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Escobar F, Friis S, Adly N, Brinkwirth N, Gomis-Tena J, Saiz J, Klaerke DA, Stoelzle-Feix S, Romero L. Experimentally validated modeling of dynamic drug-hERG channel interactions reproducing the binding mechanisms and its importance in action potential duration. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 254:108293. [PMID: 38936153 DOI: 10.1016/j.cmpb.2024.108293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/09/2024] [Accepted: 06/16/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND AND OBJECTIVE Assessment of drug cardiotoxicity is critical in the development of new compounds and modeling of drug-binding dynamics to hERG can improve early cardiotoxicity assessment. We previously developed a methodology to generate Markovian models reproducing preferential state-dependent binding properties, trapping dynamics and the onset of IKr block using simple voltage clamp protocols. Here, we test this methodology with real IKr blockers and investigate the impact of drug dynamics on action potential prolongation. METHODS Experiments were performed on HEK cells stably transfected with hERG and using the Nanion SyncroPatch 384i. Three protocols, P-80, P0 and P 40, were applied to obtain the experimental data from the drugs and the Markovian models were generated using our pipeline. The corresponding static models were also generated and a modified version of the O´Hara-Rudy action potential model was used to simulate the action potential duration. RESULTS The experimental Hill plots and the onset of IKr block of ten compounds were obtained using our voltage clamp protocols and the models generated successfully mimicked these experimental data, unlike the CiPA dynamic models. Marked differences in APD prolongation were observed when drug effects were simulated using the dynamic models and the static models. CONCLUSIONS These new dynamic models of ten well-known IKr blockers constitute a validation of our methodology to model dynamic drug-hERG channel interactions and highlight the importance of state-dependent binding, trapping dynamics and the time-course of IKr block to assess drug effects even at the steady-state.
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Affiliation(s)
- Fernando Escobar
- Centro de Innovación e Investigación en Bioingeniería, Universitat Politècnica de València, Valencia, Spain
| | | | | | | | - Julio Gomis-Tena
- Centro de Innovación e Investigación en Bioingeniería, Universitat Politècnica de València, Valencia, Spain
| | - Javier Saiz
- Centro de Innovación e Investigación en Bioingeniería, Universitat Politècnica de València, Valencia, Spain
| | - Dan A Klaerke
- Department of Pathobiology, University of Copenhagen, Copenhagen, Denmark
| | | | - Lucia Romero
- Centro de Innovación e Investigación en Bioingeniería, Universitat Politècnica de València, Valencia, Spain.
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2
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Arab I, Egghe K, Laukens K, Chen K, Barakat K, Bittremieux W. Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction. J Chem Inf Model 2024; 64:2515-2527. [PMID: 37870574 DOI: 10.1021/acs.jcim.3c01301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
In the field of drug discovery, there is a substantial challenge in seeking out chemical structures that possess desirable pharmacological, toxicological, and pharmacokinetic properties. Complications arise when drugs interfere with the functioning of cardiac ion channels, leading to serious cardiovascular consequences. The discontinuation and removal of numerous approved drugs from the market or at late development stages in the pipeline due to such inhibitory effects further highlight the urgency of addressing this issue. Consequently, the early prediction of potential blockers targeting cardiac ion channels during the drug discovery process is of paramount importance. This study introduces a deep learning framework that computationally determines the cardiotoxicity associated with the voltage-gated potassium channel (hERG), the voltage-gated calcium channel (Cav1.2), and the voltage-gated sodium channel (Nav1.5) for drug candidates. The predictive capabilities of three feature representations─molecular fingerprints, descriptors, and graph-based numerical representations─are rigorously benchmarked. Additionally, a novel training and evaluation data set framework is presented, enabling predictive model training of drug off-target cardiotoxicity using a comprehensive and large curated data set covering these three cardiac ion channels. To facilitate these predictions, a robust and comprehensive small molecule cardiotoxicity prediction tool named CToxPred has been developed. It is made available as open source under the permissive MIT license at https://github.com/issararab/CToxPred.
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Affiliation(s)
- Issar Arab
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Biomedical Informatics Network Antwerpen (Biomina), 2020 Antwerp, Belgium
| | - Kristof Egghe
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Biomedical Informatics Network Antwerpen (Biomina), 2020 Antwerp, Belgium
| | - Ke Chen
- Chair for Theoretical Chemistry, Catalysis Research Center, Technische Universität München, Lichtenbergstraße 4, D-85747 Garching, Germany
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta 8613, Canada
| | - Wout Bittremieux
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Biomedical Informatics Network Antwerpen (Biomina), 2020 Antwerp, Belgium
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3
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Lei CL, Whittaker DG, Mirams GR. The impact of uncertainty in hERG binding mechanism on in silico predictions of drug-induced proarrhythmic risk. Br J Pharmacol 2024; 181:987-1004. [PMID: 37740435 DOI: 10.1111/bph.16250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND AND PURPOSE Drug-induced reduction of the rapid delayed rectifier potassium current carried by the human Ether-à-go-go-Related Gene (hERG) channel is associated with increased risk of arrhythmias. Recent updates to drug safety regulatory guidelines attempt to capture each drug's hERG binding mechanism by combining in vitro assays with in silico simulations. In this study, we investigate the impact on in silico proarrhythmic risk predictions due to uncertainty in the hERG binding mechanism and physiological hERG current model. EXPERIMENTAL APPROACH Possible pharmacological binding models were designed for the hERG channel to account for known and postulated small molecule binding mechanisms. After selecting a subset of plausible binding models for each compound through calibration to available voltage-clamp electrophysiology data, we assessed their effects, and the effects of different physiological models, on proarrhythmic risk predictions. KEY RESULTS For some compounds, multiple binding mechanisms can explain the same data produced under the safety testing guidelines, which results in different inferred binding rates. This can result in substantial uncertainty in the predicted torsade risk, which often spans more than one risk category. By comparison, we found that the effect of a different hERG physiological current model on risk classification was subtle. CONCLUSION AND IMPLICATIONS The approach developed in this study assesses the impact of uncertainty in hERG binding mechanisms on predictions of drug-induced proarrhythmic risk. For some compounds, these results imply the need for additional binding data to decrease uncertainty in safety-critical applications.
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Affiliation(s)
- Chon Lok Lei
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau, China
| | - Dominic G Whittaker
- Centre for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Gary R Mirams
- Centre for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
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4
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Farm HJ, Clerx M, Cooper F, Polonchuk L, Wang K, Gavaghan DJ, Lei CL. Importance of modelling hERG binding in predicting drug-induced action potential prolongations for drug safety assessment. Front Pharmacol 2023; 14:1110555. [PMID: 37021055 PMCID: PMC10067903 DOI: 10.3389/fphar.2023.1110555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/22/2023] [Indexed: 03/30/2023] Open
Abstract
Reduction of the rapid delayed rectifier potassium current (IKr) via drug binding to the human Ether-à-go-go-Related Gene (hERG) channel is a well recognised mechanism that can contribute to an increased risk of Torsades de Pointes. Mathematical models have been created to replicate the effects of channel blockers, such as reducing the ionic conductance of the channel. Here, we study the impact of including state-dependent drug binding in a mathematical model of hERG when translating hERG inhibition to action potential changes. We show that the difference in action potential predictions when modelling drug binding of hERG using a state-dependent model versus a conductance scaling model depends not only on the properties of the drug and whether the experiment achieves steady state, but also on the experimental protocols. Furthermore, through exploring the model parameter space, we demonstrate that the state-dependent model and the conductance scaling model generally predict different action potential prolongations and are not interchangeable, while at high binding and unbinding rates, the conductance scaling model tends to predict shorter action potential prolongations. Finally, we observe that the difference in simulated action potentials between the models is determined by the binding and unbinding rate, rather than the trapping mechanism. This study demonstrates the importance of modelling drug binding and highlights the need for improved understanding of drug trapping which can have implications for the uses in drug safety assessment.
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Affiliation(s)
- Hui Jia Farm
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Michael Clerx
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Fergus Cooper
- Doctoral Training Centre, University of Oxford, Oxford, United Kingdom
| | - Liudmila Polonchuk
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Ken Wang
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - David J. Gavaghan
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
- Doctoral Training Centre, University of Oxford, Oxford, United Kingdom
- *Correspondence: David J. Gavaghan, ; Chon Lok Lei,
| | - Chon Lok Lei
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau, China
- *Correspondence: David J. Gavaghan, ; Chon Lok Lei,
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5
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Whittaker DG, Wang J, Shuttleworth JG, Venkateshappa R, Kemp JM, Claydon TW, Mirams GR. Ion channel model reduction using manifold boundaries. JOURNAL OF THE ROYAL SOCIETY, INTERFACE 2022; 19:20220193. [PMID: 35946166 PMCID: PMC9363999 DOI: 10.1098/rsif.2022.0193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Mathematical models of voltage-gated ion channels are used in basic research, industrial and clinical settings. These models range in complexity, but typically contain numerous variables representing the proportion of channels in a given state, and parameters describing the voltage-dependent rates of transition between states. An open problem is selecting the appropriate degree of complexity and structure for an ion channel model given data availability. Here, we simplify a model of the cardiac human Ether-à-go-go related gene (hERG) potassium ion channel, which carries cardiac IKr, using the manifold boundary approximation method (MBAM). The MBAM approximates high-dimensional model-output manifolds by reduced models describing their boundaries, resulting in models with fewer parameters (and often variables). We produced a series of models of reducing complexity starting from an established five-state hERG model with 15 parameters. Models with up to three fewer states and eight fewer parameters were shown to retain much of the predictive capability of the full model and were validated using experimental hERG1a data collected in HEK293 cells at 37°C. The method provides a way to simplify complex models of ion channels that improves parameter identifiability and will aid in future model development.
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Affiliation(s)
- Dominic G Whittaker
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Jiahui Wang
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Joseph G Shuttleworth
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | | | - Jacob M Kemp
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - Thomas W Claydon
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - Gary R Mirams
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
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6
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Pesti K, Földi MC, Zboray K, Toth AV, Lukacs P, Mike A. Characterization of Compound-Specific, Concentration-Independent Biophysical Properties of Sodium Channel Inhibitor Mechanism of Action Using Automated Patch-Clamp Electrophysiology. Front Pharmacol 2021; 12:738460. [PMID: 34497526 PMCID: PMC8419314 DOI: 10.3389/fphar.2021.738460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/10/2021] [Indexed: 01/15/2023] Open
Abstract
We have developed an automated patch-clamp protocol that allows high information content screening of sodium channel inhibitor compounds. We have observed that individual compounds had their specific signature patterns of inhibition, which were manifested irrespective of the concentration. Our aim in this study was to quantify these properties. Primary biophysical data, such as onset rate, the shift of the half inactivation voltage, or the delay of recovery from inactivation, are concentration-dependent. We wanted to derive compound-specific properties, therefore, we had to neutralize the effect of concentration. This study describes how this is done, and shows how compound-specific properties reflect the mechanism of action, including binding dynamics, cooperativity, and interaction with the membrane phase. We illustrate the method using four well-known sodium channel inhibitor compounds, riluzole, lidocaine, benzocaine, and bupivacaine. Compound-specific biophysical properties may also serve as a basis for deriving parameters for kinetic modeling of drug action. We discuss how knowledge about the mechanism of action may help to predict the frequency-dependence of individual compounds, as well as their potential persistent current component selectivity. The analysis method described in this study, together with the experimental protocol described in the accompanying paper, allows screening for inhibitor compounds with specific kinetic properties, or with specific mechanisms of inhibition.
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Affiliation(s)
- Krisztina Pesti
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
- School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
| | - Mátyás C. Földi
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Katalin Zboray
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Adam V. Toth
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Peter Lukacs
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Arpad Mike
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
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7
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Kemp JM, Whittaker DG, Venkateshappa R, Pang Z, Johal R, Sergeev V, Tibbits GF, Mirams GR, Claydon TW. Electrophysiological characterization of the hERG R56Q LQTS variant and targeted rescue by the activator RPR260243. J Gen Physiol 2021; 153:212555. [PMID: 34398210 PMCID: PMC8493834 DOI: 10.1085/jgp.202112923] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/11/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
Human Ether-à-go-go (hERG) channels contribute to cardiac repolarization, and inherited variants or drug block are associated with long QT syndrome type 2 (LQTS2) and arrhythmia. Therefore, hERG activator compounds present a therapeutic opportunity for targeted treatment of LQTS. However, a limiting concern is over-activation of hERG resurgent current during the action potential and abbreviated repolarization. Activators that slow deactivation gating (type I), such as RPR260243, may enhance repolarizing hERG current during the refractory period, thus ameliorating arrhythmogenicity with reduced early repolarization risk. Here, we show that, at physiological temperature, RPR260243 enhances hERG channel repolarizing currents conducted in the refractory period in response to premature depolarizations. This occurs with little effect on the resurgent hERG current during the action potential. The effects of RPR260243 were particularly evident in LQTS2-associated R56Q mutant channels, whereby RPR260243 restored WT-like repolarizing drive in the early refractory period and diastolic interval, combating attenuated protective currents. In silico kinetic modeling of channel gating predicted little effect of the R56Q mutation on hERG current conducted during the action potential and a reduced repolarizing protection against afterdepolarizations in the refractory period and diastolic interval, particularly at higher pacing rates. These simulations predicted partial rescue from the arrhythmic effects of R56Q by RPR260243 without risk of early repolarization. Our findings demonstrate that the pathogenicity of some hERG variants may result from reduced repolarizing protection during the refractory period and diastolic interval with limited effect on action potential duration, and that the hERG channel activator RPR260243 may provide targeted antiarrhythmic potential in these cases.
