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Sanches IH, Braga RC, Alves VM, Andrade CH. Enhancing hERG Risk Assessment with Interpretable Classificatory and Regression Models. Chem Res Toxicol 2024; 37:910-922. [PMID: 38781421 PMCID: PMC11187631 DOI: 10.1021/acs.chemrestox.3c00400] [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: 12/15/2023] [Revised: 04/22/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
The human Ether-à-go-go-Related Gene (hERG) is a transmembrane protein that regulates cardiac action potential, and its inhibition can induce a potentially deadly cardiac syndrome. In vitro tests help identify hERG blockers at early stages; however, the high cost motivates searching for alternative, cost-effective methods. The primary goal of this study was to enhance the Pred-hERG tool for predicting hERG blockage. To achieve this, we developed new QSAR models that incorporated additional data, updated existing classificatory and multiclassificatory models, and introduced new regression models. Notably, we integrated SHAP (SHapley Additive exPlanations) values to offer a visual interpretation of these models. Utilizing the latest data from ChEMBL v30, encompassing over 14,364 compounds with hERG data, our binary and multiclassification models outperformed both the previous iteration of Pred-hERG and all publicly available models. Notably, the new version of our tool introduces a regression model for predicting hERG activity (pIC50). The optimal model demonstrated an R2 of 0.61 and an RMSE of 0.48, surpassing the only available regression model in the literature. Pred-hERG 5.0 now offers users a swift, reliable, and user-friendly platform for the early assessment of chemically induced cardiotoxicity through hERG blockage. The tool provides versatile outcomes, including (i) classificatory predictions of hERG blockage with prediction reliability, (ii) multiclassificatory predictions of hERG blockage with reliability, (iii) regression predictions with estimated pIC50 values, and (iv) probability maps illustrating the contribution of chemical fragments for each prediction. Furthermore, we implemented explainable AI analysis (XAI) to visualize SHAP values, providing insights into the contribution of each feature to binary classification predictions. A consensus prediction calculated based on the predictions of the three developed models is also present to assist the user's decision-making process. Pred-hERG 5.0 has been designed to be user-friendly, making it accessible to users without computational or programming expertise. The tool is freely available at http://predherg.labmol.com.br.
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Affiliation(s)
- Igor H. Sanches
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, GO 74690-900, Brazil
- Center
for Excellence in Artificial Intelligence (CEIA), Institute of Informatics, Universidade Federal de Goiás, Goiânia, GO 74690-900, Brazil
- Center
for the Research and Advancement in Fragments and Molecular Targets
(CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto, SP 05508-220, Brazil
| | | | - Vinicius M. Alves
- University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Carolina Horta Andrade
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, GO 74690-900, Brazil
- Center
for Excellence in Artificial Intelligence (CEIA), Institute of Informatics, Universidade Federal de Goiás, Goiânia, GO 74690-900, Brazil
- Center
for the Research and Advancement in Fragments and Molecular Targets
(CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto, SP 05508-220, Brazil
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Santos TP, da Silva Bastos PE, da Silva JF, de Medeiros Vieira SM, da Silva MCG, de Andrade ALC, Padilha RMO, Dos Santos Magnabosco AR, Cadena MRS, Cadena PG. Single and joint toxic effects of thyroid hormone, levothyroxine, and amiodarone on embryo-larval stages of zebrafish (Danio rerio). ECOTOXICOLOGY (LONDON, ENGLAND) 2023; 32:525-535. [PMID: 37119427 DOI: 10.1007/s10646-023-02655-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/20/2023] [Indexed: 05/22/2023]
Abstract
This study evaluates single and joint endocrine disruptor toxicities of thyroid hormone, levothyroxine, and amiodarone in the embryo-larval stages of Danio rerio. Single toxicity experiments were carried out in concentrations based on the environmental concentration and increasing concentrations of 10, 100, and 1000 times the environmental concentration. Joint toxicity experiments evaluated the combined effects of these compounds. Toxic effects were examined during zebrafish embryonic development, and the parameters analyzed were apical sublethal, teratogenicity, mortality endpoints, and morphometry. Thyroid hormone exhibited the highest toxicity. However, the results showed that the environmental concentrations for all 3 compounds had low risk in relation to the parameters studied, such as teratogenic effects and morphometry. The larvae were more affected than embryos, where embryos needed higher concentrations in all experiments, possibly due to the absence of the chorion. The same type of effects were observed in the joint toxicity test, except that a possible antagonistic effect was detected. However, high concentrations showed stronger effects of these toxic compounds on fish development.
