1
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Varsou DD, Kolokathis PD, Antoniou M, Sidiropoulos NK, Tsoumanis A, Papadiamantis AG, Melagraki G, Lynch I, Afantitis A. In silico assessment of nanoparticle toxicity powered by the Enalos Cloud Platform: Integrating automated machine learning and synthetic data for enhanced nanosafety evaluation. Comput Struct Biotechnol J 2024; 25:47-60. [PMID: 38646468 PMCID: PMC11026727 DOI: 10.1016/j.csbj.2024.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/23/2024] Open
Abstract
The rapid advance of nanotechnology has led to the development and widespread application of nanomaterials, raising concerns regarding their potential adverse effects on human health and the environment. Traditional (experimental) methods for assessing the nanoparticles (NPs) safety are time-consuming, expensive, and resource-intensive, and raise ethical concerns due to their reliance on animals. To address these challenges, we propose an in silico workflow that serves as an alternative or complementary approach to conventional hazard and risk assessment strategies, which incorporates state-of-the-art computational methodologies. In this study we present an automated machine learning (autoML) scheme that employs dose-response toxicity data for silver (Ag), titanium dioxide (TiO2), and copper oxide (CuO) NPs. This model is further enriched with atomistic descriptors to capture the NPs' underlying structural properties. To overcome the issue of limited data availability, synthetic data generation techniques are used. These techniques help in broadening the dataset, thus improving the representation of different NP classes. A key aspect of this approach is a novel three-step applicability domain method (which includes the development of a local similarity approach) that enhances user confidence in the results by evaluating the prediction's reliability. We anticipate that this approach will significantly expedite the nanosafety assessment process enabling regulation to keep pace with innovation, and will provide valuable insights for the design and development of safe and sustainable NPs. The ML model developed in this study is made available to the scientific community as an easy-to-use web-service through the Enalos Cloud Platform (www.enaloscloud.novamechanics.com/sabydoma/safenanoscope/), facilitating broader access and collaborative advancements in nanosafety.
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Affiliation(s)
- Dimitra-Danai Varsou
- NovaMechanics MIKE, Piraeus 18545, Greece
- Entelos Institute, Larnaca 6059, Cyprus
| | | | | | | | - Andreas Tsoumanis
- Entelos Institute, Larnaca 6059, Cyprus
- NovaMechanics Ltd, Nicosia 1070, Cyprus
| | - Anastasios G. Papadiamantis
- Entelos Institute, Larnaca 6059, Cyprus
- NovaMechanics Ltd, Nicosia 1070, Cyprus
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, UK
| | - Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, Vari 16672, Greece
| | - Iseult Lynch
- Entelos Institute, Larnaca 6059, Cyprus
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, UK
| | - Antreas Afantitis
- NovaMechanics MIKE, Piraeus 18545, Greece
- Entelos Institute, Larnaca 6059, Cyprus
- NovaMechanics Ltd, Nicosia 1070, Cyprus
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2
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Kromer C, Katz A, Feldmann I, Laux P, Luch A, Tschiche HR. A targeted fluorescent nanosensor for ratiometric pH sensing at the cell surface. Sci Rep 2024; 14:12302. [PMID: 38811698 PMCID: PMC11137054 DOI: 10.1038/s41598-024-62976-2] [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: 03/03/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024] Open
Abstract
The correlation between altered extracellular pH and various pathological conditions, including cancer, inflammation and metabolic disorders, is well known. Bulk pH measurements cannot report the extracellular pH value at the cell surface. However, there is a limited number of suitable tools for measuring the extracellular pH of cells with high spatial resolution, and none of them are commonly used in laboratories around the world. In this study, a versatile ratiometric nanosensor for the measurement of extracellular pH was developed. The nanosensor consists of biocompatible polystyrene nanoparticles loaded with the pH-inert reference dye Nile red and is surface functionalized with a pH-responsive fluorescein dye. Equipped with a targeting moiety, the nanosensor can adhere to cell membranes, allowing direct measurement of extracellular pH at the cell surface. The nanosensor exhibits a sensitive ratiometric pH response within the range of 5.5-9.0, with a calculated pKa of 7.47. This range optimally covers the extracellular pH (pHe) of most healthy cells and cells in which the pHe is abnormal, such as cancer cells. In combination with the nanosensors ability to target cell membranes, its high robustness, reversibility and its biocompatibility, the pHe nanosensor proves to be well suited for in-situ measurement of extracellular pH, even over extended time periods. This pH nanosensor has the potential to advance biomedical research by improving our understanding of cellular microenvironments, where extracellular pH plays an important role.
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Affiliation(s)
- Charlotte Kromer
- Product Materials and Nanotechnology, Department Chemical and Product Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany.
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - Aaron Katz
- Product Materials and Nanotechnology, Department Chemical and Product Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Ines Feldmann
- Material-Microbiome Interactions, Department Materials and the Environment, Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Peter Laux
- Product Materials and Nanotechnology, Department Chemical and Product Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Andreas Luch
- Product Materials and Nanotechnology, Department Chemical and Product Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Harald R Tschiche
- Product Materials and Nanotechnology, Department Chemical and Product Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
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3
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Huang J, Zhang J, Sun J, Gong M, Yuan Z. Exposure to polystyrene microplastics and perfluorooctane sulfonate disrupt the homeostasis of intact planarians and the growth of regenerating planarians. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171653. [PMID: 38485023 DOI: 10.1016/j.scitotenv.2024.171653] [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: 12/25/2023] [Revised: 03/09/2024] [Accepted: 03/09/2024] [Indexed: 03/17/2024]
Abstract
Microplastics (MPs) and perfluorinated compounds (PFAS) are widespread in the global ecosystem. MPs have the ability to adsorb organic contaminants such as perfluorooctane sulfonate (PFOS), leading to combined effects. The current work aims to explore the individual and combined toxicological effects of polystyrene (PS) and PFOS on the growth and nerves of the freshwater planarian (Dugesia japonica). The results showed that PS particles could adsorb PFOS. PS and PFOS impeded the regeneration of decapitated planarians eyespots, whereas the combined treatment increased the locomotor speed of intact planarians. PS and PFOS caused significant DNA damage, while co-treatment with different PS concentrations aggravated and attenuated DNA damage, respectively. Further studies at the molecular level have shown that PS and PFOS affect the proliferation and differentiation of neoblasts in both intact and regenerating planarians, alter the expression levels of neuronal genes, and impede the development of the nervous system. PS and PFOS not only disrupted the homeostasis of intact planarians, but also inhibited the regeneration of decapitated planarians. This study is the first to assess the multiple toxicity of PS and PFOS to planarians after combined exposure. It provides a basis for the environmental and human health risks of MPs and PFAS.
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Affiliation(s)
- Jinying Huang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong, China
| | - Jianyong Zhang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong, China
| | - Jingyi Sun
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong, China
| | - Mengxin Gong
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong, China
| | - Zuoqing Yuan
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, Shandong, China.
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4
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Antoniou M, Papavasileiou KD, Melagraki G, Dondero F, Lynch I, Afantitis A. Development of a Robust Read-Across Model for the Prediction of Biological Potency of Novel Peroxisome Proliferator-Activated Receptor Delta Agonists. Int J Mol Sci 2024; 25:5216. [PMID: 38791255 PMCID: PMC11121726 DOI: 10.3390/ijms25105216] [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: 04/01/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
A robust predictive model was developed using 136 novel peroxisome proliferator-activated receptor delta (PPARδ) agonists, a distinct subtype of lipid-activated transcription factors of the nuclear receptor superfamily that regulate target genes by binding to characteristic sequences of DNA bases. The model employs various structural descriptors and docking calculations and provides predictions of the biological activity of PPARδ agonists, following the criteria of the Organization for Economic Co-operation and Development (OECD) for the development and validation of quantitative structure-activity relationship (QSAR) models. Specifically focused on small molecules, the model facilitates the identification of highly potent and selective PPARδ agonists and offers a read-across concept by providing the chemical neighbours of the compound under study. The model development process was conducted on Isalos Analytics Software (v. 0.1.17) which provides an intuitive environment for machine-learning applications. The final model was released as a user-friendly web tool and can be accessed through the Enalos Cloud platform's graphical user interface (GUI).
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Affiliation(s)
- Maria Antoniou
- Department of Chemoinformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus; (M.A.); (K.D.P.)
- Department of ChemoInformatics, NovaMechanics MIKE, 18545 Piraeus, Greece
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
| | - Konstantinos D. Papavasileiou
- Department of Chemoinformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus; (M.A.); (K.D.P.)