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Affiliation(s)
- Jacob M Kemp
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - Dominic G Whittaker
- Centre for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | | | - ZhaoKai Pang
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - Raj Johal
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - Valentine Sergeev
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - Glen F Tibbits
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - Gary R Mirams
- Centre for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Thomas W Claydon
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
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8
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Mousaei M, Kudaibergenova M, MacKerell AD, Noskov S. Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations. J Chem Inf Model 2020; 60:6489-6501. [PMID: 33196188 PMCID: PMC7839320 DOI: 10.1021/acs.jcim.0c01065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Drug-induced cardiotoxicity is a potentially lethal and yet one of the most common side effects with the drugs in clinical use. Most of the drug-induced cardiotoxicity is associated with an off-target pharmacological blockade of K+ currents carried out by the cardiac Human-Ether-a-go-go-Related (hERG1) potassium channel. There is a compulsory preclinical stage safety assessment for the hERG1 blockade for all classes of drugs, which adds substantially to the cost of drug development. The availability of a high-resolution cryogenic electron microscopy (cryo-EM) structure for the channel in its open/depolarized state solved in 2017 enabled the application of molecular modeling for rapid assessment of drug blockade by molecular docking and simulation techniques. More importantly, if successful, in silico methods may allow a path to lead-compound salvaging by mapping out key block determinants. Here, we report the blind application of the site identification by the ligand competitive saturation (SILCS) protocol to map out druggable/regulatory hotspots in the hERG1 channel available for blockers and activators. The SILCS simulations use small solutes representative of common functional groups to sample the chemical space for the entire protein and its environment using all-atom simulations. The resulting chemical maps, FragMaps, explicitly account for receptor flexibility, protein-fragment interactions, and fragment desolvation penalty allowing for rapid ranking of potential ligands as blockers or nonblockers of hERG1. To illustrate the power of the approach, SILCS was applied to a test set of 55 blockers with diverse chemical scaffolds and pIC50 values measured under uniform conditions. The original SILCS model was based on the all-atom modeling of the hERG1 channel in an explicit lipid bilayer and was further augmented with a Bayesian-optimization/machine-learning (BML) stage employing an independent literature-derived training set of 163 molecules. BML approach was used to determine weighting factors for the FragMaps contributions to the scoring function. pIC50 predictions from the combined SILCS/BML approach to the 55 blockers showed a Pearson correlation (PC) coefficient of >0.535 relative to the experimental data. SILCS/BML model was shown to yield substantially improved performance as compared to commonly used rigid and flexible molecular docking methods for a well-established cohort of hERG1 blockers, where no correlation with experimental data was recorded. SILCS/BML results also suggest that a proper weighting of protonation states of common blockers present at physiological pH is essential for accurate predictions of blocker potency. The precalculated and optimized SILCS FragMaps can now be used for the rapid screening of small molecules for their cardiotoxic potential as well as for exploring alternative binding pockets in the hERG1 channel with applications to the rational design of activators.
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Affiliation(s)
- Mahdi Mousaei
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Meruyert Kudaibergenova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Alexander D. MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Sergei Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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9
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Lei CL, Ghosh S, Whittaker DG, Aboelkassem Y, Beattie KA, Cantwell CD, Delhaas T, Houston C, Novaes GM, Panfilov AV, Pathmanathan P, Riabiz M, dos Santos RW, Walmsley J, Worden K, Mirams GR, Wilkinson RD. Considering discrepancy when calibrating a mechanistic electrophysiology model. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190349. [PMID: 32448065 PMCID: PMC7287333 DOI: 10.1098/rsta.2019.0349] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/21/2020] [Indexed: 05/21/2023]
Abstract
Uncertainty quantification (UQ) is a vital step in using mathematical models and simulations to take decisions. The field of cardiac simulation has begun to explore and adopt UQ methods to characterize uncertainty in model inputs and how that propagates through to outputs or predictions; examples of this can be seen in the papers of this issue. In this review and perspective piece, we draw attention to an important and under-addressed source of uncertainty in our predictions-that of uncertainty in the model structure or the equations themselves. The difference between imperfect models and reality is termed model discrepancy, and we are often uncertain as to the size and consequences of this discrepancy. Here, we provide two examples of the consequences of discrepancy when calibrating models at the ion channel and action potential scales. Furthermore, we attempt to account for this discrepancy when calibrating and validating an ion channel model using different methods, based on modelling the discrepancy using Gaussian processes and autoregressive-moving-average models, then highlight the advantages and shortcomings of each approach. Finally, suggestions and lines of enquiry for future work are provided. This article is part of the theme issue 'Uncertainty quantification in cardiac and cardiovascular modelling and simulation'.
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Affiliation(s)
- Chon Lok Lei
- Computational Biology and Health Informatics, Department of Computer Science, University of Oxford, Oxford, UK
| | - Sanmitra Ghosh
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Dominic G. Whittaker
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Yasser Aboelkassem
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Kylie A. Beattie
- Systems Modeling and Translational Biology, GlaxoSmithKline R&D, Stevenage, UK
| | - Chris D. Cantwell
- ElectroCardioMaths Programme, Centre for Cardiac Engineering, Imperial College London, London, UK
| | - Tammo Delhaas
- CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Charles Houston
- ElectroCardioMaths Programme, Centre for Cardiac Engineering, Imperial College London, London, UK
| | - Gustavo Montes Novaes
- Graduate Program in Computational Modeling, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Alexander V. Panfilov
- Department of Physics and Astronomy, Ghent University, Ghent, Belgium
- Laboratory of Computational Biology and Medicine, Ural Federal University, Ekaterinburg, Russia
| | - Pras Pathmanathan
- US Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Silver Spring, MD, USA
| | - Marina Riabiz
- Department of Biomedical Engineering King’s College London and Alan Turing Institute, London, UK
| | - Rodrigo Weber dos Santos
- Graduate Program in Computational Modeling, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - John Walmsley
- James T. Willerson Center for Cardiovascular Modeling and Simulation, Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Keith Worden
- Dynamics Research Group, Department of Mechanical Engineering, University of Sheffield, Sheffield, UK
| | - Gary R. Mirams
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
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10
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Shou WZ. Current status and future directions of high-throughput ADME screening in drug discovery. J Pharm Anal 2020; 10:201-208. [PMID: 32612866 PMCID: PMC7322755 DOI: 10.1016/j.jpha.2020.05.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
During the last decade high-throughput in vitro absorption, distribution, metabolism and excretion (HT-ADME) screening has become an essential part of any drug discovery effort of synthetic molecules. The conduct of HT-ADME screening has been "industrialized" due to the extensive development of software and automation tools in cell culture, assay incubation, sample analysis and data analysis. The HT-ADME assay portfolio continues to expand in emerging areas such as drug-transporter interactions, early soft spot identification, and ADME screening of peptide drug candidates. Additionally, thanks to the very large and high-quality HT-ADME data sets available in many biopharma companies, in silico prediction of ADME properties using machine learning has also gained much momentum in recent years. In this review, we discuss the current state-of-the-art practices in HT-ADME screening including assay portfolio, assay automation, sample analysis, data processing, and prediction model building. In addition, we also offer perspectives in future development of this exciting field.
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Affiliation(s)
- Wilson Z. Shou
- Bristol-Myers Squibb, PO Box 4000, Princeton, NJ, 08540, USA
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11
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Lei CL, Clerx M, Beattie KA, Melgari D, Hancox JC, Gavaghan DJ, Polonchuk L, Wang K, Mirams GR. Rapid Characterization of hERG Channel Kinetics II: Temperature Dependence. Biophys J 2019; 117:2455-2470. [PMID: 31451180 PMCID: PMC6990152 DOI: 10.1016/j.bpj.2019.07.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/20/2019] [Accepted: 07/17/2019] [Indexed: 11/29/2022] Open
Abstract
Ion channel behavior can depend strongly on temperature, with faster kinetics at physiological temperatures leading to considerable changes in currents relative to room temperature. These temperature-dependent changes in voltage-dependent ion channel kinetics (rates of opening, closing, inactivating, and recovery) are commonly represented with Q10 coefficients or an Eyring relationship. In this article, we assess the validity of these representations by characterizing channel kinetics at multiple temperatures. We focus on the human Ether-à-go-go-Related Gene (hERG) channel, which is important in drug safety assessment and commonly screened at room temperature so that results require extrapolation to physiological temperature. In Part I of this study, we established a reliable method for high-throughput characterization of hERG1a (Kv11.1) kinetics, using a 15-second information-rich optimized protocol. In this Part II, we use this protocol to study the temperature dependence of hERG kinetics using Chinese hamster ovary cells overexpressing hERG1a on the Nanion SyncroPatch 384PE, a 384-well automated patch-clamp platform, with temperature control. We characterize the temperature dependence of hERG gating by fitting the parameters of a mathematical model of hERG kinetics to data obtained at five distinct temperatures between 25 and 37°C and validate the models using different protocols. Our models reveal that activation is far more temperature sensitive than inactivation, and we observe that the temperature dependency of the kinetic parameters is not represented well by Q10 coefficients; it broadly follows a generalized, but not the standardly-used, Eyring relationship. We also demonstrate that experimental estimations of Q10 coefficients are protocol dependent. Our results show that a direct fit using our 15-s protocol best represents hERG kinetics at any given temperature and suggests that using the Generalized Eyring theory is preferable if no experimental data are available to derive model parameters at a given temperature.
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Affiliation(s)
- Chon Lok Lei
- Computational Biology, Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Michael Clerx
- Computational Biology, Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Kylie A Beattie
- Computational Biology, Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Dario Melgari
- School of Physiology, Pharmacology and Neuroscience, and Cardiovascular Research Laboratories, School of Medical Sciences, University of Bristol, Bristol, United Kingdom
| | - Jules C Hancox
- School of Physiology, Pharmacology and Neuroscience, and Cardiovascular Research Laboratories, School of Medical Sciences, University of Bristol, Bristol, United Kingdom
| | - David J Gavaghan
- Computational Biology, Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Liudmila Polonchuk
- Pharma Research and Early Development, Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Ken Wang
- Pharma Research and Early Development, Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Gary R Mirams
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom.
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Perissinotti L, Guo J, Kudaibergenova M, Lees-Miller J, Ol'khovich M, Sharapova A, Perlovich GL, Muruve DA, Gerull B, Noskov SY, Duff HJ. The Pore-Lipid Interface: Role of Amino-Acid Determinants of Lipophilic Access by Ivabradine to the hERG1 Pore Domain. Mol Pharmacol 2019; 96:259-271. [PMID: 31182542 DOI: 10.1124/mol.118.115642] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/28/2019] [Indexed: 12/14/2022] Open
Abstract
Abnormal cardiac electrical activity is a common side effect caused by unintended block of the promiscuous drug target human ether-à-go-go-related gene (hERG1), the pore-forming domain of the delayed rectifier K+ channel in the heart. hERG1 block leads to a prolongation of the QT interval, a phase of the cardiac cycle that underlies myocyte repolarization detectable on the electrocardiogram. Even newly released drugs such as heart-rate lowering agent ivabradine block the rapid delayed rectifier current IKr, prolong action potential duration, and induce potentially lethal arrhythmia known as torsades de pointes. In this study, we describe a critical drug-binding pocket located at the lateral pore surface facing the cellular membrane. Mutations of the conserved M651 residue alter ivabradine-induced block but not by the common hERG1 blocker dofetilide. As revealed by molecular dynamics simulations, binding of ivabradine to a lipophilic pore access site is coupled to a state-dependent reorientation of aromatic residues F557 and F656 in the S5 and S6 helices. We show that the M651 mutation impedes state-dependent dynamics of F557 and F656 aromatic cassettes at the protein-lipid interface, which has a potential to disrupt drug-induced block of the channel. This fundamentally new mechanism coupling the channel dynamics and small-molecule access from the membrane into the hERG1 intracavitary site provides a simple rationale for the well established state-dependence of drug blockade. SIGNIFICANCE STATEMENT: The drug interference with the function of the cardiac hERG channels represents one of the major sources of drug-induced heart disturbances. We found a novel and a critical drug-binding pocket adjacent to a lipid-facing surface of the hERG1 channel, which furthers our molecular understanding of drug-induced QT syndrome.
