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He S, Nader K, Abarrategi JS, Bediaga H, Nocedo-Mena D, Ascencio E, Casanola-Martin GM, Castellanos-Rubio I, Insausti M, Rasulev B, Arrasate S, González-Díaz H. NANO.PTML model for read-across prediction of nanosystems in neurosciences. computational model and experimental case of study. J Nanobiotechnology 2024; 22:435. [PMID: 39044265 PMCID: PMC11267683 DOI: 10.1186/s12951-024-02660-9] [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: 04/18/2024] [Accepted: 06/24/2024] [Indexed: 07/25/2024] Open
Abstract
Neurodegenerative diseases involve progressive neuronal death. Traditional treatments often struggle due to solubility, bioavailability, and crossing the Blood-Brain Barrier (BBB). Nanoparticles (NPs) in biomedical field are garnering growing attention as neurodegenerative disease drugs (NDDs) carrier to the central nervous system. Here, we introduced computational and experimental analysis. In the computational study, a specific IFPTML technique was used, which combined Information Fusion (IF) + Perturbation Theory (PT) + Machine Learning (ML) to select the most promising Nanoparticle Neuronal Disease Drug Delivery (N2D3) systems. For the application of IFPTML model in the nanoscience, NANO.PTML is used. IF-process was carried out between 4403 NDDs assays and 260 cytotoxicity NP assays conducting a dataset of 500,000 cases. The optimal IFPTML was the Decision Tree (DT) algorithm which shown satisfactory performance with specificity values of 96.4% and 96.2%, and sensitivity values of 79.3% and 75.7% in the training (375k/75%) and validation (125k/25%) set. Moreover, the DT model obtained Area Under Receiver Operating Characteristic (AUROC) scores of 0.97 and 0.96 in the training and validation series, highlighting its effectiveness in classification tasks. In the experimental part, two samples of NPs (Fe3O4_A and Fe3O4_B) were synthesized by thermal decomposition of an iron(III) oleate (FeOl) precursor and structurally characterized by different methods. Additionally, in order to make the as-synthesized hydrophobic NPs (Fe3O4_A and Fe3O4_B) soluble in water the amphiphilic CTAB (Cetyl Trimethyl Ammonium Bromide) molecule was employed. Therefore, to conduct a study with a wider range of NP system variants, an experimental illustrative simulation experiment was performed using the IFPTML-DT model. For this, a set of 500,000 prediction dataset was created. The outcome of this experiment highlighted certain NANO.PTML systems as promising candidates for further investigation. The NANO.PTML approach holds potential to accelerate experimental investigations and offer initial insights into various NP and NDDs compounds, serving as an efficient alternative to time-consuming trial-and-error procedures.
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Affiliation(s)
- Shan He
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, 58108, USA
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain
- IKERDATA S.L., ZITEK, UPV/EHU, Rectorate Building, nº 6, Leioa, 48940, Greater Bilbao, Basque Country, Spain
| | - Karam Nader
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain
| | - Julen Segura Abarrategi
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain
| | - Harbil Bediaga
- IKERDATA S.L., ZITEK, UPV/EHU, Rectorate Building, nº 6, Leioa, 48940, Greater Bilbao, Basque Country, Spain
| | - Deyani Nocedo-Mena
- Faculty of Physical Mathematical Sciences, Autonomous University of Nuevo León, San Nicolás de los Garza, 66455, Nuevo León, México
| | - Estefania Ascencio
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, 58108, USA
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain
- IKERDATA S.L., ZITEK, UPV/EHU, Rectorate Building, nº 6, Leioa, 48940, Greater Bilbao, Basque Country, Spain
| | - Gerardo M Casanola-Martin
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, 58108, USA
| | - Idoia Castellanos-Rubio
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain.
| | - Maite Insausti
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Leioa, 48940, Spain
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, 58108, USA
| | - Sonia Arrasate
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain.
| | - Humberto González-Díaz
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa, 48940, Spain
- BIOFISIKA: Basque Center for Biophysics CSIC, University of The Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Bizkaia, Basque Country, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48011, Biscay, Spain
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Saeedimasine M, Rahmani R, Lyubartsev AP. Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning. J Chem Inf Model 2024; 64:3799-3811. [PMID: 38623916 PMCID: PMC11094735 DOI: 10.1021/acs.jcim.3c01606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Adsorption free energies of 32 small biomolecules (amino acids side chains, fragments of lipids, and sugar molecules) on 33 different nanomaterials, computed by the molecular dynamics - metadynamics methodology, have been analyzed using statistical machine learning approaches. Multiple unsupervised learning algorithms (principal component analysis, agglomerative clustering, and K-means) as well as supervised linear and nonlinear regression algorithms (linear regression, AdaBoost ensemble learning, artificial neural network) have been applied. As a result, a small set of biomolecules has been identified, knowledge of adsorption free energies of which to a specific nanomaterial can be used to predict, within the developed machine learning model, adsorption free energies of other biomolecules. Furthermore, the methodology of grouping of nanomaterials according to their interactions with biomolecules has been presented.
