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Djelassi I, Lancia P, Thuillier I, Ginestar J, Fioravanzo E, Baleydier A. Strategy proposal using QSAR models to approach mutagenicity assessment of non intentionally added substances in recycled plastic resins. Food Chem Toxicol 2024; 187:114597. [PMID: 38492856 DOI: 10.1016/j.fct.2024.114597] [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: 01/04/2024] [Revised: 02/20/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
CONTEXT Transition to the use of recycled plastics raises an issue concerning safety assessment of Non Intentionally Added Substances (NIAS). To assess the mutagenic potential of the recycled polyethylene impurities and to evaluate the need to perform in vitro assays on recycled resins, this study lies in identifying existing NIAS associated with recycled Low/High Density Polyethylene and assessing the mutagenicity data-gaps by employing in silico tools. METHODS Quantitative Structure-Activity Relationship (QSAR) models predicting Ames mutagenicity were selected from literature, then NIAS were run to 1/evaluate performances of each model, 2/apply a QSAR strategy on the NIAS molecular space and address data-gaps. RESULTS Among the 165 NIAS identified, experimental Ames results were not found for 50 substances while the substances with experimental data were predominantly negatives. No individual model was able to predict all NIAS due to applicability domain limitations. Taking into account 1/calculated performances, 2/availability of applicability domain, 3/description of the Training Set, an Integrated Strategy was founded including Sarpy, Consensus and Protox to extend the applicability domain. CONCLUSION & PERSPECTIVES Existing data and predictions generated by this strategy suggest a low mutagenic potential of NIAS. Further investigation is needed to explore other genotoxicity mechanisms.
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Affiliation(s)
- Ishan Djelassi
- C.F.E.B Sisley Paris, 32 Avenue des Bethunes, 95310, Saint Ouen L'Aumône, France
| | - Pauline Lancia
- C.F.E.B Sisley Paris, 32 Avenue des Bethunes, 95310, Saint Ouen L'Aumône, France.
| | - Isabelle Thuillier
- C.F.E.B Sisley Paris, 32 Avenue des Bethunes, 95310, Saint Ouen L'Aumône, France
| | - José Ginestar
- C.F.E.B Sisley Paris, 32 Avenue des Bethunes, 95310, Saint Ouen L'Aumône, France
| | - Elena Fioravanzo
- ToxNavigation Ltd., Mole View, 158 Bridge Road, East Molesey, KT9 8HW, UK
| | - Aurélie Baleydier
- C.F.E.B Sisley Paris, 32 Avenue des Bethunes, 95310, Saint Ouen L'Aumône, France
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Arora S, Satija S, Mittal A, Solanki S, Mohanty SK, Srivastava V, Sengupta D, Rout D, Arul Murugan N, Borkar RM, Ahuja G. Unlocking The Mysteries of DNA Adducts with Artificial Intelligence. Chembiochem 2024; 25:e202300577. [PMID: 37874183 DOI: 10.1002/cbic.202300577] [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: 08/16/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
Cellular genome is considered a dynamic blueprint of a cell since it encodes genetic information that gets temporally altered due to various endogenous and exogenous insults. Largely, the extent of genomic dynamicity is controlled by the trade-off between DNA repair processes and the genotoxic potential of the causative agent (genotoxins or potential carcinogens). A subset of genotoxins form DNA adducts by covalently binding to the cellular DNA, triggering structural or functional changes that lead to significant alterations in cellular processes via genetic (e. g., mutations) or non-genetic (e. g., epigenome) routes. Identification, quantification, and characterization of DNA adducts are indispensable for their comprehensive understanding and could expedite the ongoing efforts in predicting carcinogenicity and their mode of action. In this review, we elaborate on using Artificial Intelligence (AI)-based modeling in adducts biology and present multiple computational strategies to gain advancements in decoding DNA adducts. The proposed AI-based strategies encompass predictive modeling for adduct formation via metabolic activation, novel adducts' identification, prediction of biochemical routes for adduct formation, adducts' half-life predictions within biological ecosystems, and, establishing methods to predict the link between adducts chemistry and its location within the genomic DNA. In summary, we discuss some futuristic AI-based approaches in DNA adduct biology.
