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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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Trayanova NA, Lyon A, Shade J, Heijman J. Computational modeling of cardiac electrophysiology and arrhythmogenesis: toward clinical translation. Physiol Rev 2024; 104:1265-1333. [PMID: 38153307 DOI: 10.1152/physrev.00017.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023] Open
Abstract
The complexity of cardiac electrophysiology, involving dynamic changes in numerous components across multiple spatial (from ion channel to organ) and temporal (from milliseconds to days) scales, makes an intuitive or empirical analysis of cardiac arrhythmogenesis challenging. Multiscale mechanistic computational models of cardiac electrophysiology provide precise control over individual parameters, and their reproducibility enables a thorough assessment of arrhythmia mechanisms. This review provides a comprehensive analysis of models of cardiac electrophysiology and arrhythmias, from the single cell to the organ level, and how they can be leveraged to better understand rhythm disorders in cardiac disease and to improve heart patient care. Key issues related to model development based on experimental data are discussed, and major families of human cardiomyocyte models and their applications are highlighted. An overview of organ-level computational modeling of cardiac electrophysiology and its clinical applications in personalized arrhythmia risk assessment and patient-specific therapy of atrial and ventricular arrhythmias is provided. The advancements presented here highlight how patient-specific computational models of the heart reconstructed from patient data have achieved success in predicting risk of sudden cardiac death and guiding optimal treatments of heart rhythm disorders. Finally, an outlook toward potential future advances, including the combination of mechanistic modeling and machine learning/artificial intelligence, is provided. As the field of cardiology is embarking on a journey toward precision medicine, personalized modeling of the heart is expected to become a key technology to guide pharmaceutical therapy, deployment of devices, and surgical interventions.
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Affiliation(s)
- Natalia A Trayanova
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
- Alliance for Cardiovascular Diagnostic and Treatment Innovation, Johns Hopkins University, Baltimore, Maryland, United States
| | - Aurore Lyon
- Department of Biomedical Engineering, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
- Division of Heart and Lungs, Department of Medical Physiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Julie Shade
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
- Alliance for Cardiovascular Diagnostic and Treatment Innovation, Johns Hopkins University, Baltimore, Maryland, United States
| | - Jordi Heijman
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
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3
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Riaz Gondal MU, Atta Mehdi H, Khenhrani RR, Kumari N, Ali MF, Kumar S, Faraz M, Malik J. Role of Machine Learning and Artificial Intelligence in Arrhythmias and Electrophysiology. Cardiol Rev 2024:00045415-990000000-00270. [PMID: 38761137 DOI: 10.1097/crd.0000000000000715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Machine learning (ML), a subset of artificial intelligence (AI) centered on machines learning from extensive datasets, stands at the forefront of a technological revolution shaping various facets of society. Cardiovascular medicine has emerged as a key domain for ML applications, with considerable efforts to integrate these innovations into routine clinical practice. Within cardiac electrophysiology, ML applications, especially in the automated interpretation of electrocardiograms, have garnered substantial attention in existing literature. However, less recognized are the diverse applications of ML in cardiac electrophysiology and arrhythmias, spanning basic science research on arrhythmia mechanisms, both experimental and computational, as well as contributions to enhanced techniques for mapping cardiac electrical function and translational research related to arrhythmia management. This comprehensive review delves into various ML applications within the scope of this journal, organized into 3 parts. The first section provides a fundamental understanding of general ML principles and methodologies, serving as a foundational resource for readers interested in exploring ML applications in arrhythmia research. The second part offers an in-depth review of studies in arrhythmia and electrophysiology that leverage ML methodologies, showcasing the broad potential of ML approaches. Each subject is thoroughly outlined, accompanied by a review of notable ML research advancements. Finally, the review delves into the primary challenges and future perspectives surrounding ML-driven cardiac electrophysiology and arrhythmias research.
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Affiliation(s)
| | - Hassan Atta Mehdi
- Department of Medicine, Jinnah Postgraduate Medical Centre, Karachi, Pakistan
| | - Raja Ram Khenhrani
- Department of Medicine, Internal Medicine Fellow, Shaheed Mohtarma Benazir Bhutto Medical College and Lyari General Hospital, Karachi, Pakistan
| | - Neha Kumari
- Department of Medicine, Jinnah Postgraduate Medical Centre, Karachi, Pakistan
| | - Muhammad Faizan Ali
- Department of Medicine, Jinnah Postgraduate Medical Centre, Karachi, Pakistan
| | - Sooraj Kumar
- Department of Medicine, Jinnah Sindh Medical University, Karachi, Pakistan; and
| | - Maria Faraz
- Department of Cardiovascular Medicine, Cardiovascular Analytics Group, Rawalpindi, Pakistan
| | - Jahanzeb Malik
- Department of Cardiovascular Medicine, Cardiovascular Analytics Group, Rawalpindi, Pakistan
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4
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Chandy M, Hill T, Jimenez-Tellez N, Wu JC, Sarles SE, Hensel E, Wang Q, Rahman I, Conklin DJ. Addressing Cardiovascular Toxicity Risk of Electronic Nicotine Delivery Systems in the Twenty-First Century: "What Are the Tools Needed for the Job?" and "Do We Have Them?". Cardiovasc Toxicol 2024; 24:435-471. [PMID: 38555547 DOI: 10.1007/s12012-024-09850-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024]
Abstract
Cigarette smoking is positively and robustly associated with cardiovascular disease (CVD), including hypertension, atherosclerosis, cardiac arrhythmias, stroke, thromboembolism, myocardial infarctions, and heart failure. However, after more than a decade of ENDS presence in the U.S. marketplace, uncertainty persists regarding the long-term health consequences of ENDS use for CVD. New approach methods (NAMs) in the field of toxicology are being developed to enhance rapid prediction of human health hazards. Recent technical advances can now consider impact of biological factors such as sex and race/ethnicity, permitting application of NAMs findings to health equity and environmental justice issues. This has been the case for hazard assessments of drugs and environmental chemicals in areas such as cardiovascular, respiratory, and developmental toxicity. Despite these advances, a shortage of widely accepted methodologies to predict the impact of ENDS use on human health slows the application of regulatory oversight and the protection of public health. Minimizing the time between the emergence of risk (e.g., ENDS use) and the administration of well-founded regulatory policy requires thoughtful consideration of the currently available sources of data, their applicability to the prediction of health outcomes, and whether these available data streams are enough to support an actionable decision. This challenge forms the basis of this white paper on how best to reveal potential toxicities of ENDS use in the human cardiovascular system-a primary target of conventional tobacco smoking. We identify current approaches used to evaluate the impacts of tobacco on cardiovascular health, in particular emerging techniques that replace, reduce, and refine slower and more costly animal models with NAMs platforms that can be applied to tobacco regulatory science. The limitations of these emerging platforms are addressed, and systems biology approaches to close the knowledge gap between traditional models and NAMs are proposed. It is hoped that these suggestions and their adoption within the greater scientific community will result in fresh data streams that will support and enhance the scientific evaluation and subsequent decision-making of tobacco regulatory agencies worldwide.
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Affiliation(s)
- Mark Chandy
- Robarts Research Institute, Western University, London, N6A 5K8, Canada
| | - Thomas Hill
- Division of Nonclinical Science, Center for Tobacco Products, US Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Nerea Jimenez-Tellez
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - S Emma Sarles
- Biomedical and Chemical Engineering PhD Program, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Edward Hensel
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Qixin Wang
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Daniel J Conklin
- Division of Environmental Medicine, Department of Medicine, Center for Cardiometabolic Science, Christina Lee Brown Envirome Institute, University of Louisville, 580 S. Preston St., Delia Baxter, Rm. 404E, Louisville, KY, 40202, USA.
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Armoundas AA, Narayan SM, Arnett DK, Spector-Bagdady K, Bennett DA, Celi LA, Friedman PA, Gollob MH, Hall JL, Kwitek AE, Lett E, Menon BK, Sheehan KA, Al-Zaiti SS. Use of Artificial Intelligence in Improving Outcomes in Heart Disease: A Scientific Statement From the American Heart Association. Circulation 2024; 149:e1028-e1050. [PMID: 38415358 PMCID: PMC11042786 DOI: 10.1161/cir.0000000000001201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
A major focus of academia, industry, and global governmental agencies is to develop and apply artificial intelligence and other advanced analytical tools to transform health care delivery. The American Heart Association supports the creation of tools and services that would further the science and practice of precision medicine by enabling more precise approaches to cardiovascular and stroke research, prevention, and care of individuals and populations. Nevertheless, several challenges exist, and few artificial intelligence tools have been shown to improve cardiovascular and stroke care sufficiently to be widely adopted. This scientific statement outlines the current state of the art on the use of artificial intelligence algorithms and data science in the diagnosis, classification, and treatment of cardiovascular disease. It also sets out to advance this mission, focusing on how digital tools and, in particular, artificial intelligence may provide clinical and mechanistic insights, address bias in clinical studies, and facilitate education and implementation science to improve cardiovascular and stroke outcomes. Last, a key objective of this scientific statement is to further the field by identifying best practices, gaps, and challenges for interested stakeholders.
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6
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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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7
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Aguado-Sierra J, Dominguez-Gomez P, Amar A, Butakoff C, Leitner M, Schaper S, Kriegl JM, Darpo B, Vazquez M, Rast G. Virtual clinical QT exposure-response studies - A translational computational approach. J Pharmacol Toxicol Methods 2024; 126:107498. [PMID: 38432528 DOI: 10.1016/j.vascn.2024.107498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 12/13/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND AND PURPOSE A recent paradigm shift in proarrhythmic risk assessment suggests that the integration of clinical, non-clinical, and computational evidence can be used to reach a comprehensive understanding of the proarrhythmic potential of drug candidates. While current computational methodologies focus on predicting the incidence of proarrhythmic events after drug administration, the objective of this study is to predict concentration-response relationships of QTc as a clinical endpoint. EXPERIMENTAL APPROACH Full heart computational models reproducing human cardiac populations were created to predict the concentration-response relationship of changes in the QT interval as recommended for clinical trials. The concentration-response relationship of the QT-interval prolongation obtained from the computational cardiac population was compared against the relationship from clinical trial data for a set of well-characterized compounds: moxifloxacin, dofetilide, verapamil, and ondansetron. KEY RESULTS Computationally derived concentration-response relationships of QT interval changes for three of the four drugs had slopes within the confidence interval of clinical trials (dofetilide, moxifloxacin and verapamil) when compared to placebo-corrected concentration-ΔQT and concentration-ΔQT regressions. Moxifloxacin showed a higher intercept, outside the confidence interval of the clinical data, demonstrating that in this example, the standard linear regression does not appropriately capture the concentration-response results at very low concentrations. The concentrations corresponding to a mean QTc prolongation of 10 ms were consistently lower in the computational model than in clinical data. The critical concentration varied within an approximate ratio of 0.5 (moxifloxacin and ondansetron) and 1 times (dofetilide, verapamil) the critical concentration observed in human clinical trials. Notably, no other in silico methodology can approximate the human critical concentration values for a QT interval prolongation of 10 ms. CONCLUSION AND IMPLICATIONS Computational concentration-response modelling of a virtual population of high-resolution, 3-dimensional cardiac models can provide comparable information to clinical data and could be used to complement pre-clinical and clinical safety packages. It provides access to an unlimited exposure range to support trial design and can improve the understanding of pre-clinical-clinical translation.
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Affiliation(s)
- Jazmin Aguado-Sierra
- Elem Biotech, Barcelona, Spain; Barcelona Supercomputing Center, Barcelona, Spain.
| | | | | | | | - Michael Leitner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach, Germany.
| | - Stefan Schaper
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach, Germany.
| | - Jan M Kriegl
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach, Germany.
| | | | - Mariano Vazquez
- Elem Biotech, Barcelona, Spain; Barcelona Supercomputing Center, Barcelona, Spain.
| | - Georg Rast
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach, Germany.
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8
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Yang PC, Jeng MT, Yarov-Yarovoy V, Santana LF, Vorobyov I, Clancy CE. Toward Digital Twin Technology for Precision Pharmacology. JACC Clin Electrophysiol 2024; 10:359-364. [PMID: 38069976 DOI: 10.1016/j.jacep.2023.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/26/2023] [Accepted: 10/20/2023] [Indexed: 03/01/2024]
Abstract
The authors demonstrate the feasibility of technological innovation for personalized medicine in the context of drug-induced arrhythmia. The authors use atomistic-scale structural models to predict rates of drug interaction with ion channels and make predictions of their effects in digital twins of induced pluripotent stem cell-derived cardiac myocytes. The authors construct a simplified multilayer, 1-dimensional ring model with sufficient path length to enable the prediction of arrhythmogenic dispersion of repolarization. Finally, the authors validate the computational pipeline prediction of drug effects with data and quantify drug-induced propensity to repolarization abnormalities in cardiac tissue. The technology is high throughput, computationally efficient, and low cost toward personalized pharmacologic prediction.
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Affiliation(s)
- Pei-Chi Yang
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California, USA
| | - Mao-Tsuen Jeng
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California, USA
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California, USA; Department of Anesthesiology and Pain Medicine, University of California-Davis, Davis, California, USA
| | - L Fernando Santana
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California, USA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California, USA; Department of Pharmacology, University of California-Davis, Davis, California, USA.
| | - Colleen E Clancy
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California, USA; Department of Pharmacology, University of California-Davis, Davis, California, USA; Center for Precision Medicine, University of California-Davis, Davis, California, USA.