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Affiliation(s)
- Marzieh Saeedimasine
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Roja Rahmani
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Alexander P. Lyubartsev
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
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Singh AV, Shelar A, Rai M, Laux P, Thakur M, Dosnkyi I, Santomauro G, Singh AK, Luch A, Patil R, Bill J. Harmonization Risks and Rewards: Nano-QSAR for Agricultural Nanomaterials. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2835-2852. [PMID: 38315814 DOI: 10.1021/acs.jafc.3c06466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
This comprehensive review explores the emerging landscape of Nano-QSAR (quantitative structure-activity relationship) for assessing the risk and potency of nanomaterials in agricultural settings. The paper begins with an introduction to Nano-QSAR, providing background and rationale, and explicitly states the hypotheses guiding the review. The study navigates through various dimensions of nanomaterial applications in agriculture, encompassing their diverse properties, types, and associated challenges. Delving into the principles of QSAR in nanotoxicology, this article elucidates its application in evaluating the safety of nanomaterials, while addressing the unique limitations posed by these materials. The narrative then transitions to the progression of Nano-QSAR in the context of agricultural nanomaterials, exemplified by insightful case studies that highlight both the strengths and the limitations inherent in this methodology. Emerging prospects and hurdles tied to Nano-QSAR in agriculture are rigorously examined, casting light on important pathways forward, existing constraints, and avenues for research enhancement. Culminating in a synthesis of key insights, the review underscores the significance of Nano-QSAR in shaping the future of nanoenabled agriculture. It provides strategic guidance to steer forthcoming research endeavors in this dynamic field.
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Affiliation(s)
- Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR), Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Amruta Shelar
- Department of Technology, Savitribai Phule Pune University, Pune 411007, India
| | - Mansi Rai
- Department of Microbiology, Central University of Rajasthan NH-8, Bandar Sindri, Dist-Ajmer-305817, Rajasthan, India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR), Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Manali Thakur
- Uniklinik Köln, Kerpener Strasse 62, 50937 Köln Germany
| | - Ievgen Dosnkyi
- Institute of Chemistry and Biochemistry Department of Organic ChemistryFreie Universität Berlin Takustr. 3 14195 Berlin, Germany
| | - Giulia Santomauro
- Institute for Materials Science, Department of Bioinspired Materials, University of Stuttgart, 70569, Stuttgart, Germany
| | - Alok Kumar Singh
- Department of Plant Molecular Biology & Genetic Engineering, ANDUA&T, Ayodhya 224229, Uttar Pradesh, India
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR), Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Rajendra Patil
- Department of Technology, Savitribai Phule Pune University, Pune 411007, India
| | - Joachim Bill
- Institute for Materials Science, Department of Bioinspired Materials, University of Stuttgart, 70569, Stuttgart, Germany
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4
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Furxhi I, Willighagen E, Evelo C, Costa A, Gardini D, Ammar A. A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability. NANOIMPACT 2023; 31:100475. [PMID: 37423508 DOI: 10.1016/j.impact.2023.100475] [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: 03/28/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
INTRODUCTION The current effort towards the digital transformation across multiple scientific domains requires data that is Findable, Accessible, Interoperable and Reusable (FAIR). In addition to the FAIR data, what is required for the application of computational tools, such as Quantitative Structure Activity Relationships (QSARs), is a sufficient data volume and the ability to merge sources into homogeneous digital assets. In the nanosafety domain there is a lack of FAIR available metadata. METHODOLOGY To address this challenge, we utilized 34 datasets from the nanosafety domain by exploiting the NanoSafety Data Reusability Assessment (NSDRA) framework, which allowed the annotation and assessment of dataset's reusability. From the framework's application results, eight datasets targeting the same endpoint (i.e. numerical cellular viability) were selected, processed and merged to test several hypothesis including universal versus nanogroup-specific QSAR models (metal oxide and nanotubes), and regression versus classification Machine Learning (ML) algorithms. RESULTS Universal regression and classification QSARs reached an 0.86 R2 and 0.92 accuracy, respectively, for the test set. Nanogroup-specific regression models reached 0.88 R2 for nanotubes test set followed by metal oxide (0.78). Nanogroup-specific classification models reached 0.99 accuracy for nanotubes test set, followed by metal oxide (0.91). Feature importance revealed different patterns depending on the dataset with common influential features including core size, exposure conditions and toxicological assay. Even in the case where the available experimental knowledge was merged, the models still failed to correctly predict the outputs of an unseen dataset, revealing the cumbersome conundrum of scientific reproducibility in realistic applications of QSAR for nanosafety. To harness the full potential of computational tools and ensure their long-term applications, embracing FAIR data practices is imperative in driving the development of responsible QSAR models. CONCLUSIONS This study reveals that the digitalization of nanosafety knowledge in a reproducible manner has a long way towards its successful pragmatic implementation. The workflow carried out in the study shows a promising approach to increase the FAIRness across all the elements of computational studies, from dataset's annotation, selection, merging to FAIR modeling reporting. This has significant implications for future research as it provides an example of how to utilize and report different tools available in the nanosafety knowledge system, while increasing the transparency of the results. One of the main benefits of this workflow is that it promotes data sharing and reuse, which is essential for advancing scientific knowledge by making data and metadata FAIR compliant. In addition, the increased transparency and reproducibility of the results can enhance the trustworthiness of the computational findings.