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Affiliation(s)
- Thamiris Pinheiro Santos
- Departamento de Morfologia e Fisiologia Animal (DMFA), Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros s/n Dois Irmãos, 52171-900, Recife, PE, Brazil
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, 50780-901, Recife, PE, Brazil
| | - Paulo Eduardo da Silva Bastos
- Departamento de Morfologia e Fisiologia Animal (DMFA), Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros s/n Dois Irmãos, 52171-900, Recife, PE, Brazil
| | - Jadson Freitas da Silva
- Departamento de Morfologia e Fisiologia Animal (DMFA), Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros s/n Dois Irmãos, 52171-900, Recife, PE, Brazil
| | - Stefânia Maria de Medeiros Vieira
- Departamento de Morfologia e Fisiologia Animal (DMFA), Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros s/n Dois Irmãos, 52171-900, Recife, PE, Brazil
| | - Marília Cordeiro Galvão da Silva
- Departamento de Morfologia e Fisiologia Animal (DMFA), Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros s/n Dois Irmãos, 52171-900, Recife, PE, Brazil
| | - André Lucas Corrêa de Andrade
- Departamento de Morfologia e Fisiologia Animal (DMFA), Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros s/n Dois Irmãos, 52171-900, Recife, PE, Brazil
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, 50780-901, Recife, PE, Brazil
| | - Renata Meireles Oliveira Padilha
- Departamento de Morfologia e Fisiologia Animal (DMFA), Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros s/n Dois Irmãos, 52171-900, Recife, PE, Brazil
| | - Amanda Rodrigues Dos Santos Magnabosco
- Departamento de Morfologia e Fisiologia Animal (DMFA), Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros s/n Dois Irmãos, 52171-900, Recife, PE, Brazil
| | - Marilia Ribeiro Sales Cadena
- Departamento de Biologia (DB), Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros s/n Dois Irmãos, 52171-900, Recife, PE, Brazil
| | - Pabyton Gonçalves Cadena
- Departamento de Morfologia e Fisiologia Animal (DMFA), Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros s/n Dois Irmãos, 52171-900, Recife, PE, Brazil.
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, 50780-901, Recife, PE, Brazil.
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Melnikov F, Anger LT, Hasselgren C. Toward Quantitative Models in Safety Assessment: A Case Study to Show Impact of Dose-Response Inference on hERG Inhibition Models. Int J Mol Sci 2022; 24:ijms24010635. [PMID: 36614078 PMCID: PMC9820331 DOI: 10.3390/ijms24010635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/31/2022] Open
Abstract
Due to challenges with historical data and the diversity of assay formats, in silico models for safety-related endpoints are often based on discretized data instead of the data on a natural continuous scale. Models for discretized endpoints have limitations in usage and interpretation that can impact compound design. Here, we present a consistent data inference approach, exemplified on two data sets of Ether-à-go-go-Related Gene (hERG) K+ inhibition data, for dose-response and screening experiments that are generally applicable for in vitro assays. hERG inhibition has been associated with severe cardiac effects and is one of the more prominent safety targets assessed in drug development, using a wide array of in vitro and in silico screening methods. In this study, the IC50 for hERG inhibition is estimated from diverse historical proprietary data. The IC50 derived from a two-point proprietary screening data set demonstrated high correlation (R = 0.98, MAE = 0.08) with IC50s derived from six-point dose-response curves. Similar IC50 estimation accuracy was obtained on a public thallium flux assay data set (R = 0.90, MAE = 0.2). The IC50 data were used to develop a robust quantitative model. The model's MAE (0.47) and R2 (0.46) were on par with literature statistics and approached assay reproducibility. Using a continuous model has high value for pharmaceutical projects, as it enables rank ordering of compounds and evaluation of compounds against project-specific inhibition thresholds. This data inference approach can be widely applicable to assays with quantitative readouts and has the potential to impact experimental design and improve model performance, interpretation, and acceptance across many standard safety endpoints.
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Ding W, Nan Y, Wu J, Han C, Xin X, Li S, Liu H, Zhang L. Combining multi-dimensional molecular fingerprints to predict the hERG cardiotoxicity of compounds. Comput Biol Med 2022; 144:105390. [DOI: 10.1016/j.compbiomed.2022.105390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 01/28/2023]
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Zhang Y, Xia Q, Wang J, Zhuang K, Jin H, Liu K. Progress in using zebrafish as a toxicological model for traditional Chinese medicine. JOURNAL OF ETHNOPHARMACOLOGY 2022; 282:114638. [PMID: 34530096 DOI: 10.1016/j.jep.2021.114638] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/25/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Traditional Chinese medicine (TCM) has been applied for more than 2000 years. However, modern basic research on the safety of TCMs is limited. Establishing safety evaluation technology in line with the characteristics of TCM and conducting large-scale basic toxicity research are keys to comprehensively understand the toxicity of TCMs. In recent years, zebrafish has been used as a model organism for toxicity assessment and is increasingly utilized for toxicity research of TCMs. Yet, a comprehensive review in using zebrafish as a toxicological model for TCMs is lacked. AIM OF THE STUDY We aim to summarize the progress and limitation in toxicity evaluation of TCMs using zebrafish and put forward the future research ideas. MATERIALS AND METHODS The scientific databases, including Springer, Science Direct, Wiley, Pubmed and China Knowledge Resource Integrated (CNKI) were searched using the key words of zebrafish, toxicology, traditional Chinese medicine, acute toxicity, liver injury, cardiotoxicity, kidney toxicity, developmental toxicity, neurotoxicity, gastrointestinal irritation, immunotoxicity, ototoxicity, and osteotoxicity. RESULTS Zebrafish assays are low experimental cost and short cycle, easily achieving high-throughput toxicity screening, and exemption from ethical legislation up to 5 dpf. It has been widely used to evaluate the acute toxicity, liver toxicity, cardiotoxicity, nephrotoxicity, developmental toxicity, neurotoxicity, gastrointestinal irritation, immunotoxicity, and ototoxicity caused by TCMs, although some physiological difference limited its application. CONCLUSIONS Zebrafish is a powerful model for TCMs toxicity evaluation, but it is not flawless. The toxicity testing criterion and high throughput assays are urgent to be established. This review provides references for future studies.
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Affiliation(s)
- Yun Zhang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China; Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong Province, Jinan, China
| | - Qing Xia
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China; Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong Province, Jinan, China
| | - Jiabo Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Kaiyan Zhuang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China; Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong Province, Jinan, China
| | - Hongtao Jin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Kechun Liu
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China; Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong Province, Jinan, China.
