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Eleazar EG, Carrera ARM, Quiambao JIR, Caparanga AR, Tayo LL. QSTR Models in Dioxins and Dioxin-like Compounds Provide Insights into Gene Expression Dysregulation. TOXICS 2024; 12:597. [PMID: 39195699 DOI: 10.3390/toxics12080597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/11/2024] [Accepted: 08/15/2024] [Indexed: 08/29/2024]
Abstract
Polychlorinated dibenzo-p-dioxins and polychlorinated dibenzo-p-furans (PCDD/Fs) are a group of organic chemicals containing three-ring structures that can be substituted with one to eight chlorine atoms, leading to 75 dioxin and 135 furan congeners. As endocrine-disrupting chemicals (EDCs), they can alter physiological processes causing a number of disorders. In this study, quantitative structure-toxicity relationship (QSTR) studies were used to determine the correlations between the PCDD/Fs' molecular structures and various toxicity endpoints. Strong QSTR models, with the coefficients of determination (r2) values greater than 0.95 and ANOVA p-values less than 0.0001 were established between molecular descriptors and the endpoints of bioconcentration, fathead minnow LC50, and Daphnia magna LC50. The ability of PCDD/Fs to bind to several nuclear receptors was investigated via molecular docking studies. The results show comparable, and in some instances better, binding affinities of PCDD/Fs toward the receptors relative to their natural agonistic and antagonistic ligands, signifying possible interference with the receptors' natural biological activities. These studies were accompanied by the molecular dynamics simulations of the top-binding PCDD/Fs to show changes in the receptor-ligand complexes during binding and provide insights into these compounds' ability to interfere with transcription and thereby modify gene expression. This introspection of PCDD/Fs at the molecular level provides a deeper understanding of these compounds' toxicity and opens avenues for future studies.
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Affiliation(s)
- Elisa G Eleazar
- School of Graduate Studies, Mapua University, Manila 1002, Philippines
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapua University, Manila 1002, Philippines
| | - Andrei Raphael M Carrera
- School of Graduate Studies, Mapua University, Manila 1002, Philippines
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapua University, Manila 1002, Philippines
| | - Janus Isaiah R Quiambao
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapua University, Manila 1002, Philippines
| | - Alvin R Caparanga
- School of Graduate Studies, Mapua University, Manila 1002, Philippines
| | - Lemmuel L Tayo
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapua University, Manila 1002, Philippines
- Department of Biology, School of Health Sciences, Mapua University, Makati 1200, Philippines
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2
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Lu X, Wang X, Chen S, Fan T, Zhao L, Zhong R, Sun G. The rat acute oral toxicity of trifluoromethyl compounds (TFMs): a computational toxicology study combining the 2D-QSTR, read-across and consensus modeling methods. Arch Toxicol 2024; 98:2213-2229. [PMID: 38627326 DOI: 10.1007/s00204-024-03739-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/18/2024] [Indexed: 06/13/2024]
Abstract
All areas of the modern society are affected by fluorine chemistry. In particular, fluorine plays an important role in medical, pharmaceutical and agrochemical sciences. Amongst various fluoro-organic compounds, trifluoromethyl (CF3) group is valuable in applications such as pharmaceuticals, agrochemicals and industrial chemicals. In the present study, following the strict OECD modelling principles, a quantitative structure-toxicity relationship (QSTR) modelling for the rat acute oral toxicity of trifluoromethyl compounds (TFMs) was established by genetic algorithm-multiple linear regression (GA-MLR) approach. All developed models were evaluated by various state-of-the-art validation metrics and the OECD principles. The best QSTR model included nine easily interpretable 2D molecular descriptors with clear physical and chemical significance. The mechanistic interpretation showed that the atom-type electro-topological state indices, molecular connectivity, ionization potential, lipophilicity and some autocorrelation coefficients are the main factors contributing to the acute oral toxicity of TFMs against rats. To validate that the selected 2D descriptors can effectively characterize the toxicity, we performed the chemical read-across analysis. We also compared the best QSTR model with public OPERA tool to demonstrate the reliability of the predictions. To further improve the prediction range of the QSTR model, we performed the consensus modelling. Finally, the optimum QSTR model was utilized to predict a true external set containing many untested/unknown TFMs for the first time. Overall, the developed model contributes to a more comprehensive safety assessment approach for novel CF3-containing pharmaceuticals or chemicals, reducing unnecessary chemical synthesis whilst saving the development cost of new drugs.