- Department of ChemoInformatics, NovaMechanics MIKE, 18545 Piraeus, Greece
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, 16672 Vari, Greece;
| | - Francesco Dondero
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
- Department of Science and Technological Innovation, Università del Piemonte Orientale, 15121 Alessandria, Italy
| | - Iseult Lynch
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
- School of Geography, Earth and Environmental Sciences, University of Birmingham Edgbaston, Birmingham B15 2TT, UK
| | - Antreas Afantitis
- Department of Chemoinformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus; (M.A.); (K.D.P.)
- Department of ChemoInformatics, NovaMechanics MIKE, 18545 Piraeus, Greece
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
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5
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Varsou DD, Sarimveis H. Deimos: A novel automated methodology for optimal grouping. Application to nanoinformatics case studies. Mol Inform 2023; 42:e2300019. [PMID: 37258455 DOI: 10.1002/minf.202300019] [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: 01/22/2023] [Revised: 05/05/2023] [Accepted: 05/31/2023] [Indexed: 06/02/2023]
Abstract
In this study we present deimos, a computational methodology for optimal grouping, applied on the read-across prediction of engineered nanomaterials' (ENMs) toxicity-related properties. The method is based on the formulation and the solution of a mixed-integer optimization program (MILP) problem that automatically and simultaneously performs feature selection, defines the grouping boundaries according to the response variable and develops linear regression models in each group. For each group/region, the characteristic centroid is defined in order to allocate untested ENMs to the groups. The deimos MILP problem is integrated in a broader optimization workflow that selects the best performing methodology between the standard multiple linear regression (MLR), the least absolute shrinkage and selection operator (LASSO) models and the proposed deimos multiple-region model. The performance of the suggested methodology is demonstrated through the application to benchmark ENMs datasets and comparison with other predictive modelling approaches. However, the proposed method can be applied to property prediction of other than ENM chemical entities and it is not limited to ENMs toxicity prediction.
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Affiliation(s)
- Dimitra-Danai Varsou
- School of Chemical Engineering, National Technical University of Athens, 157 80, Athens, Greece
| | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, 157 80, Athens, Greece
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6
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Yan X, Yue T, Winkler DA, Yin Y, Zhu H, Jiang G, Yan B. Converting Nanotoxicity Data to Information Using Artificial Intelligence and Simulation. Chem Rev 2023. [PMID: 37262026 DOI: 10.1021/acs.chemrev.3c00070] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Decades of nanotoxicology research have generated extensive and diverse data sets. However, data is not equal to information. The question is how to extract critical information buried in vast data streams. Here we show that artificial intelligence (AI) and molecular simulation play key roles in transforming nanotoxicity data into critical information, i.e., constructing the quantitative nanostructure (physicochemical properties)-toxicity relationships, and elucidating the toxicity-related molecular mechanisms. For AI and molecular simulation to realize their full impacts in this mission, several obstacles must be overcome. These include the paucity of high-quality nanomaterials (NMs) and standardized nanotoxicity data, the lack of model-friendly databases, the scarcity of specific and universal nanodescriptors, and the inability to simulate NMs at realistic spatial and temporal scales. This review provides a comprehensive and representative, but not exhaustive, summary of the current capability gaps and tools required to fill these formidable gaps. Specifically, we discuss the applications of AI and molecular simulation, which can address the large-scale data challenge for nanotoxicology research. The need for model-friendly nanotoxicity databases, powerful nanodescriptors, new modeling approaches, molecular mechanism analysis, and design of the next-generation NMs are also critically discussed. Finally, we provide a perspective on future trends and challenges.
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Affiliation(s)
- Xiliang Yan
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Tongtao Yue
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Institute of Coastal Environmental Pollution Control, Ocean University of China, Qingdao 266100, China
| | - David A Winkler
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- School of Pharmacy, University of Nottingham, Nottingham NG7 2QL, U.K
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Yongguang Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hao Zhu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Bing Yan
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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7
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Blekos K, Chairetakis K, Lynch I, Marcoulaki E. Principles and requirements for nanomaterial representations to facilitate machine processing and cooperation with nanoinformatics tools. J Cheminform 2023; 15:44. [PMID: 37046286 PMCID: PMC10099932 DOI: 10.1186/s13321-022-00669-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 12/10/2022] [Indexed: 04/14/2023] Open
Abstract
Efficient and machine-readable representations are needed to accurately identify, validate and communicate information of chemical structures. Many such representations have been developed (as, for example, the Simplified Molecular-Input Line-Entry System and the IUPAC International Chemical Identifier), each offering advantages specific to various use-cases. Representation of the multi-component structures of nanomaterials (NMs), though, remains out of scope for all the currently available standards, as the nature of NMs sets new challenges on formalizing the encoding of their structure, interactions and environmental parameters. In this work we identify a set of principles that a NM representation should adhere to in order to provide "machine-friendly" encodings of NMs, i.e. encodings that facilitate machine processing and cooperation with nanoinformatics tools. We illustrate our principles by showing how the recently introduced InChI-based NM representation, might be augmented, in principle, to also encode morphology and mixture properties, distributions of properties, and also to capture auxiliary information and allow data reuse.
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Affiliation(s)
- Kostas Blekos
- Institute of Nuclear and Radiological Sciences and Technology, Energy and Safety, National Centre for Scientific Research "Demokritos", 15341, Agia Paraskevi, Greece
| | - Kostas Chairetakis
- Institute of Nuclear and Radiological Sciences and Technology, Energy and Safety, National Centre for Scientific Research "Demokritos", 15341, Agia Paraskevi, Greece
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Effie Marcoulaki
- Institute of Nuclear and Radiological Sciences and Technology, Energy and Safety, National Centre for Scientific Research "Demokritos", 15341, Agia Paraskevi, Greece.
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8
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Sengottiyan S, Mikolajczyk A, Jagiełło K, Swirog M, Puzyn T. Core, Coating, or Corona? The Importance of Considering Protein Coronas in nano-QSPR Modeling of Zeta Potential. ACS NANO 2023; 17:1989-1997. [PMID: 36651824 PMCID: PMC9933600 DOI: 10.1021/acsnano.2c06977] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
To control stability in a biological medium, several factors affecting the zeta potential (ζ) of nanoparticles (NPs) must be considered, including complex interactions between the nanostructure and the composition of the protein corona (PC). Effective in silico methods (based on machine learning and quantitative structure-property relationship (QSPR) models) could help predict and characterize the relationship between the physicochemical properties of NP and the formation of PC and biological outcomes in the medium at an early stage of the experiment. However, the models currently developed are limited to simple descriptors that do not represent the complex interactions between the core, the coating, and their PC fingerprints. To be useful, the models developed should be described as a function of both the structural properties determined by the core and coating of the NPs and the biological medium determined by the formation of the protein corona. We have developed a set of complex descriptors that describe the quantitative relationship between the value of the zeta potential (ζ), core, the coating of NPs, and their PC fingerprints (the so-called nano-QSPR model). The nano-QSPR model was developed based on a genetic algorithm using a partial least-squares regression method (GA-PLS), which is characterized by high external predictive power (Q2EXT = 0.89). The GA-PLS model was developed using descriptors that describe (i) the core structure (determined by 7 different types of polymer-based NMs in the range of 20 different sizes), (ii) the coating structure with 7 different functional groups, and (iii) 80 different types of protein compositions adsorbed on the surface of the NPs. The presented study answers the question of how complex interactions between the corona and NP determine the zeta potential (ζ) of NP in a given medium. Moreover, our current study is a proof-of-concept that the zeta potential of NPs modeled on the original structure depends not only on the NPs themselves but also on the structure and properties determined by the NP core and coating, as well as the biological medium determined by the formation of the protein corona. On the basis of these results, our studies will be useful in determining the stability and mechanism of cell uptake, toxicity, and ability to predict the zeta potential of compounds not yet tested.