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9
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Weinberg SH, Hund TJ. Building A Pipeline for Precision Antiarrhythmic Therapy. JACC Clin Electrophysiol 2024; 10:365-366. [PMID: 38180434 DOI: 10.1016/j.jacep.2023.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024]
Affiliation(s)
- Seth H Weinberg
- Dorothy M. Davis Heart and Lung Research Institute, Ohio State University, Columbus, Ohio, USA; Department of Biomedical Engineering, Ohio State University, Columbus, Ohio, USA
| | - Thomas J Hund
- Dorothy M. Davis Heart and Lung Research Institute, Ohio State University, Columbus, Ohio, USA; Department of Biomedical Engineering, Ohio State University, Columbus, Ohio, USA; Division of Cardiovascular Medicine, Department of Internal Medicine, Ohio State University, Columbus, Ohio, USA.
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10
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Ngo K, Yarov-Yarovoy V, Clancy CE, Vorobyov I. Harnessing AlphaFold to reveal state secrets: Prediction of hERG closed and inactivated states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.27.577468. [PMID: 38352360 PMCID: PMC10862728 DOI: 10.1101/2024.01.27.577468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
To design safe, selective, and effective new therapies, there must be a deep understanding of the structure and function of the drug target. One of the most difficult problems to solve has been resolution of discrete conformational states of transmembrane ion channel proteins. An example is KV11.1 (hERG), comprising the primary cardiac repolarizing current, IKr. hERG is a notorious drug anti-target against which all promising drugs are screened to determine potential for arrhythmia. Drug interactions with the hERG inactivated state are linked to elevated arrhythmia risk, and drugs may become trapped during channel closure. However, the structural details of multiple conformational states have remained elusive. Here, we guided AlphaFold2 to predict plausible hERG inactivated and closed conformations, obtaining results consistent with myriad available experimental data. Drug docking simulations demonstrated hERG state-specific drug interactions aligning well with experimental results, revealing that most drugs bind more effectively in the inactivated state and are trapped in the closed state. Molecular dynamics simulations demonstrated ion conduction that aligned with earlier studies. Finally, we identified key molecular determinants of state transitions by analyzing interaction networks across closed, open, and inactivated states in agreement with earlier mutagenesis studies. Here, we demonstrate a readily generalizable application of AlphaFold2 as a novel method to predict discrete protein conformations and novel linkages from structure to function.
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Affiliation(s)
- Khoa Ngo
- Biophysics Graduate Group, University of California, Davis, CA
- Department of Physiology and Membrane Biology, University of California, Davis, CA
- Center for Precision Medicine and Data Science, University of California, Davis, CA
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, CA
- Department of Anesthesiology and Pain Medicine, University of California, Davis, CA
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, CA
- Department of Pharmacology, University of California, Davis, CA
- Center for Precision Medicine and Data Science, University of California, Davis, CA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, CA
- Department of Pharmacology, University of California, Davis, CA
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11
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Aguado-Sierra J, Brigham R, Baron AK, Gomez PD, Houzeaux G, Guerra JM, Carreras F, Filgueiras-Rama D, Vazquez M, Iaizzo PA, Iles TL, Butakoff C. HPC Framework for Performing in Silico Trials Using a 3D Virtual Human Cardiac Population as Means to Assess Drug-Induced Arrhythmic Risk. Methods Mol Biol 2024; 2716:307-334. [PMID: 37702946 DOI: 10.1007/978-1-0716-3449-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Following the 3 R's principles of animal research-replacement, reduction, and refinement-a high-performance computational framework was produced to generate a platform to perform human cardiac in-silico clinical trials as means to assess the pro-arrhythmic risk after the administrations of one or combination of two potentially arrhythmic drugs. The drugs assessed in this study were hydroxychloroquine and azithromycin. The framework employs electrophysiology simulations on high-resolution three-dimensional, biventricular human heart anatomies including phenotypic variabilities, so as to determine if differential QT-prolongation responds to drugs as observed clinically. These simulations also reproduce sex-specific ionic channel characteristics. The derived changes in the pseudo-electrocardiograms, calcium concentrations, as well as activation patterns within 3D geometries were evaluated for signs of induced arrhythmia. The virtual subjects could be evaluated at two different cycle lengths: at a normal heart rate and at a heart rate associated with stress as means to analyze the proarrhythmic risks after the administrations of hydroxychloroquine and azithromycin. Additionally, a series of experiments performed on reanimated swine hearts utilizing Visible Heart® methodologies in a four-chamber working heart model were performed to verify the arrhythmic behaviors observed in the in silico trials.The obtained results indicated similar pro-arrhythmic risk assessments within the virtual population as compared to published clinical trials (21% clinical risk vs 21.8% in silico trial risk). Evidence of transmurally heterogeneous action potential prolongations after providing a large dose of hydroxychloroquine was found as the observed mechanisms for elicited arrhythmias, both in the in vitro and the in silico models. The proposed workflow for in silico clinical drug cardiotoxicity trials allows for reproducing the complex behavior of cardiac electrophysiology in a varied population, in a matter of a few days as compared to the months or years it requires for most in vivo human clinical trials. Importantly, our results provided evidence of the common phenotype variants that produce distinct drug-induced arrhythmogenic outcomes.
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Affiliation(s)
- Jazmin Aguado-Sierra
- Barcelona Supercomputing Center, Barcelona, Spain.
- Elem Biotech S.L., Barcelona, Spain.
| | - Renee Brigham
- Visible Heart® Laboratories, Department of Surgery and the Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | | | | | - Jose M Guerra
- Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, CIBERCV, Barcelona, Spain
| | - Francesc Carreras
- Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, CIBERCV, Barcelona, Spain
| | - David Filgueiras-Rama
- Fundación Centro Nacional de Investigaciones Cardiovasculares (CNIC), Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), CIBERCV, Madrid, Spain
| | - Mariano Vazquez
- Barcelona Supercomputing Center, Barcelona, Spain
- Elem Biotech S.L., Barcelona, Spain
| | - Paul A Iaizzo
- Visible Heart® Laboratories, Department of Surgery and the Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Tinen L Iles
- Department of Surgery, Medical School, University of Minnesota, Minneapolis, MN, USA
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12
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Casson CL, John SA, Ferrall-Fairbanks MC. Mathematical modeling of cardio-oncology: Modeling the systemic effects of cancer therapeutics on the cardiovascular system. Semin Cancer Biol 2023; 97:30-41. [PMID: 37979714 DOI: 10.1016/j.semcancer.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 08/25/2023] [Accepted: 11/12/2023] [Indexed: 11/20/2023]
Abstract
Cardiotoxicity is a common side-effect of many cancer therapeutics; however, to-date there has been very little push to understand the mechanisms underlying this group of pathologies. This has led to the emergence of cardio-oncology, a field of medicine focused on understanding the effects of cancer and its treatment on the human heart. Here, we describe how mechanistic modeling approaches have been applied to study open questions in the cardiovascular system and how these approaches are being increasingly applied to advance knowledge of the underlying effects of cancer treatments on the human heart. A variety of mechanistic, mathematical modeling techniques have been applied to explore the link between common cancer treatments, such as chemotherapy, radiation, targeted therapy, and immunotherapy, and cardiotoxicity, nevertheless there is limited coverage in the different types of cardiac dysfunction that may be associated with these treatments. Moreover, cardiac modeling has a rich heritage of mathematical modeling and is well suited for the further development of novel approaches for understanding the cardiotoxicities associated with cancer therapeutics. There are many opportunities to combine mechanistic, bottom-up approaches with data-driven, top-down approaches to improve personalized, precision oncology to better understand, and ultimately mitigate, cardiac dysfunction in cancer patients.
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Affiliation(s)
- Camara L Casson
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Sofia A John
- Department of Statistics, University of Florida, Gainesville, FL 32611, USA
| | - Meghan C Ferrall-Fairbanks
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA; University of Florida Health Cancer Center, University of Florida, Gainesville, FL 32611, USA.
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13
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Emigh Cortez AM, DeMarco KR, Furutani K, Bekker S, Sack JT, Wulff H, Clancy CE, Vorobyov I, Yarov-Yarovoy V. Structural modeling of hERG channel-drug interactions using Rosetta. Front Pharmacol 2023; 14:1244166. [PMID: 38035013 PMCID: PMC10682396 DOI: 10.3389/fphar.2023.1244166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
The human ether-a-go-go-related gene (hERG) not only encodes a potassium-selective voltage-gated ion channel essential for normal electrical activity in the heart but is also a major drug anti-target. Genetic hERG mutations and blockage of the channel pore by drugs can cause long QT syndrome, which predisposes individuals to potentially deadly arrhythmias. However, not all hERG-blocking drugs are proarrhythmic, and their differential affinities to discrete channel conformational states have been suggested to contribute to arrhythmogenicity. We used Rosetta electron density refinement and homology modeling to build structural models of open-state hERG channel wild-type and mutant variants (Y652A, F656A, and Y652A/F656 A) and a closed-state wild-type channel based on cryo-electron microscopy structures of hERG and EAG1 channels. These models were used as protein targets for molecular docking of charged and neutral forms of amiodarone, nifekalant, dofetilide, d/l-sotalol, flecainide, and moxifloxacin. We selected these drugs based on their different arrhythmogenic potentials and abilities to facilitate hERG current. Our docking studies and clustering provided atomistic structural insights into state-dependent drug-channel interactions that play a key role in differentiating safe and harmful hERG blockers and can explain hERG channel facilitation through drug interactions with its open-state hydrophobic pockets.
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Affiliation(s)
- Aiyana M. Emigh Cortez
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Kevin R. DeMarco
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Kazuharu Furutani
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, Tokushima Bunri University, Tokushima, Japan
| | - Slava Bekker
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- American River College, Sacramento, CA, United States
| | - Jon T. Sack
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, United States
| | - Heike Wulff
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
- Center for Precision Medicine and Data Sciences, University of California, Davis, Davis, CA, United States
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, United States
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14
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Docken SS, Clancy CE, Lewis TJ. Rate-dependent effects of state-specific sodium channel blockers in cardiac tissue: Insights from idealized models. J Theor Biol 2023; 573:111595. [PMID: 37562674 DOI: 10.1016/j.jtbi.2023.111595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 06/08/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
A common side effect of pharmaceutical drugs is an increased propensity for cardiac arrhythmias. Many drugs bind to cardiac ion-channels in a state-specific manner, which alters the ionic conductances in complicated ways, making it difficult to identify the mechanisms underlying pro-arrhythmic drug effects. To better understand the fundamental mechanisms underlying the diverse effects of state-dependent sodium (Na+) channel blockers on cellular excitability, we consider two canonical motifs of drug-ion-channel interactions and compare the effects of Na+ channel blockers on the rate-dependence of peak upstroke velocity, conduction velocity, and vulnerable window size. In the literature, both motifs are referred to as "guarded receptor," but here we distinguish between state-specific binding that does not alter channel gating (referred to here as "guarded receptor") and state-specific binding that blocks certain gating transitions ("gate immobilization"). For each drug binding motif, we consider drugs that bind to the inactivated state and drugs that bind to the non-inactivated state of the Na+ channel. Exploiting the idealized nature of the canonical binding motifs, we identify the fundamental mechanisms underlying the effects on excitability of the various binding interactions. Specifically, we derive the voltage-dependence of the drug binding time constants and the equilibrium fractions of channels bound to drug, and we then derive a formula that incorporates these time constants and equilibrium fractions to elucidate the fundamental mechanisms. In the case of charged drug, we find that drugs that bind to inactivated channels exhibit greater rate-dependence than drugs that bind to non-inactivated channels. For neutral drugs, the effects of guarded receptor interactions are rate-independent, and we describe a novel mechanism for reverse rate-dependence resulting from neutral drug binding to non-inactivated channels via the gate immobilization motif.
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Affiliation(s)
- Steffen S Docken
- Department of Mathematics, University of California Davis, Davis, CA, USA; Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA.
| | - Colleen E Clancy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Timothy J Lewis
- Department of Mathematics, University of California Davis, Davis, CA, USA
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15
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Yang PC, Rose A, DeMarco KR, Dawson JRD, Han Y, Jeng MT, Harvey RD, Santana LF, Ripplinger CM, Vorobyov I, Lewis TJ, Clancy CE. A multiscale predictive digital twin for neurocardiac modulation. J Physiol 2023; 601:3789-3812. [PMID: 37528537 PMCID: PMC10528740 DOI: 10.1113/jp284391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/11/2023] [Indexed: 08/03/2023] Open
Abstract
Cardiac function is tightly regulated by the autonomic nervous system (ANS). Activation of the sympathetic nervous system increases cardiac output by increasing heart rate and stroke volume, while parasympathetic nerve stimulation instantly slows heart rate. Importantly, imbalance in autonomic control of the heart has been implicated in the development of arrhythmias and heart failure. Understanding of the mechanisms and effects of autonomic stimulation is a major challenge because synapses in different regions of the heart result in multiple changes to heart function. For example, nerve synapses on the sinoatrial node (SAN) impact pacemaking, while synapses on contractile cells alter contraction and arrhythmia vulnerability. Here, we present a multiscale neurocardiac modelling and simulator tool that predicts the effect of efferent stimulation of the sympathetic and parasympathetic branches of the ANS on the cardiac SAN and ventricular myocardium. The model includes a layered representation of the ANS and reproduces firing properties measured experimentally. Model parameters are derived from experiments and atomistic simulations. The model is a first prototype of a digital twin that is applied to make predictions across all system scales, from subcellular signalling to pacemaker frequency to tissue level responses. We predict conditions under which autonomic imbalance induces proarrhythmia and can be modified to prevent or inhibit arrhythmia. In summary, the multiscale model constitutes a predictive digital twin framework to test and guide high-throughput prediction of novel neuromodulatory therapy. KEY POINTS: A multi-layered model representation of the autonomic nervous system that includes sympathetic and parasympathetic branches, each with sparse random intralayer connectivity, synaptic dynamics and conductance based integrate-and-fire neurons generates firing patterns in close agreement with experiment. A key feature of the neurocardiac computational model is the connection between the autonomic nervous system and both pacemaker and contractile cells, where modification to pacemaker frequency drives initiation of electrical signals in the contractile cells. We utilized atomic-scale molecular dynamics simulations to predict the association and dissociation rates of noradrenaline with the β-adrenergic receptor. Multiscale predictions demonstrate how autonomic imbalance may increase proclivity to arrhythmias or be used to terminate arrhythmias. The model serves as a first step towards a digital twin for predicting neuromodulation to prevent or reduce disease.