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Affiliation(s)
- Xinyi Lu
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing, 100124, People's Republic of China
| | - Xin Wang
- Department of Clinical Trials Center, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, People's Republic of China
| | - Shuo Chen
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing, 100124, People's Republic of China
| | - Tengjiao Fan
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing, 100124, People's Republic of China
- Department of Medical Technology, Beijing Pharmaceutical University of Staff and Workers, Beijing, 100079, China
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing, 100124, People's Republic of China
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing, 100124, People's Republic of China
| | - Guohui Sun
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing, 100124, People's Republic of China.
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Jiang JR, Cai WX, Chen ZF, Liao XL, Cai Z. Prediction of acute toxicity for Chlorella vulgaris caused by tire wear particle-derived compounds using quantitative structure-activity relationship models. WATER RESEARCH 2024; 256:121643. [PMID: 38663211 DOI: 10.1016/j.watres.2024.121643] [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: 11/29/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Tire wear particles (TWPs) enter aquatic ecosystems through various pathways, such as rainwater and urban runoff. Additives in TWPs can harm aquatic organisms in these ecosystems. Therefore, it is essential to investigate their toxicity to aquatic organisms. In our study, we initially recorded the median effective concentrations of 21 TWP-derived compounds on Chlorella vulgaris growth, ranging from 0.04 to 8.60 mg/L. Subsequently, through an extensive review of the literature, we incorporated 112 compounds with specific toxicity endpoints to construct the QSAR model using genetic algorithm and multiple linear regression techniques, followed by the construction of the consensus model and the quantitative read-across structure-activity relationship (q-RASAR) model. Meanwhile, we employed rigorous internal and external validation measures to assess the performance of the model. The results indicated that the developed q-RASAR model exhibited strong adaptation, robustness, and reliable prediction, with q-RASAR indicators of Q2LOO = 0.7673, R2tr = 0.8079, R2test = 0.8610, Q2Fn = 0.8285-0.8614, and CCCtest = 0.9222. Based on an external dataset containing 128 emerging TWP-derived compounds, the model's applicability domain coverage was 90.6 %. The q-RASAR model predicted that the structure of diphenylamine was associated with higher toxicity, possibly liked to the SpMax2_Bhm and LogBCF descriptors. The established model reliably provides prediction and fills a critical data gap. These findings highlight the potential risks posed by emerging TWP-derived compounds to aquatic organisms.
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Affiliation(s)
- Jie-Ru Jiang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Wen-Xi Cai
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhi-Feng Chen
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Xiao-Liang Liao
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Zongwei Cai
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China; State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong 999077, China.
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Yang L, Li P, Han Y, Han D, Yan H. Porous chlorine-functionalized covalent organic framework anchored graphene aerogel composite for synergically enhanced solid phase microextraction of polychlorinated naphthalene in environmental water. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133909. [PMID: 38432094 DOI: 10.1016/j.jhazmat.2024.133909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/17/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
The residues of polychlorinated naphthalenes (PCNs) produced in multiple industrial production and life processes are continuously entering environmental waters through atmospheric deposition and land drainage, and the water pollution caused by PCNs is continuing public concern due to their potential threat to aquatic ecosystems and public health. Herein, a new chlorine-functionalized covalent organic framework anchored graphene aerogel (COF-GA) was synthesized by covalent modification technology and used as fiber coating of solid-phase microextraction for synergically enhanced extraction of PCNs in environmental water. The extraction efficiency of COF-GA coated fiber was superior to commercial fiber due to the multiple interactions (π-π, hydrophobic interaction, and halogen bonding interaction). The COF-GA coated fiber has good stability, can avoid water vapor interference at 80 °C for a long time (30 -50 min) to maintain adsorption equilibrium, and can be reused at least 96 times. Combined with gas chromatography-tandem mass spectrometry, a sensitive method for the high-efficient enrichment (enrichment factors were 501 -7453 folds) and ultra-sensitive detection (LODs were 0.001 -0.428 pg/mL) of PCNs in environmental water was established. The enrichment factor for PCNs is significantly higher than in previous studies. This proposed method provides new technical support for the daily monitoring and risk assessment of trace PCNs in environmental water.