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Affiliation(s)
- Selvaraj Sengottiyan
- Laboratory
of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk80-308, Poland
| | - Alicja Mikolajczyk
- Laboratory
of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk80-308, Poland
- QSARLab, Trzy Lipy 3, 80-172Gdansk, Poland
| | - Karolina Jagiełło
- Laboratory
of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk80-308, Poland
- QSARLab, Trzy Lipy 3, 80-172Gdansk, Poland
| | - Marta Swirog
- Laboratory
of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk80-308, Poland
| | - Tomasz Puzyn
- Laboratory
of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk80-308, Poland
- QSARLab, Trzy Lipy 3, 80-172Gdansk, Poland
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9
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Auclair J, Gagné F. Shape-Dependent Toxicity of Silver Nanoparticles on Freshwater Cnidarians. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12183107. [PMID: 36144895 PMCID: PMC9503847 DOI: 10.3390/nano12183107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 05/27/2023]
Abstract
Silver nanoparticles (AgNPs) are increasingly used in various consumer products, leading to their inadvertent release in aquatic ecosystems. The toxicity of AgNPs could be associated with the leaching of ionic Ag but also with the size, shape and surface properties. The purpose of this study was to test the null hypothesis that toxicity of AgNPs was independent of shape in the invertebrate Hydra vulgaris. The hydranths were exposed to increasing concentrations of ionic Ag and AgNPs of three different shapes (spherical, cubic and prismatic) with the same size and coating (polyvinylpyrrolidone). The data revealed that between 68% and 75% of total Ag remained in solution after the 96 h exposure period, while 85−90% of ionic Ag remained in solution. The 96 h lethal concentration (LC50) was lower with ionic (4 µg/L) and spherical AgNPs (56 µg/L), based on irreversible morphological changes such as loss of tentacles and body disintegration. Cubic and prismatic AgNPs were not toxic at a concentration of <100 µg/L. The sublethal toxicity was also determined at 96 h based on characteristic morphological changes (clubbed and/or shortened tentacles) and showed the following toxicity: ionic (2.6 µg/L), spherical (22 µg/L) and prismatic (32.5 µg/L) AgNPs. The nanocube was not toxic at this level. The data indicated that toxicity was shape-dependent where nanoparticles with a low aspect ratio in addition to high circularity and elongation properties were more toxic at both the lethal and sublethal levels. In conclusion, the shape of AgNPs could influence toxicity and warrants further research to better understand the mechanisms of action at play.
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10
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Stoliński F, Rybińska-Fryca A, Gromelski M, Mikolajczyk A, Puzyn T. NanoMixHamster: a web-based tool for predicting cytotoxicity of TiO 2-based multicomponent nanomaterials toward Chinese hamster ovary (CHO-K1) cells. Nanotoxicology 2022; 16:276-289. [PMID: 35713578 DOI: 10.1080/17435390.2022.2080609] [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: 10/18/2022]
Abstract
Nano-QSAR models can be effectively used for prediction of the biological activity of nanomaterials that have not been experimentally tested before. However, their use is associated with the need to have appropriate knowledge and skills in chemoinformatics. Thus, they are mainly aimed at specialists in the field. This significantly limits the potential group of recipients of the developed solutions. In this perspective, the purpose of the presented research was to develop an easily accessible and user-friendly web-based application that could enable the prediction of TiO2-based multicomponent nanomaterials cytotoxicity toward Chinese Hamster Ovary (CHO-K1) cells. The graphical user interface is clear and intuitive and the only information required from the user is the type and concentration of the metals which will be modifying TiO2-based nanomaterial. Thanks to this, the application will be easy to use not only by cheminformatics but also by specialists in the field of nanotechnology or toxicology, who will be able to quickly predict cytotoxicity of desired nanoclusters. We have performed case studies to demonstrate the features and utilities of developed application. The NanoMixHamster application is freely available at https://nanomixhamster.cloud.nanosolveit.eu/.
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Affiliation(s)
- Filip Stoliński
- QSAR Lab Ltd, Gdansk, Poland.,Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | | | | | - Alicja Mikolajczyk
- QSAR Lab Ltd, Gdansk, Poland.,Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Tomasz Puzyn
- QSAR Lab Ltd, Gdansk, Poland.,Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
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11
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Gromelski M, Stoliński F, Jagiello K, Rybińska-Fryca A, Williams A, Halappanavar S, Vogel U, Puzyn T. AOP173 key event associated pathway predictor - online application for the prediction of benchmark dose lower bound (BMDLs) of a transcriptomic pathway involved in MWCNTs-induced lung fibrosis. Nanotoxicology 2022; 16:183-194. [PMID: 35452346 DOI: 10.1080/17435390.2022.2064250] [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: 10/18/2022]
Abstract
Nano-QSAR model allows for prediction of the toxicity of materials that have not been experimentally tested before by linking the nano-related structural properties with the biological responses induced by nanomaterials. Prediction of adverse effects caused by substances without having to perform time- and cost-consuming experiments makes QSAR models promising tools for supporting risk assessment. However, very often, newly developed nano-QSAR models are not used in practice due to the complexity of their algorithms, the necessity to have experience in chemoinformatics, and their poor accessibility. In this perspective, the aim of this paper is to encourage developers of the QSAR models to take the effort to prepare user-friendly applications based on predictive models. This would make the developed models accessible to a wider community, and, in effect, promote their further application by regulators and decision-makers. Here, we describe a web-based application that enables to predict the transcriptomic pathway-level response perturbated in the lungs of mice exposed to multiwalled carbon nanotubes. The developed application is freely available at http://aop173-event1.nanoqsar-aop.com/apps/aop_app. It requires only two types of input information related to analyzed nanotubes (their length and diameter) to assess the doses that initiate the inflammation process that may lead to lung fibrosis.
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Affiliation(s)
| | | | - Karolina Jagiello
- QSAR Lab, ul. Trzy Lipy 3, Gdańsk, Poland.,Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | | | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Tomasz Puzyn
- QSAR Lab, ul. Trzy Lipy 3, Gdańsk, Poland.,Faculty of Chemistry, University of Gdansk, Gdansk, Poland
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12
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Hofer S, Hofstätter N, Punz B, Hasenkopf I, Johnson L, Himly M. Immunotoxicity of nanomaterials in health and disease: Current challenges and emerging approaches for identifying immune modifiers in susceptible populations. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1804. [PMID: 36416020 PMCID: PMC9787548 DOI: 10.1002/wnan.1804] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 11/24/2022]
Abstract
Nanosafety assessment has experienced an intense era of research during the past decades driven by a vivid interest of regulators, industry, and society. Toxicological assays based on in vitro cellular models have undergone an evolution from experimentation using nanoparticulate systems on singular epithelial cell models to employing advanced complex models more realistically mimicking the respective body barriers for analyzing their capacity to alter the immune state of exposed individuals. During this phase, a number of lessons were learned. We have thus arrived at a state where the next chapters have to be opened, pursuing the following objectives: (1) to elucidate underlying mechanisms, (2) to address effects on vulnerable groups, (3) to test material mixtures, and (4) to use realistic doses on (5) sophisticated models. Moreover, data reproducibility has become a significant demand. In this context, we studied the emerging concept of adverse outcome pathways (AOPs) from the perspective of immune activation and modulation resulting in pro-inflammatory versus tolerogenic responses. When considering the interaction of nanomaterials with biological systems, protein corona formation represents the relevant molecular initiating event (e.g., by potential alterations of nanomaterial-adsorbed proteins). Using this as an example, we illustrate how integrated experimental-computational workflows combining in vitro assays with in silico models aid in data enrichment and upon comprehensive ontology-annotated (meta)data upload to online repositories assure FAIRness (Findability, Accessibility, Interoperability, Reusability). Such digital twinning may, in future, assist in early-stage decision-making during therapeutic development, and hence, promote safe-by-design innovation in nanomedicine. Moreover, it may, in combination with in silico-based exposure-relevant dose-finding, serve for risk monitoring in particularly loaded areas, for example, workplaces, taking into account pre-existing health conditions. This article is categorized under: Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials.
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Affiliation(s)
- Sabine Hofer
- Division of Allergy & Immunology, Department of Biosciences & Medical BiologyParis Lodron University of SalzburgSalzburgAustria
| | - Norbert Hofstätter
- Division of Allergy & Immunology, Department of Biosciences & Medical BiologyParis Lodron University of SalzburgSalzburgAustria
| | - Benjamin Punz
- Division of Allergy & Immunology, Department of Biosciences & Medical BiologyParis Lodron University of SalzburgSalzburgAustria
| | - Ingrid Hasenkopf
- Division of Allergy & Immunology, Department of Biosciences & Medical BiologyParis Lodron University of SalzburgSalzburgAustria
| | - Litty Johnson
- Division of Allergy & Immunology, Department of Biosciences & Medical BiologyParis Lodron University of SalzburgSalzburgAustria
| | - Martin Himly
- Division of Allergy & Immunology, Department of Biosciences & Medical BiologyParis Lodron University of SalzburgSalzburgAustria
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Varsou DD, Ellis LJA, Afantitis A, Melagraki G, Lynch I. Ecotoxicological read-across models for predicting acute toxicity of freshly dispersed versus medium-aged NMs to Daphnia magna. CHEMOSPHERE 2021; 285:131452. [PMID: 34265725 DOI: 10.1016/j.chemosphere.2021.131452] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/29/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Nanoinformatics models to predict the toxicity/ecotoxicity of nanomaterials (NMs) are urgently needed to support commercialization of nanotechnologies and allow grouping of NMs based on their physico-chemical and/or (eco)toxicological properties, to facilitate read-across of knowledge from data-rich NMs to data-poor ones. Here we present the first ecotoxicological read-across models for predicting NMs ecotoxicity, which were developed in accordance with ECHA's recommended strategy for grouping of NMs as a means to explore in silico the effects of a panel of freshly dispersed versus environmentally aged (in various media) Ag and TiO2 NMs on the freshwater zooplankton Daphnia magna, a keystone species used in regulatory testing. The dataset used to develop the models consisted of dose-response data from 11 NMs (5 TiO2 NMs of identical cores with different coatings, and 6 Ag NMs with different capping agents/coatings) each dispersed in three different media (a high hardness medium (HH Combo) and two representative river waters containing different amounts of natural organic matter (NOM) and having different ionic strengths), generated in accordance with the OECD 202 immobilization test. The experimental hypotheses being tested were (1) that the presence of NOM in the medium would reduce the toxicity of the NMs by forming an ecological corona, and (2) that environmental ageing of NMs reduces their toxicity compared to the freshly dispersed NMs irrespective of the medium composition (salt only or NOM-containing). As per the ECHA guidance, the NMs were grouped into two categories - freshly dispersed and 2-year-aged and explored in silico to identify the most important features driving the toxicity in each group. The final predictive models have been validated according to the OECD criteria and a QSAR model report form (QMRF) report included in the supplementary information to support adoption of the models for regulatory purposes.
