clinical applications. However, most available drugs do not seem to have a sufficient tissue selectivity to be useful therapeutic alternatives. Before the potential of the new members of the group on clinical trials can be properly evaluated, clinical experiences are needed.