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Affiliation(s)
- Laura Perissinotti
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Jiqing Guo
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Meruyert Kudaibergenova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - James Lees-Miller
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Marina Ol'khovich
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Angelica Sharapova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - German L Perlovich
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Daniel A Muruve
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Brenda Gerull
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Sergei Yu Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Henry J Duff
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
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13
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Li Z, Garnett C, Strauss DG. Quantitative Systems Pharmacology Models for a New International Cardiac Safety Regulatory Paradigm: An Overview of the Comprehensive In Vitro Proarrhythmia Assay In Silico Modeling Approach. CPT Pharmacometrics Syst Pharmacol 2019; 8:371-379. [PMID: 31044559 PMCID: PMC6617836 DOI: 10.1002/psp4.12423] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/15/2019] [Indexed: 12/17/2022] Open
Abstract
As a relatively new discipline, quantitative systems pharmacology has seen a significant increase in the application and utility of drug development. One area that could greatly benefit from such an approach is in the proarrhythmia assessment of new drugs. The Comprehensive In Vitro Proarrhythmia Assay (CiPA) Initiative is a global public-private partnership project that has developed an integrated approach using mechanistic in silico models for proarrhythmia risk prediction. Progress to date has led to the formation of the International Council on Harmonisation Implementation Working Group to revise regulatory guidelines via the Questions-and-Answers process to address the best practices for proarrhythmia models and how they can impact clinical drug development. This article reviews the CiPA in silico model-development process, focusing on its unique development and validation strategy, and summarizes the lessons learned as consideration points for the ongoing implementation of CiPA-like in silico models in drug development.
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Affiliation(s)
- Zhihua Li
- Division of Applied Regulatory ScienceOffice of Clinical PharmacologyOffice of Translational SciencesCenter for Drug Evaluation and ResearchUS Food and Drug AdministrationSilver SpringMarylandUSA
| | - Christine Garnett
- Division of Cardiovascular and Renal ProductsOffice of Drug Evaluation IOffice of New DrugsCenter for Drug Evaluation and ResearchUS Food and Drug AdministrationSilver SpringMarylandUSA
| | - David G. Strauss
- Division of Applied Regulatory ScienceOffice of Clinical PharmacologyOffice of Translational SciencesCenter for Drug Evaluation and ResearchUS Food and Drug AdministrationSilver SpringMarylandUSA
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14
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Yang PC, Purawat S, Ieong PU, Jeng MT, DeMarco KR, Vorobyov I, McCulloch AD, Altintas I, Amaro RE, Clancy CE. A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows. PLoS Comput Biol 2019; 15:e1006856. [PMID: 30849072 PMCID: PMC6426265 DOI: 10.1371/journal.pcbi.1006856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 03/20/2019] [Accepted: 02/08/2019] [Indexed: 01/18/2023] Open
Abstract
Multi-scale computational modeling is a major branch of computational biology as evidenced by the US federal interagency Multi-Scale Modeling Consortium and major international projects. It invariably involves specific and detailed sequences of data analysis and simulation, often with multiple tools and datasets, and the community recognizes improved modularity, reuse, reproducibility, portability and scalability as critical unmet needs in this area. Scientific workflows are a well-recognized strategy for addressing these needs in scientific computing. While there are good examples if the use of scientific workflows in bioinformatics, medical informatics, biomedical imaging and data analysis, there are fewer examples in multi-scale computational modeling in general and cardiac electrophysiology in particular. Cardiac electrophysiology simulation is a mature area of multi-scale computational biology that serves as an excellent use case for developing and testing new scientific workflows. In this article, we develop, describe and test a computational workflow that serves as a proof of concept of a platform for the robust integration and implementation of a reusable and reproducible multi-scale cardiac cell and tissue model that is expandable, modular and portable. The workflow described leverages Python and Kepler-Python actor for plotting and pre/post-processing. During all stages of the workflow design, we rely on freely available open-source tools, to make our workflow freely usable by scientists. We present a computational workflow as a proof of concept for integration and implementation of a reusable and reproducible cardiac multi-scale electrophysiology model that is expandable, modular and portable. This framework enables scientists to create intuitive, user-friendly and flexible end-to-end automated scientific workflows using a graphical user interface. Kepler is an advanced open-source platform that supports multiple models of computation. The underlying workflow engine handles scalability, provenance, reproducibility aspects of the code, performs orchestration of data flow, and automates execution on heterogeneous computing resources. One of the main advantages of workflow utilization is the integration of code written in multiple languages Standardization occurs at the interfaces of the workflow elements and allows for general applications and easy comparison and integration of code from different research groups or even multiple programmers coding in different languages for various purposes from the same group. A workflow driven problem-solving approach enables domain scientists to focus on resolving the core science questions, and delegates the computational and process management burden to the underlying Workflow. The workflow driven approach allows scaling the computational experiment with distributed data-parallel execution on multiple computing platforms, such as, HPC resources, GPU clusters, Cloud etc. The workflow framework tracks software version information along with hardware information to allow users an opportunity to trace any variation in workflow outcome to the system configurations.
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Affiliation(s)
- Pei-Chi Yang
- Department of Physiology and Membrane Biology, Department of Pharmacology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Shweta Purawat
- San Diego Supercomputer Center (SDSC), University of California, San Diego, La Jolla, California, United States of America
| | - Pek U. Ieong
- Department of Chemistry and Biochemistry, National Biomedical Computation Resource, Drug Design Data Resource (D3R), University of California San Diego, La Jolla, California, United States of America
| | - Mao-Tsuen Jeng
- Department of Physiology and Membrane Biology, Department of Pharmacology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Kevin R. DeMarco
- Department of Physiology and Membrane Biology, Department of Pharmacology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, Department of Pharmacology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Andrew D. McCulloch
- Departments of Bioengineering and Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Ilkay Altintas
- San Diego Supercomputer Center (SDSC), University of California, San Diego, La Jolla, California, United States of America
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, National Biomedical Computation Resource, Drug Design Data Resource (D3R), University of California San Diego, La Jolla, California, United States of America
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, Department of Pharmacology, School of Medicine, University of California Davis, Davis, California, United States of America
- * E-mail:
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15
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Lee W, Windley MJ, Perry MD, Vandenberg JI, Hill AP. Protocol-Dependent Differences in IC 50 Values Measured in Human Ether-Á-Go-Go-Related Gene Assays Occur in a Predictable Way and Can Be Used to Quantify State Preference of Drug Binding. Mol Pharmacol 2019; 95:537-550. [PMID: 30770456 DOI: 10.1124/mol.118.115220] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/10/2019] [Indexed: 12/22/2022] Open
Abstract
Current guidelines around preclinical screening for drug-induced arrhythmias require the measurement of the potency of block of voltage-gated potassium channel subtype 11.1 (Kv11.1) as a surrogate for risk. A shortcoming of this approach is that the measured IC50 of Kv11.1 block varies widely depending on the voltage protocol used in electrophysiological assays. In this study, we aimed to investigate the factors that contribute to these differences and to identify whether it is possible to make predictions about protocol-dependent block that might facilitate the comparison of potencies measured using different assays. Our data demonstrate that state preferential binding, together with drug-binding kinetics and trapping, is an important determinant of the protocol dependence of Kv11.1 block. We show for the first time that differences in IC50 measured between protocols occurs in a predictable way, such that machine-learning algorithms trained using a selection of simple voltage protocols can indeed predict protocol-dependent potency. Furthermore, we also show that the preference of a drug for binding to the open versus the inactivated state of Kv11.1 can also be inferred from differences in IC50 values measured between protocols. Our work therefore identifies how state preferential drug binding is a major determinant of the protocol dependence of IC50 values measured in preclinical Kv11.1 assays. It also provides a novel method for quantifying the state dependence of Kv11.1 drug binding that will facilitate the development of more complete models of drug binding to Kv11.1 and improve our understanding of proarrhythmic risk associated with compounds that block Kv11.1.
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Affiliation(s)
- William Lee
- Victor Chang Cardiac Research Institute (W.L., M.J.W., M.D.P., J.I.V., A.P.H.) and St Vincent's Clinical School (W.L., M.J.W., M.D.P., J.I.V., A.P.H.), University of New South Wales, Darlinghurst, New South Wales, Australia
| | - Monique J Windley
- Victor Chang Cardiac Research Institute (W.L., M.J.W., M.D.P., J.I.V., A.P.H.) and St Vincent's Clinical School (W.L., M.J.W., M.D.P., J.I.V., A.P.H.), University of New South Wales, Darlinghurst, New South Wales, Australia
| | - Matthew D Perry
- Victor Chang Cardiac Research Institute (W.L., M.J.W., M.D.P., J.I.V., A.P.H.) and St Vincent's Clinical School (W.L., M.J.W., M.D.P., J.I.V., A.P.H.), University of New South Wales, Darlinghurst, New South Wales, Australia
| | - Jamie I Vandenberg
- Victor Chang Cardiac Research Institute (W.L., M.J.W., M.D.P., J.I.V., A.P.H.) and St Vincent's Clinical School (W.L., M.J.W., M.D.P., J.I.V., A.P.H.), University of New South Wales, Darlinghurst, New South Wales, Australia
| | - Adam P Hill
- Victor Chang Cardiac Research Institute (W.L., M.J.W., M.D.P., J.I.V., A.P.H.) and St Vincent's Clinical School (W.L., M.J.W., M.D.P., J.I.V., A.P.H.), University of New South Wales, Darlinghurst, New South Wales, Australia
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16
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Vagos M, van Herck IGM, Sundnes J, Arevalo HJ, Edwards AG, Koivumäki JT. Computational Modeling of Electrophysiology and Pharmacotherapy of Atrial Fibrillation: Recent Advances and Future Challenges. Front Physiol 2018; 9:1221. [PMID: 30233399 PMCID: PMC6131668 DOI: 10.3389/fphys.2018.01221] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022] Open
Abstract
The pathophysiology of atrial fibrillation (AF) is broad, with components related to the unique and diverse cellular electrophysiology of atrial myocytes, structural complexity, and heterogeneity of atrial tissue, and pronounced disease-associated remodeling of both cells and tissue. A major challenge for rational design of AF therapy, particularly pharmacotherapy, is integrating these multiscale characteristics to identify approaches that are both efficacious and independent of ventricular contraindications. Computational modeling has long been touted as a basis for achieving such integration in a rapid, economical, and scalable manner. However, computational pipelines for AF-specific drug screening are in their infancy, and while the field is progressing quite rapidly, major challenges remain before computational approaches can fill the role of workhorse in rational design of AF pharmacotherapies. In this review, we briefly detail the unique aspects of AF pathophysiology that determine requirements for compounds targeting AF rhythm control, with emphasis on delimiting mechanisms that promote AF triggers from those providing substrate or supporting reentry. We then describe modeling approaches that have been used to assess the outcomes of drugs acting on established AF targets, as well as on novel promising targets including the ultra-rapidly activating delayed rectifier potassium current, the acetylcholine-activated potassium current and the small conductance calcium-activated potassium channel. Finally, we describe how heterogeneity and variability are being incorporated into AF-specific models, and how these approaches are yielding novel insights into the basic physiology of disease, as well as aiding identification of the important molecular players in the complex AF etiology.
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Affiliation(s)
- Márcia Vagos
- Computational Physiology Department, Simula Research Laboratory, Lysaker, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Ilsbeth G. M. van Herck
- Computational Physiology Department, Simula Research Laboratory, Lysaker, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Joakim Sundnes
- Computational Physiology Department, Simula Research Laboratory, Lysaker, Norway
- Center for Cardiological Innovation, Oslo, Norway
| | - Hermenegild J. Arevalo
- Computational Physiology Department, Simula Research Laboratory, Lysaker, Norway
- Center for Cardiological Innovation, Oslo, Norway
| | - Andrew G. Edwards
- Computational Physiology Department, Simula Research Laboratory, Lysaker, Norway
- Center for Cardiological Innovation, Oslo, Norway
| | - Jussi T. Koivumäki
- BioMediTech Institute and Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere, Finland
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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17
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Beattie KA, Hill AP, Bardenet R, Cui Y, Vandenberg JI, Gavaghan DJ, de Boer TP, Mirams GR. Sinusoidal voltage protocols for rapid characterisation of ion channel kinetics. J Physiol 2018; 596:1813-1828. [PMID: 29573276 PMCID: PMC5978315 DOI: 10.1113/jp275733] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/19/2018] [Indexed: 12/21/2022] Open
Abstract
Key points Ion current kinetics are commonly represented by current–voltage relationships, time constant–voltage relationships and subsequently mathematical models fitted to these. These experiments take substantial time, which means they are rarely performed in the same cell. Rather than traditional square‐wave voltage clamps, we fitted a model to the current evoked by a novel sum‐of‐sinusoids voltage clamp that was only 8 s long. Short protocols that can be performed multiple times within a single cell will offer many new opportunities to measure how ion current kinetics are affected by changing conditions. The new model predicts the current under traditional square‐wave protocols well, with better predictions of underlying currents than literature models. The current under a novel physiologically relevant series of action potential clamps is predicted extremely well. The short sinusoidal protocols allow a model to be fully fitted to individual cells, allowing us to examine cell–cell variability in current kinetics for the first time.