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Affiliation(s)
- Pei-Chi Yang
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA
| | - Adam Rose
- Department of Mathematics, University of California Davis, Davis, CA
| | - Kevin R. DeMarco
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA
| | - John R. D. Dawson
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA
| | - Yanxiao Han
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA
| | - Mao-Tsuen Jeng
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA
| | | | - L. Fernando Santana
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA
| | | | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA
| | - Timothy J. Lewis
- Department of Mathematics, University of California Davis, Davis, CA
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA
- Center for Precision Medicine and Data Science, University of California Davis, Sacramento, CA
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16
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Moreno JD, Silva JR. Emerging methods to model cardiac ion channel and myocyte electrophysiology. BIOPHYSICS REVIEWS 2023; 4:011315. [PMID: 37034130 PMCID: PMC10071990 DOI: 10.1063/5.0127713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/28/2023] [Indexed: 04/03/2023]
Abstract
In the field of cardiac electrophysiology, modeling has played a central role for many decades. However, even though the effort is well-established, it has recently seen a rapid and sustained evolution in the complexity and predictive power of the models being created. In particular, new approaches to modeling have allowed the tracking of parallel and interconnected processes that span from the nanometers and femtoseconds that determine ion channel gating to the centimeters and minutes needed to describe an arrhythmia. The connection between scales has brought unprecedented insight into cardiac arrhythmia mechanisms and drug therapies. This review focuses on the generation of these models from first principles, generation of detailed models to describe ion channel kinetics, algorithms to create and numerically solve kinetic models, and new approaches toward data gathering that parameterize these models. While we focus on application of these models for cardiac arrhythmia, these concepts are widely applicable to model the physiology and pathophysiology of any excitable cell.
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Affiliation(s)
- Jonathan D. Moreno
- Division of Cardiology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Jonathan R. Silva
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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17
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Qu Z, Yan D, Song Z. Modeling Calcium Cycling in the Heart: Progress, Pitfalls, and Challenges. Biomolecules 2022; 12:1686. [PMID: 36421700 PMCID: PMC9687412 DOI: 10.3390/biom12111686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Intracellular calcium (Ca) cycling in the heart plays key roles in excitation-contraction coupling and arrhythmogenesis. In cardiac myocytes, the Ca release channels, i.e., the ryanodine receptors (RyRs), are clustered in the sarcoplasmic reticulum membrane, forming Ca release units (CRUs). The RyRs in a CRU act collectively to give rise to discrete Ca release events, called Ca sparks. A cell contains hundreds to thousands of CRUs, diffusively coupled via Ca to form a CRU network. A rich spectrum of spatiotemporal Ca dynamics is observed in cardiac myocytes, including Ca sparks, spark clusters, mini-waves, persistent whole-cell waves, and oscillations. Models of different temporal and spatial scales have been developed to investigate these dynamics. Due to the complexities of the CRU network and the spatiotemporal Ca dynamics, it is challenging to model the Ca cycling dynamics in the cardiac system, particularly at the tissue sales. In this article, we review the progress of modeling of Ca cycling in cardiac systems from single RyRs to the tissue scale, the pros and cons of the current models and different modeling approaches, and the challenges to be tackled in the future.
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Affiliation(s)
- Zhilin Qu
- Department of Medicine, David Geffen School of Medicine, University of California, A2-237 CHS, 650 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Dasen Yan
- Peng Cheng Laboratory, Shenzhen 518066, China
| | - Zhen Song
- Peng Cheng Laboratory, Shenzhen 518066, China
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18
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Escobar F, Gomis-Tena J, Saiz J, Romero L. Automatic modeling of dynamic drug-hERG channel interactions using three voltage protocols and machine learning techniques: A simulation study. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 226:107148. [PMID: 36170760 DOI: 10.1016/j.cmpb.2022.107148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 09/12/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Assessment of drug cardiac safety is critical in the development of new compounds and is commonly addressed by evaluating the half-maximal blocking concentration of the potassium human ether-à-go-go related gene (hERG) channels. However, recent works have evidenced that the modelling of drug-binding dynamics to hERG can help to improve early cardiac safety assessment. Our goal is to develop a methodology to automatically generate Markovian models of the drug-hERG channel interactions. METHODS The training and the test sets consisted of 20800 and 5200 virtual drugs, respectively, distributed into 104 groups with different affinities and kinetics to the conformational states of the channel. In our system, drugs may bind to any state (individually or simultaneously), with different degrees of preference for a conformational state and the change of the conformational state of the drug bound channels may be restricted or allowed. To model such a wide range of possibilities, 12 Markovian chains are considered. Our approach uses the response of the drugs to our three previously developed voltage clamp protocols, which enhance the differences in the probabilities of occupying a certain conformational state of the channel (open, closed and inactivated). The computing tool is comprised of a classifier and a parameter optimizer and uses linear interpolation, support vector machines and a simplex method for function minimization. RESULTS We propose a novel methodology that automatically generates dynamic drug models using Markov model formulations and that elucidates the states where the drug binds and unbinds and the preferential binding state using data obtained from simple voltage clamp protocols that captures the preferential state-dependent binding properties, the relative affinities, trapping and non-trapping dynamics and the onset of IKr block. Overall, the tool correctly predicted the class of 92.04% of the drugs and the model provided by the tool accurately fitted the response of the target compound, the mean accuracy being 97.53%. Moreover, generation of the dynamic model of an IKr blocker from its response to our voltage clamp protocols usually takes less than an hour on a common desktop computer. CONCLUSION Our methodology could be very useful to model and simulate dynamic drug-hERG channel interactions. It would contribute to the improvement of the preclinical assessment of the proarrhythmic risk of drugs that inhibit IKr and the efficacy of antiarrhythmic IKr blockers.
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Affiliation(s)
- Fernando Escobar
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València
| | - Julio Gomis-Tena
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València
| | - Javier Saiz
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València
| | - Lucía Romero
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València.
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19
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Clark AP, Wei S, Kalola D, Krogh‐Madsen T, Christini DJ. An in silico-in vitro pipeline for drug cardiotoxicity screening identifies ionic pro-arrhythmia mechanisms. Br J Pharmacol 2022; 179:4829-4843. [PMID: 35781252 PMCID: PMC9489646 DOI: 10.1111/bph.15915] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 05/25/2022] [Accepted: 06/24/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND AND PURPOSE Before advancing to clinical trials, new drugs are screened for their pro-arrhythmic potential using a method that is overly conservative and provides limited mechanistic insight. The shortcomings of this approach can lead to the mis-classification of beneficial drugs as pro-arrhythmic. EXPERIMENTAL APPROACH An in silico-in vitro pipeline was developed to circumvent these shortcomings. A computational human induced pluripotent stem cell-derived cardiomyocyte (iPSC-CM) model was used as part of a genetic algorithm to design experiments, specifically electrophysiological voltage clamp (VC) protocols, to identify which of several cardiac ion channels were blocked during in vitro drug studies. Such VC data, along with dynamically clamped action potentials (AP), were acquired from iPSC-CMs before and after treatment with a control solution or a low- (verapamil), intermediate- (cisapride or quinine) or high-risk (quinidine) drug. KEY RESULTS Significant AP prolongation (a pro-arrhythmia marker) was seen in response to quinidine and quinine. The VC protocol identified block of IKr (a source of arrhythmias) by all strong IKr blockers, including cisapride, quinidine and quinine. The protocol also detected block of ICaL by verapamil and Ito by quinidine. Further demonstrating the power of the approach, the VC data uncovered a previously unidentified If block by quinine, which was confirmed with experiments using a HEK-293 expression system and automated patch-clamp. CONCLUSION AND IMPLICATIONS We developed an in silico-in vitro pipeline that simultaneously identifies pro-arrhythmia risk and mechanism of ion channel-blocking drugs. The approach offers a new tool for evaluating cardiotoxicity during preclinical drug screening.
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Affiliation(s)
| | - Siyu Wei
- Department of Physiology and PharmacologySUNY Downstate Medical CenterBrooklynNew YorkUSA
| | - Darshan Kalola
- Computational Biology Summer ProgramWeill Cornell Medicine & Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Trine Krogh‐Madsen
- Department of Physiology & BiophysicsWeill Cornell MedicineNew YorkNew YorkUSA
- Institute for Computational BiomedicineWeill Cornell MedicineNew YorkNew YorkUSA
| | - David J. Christini
- Department of Biomedical EngineeringCornell UniversityIthacaNew YorkUSA
- Department of Physiology and PharmacologySUNY Downstate Medical CenterBrooklynNew YorkUSA
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20
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Li G, Brumback BD, Huang L, Zhang DM, Yin T, Lipovsky CE, Hicks SC, Jimenez J, Boyle PM, Rentschler SL. Acute Glycogen Synthase Kinase-3 Inhibition Modulates Human Cardiac Conduction. JACC Basic Transl Sci 2022; 7:1001-1017. [PMID: 36337924 PMCID: PMC9626903 DOI: 10.1016/j.jacbts.2022.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 01/14/2023]
Abstract
Glycogen synthase kinase 3 (GSK-3) inhibition has emerged as a potential therapeutic target for several diseases, including cancer. However, the role for GSK-3 regulation of human cardiac electrophysiology remains ill-defined. We demonstrate that SB216763, a GSK-3 inhibitor, can acutely reduce conduction velocity in human cardiac slices. Combined computational modeling and experimental approaches provided mechanistic insight into GSK-3 inhibition-mediated changes, revealing that decreased sodium-channel conductance and tissue conductivity may underlie the observed phenotypes. Our study demonstrates that GSK-3 inhibition in human myocardium alters electrophysiology and may predispose to an arrhythmogenic substrate; therefore, monitoring for adverse arrhythmogenic events could be considered.
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Key Words
- ABC, active β-catenin
- APD, action potential duration
- BDM, 2,3-butanedione monoxime
- CV, conduction velocity
- Cx43, connexin 43
- GNa, sodium-channel conductance
- GOF, gain of function
- GSK-3 inhibitor
- GSK-3, glycogen synthase kinase 3
- INa, sodium current
- LV, left ventricle
- NaV1.5, pore-forming α-subunit protein of the voltage-gated cardiac sodium channel
- PCR, polymerase chain reaction
- RMP, resting membrane potential
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- SB2, SB216763
- SB216763
- cDNA, complementary DNA
- dVm/dtmax, maximum upstroke velocity
- electrophysiology
- human cardiac slices
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Affiliation(s)
- Gang Li
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University McKelvey School of Engineering in St. Louis, Missouri, USA
| | - Brittany D. Brumback
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University McKelvey School of Engineering in St. Louis, Missouri, USA
| | - Lei Huang
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
| | - David M. Zhang
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
| | - Tiankai Yin
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
| | - Catherine E. Lipovsky
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, Missouri, USA
| | - Stephanie C. Hicks
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
| | - Jesus Jimenez
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
| | - Patrick M. Boyle
- Department of Bioengineering, Center for Cardiovascular Biology, and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - Stacey L. Rentschler
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University McKelvey School of Engineering in St. Louis, Missouri, USA
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, Missouri, USA
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21
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Turk A, Kunej T. Shared Genetic Risk Factors Between Cancer and Cardiovascular Diseases. Front Cardiovasc Med 2022; 9:931917. [PMID: 35872888 PMCID: PMC9300967 DOI: 10.3389/fcvm.2022.931917] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/21/2022] [Indexed: 11/22/2022] Open
Abstract
Cancer and cardiovascular diseases (CVD) account for approximately 27.5 million deaths every year. While they share some common environmental risk factors, their shared genetic risk factors are not yet fully understood. The aim of the present study was to aggregate genetic risk factors associated with the comorbidity of cancer and CVDs. For this purpose, we: (1) created a catalog of genes associated with cancer and CVDs, (2) visualized retrieved data as a gene-disease network, and (3) performed a pathway enrichment analysis. We performed screening of PubMed database for literature reporting genetic risk factors in patients with both cancer and CVD. The gene-disease network was visualized using Cytoscape and the enrichment analysis was conducted using Enrichr software. We manually reviewed the 181 articles fitting the search criteria and included 13 articles in the study. Data visualization revealed a highly interconnected network containing a single subnetwork with 56 nodes and 146 edges. Genes in the network with the highest number of disease interactions were JAK2, TTN, TET2, and ATM. The pathway enrichment analysis revealed that genes included in the study were significantly enriched in DNA damage repair (DDR) pathways, such as homologous recombination. The role of DDR mechanisms in the development of CVDs has been studied in previously published research; however, additional functional studies are required to elucidate their contribution to the pathophysiology to CVDs.
