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Naveed M, Azeem A, Aziz T, Javed K, Ali I, Ali Khan A, Alasmari AF, Albekairi TH. Evaluating the MDCK cell permeability of greenly synthesize bimetallic Ag/Zn Nanoparticles using leaf extract of Vallaris solanacea as a potential antipesticide-resistant agent. Z NATURFORSCH C 2024; 0:znc-2024-0065. [PMID: 38898802 DOI: 10.1515/znc-2024-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
Bimetallic nanoparticles, particularly Ag/Zn bimetallic nanoparticles, have gained increasing attention due to their unique properties, making them suitable for a variety of applications such as catalysis, water treatment, and environmental remediation. This study aimed to elucidate the use of bimetallic nanoparticles of Ag/Zn as an alternative to resistant pesticides for pest control. Furthermore, this research demonstrates that BNPs can target specific pollutants and degrade them through various mechanisms. BNP docking with the Nilaparvata lugens cytochrome P450 (CYP6ER1) protein exhibited the lowest binding energy of -7.5 kcal/mol. The cell permeability analysis of BNP in plant cells reveals that the BNP has 0 % permeability towards any cell at -10 kcal/mol energy, which is the lowest free energy translocation pathway. The harmful leftover residues of the pesticides have a higher chance of degradability in case of interaction with BNP validated by chemical-chemical interaction analysis. Additionally, MDCK permeability coefficient of small molecules based on the regression model was calculated for BNP which authenticated the efficiency of BNP. Moreover, Swiss ADMET simulated absorption using a boiled egg model with no blood-brain barrier and gastrointestinal crossing for the expected BNP molecule has been observed. Significantly, the findings indicate that employing bimetallic nanoparticles like Ag/Zn is a crucial strategy for bioremediation because they proficiently decompose pesticides while posing no risk to humans. Our results will facilitate the design of novel BNPs materials for environmental remediation and pest control ensuring human health safety that are predicated on bimetallic nanoparticles.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, 66901 Faculty of Science and Technology, University of Central Punjab , Lahore, 54590, Pakistan
| | - Arooj Azeem
- Department of Biotechnology, 66901 Faculty of Science and Technology, University of Central Punjab , Lahore, 54590, Pakistan
| | - Tariq Aziz
- 37796 Laboratory of Animal Health Food Hygiene and Quality University of Ioannina , Arta, 47132, Greece
| | - Khushbakht Javed
- Department of Biotechnology, 66901 Faculty of Science and Technology, University of Central Punjab , Lahore, 54590, Pakistan
| | - Imran Ali
- Department of Biotechnology, 66901 Faculty of Science and Technology, University of Central Punjab , Lahore, 54590, Pakistan
| | - Ayaz Ali Khan
- Department of Biotechnology, 66714 University of Malakand , Chakdara, 18800, Pakistan
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, 37850 College of Pharmacy, King Saud University , P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Thamer H Albekairi
- Department of Pharmacology and Toxicology, 37850 College of Pharmacy, King Saud University , P.O. Box 2455, Riyadh, 11451, Saudi Arabia
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Seo M, Choi J, Park J, Yu WJ, Kim S. Computational modeling approaches for developing a synergistic effect prediction model of estrogen agonistic activity. CHEMOSPHERE 2024; 349:140926. [PMID: 38092168 DOI: 10.1016/j.chemosphere.2023.140926] [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: 09/27/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
The concerns regarding the potential health threats caused by estrogenic endocrine-disrupting chemicals (EDCs) and their mixtures manufactured by the chemical industry are increasing worldwide. Conventional experimental tests for understanding the estrogenic activity of mixtures are expensive and time-consuming. Although non-testing methods using computational modeling approaches have been developed to reduce the number of traditional tests, they are unsuitable for predicting synergistic effects because current prediction models consider only a single chemical. Thus, the development of predictive models is essential for predicting the mixture toxicity, including chemical interactions. However, selecting suitable computational modeling approaches to develop a high-performance prediction model requires considerable time and effort. In this study, we provide a suitable computational approach to develop a predictive model for the synergistic effects of estrogenic activity. We collected datasets on mixture toxicity based on the synergistic effect of estrogen agonistic activity in binary mixtures. Using the model deviation ratio approach, we classified the labels of the binary mixtures as synergistic or non-synergistic effects. We assessed five molecular descriptors, four machine learning-based algorithms, and a deep learning-based algorithm to provide a suitable computational modeling approach. Compared with other modeling approaches, the prediction model using the deep learning-based algorithm and chemical-protein network descriptors exhibited the best performance in predicting the synergistic effects. In conclusion, we developed a new high-performance binary classification model using a deep neural network and chemical-protein network-based descriptors. The developed model will be helpful for the preliminary screening of the synergistic effects of binary mixtures during the development process of chemical products.