Abstract Understanding the roles of ion currents is crucial to predict the action of pharmaceuticals and mutations in different scenarios, and thereby to guide clinical interventions in the heart, brain and other electrophysiological systems. Our ability to predict how ion currents contribute to cellular electrophysiology is in turn critically dependent on our characterisation of ion channel kinetics – the voltage‐dependent rates of transition between open, closed and inactivated channel states. We present a new method for rapidly exploring and characterising ion channel kinetics, applying it to the hERG potassium channel as an example, with the aim of generating a quantitatively predictive representation of the ion current. We fitted a mathematical model to currents evoked by a novel 8 second sinusoidal voltage clamp in CHO cells overexpressing hERG1a. The model was then used to predict over 5 minutes of recordings in the same cell in response to further protocols: a series of traditional square step voltage clamps, and also a novel voltage clamp comprising a collection of physiologically relevant action potentials. We demonstrate that we can make predictive cell‐specific models that outperform the use of averaged data from a number of different cells, and thereby examine which changes in gating are responsible for cell–cell variability in current kinetics. Our technique allows rapid collection of consistent and high quality data, from single cells, and produces more predictive mathematical ion channel models than traditional approaches. Ion current kinetics are commonly represented by current–voltage relationships, time constant–voltage relationships and subsequently mathematical models fitted to these. These experiments take substantial time, which means they are rarely performed in the same cell. Rather than traditional square‐wave voltage clamps, we fitted a model to the current evoked by a novel sum‐of‐sinusoids voltage clamp that was only 8 s long. Short protocols that can be performed multiple times within a single cell will offer many new opportunities to measure how ion current kinetics are affected by changing conditions. The new model predicts the current under traditional square‐wave protocols well, with better predictions of underlying currents than literature models. The current under a novel physiologically relevant series of action potential clamps is predicted extremely well. The short sinusoidal protocols allow a model to be fully fitted to individual cells, allowing us to examine cell–cell variability in current kinetics for the first time.
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Affiliation(s)
- Kylie A Beattie
- Computational Biology, Department of Computer Science, University of Oxford, Oxford, OX1 3QD, UK.,Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Adam P Hill
- Department of Molecular Cardiology and Biophysics, Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW, 2010, Australia
| | - Rémi Bardenet
- CNRS & CRIStAL, Université de Lille, 59651 Villeneuve d'Ascq, Lille, France
| | - Yi Cui
- Safety Evaluation and Risk Management, Global Clinical Safety and Pharmacovigilance, GlaxoSmithKline, Uxbridge, UB11 1BS, UK
| | - Jamie I Vandenberg
- Department of Molecular Cardiology and Biophysics, Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW, 2010, Australia
| | - David J Gavaghan
- Computational Biology, Department of Computer Science, University of Oxford, Oxford, OX1 3QD, UK
| | - Teun P de Boer
- Department of Medical Physiology, Division of Heart & Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gary R Mirams
- Centre for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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18
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Perissinotti LL, De Biase PM, Guo J, Yang PC, Lee MC, Clancy CE, Duff HJ, Noskov SY. Determinants of Isoform-Specific Gating Kinetics of hERG1 Channel: Combined Experimental and Simulation Study. Front Physiol 2018; 9:207. [PMID: 29706893 PMCID: PMC5907531 DOI: 10.3389/fphys.2018.00207] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/23/2018] [Indexed: 12/22/2022] Open
Abstract
IKr is the rapidly activating component of the delayed rectifier potassium current, the ion current largely responsible for the repolarization of the cardiac action potential. Inherited forms of long QT syndrome (LQTS) (Lees-Miller et al., 1997) in humans are linked to functional modifications in the Kv11.1 (hERG) ion channel and potentially life threatening arrhythmias. There is little doubt now that hERG-related component of IKr in the heart depends on the tetrameric (homo- or hetero-) channels formed by two alternatively processed isoforms of hERG, termed hERG1a and hERG1b. Isoform composition (hERG1a- vs. the b-isoform) has recently been reported to alter pharmacologic responses to some hERG blockers and was proposed to be an essential factor pre-disposing patients for drug-induced QT prolongation. Very little is known about the gating and pharmacological properties of two isoforms in heart membranes. For example, how gating mechanisms of the hERG1a channels differ from that of hERG1b is still unknown. The mechanisms by which hERG 1a/1b hetero-tetramers contribute to function in the heart, or what role hERG1b might play in disease are all questions to be answered. Structurally, the two isoforms differ only in the N-terminal region located in the cytoplasm: hERG1b is 340 residues shorter than hERG1a and the initial 36 residues of hERG1b are unique to this isoform. In this study, we combined electrophysiological measurements for HEK cells, kinetics and structural modeling to tease out the individual contributions of each isoform to Action Potential formation and then make predictions about the effects of having various mixture ratios of the two isoforms. By coupling electrophysiological data with computational kinetic modeling, two proposed mechanisms of hERG gating in two homo-tetramers were examined. Sets of data from various experimental stimulation protocols (HEK cells) were analyzed simultaneously and fitted to Markov-chain models (M-models). The minimization procedure presented here, allowed assessment of suitability of different Markov model topologies and the corresponding parameters that describe the channel kinetics. The kinetics modeling pointed to key differences in the gating kinetics that were linked to the full channel structure. Interactions between soluble domains and the transmembrane part of the channel appeared to be critical determinants of the gating kinetics. The structures of the full channel in the open and closed states were compared for the first time using the recent Cryo-EM resolved structure for full open hERG channel and an homology model for the closed state, based on the highly homolog EAG1 channel. Key potential interactions which emphasize the importance of electrostatic interactions between N-PAS cap, S4-S5, and C-linker are suggested based on the structural analysis. The derived kinetic parameters were later used in higher order models of cells and tissue to track down the effect of varying the ratios of hERG1a and hERG1b on cardiac action potentials and computed electrocardiograms. Simulations suggest that the recovery from inactivation of hERG1b may contribute to its physiologic role of this isoform in the action potential. Finally, the results presented here contribute to the growing body of evidence that hERG1b significantly affects the generation of the cardiac Ikr and plays an important role in cardiac electrophysiology. We highlight the importance of carefully revisiting the Markov models previously proposed in order to properly account for the relative abundance of the hERG1 a- and b- isoforms.
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Affiliation(s)
- Laura L Perissinotti
- Centre for Molecular Simulations, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Pablo M De Biase
- Centre for Molecular Simulations, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Jiqing Guo
- Libin Cardiovascular Institute of Alberta, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
| | - Pei-Chi Yang
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Miranda C Lee
- Centre for Molecular Simulations, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Colleen E Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Henry J Duff
- Libin Cardiovascular Institute of Alberta, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
| | - Sergei Y Noskov
- Centre for Molecular Simulations, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
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19
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Grandi E. Keeping it short and (not so) simple: characterizing hERG kinetics with sinusoidal waves. J Physiol 2018. [PMID: 29521425 DOI: 10.1113/jp276068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Eleonora Grandi
- Department of Pharmacology, University of California Davis, Davis, CA, USA
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20
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Vicente J, Zusterzeel R, Johannesen L, Mason J, Sager P, Patel V, Matta MK, Li Z, Liu J, Garnett C, Stockbridge N, Zineh I, Strauss DG. Mechanistic Model-Informed Proarrhythmic Risk Assessment of Drugs: Review of the "CiPA" Initiative and Design of a Prospective Clinical Validation Study. Clin Pharmacol Ther 2018; 103:54-66. [PMID: 28986934 PMCID: PMC5765372 DOI: 10.1002/cpt.896] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/20/2017] [Accepted: 10/01/2017] [Indexed: 12/19/2022]
Abstract
The Comprehensive in vitro Proarrhythmia Assay (CiPA) initiative is developing and validating a mechanistic-based assessment of the proarrhythmic risk of drugs. CiPA proposes to assess a drug's effect on multiple ion channels and integrate the effects in a computer model of the human cardiomyocyte to predict proarrhythmic risk. Unanticipated or missed effects will be assessed with human stem cell-derived cardiomyocytes and electrocardiogram (ECG) analysis in early phase I clinical trials. This article provides an overview of CiPA and the rationale and design of the CiPA phase I ECG validation clinical trial, which involves assessing an additional ECG biomarker (J-Tpeak) for QT prolonging drugs. If successful, CiPA will 1) create a pathway for drugs with hERG block / QT prolongation to advance without intensive ECG monitoring in phase III trials if they have low proarrhythmic risk; and 2) enable updating drug labels to be more informative about proarrhythmic risk, not just QT prolongation.
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Affiliation(s)
- Jose Vicente
- Office of New Drugs, Center for Drug Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMarylandUSA
| | - Robbert Zusterzeel
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMarylandUSA
| | - Lars Johannesen
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMarylandUSA
| | - Jay Mason
- Department of Medicine, Division of CardiologyUniversity of UtahSalt Lake CityUtahUSA
- Spaulding Clinical ResearchWest BendWisconsinUSA
| | | | - Vikram Patel
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMarylandUSA
| | - Murali K. Matta
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMarylandUSA
| | - Zhihua Li
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMarylandUSA
| | - Jiang Liu
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMarylandUSA
| | - Christine Garnett
- Office of New Drugs, Center for Drug Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMarylandUSA
| | - Norman Stockbridge
- Office of New Drugs, Center for Drug Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMarylandUSA
| | - Issam Zineh
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMarylandUSA
| | - David G. Strauss
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMarylandUSA
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21
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Berridge BR, Schultze AE, Heyen JR, Searfoss GH, Sarazan RD. Technological Advances in Cardiovascular Safety Assessment Decrease Preclinical Animal Use and Improve Clinical Relevance. ILAR J 2017; 57:120-132. [PMID: 28053066 DOI: 10.1093/ilar/ilw028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 10/09/2016] [Indexed: 12/11/2022] Open
Abstract
Cardiovascular (CV) safety liabilities are significant concerns for drug developers and preclinical animal studies are predominately where those liabilities are characterized before patient exposures. Steady progress in technology and laboratory capabilities is enabling a more refined and informative use of animals in those studies. The application of surgically implantable and telemetered instrumentation in the acute assessment of drug effects on CV function has significantly improved historical approaches that involved anesthetized or restrained animals. More chronically instrumented animals and application of common clinical imaging assessments like echocardiography and MRI extend functional and in-life structural assessments into the repeat-dose setting. A growing portfolio of circulating CV biomarkers is allowing longitudinal and repeated measures of cardiac and vascular injury and dysfunction better informing an understanding of temporal pathogenesis and allowing earlier detection of undesirable effects. In vitro modeling systems of the past were limited by their lack of biological relevance to the in vivo human condition. Advances in stem cell technology and more complex in vitro modeling platforms are quickly creating more opportunity to supplant animals in our earliest assessments for liabilities. Continuing improvement in our capabilities in both animal and nonanimal modeling should support a steady decrease in animal use for primary liability identification and optimize the translational relevance of the animal studies we continue to do.