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22
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An Automata-Based Cardiac Electrophysiology Simulator to Assess Arrhythmia Inducibility. MATHEMATICS 2022. [DOI: 10.3390/math10081293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Personalized cardiac electrophysiology simulations have demonstrated great potential to study cardiac arrhythmias and help in therapy planning of radio-frequency ablation. Its application to analyze vulnerability to ventricular tachycardia and sudden cardiac death in infarcted patients has been recently explored. However, the detailed multi-scale biophysical simulations used in these studies are very demanding in terms of memory and computational resources, which prevents their clinical translation. In this work, we present a fast phenomenological system based on cellular automata (CA) to simulate personalized cardiac electrophysiology. The system is trained on biophysical simulations to reproduce cellular and tissue dynamics in healthy and pathological conditions, including action potential restitution, conduction velocity restitution and cell safety factor. We show that a full ventricular simulation can be performed in the order of seconds, emulate the results of a biophysical simulation and reproduce a patient’s ventricular tachycardia in a model that includes a heterogeneous scar region. The system could be used to study the risk of arrhythmia in infarcted patients for a large number of scenarios.
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23
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Lagoutte-Renosi J, Allemand F, Ramseyer C, Yesylevskyy S, Davani S. Molecular modeling in cardiovascular pharmacology: Current state of the art and perspectives. Drug Discov Today 2021; 27:985-1007. [PMID: 34863931 DOI: 10.1016/j.drudis.2021.11.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/02/2021] [Accepted: 11/25/2021] [Indexed: 01/10/2023]
Abstract
Molecular modeling in pharmacology is a promising emerging tool for exploring drug interactions with cellular components. Recent advances in molecular simulations, big data analysis, and artificial intelligence (AI) have opened new opportunities for rationalizing drug interactions with their pharmacological targets. Despite the obvious utility and increasing impact of computational approaches, their development is not progressing at the same speed in different fields of pharmacology. Here, we review current in silico techniques used in cardiovascular diseases (CVDs), cardiological drug discovery, and assessment of cardiotoxicity. In silico techniques are paving the way to a new era in cardiovascular medicine, but their use somewhat lags behind that in other fields.
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Affiliation(s)
- Jennifer Lagoutte-Renosi
- EA 3920 Université Bourgogne Franche-Comté, 25000 Besançon, France; Laboratoire de Pharmacologie Clinique et Toxicologie-CHU de Besançon, 25000 Besançon, France
| | - Florentin Allemand
- EA 3920 Université Bourgogne Franche-Comté, 25000 Besançon, France; Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France
| | - Christophe Ramseyer
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France
| | - Semen Yesylevskyy
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France; Department of Physics of Biological Systems, Institute of Physics of The National Academy of Sciences of Ukraine, Nauky Sve. 46, Kyiv, Ukraine; Receptor.ai inc, 16192 Coastal Highway, Lewes, DE, USA
| | - Siamak Davani
- EA 3920 Université Bourgogne Franche-Comté, 25000 Besançon, France; Laboratoire de Pharmacologie Clinique et Toxicologie-CHU de Besançon, 25000 Besançon, France.
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24
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Maleckar MM, Myklebust L, Uv J, Florvaag PM, Strøm V, Glinge C, Jabbari R, Vejlstrup N, Engstrøm T, Ahtarovski K, Jespersen T, Tfelt-Hansen J, Naumova V, Arevalo H. Combined In-silico and Machine Learning Approaches Toward Predicting Arrhythmic Risk in Post-infarction Patients. Front Physiol 2021; 12:745349. [PMID: 34819872 PMCID: PMC8606551 DOI: 10.3389/fphys.2021.745349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
Background: Remodeling due to myocardial infarction (MI) significantly increases patient arrhythmic risk. Simulations using patient-specific models have shown promise in predicting personalized risk for arrhythmia. However, these are computationally- and time- intensive, hindering translation to clinical practice. Classical machine learning (ML) algorithms (such as K-nearest neighbors, Gaussian support vector machines, and decision trees) as well as neural network techniques, shown to increase prediction accuracy, can be used to predict occurrence of arrhythmia as predicted by simulations based solely on infarct and ventricular geometry. We present an initial combined image-based patient-specific in silico and machine learning methodology to assess risk for dangerous arrhythmia in post-infarct patients. Furthermore, we aim to demonstrate that simulation-supported data augmentation improves prediction models, combining patient data, computational simulation, and advanced statistical modeling, improving overall accuracy for arrhythmia risk assessment. Methods: MRI-based computational models were constructed from 30 patients 5 days post-MI (the “baseline” population). In order to assess the utility biophysical model-supported data augmentation for improving arrhythmia prediction, we augmented the virtual baseline patient population. Each patient ventricular and ischemic geometry in the baseline population was used to create a subfamily of geometric models, resulting in an expanded set of patient models (the “augmented” population). Arrhythmia induction was attempted via programmed stimulation at 17 sites for each virtual patient corresponding to AHA LV segments and simulation outcome, “arrhythmia,” or “no-arrhythmia,” were used as ground truth for subsequent statistical prediction (machine learning, ML) models. For each patient geometric model, we measured and used choice data features: the myocardial volume and ischemic volume, as well as the segment-specific myocardial volume and ischemia percentage, as input to ML algorithms. For classical ML techniques (ML), we trained k-nearest neighbors, support vector machine, logistic regression, xgboost, and decision tree models to predict the simulation outcome from these geometric features alone. To explore neural network ML techniques, we trained both a three - and a four-hidden layer multilayer perceptron feed forward neural networks (NN), again predicting simulation outcomes from these geometric features alone. ML and NN models were trained on 70% of randomly selected segments and the remaining 30% was used for validation for both baseline and augmented populations. Results: Stimulation in the baseline population (30 patient models) resulted in reentry in 21.8% of sites tested; in the augmented population (129 total patient models) reentry occurred in 13.0% of sites tested. ML and NN models ranged in mean accuracy from 0.83 to 0.86 for the baseline population, improving to 0.88 to 0.89 in all cases. Conclusion: Machine learning techniques, combined with patient-specific, image-based computational simulations, can provide key clinical insights with high accuracy rapidly and efficiently. In the case of sparse or missing patient data, simulation-supported data augmentation can be employed to further improve predictive results for patient benefit. This work paves the way for using data-driven simulations for prediction of dangerous arrhythmia in MI patients.
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Affiliation(s)
- Mary M Maleckar
- Computational Physiology, Simula Research Laboratory, Oslo, Norway
| | - Lena Myklebust
- Computational Physiology, Simula Research Laboratory, Oslo, Norway
| | - Julie Uv
- Computational Physiology, Simula Research Laboratory, Oslo, Norway
| | | | - Vilde Strøm
- Computational Physiology, Simula Research Laboratory, Oslo, Norway
| | - Charlotte Glinge
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Reza Jabbari
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Niels Vejlstrup
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas Engstrøm
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Kiril Ahtarovski
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas Jespersen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Forensic Medicine, Faculty of Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Valeriya Naumova
- Computational Physiology, Simula Research Laboratory, Oslo, Norway
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25
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Chen L, He Y, Wang X, Ge J, Li H. Ventricular voltage-gated ion channels: Detection, characteristics, mechanisms, and drug safety evaluation. Clin Transl Med 2021; 11:e530. [PMID: 34709746 PMCID: PMC8516344 DOI: 10.1002/ctm2.530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 02/06/2023] Open
Abstract
Cardiac voltage-gated ion channels (VGICs) play critical roles in mediating cardiac electrophysiological signals, such as action potentials, to maintain normal heart excitability and contraction. Inherited or acquired alterations in the structure, expression, or function of VGICs, as well as VGIC-related side effects of pharmaceutical drug delivery can result in abnormal cellular electrophysiological processes that induce life-threatening cardiac arrhythmias or even sudden cardiac death. Hence, to reduce possible heart-related risks, VGICs must be acknowledged as important targets in drug discovery and safety studies related to cardiac disease. In this review, we first summarize the development and application of electrophysiological techniques that are employed in cardiac VGIC studies alone or in combination with other techniques such as cryoelectron microscopy, optical imaging and optogenetics. Subsequently, we describe the characteristics, structure, mechanisms, and functions of various well-studied VGICs in ventricular myocytes and analyze their roles in and contributions to both physiological cardiac excitability and inherited cardiac diseases. Finally, we address the implications of the structure and function of ventricular VGICs for drug safety evaluation. In summary, multidisciplinary studies on VGICs help researchers discover potential targets of VGICs and novel VGICs in heart, enrich their knowledge of the properties and functions, determine the operation mechanisms of pathological VGICs, and introduce groundbreaking trends in drug therapy strategies, and drug safety evaluation.
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Affiliation(s)
- Lulan Chen
- Department of Cardiology, Shanghai Institute of Cardiovascular DiseasesShanghai Xuhui District Central Hospital & Zhongshan‐xuhui Hospital, Zhongshan Hospital, Fudan UniversityShanghaiChina
| | - Yue He
- Department of CardiologyShanghai Xuhui District Central Hospital & Zhongshan‐xuhui HospitalShanghaiChina
| | - Xiangdong Wang
- Institute of Clinical Science, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Junbo Ge
- Department of Cardiology, Shanghai Institute of Cardiovascular DiseasesShanghai Xuhui District Central Hospital & Zhongshan‐xuhui Hospital, Zhongshan Hospital, Fudan UniversityShanghaiChina
| | - Hua Li
- Department of Cardiology, Shanghai Institute of Cardiovascular DiseasesShanghai Xuhui District Central Hospital & Zhongshan‐xuhui Hospital, Zhongshan Hospital, Fudan UniversityShanghaiChina
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26
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Lee KH, Fant AD, Guo J, Guan A, Jung J, Kudaibergenova M, Miranda WE, Ku T, Cao J, Wacker S, Duff HJ, Newman AH, Noskov SY, Shi L. Toward Reducing hERG Affinities for DAT Inhibitors with a Combined Machine Learning and Molecular Modeling Approach. J Chem Inf Model 2021; 61:4266-4279. [PMID: 34420294 DOI: 10.1021/acs.jcim.1c00856] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Psychostimulant drugs, such as cocaine, inhibit dopamine reuptake via blockading the dopamine transporter (DAT), which is the primary mechanism underpinning their abuse. Atypical DAT inhibitors are dissimilar to cocaine and can block cocaine- or methamphetamine-induced behaviors, supporting their development as part of a treatment regimen for psychostimulant use disorders. When developing these atypical DAT inhibitors as medications, it is necessary to avoid off-target binding that can produce unwanted side effects or toxicities. In particular, the blockade of a potassium channel, human ether-a-go-go (hERG), can lead to potentially lethal ventricular tachycardia. In this study, we established a counter screening platform for DAT and against hERG binding by combining machine learning-based quantitative structure-activity relationship (QSAR) modeling, experimental validation, and molecular modeling and simulations. Our results show that the available data are adequate to establish robust QSAR models, as validated by chemical synthesis and pharmacological evaluation of a validation set of DAT inhibitors. Furthermore, the QSAR models based on subsets of the data according to experimental approaches used have predictive power as well, which opens the door to target specific functional states of a protein. Complementarily, our molecular modeling and simulations identified the structural elements responsible for a pair of DAT inhibitors having opposite binding affinity trends at DAT and hERG, which can be leveraged for rational optimization of lead atypical DAT inhibitors with desired pharmacological properties.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Andrew D Fant
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Jiqing Guo
- Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Andy Guan
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Joslyn Jung
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Mary Kudaibergenova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Williams E Miranda
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Therese Ku
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Jianjing Cao
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Soren Wacker
- Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.,Achlys Inc., 7-126 Li Ka Shing Center for Health and Innovation, Edmonton, Alberta T6G 2E1, Canada
| | - Henry J Duff
- Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Sergei Y Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
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27
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Prediction of arrhythmia susceptibility through mathematical modeling and machine learning. Proc Natl Acad Sci U S A 2021; 118:2104019118. [PMID: 34493665 DOI: 10.1073/pnas.2104019118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 01/08/2023] Open
Abstract
At present, the QT interval on the electrocardiographic (ECG) waveform is the most common metric for assessing an individual's susceptibility to ventricular arrhythmias, with a long QT, or, at the cellular level, a long action potential duration (APD) considered high risk. However, the limitations of this simple approach have long been recognized. Here, we sought to improve prediction of arrhythmia susceptibility by combining mechanistic mathematical modeling with machine learning (ML). Simulations with a model of the ventricular myocyte were performed to develop a large heterogenous population of cardiomyocytes (n = 10,586), and we tested each variant's ability to withstand three arrhythmogenic triggers: 1) block of the rapid delayed rectifier potassium current (IKr Block), 2) augmentation of the L-type calcium current (ICaL Increase), and 3) injection of inward current (Current Injection). Eight ML algorithms were trained to predict, based on simulated AP features in preperturbed cells, whether each cell would develop arrhythmic dynamics in response to each trigger. We found that APD can accurately predict how cells respond to the simple Current Injection trigger but cannot effectively predict the response to IKr Block or ICaL Increase. ML predictive performance could be improved by incorporating additional AP features and simulations of additional experimental protocols. Importantly, we discovered that the most relevant features and experimental protocols were trigger specific, which shed light on the mechanisms that promoted arrhythmia formation in response to the triggers. Overall, our quantitative approach provides a means to understand and predict differences between individuals in arrhythmia susceptibility.