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Affiliation(s)
- Sakshi Arora
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Shiva Satija
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Aayushi Mittal
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Saveena Solanki
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Sanjay Kumar Mohanty
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry CBH School, Royal Institute of Technology (KTH) AlbaNova University Center, 10691, Stockholm, Sweden
| | - Debarka Sengupta
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Diptiranjan Rout
- Department of Transfusion Medicine National Cancer Institute, AIIMS, New Delhi, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110608, India
| | - Natarajan Arul Murugan
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Roshan M Borkar
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER)-Guwahati, Sila Katamur Halugurisuk P.O.: Changsari, Dist, Guwahati, Assam, 781101, India
| | - Gaurav Ahuja
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
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Tumskiy R, Khlebtsov B, Tumskaia A, Evstigneeva S, Antoshkina E, Zakharevich A, Khlebtsov NG. Enhanced Antibacterial Activity of Novel Fluorescent Glutathione-Capped Ag Nanoclusters. Int J Mol Sci 2023; 24:ijms24098306. [PMID: 37176012 PMCID: PMC10179335 DOI: 10.3390/ijms24098306] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Ag nanomaterials are promising candidates for the discovery of next-generation antibiotics with a high antibacterial effect against multi-drug resistant strains. This paper reports a simple synthesis of novel water-soluble glutathione-capped silver nanoclusters (GSH-Ag NCs) with an enhanced antibacterial activity. According to thin layer chromatography (TLC), the synthesized GSH-Ag NCs are an individual fraction of the same composition without any impurities. According to matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and energy dispersive X-ray (EDX) analyses, the silver core of the GSH-Ag NCs contains approximately 35 silver atoms, and the molecular weight of these nanoclusters is about 11 kDa. The fabricated silver nanoclusters have a reddish fluorescence (λex/λem = 509/645 nm), with a large Stokes shift (>130 nm), and ultra-small size (less than 2 nm) according to transmission electron microscopy (TEM) data and dynamic light scattering (DLS) analysis. The antibacterial activity and minimal inhibitory concentrations of the silver nanoclusters towards Escherichia coli, Staphylococcus aureus, Bacillus cereus and Enterobacter cloacae were evaluated using the agar well-diffusion method and resazurin metabolism assay. The antibacterial activity of chelated silver in the nanoclusters was found to be significantly higher compared to the activity of free silver ions. To explain the possible mechanisms underlying the antibacterial actions of the GSH-Ag nanoclusters, molecular docking was performed, and prospective bacterial targets were identified using AutoDock.
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Affiliation(s)
- Roman Tumskiy
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Boris Khlebtsov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | | | - Stella Evstigneeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Evgeniya Antoshkina
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences (INEOS RAS), 28 Vavilova Str, Bld.1, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 9 Institutskiy per., 141700 Dolgoprudny, Russia
| | | | - Nikolai G Khlebtsov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
- Institute of Physics, Saratov State University, 410012 Saratov, Russia
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Pereira M, Macmillan DS, Willett C, Seidle T. REACHing for solutions: Essential revisions to the EU chemicals regulation to modernise safety assessment. Regul Toxicol Pharmacol 2022; 136:105278. [DOI: 10.1016/j.yrtph.2022.105278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/05/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022]
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Zhang X, Wang L, Chen S, Huang P, Ma L, Ding H, Basappa B, Zhu T, Lobie PE, Pandey V. Combined inhibition of BADSer99 phosphorylation and PARP ablates models of recurrent ovarian carcinoma. COMMUNICATIONS MEDICINE 2022; 2:82. [PMID: 35791346 PMCID: PMC9250505 DOI: 10.1038/s43856-022-00142-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
Background Poly (ADP-ribose) polymerase inhibitors (PARPis) have been approved for the treatment of recurrent epithelial ovarian cancer (EOC), regardless of BRCA status or homologous recombination repair deficiency. However, the low response of platinum-resistant EOC, the emergence of resistance in BRCA-deficient cancer, and therapy-associated toxicities in patients limit the clinical utility of PARPis in recurrent EOC. Methods The association of phosphorylated (p) BADS99 with clinicopathological parameters and survival outcomes in an EOC cohort was assessed by immunohistochemistry. The therapeutic synergy, and mechanisms thereof, between a pBADS99 inhibitor and PARPis in EOC was determined in vitro and in vivo using cell line and patient-derived models. Results A positive correlation between pBADS99 in EOC with higher disease stage and poorer survival is observed. Increased pBADS99 in EOC cells is significantly associated with BRCA-deficiency and decreased Cisplatin or Olaparib sensitivity. Pharmacological inhibition of pBADS99 synergizes with PARPis to enhance PARPi IC50 and decreases survival, foci formation, and growth in ex vivo culture of EOC cells and patient-derived organoids (PDOs). Combined inhibition of pBADS99 and PARP in EOC cells or PDOs enhances DNA damage but impairs PARPi stimulated DNA repair with a consequent increase in apoptosis. Inhibition of BADS99 phosphorylation synergizes with Olaparib to suppress the xenograft growth of platinum-sensitive and resistant EOC. Combined pBADS99-PARP inhibition produces a complete response in a PDX derived from a patient with metastatic and chemoresistant EOC. Conclusions A rational and efficacious combination strategy involving combined inhibition of pBADS99 and PARP for the treatment of recurrent EOC is presented. Ovarian cancer is difficult to successfully treat because it often recurs as the cancer becomes resistant to drugs used to treat it. As such, new drugs or combinations of drugs are needed to treat patients with recurrent ovarian cancer. Here, a drug combination is reported that is effective in experimental models of ovarian cancer, including those derived from patients. The combination approach uses drugs that have previously been approved for use in patients, known as PARP inhibitors, and another drug to inhibit cancer cell survival by targeting activation of a specific protein involved in cancer cell survival. The net effect of this drug combination in ovarian cancer models is greater than the sum of the drugs used individually. With further testing, this combination may offer a potential strategy to treat patients with recurrent ovarian cancer. Zhang et al. test the therapeutic potential of an inhibitor of BAD phosphorylation, NPB, in epithelial ovarian cancer. The authors show that the small molecule synergises with PARP inhibition to kill patient-derived ovarian cancer organoids and suppress the growth of xenograft tumours, including a cisplatin-resistant model.