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Affiliation(s)
- Brian R Berridge
- Brian R. Berridge, DVM, PhD, is a Senior GSK Fellow and Head of Worldwide Animal Research Strategy at GlaxoSmithKline in King of Prussia, Pennsylvania. A. Eric Schultze, DVM, PhD, is a Senior Research Advisor-Pathologist at Lilly Research Laboratories in Indianapolis, Indiana. Jon R. Heyen, MS, is a Senior Principal Scientist at Pfizer in La Jolla, California. George H. Searfoss, MS, is a Consultant Toxicologist at Lilly Research Laboratories in Indianapolis, Indiana. R. Dustan Sarazan, DVM, PhD, is a cardiovascular consultant currently residing in Rhinelander, Wisconsin
| | - A Eric Schultze
- Brian R. Berridge, DVM, PhD, is a Senior GSK Fellow and Head of Worldwide Animal Research Strategy at GlaxoSmithKline in King of Prussia, Pennsylvania. A. Eric Schultze, DVM, PhD, is a Senior Research Advisor-Pathologist at Lilly Research Laboratories in Indianapolis, Indiana. Jon R. Heyen, MS, is a Senior Principal Scientist at Pfizer in La Jolla, California. George H. Searfoss, MS, is a Consultant Toxicologist at Lilly Research Laboratories in Indianapolis, Indiana. R. Dustan Sarazan, DVM, PhD, is a cardiovascular consultant currently residing in Rhinelander, Wisconsin
| | - Jon R Heyen
- Brian R. Berridge, DVM, PhD, is a Senior GSK Fellow and Head of Worldwide Animal Research Strategy at GlaxoSmithKline in King of Prussia, Pennsylvania. A. Eric Schultze, DVM, PhD, is a Senior Research Advisor-Pathologist at Lilly Research Laboratories in Indianapolis, Indiana. Jon R. Heyen, MS, is a Senior Principal Scientist at Pfizer in La Jolla, California. George H. Searfoss, MS, is a Consultant Toxicologist at Lilly Research Laboratories in Indianapolis, Indiana. R. Dustan Sarazan, DVM, PhD, is a cardiovascular consultant currently residing in Rhinelander, Wisconsin
| | - George H Searfoss
- Brian R. Berridge, DVM, PhD, is a Senior GSK Fellow and Head of Worldwide Animal Research Strategy at GlaxoSmithKline in King of Prussia, Pennsylvania. A. Eric Schultze, DVM, PhD, is a Senior Research Advisor-Pathologist at Lilly Research Laboratories in Indianapolis, Indiana. Jon R. Heyen, MS, is a Senior Principal Scientist at Pfizer in La Jolla, California. George H. Searfoss, MS, is a Consultant Toxicologist at Lilly Research Laboratories in Indianapolis, Indiana. R. Dustan Sarazan, DVM, PhD, is a cardiovascular consultant currently residing in Rhinelander, Wisconsin
| | - R Dustan Sarazan
- Brian R. Berridge, DVM, PhD, is a Senior GSK Fellow and Head of Worldwide Animal Research Strategy at GlaxoSmithKline in King of Prussia, Pennsylvania. A. Eric Schultze, DVM, PhD, is a Senior Research Advisor-Pathologist at Lilly Research Laboratories in Indianapolis, Indiana. Jon R. Heyen, MS, is a Senior Principal Scientist at Pfizer in La Jolla, California. George H. Searfoss, MS, is a Consultant Toxicologist at Lilly Research Laboratories in Indianapolis, Indiana. R. Dustan Sarazan, DVM, PhD, is a cardiovascular consultant currently residing in Rhinelander, Wisconsin
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22
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Lee W, Windley MJ, Vandenberg JI, Hill AP. In Vitro and In Silico Risk Assessment in Acquired Long QT Syndrome: The Devil Is in the Details. Front Physiol 2017; 8:934. [PMID: 29201009 PMCID: PMC5696636 DOI: 10.3389/fphys.2017.00934] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/03/2017] [Indexed: 12/16/2022] Open
Abstract
Acquired long QT syndrome, mostly as a result of drug block of the Kv11. 1 potassium channel in the heart, is characterized by delayed cardiac myocyte repolarization, prolongation of the T interval on the ECG, syncope and sudden cardiac death due to the polymorphic ventricular arrhythmia Torsade de Pointes (TdP). In recent years, efforts are underway through the Comprehensive in vitro proarrhythmic assay (CiPA) initiative, to develop better tests for this drug induced arrhythmia based in part on in silico simulations of pharmacological disruption of repolarization. However, drug binding to Kv11.1 is more complex than a simple binary molecular reaction, meaning simple steady state measures of potency are poor surrogates for risk. As a result, there is a plethora of mechanistic detail describing the drug/Kv11.1 interaction—such as drug binding kinetics, state preference, temperature dependence and trapping—that needs to be considered when developing in silico models for risk prediction. In addition to this, other factors, such as multichannel pharmacological profile and the nature of the ventricular cell models used in simulations also need to be considered in the search for the optimum in silico approach. Here we consider how much of mechanistic detail needs to be included for in silico models to accurately predict risk and further, how much of this detail can be retrieved from protocols that are practical to implement in high throughout screens as part of next generation of preclinical in silico drug screening approaches?
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Affiliation(s)
- William Lee
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Monique J Windley
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Jamie I Vandenberg
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Adam P Hill
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
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23
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Dutta S, Chang KC, Beattie KA, Sheng J, Tran PN, Wu WW, Wu M, Strauss DG, Colatsky T, Li Z. Optimization of an In silico Cardiac Cell Model for Proarrhythmia Risk Assessment. Front Physiol 2017; 8:616. [PMID: 28878692 PMCID: PMC5572155 DOI: 10.3389/fphys.2017.00616] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/09/2017] [Indexed: 12/19/2022] Open
Abstract
Drug-induced Torsade-de-Pointes (TdP) has been responsible for the withdrawal of many drugs from the market and is therefore of major concern to global regulatory agencies and the pharmaceutical industry. The Comprehensive in vitro Proarrhythmia Assay (CiPA) was proposed to improve prediction of TdP risk, using in silico models and in vitro multi-channel pharmacology data as integral parts of this initiative. Previously, we reported that combining dynamic interactions between drugs and the rapid delayed rectifier potassium current (IKr) with multi-channel pharmacology is important for TdP risk classification, and we modified the original O'Hara Rudy ventricular cell mathematical model to include a Markov model of IKr to represent dynamic drug-IKr interactions (IKr-dynamic ORd model). We also developed a novel metric that could separate drugs with different TdP liabilities at high concentrations based on total electronic charge carried by the major inward ionic currents during the action potential. In this study, we further optimized the IKr-dynamic ORd model by refining model parameters using published human cardiomyocyte experimental data under control and drug block conditions. Using this optimized model and manual patch clamp data, we developed an updated version of the metric that quantifies the net electronic charge carried by major inward and outward ionic currents during the steady state action potential, which could classify the level of drug-induced TdP risk across a wide range of concentrations and pacing rates. We also established a framework to quantitatively evaluate a system's robustness against the induction of early afterdepolarizations (EADs), and demonstrated that the new metric is correlated with the cell's robustness to the pro-EAD perturbation of IKr conductance reduction. In summary, in this work we present an optimized model that is more consistent with experimental data, an improved metric that can classify drugs at concentrations both near and higher than clinical exposure, and a physiological framework to check the relationship between a metric and EAD. These findings provide a solid foundation for using in silico models for the regulatory assessment of TdP risk under the CiPA paradigm.
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Affiliation(s)
- Sara Dutta
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug AdministrationSilver Spring, MD, United States
| | - Kelly C Chang
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug AdministrationSilver Spring, MD, United States
| | - Kylie A Beattie
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug AdministrationSilver Spring, MD, United States
| | - Jiansong Sheng
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug AdministrationSilver Spring, MD, United States
| | - Phu N Tran
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug AdministrationSilver Spring, MD, United States
| | - Wendy W Wu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug AdministrationSilver Spring, MD, United States
| | - Min Wu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug AdministrationSilver Spring, MD, United States
| | - David G Strauss
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug AdministrationSilver Spring, MD, United States
| | - Thomas Colatsky
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug AdministrationSilver Spring, MD, United States
| | - Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug AdministrationSilver Spring, MD, United States
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24
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Li Z, Dutta S, Sheng J, Tran PN, Wu W, Chang K, Mdluli T, Strauss DG, Colatsky T. Improving the In Silico Assessment of Proarrhythmia Risk by Combining hERG (Human Ether-à-go-go-Related Gene) Channel-Drug Binding Kinetics and Multichannel Pharmacology. Circ Arrhythm Electrophysiol 2017; 10:e004628. [PMID: 28202629 DOI: 10.1161/circep.116.004628] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/19/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND The current proarrhythmia safety testing paradigm, although highly efficient in preventing new torsadogenic drugs from entering the market, has important limitations that can restrict the development and use of valuable new therapeutics. The CiPA (Comprehensive in vitro Proarrhythmia Assay) proposes to overcome these limitations by evaluating drug effects on multiple cardiac ion channels in vitro and using these data in a predictive in silico model of the adult human ventricular myocyte. A set of drugs with known clinical torsade de pointes risk was selected to develop and calibrate the in silico model. METHODS AND RESULTS Manual patch-clamp data assessing drug effects on expressed cardiac ion channels were integrated into the O'Hara-Rudy myocyte model modified to include dynamic drug-hERG channel (human Ether-à-go-go-Related Gene) interactions. Together with multichannel pharmacology data, this model predicts that compounds with high torsadogenic risk are more likely to be trapped within the hERG channel and show stronger reverse use dependency of action potential prolongation. Furthermore, drug-induced changes in the amount of electronic charge carried by the late sodium and L-type calcium currents was evaluated as a potential metric for assigning torsadogenic risk. CONCLUSIONS Modeling dynamic drug-hERG channel interactions and multi-ion channel pharmacology improves the prediction of torsadogenic risk. With further development, these methods have the potential to improve the regulatory assessment of drug safety models under the CiPA paradigm.
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Affiliation(s)
- Zhihua Li
- From the Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD.
| | - Sara Dutta
- From the Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD
| | - Jiansong Sheng
- From the Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD
| | - Phu N Tran
- From the Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD
| | - Wendy Wu
- From the Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD
| | - Kelly Chang
- From the Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD
| | - Thembi Mdluli
- From the Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD
| | - David G Strauss
- From the Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD
| | - Thomas Colatsky
- From the Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD
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25
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Wacker S, Noskov SY. Performance of Machine Learning Algorithms for Qualitative and Quantitative Prediction Drug Blockade of hERG1 channel. ACTA ACUST UNITED AC 2017; 6:55-63. [PMID: 29806042 DOI: 10.1016/j.comtox.2017.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Drug-induced abnormal heart rhythm known as Torsades de Pointes (TdP) is a potential lethal ventricular tachycardia found in many patients. Even newly released anti-arrhythmic drugs, like ivabradine with HCN channel as a primary target, block the hERG potassium current in overlapping concentration interval. Promiscuous drug block to hERG channel may potentially lead to perturbation of the action potential duration (APD) and TdP, especially when with combined with polypharmacy and/or electrolyte disturbances. The example of novel anti-arrhythmic ivabradine illustrates clinically important and ongoing deficit in drug design and warrants for better screening methods. There is an urgent need to develop new approaches for rapid and accurate assessment of how drugs with complex interactions and multiple subcellular targets can predispose or protect from drug-induced TdP. One of the unexpected outcomes of compulsory hERG screening implemented in USA and European Union resulted in large datasets of IC50 values for various molecules entering the market. The abundant data allows now to construct predictive machine-learning (ML) models. Novel ML algorithms and techniques promise better accuracy in determining IC50 values of hERG blockade that is comparable or surpassing that of the earlier QSAR or molecular modeling technique. To test the performance of modern ML techniques, we have developed a computational platform integrating various workflows for quantitative structure activity relationship (QSAR) models using data from the ChEMBL database. To establish predictive powers of ML-based algorithms we computed IC50 values for large dataset of molecules and compared it to automated patch clamp system for a large dataset of hERG blocking and non-blocking drugs, an industry gold standard in studies of cardiotoxicity. The optimal protocol with high sensitivity and predictive power is based on the novel eXtreme gradient boosting (XGBoost) algorithm. The ML-platform with XGBoost displays excellent performance with a coefficient of determination of up to R2 ~0.8 for pIC50 values in evaluation datasets, surpassing other metrics and approaches available in literature. Ultimately, the ML-based platform developed in our work is a scalable framework with automation potential to interact with other developing technologies in cardiotoxicity field, including high-throughput electrophysiology measurements delivering large datasets of profiled drugs, rapid synthesis and drug development via progress in synthetic biology.
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Affiliation(s)
- Soren Wacker
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB, Canada, T2N 1N4.,Achlys Inc. and Li Ka Shing Institute of Applied Virology, 6-020 Katz Group Centre for Health Research, University of Alberta, Edmonton, AB T6G 2E1
| | - Sergei Yu Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB, Canada, T2N 1N4
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26
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Hartung T, FitzGerald RE, Jennings P, Mirams GR, Peitsch MC, Rostami-Hodjegan A, Shah I, Wilks MF, Sturla SJ. Systems Toxicology: Real World Applications and Opportunities. Chem Res Toxicol 2017; 30:870-882. [PMID: 28362102 PMCID: PMC5396025 DOI: 10.1021/acs.chemrestox.7b00003] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Indexed: 01/14/2023]
Abstract
Systems Toxicology aims to change the basis of how adverse biological effects of xenobiotics are characterized from empirical end points to describing modes of action as adverse outcome pathways and perturbed networks. Toward this aim, Systems Toxicology entails the integration of in vitro and in vivo toxicity data with computational modeling. This evolving approach depends critically on data reliability and relevance, which in turn depends on the quality of experimental models and bioanalysis techniques used to generate toxicological data. Systems Toxicology involves the use of large-scale data streams ("big data"), such as those derived from omics measurements that require computational means for obtaining informative results. Thus, integrative analysis of multiple molecular measurements, particularly acquired by omics strategies, is a key approach in Systems Toxicology. In recent years, there have been significant advances centered on in vitro test systems and bioanalytical strategies, yet a frontier challenge concerns linking observed network perturbations to phenotypes, which will require understanding pathways and networks that give rise to adverse responses. This summary perspective from a 2016 Systems Toxicology meeting, an international conference held in the Alps of Switzerland, describes the limitations and opportunities of selected emerging applications in this rapidly advancing field. Systems Toxicology aims to change the basis of how adverse biological effects of xenobiotics are characterized, from empirical end points to pathways of toxicity. This requires the integration of in vitro and in vivo data with computational modeling. Test systems and bioanalytical technologies have made significant advances, but ensuring data reliability and relevance is an ongoing concern. The major challenge facing the new pathway approach is determining how to link observed network perturbations to phenotypic toxicity.