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Affiliation(s)
- Irini Furxhi
- Transgero Limited, Cullinagh, Newcastle West, Co. Limerick, Ireland; Dept. of Accounting and Finance, Kemmy Business School, University of Limerick, V94PH93, Ireland.
| | - Egon Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, the Netherlands.
| | - Chris Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, the Netherlands.
| | - Anna Costa
- National Research Council, Institute of Science, Technology and Sustainability for Ceramics, Faenza, Italy.
| | - Davide Gardini
- National Research Council, Institute of Science, Technology and Sustainability for Ceramics, Faenza, Italy.
| | - Ammar Ammar
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, the Netherlands.
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5
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Furxhi I, Bengalli R, Motta G, Mantecca P, Kose O, Carriere M, Haq EU, O’Mahony C, Blosi M, Gardini D, Costa A. Data-Driven Quantitative Intrinsic Hazard Criteria for Nanoproduct Development in a Safe-by-Design Paradigm: A Case Study of Silver Nanoforms. ACS APPLIED NANO MATERIALS 2023; 6:3948-3962. [PMID: 36938492 PMCID: PMC10012170 DOI: 10.1021/acsanm.3c00173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The current European (EU) policies, that is, the Green Deal, envisage safe and sustainable practices for chemicals, which include nanoforms (NFs), at the earliest stages of innovation. A theoretically safe and sustainable by design (SSbD) framework has been established from EU collaborative efforts toward the definition of quantitative criteria in each SSbD dimension, namely, the human and environmental safety dimension and the environmental, social, and economic sustainability dimensions. In this study, we target the safety dimension, and we demonstrate the journey toward quantitative intrinsic hazard criteria derived from findable, accessible, interoperable, and reusable data. Data were curated and merged for the development of new approach methodologies, that is, quantitative structure-activity relationship models based on regression and classification machine learning algorithms, with the intent to predict a hazard class. The models utilize system (i.e., hydrodynamic size and polydispersity index) and non-system (i.e., elemental composition and core size)-dependent nanoscale features in combination with biological in vitro attributes and experimental conditions for various silver NFs, functional antimicrobial textiles, and cosmetics applications. In a second step, interpretable rules (criteria) followed by a certainty factor were obtained by exploiting a Bayesian network structure crafted by expert reasoning. The probabilistic model shows a predictive capability of ≈78% (average accuracy across all hazard classes). In this work, we show how we shifted from the conceptualization of the SSbD framework toward the realistic implementation with pragmatic instances. This study reveals (i) quantitative intrinsic hazard criteria to be considered in the safety aspects during synthesis stage, (ii) the challenges within, and (iii) the future directions for the generation and distillation of such criteria that can feed SSbD paradigms. Specifically, the criteria can guide material engineers to synthesize NFs that are inherently safer from alternative nanoformulations, at the earliest stages of innovation, while the models enable a fast and cost-efficient in silico toxicological screening of previously synthesized and hypothetical scenarios of yet-to-be synthesized NFs.
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Affiliation(s)
- Irini Furxhi
- Transgero
Ltd, Limerick V42V384, Ireland
- Department
of Accounting and Finance, Kemmy Business School, University of Limerick, Limerick V94T9PX, Ireland
| | - Rossella Bengalli
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza
della Scienza 1, Milano 20126, Italy
| | - Giulia Motta
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza
della Scienza 1, Milano 20126, Italy
| | - Paride Mantecca
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza
della Scienza 1, Milano 20126, Italy
| | - Ozge Kose
- Univ.
Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SYMMES, Grenoble 38000, France
| | - Marie Carriere
- Univ.
Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SYMMES, Grenoble 38000, France
| | - Ehtsham Ul Haq
- Department
of Physics, and Bernal Institute, University
of Limerick, Limerick V94TC9PX, Ireland
| | - Charlie O’Mahony
- Department
of Physics, and Bernal Institute, University
of Limerick, Limerick V94TC9PX, Ireland
| | - Magda Blosi
- Istituto
di Scienza e Tecnologia dei Materiali Ceramici (CNR-ISTEC), Via Granarolo, 64, Faenza 48018, Ravenna, Italy
| | - Davide Gardini
- Istituto
di Scienza e Tecnologia dei Materiali Ceramici (CNR-ISTEC), Via Granarolo, 64, Faenza 48018, Ravenna, Italy
| | - Anna Costa
- Istituto
di Scienza e Tecnologia dei Materiali Ceramici (CNR-ISTEC), Via Granarolo, 64, Faenza 48018, Ravenna, Italy
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Tan P, Chen X, Zhang H, Wei Q, Luo K. Artificial intelligence aids in development of nanomedicines for cancer management. Semin Cancer Biol 2023; 89:61-75. [PMID: 36682438 DOI: 10.1016/j.semcancer.2023.01.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/28/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023]
Abstract
Over the last decade, the nanomedicine has experienced unprecedented development in diagnosis and management of diseases. A number of nanomedicines have been approved in clinical use, which has demonstrated the potential value of clinical transition of nanotechnology-modified medicines from bench to bedside. The application of artificial intelligence (AI) in development of nanotechnology-based products could transform the healthcare sector by realizing acquisition and analysis of large datasets, and tailoring precision nanomedicines for cancer management. AI-enabled nanotechnology could improve the accuracy of molecular profiling and early diagnosis of patients, and optimize the design pipeline of nanomedicines by tuning the properties of nanomedicines, achieving effective drug synergy, and decreasing the nanotoxicity, thereby, enhancing the targetability, personalized dosing and treatment potency of nanomedicines. Herein, the advances in AI-enabled nanomedicines in cancer management are elaborated and their application in diagnosis, monitoring and therapy as well in precision medicine development is discussed.
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Affiliation(s)
- Ping Tan
- Department of Urology, and Department of Radiology, Institute of Urology, and Huaxi MR Research Center (HMRRC), Animal Experimental Center, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoting Chen
- Department of Urology, and Department of Radiology, Institute of Urology, and Huaxi MR Research Center (HMRRC), Animal Experimental Center, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hu Zhang
- Amgen Bioprocessing Centre, Keck Graduate Institute, Claremont, CA 91711, USA
| | - Qiang Wei
- Department of Urology, and Department of Radiology, Institute of Urology, and Huaxi MR Research Center (HMRRC), Animal Experimental Center, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Kui Luo
- Department of Urology, and Department of Radiology, Institute of Urology, and Huaxi MR Research Center (HMRRC), Animal Experimental Center, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
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Ahmad A, Imran M, Sharma N. Precision Nanotoxicology in Drug Development: Current Trends and Challenges in Safety and Toxicity Implications of Customized Multifunctional Nanocarriers for Drug-Delivery Applications. Pharmaceutics 2022; 14:2463. [PMID: 36432653 PMCID: PMC9697541 DOI: 10.3390/pharmaceutics14112463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/06/2022] [Accepted: 11/13/2022] [Indexed: 11/17/2022] Open
Abstract
The dire need for the assessment of human and environmental endangerments of nanoparticulate material has motivated the formulation of novel scientific tools and techniques to detect, quantify, and characterize these nanomaterials. Several of these paradigms possess enormous possibilities for applications in many of the realms of nanotoxicology. Furthermore, in a large number of cases, the limited capabilities to assess the environmental and human toxicological outcomes of customized and tailored multifunctional nanoparticles used for drug delivery have hindered their full exploitation in preclinical and clinical settings. With the ever-compounded availability of nanoparticulate materials in commercialized settings, an ever-arising popular debate has been egressing on whether the social, human, and environmental costs associated with the risks of nanomaterials outweigh their profits. Here we briefly review the various health, pharmaceutical, and regulatory aspects of nanotoxicology of engineered multifunctional nanoparticles in vitro and in vivo. Several aspects and issues encountered during the safety and toxicity assessments of these drug-delivery nanocarriers have also been summarized. Furthermore, recent trends implicated in the nanotoxicological evaluations of nanoparticulate matter in vitro and in vivo have also been discussed. Due to the absence of robust and rigid regulatory guidelines, researchers currently frequently encounter a larger number of challenges in the toxicology assessment of nanocarriers, which have also been briefly discussed here. Nanotoxicology has an appreciable and significant part in the clinical translational development as well as commercialization potential of nanocarriers; hence these aspects have also been touched upon. Finally, a brief overview has been provided regarding some of the nanocarrier-based medicines that are currently undergoing clinical trials, and some of those which have recently been commercialized and are available for patients. It is expected that this review will instigate an appreciable interest in the research community working in the arena of pharmaceutical drug development and nanoformulation-based drug delivery.
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Affiliation(s)
- Anas Ahmad
- Julia McFarlane Diabetes Research Centre (JMDRC), Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mohammad Imran
- Therapeutics Research Group, Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane 4102, Australia
| | - Nisha Sharma
- Division of Nephrology, Department of Internal Medicine, University of Utah, Salt Lake City, UT 84132, USA
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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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9
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Furxhi I. Health and environmental safety of nanomaterials: O Data, Where Art Thou? NANOIMPACT 2022; 25:100378. [PMID: 35559884 DOI: 10.1016/j.impact.2021.100378] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 06/15/2023]
Abstract
Nanotechnology keeps drawing attention due to the great tunable properties of nanomaterials in comparison to their bulk conventional materials. The growth of nanotechnology in combination with the digitization era has led to an increased need of safety related data. In addition to safety, new data-driven paradigms on safe and sustainable by design materials are stressing the necessity of data even more. Data is a fundamental asset to the scientific community in studying and analysing the entire life-cycle of nanomaterials. Unfortunately, data exist in a scattered fashion, in different sources and formats. To our knowledge, there is no study focusing on aspects of actual data-structure knowledge that exists in literature and databases. The purpose of this review research is to transparently and comprehensively, display to the nanoscience community the datasets readily available for machine learning purposes making it convenient and more efficient for the next users such as modellers or data curators to retrieve information. We systematically recorded the features and descriptors available in the datasets and provide synopsised information on their ranges, forms and metrics in the supplementary material.