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Liu F, Gao C, Zhang C, Gang H, Mu B, Yang S. A new zwitterionic surfactant with high interfacial activity and high salt tolerance derived from methyl oleate through an eco‐friendly aryl‐introducing method. J SURFACTANTS DETERG 2022. [DOI: 10.1002/jsde.12635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fang‐Hui Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering East China University of Science and Technology Shanghai China
| | - Cheng‐Long Gao
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering East China University of Science and Technology Shanghai China
| | - Cui‐Cui Zhang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering East China University of Science and Technology Shanghai China
| | - Hong‐Ze Gang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering East China University of Science and Technology Shanghai China
- Engineering Research Center of Microbial Enhanced Oil Recovery, MOE East China University of Science and Technology Shanghai China
| | - Bo‐Zhong Mu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering East China University of Science and Technology Shanghai China
- Engineering Research Center of Microbial Enhanced Oil Recovery, MOE East China University of Science and Technology Shanghai China
| | - Shi‐Zhong Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering East China University of Science and Technology Shanghai China
- Engineering Research Center of Microbial Enhanced Oil Recovery, MOE East China University of Science and Technology Shanghai China
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OUP accepted manuscript. Toxicol Res (Camb) 2022; 11:520-528. [DOI: 10.1093/toxres/tfac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/01/2022] [Accepted: 05/05/2022] [Indexed: 11/14/2022] Open
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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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Rasinger JD, Frenzel F, Braeuning A, Bernhard A, Ørnsrud R, Merel S, Berntssen MHG. Use of (Q)SAR genotoxicity predictions and fuzzy multicriteria decision-making for priority ranking of ethoxyquin transformation products. ENVIRONMENT INTERNATIONAL 2022; 158:106875. [PMID: 34607038 DOI: 10.1016/j.envint.2021.106875] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/16/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Ethoxyquin (EQ; 6-ethoxy-2,2,4-trimethyl-1,2-dihydroquinoline) has been used as an antioxidant in feed for pets and food-producing animals, including farmed fish such as Atlantic salmon. In Europe, the authorization for use of EQ as a feed additive was suspended, due to knowledge gaps concerning the presence and toxicity of EQ transformation products (TPs). Recent analytical studies focusing on the detection of EQ TPs in farmed Atlantic salmon feed and fillets reported the detection of a total of 27 EQ TPs, comprising both known and previously not described EQ TPs. We devised and applied an in silico workflow to rank these EQ TPs according to their genotoxic potential and their occurrence data in Atlantic salmon feed and fillet. Ames genotoxicity predictions were obtained applying a suite of five (quantitative) structure-activity relationship ((Q)SAR) tools, namely VEGA, TEST, LAZAR, Derek Nexus and Sarah Nexus. (Q)SAR Ames genotoxicity predictions were aggregated using fuzzy analytic hierarchy process (fAHP) multicriteria decision-making (MCDM). A priority ranking of EQ TPs was performed based on combining both fAHP ranked (Q)SAR predictions and analytical occurrence data. The applied workflow prioritized four newly identified EQ TPs for further investigation of genotoxicity. The fAHP-based prioritization strategy described here, can easily be applied to other toxicity endpoints and groups of chemicals for priority ranking of compounds of most concern for subsequent experimental and mechanistic toxicology analyses.
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Affiliation(s)
- J D Rasinger
- Institute of Marine Research (IMR), Bergen, Norway.