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Affiliation(s)
- Myungwon Seo
- Chemical Analysis Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea.
| | - Jiwon Choi
- Chemical Analysis Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea.
| | - Jongseo Park
- Chemical Analysis Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea.
| | - Wook-Joon Yu
- Developmental and Reproductive Toxicology Research Group, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea.
| | - Sunmi Kim
- Chemical Analysis Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea.
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3
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Lakshmi SG, Kamaraj M, Nithya TG, Chidambaranathan N, Pushpalatha GGL, Santhosh P, Balavaishnavi B, Mahajan M. Network pharmacology integrated with molecular docking reveals the anticancer mechanism of Jasminum sambac Linn. essential oil against human breast cancer and experimental validation by in vitro and in vivo studies. Appl Biochem Biotechnol 2024; 196:350-381. [PMID: 37129744 DOI: 10.1007/s12010-023-04481-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Jasminum sambac L. (J. sambac) belongs to the family Oleaceae and it is an ornamental subtropical evergreen shrub used in traditional treatments of certain ailments and diseases. This study aimed at devising an integrated strategy attempts to evaluate the bioactive components in the J. sambac essential oil (JEO) against human breast cancer. JEO extracted by distillation process and analyzed by GC-MS was subjected to screening of therapeutic components in their allegiance to the drug-likeness index. The utility and efficacy of its molecular mechanism relating to anticancer potential were probed with network pharmacology analysis. Gene ontology, pathway enrichment, and compound-target-pathway network by Cytoscape helped to harp on hub targets and pathways involved in curative action. Drawing from the network data, molecular docking analysis of selected compounds on breast cancer targets was approached. The anti-proliferative study was carried out in MCF-7 and MDA-MB-231 to evaluate the cytotoxicity of JEO. Finally, in vivo anticancer activity was verified using rat models. The results showed MDA-MB-231 cell growth was highly inhibited than the MCF-7 cell line. Alongside this in vitro trial, in situ effectiveness of JEO was evaluated using female Sprague-Dawley rat animal models. In vivo experiments and histopathological analysis showed convincing results in DMBA tumor-induced rats. The larger aim of this study is to identify the potential ingredients of the JEO in cancer apoptosis by integrating network pharmacology and experimental validation achieved to certain extent confers credence to the concept of hiring J. sambac as floral therapy in dealing with the disastrous disease.
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Affiliation(s)
- S Gokila Lakshmi
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - M Kamaraj
- Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology-Ramapuram Campus, Chennai, Tamil Nadu, 600089, India
| | - T G Nithya
- Department of Biochemistry, College of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India.