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Affiliation(s)
- Lansen Yang
- Hebei Key Laboratory of Public Health Safety, College of Public Health, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China; State Key Laboratory of New Pharmaceutical Preparations and Excipients, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, China
| | - Pengfei Li
- State Key Laboratory of New Pharmaceutical Preparations and Excipients, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, China
| | - Yehong Han
- Hebei Key Laboratory of Public Health Safety, College of Public Health, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
| | - Dandan Han
- Hebei Key Laboratory of Public Health Safety, College of Public Health, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
| | - Hongyuan Yan
- Hebei Key Laboratory of Public Health Safety, College of Public Health, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China; State Key Laboratory of New Pharmaceutical Preparations and Excipients, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, China.
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5
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Dong S, Wu X, Zhang S, Cao J, Huang N, Zou Y, Liu P, Gu X, Zheng X, Wang P. Polychlorinated naphthalenes in freshwater fish from Beijing markets: Species-specific differences, effects of cooking, and health risk assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170605. [PMID: 38307290 DOI: 10.1016/j.scitotenv.2024.170605] [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: 11/30/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/04/2024]
Abstract
Fish are an important source of human dietary exposure to polychlorinated naphthalenes (PCNs). The occurrence and sources of PCNs in different species of freshwater fish are unknown, and few studies have assessed human exposure risks to PCNs through freshwater fish. In this study, 140 freshwater fish samples from 10 species were collected from Beijing markets, China. The Σ75CNs concentration range in the fish was 20.7-1310 pg/g wet weight (ww). The highest median Σ75PCNs concentration (80.4 pg/g ww) was found in mandarin fish (Siniperca chuatsi), and the lowest (29.6 pg/g ww) in snakehead (Channa argus). Di- and tri-CNs were the dominant PCN homologues with contributions of 35.3 % and 30.8 %, respectively. Unintentionally produced PCNs from metal smelting might be the source of PCN contamination in freshwater fish. The cooking temperature and time did not significantly affect the PCN concentrations in fish or the PCN homologue profiles. The highest toxic equivalent (TEQ) value was observed in sturgeon (Acipenser sinensis), followed by mandarin fish. Hexa-CNs were the most abundant homologue for the PCN TEQs. A risk assessment indicated that the dietary exposure risks for local residents to PCNs through freshwater fish were low. However, the relatively high concentrations of PCNs in the samples deserve attention to avoid PCNs exposure risks for groups with high fish consumption rates. Furthermore, freshwater fish likely contain a mixture of contaminants including dioxin and furans which also display a similar mode of toxicity as the PCNs and could enhance the risk to fish consumers.
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Affiliation(s)
- Shujun Dong
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xingyi Wu
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Science, China Agricultural University, Beijing 10081, China
| | - Su Zhang
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jun Cao
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Na Huang
- Chinese Academy of Inspection and Quarantine Comprehensive Test Center, Beijing 100123, China
| | - Yun Zou
- Organic Biological Analytical Chemistry Group, Department of Chemistry, University of Liège, Liège 4000, Belgium
| | - Puying Liu
- Guangdong Ocean University, Zhanjiang 524088, China
| | - Xiaoyao Gu
- Chinese Academy of Inspection and Quarantine Comprehensive Test Center, Beijing 100123, China
| | - Xue Zheng
- Chinese Academy of Inspection and Quarantine Comprehensive Test Center, Beijing 100123, China.