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28
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Personalized Evaluation of Atrial Complexity of Patients Undergoing Atrial Fibrillation Ablation: A Clinical Computational Study. BIOLOGY 2021; 10:biology10090838. [PMID: 34571716 PMCID: PMC8469429 DOI: 10.3390/biology10090838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Atrial fibrillation is a type of arrhythmia that occurs when the electrical activity of the heart in the atrium is not coordinated, and its consequences can be lethal. The driving source that initiates this chaotic activity can be located anywhere in the atrium, but most frequently appears in certain areas such as the pulmonary veins. In this study, we developed a new estimation method to evaluate possible source location and complexity of the arrhythmia using computer simulations. This method represents mathematical descriptions of natural processes that can be used to mimic a real scenario, including specific information such as the atrial anatomy. Here, we identified a specific biomarker the enabled obtaining a foci distribution map and found that elimination of pulmonary vein drivers was associated with a successful long-term ablation outcome. This study could, therefore, help to identify and characterize patients in order to better plan the ablation procedure. Abstract Current clinical guidelines establish Pulmonary Vein (PV) isolation as the indicated treatment for Atrial Fibrillation (AF). However, AF can also be triggered or sustained due to atrial drivers located elsewhere in the atria. We designed a new simulation workflow based on personalized computer simulations to characterize AF complexity of patients undergoing PV ablation, validated with non-invasive electrocardiographic imaging and evaluated at one year after ablation. We included 30 patients using atrial anatomies segmented from MRI and simulated an automata model for the electrical modelling, consisting of three states (resting, excited and refractory). In total, 100 different scenarios were simulated per anatomy varying rotor number and location. The 3 states were calibrated with Koivumaki action potential, entropy maps were obtained from the electrograms and compared with ECGi for each patient to analyze PV isolation outcome. The completion of the workflow indicated that successful AF ablation occurred in patients with rotors mainly located at the PV antrum, while unsuccessful procedures presented greater number of driving sites outside the PV area. The number of rotors attached to the PV was significantly higher in patients with favorable long-term ablation outcome (1-year freedom from AF: 1.61 ± 0.21 vs. AF recurrence: 1.40 ± 0.20; p-value = 0.018). The presented workflow could improve patient stratification for PV ablation by screening the complexity of the atria.
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29
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Peirlinck M, Sahli Costabal F, Kuhl E. Sex Differences in Drug-Induced Arrhythmogenesis. Front Physiol 2021; 12:708435. [PMID: 34489728 PMCID: PMC8417068 DOI: 10.3389/fphys.2021.708435] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/14/2021] [Indexed: 12/25/2022] Open
Abstract
The electrical activity in the heart varies significantly between men and women and results in a sex-specific response to drugs. Recent evidence suggests that women are more than twice as likely as men to develop drug-induced arrhythmia with potentially fatal consequences. Yet, the sex-specific differences in drug-induced arrhythmogenesis remain poorly understood. Here we integrate multiscale modeling and machine learning to gain mechanistic insight into the sex-specific origin of drug-induced cardiac arrhythmia at differing drug concentrations. To quantify critical drug concentrations in male and female hearts, we identify the most important ion channels that trigger male and female arrhythmogenesis, and create and train a sex-specific multi-fidelity arrhythmogenic risk classifier. Our study reveals that sex differences in ion channel activity, tissue conductivity, and heart dimensions trigger longer QT-intervals in women than in men. We quantify the critical drug concentration for dofetilide, a high risk drug, to be seven times lower for women than for men. Our results emphasize the importance of including sex as an independent biological variable in risk assessment during drug development. Acknowledging and understanding sex differences in drug safety evaluation is critical when developing novel therapeutic treatments on a personalized basis. The general trends of this study have significant implications on the development of safe and efficacious new drugs and the prescription of existing drugs in combination with other drugs.
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Affiliation(s)
- Mathias Peirlinck
- Department of Mechanical Engineering, Stanford University, Stanford, CA, United States
| | - Francisco Sahli Costabal
- Department of Mechanical and Metallurgical Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
| | - Ellen Kuhl
- Department of Mechanical Engineering, Stanford University, Stanford, CA, United States
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30
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Iseppe AF, Ni H, Zhu S, Zhang X, Coppini R, Yang PC, Srivatsa U, Clancy CE, Edwards AG, Morotti S, Grandi E. Sex-Specific Classification of Drug-Induced Torsade de Pointes Susceptibility Using Cardiac Simulations and Machine Learning. Clin Pharmacol Ther 2021; 110:380-391. [PMID: 33772748 PMCID: PMC8316283 DOI: 10.1002/cpt.2240] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/16/2021] [Indexed: 11/09/2022]
Abstract
Torsade de Pointes (TdP), a rare but lethal ventricular arrhythmia, is a toxic side effect of many drugs. To assess TdP risk, safety regulatory guidelines require quantification of hERG channel block in vitro and QT interval prolongation in vivo for all new therapeutic compounds. Unfortunately, these have proven to be poor predictors of torsadogenic risk, and are likely to have prevented safe compounds from reaching clinical phases. Although this has stimulated numerous efforts to define new paradigms for cardiac safety, none of the recently developed strategies accounts for patient conditions. In particular, despite being a well-established independent risk factor for TdP, female sex is vastly under-represented in both basic research and clinical studies, and thus current TdP metrics are likely biased toward the male sex. Here, we apply statistical learning to synthetic data, generated by simulating drug effects on cardiac myocyte models capturing male and female electrophysiology, to develop new sex-specific classification frameworks for TdP risk. We show that (i) TdP classifiers require different features in females vs. males; (ii) male-based classifiers perform more poorly when applied to female data; and (iii) female-based classifier performance is largely unaffected by acute effects of hormones (i.e., during various phases of the menstrual cycle). Notably, when predicting TdP risk of intermediate drugs on female simulated data, male-biased predictive models consistently underestimate TdP risk in women. Therefore, we conclude that pipelines for preclinical cardiotoxicity risk assessment should consider sex as a key variable to avoid potentially life-threatening consequences for the female population.
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Affiliation(s)
- Alex Fogli Iseppe
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Haibo Ni
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Sicheng Zhu
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Xianwei Zhang
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Raffaele Coppini
- Department of Neuroscience, Psychology, Drug Sciences and Child Health (NeuroFarBa), University of Florence, Italy
| | - Pei-Chi Yang
- Department of Physiology and Membrane Biology, University of California, Davis, CA, USA
| | - Uma Srivatsa
- Department of Internal Medicine, University of California, Davis, CA, USA
| | - Colleen E. Clancy
- Department of Pharmacology, University of California, Davis, CA, USA
- Department of Physiology and Membrane Biology, University of California, Davis, CA, USA
| | - Andrew G. Edwards
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Stefano Morotti
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Eleonora Grandi
- Department of Pharmacology, University of California, Davis, CA, USA
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31
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The Role of Artificial Intelligence and Machine Learning in Clinical Cardiac Electrophysiology. Can J Cardiol 2021; 38:246-258. [PMID: 34333029 DOI: 10.1016/j.cjca.2021.07.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/11/2021] [Accepted: 07/25/2021] [Indexed: 11/21/2022] Open
Abstract
In recent years, artificial intelligence (AI) has found numerous applications in cardiology due in part to large digitized datasets and the evolution of high performance computing. In the discipline of cardiac electrophysiology (EP), a number of clinical, imaging, and electrical waveform data are considered in the diagnosis, prognostication and management of arrhythmias, which lend themselves well to automation through AI. But equally relevant, AI offers a unique opportunity to discover novel EP concepts and improve clinical care through its inherent, hierarchical tenets of self-learning. This review will focus on the application of AI in clinical EP and summarize state-of-the art, large, clinical studies in the following key domains: (1) ECG-based arrhythmia and disease classification, (2) atrial fibrillation source detection, (3) substrate and risk assessment for atrial fibrillation and ventricular tachyarrhythmias, and (4) predicting outcomes after cardiac resynchronization therapy. Many are small, single-center, proof-of-concept investigations, but they still demonstrate groundbreaking performance of deep learning, a subdomain of AI, which surpasses traditional statistical analysis. Larger studies, for instance classifying arrhythmias from ECG recordings, have further provided external validation of their high accuracy. Ultimately, the performance of AI is dependent on the quality of the input data and the rigor of algorithm development. The field is still nascent and several barriers will need to be overcome, including prospective validation in large, well-labelled datasets and more seamless information technology-based data collection/integration, before AI can be adopted into broader clinical EP practice. This review will conclude with a discussion of these challenges and future work.
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32
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Odening KE, Gomez AM, Dobrev D, Fabritz L, Heinzel FR, Mangoni ME, Molina CE, Sacconi L, Smith G, Stengl M, Thomas D, Zaza A, Remme CA, Heijman J. ESC working group on cardiac cellular electrophysiology position paper: relevance, opportunities, and limitations of experimental models for cardiac electrophysiology research. Europace 2021; 23:1795-1814. [PMID: 34313298 DOI: 10.1093/europace/euab142] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/19/2021] [Indexed: 12/19/2022] Open
Abstract
Cardiac arrhythmias are a major cause of death and disability. A large number of experimental cell and animal models have been developed to study arrhythmogenic diseases. These models have provided important insights into the underlying arrhythmia mechanisms and translational options for their therapeutic management. This position paper from the ESC Working Group on Cardiac Cellular Electrophysiology provides an overview of (i) currently available in vitro, ex vivo, and in vivo electrophysiological research methodologies, (ii) the most commonly used experimental (cellular and animal) models for cardiac arrhythmias including relevant species differences, (iii) the use of human cardiac tissue, induced pluripotent stem cell (hiPSC)-derived and in silico models to study cardiac arrhythmias, and (iv) the availability, relevance, limitations, and opportunities of these cellular and animal models to recapitulate specific acquired and inherited arrhythmogenic diseases, including atrial fibrillation, heart failure, cardiomyopathy, myocarditis, sinus node, and conduction disorders and channelopathies. By promoting a better understanding of these models and their limitations, this position paper aims to improve the quality of basic research in cardiac electrophysiology, with the ultimate goal to facilitate the clinical translation and application of basic electrophysiological research findings on arrhythmia mechanisms and therapies.
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Affiliation(s)
- Katja E Odening
- Translational Cardiology, Department of Cardiology, Inselspital, Bern University Hospital, Bern, Switzerland.,Institute of Physiology, University of Bern, Bern, Switzerland
| | - Ana-Maria Gomez
- Signaling and cardiovascular pathophysiology-UMR-S 1180, Inserm, Université Paris-Saclay, 92296 Châtenay-Malabry, France
| | - Dobromir Dobrev
- Institute of Pharmacology, West German Heart and Vascular Center, University Duisburg-Essen, Essen, Germany
| | - Larissa Fabritz
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, UK.,Department of Cardiology, University Hospital Birmingham NHS Trust, Birmingham, UK
| | - Frank R Heinzel
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site, Berlin, Germany
| | - Matteo E Mangoni
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Cristina E Molina
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site, Hamburg/Kiel/Lübeck, Germany
| | - Leonardo Sacconi
- National Institute of Optics and European Laboratory for Non Linear Spectroscopy, Italy.,Institute for Experimental Cardiovascular Medicine, University Freiburg, Germany
| | - Godfrey Smith
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
| | - Milan Stengl
- Department of Physiology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Dierk Thomas
- Department of Cardiology, University Hospital Heidelberg, Heidelberg, Germany; Heidelberg Center for Heart Rhythm Disorders (HCR), University Hospital Heidelberg, Heidelberg, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site, Heidelberg/Mannheim, Germany
| | - Antonio Zaza
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milano, Italy
| | - Carol Ann Remme
- Department of Experimental Cardiology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Jordi Heijman
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
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33
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Aghasafari P, Yang PC, Kernik DC, Sakamoto K, Kanda Y, Kurokawa J, Vorobyov I, Clancy CE. A deep learning algorithm to translate and classify cardiac electrophysiology. eLife 2021; 10:68335. [PMID: 34212860 PMCID: PMC8282335 DOI: 10.7554/elife.68335] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/29/2021] [Indexed: 01/15/2023] Open
Abstract
The development of induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) has been a critical in vitro advance in the study of patient-specific physiology, pathophysiology, and pharmacology. We designed a new deep learning multitask network approach intended to address the low throughput, high variability, and immature phenotype of the iPSC-CM platform. The rationale for combining translation and classification tasks is because the most likely application of the deep learning technology we describe here is to translate iPSC-CMs following application of a perturbation. The deep learning network was trained using simulated action potential (AP) data and applied to classify cells into the drug-free and drugged categories and to predict the impact of electrophysiological perturbation across the continuum of aging from the immature iPSC-CMs to the adult ventricular myocytes. The phase of the AP extremely sensitive to perturbation due to a steep rise of the membrane resistance was found to contain the key information required for successful network multitasking. We also demonstrated successful translation of both experimental and simulated iPSC-CM AP data validating our network by prediction of experimental drug-induced effects on adult cardiomyocyte APs by the latter.