| | - F Frenzel
- German Federal Institute for Risk Assessment (BfR), Dept. Food Safety, Berlin, Germany
| | - A Braeuning
- German Federal Institute for Risk Assessment (BfR), Dept. Food Safety, Berlin, Germany
| | - A Bernhard
- Institute of Marine Research (IMR), Bergen, Norway
| | - R Ørnsrud
- Institute of Marine Research (IMR), Bergen, Norway
| | - S Merel
- Institute of Marine Research (IMR), Bergen, Norway; National Research Institute for Agriculture, Food and Environment (INRAE), Lyon-Villeurbanne, France
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Hakura A, Awogi T, Shiragiku T, Ohigashi A, Yamamoto M, Kanasaki K, Oka H, Dewa Y, Ozawa S, Sakamoto K, Kato T, Yamamura E. Bacterial mutagenicity test data: collection by the task force of the Japan pharmaceutical manufacturers association. Genes Environ 2021; 43:41. [PMID: 34593056 PMCID: PMC8482598 DOI: 10.1186/s41021-021-00206-1] [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] [Received: 03/21/2021] [Accepted: 07/07/2021] [Indexed: 12/04/2022] Open
Abstract
Background Ames test is used worldwide for detecting the bacterial mutagenicity of chemicals. In silico analyses of bacterial mutagenicity have recently gained acceptance by regulatory agencies; however, current in silico models for prediction remain to be improved. The Japan Pharmaceutical Manufacturers Association (JPMA) organized a task force in 2017 in which eight Japanese pharmaceutical companies had participated. The purpose of this task force was to disclose a piece of pharmaceutical companies’ proprietary Ames test data. Results Ames test data for 99 chemicals of various chemical classes were collected for disclosure in this study. These chemicals are related to the manufacturing process of pharmaceutical drugs, including reagents, synthetic intermediates, and drug substances. The structure-activity (mutagenicity) relationships are discussed in relation to structural alerts for each chemical class. In addition, in silico analyses of these chemicals were conducted using a knowledge-based model of Derek Nexus (Derek) and a statistics-based model (GT1_BMUT module) of CASE Ultra. To calculate the effectiveness of these models, 89 chemicals for Derek and 54 chemicals for CASE Ultra were selected; major exclusions were the salt form of four chemicals that were tested both in the salt and free forms for both models, and 35 chemicals called “known” positives or negatives for CASE Ultra. For Derek, the sensitivity, specificity, and accuracy were 65% (15/23), 71% (47/66), and 70% (62/89), respectively. The sensitivity, specificity, and accuracy were 50% (6/12), 60% (25/42), and 57% (31/54) for CASE Ultra, respectively. The ratio of overall disagreement between the CASE Ultra “known” positives/negatives and the actual test results was 11% (4/35). In this study, 19 out of 28 mutagens (68%) were detected with TA100 and/or TA98, and 9 out of 28 mutagens (32%) were detected with either TA1535, TA1537, WP2uvrA, or their combination. Conclusion The Ames test data presented here will help avoid duplicated Ames testing in some cases, support duplicate testing in other cases, improve in silico models, and enhance our understanding of the mechanisms of mutagenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s41021-021-00206-1.
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Affiliation(s)
- Atsushi Hakura
- Global Drug Safety, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki, 300-2635, Japan.
| | - Takumi Awogi
- Manufacturing Process Development Department, Otsuka Pharmaceutical Co., Ltd., 224-18 Hiraishi-Ebisuno, Kawauchi-cho, Tokushima-shi, Tokushima, 771-0182, Japan
| | - Toshiyuki Shiragiku
- Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima-shi, Tokushima, 771-0192, Japan
| | - Atsushi Ohigashi
- Process Chemistry Labs, Astellas Pharma Inc., 160-2 Akahama, Takahagi, Ibaraki, 318-0001, Japan
| | - Mika Yamamoto
- Drug Safety Research Labs, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan
| | - Kayoko Kanasaki
- Laboratory for Drug Discovery and Development, Shionogi & Co., Ltd., 3-1-1 Futaba-cho, Osaka, Toyonaka-shi, 561-0825, Japan
| | - Hiroaki Oka
- Toxicology Laboratory, Taiho pharmaceutical Co., Ltd., 224-2 Ebisuno, Hiraishi, Kawauchi-cho, Tokushima, 771-0194, Japan
| | - Yasuaki Dewa
- Toxicology Research Laboratory, Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi, 329-0114, Japan
| | - Shunsuke Ozawa
- Toxicology Research Laboratory, Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi, 329-0114, Japan
| | - Kouji Sakamoto
- Drug Safety, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-cho, Kita-ku, Saitama-shi, 331-9530, Japan
| | - Tatsuya Kato
- Safety Research Laboratories, Mitsubishi Tanabe Pharma Co., 2-2-50 Kawagishi, Toda-shi, Saitama, 335-8505, Japan
| | - Eiji Yamamura
- Safety Research Laboratories, Mitsubishi Tanabe Pharma Co., 2-2-50 Kawagishi, Toda-shi, Saitama, 335-8505, Japan
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Benigni R. In silico assessment of genotoxicity. Combinations of sensitive structural alerts minimize false negative predictions for all genotoxicity endpoints and can single out chemicals for which experimentation can be avoided. Regul Toxicol Pharmacol 2021; 126:105042. [PMID: 34506881 DOI: 10.1016/j.yrtph.2021.105042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 11/15/2022]
Abstract
Genotoxicity assessment of chemicals has a crucial role in most regulations. Due to labor, time, cost, and animal welfare issues, attention is being given to (Q)SAR methods. A strategic application of alternative methods is to first use a sequence of conservative (very sensitive) (Q)SARs and/or in vitro models to arrive at the conclusion that no further testing is necessary for negatives, and to use mechanistically based, Weight-Of-Evidence approach to evaluate the chemicals showing positive results. The ICH M7 guideline to detect DNA-reactive impurities in drugs follows these lines (recommending solely (Q)SAR in step 1). However, ICH M7 focuses only on Ames test. Here a large database of more than 6000 chemicals positive in at least one endpoint (in vitro gene mutations or chromosomal aberrations, in vivo micronucleus, aneugenicity) were analyzed with structural alerts implemented in the OECD QSAR Toolbox, resulting in maximum 3% false negatives. These promising results indicate that it may be possible to extend the approach to the whole range of genotoxicity endpoints required by regulations. Since structural alerts may generate false positives, cautious follow-up of positives is recommended (with e.g., statistically based QSARs, read across of similar chemicals, expert judgement, and experimentation when necessary).