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Affiliation(s)
- Thomas Hartung
- Center
for Alternatives to Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
- University
of Konstanz, CAAT-Europe, 78457 Konstanz, Germany
| | - Rex E. FitzGerald
- Swiss
Centre for Applied Human Toxicology, University
of Basel, 4055 Basel, Switzerland
| | - Paul Jennings
- Division
of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Gary R. Mirams
- Centre
for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Manuel C. Peitsch
- Department
of Research and Development, Philip Morris
International, 2000 Neuchâtel, Switzerland
| | - Amin Rostami-Hodjegan
- Centre
for Applied Pharmacokinetic Research, University
of Manchester, Manchester M13 9PL, U.K.
- Simcyp
Limited (a Certara Company), Blades Enterprise
Centre, Sheffield S2 4SU, U.K.
| | - Imran Shah
- National
Center for Computational Toxicology, Research Triangle Park, North Carolina 27711, United States
| | - Martin F. Wilks
- Swiss
Centre for Applied Human Toxicology, University
of Basel, 4055 Basel, Switzerland
| | - Shana J. Sturla
- Department
of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland
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Onal B, Hund TJ. Integrative approaches for prediction of cardiotoxic drug effects and mitigation strategies. J Mol Cell Cardiol 2016; 102:1-2. [PMID: 27894864 DOI: 10.1016/j.yjmcc.2016.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Birce Onal
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center and The Ohio State University College of Engineering, USA; Department of Biomedical Engineering, The Ohio State University Wexner Medical Center and The Ohio State University College of Engineering, USA
| | - Thomas J Hund
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center and The Ohio State University College of Engineering, USA; Department of Biomedical Engineering, The Ohio State University Wexner Medical Center and The Ohio State University College of Engineering, USA; Department of Internal Medicine, The Ohio State University Wexner Medical Center and The Ohio State University College of Engineering, USA.
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Gotta V, Yu Z, Cools F, van Ammel K, Gallacher DJ, Visser SAG, Sannajust F, Morissette P, Danhof M, van der Graaf PH. Application of a systems pharmacology model for translational prediction of hERG-mediated QTc prolongation. Pharmacol Res Perspect 2016; 4:e00270. [PMID: 28097003 PMCID: PMC5226282 DOI: 10.1002/prp2.270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 09/14/2016] [Indexed: 02/06/2023] Open
Abstract
Drug‐induced QTc interval prolongation (ΔQTc) is a main surrogate for proarrhythmic risk assessment. A higher in vivo than in vitro potency for hERG‐mediated QTc prolongation has been suggested. Also, in vivo between‐species and patient populations’ sensitivity to drug‐induced QTc prolongation seems to differ. Here, a systems pharmacology model integrating preclinical in vitro (hERG binding) and in vivo (conscious dog ΔQTc) data of three hERG blockers (dofetilide, sotalol, moxifloxacin) was applied (1) to compare the operational efficacy of the three drugs in vivo and (2) to quantify dog–human differences in sensitivity to drug‐induced QTc prolongation (for dofetilide only). Scaling parameters for translational in vivo extrapolation of drug effects were derived based on the assumption of system‐specific myocardial ion channel densities and transduction of ion channel block: the operational efficacy (transduction of hERG block) in dogs was drug specific (1–19% hERG block corresponded to ≥10 msec ΔQTc). System‐specific maximal achievable ΔQTc was estimated to 28% from baseline in both dog and human, while %hERG block leading to half‐maximal effects was 58% lower in human, suggesting a higher contribution of hERG‐mediated potassium current to cardiac repolarization. These results suggest that differences in sensitivity to drug‐induced QTc prolongation may be well explained by drug‐ and system‐specific differences in operational efficacy (transduction of hERG block), consistent with experimental reports. The proposed scaling approach may thus assist the translational risk assessment of QTc prolongation in different species and patient populations, if mediated by the hERG channel.
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Affiliation(s)
- Verena Gotta
- Systems Pharmacology Leiden Academic Centre for Drug Research (LACDR) Leiden University Leiden The Netherlands; Pediatric Pharmacology and Pharmacometrics University of Basel Children's Hospital (UKBB) Basel Switzerland
| | - Zhiyi Yu
- Division of Medicinal Chemistry Leiden Academic Centre for Drug Research (LACDR) Leiden University Leiden The Netherlands
| | - Frank Cools
- Global Safety Pharmacology Janssen Research & Development Janssen Pharmaceutica NV Beerse Belgium
| | - Karel van Ammel
- Global Safety Pharmacology Janssen Research & Development Janssen Pharmaceutica NV Beerse Belgium
| | - David J Gallacher
- Global Safety Pharmacology Janssen Research & Development Janssen Pharmaceutica NV Beerse Belgium
| | - Sandra A G Visser
- Quantitative Pharmacology and Pharmacometrics/Merck Research Laboratories Merck & Co., Inc. Upper Gwynedd Pennsylvania
| | - Frederick Sannajust
- SALAR-Safety and Exploratory Pharmacology Department/Merck Research Laboratories Merck & Co., Inc. West Point Pennsylvania
| | - Pierre Morissette
- SALAR-Safety and Exploratory Pharmacology Department/Merck Research Laboratories Merck & Co., Inc. West Point Pennsylvania
| | - Meindert Danhof
- Systems Pharmacology Leiden Academic Centre for Drug Research (LACDR) Leiden University Leiden The Netherlands
| | - Piet H van der Graaf
- Systems Pharmacology Leiden Academic Centre for Drug Research (LACDR) Leiden University Leiden The Netherlands; Certara Quantitative Systems Pharmacology Canterbury United Kingdom
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Clancy CE, An G, Cannon WR, Liu Y, May EE, Ortoleva P, Popel AS, Sluka JP, Su J, Vicini P, Zhou X, Eckmann DM. Multiscale Modeling in the Clinic: Drug Design and Development. Ann Biomed Eng 2016; 44:2591-610. [PMID: 26885640 PMCID: PMC4983472 DOI: 10.1007/s10439-016-1563-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/02/2016] [Indexed: 01/30/2023]
Abstract
A wide range of length and time scales are relevant to pharmacology, especially in drug development, drug design and drug delivery. Therefore, multiscale computational modeling and simulation methods and paradigms that advance the linkage of phenomena occurring at these multiple scales have become increasingly important. Multiscale approaches present in silico opportunities to advance laboratory research to bedside clinical applications in pharmaceuticals research. This is achievable through the capability of modeling to reveal phenomena occurring across multiple spatial and temporal scales, which are not otherwise readily accessible to experimentation. The resultant models, when validated, are capable of making testable predictions to guide drug design and delivery. In this review we describe the goals, methods, and opportunities of multiscale modeling in drug design and development. We demonstrate the impact of multiple scales of modeling in this field. We indicate the common mathematical and computational techniques employed for multiscale modeling approaches used in pharmacometric and systems pharmacology models in drug development and present several examples illustrating the current state-of-the-art models for (1) excitable systems and applications in cardiac disease; (2) stem cell driven complex biosystems; (3) nanoparticle delivery, with applications to angiogenesis and cancer therapy; (4) host-pathogen interactions and their use in metabolic disorders, inflammation and sepsis; and (5) computer-aided design of nanomedical systems. We conclude with a focus on barriers to successful clinical translation of drug development, drug design and drug delivery multiscale models.
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Affiliation(s)
- Colleen E Clancy
- Department of Pharmacology, University of California, Davis, CA, USA.
| | - Gary An
- Department of Surgery, University of Chicago, Chicago, IL, USA
| | - William R Cannon
- Computational Biology Group, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yaling Liu
- Department of Mechanical Engineering and Mechanics, Bioengineering Program, Lehigh University, Bethlehem, PA, USA
| | - Elebeoba E May
- Department of Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Peter Ortoleva
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - James P Sluka
- Biocomplexity Institute, Indiana University, Bloomington, IN, USA
| | - Jing Su
- Department of Radiology, Wake Forest University, Winston-Salem, NC, USA
| | - Paolo Vicini
- Clinical Pharmacology and DMPK, MedImmune, Cambridge, UK
| | - Xiaobo Zhou
- Department of Radiology, Wake Forest University, Winston-Salem, NC, USA
| | - David M Eckmann
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA, USA.
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McCauley MD, Darbar D. A new paradigm for predicting risk of Torsades de Pointes during drug development: Commentary on: "Improved prediction of drug-induced Torsades de Pointes through simulations of dynamics and machine learning algorithms". Clin Pharmacol Ther 2016; 100:324-6. [PMID: 27301674 DOI: 10.1002/cpt.408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/26/2016] [Accepted: 06/06/2016] [Indexed: 01/10/2023]
Abstract
Drug-induced long QT syndrome (diLQTS) is a clinical entity in which administration of a drug produces marked prolongation of the QT interval on the ECG. DiLQTS places a patient at risk of developing Torsades de Pointes (TdP), a malignant polymorphic ventricular tachycardia associated with arrhythmic sudden cardiac death (SCD). In addition to diLQTS, other clinical risk factors for TdP include female gender, bradycardia, electrolyte disturbances, recent conversion to normal (sinus) rhythm, and congenital LQTS.
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Affiliation(s)
- M D McCauley
- Division of Cardiology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - D Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, Illinois, USA.
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Hill AP, Perry MD, Abi-Gerges N, Couderc JP, Fermini B, Hancox JC, Knollmann BC, Mirams GR, Skinner J, Zareba W, Vandenberg JI. Computational cardiology and risk stratification for sudden cardiac death: one of the grand challenges for cardiology in the 21st century. J Physiol 2016; 594:6893-6908. [PMID: 27060987 PMCID: PMC5134408 DOI: 10.1113/jp272015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/16/2016] [Indexed: 12/25/2022] Open
Abstract
Risk stratification in the context of sudden cardiac death has been acknowledged as one of the major challenges facing cardiology for the past four decades. In recent years, the advent of high performance computing has facilitated organ-level simulation of the heart, meaning we can now examine the causes, mechanisms and impact of cardiac dysfunction in silico. As a result, computational cardiology, largely driven by the Physiome project, now stands at the threshold of clinical utility in regards to risk stratification and treatment of patients at risk of sudden cardiac death. In this white paper, we outline a roadmap of what needs to be done to make this translational step, using the relatively well-developed case of acquired or drug-induced long QT syndrome as an exemplar case.
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Affiliation(s)
- Adam P Hill
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Matthew D Perry
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Najah Abi-Gerges
- AnaBios Corporation, 3030 Bunker Hill St., San Diego, CA, 92109, USA
| | | | - Bernard Fermini
- Global Safety Pharmacology, Pfizer Inc, MS8274-1347 Eastern Point Road, Groton, CT, 06340, USA
| | - Jules C Hancox
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Bjorn C Knollmann
- Vanderbilt University School of Medicine, 1285 Medical Research Building IV, Nashville, Tennessee, 37232, USA
| | - Gary R Mirams
- Computational Biology, Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Jon Skinner
- Cardiac Inherited Disease Group, Starship Hospital, Auckland, New Zealand
| | - Wojciech Zareba
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Jamie I Vandenberg
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2052, Australia
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Colatsky T, Fermini B, Gintant G, Pierson JB, Sager P, Sekino Y, Strauss DG, Stockbridge N. The Comprehensive in Vitro Proarrhythmia Assay (CiPA) initiative - Update on progress. J Pharmacol Toxicol Methods 2016; 81:15-20. [PMID: 27282641 DOI: 10.1016/j.vascn.2016.06.002] [Citation(s) in RCA: 288] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/01/2016] [Accepted: 06/04/2016] [Indexed: 11/17/2022]
Abstract
The implementation of the ICH S7B and E14 guidelines has been successful in preventing the introduction of potentially torsadogenic drugs to the market, but it has also unduly constrained drug development by focusing on hERG block and QT prolongation as essential determinants of proarrhythmia risk. The Comprehensive in Vitro Proarrhythmia Assay (CiPA) initiative was established to develop a new paradigm for assessing proarrhythmic risk, building on the emergence of new technologies and an expanded understanding of torsadogenic mechanisms beyond hERG block. An international multi-disciplinary team of regulatory, industry and academic scientists are working together to develop and validate a set of predominantly nonclinical assays and methods that eliminate the need for the thorough-QT study and enable a more precise prediction of clinical proarrhythmia risk. The CiPA effort is led by a Steering Team that provides guidance, expertise and oversight to the various working groups and includes partners from US FDA, HESI, CSRC, SPS, EMA, Health Canada, Japan NIHS, and PMDA. The working groups address the three pillars of CiPA that evaluate drug effects on: 1) human ventricular ionic channel currents in heterologous expression systems, 2) in silico integration of cellular electrophysiologic effects based on ionic current effects, the ion channel effects, and 3) fully integrated biological systems (stem-cell-derived cardiac myocytes and the human ECG). This article provides an update on the progress of the initiative towards its target date of December 2017 for completing validation.