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Affiliation(s)
- Parya Aghasafari
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States
| | - Pei-Chi Yang
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States
| | - Divya C Kernik
- Washington University in St. Louis, St. Louis, United States
| | - Kazuho Sakamoto
- Department of Bio-Informational Pharmacology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yasunari Kanda
- Division of Pharmacology, National Institute of Health Sciences, Kanagawa, Japan
| | - Junko Kurokawa
- Department of Bio-Informational Pharmacology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States.,Department of Pharmacology, University of California, Davis, Davis, United States
| | - Colleen E Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States
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Lazzerini PE, Cartocci A, Qu YS, Saponara S, Furini S, Fusi F, Fabris F, Gamberucci A, El-Sherif N, Cevenini G, Pettini F, Laghi-Pasini F, Acampa M, Bertolozzi I, Capecchi PL, Lazaro D, Boutjdir M. Proton Pump Inhibitors Directly Block hERG-Potassium Channel and Independently Increase the Risk of QTc Prolongation in a Large Cohort of US Veterans. Circ Arrhythm Electrophysiol 2021; 14:e010042. [PMID: 34143643 DOI: 10.1161/circep.121.010042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Pietro Enea Lazzerini
- Department of Medical Sciences, Surgery and Neurosciences (P.E.L., F.L.-P., P.L.C.), University of Siena, Italy
| | - Alessandra Cartocci
- Department of Medical Biotechnologies (A.C., S.F., G.C., F.P.), University of Siena, Italy
| | - Yongxia Sarah Qu
- Research and Development Department, VA New York Harbor Healthcare System, SUNY Downstate Medical Center (Y.S.Q., F.F., N.E.-S., D.L., M.B.).,Department of Cardiology, New York Presbyterian Brooklyn Methodist Hospital (Y.S.Q.)
| | - Simona Saponara
- Department of Life Sciences (S.S.), University of Siena, Italy
| | - Simone Furini
- Department of Medical Biotechnologies (A.C., S.F., G.C., F.P.), University of Siena, Italy
| | - Fabio Fusi
- Department of Biotechnology, Chemistry and Pharmacy (F.F.), University of Siena, Italy
| | | | - Alessandra Gamberucci
- Department of Molecular and Developmental Medicine (A.G.), University of Siena, Italy
| | | | - Gabriele Cevenini
- Department of Medical Biotechnologies (A.C., S.F., G.C., F.P.), University of Siena, Italy.,Research and Development Department, VA New York Harbor Healthcare System, SUNY Downstate Medical Center (Y.S.Q., F.F., N.E.-S., D.L., M.B.)
| | - Francesco Pettini
- Department of Medical Biotechnologies (A.C., S.F., G.C., F.P.), University of Siena, Italy
| | - Franco Laghi-Pasini
- Department of Medical Sciences, Surgery and Neurosciences (P.E.L., F.L.-P., P.L.C.), University of Siena, Italy
| | - Maurizio Acampa
- Research and Development Department, VA New York Harbor Healthcare System, SUNY Downstate Medical Center (Y.S.Q., F.F., N.E.-S., D.L., M.B.).,Department of Neurological and Sensorineural Sciences, Stroke Unit, University Hospital of Siena, Italy (M.A.)
| | - Iacopo Bertolozzi
- Cardiology Intensive Therapy Unit, Department of Internal Medicine, Nuovo Ospedale San Giovanni di Dio, Florence, Italy (I.B.)
| | - Pier Leopoldo Capecchi
- Department of Medical Sciences, Surgery and Neurosciences (P.E.L., F.L.-P., P.L.C.), University of Siena, Italy
| | - Deana Lazaro
- Research and Development Department, VA New York Harbor Healthcare System, SUNY Downstate Medical Center (Y.S.Q., F.F., N.E.-S., D.L., M.B.)
| | - Mohamed Boutjdir
- Research and Development Department, VA New York Harbor Healthcare System, SUNY Downstate Medical Center (Y.S.Q., F.F., N.E.-S., D.L., M.B.).,Department of Medicine, NYU School of Medicine, New York, NY (M.B.)
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35
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Heijman J, Sutanto H, Crijns HJGM, Nattel S, Trayanova NA. Computational models of atrial fibrillation: achievements, challenges, and perspectives for improving clinical care. Cardiovasc Res 2021; 117:1682-1699. [PMID: 33890620 PMCID: PMC8208751 DOI: 10.1093/cvr/cvab138] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Indexed: 12/11/2022] Open
Abstract
Despite significant advances in its detection, understanding and management, atrial fibrillation (AF) remains a highly prevalent cardiac arrhythmia with a major impact on morbidity and mortality of millions of patients. AF results from complex, dynamic interactions between risk factors and comorbidities that induce diverse atrial remodelling processes. Atrial remodelling increases AF vulnerability and persistence, while promoting disease progression. The variability in presentation and wide range of mechanisms involved in initiation, maintenance and progression of AF, as well as its associated adverse outcomes, make the early identification of causal factors modifiable with therapeutic interventions challenging, likely contributing to suboptimal efficacy of current AF management. Computational modelling facilitates the multilevel integration of multiple datasets and offers new opportunities for mechanistic understanding, risk prediction and personalized therapy. Mathematical simulations of cardiac electrophysiology have been around for 60 years and are being increasingly used to improve our understanding of AF mechanisms and guide AF therapy. This narrative review focuses on the emerging and future applications of computational modelling in AF management. We summarize clinical challenges that may benefit from computational modelling, provide an overview of the different in silico approaches that are available together with their notable achievements, and discuss the major limitations that hinder the routine clinical application of these approaches. Finally, future perspectives are addressed. With the rapid progress in electronic technologies including computing, clinical applications of computational modelling are advancing rapidly. We expect that their application will progressively increase in prominence, especially if their added value can be demonstrated in clinical trials.
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Affiliation(s)
- Jordi Heijman
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Faculty of Health, Medicine, and Life Sciences, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Henry Sutanto
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Faculty of Health, Medicine, and Life Sciences, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Harry J G M Crijns
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Faculty of Health, Medicine, and Life Sciences, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Stanley Nattel
- Department of Medicine, Montreal Heart Institute and Université de Montréal, Montreal, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
- Institute of Pharmacology, West German Heart and Vascular Center, Faculty of Medicine, University Duisburg-Essen, Duisburg, Germany
- IHU Liryc and Fondation Bordeaux Université, Bordeaux, France
| | - Natalia A Trayanova
- Alliance for Cardiovascular Diagnostic and Treatment Innovation, and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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36
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DeMarco KR, Yang PC, Singh V, Furutani K, Dawson JRD, Jeng MT, Fettinger JC, Bekker S, Ngo VA, Noskov SY, Yarov-Yarovoy V, Sack JT, Wulff H, Clancy CE, Vorobyov I. Molecular determinants of pro-arrhythmia proclivity of d- and l-sotalol via a multi-scale modeling pipeline. J Mol Cell Cardiol 2021; 158:163-177. [PMID: 34062207 PMCID: PMC8906354 DOI: 10.1016/j.yjmcc.2021.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/03/2021] [Accepted: 05/24/2021] [Indexed: 11/20/2022]
Abstract
Drug isomers may differ in their proarrhythmia risk. An interesting example is the drug sotalol, an antiarrhythmic drug comprising d- and l- enantiomers that both block the hERG cardiac potassium channel and confer differing degrees of proarrhythmic risk. We developed a multi-scale in silico pipeline focusing on hERG channel – drug interactions and used it to probe and predict the mechanisms of pro-arrhythmia risks of the two enantiomers of sotalol. Molecular dynamics (MD) simulations predicted comparable hERG channel binding affinities for d- and l-sotalol, which were validated with electrophysiology experiments. MD derived thermodynamic and kinetic parameters were used to build multi-scale functional computational models of cardiac electrophysiology at the cell and tissue scales. Functional models were used to predict inactivated state binding affinities to recapitulate electrocardiogram (ECG) QT interval prolongation observed in clinical data. Our study demonstrates how modeling and simulation can be applied to predict drug effects from the atom to the rhythm for dl-sotalol and also increased proarrhythmia proclivity of d- vs. l-sotalol when accounting for stereospecific beta-adrenergic receptor blocking.
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Affiliation(s)
- Kevin R DeMarco
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
| | - Pei-Chi Yang
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
| | - Vikrant Singh
- Department of Pharmacology, University of California Davis, Davis, CA 95616, USA
| | - Kazuharu Furutani
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Department of Pharmacology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, Tokushima 770-8514, Japan
| | - John R D Dawson
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Biophysics Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Mao-Tsuen Jeng
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
| | - James C Fettinger
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA
| | - Slava Bekker
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Department of Science and Engineering, American River College, Sacramento, CA 95841, USA
| | - Van A Ngo
- Centre for Molecular Simulation and Biochemistry Research Cluster, Department of Biological Sciences, University of Calgary, Calgary, AB T2N1N4, Canada
| | - Sergei Y Noskov
- Centre for Molecular Simulation and Biochemistry Research Cluster, Department of Biological Sciences, University of Calgary, Calgary, AB T2N1N4, Canada
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Department of Anesthesiology and Pain Medicine, University of California Davis, Davis, CA 95616, USA
| | - Jon T Sack
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Department of Anesthesiology and Pain Medicine, University of California Davis, Davis, CA 95616, USA
| | - Heike Wulff
- Department of Pharmacology, University of California Davis, Davis, CA 95616, USA
| | - Colleen E Clancy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Department of Pharmacology, University of California Davis, Davis, CA 95616, USA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Department of Pharmacology, University of California Davis, Davis, CA 95616, USA.
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37
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Clerx M, Mirams GR, Rogers AJ, Narayan SM, Giles WR. Immediate and Delayed Response of Simulated Human Atrial Myocytes to Clinically-Relevant Hypokalemia. Front Physiol 2021; 12:651162. [PMID: 34122128 PMCID: PMC8188899 DOI: 10.3389/fphys.2021.651162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Although plasma electrolyte levels are quickly and precisely regulated in the mammalian cardiovascular system, even small transient changes in K+, Na+, Ca2+, and/or Mg2+ can significantly alter physiological responses in the heart, blood vessels, and intrinsic (intracardiac) autonomic nervous system. We have used mathematical models of the human atrial action potential (AP) to explore the electrophysiological mechanisms that underlie changes in resting potential (Vr) and the AP following decreases in plasma K+, [K+]o, that were selected to mimic clinical hypokalemia. Such changes may be associated with arrhythmias and are commonly encountered in patients (i) in therapy for hypertension and heart failure; (ii) undergoing renal dialysis; (iii) with any disease with acid-base imbalance; or (iv) post-operatively. Our study emphasizes clinically-relevant hypokalemic conditions, corresponding to [K+]o reductions of approximately 1.5 mM from the normal value of 4 to 4.5 mM. We show how the resulting electrophysiological responses in human atrial myocytes progress within two distinct time frames: (i) Immediately after [K+]o is reduced, the K+-sensing mechanism of the background inward rectifier current (IK1) responds. Specifically, its highly non-linear current-voltage relationship changes significantly as judged by the voltage dependence of its region of outward current. This rapidly alters, and sometimes even depolarizes, Vr and can also markedly prolong the final repolarization phase of the AP, thus modulating excitability and refractoriness. (ii) A second much slower electrophysiological response (developing 5-10 minutes after [K+]o is reduced) results from alterations in the intracellular electrolyte balance. A progressive shift in intracellular [Na+]i causes a change in the outward electrogenic current generated by the Na+/K+ pump, thereby modifying Vr and AP repolarization and changing the human atrial electrophysiological substrate. In this study, these two effects were investigated quantitatively, using seven published models of the human atrial AP. This highlighted the important role of IK1 rectification when analyzing both the mechanisms by which [K+]o regulates Vr and how the AP waveform may contribute to "trigger" mechanisms within the proarrhythmic substrate. Our simulations complement and extend previous studies aimed at understanding key factors by which decreases in [K+]o can produce effects that are known to promote atrial arrhythmias in human hearts.
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Affiliation(s)
- Michael Clerx
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Gary R Mirams
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Albert J Rogers
- Department of Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, United States
| | - Sanjiv M Narayan
- Department of Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, United States
| | - Wayne R Giles
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
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38
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Campana C, Dariolli R, Boutjdir M, Sobie EA. Inflammation as a Risk Factor in Cardiotoxicity: An Important Consideration for Screening During Drug Development. Front Pharmacol 2021; 12:598549. [PMID: 33953668 PMCID: PMC8091045 DOI: 10.3389/fphar.2021.598549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/31/2021] [Indexed: 01/08/2023] Open
Abstract
Numerous commonly prescribed drugs, including antiarrhythmics, antihistamines, and antibiotics, carry a proarrhythmic risk and may induce dangerous arrhythmias, including the potentially fatal Torsades de Pointes. For this reason, cardiotoxicity testing has become essential in drug development and a required step in the approval of any medication for use in humans. Blockade of the hERG K+ channel and the consequent prolongation of the QT interval on the ECG have been considered the gold standard to predict the arrhythmogenic risk of drugs. In recent years, however, preclinical safety pharmacology has begun to adopt a more integrative approach that incorporates mathematical modeling and considers the effects of drugs on multiple ion channels. Despite these advances, early stage drug screening research only evaluates QT prolongation in experimental and computational models that represent healthy individuals. We suggest here that integrating disease modeling with cardiotoxicity testing can improve drug risk stratification by predicting how disease processes and additional comorbidities may influence the risks posed by specific drugs. In particular, chronic systemic inflammation, a condition associated with many diseases, affects heart function and can exacerbate medications’ cardiotoxic effects. We discuss emerging research implicating the role of inflammation in cardiac electrophysiology, and we offer a perspective on how in silico modeling of inflammation may lead to improved evaluation of the proarrhythmic risk of drugs at their early stage of development.