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El-Wakil MH, Teleb M, Abu-Serie MM, Huang S, Zamponi GW, Fahmy H. Structural optimization, synthesis and in vitro synergistic anticancer activities of combinations of new N3-substituted dihydropyrimidine calcium channel blockers with cisplatin and etoposide. Bioorg Chem 2021; 115:105262. [PMID: 34411980 DOI: 10.1016/j.bioorg.2021.105262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/19/2021] [Accepted: 08/07/2021] [Indexed: 01/09/2023]
Abstract
T-type calcium channels are considered potential drug targets to combat cancer. Combining T-type calcium channel blockers with conventional chemotherapy drugs represents a promising strategy towards successful cancer treatment. From this perspective, we report in this study the design and synthesis of a novel series of N3-sustituted dihydropyrimidines (DHPMs) as anticancer adjuvants to cisplatin (Cis) and etoposide (Eto). Full spectral characterization of the new compounds was done using FT-IR, 1H NMR, 13C NMR, and HRMS. Structure elucidation was confirmed by 2D NMR 1H-H COSY, HSQC and NOESY experiments. Novel derivatives were tested for their Ca2+ channel blocking activity by employing the whole cell patch-clamp technique. Results demonstrated that most compounds were potential T-type calcium channel blockers with the triazole-based C12 and C13 being the most selective agents against CaV3.2 channel. Further electrophysiological studies demonstrated that C12 and C13 inhibited CaV3.2 currents with respective affinity of 2.26 and 1.27 µM, and induced 5 mV hyperpolarizing shifts in the half-inactivation potential. Subsequently, C12 and C13 were evaluated for their anticancer activities alone and in combination with Cis and Eto against A549 and MDA-MB 231 cancer cells. Interestingly, both compounds exhibited potential anticancer effects with IC50 values < 5 µM. Combination studies revealed that both compounds had synergistic effects (combination index CI < 1) on Cis and Eto through induction of apoptosis (p53 activation and up-regulation of BAX and p21 gene expression). Importantly, in silico physicochemical and ADMET assessment of both compounds revealed their potential drug-like properties with decreased risk of cardiac toxicity. Hence, C12 and C13 are promising anticancer adjuvants through inhibition of CaV3.2 T-type calcium channels, thereby serving as eminent leads for further modification.
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Affiliation(s)
- Marwa H El-Wakil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Mohamed Teleb
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt.
| | - Marwa M Abu-Serie
- Department of Medical Biotechnology, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Egypt
| | - Sun Huang
- Department of Physiology & Pharmacology, Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary T2N 4N1, Canada
| | - Gerald W Zamponi
- Department of Physiology & Pharmacology, Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary T2N 4N1, Canada
| | - Hesham Fahmy
- Department of Pharmaceutical Sciences, College of Pharmacy & Allied Health Sciences, South Dakota State University, Brookings, SD 57006, USA.
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Tcheremenskaia O, Benigni R. Toward regulatory acceptance and improving the prediction confidence of in silico approaches: a case study of genotoxicity. Expert Opin Drug Metab Toxicol 2021; 17:987-1005. [PMID: 34078212 DOI: 10.1080/17425255.2021.1938540] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: Genotoxicity is an imperative component of the human health safety assessment of chemicals. Its secure forecast is of the utmost importance for all health prevention strategies and regulations.Areas covered: We surveyed several types of alternative, animal-free approaches ((quantitative) structure-activity relationship (Q)SAR, read-across, Adverse Outcome Pathway, Integrated Approaches to Testing and Assessment) for genotoxicity prediction within the needs of regulatory frameworks, putting special emphasis on data quality and uncertainties issues.Expert opinion: (Q)SAR models and read-across approaches for in vitro bacterial mutagenicity have sufficient reliability for use in prioritization processes, and as support in regulatory decisions in combination with other types of evidence. (Q)SARs and read-across methodologies for other genotoxicity endpoints need further improvements and should be applied with caution. It appears that there is still large room for improvement of genotoxicity prediction methods. Availability of well-curated high-quality databases, covering a broader chemical space, is one of the most important needs. Integration of in silico predictions with expert knowledge, weight-of-evidence-based assessment, and mechanistic understanding of genotoxicity pathways are other key points to be addressed for the generation of more accurate and trustable results.