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Gosset A, Wiest L, Fildier A, Libert C, Giroud B, Hammada M, Hervé M, Sibeud E, Vulliet E, Polomé P, Perrodin Y. Ecotoxicological risk assessment of contaminants of emerging concern identified by "suspect screening" from urban wastewater treatment plant effluents at a territorial scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146275. [PMID: 33714835 DOI: 10.1016/j.scitotenv.2021.146275] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/28/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Urban wastewater treatment plants (WWTP) are a major vector of highly ecotoxic contaminants of emerging concern (CECs) for urban and sub-urban streams. Ecotoxicological risk assessments (ERAs) provide essential information to public environmental authorities. Nevertheless, ERAs are mainly performed at very local scale (one or few WWTPs) and on pre-selected list of CECs. To cope with these limits, the present study aims to develop a territorial-scale ERA on CECs previously identified by a "suspect screening" analytical approach (LC-QToF-MS) and quantified in the effluents of 10 WWTPs of a highly urbanized territory during three periods of the year. Among CECs, this work focused on pharmaceutical residue and pesticides. ERA was conducted following two complementary methods: (1) a single substance approach, based on the calculation for each CEC of risk quotients (RQs) by the ratio of Predicted Environmental Concentration (PEC) and Predicted No Effect Concentration (PNEC), and (2) mixture risk assessment ("cocktail effect") based on a concentration addition model (CA), summing individual RQs. Chemical results led to an ERA for 41 CEC (37 pharmaceuticals and 4 pesticides) detected in treated effluents. Single substance ERA identified 19 CECs implicated in at least one significant risk for streams, with significant risks for DEET, diclofenac, lidocaine, atenolol, terbutryn, atorvastatin, methocarbamol, and venlafaxine (RQs reaching 39.84, 62.10, 125.58, 179.11, 348.24, 509.27, 1509.71 and 3097.37, respectively). Mixture ERA allowed the identification of a risk (RQmix > 1) for 9 of the 10 WWTPs studied. It was also remarked that CECs leading individually to a negligible risk could imply a significant risk in a mixture. Finally, the territorial ERA showed a diversity of risk situations, with the highest concerns for 3 WWTPs: the 2 biggest of the territory discharging into a large French river, the Rhône, and for the smallest WWTP that releases into a small intermittent stream.
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Affiliation(s)
- Antoine Gosset
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, F-69518 Vaulx-en-Velin, France; Université de Lyon & Université Lyon 2, Lyon, F-69007, CNRS, UMR 5824 GATE Lyon Saint-Etienne, Ecully F-69130, France; Ecole Urbaine de Lyon, Institut Convergences, Commissariat général aux investissements d'avenir, Bât. Atrium, 43 Boulevard du 11 Novembre 1918, F-69616 Villeurbanne, France.
| | - Laure Wiest
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Aurélie Fildier
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Christine Libert
- Grand Lyon Urban Community, Water and Urban Planning Department, 69003 Lyon, 9, France
| | - Barbara Giroud
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Myriam Hammada
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, F-69518 Vaulx-en-Velin, France
| | - Matthieu Hervé
- Grand Lyon Urban Community, Water and Urban Planning Department, 69003 Lyon, 9, France
| | - Elisabeth Sibeud
- Grand Lyon Urban Community, Water and Urban Planning Department, 69003 Lyon, 9, France
| | - Emmanuelle Vulliet
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Philippe Polomé
- Université de Lyon & Université Lyon 2, Lyon, F-69007, CNRS, UMR 5824 GATE Lyon Saint-Etienne, Ecully F-69130, France
| | - Yves Perrodin
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, F-69518 Vaulx-en-Velin, France
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Lane S, More LA, Asnani A. Zebrafish Models of Cancer Therapy-Induced Cardiovascular Toxicity. J Cardiovasc Dev Dis 2021; 8:jcdd8020008. [PMID: 33499052 PMCID: PMC7911266 DOI: 10.3390/jcdd8020008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
Purpose of review: Both traditional and novel cancer therapies can cause cardiovascular toxicity in patients. In vivo models integrating both cardiovascular and cancer phenotypes allow for the study of on- and off-target mechanisms of toxicity arising from these agents. The zebrafish is the optimal whole organism model to screen for cardiotoxicity in a high throughput manner, while simultaneously assessing the role of cardiotoxicity pathways on the cancer therapy’s antitumor effect. Here we highlight established zebrafish models of human cardiovascular disease and cancer, the unique advantages of zebrafish to study mechanisms of cancer therapy-associated cardiovascular toxicity, and finally, important limitations to consider when using the zebrafish to study toxicity. Recent findings: Cancer therapy-associated cardiovascular toxicities range from cardiomyopathy with traditional agents to arrhythmias and thrombotic complications associated with newer targeted therapies. The zebrafish can be used to identify novel therapeutic strategies that selectively protect the heart from cancer therapy without affecting antitumor activity. Advances in genome editing technology have enabled the creation of several transgenic zebrafish lines valuable to the study of cardiovascular and cancer pathophysiology. Summary: The high degree of genetic conservation between zebrafish and humans, as well as the ability to recapitulate cardiotoxic phenotypes observed in patients with cancer, make the zebrafish an effective model to study cancer therapy-associated cardiovascular toxicity. Though this model provides several key benefits over existing in vitro and in vivo models, limitations of the zebrafish model include the early developmental stage required for most high-throughput applications.