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Affiliation(s)
- Thomas Colatsky
- US FDA, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States.
| | - Bernard Fermini
- Pfizer, Eastern Point Road MS 4083, Groton, CT 06340, United States.
| | - Gary Gintant
- AbbVie, R46R AP-9, 1 North Waukegan Rd, North Chicago, IL 60064-6118, United States.
| | - Jennifer B Pierson
- ILSI-Health and Environmental Sciences Institute, 1156 15th Street NW, Suite 200, Washington, DC 20005, United States.
| | - Philip Sager
- Stanford University, 719 Carolina St., San Francisco, CA 94107, United States.
| | - Yuko Sekino
- NIHS Japan, Kamiyoga 1-18-1, Setagaya-ku, Tokyo 158-8501, Japan.
| | - David G Strauss
- US FDA, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States.
| | - Norman Stockbridge
- US FDA, 10903 New Hampshire Ave, Silver Spring, MD 20993, United States.
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Comparison between Hodgkin–Huxley and Markov formulations of cardiac ion channels. J Theor Biol 2016; 399:92-102. [DOI: 10.1016/j.jtbi.2016.03.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 03/22/2016] [Accepted: 03/28/2016] [Indexed: 11/18/2022]
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Li Z, Dutta S, Sheng J, Tran PN, Wu W, Colatsky T. A temperature-dependent in silico model of the human ether-à-go-go-related (hERG) gene channel. J Pharmacol Toxicol Methods 2016; 81:233-9. [PMID: 27178106 DOI: 10.1016/j.vascn.2016.05.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/20/2016] [Accepted: 05/09/2016] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Current regulatory guidelines for assessing the risk of QT prolongation include in vitro assays assessing drug effects on the human ether-à-go-go-related (hERG; also known as Kv11.1) channel expressed in cell lines. These assays are typically conducted at room temperature to promote the ease and stability of recording hERG currents. However, the new Comprehensive in vitro Proarrhythmia Assay (CiPA) paradigm proposes to use an in silico model of the human ventricular myocyte to assess risk, requiring as input hERG channel pharmacology data obtained at physiological temperatures. To accommodate current industry safety pharmacology practices for measuring hERG channel activity, an in silico model of hERG channel that allows for the extrapolation of hERG assay data across different temperatures is desired. Because temperature may have an effect on both channel gating and drug binding rate, such models may need to have two components: a base model dealing with temperature-dependent gating changes without drug, and a pharmacodynamic component simulating temperature-dependent drug binding kinetics. As a first step, a base mode that can capture temperature effects on hERG channel gating without drug is needed. METHODS AND RESULTS To meet this need for a temperature-dependent base model, a Markov model of the hERG channel with state transition rates explicitly dependent on temperature was developed and calibrated using data from a variety of published experiments conducted over a range of temperatures. The model was able to reproduce observed temperature-dependent changes in key channel gating properties and also to predict the results obtained in independent sets of new experiments. DISCUSSION This new temperature-sensitive model of hERG gating represents an attempt to improve the predictivity of safety pharmacology testing by enabling the translation of room temperature hERG assay data to more physiological conditions. With further development, this model can be incorporated into the CiPA paradigm and also be used as a tool for developing insights into the thermodynamics of hERG channel gating mechanisms and the temperature-dependence of hERG channel block by drugs.
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Affiliation(s)
- Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, United States.
| | - Sara Dutta
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, United States
| | - Jiansong Sheng
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, United States
| | - Phu N Tran
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, United States
| | - Wendy Wu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, United States
| | - Thomas Colatsky
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, United States
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36
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Davies MR, Wang K, Mirams GR, Caruso A, Noble D, Walz A, Lavé T, Schuler F, Singer T, Polonchuk L. Recent developments in using mechanistic cardiac modelling for drug safety evaluation. Drug Discov Today 2016; 21:924-38. [PMID: 26891981 PMCID: PMC4909717 DOI: 10.1016/j.drudis.2016.02.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/13/2016] [Accepted: 02/05/2016] [Indexed: 01/21/2023]
Abstract
Modelling and simulation can streamline decision making in drug safety testing. Computational cardiac electrophysiology is a mature technology with a long heritage. There are many challenges and opportunities in using in silico techniques in future. We discuss how models can be used at different stages of drug discovery. CiPA will combine screening platforms, human cell assays and in silico predictions.
On the tenth anniversary of two key International Conference on Harmonisation (ICH) guidelines relating to cardiac proarrhythmic safety, an initiative aims to consider the implementation of a new paradigm that combines in vitro and in silico technologies to improve risk assessment. The Comprehensive In Vitro Proarrhythmia Assay (CiPA) initiative (co-sponsored by the Cardiac Safety Research Consortium, Health and Environmental Sciences Institute, Safety Pharmacology Society and FDA) is a bold and welcome step in using computational tools for regulatory decision making. This review compares and contrasts the state-of-the-art tools from empirical to mechanistic models of cardiac electrophysiology, and how they can and should be used in combination with experimental tests for compound decision making.
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Affiliation(s)
| | - Ken Wang
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Switzerland
| | - Gary R Mirams
- Computational Biology, Department of Computer Science, University of Oxford, OX1 3QD, UK
| | - Antonello Caruso
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Switzerland
| | - Denis Noble
- Department of Physiology, Anatomy & Genetics, University of Oxford, OX1 3PT, UK
| | - Antje Walz
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Switzerland
| | - Thierry Lavé
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Switzerland
| | - Franz Schuler
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Switzerland
| | - Thomas Singer
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Switzerland
| | - Liudmila Polonchuk
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Switzerland
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37
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Paci M, Hyttinen J, Rodriguez B, Severi S. Human induced pluripotent stem cell-derived versus adult cardiomyocytes: an in silico electrophysiological study on effects of ionic current block. Br J Pharmacol 2015; 172:5147-60. [PMID: 26276951 PMCID: PMC4629192 DOI: 10.1111/bph.13282] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/29/2015] [Accepted: 08/03/2015] [Indexed: 12/28/2022] Open
Abstract
Background and Purpose Two new technologies are likely to revolutionize cardiac safety and drug development: in vitro experiments on human‐induced pluripotent stem cell‐derived cardiomyocytes (hiPSC‐CMs) and in silico human adult ventricular cardiomyocyte (hAdultV‐CM) models. Their combination was recently proposed as a potential replacement for the present hERG‐based QT study for pharmacological safety assessments. Here, we systematically compared in silico the effects of selective ionic current block on hiPSC‐CM and hAdultV‐CM action potentials (APs), to identify similarities/differences and to illustrate the potential of computational models as supportive tools for evaluating new in vitro technologies. Experimental Approach In silico AP models of ventricular‐like and atrial‐like hiPSC‐CMs and hAdultV‐CM were used to simulate the main effects of four degrees of block of the main cardiac transmembrane currents. Key Results Qualitatively, hiPSC‐CM and hAdultV‐CM APs showed similar responses to current block, consistent with results from experiments. However, quantitatively, hiPSC‐CMs were more sensitive to block of (i) L‐type Ca2+ currents due to the overexpression of the Na+/Ca2+ exchanger (leading to shorter APs) and (ii) the inward rectifier K+ current due to reduced repolarization reserve (inducing diastolic potential depolarization and repolarization failure). Conclusions and Implications In silico hiPSC‐CMs and hAdultV‐CMs exhibit a similar response to selective current blocks. However, overall hiPSC‐CMs show greater sensitivity to block, which may facilitate in vitro identification of drug‐induced effects. Extrapolation of drug effects from hiPSC‐CM to hAdultV‐CM and pro‐arrhythmic risk assessment can be facilitated by in silico predictions using biophysically‐based computational models.
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Affiliation(s)
- M Paci
- Department of Electronics and Communications Engineering, Tampere University of Technology, BioMediTech, Tampere, Finland
| | - J Hyttinen
- Department of Electronics and Communications Engineering, Tampere University of Technology, BioMediTech, Tampere, Finland
| | - B Rodriguez
- Department of Computer Science, University of Oxford, Oxford, UK
| | - S Severi
- Department of Electrical, Electronic and Information Engineering 'Guglielmo Marconi', University of Bologna, Cesena (FC), Italy
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Yu Z, van Veldhoven JPD, Louvel J, ’t Hart IME, Rook MB, van der Heyden MAG, Heitman LH, IJzerman AP. Structure–Affinity Relationships (SARs) and Structure–Kinetics Relationships (SKRs) of Kv11.1 Blockers. J Med Chem 2015; 58:5916-29. [DOI: 10.1021/acs.jmedchem.5b00518] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Zhiyi Yu
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jacobus P. D. van Veldhoven
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Julien Louvel
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Ingrid M. E. ’t Hart
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Martin B. Rook
- Department of Medical Physiology, Division Heart & Lungs, University Medical Centre Utrecht, 3584 CM Utrecht, The Netherlands
| | - Marcel A. G. van der Heyden
- Department of Medical Physiology, Division Heart & Lungs, University Medical Centre Utrecht, 3584 CM Utrecht, The Netherlands
| | - Laura H. Heitman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
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Fermini B, Hancox JC, Abi-Gerges N, Bridgland-Taylor M, Chaudhary KW, Colatsky T, Correll K, Crumb W, Damiano B, Erdemli G, Gintant G, Imredy J, Koerner J, Kramer J, Levesque P, Li Z, Lindqvist A, Obejero-Paz CA, Rampe D, Sawada K, Strauss DG, Vandenberg JI. A New Perspective in the Field of Cardiac Safety Testing through the Comprehensive In Vitro Proarrhythmia Assay Paradigm. ACTA ACUST UNITED AC 2015; 21:1-11. [PMID: 26170255 DOI: 10.1177/1087057115594589] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/11/2015] [Indexed: 12/31/2022]
Abstract
For the past decade, cardiac safety screening to evaluate the propensity of drugs to produce QT interval prolongation and Torsades de Pointes (TdP) arrhythmia has been conducted according to ICH S7B and ICH E14 guidelines. Central to the existing approach are hERG channel assays and in vivo QT measurements. Although effective, the present paradigm carries a risk of unnecessary compound attrition and high cost, especially when considering costly thorough QT (TQT) studies conducted later in drug development. The C: omprehensive I: n Vitro P: roarrhythmia A: ssay (CiPA) initiative is a public-private collaboration with the aim of updating the existing cardiac safety testing paradigm to better evaluate arrhythmia risk and remove the need for TQT studies. It is hoped that CiPA will produce a standardized ion channel assay approach, incorporating defined tests against major cardiac ion channels, the results of which then inform evaluation of proarrhythmic actions in silico, using human ventricular action potential reconstructions. Results are then to be confirmed using human (stem cell-derived) cardiomyocytes. This perspective article reviews the rationale, progress of, and challenges for the CiPA initiative, if this new paradigm is to replace existing practice and, in time, lead to improved and widely accepted cardiac safety testing guidelines.
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Affiliation(s)
| | - Jules C Hancox
- School of Physiology and Pharmacology, University of Bristol, Bristol, UK
| | - Najah Abi-Gerges
- Translational Safety, Drug Safety and Metabolism, Innovative Medicines and Early Development, AstraZeneca R&D, Macclesfield, UK AnaBios Corporation, San Diego, CA, USA
| | - Matthew Bridgland-Taylor
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca R&D, Macclesfield, UK
| | | | - Thomas Colatsky
- Division of Applied Regulatory Science, CDER, US Food and Drug Administration, Silver Spring, MD, USA
| | | | | | - Bruce Damiano
- Global Safety Pharmacology, Discovery Sciences, Janssen Research & Development LLC, Spring House, PA, USA
| | - Gul Erdemli
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Inc, Cambridge, MA, USA
| | - Gary Gintant
- Department of Integrative Pharmacology, Integrated Sciences & Technology, AbbVie, North Chicago, IL, USA
| | - John Imredy
- Department of Safety Assessment, Merck & Co, Kenilworth, NJ, USA
| | - John Koerner
- Division of Cardiovascular and Renal Products, CDER, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - James Kramer
- ChanTest, A Charles River Company, Cleveland, OH, USA
| | - Paul Levesque
- Bristol Myers Squibb Research & Development, Princeton, NJ, USA
| | - Zhihua Li
- Division of Applied Regulatory Science, CDER, US Food and Drug Administration, Silver Spring, MD, USA
| | | | | | - David Rampe
- Preclinical Safety, Sanofi, Bridgewater, NJ, USA
| | - Kohei Sawada
- Global Cardiovascular Assessment, Eisai Co., Ltd., Ibaraki, Japan
| | - David G Strauss
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Jamie I Vandenberg
- Victor Chang Cardiac Research Institute, St Vincent's Clinical School, University of NSW, Darlinghurst, NSW, Australia
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Computational investigations of hERG channel blockers: New insights and current predictive models. Adv Drug Deliv Rev 2015; 86:72-82. [PMID: 25770776 DOI: 10.1016/j.addr.2015.03.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 01/13/2015] [Accepted: 03/04/2015] [Indexed: 01/08/2023]
Abstract
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.