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Affiliation(s)
- Olga Tcheremenskaia
- Environmental and Health Department, Istituto Superiore Di Sanità (ISS), Rome, Italy, Rome, Italy
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14
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Pradeep P, Judson R, DeMarini DM, Keshava N, Martin TM, Dean J, Gibbons CF, Simha A, Warren SH, Gwinn MR, Patlewicz G. Evaluation of Existing QSAR Models and Structural Alerts and Development of New Ensemble Models for Genotoxicity Using a Newly Compiled Experimental Dataset. ACTA ACUST UNITED AC 2021; 18. [PMID: 34504984 DOI: 10.1016/j.comtox.2021.100167] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Regulatory agencies world-wide face the challenge of performing risk-based prioritization of thousands of substances in commerce. In this study, a major effort was undertaken to compile a large genotoxicity dataset (54,805 records for 9299 substances) from several public sources (e.g., TOXNET, COSMOS, eChemPortal). The names and outcomes of the different assays were harmonized, and assays were annotated by type: gene mutation in Salmonella bacteria (Ames assay) and chromosome mutation (clastogenicity) in vitro or in vivo (chromosome aberration, micronucleus, and mouse lymphoma Tk +/- assays). This dataset was then evaluated to assess genotoxic potential using a categorization scheme, whereby a substance was considered genotoxic if it was positive in at least one Ames or clastogen study. The categorization dataset comprised 8442 chemicals, of which 2728 chemicals were genotoxic, 5585 were not and 129 were inconclusive. QSAR models (TEST and VEGA) and the OECD Toolbox structural alerts/profilers (e.g., OASIS DNA alerts for Ames and chromosomal aberrations) were used to make in silico predictions of genotoxicity potential. The performance of the individual QSAR tools and structural alerts resulted in balanced accuracies of 57-73%. A Naïve Bayes consensus model was developed using combinations of QSAR models and structural alert predictions. The 'best' consensus model selected had a balanced accuracy of 81.2%, a sensitivity of 87.24% and a specificity of 75.20%. This in silico scheme offers promise as a first step in ranking thousands of substances as part of a prioritization approach for genotoxicity.
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Affiliation(s)
- Prachi Pradeep
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Richard Judson
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - David M DeMarini
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Nagalakshmi Keshava
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Todd M Martin
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Jeffry Dean
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Catherine F Gibbons
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Washington, District of Columbia, USA
| | - Anita Simha
- ORAU, contractor to U.S. Environmental Protection Agency through the National Student Services Contract, Research Triangle Park, North Carolina, USA
| | - Sarah H Warren
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Maureen R Gwinn
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Grace Patlewicz
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
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15
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Docking and antibacterial activity of novel nontoxic 5-arylidenepyrimidine-triones as inhibitors of NDM-1 and MetAP-1. Future Med Chem 2021; 13:1041-1055. [PMID: 33913733 DOI: 10.4155/fmc-2021-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Antibiotic resistance, which occurs through the action of metallo-β-lactamases (NDM-1), is a serious problem in the treatment of infectious diseases. Therefore, the discovery of new NDM-1 inhibitors and promising antibacterial agents as inhibitors of alternative targets (MetAP-1) is important. Method & results: In this study, a virtual library of 5-arylidene barbituric acids was created and molecular docking was performed for identification of novel possible inhibitors of NDM-1 and MetAP-1. Antibacterial activity (agar well-diffusion assay) and cytotoxicity (alamarBlue assay) of perspective compounds were evaluated. Pharmacokinetic profiles and molecular properties were predicted. Conclusion: We have identified possible novel inhibitors of NDM-1 and MetAP-1 with bacteriostatic activity, most of which are not cytotoxic and have potential excellent drug-likeness properties.
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Krebs J, McKeague M. Green Toxicology: Connecting Green Chemistry and Modern Toxicology. Chem Res Toxicol 2020; 33:2919-2931. [DOI: 10.1021/acs.chemrestox.0c00260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Johanna Krebs
- Pharmacology and Therapeutics, Faculty of Medicine, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 1Y6
- Department of Health Sciences and Technology, ETH Zürich, Universitätstrasse 2, Zurich, Switzerland CH 8092
| | - Maureen McKeague
- Pharmacology and Therapeutics, Faculty of Medicine, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 1Y6
- Faculty of Science, Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
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17
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Herrmann K, Holzwarth A, Rime S, Fischer BC, Kneuer C. (Q)SAR tools for the prediction of mutagenic properties: Are they ready for application in pesticide regulation? PEST MANAGEMENT SCIENCE 2020; 76:3316-3325. [PMID: 32223060 DOI: 10.1002/ps.5828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 03/29/2020] [Indexed: 06/10/2023]
Abstract