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Affiliation(s)
- Sarah Lane
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; (S.L.); (L.A.M.)
| | - Luis Alberto More
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; (S.L.); (L.A.M.)
| | - Aarti Asnani
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; (S.L.); (L.A.M.)
- Harvard Medical School, Boston, MA 02115, USA
- Correspondence:
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Miyawaki I. Application of zebrafish to safety evaluation in drug discovery. J Toxicol Pathol 2020; 33:197-210. [PMID: 33239838 PMCID: PMC7677624 DOI: 10.1293/tox.2020-0021] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
Traditionally, safety evaluation at the early stage of drug discovery research has been done using in silico, in vitro, and in vivo systems in this order because of limitations on the amount of compounds available and the throughput ability of the assay systems. While these in vitro assays are very effective tools for detecting particular tissue-specific toxicity phenotypes, it is difficult to detect toxicity based on complex mechanisms involving multiple organs and tissues. Therefore, the development of novel high throughput in vivo evaluation systems has been expected for a long time. The zebrafish (Danio rerio) is a vertebrate with many attractive characteristics for use in drug discovery, such as a small size, transparency, gene and protein similarity with mammals (80% or more), and ease of genetic modification to establish human disease models. Actually, in recent years, the zebrafish has attracted interest as a novel experimental animal. In this article, the author summarized the features of zebrafish that make it a suitable laboratory animal, and introduced and discussed the applications of zebrafish to preclinical toxicity testing, including evaluations of teratogenicity, hepatotoxicity, and nephrotoxicity based on morphological findings, evaluation of cardiotoxicity using functional endpoints, and assessment of seizure and drug abuse liability.
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Affiliation(s)
- Izuru Miyawaki
- Preclinical Research Laboratories, Sumitomo Dainippon Pharma
Co., Ltd., 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-0022, Japan
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Ietswaart R, Arat S, Chen AX, Farahmand S, Kim B, DuMouchel W, Armstrong D, Fekete A, Sutherland JJ, Urban L. Machine learning guided association of adverse drug reactions with in vitro target-based pharmacology. EBioMedicine 2020; 57:102837. [PMID: 32565027 PMCID: PMC7379147 DOI: 10.1016/j.ebiom.2020.102837] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/08/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Adverse drug reactions (ADRs) are one of the leading causes of morbidity and mortality in health care. Understanding which drug targets are linked to ADRs can lead to the development of safer medicines. METHODS Here, we analyse in vitro secondary pharmacology of common (off) targets for 2134 marketed drugs. To associate these drugs with human ADRs, we utilized FDA Adverse Event Reports and developed random forest models that predict ADR occurrences from in vitro pharmacological profiles. FINDINGS By evaluating Gini importance scores of model features, we identify 221 target-ADR associations, which co-occur in PubMed abstracts to a greater extent than expected by chance. Amongst these are established relations, such as the association of in vitro hERG binding with cardiac arrhythmias, which further validate our machine learning approach. Evidence on bile acid metabolism supports our identification of associations between the Bile Salt Export Pump and renal, thyroid, lipid metabolism, respiratory tract and central nervous system disorders. Unexpectedly, our model suggests PDE3 is associated with 40 ADRs. INTERPRETATION These associations provide a comprehensive resource to support drug development and human biology studies. FUNDING This study was not supported by any formal funding bodies.
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Affiliation(s)
- Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States.
| | - Seda Arat
- The Jackson Laboratory, Farmington, CT 06032, United States.
| | - Amanda X Chen
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, United States; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Saman Farahmand
- Computational Sciences PhD program, University of Massachusetts Boston, Boston, MA 02125, United States
| | - Bumjun Kim
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, United States
| | | | - Duncan Armstrong
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, United States
| | - Alexander Fekete
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, United States
| | - Jeffrey J Sutherland
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, United States.
| | - Laszlo Urban
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, United States.
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Liu H, Chen X, Zhao X, Zhao B, Qian K, Shi Y, Baruscotti M, Wang Y. Screening and Identification of Cardioprotective Compounds From Wenxin Keli by Activity Index Approach and in vivo Zebrafish Model. Front Pharmacol 2018; 9:1288. [PMID: 30483130 PMCID: PMC6243390 DOI: 10.3389/fphar.2018.01288] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/22/2018] [Indexed: 12/12/2022] Open
Abstract
Wenxin Keli (WXKL) is a widely used Chinese botanical drug for the treatment of arrhythmia, which is consisted of four herbs and amber. In the present study, we analyzed the chemical composition of WXKL using liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) to tentatively identify 71 compounds. Through typical separate procession, the total extract of WXKL was divided into fractions for further bioassays. Cardiomyocytes and zebrafish larvae were applied for assessment. In vivo arrhythmia model in Cmlc2-GFP transgenic zebrafish was induced by terfenadine, which exhibited obvious reduction of heart rate and occurrence of atrioventricular block. Dynamic beating of heart was recorded by fluorescent microscope and sensitive camera to automatically recognize the rhythm of heartbeat in zebrafish larvae. By integrating the chemical information of WXKL and corresponding bioactivities of these fractions, activity index (AI) of each identified compound was calculated to screen potential active compounds. The results showed that dozens of compounds including ginsenoside Rg1, ginsenoside Re, notoginsenoside R1, lobetyolin, and lobetyolinin were contributed to cardioprotective effects of WXKL. The anti-arrhythmic activities of five compounds were further validated in larvae model and mature zebrafish by measuring electrocardiogram (ECG). Our findings provide a successful example for rapid discovery of bioactive compounds from traditional Chinese medicine (TCM) by activity index based approach coupled with in vivo zebrafish model.