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Affiliation(s)
| | - Laura-Jayne A Ellis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT, Birmingham, UK
| | | | - Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, Vari, Greece.
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT, Birmingham, UK.
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14
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Zheng M, Lin H, Zhang W, Tang S, Liu D, Cai J. Poly(l-ornithine)-Grafted Zinc Phthalocyanines as Dual-Functional Antimicrobial Agents with Intrinsic Membrane Damage and Photothermal Ablation Capacity. ACS Infect Dis 2021; 7:2917-2929. [PMID: 34570483 DOI: 10.1021/acsinfecdis.1c00392] [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] [Indexed: 02/05/2023]
Abstract
Multifunctional antimicrobial peptides that combine the intrinsic microbicidal property of cationic polypeptide chains and additional antibacterial strategy hold promising applications for the treatment of infections caused by antibiotic-resistant bacteria, especially "superbugs". In the present study, star-shaped copolymers ZnPc-g-PLO with a zinc phthalocyanine (ZnPc) core and four poly(l-ornithine) (PLO) arms were designed, synthesized, and evaluated as dual-functional antimicrobial agents, that is, intrinsic membrane damage and photothermal ablation capacity. In an aqueous solution, amphiphilic ZnPc-g-PLO molecules self-assemble into nanosized polymeric micelles with an aggregated ZnPc core and star-shaped PLO periphery, where the ZnPc core exhibits appreciable aggregation-induced photothermal conversion efficiency. In the absence of laser irradiation, ZnPc-g-PLO micelles display potent and broad-spectrum antibacterial activities via physical bacterial membrane disruption as a result of the high cationic charge density of the star-shaped PLO. Upon laser irradiation, significant improvement in bactericidal potency was realized due to the efficacious photothermal sterilization from the ZnPc core. Notably, ZnPc-g-PLO micelles did not induce drug-resistance upon subinhibitory passages. In summary, dual-functional ZnPc-g-PLO copolymers can serve as promising antibacterial agents for the treatment of infectious diseases caused by antibiotic-resistant bacteria.
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Affiliation(s)
- Maochao Zheng
- Department of Pharmacy, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
- Department of Pharmacy, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310022, China
| | - Huanchang Lin
- Department of Pharmacy, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Wancong Zhang
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, 69 Dongxiabei Road, Shantou 515041, China
- Plastic Surgery Institute of Shantou University Medical College, 69 Dongxiabei Road, Shantou 515041, China
| | - Shijie Tang
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, 69 Dongxiabei Road, Shantou 515041, China
- Plastic Surgery Institute of Shantou University Medical College, 69 Dongxiabei Road, Shantou 515041, China
| | - Daojun Liu
- Department of Pharmacy, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
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15
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Zhang P, Guo Z, Ullah S, Melagraki G, Afantitis A, Lynch I. Nanotechnology and artificial intelligence to enable sustainable and precision agriculture. NATURE PLANTS 2021; 7:864-876. [PMID: 34168318 DOI: 10.1038/s41477-021-00946-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
Abstract
Climate change, increasing populations, competing demands on land for production of biofuels and declining soil quality are challenging global food security. Finding sustainable solutions requires bold new approaches and integration of knowledge from diverse fields, such as materials science and informatics. The convergence of precision agriculture, in which farmers respond in real time to changes in crop growth with nanotechnology and artificial intelligence, offers exciting opportunities for sustainable food production. Coupling existing models for nutrient cycling and crop productivity with nanoinformatics approaches to optimize targeting, uptake, delivery, nutrient capture and long-term impacts on soil microbial communities will enable design of nanoscale agrochemicals that combine optimal safety and functionality profiles.
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Affiliation(s)
- Peng Zhang
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK.
| | - Zhiling Guo
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Sami Ullah
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, Vari, Greece
| | | | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
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16
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Marcoulaki E, López de Ipiña JM, Vercauteren S, Bouillard J, Himly M, Lynch I, Witters H, Shandilya N, van Duuren-Stuurman B, Kunz V, Unger WES, Hodoroaba VD, Bard D, Evans G, Jensen KA, Pilou M, Viitanen AK, Bochon A, Duschl A, Geppert M, Persson K, Cotgreave I, Niga P, Gini M, Eleftheriadis K, Scalbi S, Caillard B, Arevalillo A, Frejafon E, Aguerre-Chariol O, Dulio V. Blueprint for a self-sustained European Centre for service provision in safe and sustainable innovation for nanotechnology. NANOIMPACT 2021; 23:100337. [PMID: 35559838 DOI: 10.1016/j.impact.2021.100337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/05/2021] [Accepted: 06/17/2021] [Indexed: 06/15/2023]
Abstract
The coming years are expected to bring rapid changes in the nanotechnology regulatory landscape, with the establishment of a new framework for nano-risk governance, in silico approaches for characterisation and risk assessment of nanomaterials, and novel procedures for the early identification and management of nanomaterial risks. In this context, Safe(r)-by-Design (SbD) emerges as a powerful preventive approach to support the development of safe and sustainable (SSbD) nanotechnology-based products and processes throughout the life cycle. This paper summarises the work undertaken to develop a blueprint for the deployment and operation of a permanent European Centre of collaborating laboratories and research organisations supporting safe innovation in nanotechnologies. The proposed entity, referred to as "the Centre", will establish a 'one-stop shop' for nanosafety-related services and a central contact point for addressing stakeholder questions about nanosafety. Its operation will rely on significant business, legal and market knowledge, as well as other tools developed and acquired through the EU-funded EC4SafeNano project and subsequent ongoing activities. The proposed blueprint adopts a demand-driven service update scheme to allow the necessary vigilance and flexibility to identify opportunities and adjust its activities and services in the rapidly evolving regulatory and nano risk governance landscape. The proposed Centre will play a major role as a conduit to transfer scientific knowledge between the research and commercial laboratories or consultants able to provide high quality nanosafety services, and the end-users of such services (e.g., industry, SMEs, consultancy firms, and regulatory authorities). The Centre will harmonise service provision, and bring novel risk assessment and management approaches, e.g. in silico methodologies, closer to practice, notably through SbD/SSbD, and decisively support safe and sustainable innovation of industrial production in the nanotechnology industry according to the European Chemicals Strategy for Sustainability.