The assessment of human health risks resulting from the presence of metabolites in groundwater and food residues has become an important element in pesticide authorisation. In this context, the evaluation of mutagenicity is of particular interest and a paradigm shift from exposure-triggered testing to in silico-based screening has been recommended in the European Food Safety Authority (EFSA) Guidance on the establishment of the residue definition for dietary risk assessment. In addition, it is proposed to apply in silico predictions when experimental mutagenicity testing is not possible due to a lack of sufficient quantities of the pesticide metabolite. This, combined with animal welfare and economic considerations, has led to a situation where an increasing number of in silico studies are submitted to regulatory authorities. Whilst there is extensive experience with in silico predictions for mutagenicity in the chemical and pharmaceutical industry, their suitability in pesticide regulation is still insufficiently considered. Therefore, we herein discuss critical issues that need to be resolved to successfully implement (Quantitative) Structure-Activity Relationship ((Q)SAR) as an accepted tool in pesticide regulation. For illustration purposes, the results of a pilot study are included. The presented study highlights a need for further improvement regarding the predictivity and applicability domain of (Q)SAR systems for pesticides and their metabolites, but also raises other questions such as model selection, establishment of acceptance criteria, harmonised approaches to the combination of model outputs into overall conclusions, adequate reporting and data sharing. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Kristin Herrmann
- Department Pesticides Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Andrea Holzwarth
- Department Pesticides Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Soyub Rime
- Department Pesticides Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Benjamin C Fischer
- Department Pesticides Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Carsten Kneuer
- Department Pesticides Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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18
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Goel R, Valerio LG. Predicting the mutagenic potential of chemicals in tobacco products using in silico toxicology tools. Toxicol Mech Methods 2020; 30:672-678. [DOI: 10.1080/15376516.2020.1805836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Reema Goel
- United States Food and Drug Administration, Division of Nonclinical Science, Office of Science, Center for Tobacco Products, Calverton, MD, USA
| | - Luis G. Valerio
- United States Food and Drug Administration, Division of Nonclinical Science, Office of Science, Center for Tobacco Products, Calverton, MD, USA
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Moon J, Lee B, Ra JS, Kim KT. Predicting PBT and CMR properties of substances of very high concern (SVHCs) using QSAR models, and application for K-REACH. Toxicol Rep 2020; 7:995-1000. [PMID: 32874922 PMCID: PMC7451722 DOI: 10.1016/j.toxrep.2020.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/29/2020] [Accepted: 08/10/2020] [Indexed: 11/26/2022] Open
Abstract
BIOWIN is effective for predicting persistence and bioaccumulation. Toxtree is effective for predicting carcinogenicity and mutagenicity. WoE approach enhances the sensitivity. It is recommended to set a conservative criteria of log Kow more than 4.5 in K-REACH.
Quantitative structure-activity relationship (QSAR) models have been applied to predict a variety of toxicity endpoints. Their performance needs to be validated, in a variety of cases, to increase their applicability to chemical regulation. Using the data set of substances of very high concern (SVHCs), the performance of QSAR models were evaluated to predict the persistence and bioaccumulation of PBT, and the carcinogenicity and mutagenicity of CMR. BIOWIN and Toxtree showed higher sensitivity than other QSAR models – the former for persistence and bioaccumulation, the latter for carcinogenicity. In terms of mutagenicity, the sensitivities of QSAR models were underestimated, Toxtree was more accurate and specific than lazy structure–activity relationships (LAZARs) and Computer Assisted Evaluation of industrial chemical Substances According to Regulations (CAESAR). Using the weight of evidence (WoE) approach, which integrates results of individual QSAR models, enhanced the sensitivity of each toxicity endpoint. On the basis of obtained results, in particular the prediction of persistence and bioaccumulation by KOWWIN, a conservative criterion is recommended of log Kow greater than 4.5 in K-REACH, without an upper limit. This study suggests that reliable production of toxicity data by QSAR models is facilitated by a better understanding of the performance of these models.
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Key Words
- AD, applicability domain
- AFC, atom/fragment contribution
- BCF, bioconcentration factor
- CAESAR, Computer Assisted Evaluation of industrial chemical Substances According to Regulations
- CAS, chemicals abstracts service
- CMR
- CMR, carcinogenic, mutagenic or toxic for reproduction
- DSSTox, distributed structure-searchable toxicity
- ECHA, European Chemical Agency
- EDC, endocrine disrupting chemicals
- EPI, estimation programs interface
- FN, false negative
- FP, false positive
- GHS, globally harmonized system of classification and labelling of chemicals
- K-REACH
- Kow, octanol-water coefficient
- LAZAR, lazy structure–activity relationships
- PBT
- PBT, persistent, bioaccumulative and toxic
- PFCAs, perfluorinated carboxylic acids
- PFDA, nonadecafluorodecanoic acid
- QMRF, QSAR model reporting format
- QPRF, QSAR prediction reporting format
- QSAR
- QSAR, quantitative structure-activity relationship
- REACH, registration, evaluation, authorization and restriction of chemicals
- SA, structure alters
- SMILES, simplified molecular-input line-entry system
- SVHCs
- SVHCs, substances of very high concern
- TN, ture negative
- TP, ture positive
- US EPA, United States Environmental Protection Agency
- UVCBs, complex reaction products or biological materials
- WoE, weight of evidence
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Affiliation(s)
- Joonsik Moon
- Department of Environmental Energy Engineering, Seoul National University of Science and Technology, Seoul, 01811, Republic of Korea
| | - Byongcheun Lee
- Risk Assessment Division, National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Jin-Sung Ra
- Eco-testing and Risk Assessment Center, Korea Institute of Industrial Technology (KITECH), Ansan, 15588, Republic of Korea
| | - Ki-Tae Kim
- Department of Environmental Energy Engineering, Seoul National University of Science and Technology, Seoul, 01811, Republic of Korea
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Benigni R, Bassan A, Pavan M. In silico models for genotoxicity and drug regulation. Expert Opin Drug Metab Toxicol 2020; 16:651-662. [DOI: 10.1080/17425255.2020.1785428] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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21