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Affiliation(s)
- Hao Liu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xuechun Chen
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoping Zhao
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Buchang Zhao
- Shandong Danhong Pharmaceutical Co., Ltd., Heze, China
| | - Ke Qian
- Shandong Danhong Pharmaceutical Co., Ltd., Heze, China
| | - Yang Shi
- Shandong Danhong Pharmaceutical Co., Ltd., Heze, China
| | - Mirko Baruscotti
- Department of Bioscienze, The PaceLab, University of Milano, Milan, Italy
| | - Yi Wang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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11
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Siramshetty VB, Chen Q, Devarakonda P, Preissner R. The Catch-22 of Predicting hERG Blockade Using Publicly Accessible Bioactivity Data. J Chem Inf Model 2018; 58:1224-1233. [PMID: 29772901 DOI: 10.1021/acs.jcim.8b00150] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Drug-induced inhibition of the human ether-à-go-go-related gene (hERG)-encoded potassium ion channels can lead to fatal cardiotoxicity. Several marketed drugs and promising drug candidates were recalled because of this concern. Diverse modeling methods ranging from molecular similarity assessment to quantitative structure-activity relationship analysis employing machine learning techniques have been applied to data sets of varying size and composition (number of blockers and nonblockers). In this study, we highlight the challenges involved in the development of a robust classifier for predicting the hERG end point using bioactivity data extracted from the public domain. To this end, three different modeling methods, nearest neighbors, random forests, and support vector machines, were employed to develop predictive models using different molecular descriptors, activity thresholds, and training set compositions. Our models demonstrated superior performance in external validations in comparison with those reported in the previous studies from which the data sets were extracted. The choice of descriptors had little influence on the model performance, with minor exceptions. The criteria used to filter bioactivity data, the activity threshold settings used to separate blockers from nonblockers, and the structural diversity of blockers in training data set were found to be the crucial indicators of model performance. Training sets based on a binary threshold of 1 μM/10 μM to separate blockers (IC50/ Ki ≤ 1 μM) from nonblockers (IC50/ Ki > 10 μM) provided superior performance in comparison with those defined using a single threshold (1 μM or 10 μM). A major limitation in using the public domain hERG activity data is the abundance of blockers in comparison with nonblockers at usual activity thresholds, since not many studies report the latter.
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Affiliation(s)
- Vishal B Siramshetty
- Structural Bioinformatics Group , Charité - University Medicine Berlin , 10115 Berlin , Germany.,BB3R - Berlin Brandenburg 3R Graduate School , Freie Universität Berlin , 14195 Berlin , Germany
| | - Qiaofeng Chen
- Structural Bioinformatics Group , Charité - University Medicine Berlin , 10115 Berlin , Germany.,China Scholarship Council (CSC) , Beijing 100044 , China
| | - Prashanth Devarakonda
- Structural Bioinformatics Group , Charité - University Medicine Berlin , 10115 Berlin , Germany
| | - Robert Preissner
- Structural Bioinformatics Group , Charité - University Medicine Berlin , 10115 Berlin , Germany.,BB3R - Berlin Brandenburg 3R Graduate School , Freie Universität Berlin , 14195 Berlin , Germany
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12
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Enzalutamide inhibits testosterone-induced growth of human prostate cancer xenografts in zebrafish and can induce bradycardia. Sci Rep 2017; 7:14698. [PMID: 29089623 PMCID: PMC5665934 DOI: 10.1038/s41598-017-14413-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 10/11/2017] [Indexed: 12/20/2022] Open
Abstract
The zebrafish has become a popular human tumour xenograft model, particularly for solid tumours including prostate cancer (PCa). To date PCa xenotransplantation studies in zebrafish have not been performed in the presence of testosterone, even when employing androgen-dependent cell models, such as the LNCaP cell line. Thus, with the goal of more faithfully modelling the hormonal milieu in which PCa develops in humans, we sought to determine the effects of exogenous testosterone on the growth of LNCaP, or androgen-independent C4-2 cells xenografted into zebrafish embryos. Testosterone significantly increased engrafted LNCaP proliferation compared to control xenografts, which could be inhibited by co-administration of the anti-androgen receptor drug, enzalutamide. By contrast, C4-2 cell growth was not affected by either testosterone or enzalutamide. Enzalutamide also induced bradycardia and death in zebrafish embryos in a dose-dependent manner and strongly synergized with the potassium-channel blocking agent, terfenadine, known to induce long QT syndrome and cardiac arrhythmia. Together, these data not only indicate that testosterone administration should be considered in all PCa xenograft studies in zebrafish but also highlights the unique opportunity of this preclinical platform to simultaneously evaluate efficacy and toxicity of novel therapies and/or protective agents towards developing safer and more effective PCa treatments.
