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Tsai HHD, Ford LC, Burnett SD, Dickey AN, Wright FA, Chiu WA, Rusyn I. Informing Hazard Identification and Risk Characterization of Environmental Chemicals by Combining Transcriptomic and Functional Data from Human-Induced Pluripotent Stem-Cell-Derived Cardiomyocytes. Chem Res Toxicol 2024; 37:1428-1444. [PMID: 39046974 DOI: 10.1021/acs.chemrestox.4c00193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Environmental chemicals may contribute to the global burden of cardiovascular disease, but experimental data are lacking to determine which substances pose the greatest risk. Human-induced pluripotent stem cell (iPSC)-derived cardiomyocytes are a high-throughput cardiotoxicity model that is widely used to test drugs and chemicals; however, most studies focus on exploring electro-physiological readouts. Gene expression data may provide additional molecular insights to be used for both mechanistic interpretation and dose-response analyses. Therefore, we hypothesized that both transcriptomic and functional data in human iPSC-derived cardiomyocytes may be used as a comprehensive screening tool to identify potential cardiotoxicity hazards and risks of the chemicals. To test this hypothesis, we performed concentration-response analysis of 464 chemicals from 12 classes, including both pharmaceuticals and nonpharmaceutical substances. Functional effects (beat frequency, QT prolongation, and asystole), cytotoxicity, and whole transcriptome response were evaluated. Points of departure were derived from phenotypic and transcriptomic data, and risk characterization was performed. Overall, 244 (53%) substances were active in at least one phenotype; as expected, pharmaceuticals with known cardiac liabilities were the most active. Positive chronotropy was the functional phenotype activated by the largest number of tested chemicals. No chemical class was particularly prone to pose a potential hazard to cardiomyocytes; a varying proportion (10-44%) of substances in each class had effects on cardiomyocytes. Transcriptomic data showed that 69 (15%) substances elicited significant gene expression changes; most perturbed pathways were highly relevant to known key characteristics of human cardiotoxicants. The bioactivity-to-exposure ratios showed that phenotypic- and transcriptomic-based POD led to similar results for risk characterization. Overall, our findings demonstrate how the integrative use of in vitro transcriptomic and phenotypic data from iPSC-derived cardiomyocytes not only offers a complementary approach for hazard and risk prioritization, but also enables mechanistic interpretation of the in vitro test results to increase confidence in decision-making.
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Affiliation(s)
- Han-Hsuan D Tsai
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| | - Lucie C Ford
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| | - Sarah D Burnett
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| | - Allison N Dickey
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, United States
| | - Fred A Wright
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, United States
- Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, United States
| | - Weihsueh A Chiu
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
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Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. J Chem Inf Model 2024; 64:1172-1186. [PMID: 38300851 PMCID: PMC10900289 DOI: 10.1021/acs.jcim.3c01834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024]
Abstract
Drug-induced cardiotoxicity (DICT) is a major concern in drug development, accounting for 10-14% of postmarket withdrawals. In this study, we explored the capabilities of chemical and biological data to predict cardiotoxicity, using the recently released DICTrank data set from the United States FDA. We found that such data, including protein targets, especially those related to ion channels (e.g., hERG), physicochemical properties (e.g., electrotopological state), and peak concentration in plasma offer strong predictive ability for DICT. Compounds annotated with mechanisms of action such as cyclooxygenase inhibition could distinguish between most-concern and no-concern DICT. Cell Painting features for ER stress discerned most-concern cardiotoxic from nontoxic compounds. Models based on physicochemical properties provided substantial predictive accuracy (AUCPR = 0.93). With the availability of omics data in the future, using biological data promises enhanced predictability and deeper mechanistic insights, paving the way for safer drug development. All models from this study are available at https://broad.io/DICTrank_Predictor.
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Affiliation(s)
- Srijit Seal
- Imaging
Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Ola Spjuth
- Department
of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box
591, SE-75124 Uppsala, Sweden
| | - Layla Hosseini-Gerami
- Ignota
Labs, The Bradfield Centre, Cambridge Science Park, County Hall, Westminster Bridge Road, Cambridge CB4 0GA, U.K.