| | - N Chidambaranathan
- Department of Pharmacology, K. M. College of Pharmacy, Uthangudi, Madurai, Tamil Nadu, 625107, India
| | - G Grace Lydial Pushpalatha
- Department of Botany, Sri Meenakshi Government Arts College for Women, Madurai, Tamil Nadu, 625002, India
| | - P Santhosh
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - B Balavaishnavi
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Megha Mahajan
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
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Wawszczyk J, Wolan R, Smolik S, Kapral M. In vitro and in silico study on the effect of carvedilol and sorafenib alone and in combination on the growth and inflammatory response of melanoma cells. Saudi Pharm J 2023; 31:1306-1316. [PMID: 37323921 PMCID: PMC10265481 DOI: 10.1016/j.jsps.2023.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Melanoma is an aggressive skin cancer. Increasing evidence has shown the role of β-adrenergic receptors in the pathogenesis of melanoma. Carvedilol is a widely used non-selective β-AR antagonist with potential anticancer activity. The purpose of the study was to estimate the influence of carvedilol and sorafenib alone and in combination on the growth and inflammatory response of C32 and A2058 melanoma cells. Furthermore, this study also aimed to predict the probable interaction of carvedilol and sorafenib when administered together. Predictive study of the interaction of carvedilol and sorafenib was performed using the ChemDIS-Mixture system. Carvedilol and sorafenib alone and in combination showed a growth inhibitory effect on cells. The greatest synergistic antiproliferative effect on both cell lines was observed at Car 5 μM combined with Sor 5 μM. Analysis in silico identified diseases, proteins, and metabolic pathways that can be affected by the interaction of carvedilol and sorafenib. The results obtained demonstrated that carvedilol and sorafenib modulated the secretion of IL-8 by IL-1β-stimulated by melanoma cell lines but the use of a combination of both drugs did not intensify the effect. In summary, the results presented indicate that the combination of carvedilol and sorafenib may have a promising anticancer effect on melanoma cells.
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Souza VVD, Souza TDS, Campos JMSD, Oliveira LAD, Ribeiro YM, Hoyos DCDM, Xavier RMP, Charlie-Silva I, Lacerda SMDSN. Ecogenotoxicity of environmentally relevant atrazine concentrations: A threat to aquatic bioindicators. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 189:105297. [PMID: 36549823 DOI: 10.1016/j.pestbp.2022.105297] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/26/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Atrazine (ATZ) is a herbicide that is frequently present in surface waters and may result in damage to the health of various organisms, including humans. However, most scientific literature reports injuries caused by ATZ at high concentrations, which are not found in the environment. Therefore, the scope of this study was to investigate the impacts of realistic concentrations of ATZ found in surface waters (1, 2, 5, 10, 15 and 20 μg/L) using the bioindicators Allium cepa, Daphnia magna and zebrafish (Danio rerio). ATZ elicited a genotoxic effect in A. cepa, manifested by the induction of chromosomal aberrations, and a mutagenic effect with increased incidence of micronuclei formation, promotion of cell death and reduction in nuclear size revealed by flow cytometry analysis. D. magna exposed to 10, 15 and 20 μg/L of ATZ showed significant reduction in body size after 21 days, delayed first-brood release, decreased egg production and total offspring, as well as swimming behavioral changes. ATZ exposure promoted physiological and developmental alterations in zebrafish embryos, including an increased spontaneous movement rate, which led to premature hatching at all concentrations investigated. Increase in total body length, decrease of the yolk sac area, pericardial edema and higher heart rate were also detected in ATZ-treated zebrafish. In summary, environmentally relevant concentrations of ATZ can induce substantial alterations in the three bioindicators investigated. This study evidences the deleterious effects of ATZ on three aquatic bioindicators employing established and current techniques, and may contribute to elucidate the risks caused by this widely used herbicide even at low concentrations and short-to-medium-term exposure.