| | - Peilong Wang
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Schrenk D, Bignami M, Bodin L, Chipman JK, del Mazo J, Grasl‐Kraupp B, Hogstrand C, Hoogenboom L(R, Leblanc J, Nebbia CS, Ntzani E, Petersen A, Sand S, Schwerdtle T, Vleminckx C, Wallace H, Falandysz J, Hart A, Rose M, Anastassiadou M, Eskes C, Gergelova P, Innocenti M, Rovesti E, Whitty B, Nielsen E. Risks for animal and human health related to the presence of polychlorinated naphthalenes (PCNs) in feed and food. EFSA J 2024; 22:e8640. [PMID: 38476320 PMCID: PMC10928787 DOI: 10.2903/j.efsa.2024.8640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024] Open
Abstract
EFSA was asked for a scientific opinion on the risks for animal and human health related to the presence of polychlorinated naphthalenes (PCNs) in feed and food. The assessment focused on hexaCNs due to very limited data on other PCN congeners. For hexaCNs in feed, 217 analytical results were used to estimate dietary exposures for food-producing and non-food-producing animals; however, a risk characterisation could not be performed because none of the toxicological studies allowed identification of reference points. The oral repeated dose toxicity studies performed in rats with a hexaCN mixture containing all 10 hexaCNs indicated that the critical target was the haematological system. A BMDL20 of 0.05 mg/kg body weight (bw) per day was identified for a considerable decrease in the platelet count. For hexaCNs in food, 2317 analytical results were used to estimate dietary exposures across dietary surveys and age groups. The highest exposure ranged from 0.91 to 29.8 pg/kg bw per day in general population and from 220 to 559 pg/kg bw per day for breast-fed infants with the highest consumption of breast milk. Applying a margin of exposure (MOE) approach, the estimated MOEs for the high dietary exposures ranged from 1,700,000 to 55,000,000 for the general population and from 90,000 to 230,000 for breast-fed infants with the highest consumption of breast milk. These MOEs are far above the minimum MOE of 2000 that does not raise a health concern. Taking account of the uncertainties affecting the assessment, the Panel concluded with at least 99% certainty that dietary exposure to hexaCNs does not raise a health concern for any of the population groups considered. Due to major limitations in the available data, no assessment was possible for genotoxic effects or for health risks of PCNs other than hexaCNs.
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7
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Kumar A, Kumar V, Ojha PK, Roy K. Chronic aquatic toxicity assessment of diverse chemicals on Daphnia magna using QSAR and chemical read-across. Regul Toxicol Pharmacol 2024; 148:105572. [PMID: 38325631 DOI: 10.1016/j.yrtph.2024.105572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/06/2024] [Accepted: 01/26/2024] [Indexed: 02/09/2024]
Abstract
We have modeled here chronic Daphnia toxicity taking pNOEC (negative logarithm of no observed effect concentration in mM) and pEC50 (negative logarithm of half-maximal effective concentration in mM) as endpoints using QSAR and chemical read-across approaches. The QSAR models were developed by strictly obeying the OECD guidelines and were found to be reliable, predictive, accurate, and robust. From the selected features in the developed models, we have found that an increase in lipophilicity and saturation, the presence of electrophilic or electronegative or heavy atoms, the presence of sulphur, amine, and their related functionality, an increase in mean atomic polarizability, and higher number of (thio-) carbamates (aromatic) groups are responsible for chronic toxicity. Therefore, this information might be useful for the development of environmentally friendly and safer chemicals and data-gap filling as well as reducing the use of identified toxic chemicals which have chronic toxic effects on aquatic ecosystems. Approved classes of drugs from DrugBank databases and diverse groups of chemicals from the Chemical and Product Categories (CPDat) database were also assessed through the developed models.
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Affiliation(s)
- Ankur Kumar
- Drug Discovery and Development (DDD) Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Vinay Kumar
- Drug Theoretics and Cheminformatics (DTC) Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Probir Kumar Ojha
- Drug Discovery and Development (DDD) Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics (DTC) Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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8
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Abchir O, Khedraoui M, Nour H, Yamari I, Errougui A, Samadi A, Chtita S. Integrative Approach for Designing Novel Triazole Derivatives as α-Glucosidase Inhibitors: QSAR, Molecular Docking, ADMET, and Molecular Dynamics Investigations. Pharmaceuticals (Basel) 2024; 17:261. [PMID: 38399476 PMCID: PMC10892212 DOI: 10.3390/ph17020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
In response to the increasing prevalence of diabetes mellitus and the limitations associated with the current treatments, there is a growing need to develop novel medications for this disease. This study is focused on creating new compounds that exhibit a strong inhibition of alpha-glucosidase, which is a pivotal enzyme in diabetes control. A set of 33 triazole derivatives underwent an extensive QSAR analysis, aiming to identify the key factors influencing their inhibitory activity against α-glucosidase. Using the multiple linear regression (MLR) model, seven promising compounds were designed as potential drugs. Molecular docking and dynamics simulations were employed to shed light on the mode of interaction between the ligands and the target, and the stability of the obtained complexes. Furthermore, the pharmacokinetic properties of the designed compounds were assessed to predict their behavior in the human body. The binding free energy was also calculated using MMGBSA method and revealed favorable thermodynamic properties. The results highlighted three novel compounds with high biological activity, strong binding affinity to the target enzyme, and suitability for oral administration. These results offer interesting prospects for the development of effective and well-tolerated medications against diabetes mellitus.