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Mistry HB, Davies MR, Di Veroli GY. A new classifier-based strategy for in-silico ion-channel cardiac drug safety assessment. Front Pharmacol 2015; 6:59. [PMID: 25852560 PMCID: PMC4371651 DOI: 10.3389/fphar.2015.00059] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/08/2015] [Indexed: 11/13/2022] Open
Abstract
There is currently a strong interest in using high-throughput in-vitro ion-channel screening data to make predictions regarding the cardiac toxicity potential of a new compound in both animal and human studies. A recent FDA think tank encourages the use of biophysical mathematical models of cardiac myocytes for this prediction task. However, it remains unclear whether this approach is the most appropriate. Here we examine five literature data-sets that have been used to support the use of four different biophysical models and one statistical model for predicting cardiac toxicity in numerous species using various endpoints. We propose a simple model that represents the balance between repolarisation and depolarisation forces and compare the predictive power of the model against the original results (leave-one-out cross-validation). Our model showed equivalent performance when compared to the four biophysical models and one statistical model. We therefore conclude that this approach should be further investigated in the context of early cardiac safety screening when in-vitro potency data is generated.
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Affiliation(s)
- Hitesh B Mistry
- Manchester Pharmacy School, University of Manchester Manchester, UK
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Gunaruwan P, Howes LG. Assessing the Arrhythmogenic Potential of New Drugs: A Guide for the Pharmaceutical Physician. Pharmaceut Med 2015. [DOI: 10.1007/s40290-015-0082-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Wiśniowska B, Mendyk A, Fijorek K, Polak S. Computer-based prediction of the drug proarrhythmic effect: problems, issues, known and suspected challenges. Europace 2015; 16:724-35. [PMID: 24798962 DOI: 10.1093/europace/euu009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
It is likely that computer modelling and simulations will become an element of comprehensive cardiac safety testing. Their role would be primarily the integration and the interpretation of previously gathered data. There are still unanswered questions and issues which we list and describe below. They include sources of data used for the development of the models as well as data utilized as input information, which can come from the in vitro studies and the quantitative structure-activity relationship models. The pharmacokinetics of the drugs in question play a crucial role as their active concentration should be considered, yet the question remains where is the right place to assess it. The pharmacodynamic angle includes complications coming from multiple drugs (i.e. active metabolites) acting in parallel as well as the type of interaction with (potentially) multiple affected channels. Once established, the model and the methodology of its use should be further validated, optimistically against individual data reported at the clinical level as the physiological, anatomical, and genetic parameters play a crucial role in the drug-triggered arrhythmia induction. All the abovementioned issues should be at least considered and-hopefully-resolved, to properly utilize the mathematical models for a cardiac safety assessment.
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Affiliation(s)
- Barbara Wiśniowska
- Unit of Pharmacoepidemiology and Pharmacoeconomics, Faculty of Pharmacy, Medical College, Jagiellonian University, Medyczna 9 Street, 30-688 Kraków, Poland
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Mirams GR, Davies MR, Brough SJ, Bridgland-Taylor MH, Cui Y, Gavaghan DJ, Abi-Gerges N. Prediction of Thorough QT study results using action potential simulations based on ion channel screens. J Pharmacol Toxicol Methods 2014; 70:246-54. [PMID: 25087753 PMCID: PMC4266452 DOI: 10.1016/j.vascn.2014.07.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/18/2014] [Accepted: 07/10/2014] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Detection of drug-induced pro-arrhythmic risk is a primary concern for pharmaceutical companies and regulators. Increased risk is linked to prolongation of the QT interval on the body surface ECG. Recent studies have shown that multiple ion channel interactions can be required to predict changes in ventricular repolarisation and therefore QT intervals. In this study we attempt to predict the result of the human clinical Thorough QT (TQT) study, using multiple ion channel screening which is available early in drug development. METHODS Ion current reduction was measured, in the presence of marketed drugs which have had a TQT study, for channels encoded by hERG, CaV1.2, NaV1.5, KCNQ1/MinK, and Kv4.3/KChIP2.2. The screen was performed on two platforms - IonWorks Quattro (all 5 channels, 34 compounds), and IonWorks Barracuda (hERG & CaV1.2, 26 compounds). Concentration-effect curves were fitted to the resulting data, and used to calculate a percentage reduction in each current at a given concentration. Action potential simulations were then performed using the ten Tusscher and Panfilov (2006), Grandi et al. (2010) and O'Hara et al. (2011) human ventricular action potential models, pacing at 1Hz and running to steady state, for a range of concentrations. RESULTS We compared simulated action potential duration predictions with the QT prolongation observed in the TQT studies. At the estimated concentrations, simulations tended to underestimate any observed QT prolongation. When considering a wider range of concentrations, and conventional patch clamp rather than screening data for hERG, prolongation of ≥5ms was predicted with up to 79% sensitivity and 100% specificity. DISCUSSION This study provides a proof-of-principle for the prediction of human TQT study results using data available early in drug development. We highlight a number of areas that need refinement to improve the method's predictive power, but the results suggest that such approaches will provide a useful tool in cardiac safety assessment.
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Affiliation(s)
- Gary R Mirams
- Computational Biology, Dept. of Computer Science, University of Oxford, Oxford OX1 3QD, UK.
| | - Mark R Davies
- Clinical Informatics, R&D Information, AstraZeneca, Alderley Park, SK10 4TG, UK
| | - Stephen J Brough
- Screening & Compound Profiling, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | | | - Yi Cui
- Safety Evaluation and Risk Management, Global Clinical Safety, GlaxoSmithKline, Middlesex UB11 1BT, UK
| | - David J Gavaghan
- Computational Biology, Dept. of Computer Science, University of Oxford, Oxford OX1 3QD, UK
| | - Najah Abi-Gerges
- Translational Safety Department, Drug Safety & Metabolism, AstraZeneca, Alderley Park, SK10 4TG, UK
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Tong WC, Ghouri I, Taggart MJ. Computational modeling of inhibition of voltage-gated Ca channels: identification of different effects on uterine and cardiac action potentials. Front Physiol 2014; 5:399. [PMID: 25360118 PMCID: PMC4199256 DOI: 10.3389/fphys.2014.00399] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/26/2014] [Indexed: 11/13/2022] Open
Abstract
The uterus and heart share the important physiological feature whereby contractile activation of the muscle tissue is regulated by the generation of periodic, spontaneous electrical action potentials (APs). Preterm birth arising from premature uterine contractions is a major complication of pregnancy and there remains a need to pursue avenues of research that facilitate the use of drugs, tocolytics, to limit these inappropriate contractions without deleterious actions on cardiac electrical excitation. A novel approach is to make use of mathematical models of uterine and cardiac APs, which incorporate many ionic currents contributing to the AP forms, and test the cell-specific responses to interventions. We have used three such models-of uterine smooth muscle cells (USMC), cardiac sinoatrial node cells (SAN), and ventricular cells-to investigate the relative effects of reducing two important voltage-gated Ca currents-the L-type (ICaL) and T-type (ICaT) Ca currents. Reduction of ICaL (10%) alone, or ICaT (40%) alone, blunted USMC APs with little effect on ventricular APs and only mild effects on SAN activity. Larger reductions in either current further attenuated the USMC APs but with also greater effects on SAN APs. Encouragingly, a combination of ICaL and ICaT reduction did blunt USMC APs as intended with little detriment to APs of either cardiac cell type. Subsequent overlapping maps of ICaL and ICaT inhibition profiles from each model revealed a range of combined reductions of ICaL and ICaT over which an appreciable diminution of USMC APs could be achieved with no deleterious action on cardiac SAN or ventricular APs. This novel approach illustrates the potential for computational biology to inform us of possible uterine and cardiac cell-specific mechanisms. Incorporating such computational approaches in future studies directed at designing new, or repurposing existing, tocolytics will be beneficial for establishing a desired uterine specificity of action.
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Affiliation(s)
- Wing-Chiu Tong
- Institute of Cellular Medicine, Newcastle UniversityNewcastle upon Tyne, UK
| | | | - Michael J. Taggart
- Institute of Cellular Medicine, Newcastle UniversityNewcastle upon Tyne, UK
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Predicting QTc Prolongation in Man From Only In Vitro Data. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2014; 3:e131. [PMID: 25141222 PMCID: PMC4150928 DOI: 10.1038/psp.2014.33] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 06/16/2014] [Indexed: 11/09/2022]
Abstract
Mishra et al.(1) in their article "Interaction between domperidone and ketoconazole: toward prediction of consequent QTc prolongation using purely in vitro information" describe the use of physiologically based pharmacokinetic (PBPK) modeling and pharmacodynamic models of cardiac repolarization to predict clinical data from preclinical data. Eliminating the risk of cardiac arrhythmias through delayed repolarization often relies on preclinical data during compound selection. Although there are some limitations, there appears to be significant promise in using this modeling approach.
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47
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Yarov-Yarovoy V, Allen TW, Clancy CE. Computational Models for Predictive Cardiac Ion Channel Pharmacology. ACTA ACUST UNITED AC 2014; 14:3-10. [PMID: 26635886 DOI: 10.1016/j.ddmod.2014.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A wealth of experimental data exists describing the elementary building blocks of complex physiological systems. However, it is increasingly apparent in the biomedical sciences that mechanisms of biological function cannot be observed or readily predicted via study of constituent elements alone. This is especially clear in the longstanding failures in prediction of effects of drug treatment for heart rhythm disturbances. These failures stem in part from classical assumptions that have been made in cardiac antiarrhythmic drug development - that a drug operates by one mechanism via one target receptor that arises from one gene.
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Affiliation(s)
| | - Toby W Allen
- Department of Chemistry, University of California, Davis
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48
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Heijman J, Voigt N, Carlsson LG, Dobrev D. Cardiac safety assays. Curr Opin Pharmacol 2014; 15:16-21. [DOI: 10.1016/j.coph.2013.11.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/04/2013] [Accepted: 11/07/2013] [Indexed: 12/22/2022]
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Sager PT, Gintant G, Turner JR, Pettit S, Stockbridge N. Rechanneling the cardiac proarrhythmia safety paradigm: a meeting report from the Cardiac Safety Research Consortium. Am Heart J 2014; 167:292-300. [PMID: 24576511 DOI: 10.1016/j.ahj.2013.11.004] [Citation(s) in RCA: 387] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 11/14/2013] [Indexed: 12/18/2022]
Abstract
This white paper provides a summary of a scientific proposal presented at a Cardiac Safety Research Consortium/Health and Environmental Sciences Institute/Food and Drug Administration-sponsored Think Tank, held at Food and Drug Administration's White Oak facilities, Silver Spring, MD, on July 23, 2013, with the intention of moving toward consensus on defining a new paradigm in the field of cardiac safety in which proarrhythmic risk would be primarily assessed using nonclinical in vitro human models based on solid mechanistic considerations of torsades de pointes proarrhythmia. This new paradigm would shift the emphasis from the present approach that strongly relies on QTc prolongation (a surrogate marker of proarrhythmia) and could obviate the clinical Thorough QT study during later drug development. These discussions represent current thinking and suggestions for furthering our knowledge and understanding of the public health case for adopting a new, integrated nonclinical in vitro/in silico paradigm, the Comprehensive In Vitro Proarrhythmia Assay, for the assessment of a candidate drug's proarrhythmic liability, and for developing a public-private collaborative program to characterize the data content, quality, and approaches required to assess proarrhythmic risk in the absence of a Thorough QT study. This paper seeks to encourage multistakeholder input regarding this initiative and does not represent regulatory guidance.
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Hill AP, Perrin MJ, Heide J, Campbell TJ, Mann SA, Vandenberg JI. Kinetics of Drug Interaction with the Kv11.1 Potassium Channel. Mol Pharmacol 2014; 85:769-76. [DOI: 10.1124/mol.114.091835] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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