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13
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Gut P, Reischauer S, Stainier DYR, Arnaout R. LITTLE FISH, BIG DATA: ZEBRAFISH AS A MODEL FOR CARDIOVASCULAR AND METABOLIC DISEASE. Physiol Rev 2017; 97:889-938. [PMID: 28468832 PMCID: PMC5817164 DOI: 10.1152/physrev.00038.2016] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 12/17/2022] Open
Abstract
The burden of cardiovascular and metabolic diseases worldwide is staggering. The emergence of systems approaches in biology promises new therapies, faster and cheaper diagnostics, and personalized medicine. However, a profound understanding of pathogenic mechanisms at the cellular and molecular levels remains a fundamental requirement for discovery and therapeutics. Animal models of human disease are cornerstones of drug discovery as they allow identification of novel pharmacological targets by linking gene function with pathogenesis. The zebrafish model has been used for decades to study development and pathophysiology. More than ever, the specific strengths of the zebrafish model make it a prime partner in an age of discovery transformed by big-data approaches to genomics and disease. Zebrafish share a largely conserved physiology and anatomy with mammals. They allow a wide range of genetic manipulations, including the latest genome engineering approaches. They can be bred and studied with remarkable speed, enabling a range of large-scale phenotypic screens. Finally, zebrafish demonstrate an impressive regenerative capacity scientists hope to unlock in humans. Here, we provide a comprehensive guide on applications of zebrafish to investigate cardiovascular and metabolic diseases. We delineate advantages and limitations of zebrafish models of human disease and summarize their most significant contributions to understanding disease progression to date.
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Affiliation(s)
- Philipp Gut
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Sven Reischauer
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Didier Y R Stainier
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Rima Arnaout
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
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14
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Abstract
In the last 30 years, the zebrafish has become a widely used model organism for research on vertebrate development and disease. Through a powerful combination of genetics and experimental embryology, significant inroads have been made into the regulation of embryonic axis formation, organogenesis, and the development of neural networks. Research with this model has also expanded into other areas, including the genetic regulation of aging, regeneration, and animal behavior. Zebrafish are a popular model because of the ease with which they can be maintained, their small size and low cost, the ability to obtain hundreds of embryos on a daily basis, and the accessibility, translucency, and rapidity of early developmental stages. This primer describes the swift progress of genetic approaches in zebrafish and highlights recent advances that have led to new insights into vertebrate biology.
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15
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Cornet C, Calzolari S, Miñana-Prieto R, Dyballa S, van Doornmalen E, Rutjes H, Savy T, D'Amico D, Terriente J. ZeGlobalTox: An Innovative Approach to Address Organ Drug Toxicity Using Zebrafish. Int J Mol Sci 2017; 18:E864. [PMID: 28422076 PMCID: PMC5412445 DOI: 10.3390/ijms18040864] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/07/2017] [Accepted: 04/14/2017] [Indexed: 02/06/2023] Open
Abstract
Toxicity is one of the major attrition causes during the drug development process. In that line, cardio-, neuro-, and hepatotoxicities are among the main reasons behind the retirement of drugs in clinical phases and post market withdrawal. Zebrafish exploitation in high-throughput drug screening is becoming an important tool to assess the toxicity and efficacy of novel drugs. This animal model has, from early developmental stages, fully functional organs from a physiological point of view. Thus, drug-induced organ-toxicity can be detected in larval stages, allowing a high predictive power on possible human drug-induced liabilities. Hence, zebrafish can bridge the gap between preclinical in vitro safety assays and rodent models in a fast and cost-effective manner. ZeGlobalTox is an innovative assay that sequentially integrates in vivo cardio-, neuro-, and hepatotoxicity assessment in the same animal, thus impacting strongly in the 3Rs principles. It Reduces, by up to a third, the number of animals required to assess toxicity in those organs. It Refines the drug toxicity evaluation through novel physiological parameters. Finally, it might allow the Replacement of classical species, such as rodents and larger mammals, thanks to its high predictivity (Specificity: 89%, Sensitivity: 68% and Accuracy: 78%).
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Affiliation(s)
- Carles Cornet
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), 08003 Barcelona, Spain.
| | - Simone Calzolari
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), 08003 Barcelona, Spain.
| | - Rafael Miñana-Prieto
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), 08003 Barcelona, Spain.
| | - Sylvia Dyballa
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), 08003 Barcelona, Spain.
| | - Els van Doornmalen
- Pivot Park Screening Centre (PPSC), Kloosterstraat 9, 5349AB OSS, The Netherland.
| | - Helma Rutjes
- Pivot Park Screening Centre (PPSC), Kloosterstraat 9, 5349AB OSS, The Netherland.
| | - Thierry Savy
- Multilevel Dynamics in Morphogenesis Unit, USR3695 CNRS, 91190 Gif sur Yvette, France.
| | - Davide D'Amico
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), 08003 Barcelona, Spain.
| | - Javier Terriente
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), 08003 Barcelona, Spain.
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16
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Planchart A, Mattingly CJ, Allen D, Ceger P, Casey W, Hinton D, Kanungo J, Kullman SW, Tal T, Bondesson M, Burgess SM, Sullivan C, Kim C, Behl M, Padilla S, Reif DM, Tanguay RL, Hamm J. Advancing toxicology research using in vivo high throughput toxicology with small fish models. ALTEX 2016; 33:435-452. [PMID: 27328013 PMCID: PMC5270630 DOI: 10.14573/altex.1601281] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/31/2016] [Indexed: 12/18/2022]
Abstract
Small freshwater fish models, especially zebrafish, offer advantages over traditional rodent models, including low maintenance and husbandry costs, high fecundity, genetic diversity, physiology similar to that of traditional biomedical models, and reduced animal welfare concerns. The Collaborative Workshop on Aquatic Models and 21st Century Toxicology was held at North Carolina State University on May 5-6, 2014, in Raleigh, North Carolina, USA. Participants discussed the ways in which small fish are being used as models to screen toxicants and understand mechanisms of toxicity. Workshop participants agreed that the lack of standardized protocols is an impediment to broader acceptance of these models, whereas development of standardized protocols, validation, and subsequent regulatory acceptance would facilitate greater usage. Given the advantages and increasing application of small fish models, there was widespread interest in follow-up workshops to review and discuss developments in their use. In this article, we summarize the recommendations formulated by workshop participants to enhance the utility of small fish species in toxicology studies, as well as many of the advances in the field of toxicology that resulted from using small fish species, including advances in developmental toxicology, cardiovascular toxicology, neurotoxicology, and immunotoxicology. We alsoreview many emerging issues that will benefit from using small fish species, especially zebrafish, and new technologies that will enable using these organisms to yield results unprecedented in their information content to better understand how toxicants affect development and health.