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Affiliation(s)
- Victor Ventura de Souza
- Laboratory of Cellular Biology, Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Tatiana da Silva Souza
- Laboratory of Ecotoxicology, Department of Biology, Federal University of Espírito Santo, Alegre, Brazil
| | | | - Luiza Araújo de Oliveira
- Laboratory of Cellular Biology, Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Yves Moreira Ribeiro
- Laboratory of Ichthyohistology, Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Ives Charlie-Silva
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Wang CC, Liang YC, Wang SS, Lin P, Tung CW. A machine learning-driven approach for prioritizing food contact chemicals of carcinogenic concern based on complementary in silico methods. Food Chem Toxicol 2022; 160:112802. [PMID: 34979167 DOI: 10.1016/j.fct.2021.112802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/15/2021] [Accepted: 12/28/2021] [Indexed: 10/19/2022]
Abstract
Carcinogenicity is one of the most critical endpoints for the risk assessment of food contact chemicals (FCCs). However, the carcinogenicity of FCCs remains insufficiently investigated. To fill the data gap, the application of standard experimental methods for identifying chemicals of carcinogenic concerns from a large set of FCCs is impractical due to their resource-intensive nature. In contrast, computational methods provide an efficient way to quickly screen chemicals with carcinogenic potential for subsequent experimental validation. Since every model was developed based on a limited number of training samples, the use of single models for carcinogenicity assessment may not cover the complex mechanisms of carcinogenesis. This study proposed a novel machine learning-based weight-of-evidence (WoE) model for prioritizing chemical carcinogenesis. The WoE model can nonlinearly integrate complementary computational methods of structural alerts, quantitative structure-activity relationship models and in silico toxicogenomics models into a WoE-score. Compared to the best single method, the WoE model gained 8% and 19.7% improvement in the area under the receiver operating characteristic curve (AUC) value and chemical coverage, respectively. The prioritization of 1623 FCCs concludes 44 chemicals of high carcinogenic concern. The machine learning-based WoE approach provides a fast and comprehensive way for prioritizing chemicals of carcinogenic concern.
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Affiliation(s)
- Chia-Chi Wang
- Department and Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Chih Liang
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
| | - Shan-Shan Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County, 35053, Taiwan
| | - Pinpin Lin
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli County, 35053, Taiwan.
| | - Chun-Wei Tung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County, 35053, Taiwan; Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei, 106, Taiwan; Doctoral Degree Program in Toxicology, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
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7
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Mendonça-Gomes JM, da Costa Araújo AP, da Luz TM, Charlie-Silva I, Braz HLB, Jorge RJB, Ahmed MAI, Nóbrega RH, Vogel CFA, Malafaia G. Environmental impacts of COVID-19 treatment: Toxicological evaluation of azithromycin and hydroxychloroquine in adult zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148129. [PMID: 34380260 PMCID: PMC8164503 DOI: 10.1016/j.scitotenv.2021.148129] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 05/08/2023]
Abstract
One of the most impact issues in recent years refers to the COVID-19 pandemic, the consequences of which thousands of deaths recorded worldwide, are still inferior understood. Its impacts on the environment and aquatic biota constitute a fertile field of investigation. Thus, to predict the impact of the indiscriminate use of azithromycin (AZT) and hydroxychloroquine (HCQ) in this pandemic context, we aim to assess their toxicological risks when isolated or in combination, using zebrafish (Danio rerio) as a model system. In summary, we observed that 72 h of exposure to AZT and HCQ (alone or in binary combination, both at 2.5 μg/L) induced the reduction of total protein levels, accompanied by increased levels of thiobarbituric acid reactive substances, hydrogen peroxide, reactive oxygen species and nitrite, suggesting a REDOX imbalance and possible oxidative stress. Molecular docking analysis further supported this data by demonstrating a strong affinity of AZT and HCQ with their potential antioxidant targets (catalase and superoxide dismutase). In the protein-protein interaction network analysis, AZT showed a putative interaction with different cytochrome P450 molecules, while HCQ demonstrated interaction with caspase-3. The functional enrichment analysis also demonstrated diverse biological processes and molecular mechanisms related to the maintenance of REDOX homeostasis. Moreover, we also demonstrated an increase in the AChE activity followed by a reduction in the neuromasts of the head when zebrafish were exposed to the mixture AZT + HCQ. These data suggest a neurotoxic effect of the drugs. Altogether, our study demonstrated that short exposure to AZT, HCQ or their mixture induced physiological alterations in adult zebrafish. These effects can compromise the health of these animals, suggesting that the increase of AZT and HCQ due to COVID-19 pandemic can negatively impact freshwater ecosystems.