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Affiliation(s)
- Irini Furxhi
- Transgero Limited, Cullinagh, Newcastle West, Co. Limerick, Ireland; Dept. of Accounting and Finance, Kemmy Business School, University of Limerick, V94PH93, Ireland.
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10
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Toropova AP, Toropov AA, Leszczynski J, Sizochenko N. Using quasi-SMILES for the predictive modeling of the safety of 574 metal oxide nanoparticles measured in different experimental conditions. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 86:103665. [PMID: 33895354 DOI: 10.1016/j.etap.2021.103665] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/31/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
The production of nanomaterials continues its rapid growth; however, newly manufactured nanomaterials' environmental and health safety are among the most significant concerns. A safety assessment is usually a lengthy and costly process, so computational studies are often used to complement experimental testing. One of the most time-efficient techniques is structure-activity relationships (SAR) modeling. In this project, we analyzed the Sustainable Nanotechnology (S2NANO) dataset that contains 574 experimental cell viability and toxicity datapoints for Al2O3, CuO, Fe2O3, Fe3O4, SiO2, TiO2, and ZnO measured in different conditions. We aimed to develop classification- and regression-based structure-activity relationship models using quasi-SMILES molecular representation. Introduced quasi-SMILES took into consideration all available information, including structural features of nanoparticles (molecular structure, core size, etc.) and related experimental parameters (cell line, dose, exposure time, assay, hydrodynamic size, surface charge, etc.). Resultant regression models demonstrated sufficient predictive power, while classification models demonstrated higher accuracy.
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Affiliation(s)
- Alla P Toropova
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Science, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Andrey A Toropov
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Science, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics, and Atmospheric Sciences, Jackson State University, Jackson, MS, USA
| | - Natalia Sizochenko
- Department of Informatics, Postdoctoral Institute for Computational Studies, Enfield, NH, USA; The Ronin Institute of Independent Scholarship, Montclair, NJ, USA.
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11
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Sizochenko N, Mikolajczyk A, Syzochenko M, Puzyn T, Leszczynski J. Zeta potentials (ζ) of metal oxide nanoparticles: A meta-analysis of experimental data and a predictive neural networks modeling. NANOIMPACT 2021; 22:100317. [PMID: 35559974 DOI: 10.1016/j.impact.2021.100317] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 06/15/2023]
Abstract
Zeta potential is usually measured to estimate the surface charge and the stability of nanomaterials, as changes in these characteristics directly influence the biological activity of a given nanoparticle. Nowadays, theoretical methods are commonly used for a pre-screening safety assessments of nanomaterials. At the same time, the consistency of data on zeta potential measurements in the context of environmental impact is an important challenge. The inconsistency of data measurements leads to inaccuracies in predictive modeling. In this article, we report a new curated dataset of zeta potentials measured for 208 silica- and metal oxide nanoparticles in different media. We discuss the data curation framework for zeta potentials designed to assess the quality and usefulness of the literature data for further computational modeling. We also provide an analysis of specific trends for the datapoints harvested from different literature sources. In addition to that, we present for the first time a structure-property relationship model for nanoparticles (nano-SPR) that predicts values of zeta potential values measured in different environmental conditions (i.e., biological media and pH).
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Affiliation(s)
- Natalia Sizochenko
- Department of Informatics, Postdoctoral Institute for Computational Studies, Enfield, NH, USA; School of Informatics and Engineering, Blanchardstown Campus, Technological University Dublin, Blanchardstown, Ireland.