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Patlewicz G. Navigating the Minefield of Computational Toxicology and Informatics: Looking Back and Charting a New Horizon. FRONTIERS IN TOXICOLOGY 2020; 2:2. [PMID: 35296116 PMCID: PMC8915910 DOI: 10.3389/ftox.2020.00002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/20/2020] [Indexed: 01/07/2023] Open
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Klapacz J, Gollapudi BB. Considerations for the Use of Mutation as a Regulatory Endpoint in Risk Assessment. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:84-93. [PMID: 31301246 DOI: 10.1002/em.22318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
Assessment of a chemical's potential to cause permanent changes in the genetic code has been a common practice in the industry and regulatory settings for decades. Furthermore, the genetic toxicity battery of tests has typically been employed during the earliest stages of the research and development programs of new product development. A positive outcome from such battery has a major impact on the chemical's utility, industrial hygiene, product stewardship practices, and product life cycle analysis, among many other decisions that need to be taken by the industry, even before the registration of a chemical is undertaken. Under the prevailing regulatory paradigm, the dichotomous (yes/no) evaluation of the chemical's genotoxic potential leads to a conservative, linear no-threshold (LNT) risk assessment, unless compelling and undeniable data to the contrary can be provided to satisfy regulators, typically in a number of different global jurisdictions. With the current advent of predictive methods, new testing paradigms, mode-of-action/adverse outcome pathways, and quantitative risk assessment approaches, various stakeholders are starting to employ these state-of-the-science methodologies to further the conversation on decision making and advance the regulatory paradigm beyond the dominant LNT status quo. This commentary describes these novel methodologies, relevant biological responses, and how these can affect internal and regulatory risk assessment approaches. Environ. Mol. Mutagen. 61:84-93, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Joanna Klapacz
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, Midland, Michigan
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Chakravarti SK, Alla SRM. Descriptor Free QSAR Modeling Using Deep Learning With Long Short-Term Memory Neural Networks. Front Artif Intell 2019; 2:17. [PMID: 33733106 PMCID: PMC7861338 DOI: 10.3389/frai.2019.00017] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 08/22/2019] [Indexed: 12/15/2022] Open
Abstract
Current practice of building QSAR models usually involves computing a set of descriptors for the training set compounds, applying a descriptor selection algorithm and finally using a statistical fitting method to build the model. In this study, we explored the prospects of building good quality interpretable QSARs for big and diverse datasets, without using any pre-calculated descriptors. We have used different forms of Long Short-Term Memory (LSTM) neural networks to achieve this, trained directly using either traditional SMILES codes or a new linear molecular notation developed as part of this work. Three endpoints were modeled: Ames mutagenicity, inhibition of P. falciparum Dd2 and inhibition of Hepatitis C Virus, with training sets ranging from 7,866 to 31,919 compounds. To boost the interpretability of the prediction results, attention-based machine learning mechanism, jointly with a bidirectional LSTM was used to detect structural alerts for the mutagenicity data set. Traditional fragment descriptor-based models were used for comparison. As per the results of the external and cross-validation experiments, overall prediction accuracies of the LSTM models were close to the fragment-based models. However, LSTM models were superior in predicting test chemicals that are dissimilar to the training set compounds, a coveted quality of QSAR models in real world applications. In summary, it is possible to build QSAR models using LSTMs without using pre-computed traditional descriptors, and models are far from being “black box.” We wish that this study will be helpful in bringing large, descriptor-less QSARs to mainstream use.
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Figueiredo J, Serrano JL, Soares M, Ferreira S, Domingues FC, Almeida P, Silvestre S. 5-Hydrazinylethylidenepyrimidines effective against multidrug-resistant Acinetobacter baumannii: Synthesis and in vitro biological evaluation of antibacterial, radical scavenging and cytotoxic activities. Eur J Pharm Sci 2019; 137:104964. [DOI: 10.1016/j.ejps.2019.104964] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/03/2019] [Accepted: 06/20/2019] [Indexed: 12/14/2022]
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Towards quantitative read across: Prediction of Ames mutagenicity in a large database. Regul Toxicol Pharmacol 2019; 108:104434. [PMID: 31374229 DOI: 10.1016/j.yrtph.2019.104434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/10/2019] [Accepted: 07/30/2019] [Indexed: 11/23/2022]
Abstract
In silico chemical safety assessment can support the evaluation of hazard and risk following potential exposure to a substance, thus stimulating an increased interest for the use of Structure-Activity based approaches by regulatory authorities, particularly QSAR and Read Across. Whereas the longer history of QSAR led to recognize the crucial requirements for predictivity, there are still challenges faced by adopting Read Across to a larger extent in a regulatory setting, namely standardization and objective criteria. In previous research, suitable conditions for applying Read Across to the prediction of the Ames mutagenicity of metabolites and degradation products of pesticides were established: a standardized similarity criterion based simultaneously on basic molecular properties and Structural Similarity was successfully applied to a number of case studies. Here the investigation is extended to a large database of curated Ames mutagenicity results. For around 2,000 chemicals for which the similarity criterion was applicable, the predictivity of Read Across was high: specificity 0.72, sensitivity 0.90, accuracy 0.85. This compares favourably with the Ames test intra-assay variability, and with the predictivity of QSAR models. The need for standardization and rigorous validation of Read Across is emphasized.
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