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Affiliation(s)
| | - Amanda Pereira da Costa Araújo
- Laboratório de Pesquisas Biológicas, Instituto Federal Goiano, Urutaí, GO, Brazil; Programa de Pós-Graduação em Ciências Ambientais, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | | | - Ives Charlie-Silva
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Roberta Jeane Bezerra Jorge
- Drug Research and Development Center, Federal University of Ceará, Brazil; Department of Physiology and Pharmacology, School of Medicine, Federal University of Ceará, Brazil
| | | | - Rafael Henrique Nóbrega
- Reproductive and Molecular Biology Group, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, Brazil
| | - Christoph F A Vogel
- Department of Environmental Toxicology and Center for Health and the Environment, University of California, Davis, USA
| | - Guilherme Malafaia
- Laboratório de Pesquisas Biológicas, Instituto Federal Goiano, Urutaí, GO, Brazil; Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brazil; Programa de Pós-Graduação em Ecologia e Conservação de Recursos Naturais, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil; Programa de Pós-Graduação em Conservação de Recursos Naturais do Cerrado, Instituto Federal Goiano, Urutaí, GO, Brazil.
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8
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Liang PI, Wang CC, Cheng HJ, Wang SS, Lin YC, Lin P, Tung CW. Curation of cancer hallmark-based genes and pathways for in silico characterization of chemical carcinogenesis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5857494. [PMID: 32539087 PMCID: PMC7294774 DOI: 10.1093/database/baaa045] [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: 02/16/2020] [Revised: 05/10/2020] [Accepted: 05/19/2020] [Indexed: 01/19/2023]
Abstract
Exposure to toxic substances in the environment is one of the most important causes of cancer. However, the time-consuming process for the identification and characterization of carcinogens is not applicable to a huge amount of testing chemicals. The data gaps make the carcinogenic risk uncontrollable. An efficient and effective way of prioritizing chemicals of carcinogenic concern with interpretable mechanism information is highly desirable. This study presents a curation work for genes and pathways associated with 11 hallmarks of cancer (HOCs) reported by the Halifax Project. To demonstrate the usefulness of the curated HOC data, the interacting HOC genes and affected HOC pathways of chemicals of the three carcinogen lists from IARC, NTP and EPA were analyzed using the in silico toxicogenomics ChemDIS system. Results showed that a higher number of affected HOCs were observed for known carcinogens than the other chemicals. The curated HOC data is expected to be useful for prioritizing chemicals of carcinogenic concern. Database URL: The HOC database is available at https://github.com/hocdb-KMU-TMU/hocdb and the website of Database journal as Supplementary Data.
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Affiliation(s)
- Peir-In Liang
- Phd Program in Toxicology, Kaohsiung Medical University, 100 Shiquan 1st Road, Kaohsiung 80706, Taiwan.,Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, 100 Ziyou 1st Road, Kaohsiung 80706, Taiwan
| | - Chia-Chi Wang
- Department and Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, 1 Section 4 Roosevelt Rd, Taipei 10617, Taiwan
| | - Hsien-Jen Cheng
- National Institute of Environmental Health Sciences, National Health Research Institutes, 35 Keyan Road, Miaoli County 35053, Taiwan
| | - Shan-Shan Wang
- Graduate Institute of Data Science, College of Management, Taipei Medical University, 250 Wuxing Street, Taipei 10675, Taiwan
| | - Ying-Chi Lin
- Phd Program in Toxicology, Kaohsiung Medical University, 100 Shiquan 1st Road, Kaohsiung 80706, Taiwan.,School of Pharmacy, Kaohsiung Medical University, 100 Shiquan 1st Road, Kaohsiung 80706, Taiwan
| | - Pinpin Lin
- National Institute of Environmental Health Sciences, National Health Research Institutes, 35 Keyan Road, Miaoli County 35053, Taiwan
| | - Chun-Wei Tung
- National Institute of Environmental Health Sciences, National Health Research Institutes, 35 Keyan Road, Miaoli County 35053, Taiwan.,Graduate Institute of Data Science, College of Management, Taipei Medical University, 250 Wuxing Street, Taipei 10675, Taiwan
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Xue P, Zhang G, Zhang J, Ren L. Interaction of flavonoids with serum albumin: A review. Curr Protein Pept Sci 2020; 22:CPPS-EPUB-111278. [PMID: 33167830 DOI: 10.2174/1389203721666201109112220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/23/2020] [Accepted: 10/02/2020] [Indexed: 11/22/2022]
Abstract
Flavonoids are plant products abundant in every day diet and claimed to be beneficial for human health. After absorption, flavonoids are transported by the serum albumin (SA), the most abundant carrier blood protein, through formation of flavonoids-SA complex. This review deals with the current state of knowledge on flavonoids-SA complex over the past 10 years, mainly involved multi-spectroscopic techniques and molecular dynamics simulation studies to explore the binding mechanism, thermodynamics and structural aspects of flavonoids binding to SA. Especially, the novel method, capillary electrophoresis, high performance affinity chromatography approach, native mass spectrometry and microscale thermophoresis used in characterization of the interaction between flavonoids and SA as well as flavonoid-based fluorescent probe for SA measurement are also included in this review.