| | - Miguel García-Ortegón
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Shantanu Singh
- Imaging
Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Andreas Bender
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Anne E. Carpenter
- Imaging
Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
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Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.15.562398. [PMID: 37905146 PMCID: PMC10614794 DOI: 10.1101/2023.10.15.562398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Drug-induced cardiotoxicity (DICT) is a major concern in drug development, accounting for 10-14% of postmarket withdrawals. In this study, we explored the capabilities of various chemical and biological data to predict cardiotoxicity, using the recently released Drug-Induced Cardiotoxicity Rank (DICTrank) dataset from the United States FDA. We analyzed a diverse set of data sources, including physicochemical properties, annotated mechanisms of action (MOA), Cell Painting, Gene Expression, and more, to identify indications of cardiotoxicity. We found that such data, including protein targets, especially those related to ion channels (such as hERG), physicochemical properties (such as electrotopological state) as well as peak concentration in plasma offer strong predictive ability as well as valuable insights into DICT. We also found compounds annotated with particular mechanisms of action, such as cyclooxygenase inhibition, could distinguish between most-concern and no-concern DICT compounds. Cell Painting features related to ER stress discern the most-concern cardiotoxic compounds from non-toxic compounds. While models based on physicochemical properties currently provide substantial predictive accuracy (AUCPR = 0.93), this study also underscores the potential benefits of incorporating more comprehensive biological data in future DICT predictive models. With the availability of - omics data in the future, using biological data promises enhanced predictability and delivers deeper mechanistic insights, paving the way for safer therapeutic drug development. All models and data used in this study are publicly released at https://broad.io/DICTrank_Predictor.
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Affiliation(s)
- Srijit Seal
- Imaging Platform, Broad Institute of MIT and Harvard, US
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Sweden
| | | | | | - Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, US
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Nagoor Meeran MF, Arunachalam S, Azimullah S, Saraswathiamma D, Albawardi A, Almarzooqi S, Jha NK, Subramanya S, Beiram R, Ojha S. α-Bisabolol, a Dietary Sesquiterpene, Attenuates Doxorubicin-Induced Acute Cardiotoxicity in Rats by Inhibiting Cellular Signaling Pathways, Nrf2/Keap-1/HO-1, Akt/mTOR/GSK-3β, NF-κB/p38/MAPK, and NLRP3 Inflammasomes Regulating Oxidative Stress and Inflammatory Cascades. Int J Mol Sci 2023; 24:14013. [PMID: 37762315 PMCID: PMC10530367 DOI: 10.3390/ijms241814013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 09/29/2023] Open
Abstract
Cancer chemotherapy with doxorubicin (DOX) may have multiorgan toxicities including cardiotoxicity, and this is one of the major limitations of its clinical use. The present study aimed to evaluate the cardioprotective role of α-Bisabolol (BSB) in DOX-induced acute cardiotoxicity in rats and the underlying pharmacological and molecular mechanisms. DOX (12.5 mg/kg, single dose) was injected intraperitoneally into the rats for induction of acute cardiotoxicity. BSB was given orally to rats (25 mg/kg, p.o. twice daily) for a duration of five days. DOX administration induced cardiac dysfunction as evidenced by altered body weight, hemodynamics, and release of cardio-specific diagnostic markers. The occurrence of oxidative stress was evidenced by a significant decline in antioxidant defense along with a rise in lipid peroxidation and hyperlipidemia. Additionally, DOX also increased the levels and expression of proinflammatory cytokines and inflammatory mediators, as well as activated NF-κB/MAPK signaling in the heart, following alterations in the Nrf2/Keap-1/HO-1 and Akt/mTOR/GSK-3β signaling. DOX also perturbed NLRP3 inflammasome activation-mediated pyroptosis in the myocardium of rats. Furthermore, histopathological studies revealed cellular alterations in the myocardium. On the contrary, treatment with BSB has been observed to preserve the myocardium and restore all the cellular, molecular, and structural perturbations in the heart tissues of DOX-induced cardiotoxicity in rats. Results of the present study clearly demonstrate the protective role of BSB against DOX-induced cardiotoxicity, which is attributed to its potent antioxidant, anti-inflammatory, and antihyperlipidemic effects resulting from favorable modulation of numerous cellular signaling regulatory pathways, viz., Nrf2/Keap-1/HO-1, Akt/mTOR/GSK-3β, NF-κB/p38/MAPK, and NLRP3 inflammasomes, in countering the cascades of oxidative stress and inflammation. The observations suggest that BSB can be a promising agent or an adjuvant to limit the cardiac injury caused by DOX. Further studies including the role in tumor-bearing animals as well as regulatory toxicology are suggested.
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Affiliation(s)
- Mohamed Fizur Nagoor Meeran
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (M.F.N.M.); (R.B.)
| | - Seenipandi Arunachalam
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (M.F.N.M.); (R.B.)
| | - Sheikh Azimullah
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (M.F.N.M.); (R.B.)
| | - Dhanya Saraswathiamma
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Alia Albawardi
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Saeeda Almarzooqi
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering and Technology (SET), Sharda University, Greater Noida 201310, Uttar Pradesh, India
| | - Sandeep Subramanya
- Department of Physiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Rami Beiram
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (M.F.N.M.); (R.B.)
| | - Shreesh Ojha
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (M.F.N.M.); (R.B.)
- Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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Han R, Yoon H, Kim G, Lee H, Lee Y. Revolutionizing Medicinal Chemistry: The Application of Artificial Intelligence (AI) in Early Drug Discovery. Pharmaceuticals (Basel) 2023; 16:1259. [PMID: 37765069 PMCID: PMC10537003 DOI: 10.3390/ph16091259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/24/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Artificial intelligence (AI) has permeated various sectors, including the pharmaceutical industry and research, where it has been utilized to efficiently identify new chemical entities with desirable properties. The application of AI algorithms to drug discovery presents both remarkable opportunities and challenges. This review article focuses on the transformative role of AI in medicinal chemistry. We delve into the applications of machine learning and deep learning techniques in drug screening and design, discussing their potential to expedite the early drug discovery process. In particular, we provide a comprehensive overview of the use of AI algorithms in predicting protein structures, drug-target interactions, and molecular properties such as drug toxicity. While AI has accelerated the drug discovery process, data quality issues and technological constraints remain challenges. Nonetheless, new relationships and methods have been unveiled, demonstrating AI's expanding potential in predicting and understanding drug interactions and properties. For its full potential to be realized, interdisciplinary collaboration is essential. This review underscores AI's growing influence on the future trajectory of medicinal chemistry and stresses the importance of ongoing synergies between computational and domain experts.
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Affiliation(s)
| | | | | | | | - Yoonji Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
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Stebbeds W, Raniga K, Standing D, Wallace I, Bayliss J, Brown A, Kasprowicz R, Dalmas Wilk D, Deakyne J, Clements P, Chaudhary KW, Rossman EI, Bahinski A, Francis J. CardioMotion: identification of functional and structural cardiotoxic liabilities in small molecules through brightfield kinetic imaging. Toxicol Sci 2023; 195:61-70. [PMID: 37462734 DOI: 10.1093/toxsci/kfad065] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
Cardiovascular toxicity is an important cause of drug failures in the later stages of drug development, early clinical safety assessment, and even postmarket withdrawals. Early-stage in vitro assessment of potential cardiovascular liabilities in the pharmaceutical industry involves assessment of interactions with cardiac ion channels, as well as induced pluripotent stem cell-derived cardiomyocyte-based functional assays, such as calcium flux and multielectrode-array assays. These methods are appropriate for the identification of acute functional cardiotoxicity but structural cardiotoxicity, which manifests effects after chronic exposure, is often only captured in vivo. CardioMotion is a novel, label-free, high throughput, in vitro assay and analysis pipeline which records and assesses the spontaneous beating of cardiomyocytes and identifies compounds which impact beating. This is achieved through the acquisition of brightfield images at a high framerate, combined with an optical flow-based python analysis pipeline which transforms the images into waveform data which are then parameterized. Validation of this assay with a large dataset showed that cardioactive compounds with diverse known direct functional and structural mechanisms-of-action on cardiomyocytes are identified (sensitivity = 72.9%), importantly, known structural cardiotoxins also disrupt cardiomyocyte beating (sensitivity = 86%) in this method. Furthermore, the CardioMotion method presents a high specificity of 82.5%.
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Affiliation(s)
- William Stebbeds
- Screening Profiling and Mechanistic Biology, GSK, Stevenage, SG1 2NY, UK
| | - Kavita Raniga
- Screening Profiling and Mechanistic Biology, GSK, Stevenage, SG1 2NY, UK
- The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - David Standing
- Screening Profiling and Mechanistic Biology, GSK, Stevenage, SG1 2NY, UK
| | - Iona Wallace
- Screening Profiling and Mechanistic Biology, GSK, Stevenage, SG1 2NY, UK
| | - James Bayliss
- Screening Profiling and Mechanistic Biology, GSK, Stevenage, SG1 2NY, UK
| | - Andrew Brown
- Screening Profiling and Mechanistic Biology, GSK, Stevenage, SG1 2NY, UK
| | - Richard Kasprowicz
- Screening Profiling and Mechanistic Biology, GSK, Stevenage, SG1 2NY, UK
| | | | - Julianna Deakyne
- In vitro in vivo translation, GSK, Upper Providence, PA 19426, USA
| | | | | | - Eric I Rossman
- In vitro in vivo translation, GSK, Upper Providence, PA 19426, USA
| | - Anthony Bahinski
- In vitro in vivo translation, GSK, Upper Providence, PA 19426, USA
| | - Jo Francis
- Screening Profiling and Mechanistic Biology, GSK, Stevenage, SG1 2NY, UK
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