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Affiliation(s)
- Antonio Planchart
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Carolyn J. Mattingly
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - David Allen
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
| | - Patricia Ceger
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
| | - Warren Casey
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - David Hinton
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Jyotshna Kanungo
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Seth W. Kullman
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Tamara Tal
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Maria Bondesson
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX, USA
| | | | - Con Sullivan
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA
| | - Carol Kim
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA
| | - Mamta Behl
- Division of National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Stephanie Padilla
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - David M. Reif
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Robert L. Tanguay
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Jon Hamm
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
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17
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Braga RC, Alves VM, Silva MFB, Muratov E, Fourches D, Lião LM, Tropsha A, Andrade CH. Pred-hERG: A Novel web-Accessible Computational Tool for Predicting Cardiac Toxicity. Mol Inform 2015; 34:698-701. [PMID: 27490970 DOI: 10.1002/minf.201500040] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 05/10/2015] [Indexed: 01/17/2023]
Abstract
The blockage of the hERG K(+) channels is closely associated with lethal cardiac arrhythmia. The notorious ligand promiscuity of this channel earmarked hERG as one of the most important antitargets to be considered in early stages of drug development process. Herein we report on the development of an innovative and freely accessible web server for early identification of putative hERG blockers and non-blockers in chemical libraries. We have collected the largest publicly available curated hERG dataset of 5,984 compounds. We succeed in developing robust and externally predictive binary (CCR≈0.8) and multiclass models (accuracy≈0.7). These models are available as a web-service freely available for public at http://labmol.farmacia.ufg.br/predherg/. Three following outcomes are available for the users: prediction by binary model, prediction by multi-class model, and the probability maps of atomic contribution. The Pred-hERG will be continuously updated and upgraded as new information became available.
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Affiliation(s)
- Rodolpho C Braga
- Labmol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, Goiás 74605-170, Brazil phone: +55 62 3209-6451; fax: +55 62 3209-6037.,Chemistry Institute, Federal University of Goias, P. O. Box 131, Goiania, Goiás 74001-970, Brazil
| | - Vinicius M Alves
- Labmol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, Goiás 74605-170, Brazil phone: +55 62 3209-6451; fax: +55 62 3209-6037
| | - Meryck F B Silva
- Labmol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, Goiás 74605-170, Brazil phone: +55 62 3209-6451; fax: +55 62 3209-6037
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Denis Fourches
- Department of Chemistry, Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Luciano M Lião
- Chemistry Institute, Federal University of Goias, P. O. Box 131, Goiania, Goiás 74001-970, Brazil
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Carolina H Andrade
- Labmol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, Goiás 74605-170, Brazil phone: +55 62 3209-6451; fax: +55 62 3209-6037.
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18
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Nguyen M, Stewart AM, Kalueff AV. Aquatic blues: modeling depression and antidepressant action in zebrafish. Prog Neuropsychopharmacol Biol Psychiatry 2014; 55:26-39. [PMID: 24657522 DOI: 10.1016/j.pnpbp.2014.03.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 03/03/2014] [Accepted: 03/09/2014] [Indexed: 12/20/2022]
Abstract
Depression is a serious psychiatric condition affecting millions of patients worldwide. Unipolar depression is characterized by low mood, anhedonia, social withdrawal and other severely debilitating psychiatric symptoms. Bipolar disorder manifests in alternating depressed mood and 'hyperactive' manic/hypomanic states. Animal experimental models are an invaluable tool for research into the pathogenesis of bipolar/unipolar depression, and for the development of potential treatments. Due to their high throughput value, genetic tractability, low cost and quick reproductive cycle, zebrafish (Danio rerio) have emerged as a promising new model species for studying brain disorders. Here, we discuss the developing utility of zebrafish for studying depression disorders, and outline future areas of research in this field. We argue that zebrafish represent a useful model organism for studying depression and its behavioral, genetic and physiological mechanisms, as well as for anti-depressant drug discovery.