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Affiliation(s)
- Peiyu Xue
- School of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000. China
| | - Guangjie Zhang
- School of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000. China
| | - Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun 130062. China
| | - Li Ren
- College of Food Science and Engineering, Jilin University, Changchun 130062. China
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10
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Tung CW, Cheng HJ, Wang CC, Wang SS, Lin P. Leveraging complementary computational models for prioritizing chemicals of developmental and reproductive toxicity concern: an example of food contact materials. Arch Toxicol 2020; 94:485-494. [PMID: 31897520 DOI: 10.1007/s00204-019-02641-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/02/2019] [Indexed: 12/23/2022]
Abstract
The evaluation of developmental and reproductive toxicity of food contact materials (FCMs) is an important task for food safety. Since traditional experiments are both time-consuming and labor-intensive, only a small number of FCMs have sufficient toxicological data for evaluating their effects on human health. While computational methods such as structural alerts and quantitative structure-activity relationships can serve as first-line tools for the identification of chemicals of high toxicity concern, models with binary outputs and unsatisfied accuracy and coverage prevent the use of computational methods for prioritizing chemicals of high concern. This study proposed a genetic algorithm-based method to develop a weight-of-evidence (WoE) model leveraging complementary methods of structural alerts, quantitative structure-activity relationships and in silico toxicogenomics models for chemical prioritization. The WoE model was applied to evaluate 623 food contact chemicals and identify 26 chemicals of high toxicity concern, where 13 chemicals have been reported to be developmental or reproductive toxic and further experiments are suggested for the remaining 13 chemicals without toxicity data related to developmental and reproductive effects. The proposed WoE model is potentially useful for prioritizing chemicals of high toxicity concern and the methodology may be applied to toxicities other than developmental and reproductive toxicity.
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Affiliation(s)
- Chun-Wei Tung
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei, 10675, Taiwan. .,National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli County, 35053, Taiwan.
| | - Hsien-Jen Cheng
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli County, 35053, Taiwan
| | - Chia-Chi Wang
- Department and Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei, 10617, Taiwan
| | - Shan-Shan Wang
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei, 10675, Taiwan
| | - Pinpin Lin
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli County, 35053, Taiwan.
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11
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Madia F, Worth A, Whelan M, Corvi R. Carcinogenicity assessment: Addressing the challenges of cancer and chemicals in the environment. ENVIRONMENT INTERNATIONAL 2019; 128:417-429. [PMID: 31078876 PMCID: PMC6520474 DOI: 10.1016/j.envint.2019.04.067] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/10/2019] [Accepted: 04/27/2019] [Indexed: 05/10/2023]
Abstract
Cancer is a key public health concern, being the second leading cause of worldwide morbidity and mortality after cardiovascular diseases. At the global level, cancer prevalence, incidence and mortality rates are increasing. These trends are not fully explained by a growing and ageing population: with marked regional and socioeconomic disparities, lifestyle factors, the resources dedicated to preventive medicine, and the occupational and environmental control of hazardous chemicals all playing a role. While it is difficult to establish the contribution of chemical exposure to the societal burden of cancer, a number of measures can be taken to better assess the carcinogenic properties of chemicals and manage their risks. This paper discusses how these measures can be informed not only by the traditional data streams of regulatory toxicology, but also by using new toxicological assessment methods, along with indicators of public health status based on biomonitoring. These diverse evidence streams have the potential to form the basis of an integrated and more effective approach to cancer prevention.