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Affiliation(s)
- Effie Marcoulaki
- National Centre for Scientific Research "Demokritos", PO Box 60037, 15310 Agia Paraskevi, Greece.
| | - Jesús M López de Ipiña
- TECNALIA, Basque Research and Technology Alliance (BRTA), Parque Tecnológico de Alava, 01510 Miñano, Spain.
| | | | - Jacques Bouillard
- Institut national de l'environnement industriel et des risques (INERIS), Rue Jacques Taffanel, Parc technologique ALATA, Verneuil-en-Halatte, 60550, France.
| | - Martin Himly
- Paris Lodron University of Salzburg, Kapitelgasse 4/6, 5020 Salzburg, Austria.
| | - Iseult Lynch
- School of Geography, Earth & Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK.
| | - Hilda Witters
- VITO NV, Health Unit, Boeretang 200, 2400 Mol, Belgium.
| | - Neeraj Shandilya
- TNO, Research group Risk Analysis for Products in Development (RAPID), Princetonlaan 6, 3584 CB Utrecht, Netherlands.
| | - Birgit van Duuren-Stuurman
- TNO, Research group Risk Analysis for Products in Development (RAPID), Princetonlaan 6, 3584 CB Utrecht, Netherlands.
| | - Valentin Kunz
- Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 44-46, 12203 Berlin, Germany
| | - Wolfgang E S Unger
- Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 44-46, 12203 Berlin, Germany
| | - Vasile-Dan Hodoroaba
- Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 44-46, 12203 Berlin, Germany.
| | - Delphine Bard
- Health & Safety Executive Science and Research Centre, Harpur Hill, Buxton, Derbyshire SK17 9JN, UK.
| | - Gareth Evans
- Health & Safety Executive Science and Research Centre, Harpur Hill, Buxton, Derbyshire SK17 9JN, UK.
| | - Keld Alstrup Jensen
- National Research Center for the Work Environment (NRCWE), Lersø Parkallé 105, 2100 København, Denmark.
| | - Marika Pilou
- National Centre for Scientific Research "Demokritos", PO Box 60037, 15310 Agia Paraskevi, Greece.
| | - Anna-Kaisa Viitanen
- Finnish Institute of Occupational Health (FIOH), P.O. Box 40, FI-00032 Työterveyslaitos, Finland.
| | - Anthony Bochon
- JurisLab, Centre de droit privé, Université Libre de Bruxelles, Avenue F. Roosevelt 50, CP 137, 1050 Bruxelles, Belgium.
| | - Albert Duschl
- Paris Lodron University of Salzburg, Kapitelgasse 4/6, 5020 Salzburg, Austria.
| | - Mark Geppert
- Paris Lodron University of Salzburg, Kapitelgasse 4/6, 5020 Salzburg, Austria.
| | - Karin Persson
- RISE Surface, Process and Formulation, Box 5607, SE-114 86 Stockholm, Sweden.
| | - Ian Cotgreave
- RISE Surface, Process and Formulation, Box 5607, SE-114 86 Stockholm, Sweden.
| | - Petru Niga
- RISE Surface, Process and Formulation, Box 5607, SE-114 86 Stockholm, Sweden.
| | - Maria Gini
- National Centre for Scientific Research "Demokritos", PO Box 60037, 15310 Agia Paraskevi, Greece.
| | | | - Simona Scalbi
- ENEA, Agenzia Nazionale per le nuove tecnologie, l'energia e lo sviluppo sostenibile, SSPT-USER-RISE, Via martiri di monte sole 4, 40129 Bologna, Italy.
| | - Bastien Caillard
- European Risk Management Institute (EU-VRi), Fangelsbachstr. 14, 70178 Stuttgart, Germany.
| | - Alfonso Arevalillo
- TECNALIA, Basque Research and Technology Alliance (BRTA), Area Anardi 5, 20730 Azpeitia, Spain.
| | - Emeric Frejafon
- BRGM, 3 av. Claude-Guillemin, BP 36009, 45100 Orléans Cedex 2, France.
| | - Olivier Aguerre-Chariol
- Institut national de l'environnement industriel et des risques (INERIS), Rue Jacques Taffanel, Parc technologique ALATA, Verneuil-en-Halatte, 60550, France.
| | - Valeria Dulio
- Institut national de l'environnement industriel et des risques (INERIS), Rue Jacques Taffanel, Parc technologique ALATA, Verneuil-en-Halatte, 60550, France.
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17
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Kukkola A, Krause S, Lynch I, Sambrook Smith GH, Nel H. Nano and microplastic interactions with freshwater biota - Current knowledge, challenges and future solutions. ENVIRONMENT INTERNATIONAL 2021; 152:106504. [PMID: 33735690 DOI: 10.1016/j.envint.2021.106504] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Current understanding of nano- and microplastic movement, propagation and potential effects on biota in freshwater environments is developing rapidly. Still, there are significant disconnects in the integration of knowledge derived from laboratory and field studies. This review synthesises the current understanding of nano- and microplastic impacts on freshwater biota from field studies and combines it with the more mechanistic insights derived from laboratory studies. Several discrepancies between the field and laboratory studies, impacting progress in process understanding, were identified including that the most prevalent plastic morphologies found in the field (fibres) are not those used in most of the laboratory studies (particles). Solutions to overcome these disparities are proposed to aid comparability of future studies. For example, environmental sampling and separation of biota into its constituents is encouraged when conducting field studies to map microplastic uptake preferences. In laboratory studies, recommendations include performing toxicity studies to systematically test possible factors affecting toxicity of nano- and microplastics, including morphology, chemical makeup (e.g., additives) and effects of plastic size. Consideration should be given to environmentally relevant exposure factors in laboratory studies, such as realistic exposure medium and effects of plastic ageing. Furthermore, based on this comprehensive review recommendations of principal toxicity endpoints for each of the main trophic levels (microbes, primary producers, primary consumers and secondary consumers) that should be reported to make toxicity studies more comparable in the future are given.
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Affiliation(s)
- Anna Kukkola
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom.
| | - Stefan Krause
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom; LEHNA- Laboratoire d'ecologie des hydrosystemes naturels et anthropises, University of Lyon, Darwin C & Forel, 3-6 Rue Raphaël Dubois, 69622 Villeurbanne, France; Institute of Global Innovation, University of Birmingham, B15 2SA Birmingham, United Kingdom
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom; Institute of Global Innovation, University of Birmingham, B15 2SA Birmingham, United Kingdom
| | - Gregory H Sambrook Smith
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Holly Nel
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
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18
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Varsou DD, Koutroumpa NM, Sarimveis H. Automated Grouping of Nanomaterials and Read-Across Prediction of Their Adverse Effects Based on Mathematical Optimization. J Chem Inf Model 2021; 61:2766-2779. [PMID: 34029462 DOI: 10.1021/acs.jcim.1c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, a computational workflow is presented for grouping engineered nanomaterials (ENMs) and for predicting their toxicity-related end points. A mixed integer-linear optimization program (MILP) problem is formulated, which automatically filters out the noisy variables, defines the grouping boundaries, and develops specific to each group predictive models. The method is extended to the multidimensional space, by considering the ENM characterization categories (e.g., biological, physicochemical, biokinetics, image etc.) as different dimensions. The performance of the proposed method is illustrated through the application to benchmark data sets and comparison with alternative predictive modeling approaches. The trained models using the above data sets were made publicly available through a user-friendly web service.
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Affiliation(s)
- Dimitra-Danai Varsou
- School of Chemical Engineering, National Technical University of Athens, Athens, 157 80, Greece
| | | | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, Athens, 157 80, Greece
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19
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Yu H, Luo D, Dai L, Cheng F. In silico nanosafety assessment tools and their ecosystem-level integration prospect. NANOSCALE 2021; 13:8722-8739. [PMID: 33960351 DOI: 10.1039/d1nr00115a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Engineered nanomaterials (ENMs) have tremendous potential in many fields, but their applications and commercialization are difficult to widely implement due to their safety concerns. Recently, in silico nanosafety assessment has become an important and necessary tool to realize the safer-by-design strategy of ENMs and at the same time to reduce animal tests and exposure experiments. Here, in silico nanosafety assessment tools are classified into three categories according to their methodologies and objectives, including (i) data-driven prediction for acute toxicity, (ii) fate modeling for environmental pollution, and (iii) nano-biological interaction modeling for long-term biological effects. Released ENMs may cross environmental boundaries and undergo a variety of transformations in biological and environmental media. Therefore, the potential impacts of ENMs must be assessed from a multimedia perspective and with integrated approaches considering environmental and biological effects. Ecosystems with biodiversity and an abiotic environment may be used as an excellent integration platform to assess the community- and ecosystem-level nanosafety. In this review, the advances and challenges of in silico nanosafety assessment tools are carefully discussed. Furthermore, their integration at the ecosystem level may provide more comprehensive and reliable nanosafety assessment by establishing a site-specific interactive system among ENMs, abiotic environment, and biological communities.
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Affiliation(s)
- Hengjie Yu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
| | - Dan Luo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Limin Dai
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
| | - Fang Cheng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
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20
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Papadiamantis AG, Afantitis A, Tsoumanis A, Valsami-Jones E, Lynch I, Melagraki G. Computational enrichment of physicochemical data for the development of a ζ-potential read-across predictive model with Isalos Analytics Platform. NANOIMPACT 2021; 22:100308. [PMID: 35559965 DOI: 10.1016/j.impact.2021.100308] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/01/2021] [Accepted: 03/01/2021] [Indexed: 06/15/2023]
Abstract
The physicochemical characterisation data from a library of 69 engineered nanomaterials (ENMs) has been exploited in silico following enrichment with a set of molecular descriptors that can be easily acquired or calculated using atomic periodicity and other fundamental atomic parameters. Based on the extended set of twenty descriptors, a robust and validated nanoinformatics model has been proposed to predict the ENM ζ-potential. The five critical parameters selected as the most significant for the model development included the ENM size and coating as well as three molecular descriptors, metal ionic radius (rion), the sum of metal electronegativity divided by the number of oxygen atoms present in a particular metal oxide (Σχ/nO) and the absolute electronegativity (χabs), each of which is thoroughly discussed to interpret their influence on ζ-potential values. The model was developed using the Isalos Analytics Platform and is available to the community as a web service through the Horizon 2020 (H2020) NanoCommons Transnational Access services and the H2020 NanoSoveIT Integrated Approach to Testing and Assessment (IATA).