| | - Alicja Mikolajczyk
- Department of Informatics, Postdoctoral Institute for Computational Studies, Enfield, NH, USA; Laboratory of Environmental Chemometrics, Faculty of Chemistry, University of Gdansk, Gdansk, Poland; QSAR Lab Ltd, Gdansk, Poland
| | - Michael Syzochenko
- Department of Informatics, Postdoctoral Institute for Computational Studies, Enfield, NH, USA
| | - Tomasz Puzyn
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, University of Gdansk, Gdansk, Poland; QSAR Lab Ltd, Gdansk, Poland
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics, and Atmospheric Sciences, Jackson State University, Jackson, MS, USA
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12
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New Mechanistic Insights on Carbon Nanotubes' Nanotoxicity Using Isolated Submitochondrial Particles, Molecular Docking, and Nano-QSTR Approaches. BIOLOGY 2021; 10:biology10030171. [PMID: 33668702 PMCID: PMC7996163 DOI: 10.3390/biology10030171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 01/08/2023]
Abstract
Single-walled carbon nanotubes can induce mitochondrial F0F1-ATPase nanotoxicity through inhibition. To completely characterize the mechanistic effect triggering the toxicity, we have developed a new approach based on the combination of experimental and computational study, since the use of only one or few techniques may not fully describe the phenomena. To this end, the in vitro inhibition responses in submitochondrial particles (SMP) was combined with docking, elastic network models, fractal surface analysis, and Nano-QSTR models. In vitro studies suggest that inhibition responses in SMP of F0F1-ATPase enzyme were strongly dependent on the concentration assay (from 3 to 5 µg/mL) for both pristine and COOH single-walled carbon nanotubes types (SWCNT). Besides, both SWCNTs show an interaction inhibition pattern mimicking the oligomycin A (the specific mitochondria F0F1-ATPase inhibitor blocking the c-ring F0 subunit). Performed docking studies denote the best crystallography binding pose obtained for the docking complexes based on the free energy of binding (FEB) fit well with the in vitro evidence from the thermodynamics point of view, following an affinity order such as: FEB (oligomycin A/F0-ATPase complex) = -9.8 kcal/mol > FEB (SWCNT-COOH/F0-ATPase complex) = -6.8 kcal/mol ~ FEB (SWCNT-pristine complex) = -5.9 kcal/mol, with predominance of van der Waals hydrophobic nano-interactions with key F0-ATPase binding site residues (Phe 55 and Phe 64). Elastic network models and fractal surface analysis were performed to study conformational perturbations induced by SWCNT. Our results suggest that interaction may be triggering abnormal allosteric responses and signals propagation in the inter-residue network, which could affect the substrate recognition ligand geometrical specificity of the F0F1-ATPase enzyme in order (SWCNT-pristine > SWCNT-COOH). In addition, Nano-QSTR models have been developed to predict toxicity induced by both SWCNTs, using results of in vitro and docking studies. Results show that this method may be used for the fast prediction of the nanotoxicity induced by SWCNT, avoiding time- and money-consuming techniques. Overall, the obtained results may open new avenues toward to the better understanding and prediction of new nanotoxicity mechanisms, rational drug design-based nanotechnology, and potential biomedical application in precision nanomedicine.
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13
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Oksel Karakus C, Bilgi E, Winkler DA. Biomedical nanomaterials: applications, toxicological concerns, and regulatory needs. Nanotoxicology 2020; 15:331-351. [PMID: 33337941 DOI: 10.1080/17435390.2020.1860265] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Advances in cutting-edge technologies such as nano- and biotechnology have created an opportunity for re-engineering existing materials and generating new nano-scale products that can function beyond the limits of conventional ones. While the step change in the properties and functionalities of these new materials opens up new possibilities for a broad range of applications, it also calls for structural modifications to existing safety assessment processes that are primarily focused on bulk material properties. Decades after the need to modify existing risk management practices to include nano-specific behaviors and exposure pathways was recognized, relevant policies for evaluating, and controlling health risks of nano-enabled materials is still lacking. This review provides an overview of current progress in the field of nanobiotechnology rather than intentions and aspirations, summarizes long-recognized but still unresolved issues surrounding materials safety at the nanoscale, and discusses key barriers preventing generation and integration of reliable data in bio/nano-safety domain. Particular attention is given to nanostructured materials that are commonly used in biomedical applications.
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Affiliation(s)
| | - Eyup Bilgi
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - David A Winkler
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia.,Latrobe Institute for Molecular Science, La Trobe University, Bundoora, Australia.,School of Pharmacy, University of Nottingham, Nottingham, UK.,CSIRO Data61, Pullenvale, Australia
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14
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Giubilato E, Cazzagon V, Amorim MJB, Blosi M, Bouillard J, Bouwmeester H, Costa AL, Fadeel B, Fernandes TF, Fito C, Hauser M, Marcomini A, Nowack B, Pizzol L, Powell L, Prina-Mello A, Sarimveis H, Scott-Fordsmand JJ, Semenzin E, Stahlmecke B, Stone V, Vignes A, Wilkins T, Zabeo A, Tran L, Hristozov D. Risk Management Framework for Nano-Biomaterials Used in Medical Devices and Advanced Therapy Medicinal Products. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E4532. [PMID: 33066064 PMCID: PMC7601697 DOI: 10.3390/ma13204532] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 12/25/2022]
Abstract
The convergence of nanotechnology and biotechnology has led to substantial advancements in nano-biomaterials (NBMs) used in medical devices (MD) and advanced therapy medicinal products (ATMP). However, there are concerns that applications of NBMs for medical diagnostics, therapeutics and regenerative medicine could also pose health and/or environmental risks since the current understanding of their safety is incomplete. A scientific strategy is therefore needed to assess all risks emerging along the life cycles of these products. To address this need, an overarching risk management framework (RMF) for NBMs used in MD and ATMP is presented in this paper, as a result of a collaborative effort of a team of experts within the EU Project BIORIMA and with relevant inputs from external stakeholders. The framework, in line with current regulatory requirements, is designed according to state-of-the-art approaches to risk assessment and management of both nanomaterials and biomaterials. The collection/generation of data for NBMs safety assessment is based on innovative integrated approaches to testing and assessment (IATA). The framework can support stakeholders (e.g., manufacturers, regulators, consultants) in systematically assessing not only patient safety but also occupational (including healthcare workers) and environmental risks along the life cycle of MD and ATMP. The outputs of the framework enable the user to identify suitable safe(r)-by-design alternatives and/or risk management measures and to compare the risks of NBMs to their (clinical) benefits, based on efficacy, quality and cost criteria, in order to inform robust risk management decision-making.