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Affiliation(s)
- Federica Madia
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
| | - Andrew Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Maurice Whelan
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Raffaella Corvi
- European Commission, Joint Research Centre (JRC), Ispra, Italy
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Vakil V, Trappe W. Drug Combinations: Mathematical Modeling and Networking Methods. Pharmaceutics 2019; 11:E208. [PMID: 31052580 PMCID: PMC6571786 DOI: 10.3390/pharmaceutics11050208] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/24/2019] [Accepted: 04/27/2019] [Indexed: 12/14/2022] Open
Abstract
Treatments consisting of mixtures of pharmacological agents have been shown to have superior effects to treatments involving single compounds. Given the vast amount of possible combinations involving multiple drugs and the restrictions in time and resources required to test all such combinations in vitro, mathematical methods are essential to model the interactive behavior of the drug mixture and the target, ultimately allowing one to better predict the outcome of the combination. In this review, we investigate various mathematical methods that model combination therapies. This survey includes the methods that focus on predicting the outcome of drug combinations with respect to synergism and antagonism, as well as the methods that explore the dynamics of combination therapy and its role in combating drug resistance. This comprehensive investigation of the mathematical methods includes models that employ pharmacodynamics equations, those that rely on signaling and how the underlying chemical networks are affected by the topological structure of the target proteins, and models that are based on stochastic models for evolutionary dynamics. Additionally, this article reviews computational methods including mathematical algorithms, machine learning, and search algorithms that can identify promising combinations of drug compounds. A description of existing data and software resources is provided that can support investigations in drug combination therapies. Finally, the article concludes with a summary of future directions for investigation by the research community.
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Affiliation(s)
- Vahideh Vakil
- WINLAB, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Wade Trappe
- WINLAB, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
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Tung CW, Wang SS. ChemDIS 2: an update of chemical-disease inference system. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5057768. [PMID: 30053236 PMCID: PMC6057493 DOI: 10.1093/database/bay077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/25/2018] [Indexed: 11/14/2022]
Abstract
Computational inference of affected functions, pathways and diseases for chemicals could largely accelerate the evaluation of potential effects of chemical exposure on human beings. Previously, we have developed a ChemDIS system utilizing information of interacting targets for chemical-disease inference. With the target information, testable hypotheses can be generated for experimental validation. In this work, we present an update of ChemDIS 2 system featured with more updated datasets and several new functions, including (i) custom enrichment analysis function for single omics data; (ii) multi-omics analysis function for joint analysis of multi-omics data; (iii) mixture analysis function for the identification of interaction and overall effects; (iv) web application programming interface (API) for programmed access to ChemDIS 2. The updated ChemDIS 2 system capable of analyzing more than 430 000 chemicals is expected to be useful for both drug development and risk assessment of environmental chemicals. Database URL: ChemDIS 2 is freely accessible via https://cwtung.kmu.edu.tw/chemdis
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Affiliation(s)
- Chun-Wei Tung
- School of Pharmacy, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung, Taiwan.,PhD Program in Toxicology, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung, Taiwan.,Research Center for Environmental Medicine, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, 100 Tzyou 1st Road, Kaohsiung, Taiwan.,National Institute of Environmental Health Sciences, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, Taiwan
| | - Shan-Shan Wang
- School of Pharmacy, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung, Taiwan
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Darde TA, Chalmel F, Svingen T. Exploiting advances in transcriptomics to improve on human-relevant toxicology. CURRENT OPINION IN TOXICOLOGY 2018. [DOI: 10.1016/j.cotox.2019.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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