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Affiliation(s)
- Anastasios G Papadiamantis
- NovaMechanics Ltd, 1065 Nicosia, Cyprus; School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | | | | | - Eugenia Valsami-Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom.
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21
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Ramaye Y, Dabrio M, Roebben G, Kestens V. Development and Validation of Optical Methods for Zeta Potential Determination of Silica and Polystyrene Particles in Aqueous Suspensions. MATERIALS 2021; 14:ma14020290. [PMID: 33429974 PMCID: PMC7827561 DOI: 10.3390/ma14020290] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022]
Abstract
Zeta potential is frequently used to examine the colloidal stability of particles and macromolecules in liquids. Recently, it has been suggested that zeta potential can also play an important role for grouping and read-across of nanoforms in a regulatory context. Although the measurement of zeta potential is well established, only little information is reported on key metrological principles such as validation and measurement uncertainties. This contribution presents the results of an in-house validation of the commonly used electrophoretic light scattering (ELS) and the relatively new particle tracking analysis (PTA) methods. The performance characteristics were assessed by analyzing silica and polystyrene reference materials. The ELS and PTA methods are robust and have particle mass working ranges of 0.003 mg/kg to 30 g/kg and 0.03 mg/kg to 1.5 mg/kg, respectively. Despite different measurement principles, both methods exhibit similar uncertainties for repeatability (2%), intermediate precision (3%) and trueness (4%). These results confirm that the developed methods can accurately measure the zeta potential of silica and polystyrene particles and can be transferred to other laboratories that analyze similar types of samples. If direct implementation is impossible, the elaborated methodologies may serve as a guide to help laboratories validating their own methods.
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22
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Lynch I, Afantitis A, Exner T, Himly M, Lobaskin V, Doganis P, Maier D, Sanabria N, Papadiamantis AG, Rybinska-Fryca A, Gromelski M, Puzyn T, Willighagen E, Johnston BD, Gulumian M, Matzke M, Green Etxabe A, Bossa N, Serra A, Liampa I, Harper S, Tämm K, Jensen ACØ, Kohonen P, Slater L, Tsoumanis A, Greco D, Winkler DA, Sarimveis H, Melagraki G. Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies? NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2493. [PMID: 33322568 PMCID: PMC7764592 DOI: 10.3390/nano10122493] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/05/2020] [Accepted: 12/08/2020] [Indexed: 12/16/2022]
Abstract
Chemoinformatics has developed efficient ways of representing chemical structures for small molecules as simple text strings, simplified molecular-input line-entry system (SMILES) and the IUPAC International Chemical Identifier (InChI), which are machine-readable. In particular, InChIs have been extended to encode formalized representations of mixtures and reactions, and work is ongoing to represent polymers and other macromolecules in this way. The next frontier is encoding the multi-component structures of nanomaterials (NMs) in a machine-readable format to enable linking of datasets for nanoinformatics and regulatory applications. A workshop organized by the H2020 research infrastructure NanoCommons and the nanoinformatics project NanoSolveIT analyzed issues involved in developing an InChI for NMs (NInChI). The layers needed to capture NM structures include but are not limited to: core composition (possibly multi-layered); surface topography; surface coatings or functionalization; doping with other chemicals; and representation of impurities. NM distributions (size, shape, composition, surface properties, etc.), types of chemical linkages connecting surface functionalization and coating molecules to the core, and various crystallographic forms exhibited by NMs also need to be considered. Six case studies were conducted to elucidate requirements for unambiguous description of NMs. The suggested NInChI layers are intended to stimulate further analysis that will lead to the first version of a "nano" extension to the InChI standard.
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Affiliation(s)
- Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Antreas Afantitis
- Nanoinformatics Department, NovaMechanics Ltd., 1666 Nicosia, Cyprus; (A.A.); (A.T.)
| | - Thomas Exner
- Edelweiss Connect GmbH, Hochbergerstrasse 60C, 4057 Basel, Switzerland;
| | - Martin Himly
- Department Biosciences, Paris Lodron University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria;
| | - Vladimir Lobaskin
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Philip Doganis
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece; (P.D.); (I.L.); (H.S.)
| | - Dieter Maier
- Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany;
| | - Natasha Sanabria
- National Health Laboratory Services, 1 Modderfontein Rd, Sandringham, Johannesburg 2192, South Africa; (N.S.); (M.G.)
| | - Anastasios G. Papadiamantis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
- Nanoinformatics Department, NovaMechanics Ltd., 1666 Nicosia, Cyprus; (A.A.); (A.T.)
| | - Anna Rybinska-Fryca
- QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland; (A.R.-F.); (M.G.); (T.P.)
| | - Maciej Gromelski
- QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland; (A.R.-F.); (M.G.); (T.P.)
| | - Tomasz Puzyn
- QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland; (A.R.-F.); (M.G.); (T.P.)
| | - Egon Willighagen
- Department of Bioinformatics—BiGCaT, School of Nutrition and Translational Research in Metabolism, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands;
| | - Blair D. Johnston
- Department Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany;
| | - Mary Gulumian
- National Health Laboratory Services, 1 Modderfontein Rd, Sandringham, Johannesburg 2192, South Africa; (N.S.); (M.G.)
- Haematology and Molecular Medicine, University of the Witwatersrand, 1 Jan Smuts Ave, Johannesburg 2000, South Africa
| | - Marianne Matzke
- UK Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford OX10 8BB, UK; (M.M.); (A.G.E.)
| | - Amaia Green Etxabe
- UK Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford OX10 8BB, UK; (M.M.); (A.G.E.)
| | - Nathan Bossa
- LEITAT Technological Center, Circular Economy Business Unit, C/de La Innovació 2, 08225 Terrassa, Barcelona, Spain;
| | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (A.S.); (D.G.)
| | - Irene Liampa
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece; (P.D.); (I.L.); (H.S.)
| | - Stacey Harper
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall 105 SW 26th St., Corvallis, OR 97331, USA;
| | - Kaido Tämm
- Institute of Chemistry, University of Tartu, Ülikooli 18, 50090 Tartu, Estonia;
| | - Alexander CØ Jensen
- The National Research Center for the Work Environment, Lersø Parkallé 105, 2100 Copenhagen, Denmark;
| | - Pekka Kohonen
- Misvik Biology OY, Karjakatu 35 B, 20520 Turku, Finland;
| | - Luke Slater
- Institute of Cancer and Genomics, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Andreas Tsoumanis
- Nanoinformatics Department, NovaMechanics Ltd., 1666 Nicosia, Cyprus; (A.A.); (A.T.)
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (A.S.); (D.G.)
| | - David A. Winkler
- Institute of Molecular Sciences, La Trobe University, Kingsbury Drive, Bundoora 3086, Australia;
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
- CSIRO Data61, Pullenvale 4069, Australia
| | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece; (P.D.); (I.L.); (H.S.)
| | - Georgia Melagraki
- Nanoinformatics Department, NovaMechanics Ltd., 1666 Nicosia, Cyprus; (A.A.); (A.T.)
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23
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Rybińska-Fryca A, Mikolajczyk A, Puzyn T. Structure-activity prediction networks (SAPNets): a step beyond Nano-QSAR for effective implementation of the safe-by-design concept. NANOSCALE 2020; 12:20669-20676. [PMID: 33048104 DOI: 10.1039/d0nr05220e] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A significant number of experimental studies are supported by computational methods such as quantitative structure-activity relationship modeling of nanoparticles (Nano-QSAR). This is especially so in research focused on design and synthesis of new, safer nanomaterials using safe-by-design concepts. However, Nano-QSAR has a number of important limitations. For example, it is not clear which descriptors that describe the nanoparticle physicochemical and structural properties are essential and can be adjusted to alter the target properties. This limitation can be overcome with the use of the Structure-Activity Prediction Network (SAPNet) presented in this paper. There are three main phases of building the SAPNet. First, information about the structural characterization of a nanomaterial, its physical and chemical properties and toxicity is compiled. Then, the most relevant properties (intrinsic/extrinsic) likely to influence the ENM toxicity are identified by developing "meta-models". Finally, these "meta-models" describing the dependencies between the most relevant properties of the ENMs and their adverse biological properties are developed. In this way, the network is built layer by layer from the endpoint (e.g. toxicity or other properties of interest) to descriptors that describe the particle structure. Therefore, SAPNets go beyond the current standards and provide sufficient information on what structural features should be altered to obtain a material with desired properties.