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Affiliation(s)
- Michael Nguyen
- Department of Biomedical Engineering, University of Virginia, 415 Lane Road, Charlottesville, VA 22908, USA; ZENEREI Institute, 309 Palmer Court, Slidell, LA 70458, USA
| | - Adam Michael Stewart
- ZENEREI Institute, 309 Palmer Court, Slidell, LA 70458, USA; International Zebrafish Neuroscience Research Consortium (ZNRC), 309 Palmer Court, Slidell, LA 70458, USA; Department of Neuroscience, University of Pittsburgh, A210 Langley Hall, Pittsburgh, PA 15260, USA.
| | - Allan V Kalueff
- ZENEREI Institute, 309 Palmer Court, Slidell, LA 70458, USA; International Zebrafish Neuroscience Research Consortium (ZNRC), 309 Palmer Court, Slidell, LA 70458, USA
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19
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Developing zebrafish models relevant to PTSD and other trauma- and stressor-related disorders. Prog Neuropsychopharmacol Biol Psychiatry 2014; 55:67-79. [PMID: 25138994 DOI: 10.1016/j.pnpbp.2014.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/01/2014] [Accepted: 08/07/2014] [Indexed: 11/20/2022]
Abstract
While post-traumatic stress disorder (PTSD) and other trauma- and stress-related disorders (TSRDs) represent a serious societal and public health concern, their pathogenesis is largely unknown. Given the clinical complexity of TSRD development and susceptibility, greater investigation into candidate biomarkers and specific genetic pathways implicated in both risk and resilience to trauma becomes critical. In line with this, numerous animal models have been extensively used to better understand the pathogenic mechanisms of PTSD and related TSRD. Here, we discuss the rapidly increasing potential of zebrafish as models of these disorders, and how their use may aid researchers in uncovering novel treatments and therapies in this field.
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20
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De Luca E, Zaccaria GM, Hadhoud M, Rizzo G, Ponzini R, Morbiducci U, Santoro MM. ZebraBeat: a flexible platform for the analysis of the cardiac rate in zebrafish embryos. Sci Rep 2014. [PMCID: PMC4790192 DOI: 10.1038/srep04898] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Heartbeat measurement is important in assesssing cardiac function because variations in heart rhythm can be the cause as well as an effect of hidden pathological heart conditions. Zebrafish (Danio rerio) has emerged as one of the most useful model organisms for cardiac research. Indeed, the zebrafish heart is easily accessible for optical analyses without conducting invasive procedures and shows anatomical similarity to the human heart. In this study, we present a non-invasive, simple, cost-effective process to quantify the heartbeat in embryonic zebrafish. To achieve reproducibility, high throughput and flexibility (i.e., adaptability to any existing confocal microscope system and with a user-friendly interface that can be easily used by researchers), we implemented this method within a software program. We show here that this platform, called ZebraBeat, can successfully detect heart rate variations in embryonic zebrafish at various developmental stages, and it can record cardiac rate fluctuations induced by factors such as temperature and genetic- and chemical-induced alterations. Applications of this methodology may include the screening of chemical libraries affecting heart rhythm and the identification of heart rhythm variations in mutants from large-scale forward genetic screens.
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21
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Yozzo KL, Isales GM, Raftery TD, Volz DC. High-content screening assay for identification of chemicals impacting cardiovascular function in zebrafish embryos. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:11302-11310. [PMID: 24015875 DOI: 10.1021/es403360y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Targeted assays are needed to better evaluate effects of chemicals on organogenesis and begin classification of chemicals by toxicologically relevant modes-of-action. Using transgenic zebrafish (fli1:egfp) that stably express eGFP within vascular endothelial cells, we have developed and optimized a 384-well-based high-content screening (HCS) assay that enables us to screen and identify chemicals affecting cardiovascular function at sublethal, nonteratogenic concentrations. Following static exposure of one embryo per well from 5 to 72 h postfertilization (hpf), automated image acquisition procedures and custom image analysis protocols are used to quantify body length, circulation, heart rate, pericardial area (a biomarker for cardiac looping defects), and intersegmental vessel area within freshly hatched live embryos. After optimizing 72 hpf anesthetization procedures, we evaluated each end point across four independent control plates containing 384 initial embryos per plate. Survival and imaging success rates across these plates ranged from 93 to 99% and 42 to 74%, respectively. Criteria were then defined for assay success and analysis of treatments, and 10 chemicals were screened for targeted effects on cardiovascular function. Compared to existing zebrafish-based assays, this method provides a comprehensive discovery platform with (1) increased sample sizes; (2) broad concentration-response format; and (3) the ability to identify chemicals that target cardiovascular function at nonteratogenic concentrations.
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Affiliation(s)
- Krystle L Yozzo
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina , Columbia, South Carolina 29208, United States
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22
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Ducharme NA, Peterson LE, Benfenati E, Reif D, McCollum CW, Gustafsson JÅ, Bondesson M. Meta-analysis of toxicity and teratogenicity of 133 chemicals from zebrafish developmental toxicity studies. Reprod Toxicol 2013; 41:98-108. [PMID: 23796950 DOI: 10.1016/j.reprotox.2013.06.070] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 06/04/2013] [Accepted: 06/06/2013] [Indexed: 11/18/2022]
Abstract
Zebrafish developmental toxicity testing is an emerging field, which faces considerable challenges regarding data meta-analysis and the establishment of standardized test protocols. Here, we present an initial correlation study on toxicity of 133 chemicals based on data in the literature to ascertain predictive developmental toxicity endpoints. We found that the physical properties of chemicals (BCF or logP) did not fully predict lethality or developmental outcomes. Instead, individual outcomes such as pericardial edema and yolk sac edema were more reliable indicators of developmental toxicity. In addition, we ranked the chemicals based on toxicity with the Toxicological Priority Index (ToxPi) program and via a teratogenic ratio, and found that perfluorooctane sulfonate (PFOS) had the highest ToxPi score, triphenyltin acetate had the highest average ToxPi score (corrected for missing data and having more than 4 outcomes), and N-methyl-dithiocarbamate had the highest teratogenic ratio.
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Affiliation(s)
- Nicole A Ducharme
- University of Houston, Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, Houston, TX 77204, USA
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