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Affiliation(s)
- Elisa Giubilato
- Department of Environmental Sciences, Informatics and Statistics, University Ca’ Foscari of Venice, Via Torino 155, 30172 Venice, Italy; (E.G.); (V.C.); (A.M.); (E.S.)
| | - Virginia Cazzagon
- Department of Environmental Sciences, Informatics and Statistics, University Ca’ Foscari of Venice, Via Torino 155, 30172 Venice, Italy; (E.G.); (V.C.); (A.M.); (E.S.)
| | - Mónica J. B. Amorim
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Magda Blosi
- Institute of Science and Technology for Ceramics, National Research Council of Italy (CNR-ISTEC), Via Granarolo 64, 48018 Faenza, Italy; (M.B.); (A.L.C.)
| | - Jacques Bouillard
- Institut National de l’Environnement industriel et des Risques, Parc Technologique ALATA, 60550 Verneuil-en-Halatte, France; (J.B.); (A.V.)
| | - Hans Bouwmeester
- Division of Toxicology, Wageningen University, 6708 WE Wageningen, The Netherlands;
| | - Anna Luisa Costa
- Institute of Science and Technology for Ceramics, National Research Council of Italy (CNR-ISTEC), Via Granarolo 64, 48018 Faenza, Italy; (M.B.); (A.L.C.)
| | - Bengt Fadeel
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden;
| | - Teresa F. Fernandes
- Institute of Life and Earth Sciences, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh EH14 4AS, UK;
| | - Carlos Fito
- Instituto Tecnologico del Embalaje, Transporte y Logistica, 46980 Paterna-Valencia, Spain;
| | - Marina Hauser
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland; (M.H.); (B.N.)
| | - Antonio Marcomini
- Department of Environmental Sciences, Informatics and Statistics, University Ca’ Foscari of Venice, Via Torino 155, 30172 Venice, Italy; (E.G.); (V.C.); (A.M.); (E.S.)
| | - Bernd Nowack
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland; (M.H.); (B.N.)
| | - Lisa Pizzol
- GreenDecision Srl, Via delle Industrie, 21/8, 30175 Venice, Italy; (L.P.); (A.Z.)
| | - Leagh Powell
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK; (L.P.); (V.S.)
| | - Adriele Prina-Mello
- Trinity Translational Medicine Institute, Trinity College, The University of Dublin, Dublin 8, Ireland;
| | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece;
| | | | - Elena Semenzin
- Department of Environmental Sciences, Informatics and Statistics, University Ca’ Foscari of Venice, Via Torino 155, 30172 Venice, Italy; (E.G.); (V.C.); (A.M.); (E.S.)
| | | | - Vicki Stone
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK; (L.P.); (V.S.)
| | - Alexis Vignes
- Institut National de l’Environnement industriel et des Risques, Parc Technologique ALATA, 60550 Verneuil-en-Halatte, France; (J.B.); (A.V.)
| | - Terry Wilkins
- Nanomanufacturing Institute, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, UK;
| | - Alex Zabeo
- GreenDecision Srl, Via delle Industrie, 21/8, 30175 Venice, Italy; (L.P.); (A.Z.)
| | - Lang Tran
- Institute of Occupational Medicine, Research Avenue North, Riccarton, Edinburgh EH14 4AP, UK;
| | - Danail Hristozov
- Department of Environmental Sciences, Informatics and Statistics, University Ca’ Foscari of Venice, Via Torino 155, 30172 Venice, Italy; (E.G.); (V.C.); (A.M.); (E.S.)