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Affiliation(s)
| | - Alicja Mikolajczyk
- QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland. and University of Gdansk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Tomasz Puzyn
- QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland. and University of Gdansk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdansk, Poland
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24
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Papadiamantis AG, Klaessig FC, Exner TE, Hofer S, Hofstaetter N, Himly M, Williams MA, Doganis P, Hoover MD, Afantitis A, Melagraki G, Nolan TS, Rumble J, Maier D, Lynch I. Metadata Stewardship in Nanosafety Research: Community-Driven Organisation of Metadata Schemas to Support FAIR Nanoscience Data. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2033. [PMID: 33076428 PMCID: PMC7602672 DOI: 10.3390/nano10102033] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 12/15/2022]
Abstract
The emergence of nanoinformatics as a key component of nanotechnology and nanosafety assessment for the prediction of engineered nanomaterials (NMs) properties, interactions, and hazards, and for grouping and read-across to reduce reliance on animal testing, has put the spotlight firmly on the need for access to high-quality, curated datasets. To date, the focus has been around what constitutes data quality and completeness, on the development of minimum reporting standards, and on the FAIR (findable, accessible, interoperable, and reusable) data principles. However, moving from the theoretical realm to practical implementation requires human intervention, which will be facilitated by the definition of clear roles and responsibilities across the complete data lifecycle and a deeper appreciation of what metadata is, and how to capture and index it. Here, we demonstrate, using specific worked case studies, how to organise the nano-community efforts to define metadata schemas, by organising the data management cycle as a joint effort of all players (data creators, analysts, curators, managers, and customers) supervised by the newly defined role of data shepherd. We propose that once researchers understand their tasks and responsibilities, they will naturally apply the available tools. Two case studies are presented (modelling of particle agglomeration for dose metrics, and consensus for NM dissolution), along with a survey of the currently implemented metadata schema in existing nanosafety databases. We conclude by offering recommendations on the steps forward and the needed workflows for metadata capture to ensure FAIR nanosafety data.
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Affiliation(s)
- Anastasios G. Papadiamantis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Novamechanics Ltd., 1065 Nicosia, Cyprus; (A.A.); (G.M.)
| | | | | | - Sabine Hofer
- Department of Biosciences, Paris Lodron University of Salzburg, 5020 Salzburg, Austria; (S.H.); (N.H.); (M.H.)
| | - Norbert Hofstaetter
- Department of Biosciences, Paris Lodron University of Salzburg, 5020 Salzburg, Austria; (S.H.); (N.H.); (M.H.)
| | - Martin Himly
- Department of Biosciences, Paris Lodron University of Salzburg, 5020 Salzburg, Austria; (S.H.); (N.H.); (M.H.)
| | - Marc A. Williams
- U.S. Army Public Health Center (APHC), Aberdeen Proving Ground—South, Aberdeen, MD 21010, USA;
| | - Philip Doganis
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece;
| | | | | | | | - Tracy S. Nolan
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - John Rumble
- R&R Data Services, Gaithersburg, MD 20877, USA;
- CODATA-VAMAS Working Group on Nanomaterials, 75016 Paris, France
| | | | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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25
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Papadiamantis AG, Jänes J, Voyiatzis E, Sikk L, Burk J, Burk P, Tsoumanis A, Ha MK, Yoon TH, Valsami-Jones E, Lynch I, Melagraki G, Tämm K, Afantitis A. Predicting Cytotoxicity of Metal Oxide Nanoparticles using Isalos Analytics Platform. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2017. [PMID: 33066094 PMCID: PMC7601995 DOI: 10.3390/nano10102017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 02/07/2023]
Abstract
A literature curated dataset containing 24 distinct metal oxide (MexOy) nanoparticles (NPs), including 15 physicochemical, structural and assay-related descriptors, was enriched with 62 atomistic computational descriptors and exploited to produce a robust and validated in silico model for prediction of NP cytotoxicity. The model can be used to predict the cytotoxicity (cell viability) of MexOy NPs based on the colorimetric lactate dehydrogenase (LDH) assay and the luminometric adenosine triphosphate (ATP) assay, both of which quantify irreversible cell membrane damage. Out of the 77 total descriptors used, 7 were identified as being significant for induction of cytotoxicity by MexOy NPs. These were NP core size, hydrodynamic size, assay type, exposure dose, the energy of the MexOy conduction band (EC), the coordination number of the metal atoms on the NP surface (Avg. C.N. Me atoms surface) and the average force vector surface normal component of all metal atoms (v⟂ Me atoms surface). The significance and effect of these descriptors is discussed to demonstrate their direct correlation with cytotoxicity. The produced model has been made publicly available by the Horizon 2020 (H2020) NanoSolveIT project and will be added to the project's Integrated Approach to Testing and Assessment (IATA).
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Affiliation(s)
- Anastasios G. Papadiamantis
- NovaMechanics Ltd., Nicosia 1065, Cyprus; (A.G.P.); (E.V.); (A.T.)
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK; (E.V.-J.); (I.L.)
| | - Jaak Jänes
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia; (J.J.); (L.S.); (J.B.); (P.B.)
| | | | - Lauri Sikk
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia; (J.J.); (L.S.); (J.B.); (P.B.)
| | - Jaanus Burk
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia; (J.J.); (L.S.); (J.B.); (P.B.)
| | - Peeter Burk
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia; (J.J.); (L.S.); (J.B.); (P.B.)
| | | | - My Kieu Ha
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, Korea; (M.K.H.); (T.H.Y.)
| | - Tae Hyun Yoon
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, Korea; (M.K.H.); (T.H.Y.)
- Institute of Next Generation Material Design, Hanyang University, Seoul 04763, Korea
| | - Eugenia Valsami-Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK; (E.V.-J.); (I.L.)
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK; (E.V.-J.); (I.L.)
| | - Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, 16672 Vari, Greece;
| | - Kaido Tämm
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia; (J.J.); (L.S.); (J.B.); (P.B.)
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26
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Winkler DA. Role of Artificial Intelligence and Machine Learning in Nanosafety. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2001883. [PMID: 32537842 DOI: 10.1002/smll.202001883] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Robotics and automation provide potentially paradigm shifting improvements in the way materials are synthesized and characterized, generating large, complex data sets that are ideal for modeling and analysis by modern machine learning (ML) methods. Nanomaterials have not yet fully captured the benefits of automation, so lag behind in the application of ML methods of data analysis. Here, some key developments in, and roadblocks to the application of ML methods are reviewed to model and predict potentially adverse biological and environmental effects of nanomaterials. This work focuses on the diverse ways a range of ML algorithms are applied to understand and predict nanomaterials properties, provides examples of the application of traditional ML and deep learning methods to nanosafety, and provides context and future perspectives on developments that are likely to occur, or need to occur in the near future that allow artificial intelligence to make a deeper contribution to nanosafety.