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Affiliation(s)
- Chiara Campana
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Rafael Dariolli
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mohamed Boutjdir
- Cardiovascular Research Program, VA New York Harbor Healthcare System, Brooklyn, NY, United States.,Department of Medicine, Cell Biology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, NY, United States.,Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Eric A Sobie
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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39
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Whittaker DG, Capel RA, Hendrix M, Chan XHS, Herring N, White NJ, Mirams GR, Burton RAB. Cardiac TdP risk stratification modelling of anti-infective compounds including chloroquine and hydroxychloroquine. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210235. [PMID: 33996135 PMCID: PMC8059594 DOI: 10.1098/rsos.210235] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/30/2021] [Indexed: 05/06/2023]
Abstract
Hydroxychloroquine (HCQ), the hydroxyl derivative of chloroquine (CQ), is widely used in the treatment of rheumatological conditions (systemic lupus erythematosus, rheumatoid arthritis) and is being studied for the treatment and prevention of COVID-19. Here, we investigate through mathematical modelling the safety profile of HCQ, CQ and other QT-prolonging anti-infective agents to determine their risk categories for Torsade de Pointes (TdP) arrhythmia. We performed safety modelling with uncertainty quantification using a risk classifier based on the qNet torsade metric score, a measure of the net charge carried by major currents during the action potential under inhibition of multiple ion channels by a compound. Modelling results for HCQ at a maximum free therapeutic plasma concentration (free C max) of approximately 1.2 µM (malaria dosing) indicated it is most likely to be in the high-intermediate-risk category for TdP, whereas CQ at a free C max of approximately 0.7 µM was predicted to most likely lie in the intermediate-risk category. Combining HCQ with the antibacterial moxifloxacin or the anti-malarial halofantrine (HAL) increased the degree of human ventricular action potential duration prolongation at some or all concentrations investigated, and was predicted to increase risk compared to HCQ alone. The combination of HCQ/HAL was predicted to be the riskiest for the free C max values investigated, whereas azithromycin administered individually was predicted to pose the lowest risk. Our simulation approach highlights that the torsadogenic potentials of HCQ, CQ and other QT-prolonging anti-infectives used in COVID-19 prevention and treatment increase with concentration and in combination with other QT-prolonging drugs.
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Affiliation(s)
- Dominic G. Whittaker
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | | | - Maurice Hendrix
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
- Digital Research Service, University of Nottingham, Nottingham, UK
| | - Xin Hui S. Chan
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Neil Herring
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gary R. Mirams
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
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Abstract
Machine learning (ML), a branch of artificial intelligence, where machines learn from big data, is at the crest of a technological wave of change sweeping society. Cardiovascular medicine is at the forefront of many ML applications, and there is a significant effort to bring them into mainstream clinical practice. In the field of cardiac electrophysiology, ML applications have also seen a rapid growth and popularity, particularly the use of ML in the automatic interpretation of ECGs, which has been extensively covered in the literature. Much lesser known are the other aspects of ML application in cardiac electrophysiology and arrhythmias, such as those in basic science research on arrhythmia mechanisms, both experimental and computational; in the development of better techniques for mapping of cardiac electrical function; and in translational research related to arrhythmia management. In the current review, we examine comprehensively such ML applications as they match the scope of this journal. The current review is organized in 3 parts. The first provides an overview of general ML principles and methodologies that will afford readers of the necessary information on the subject, serving as the foundation for inviting further ML applications in arrhythmia research. The basic information we provide can serve as a guide on how one might design and conduct an ML study. The second part is a review of arrhythmia and electrophysiology studies in which ML has been utilized, highlighting the broad potential of ML approaches. For each subject, we outline comprehensively the general topics, while reviewing some of the research advances utilizing ML under the subject. Finally, we discuss the main challenges and the perspectives for ML-driven cardiac electrophysiology and arrhythmia research.
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Affiliation(s)
- Natalia A. Trayanova
- Department of Biomedical Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, USA 21218
- Alliance for Cardiovascular Diagnosis and Treatment Innovation, Whiting School of Engineering and School of Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, USA 21218
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD, USA 21205
| | - Dan M. Popescu
- Alliance for Cardiovascular Diagnosis and Treatment Innovation, Whiting School of Engineering and School of Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, USA 21218
- Department of Applied Mathematics and Statistics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, USA 21218
| | - Julie K. Shade
- Department of Biomedical Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, USA 21218
- Alliance for Cardiovascular Diagnosis and Treatment Innovation, Whiting School of Engineering and School of Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, USA 21218
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Amuzescu B, Airini R, Epureanu FB, Mann SA, Knott T, Radu BM. Evolution of mathematical models of cardiomyocyte electrophysiology. Math Biosci 2021; 334:108567. [PMID: 33607174 DOI: 10.1016/j.mbs.2021.108567] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/10/2021] [Accepted: 02/04/2021] [Indexed: 12/16/2022]
Abstract
Advanced computational techniques and mathematical modeling have become more and more important to the study of cardiac electrophysiology. In this review, we provide a brief history of the evolution of cardiomyocyte electrophysiology models and highlight some of the most important ones that had a major impact on our understanding of the electrical activity of the myocardium and associated transmembrane ion fluxes in normal and pathological states. We also present the use of these models in the study of various arrhythmogenesis mechanisms, particularly the integration of experimental pharmacology data into advanced humanized models for in silico proarrhythmogenic risk prediction as an essential component of the Comprehensive in vitro Proarrhythmia Assay (CiPA) drug safety paradigm.
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Affiliation(s)
- Bogdan Amuzescu
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, Bucharest 050095, Romania; Life, Environmental and Earth Sciences Division, Research Institute of the University of Bucharest (ICUB), 91-95 Splaiul Independentei, Bucharest 050095, Romania.
| | - Razvan Airini
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, Bucharest 050095, Romania; Life, Environmental and Earth Sciences Division, Research Institute of the University of Bucharest (ICUB), 91-95 Splaiul Independentei, Bucharest 050095, Romania
| | - Florin Bogdan Epureanu
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, Bucharest 050095, Romania; Life, Environmental and Earth Sciences Division, Research Institute of the University of Bucharest (ICUB), 91-95 Splaiul Independentei, Bucharest 050095, Romania
| | - Stefan A Mann
- Cytocentrics Bioscience GmbH, Nattermannallee 1, 50829 Cologne, Germany
| | - Thomas Knott
- CytoBioScience Inc., 3463 Magic Drive, San Antonio, TX 78229, USA
| | - Beatrice Mihaela Radu
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, Bucharest 050095, Romania; Life, Environmental and Earth Sciences Division, Research Institute of the University of Bucharest (ICUB), 91-95 Splaiul Independentei, Bucharest 050095, Romania
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42
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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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Cano J, Zorio E, Mazzanti A, Arnau MÁ, Trenor B, Priori SG, Saiz J, Romero L. Ranolazine as an Alternative Therapy to Flecainide for SCN5A V411M Long QT Syndrome Type 3 Patients. Front Pharmacol 2020; 11:580481. [PMID: 33519442 PMCID: PMC7845660 DOI: 10.3389/fphar.2020.580481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/16/2020] [Indexed: 12/14/2022] Open
Abstract
The prolongation of the QT interval represents the main feature of the long QT syndrome (LQTS), a life-threatening genetic disease. The heterozygous SCN5A V411M mutation of the human sodium channel leads to a LQTS type 3 with severe proarrhythmic effects due to an increase in the late component of the sodium current (INaL). The two sodium blockers flecainide and ranolazine are equally recommended by the current 2015 ESC guidelines to treat patients with LQTS type 3 and persistently prolonged QT intervals. However, awareness of pro-arrhythmic effects of flecainide in LQTS type 3 patients arose upon the study of the SCN5A E1784K mutation. Regarding SCN5A V411M individuals, flecainide showed good results albeit in a reduced number of patients and no evidence supporting the use of ranolazine has ever been released. Therefore, we ought to compare the effect of ranolazine and flecainide in a SCN5A V411M model using an in-silico modeling and simulation approach. We collected clinical data of four patients. Then, we fitted four Markovian models of the human sodium current (INa) to experimental and clinical data. Two of them correspond to the wild type and the heterozygous SCN5A V411M scenarios, and the other two mimic the effects of flecainide and ranolazine on INa. Next, we inserted them into three isolated cell action potential (AP) models for endocardial, midmyocardial and epicardial cells and in a one-dimensional tissue model. The SCN5A V411M mutation produced a 15.9% APD90 prolongation in the isolated endocardial cell model, which corresponded to a 14.3% of the QT interval prolongation in a one-dimensional strand model, in keeping with clinical observations. Although with different underlying mechanisms, flecainide and ranolazine partially countered this prolongation at the isolated endocardial model by reducing the APD90 by 8.7 and 4.3%, and the QT interval by 7.2 and 3.2%, respectively. While flecainide specifically targeted the mutation-induced increase in peak INaL, ranolazine reduced it during the entire AP. Our simulations also suggest that ranolazine could prevent early afterdepolarizations triggered by the SCN5A V411M mutation during bradycardia, as flecainide. We conclude that ranolazine could be used to treat SCN5A V411M patients, specifically when flecainide is contraindicated.
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Affiliation(s)
- Jordi Cano
- Centro de Investigación e Innovación en Bioingeniería (CI2B), Universitat Politècnica de València, Valencia, España
| | - Esther Zorio
- Unidad de Cardiopatías Familiares y Muerte Súbita, Servicio de Cardiología, Hospital Universitario y Politécnico La Fe, Valencia, España.,Center for Biomedical Network Research on Cardiovascular Diseases (CIBERCV), Madrid, Spain
| | - Andrea Mazzanti
- Molecular Cardiology, IRCCS, Istituti Clinici Scientifici Maugeri, Pavia, Italy.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Miguel Ángel Arnau
- Unidad de Cardiopatías Familiares y Muerte Súbita, Servicio de Cardiología, Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Beatriz Trenor
- Centro de Investigación e Innovación en Bioingeniería (CI2B), Universitat Politècnica de València, Valencia, España
| | - Silvia G Priori
- Molecular Cardiology, IRCCS, Istituti Clinici Scientifici Maugeri, Pavia, Italy.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Javier Saiz
- Centro de Investigación e Innovación en Bioingeniería (CI2B), Universitat Politècnica de València, Valencia, España
| | - Lucia Romero
- Centro de Investigación e Innovación en Bioingeniería (CI2B), Universitat Politècnica de València, Valencia, España
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Bifulco SF, Akoum N, Boyle PM. Translational applications of computational modelling for patients with cardiac arrhythmias. Heart 2020; 107:heartjnl-2020-316854. [PMID: 33303478 PMCID: PMC10896425 DOI: 10.1136/heartjnl-2020-316854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/13/2020] [Accepted: 11/19/2020] [Indexed: 11/04/2022] Open
Abstract
Cardiac arrhythmia is associated with high morbidity, and its underlying mechanisms are poorly understood. Computational modelling and simulation approaches have the potential to improve standard-of-care therapy for these disorders, offering deeper understanding of complex disease processes and sophisticated translational tools for planning clinical procedures. This review provides a clinician-friendly summary of recent advancements in computational cardiology. Organ-scale models automatically generated from clinical-grade imaging data are used to custom tailor our understanding of arrhythmia drivers, estimate future arrhythmogenic risk and personalise treatment plans. Recent mechanistic insights derived from atrial and ventricular arrhythmia simulations are highlighted, and the potential avenues to patient care (eg, by revealing new antiarrhythmic drug targets) are covered. Computational approaches geared towards improving outcomes in resynchronisation therapy have used simulations to elucidate optimal patient selection and lead location. Technology to personalise catheter ablation procedures are also covered, specifically preliminary outcomes form early-stage or pilot clinical studies. To conclude, future developments in computational cardiology are discussed, including improving the representation of patient-specific fibre orientations and fibrotic remodelling characterisation and how these might improve understanding of arrhythmia mechanisms and provide transformative tools for patient-specific therapy.