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Affiliation(s)
- Oussama Abchir
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Meriem Khedraoui
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Hassan Nour
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Imane Yamari
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Abdelkbir Errougui
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Abdelouahid Samadi
- Department of Chemistry, College of Science, United Arab Emirates University (UAEU), Al Ain P.O. Box 15551, United Arab Emirates
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
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Carrera ARM, Eleazar EG, Caparanga AR, Tayo LL. Theoretical Studies on the Quantitative Structure-Toxicity Relationship of Polychlorinated Biphenyl Congeners Reveal High Affinity Binding to Multiple Human Nuclear Receptors. TOXICS 2024; 12:49. [PMID: 38251005 PMCID: PMC10821279 DOI: 10.3390/toxics12010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Polychlorinated biphenyls (PCBs) are organic chemicals consisting of a biphenyl structure substituted with one to ten chlorine atoms, with 209 congeners depending on the number and position of the chlorine atoms. PCBs are widely known to be endocrine-disrupting chemicals (EDCs) and have been found to be involved in several diseases/disorders. This study takes various molecular descriptors of these PCBs (e.g., molecular weight) and toxicity endpoints as molecular activities, investigating the possibility of correlations via the quantitative structure-toxicity relationship (QSTR). This study then focuses on molecular docking and dynamics to investigate the docking behavior of the strongest-binding PCBs to nuclear receptors and compares these to the docking behavior of their natural ligands. Nuclear receptors are a family of transcription factors activated by steroid hormones, and they have been investigated to consider the impact of PCBs on humans in this context. It has been observed that the docking affinity of PCBs is comparable to that of the natural ligands, but they are inferior in terms of stability and interacting forces, as shown by the RMSD and total energy values. However, it is noted that most nuclear receptors respond to PCBs similarly to how they respond to their natural ligands-as shown in the RMSF plots-the most similar of which are seen in the ER, THR-β, and RAR-α. However, this study is performed purely in silico and will need experimental verification for validation.
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Affiliation(s)
- Andrei Raphael M. Carrera
- School of Graduate Studies, Mapúa University, Manila 1002, Philippines; (A.R.M.C.); (E.G.E.)
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines;
| | - Elisa G. Eleazar
- School of Graduate Studies, Mapúa University, Manila 1002, Philippines; (A.R.M.C.); (E.G.E.)
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines;
| | - Alvin R. Caparanga
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines;
| | - Lemmuel L. Tayo
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines;
- Department of Biology, School of Medicine and Health Sciences, Mapúa University, Makati 1200, Philippines
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10
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Nath A, Ojha PK, Roy K. QSAR assessment of aquatic toxicity potential of diverse agrochemicals. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023:1-20. [PMID: 37941423 DOI: 10.1080/1062936x.2023.2278074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
The fast-increasing number of commercially produced chemicals challenges the experimental ecotoxicity assessment methods, which are costly, time-consuming, and dependent on the sacrifice of animals. In this regard, Quantitative Structure-Property/Activity Relationships (QSPR/QSAR) have led the way in developing ecotoxicity assessment models. In this study, QSAR models have been developed using the pEC50 values of 82 diverse agrochemicals or agro-molecules against a planktonic crustacean Daphnia magna with easily interpretable 2D descriptors. Moreover, a link among octanol-water partition coefficient (KOW), bio-concentration factor (BCF), and critical body residue (CBR) has been addressed, and their imputation for the prediction of the toxicity endpoint (EC50) has been done with an objective of the advanced exploration of several ecotoxicological parameters for toxic chemicals. The developed partial least squares (PLS) models were validated rigorously and proved to be robust, sound, and immensely well-predictive. The final Daphnia toxicity model derived from experimental derived properties along with computed descriptors emerged better in statistical quality and predictivity than those obtained solely from computed descriptors. Additionally, the pEC50 and other important properties (log KOW, log BCF, and log CBR) for a set of external agro-molecules, not employed in model development, were predicted to show the predictive ability of the models.
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Affiliation(s)
| | - P K Ojha
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - K Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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