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Affiliation(s)
- David A Winkler
- La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, 3042, Australia
- CSIRO Data61, 1 Technology Court, Pullenvale, 4069, Australia
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2QL, UK
- Monash Institute of Pharmaceutical Sciences, Monash University, 392 Royal Parade, Parkville, 3052, Australia
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27
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Afantitis A, Melagraki G, Isigonis P, Tsoumanis A, Varsou DD, Valsami-Jones E, Papadiamantis A, Ellis LJA, Sarimveis H, Doganis P, Karatzas P, Tsiros P, Liampa I, Lobaskin V, Greco D, Serra A, Kinaret PAS, Saarimäki LA, Grafström R, Kohonen P, Nymark P, Willighagen E, Puzyn T, Rybinska-Fryca A, Lyubartsev A, Alstrup Jensen K, Brandenburg JG, Lofts S, Svendsen C, Harrison S, Maier D, Tamm K, Jänes J, Sikk L, Dusinska M, Longhin E, Rundén-Pran E, Mariussen E, El Yamani N, Unger W, Radnik J, Tropsha A, Cohen Y, Leszczynski J, Ogilvie Hendren C, Wiesner M, Winkler D, Suzuki N, Yoon TH, Choi JS, Sanabria N, Gulumian M, Lynch I. NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment. Comput Struct Biotechnol J 2020; 18:583-602. [PMID: 32226594 PMCID: PMC7090366 DOI: 10.1016/j.csbj.2020.02.023] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/18/2020] [Accepted: 02/29/2020] [Indexed: 01/26/2023] Open
Abstract
Nanotechnology has enabled the discovery of a multitude of novel materials exhibiting unique physicochemical (PChem) properties compared to their bulk analogues. These properties have led to a rapidly increasing range of commercial applications; this, however, may come at a cost, if an association to long-term health and environmental risks is discovered or even just perceived. Many nanomaterials (NMs) have not yet had their potential adverse biological effects fully assessed, due to costs and time constraints associated with the experimental assessment, frequently involving animals. Here, the available NM libraries are analyzed for their suitability for integration with novel nanoinformatics approaches and for the development of NM specific Integrated Approaches to Testing and Assessment (IATA) for human and environmental risk assessment, all within the NanoSolveIT cloud-platform. These established and well-characterized NM libraries (e.g. NanoMILE, NanoSolutions, NANoREG, NanoFASE, caLIBRAte, NanoTEST and the Nanomaterial Registry (>2000 NMs)) contain physicochemical characterization data as well as data for several relevant biological endpoints, assessed in part using harmonized Organisation for Economic Co-operation and Development (OECD) methods and test guidelines. Integration of such extensive NM information sources with the latest nanoinformatics methods will allow NanoSolveIT to model the relationships between NM structure (morphology), properties and their adverse effects and to predict the effects of other NMs for which less data is available. The project specifically addresses the needs of regulatory agencies and industry to effectively and rapidly evaluate the exposure, NM hazard and risk from nanomaterials and nano-enabled products, enabling implementation of computational 'safe-by-design' approaches to facilitate NM commercialization.
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Key Words
- (quantitative) Structure–activity relationships
- AI, Artificial Intelligence
- AOPs, Adverse Outcome Pathways
- API, Application Programming interface
- CG, coarse-grained (model)
- CNTs, carbon nanotubes
- Computational toxicology
- Engineered nanomaterials
- FAIR, Findable Accessible Inter-operable and Re-usable
- GUI, Graphical Processing Unit
- HOMO-LUMO, Highest Occupied Molecular Orbital Lowest Unoccupied Molecular Orbital
- Hazard assessment
- IATA, Integrated Approaches to Testing and Assessment
- Integrated approach for testing and assessment
- KE, key events
- MIE, molecular initiating events
- ML, machine learning
- MOA, mechanism (mode) of action
- MWCNT, multi-walled carbon nanotubes
- Machine learning
- NMs, nanomaterials
- Nanoinformatics
- OECD, Organisation for Economic Co-operation and Development
- PBPK, Physiologically Based PharmacoKinetics
- PC, Protein Corona
- PChem, Physicochemical
- PTGS, Predictive Toxicogenomics Space
- Predictive modelling
- QC, quantum-chemical
- QM, quantum-mechanical
- QSAR, quantitative structure-activity relationship
- QSPR, quantitative structure-property relationship
- RA, risk assessment
- REST, Representational State Transfer
- ROS, reactive oxygen species
- Read across
- SAR, structure-activity relationship
- SMILES, Simplified Molecular Input Line Entry System
- SOPs, standard operating procedures
- Safe-by-design
- Toxicogenomics
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Affiliation(s)
| | | | | | | | | | - Eugenia Valsami-Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, UK
| | - Anastasios Papadiamantis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, UK
| | - Laura-Jayne A. Ellis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, UK
| | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Philip Doganis
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Pantelis Karatzas
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Periklis Tsiros
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Irene Liampa
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Vladimir Lobaskin
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dario Greco
- Faculty of Medicine and Health Technology, University of Tampere, FI-33014, Finland
| | - Angela Serra
- Faculty of Medicine and Health Technology, University of Tampere, FI-33014, Finland
| | | | | | - Roland Grafström
- Misvik Biology OY, Itäinen Pitkäkatu 4, 20520 Turku, Finland
- Karolinska Institute, Institute of Environmental Medicine, Nobels väg 13, 17177 Stockholm, Sweden
| | - Pekka Kohonen
- Misvik Biology OY, Itäinen Pitkäkatu 4, 20520 Turku, Finland
- Karolinska Institute, Institute of Environmental Medicine, Nobels väg 13, 17177 Stockholm, Sweden
| | - Penny Nymark
- Misvik Biology OY, Itäinen Pitkäkatu 4, 20520 Turku, Finland
- Karolinska Institute, Institute of Environmental Medicine, Nobels väg 13, 17177 Stockholm, Sweden
| | - Egon Willighagen
- Department of Bioinformatics – BiGCaT, School of Nutrition and Translational Research in Metabolism, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, the Netherlands
| | - Tomasz Puzyn
- QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland
- University of Gdansk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdansk, Poland
| | | | - Alexander Lyubartsev
- Institutionen för material- och miljökemi, Stockholms Universitet, 106 91 Stockholm, Sweden
| | - Keld Alstrup Jensen
- The National Research Center for the Work Environment, Lersø Parkallé 105, 2100 Copenhagen, Denmark
| | - Jan Gerit Brandenburg
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Germany
- Chief Digital Organization, Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Stephen Lofts
- UK Centre for Ecology and Hydrology, Library Ave, Bailrigg, Lancaster LA1 4AP, UK
| | - Claus Svendsen
- UK Centre for Ecology and Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Samuel Harrison
- UK Centre for Ecology and Hydrology, Library Ave, Bailrigg, Lancaster LA1 4AP, UK
| | - Dieter Maier
- Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany
| | - Kaido Tamm
- Department of Chemistry, University of Tartu, Ülikooli 18, 50090 Tartu, Estonia
| | - Jaak Jänes
- Department of Chemistry, University of Tartu, Ülikooli 18, 50090 Tartu, Estonia
| | - Lauri Sikk
- Department of Chemistry, University of Tartu, Ülikooli 18, 50090 Tartu, Estonia
| | - Maria Dusinska
- NILU-Norwegian Institute for Air Research, Instituttveien 18, 2002 Kjeller, Norway
| | - Eleonora Longhin
- NILU-Norwegian Institute for Air Research, Instituttveien 18, 2002 Kjeller, Norway
| | - Elise Rundén-Pran
- NILU-Norwegian Institute for Air Research, Instituttveien 18, 2002 Kjeller, Norway
| | - Espen Mariussen
- NILU-Norwegian Institute for Air Research, Instituttveien 18, 2002 Kjeller, Norway
| | - Naouale El Yamani
- NILU-Norwegian Institute for Air Research, Instituttveien 18, 2002 Kjeller, Norway
| | - Wolfgang Unger
- Federal Institute for Material Testing and Research (BAM), Unter den Eichen 44-46, 12203 Berlin, Germany
| | - Jörg Radnik
- Federal Institute for Material Testing and Research (BAM), Unter den Eichen 44-46, 12203 Berlin, Germany
| | - Alexander Tropsha
- Eschelman School of Pharmacy, University of North Carolina at Chapel Hill, 100K Beard Hall, CB# 7568, Chapel Hill, NC 27955-7568, USA
| | - Yoram Cohen
- Samueli School Of Engineering, University of California, Los Angeles, 5531 Boelter Hall, Los Angeles, CA 90095, USA
| | - Jerzy Leszczynski
- Interdisciplinary Nanotoxicity Center, Jackson State University, 1400 J. R. Lynch Street, Jackson, MS 39217, USA
| | - Christine Ogilvie Hendren
- Center for Environmental Implications of Nanotechnologies, Duke University, 121 Hudson Hall, Durham, NC 27708-0287, USA
| | - Mark Wiesner
- Center for Environmental Implications of Nanotechnologies, Duke University, 121 Hudson Hall, Durham, NC 27708-0287, USA
| | - David Winkler
- La Trobe Institute of Molecular Sciences, La Trobe University, Plenty Rd & Kingsbury Dr, Bundoora, VIC 3086, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
- CSIRO Data61, Clayton 3168, Australia
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Noriyuki Suzuki
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-0053, Japan
| | - Tae Hyun Yoon
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
- Institute of Next Generation Material Design, Hanyang University, Seoul 04763, Republic of Korea
| | - Jang-Sik Choi
- Institute of Next Generation Material Design, Hanyang University, Seoul 04763, Republic of Korea
| | - Natasha Sanabria
- National Health Laboratory Services, 1 Modderfontein Rd, Sandringham, Johannesburg 2192, South Africa
| | - Mary Gulumian
- National Health Laboratory Services, 1 Modderfontein Rd, Sandringham, Johannesburg 2192, South Africa
- Haematology and Molecular Medicine, University of the Witwatersrand, Johannesburg, South Africa
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, UK
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