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Affiliation(s)
- Savannah F Bifulco
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Nazem Akoum
- Department of Cardiology, University of Washington, Seattle, Washington, USA
| | - Patrick M Boyle
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, USA
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA
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45
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Rogers AJ, Selvalingam A, Alhusseini MI, Krummen DE, Corrado C, Abuzaid F, Baykaner T, Meyer C, Clopton P, Giles W, Bailis P, Niederer S, Wang PJ, Rappel WJ, Zaharia M, Narayan SM. Machine Learned Cellular Phenotypes in Cardiomyopathy Predict Sudden Death. Circ Res 2020; 128:172-184. [PMID: 33167779 DOI: 10.1161/circresaha.120.317345] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RATIONALE Susceptibility to VT/VF (ventricular tachycardia/fibrillation) is difficult to predict in patients with ischemic cardiomyopathy either by clinical tools or by attempting to translate cellular mechanisms to the bedside. OBJECTIVE To develop computational phenotypes of patients with ischemic cardiomyopathy, by training then interpreting machine learning of ventricular monophasic action potentials (MAPs) to reveal phenotypes that predict long-term outcomes. METHODS AND RESULTS We recorded 5706 ventricular MAPs in 42 patients with coronary artery disease and left ventricular ejection fraction ≤40% during steady-state pacing. Patients were randomly allocated to independent training and testing cohorts in a 70:30 ratio, repeated K=10-fold. Support vector machines and convolutional neural networks were trained to 2 end points: (1) sustained VT/VF or (2) mortality at 3 years. Support vector machines provided superior classification. For patient-level predictions, we computed personalized MAP scores as the proportion of MAP beats predicting each end point. Patient-level predictions in independent test cohorts yielded c-statistics of 0.90 for sustained VT/VF (95% CI, 0.76-1.00) and 0.91 for mortality (95% CI, 0.83-1.00) and were the most significant multivariate predictors. Interpreting trained support vector machine revealed MAP morphologies that, using in silico modeling, revealed higher L-type calcium current or sodium-calcium exchanger as predominant phenotypes for VT/VF. CONCLUSIONS Machine learning of action potential recordings in patients revealed novel phenotypes for long-term outcomes in ischemic cardiomyopathy. Such computational phenotypes provide an approach which may reveal cellular mechanisms for clinical outcomes and could be applied to other conditions.
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Affiliation(s)
- Albert J Rogers
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Anojan Selvalingam
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University.,Department of Cardiology, University Medical Center Hamburg-Eppendorf, Germany (A.S., C.M.)
| | - Mahmood I Alhusseini
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - David E Krummen
- Department of Medicine (D.E.K.), University of California, San Diego
| | - Cesare Corrado
- Department of Biomedical Engineering, King's College London, United Kingdom (C.C., S.N.)
| | - Firas Abuzaid
- Department of Computer Sciences (F.A., M.Z., P.B.), Stanford University
| | - Tina Baykaner
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Christian Meyer
- Department of Cardiology, University Medical Center Hamburg-Eppendorf, Germany (A.S., C.M.)
| | - Paul Clopton
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Wayne Giles
- Department of Physiology and Pharmacology, University of Calgary, Canada (W.G.)
| | - Peter Bailis
- Department of Computer Sciences (F.A., M.Z., P.B.), Stanford University
| | - Steven Niederer
- Department of Biomedical Engineering, King's College London, United Kingdom (C.C., S.N.)
| | - Paul J Wang
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Wouter-Jan Rappel
- Department of Physics (W.-J.R.), University of California, San Diego
| | - Matei Zaharia
- Department of Computer Sciences (F.A., M.Z., P.B.), Stanford University
| | - Sanjiv M Narayan
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University
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46
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Hichri E, Selimi Z, Kucera JP. Modeling the Interactions Between Sodium Channels Provides Insight Into the Negative Dominance of Certain Channel Mutations. Front Physiol 2020; 11:589386. [PMID: 33250780 PMCID: PMC7674773 DOI: 10.3389/fphys.2020.589386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/12/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Nav1.5 cardiac Na+ channel mutations can cause arrhythmogenic syndromes. Some of these mutations exert a dominant negative effect on wild-type channels. Recent studies showed that Na+ channels can dimerize, allowing coupled gating. This leads to the hypothesis that allosteric interactions between Na+ channels modulate their function and that these interactions may contribute to the negative dominance of certain mutations. METHODS To investigate how allosteric interactions affect microscopic and macroscopic channel function, we developed a modeling paradigm in which Markovian models of two channels are combined. Allosteric interactions are incorporated by modifying the free energies of the composite states and/or barriers between states. RESULTS Simulations using two generic 2-state models (C-O, closed-open) revealed that increasing the free energy of the composite states CO/OC leads to coupled gating. Simulations using two 3-state models (closed-open-inactivated) revealed that coupled closings must also involve interactions between further composite states. Using two 6-state cardiac Na+ channel models, we replicated previous experimental results mainly by increasing the energies of the CO/OC states and lowering the energy barriers between the CO/OC and the CO/OO states. The channel model was then modified to simulate a negative dominant mutation (Nav1.5 p.L325R). Simulations of homodimers and heterodimers in the presence and absence of interactions showed that the interactions with the variant channel impair the opening of the wild-type channel and thus contribute to negative dominance. CONCLUSION Our new modeling framework recapitulates qualitatively previous experimental observations and helps identifying possible interaction mechanisms between ion channels.
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Affiliation(s)
| | | | - Jan P. Kucera
- Department of Physiology, University of Bern, Bern, Switzerland
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47
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Bystricky W, Maier C, Gintant G, Bergau D, Carter D. Identification of Drug-Induced Multichannel Block and Proarrhythmic Risk in Humans Using Continuous T Vector Velocity Effect Profiles Derived From Surface Electrocardiograms. Front Physiol 2020; 11:567383. [PMID: 33071822 PMCID: PMC7530300 DOI: 10.3389/fphys.2020.567383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/27/2020] [Indexed: 01/07/2023] Open
Abstract
We present continuous T vector velocity (TVV) effect profiles as a new method for identifying drug effects on cardiac ventricular repolarization. TVV measures the temporal change in the myocardial action potential distribution during repolarization. The T vector dynamics were measured as the time required to reach p percent of the total T vector trajectory length, denoted as Tr(p), with p in {1, …, 100%}. The Tr(p) values were individually corrected for heart rate at each trajectory length percentage p. Drug effects were measured by evaluating the placebo corrected changes from baseline of Tr(p)c jointly for all p using functional mixed effects models. The p-dependent model parameters were implemented as cubic splines, providing continuous drug effect profiles along the entire ventricular repolarization process. The effect profile distributions were approximated by bootstrap simulations. We applied this TVV-based analysis approach to ECGs available from three published studies that were conducted in the CiPA context. These studies assessed the effect of 10 drugs and drug combinations with different ion channel blocking properties on myocardial repolarization in a total of 104 healthy volunteers. TVV analysis revealed that blockade of outward potassium currents alone presents an effect profile signature of continuous accumulation of delay throughout the entire repolarization interval. In contrast, block of inward sodium or calcium currents involves acceleration, which accumulates during early repolarization. The balance of blocking inward versus outward currents was reflected in the percentage pzero of the T vector trajectory length where accelerated repolarization transitioned to delayed repolarization. Binary classification using a threshold pzero = 43% separated predominant hERG channel blocking drugs with potentially higher proarrhythmic risk (moxifloxacin, dofetilide, quinidine, chloroquine) from multichannel blocking drugs with low proarrhythmic risk (ranolazine, verapamil, lopinavir/ritonavir) with sensitivity 0.99 and specificity 0.97. The TVV-based effect profile provides a detailed view of drug effects throughout the entire ventricular repolarization interval. It enables the evaluation of drug-induced blocks of multiple cardiac repolarization currents from clinical ECGs. The proposed pzero parameter enhances identification of the proarrhythmic risk of a drug beyond QT prolongation, and therefore constitutes an important tool for cardiac arrhythmia risk assessment.
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Affiliation(s)
- Werner Bystricky
- Clinical Pharmacology and Pharmacometrics, AbbVie, Inc., North Chicago, IL, United States
| | - Christoph Maier
- Clinical Pharmacology and Pharmacometrics, AbbVie, Inc., North Chicago, IL, United States
- Department of Medical Informatics, Heilbronn University, Heilbronn, Germany
| | - Gary Gintant
- Integrated Sciences and Technology, AbbVie, Inc., North Chicago, IL, United States
| | - Dennis Bergau
- Clinical Pharmacology and Pharmacometrics, AbbVie, Inc., North Chicago, IL, United States
| | - David Carter
- Clinical Pharmacology and Pharmacometrics, AbbVie, Inc., North Chicago, IL, United States
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48
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Ni H, Fogli Iseppe A, Giles WR, Narayan SM, Zhang H, Edwards AG, Morotti S, Grandi E. Populations of in silico myocytes and tissues reveal synergy of multiatrial-predominant K + -current block in atrial fibrillation. Br J Pharmacol 2020; 177:4497-4515. [PMID: 32667679 DOI: 10.1111/bph.15198] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 06/22/2020] [Accepted: 07/03/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND AND PURPOSE Pharmacotherapy of atrial fibrillation (AF), the most common cardiac arrhythmia, remains unsatisfactory due to low efficacy and safety concerns. New therapeutic strategies target atrial-predominant ion-channels and involve multichannel block (poly)therapy. As AF is characterized by rapid and irregular atrial activations, compounds displaying potent antiarrhythmic effects at fast and minimal effects at slow rates are desirable. We present a novel systems pharmacology framework to quantitatively evaluate synergistic anti-AF effects of combined block of multiple atrial-predominant K+ currents (ultra-rapid delayed rectifier K+ current, IKur , small conductance Ca2+ -activated K+ current, IKCa , K2P 3.1 2-pore-domain K+ current, IK2P ) in AF. EXPERIMENTAL APPROACH We constructed experimentally calibrated populations of virtual atrial myocyte models in normal sinus rhythm and AF-remodelled conditions using two distinct, well-established atrial models. Sensitivity analyses on our atrial populations was used to investigate the rate dependence of action potential duration (APD) changes due to blocking IKur , IK2P or IKCa and interactions caused by blocking of these currents in modulating APD. Block was simulated in both single myocytes and one-dimensional tissue strands to confirm insights from the sensitivity analyses and examine anti-arrhythmic effects of multi-atrial-predominant K+ current block in single cells and coupled tissue. KEY RESULTS In both virtual atrial myocytes and tissues, multiple atrial-predominant K+ -current block promoted favourable positive rate-dependent APD prolongation and displayed positive rate-dependent synergy, that is, increasing synergistic antiarrhythmic effects at fast pacing versus slow rates. CONCLUSION AND IMPLICATIONS Simultaneous block of multiple atrial-predominant K+ currents may be a valuable antiarrhythmic pharmacotherapeutic strategy for AF.
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Affiliation(s)
- Haibo Ni
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Alex Fogli Iseppe
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Wayne R Giles
- Faculties of Kinesiology and Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Sanjiv M Narayan
- Division of Cardiology, Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Henggui Zhang
- Biological Physics Group, School of Physics and Astronomy, The University of Manchester, Manchester, UK
| | - Andrew G Edwards
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Stefano Morotti
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Eleonora Grandi
- Department of Pharmacology, University of California, Davis, CA, USA
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49
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Kudaibergenova M, Guo J, Khan HM, Zahid F, Lees-Miller J, Noskov SY, Duff HJ. Allosteric Coupling Between Drug Binding and the Aromatic Cassette in the Pore Domain of the hERG1 Channel: Implications for a State-Dependent Blockade. Front Pharmacol 2020; 11:914. [PMID: 32694995 PMCID: PMC7338687 DOI: 10.3389/fphar.2020.00914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/04/2020] [Indexed: 12/18/2022] Open
Abstract
Human-ether-a-go-go-related channel (hERG1) is the pore-forming domain of the delayed rectifier K+ channel in the heart which underlies the IKr current. The channel has been extensively studied due to its propensity to bind chemically diverse group of drugs. The subsequent hERG1 block can lead to a prolongation of the QT interval potentially leading to an abnormal cardiac electrical activity. The recently solved cryo-EM structure featured a striking non-swapped topology of the Voltage-Sensor Domain (VSD) which is packed against the pore-domain as well as a small and hydrophobic intra-cavity space. The small size and hydrophobicity of the cavity was unexpected and challenges the already-established hypothesis of drugs binding to the wide cavity. Recently, we showed that an amphipathic drug, ivabradine, may favorably bind the channel from the lipid-facing surface and we discovered a mutant (M651T) on the lipid facing domain between the VSD and the PD which inhibited the blocking capacity of the drug. Using multi-microseconds Molecular Dynamics (MD) simulations of wild-type and M651T mutant hERG1, we suggested the block of the channel through the lipid mediated pathway, the opening of which is facilitated by the flexible phenylalanine ring (F656). In this study, we characterize the dynamic interaction of the methionine-aromatic cassette in the S5-S6 helices by combining data from electrophysiological experiments with MD simulations and molecular docking to elucidate the complex allosteric coupling between drug binding to lipid-facing and intra-cavity sites and aromatic cassette dynamics. We investigated two well-established hERG1 blockers (ivabradine and dofetilide) for M651 sensitivity through electrophysiology and mutagenesis techniques. Our electrophysiology data reveal insensitivity of dofetilide to the mutations at site M651 on the lipid facing side of the channel, mirroring our results obtained from docking experiments. Moreover, we show that the dofetilide-induced block of hERG1 occurs through the intracellular space, whereas little to no block of ivabradine is observed during the intracellular application of the drug. The dynamic conformational rearrangement of the F656 appears to regulate the translocation of ivabradine into the central cavity. M651T mutation appears to disrupt this entry pathway by altering the molecular conformation of F656.
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Affiliation(s)
- Meruyert Kudaibergenova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.,Cumming School of Medicine, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada
| | - Jiqing Guo
- Cumming School of Medicine, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada
| | - Hanif M Khan
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Farhan Zahid
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - James Lees-Miller
- Cumming School of Medicine, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada
| | - Sergei Yu Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Henry J Duff
- Cumming School of Medicine, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada
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50
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Affiliation(s)
- Yoram Rudy
- From the Department of Biomedical Engineering, Washington University in St. Louis, MO
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