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15
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Chemometric modeling of PET imaging agents for diagnosis of Parkinson’s disease: a QSAR approach. Struct Chem 2020. [DOI: 10.1007/s11224-020-01560-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Nguyen MK, Moon JY, Lee YC. Microalgal ecotoxicity of nanoparticles: An updated review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 201:110781. [PMID: 32497816 DOI: 10.1016/j.ecoenv.2020.110781] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/05/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Nowadays, nanotechnology and its related industries are becoming a rapidly explosive industry that offers many benefits to human life. However, along with the increased production and use of nanoparticles (NPs), their presence in the environment creates a high risk of increasing toxic effects on aquatic organisms. Therefore, a large number of studies focusing on the toxicity of these NPs to the aquatic organisms are carried out which used algal species as a common biological model. In this review, the influences of the physio-chemical properties of NPs and the response mechanisms of the algae on the toxicity of the NPs were discussed focusing on the "assay" studies. Besides, the specific algal toxicities of each type of NPs along with the NP-induced changes in algal cells of these NPs are also assessed. Almost all commonly-used NPs exhibit algal toxicity. Although the algae have similarities in the symptoms under NP exposure, the sensitivity and variability of each algae species to the inherent properties of each NPs are quite different. They depend strongly on the concentration, size, characteristics of NPs, and biochemical nature of algae. Through the assessment, the review identifies several gaps that need to be further studied to make an explicit understanding. The findings in the majority of studies are mostly in laboratory conditions and there are still uncertainties and contradictory/inconsistent results about the behavioral effects of NPs under field conditions. Besides, there remains unsureness about NP-uptake pathways of microalgae. Finally, the toxicity mechanisms of NPs need to be thoughtfully understood which is essential in risk assessment.
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Affiliation(s)
- Minh Kim Nguyen
- Department of BioNano Technology, Gachon University, 1342 Seongnamdaero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea.
| | - Ju-Young Moon
- Department of Beauty Design Management, Hansung University, 116 Samseongyoro-16 gil, Seoul, 02876, Republic of Korea.
| | - Young-Chul Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnamdaero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea.
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17
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Milosevic A, Romeo D, Wick P. Understanding Nanomaterial Biotransformation: An Unmet Challenge to Achieving Predictive Nanotoxicology. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1907650. [PMID: 32402142 DOI: 10.1002/smll.201907650] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/06/2020] [Accepted: 03/08/2020] [Indexed: 06/11/2023]
Abstract
More than a decade has passed since the first concepts of predictive nanotoxicology were formulated. During this time, many advancements have been achieved in multiple disciplines, including the success stories of the fiber paradigm and the oxidative stress paradigm. However, important knowledge gaps are slowing down the development of predictive nanotoxicology and require a mutidisciplinary effort to be overcome. Among these gaps, understanding, reproducing, and modeling of nanomaterial biotransformation in biological environments is a central challenge, both in vitro and in silico. This dynamic and complex process is still a challenge for today's bioanalytics. This work explores and discusses selected approaches of the multidisciplinary efforts taken in the last decade and the challenges that remain unmet, in particular concerning nanomaterial biotransformation. It highlights some future advancements that, together, can help to understand such complex processes and accelerate the development of predictive nanotoxicology.
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Affiliation(s)
- Ana Milosevic
- Empa, Swiss Laboratories for Materials Science and Technology, Laboratory for Particles-Biology Interactions, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Daina Romeo
- Empa, Swiss Laboratories for Materials Science and Technology, Laboratory for Particles-Biology Interactions, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Peter Wick
- Empa, Swiss Laboratories for Materials Science and Technology, Laboratory for Particles-Biology Interactions, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
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18
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Sharma N, Sharma M, Sajid Jamal QM, Kamal MA, Akhtar S. Nanoinformatics and biomolecular nanomodeling: a novel move en route for effective cancer treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:19127-19141. [PMID: 31025282 DOI: 10.1007/s11356-019-05152-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Empowering role of nanoinformatics in design and elucidation of nanoparticles for effective cancer treatment has made this field a fascinating area for researchers, inspiring them to enhance up the quality and efficacy of existing anticancer medicines. Theoretical and computational modeling is being seen as a forefront solution for problems related to surface chemistry, optimized geometry, or other properties in nanoparticle designing and drug delivery. The current review aims to acquaint with the insight story of the incubation of in silico tools and techniques in nanotechnology to develop better anticancer nanomedicines. The review also recapitulates the assets and liabilities of this field and present an outline of existing inventiveness and endeavors of nanoinformatics. We propose how nanoinformatics could hasten up the advancements in anticancer nanomedicines through use of computational tools, nanoparticles repositories & various modeling and simulation methods.
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Affiliation(s)
- Neha Sharma
- Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow, UP, 226026, India
- Advanced Center of Bioengineering and Bioinformatics, Integral Information and Research Centre, Integral University, Lucknow, UP, 226026, India
| | - Mala Sharma
- Advanced Center of Bioengineering and Bioinformatics, Integral Information and Research Centre, Integral University, Lucknow, UP, 226026, India
- Department of Biosciences, Integral University, Lucknow, UP, 226026, India
| | - Qazi M Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, King Abdulaziz Rd, Al Bukayriyah, 52741, Al Qassim, Saudi Arabia
| | - Mohammad A Kamal
- King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Enzymoics, 7, Peterlee Place, Hebersham, NSW, 2770, Australia
- Novel Global Community Educational Foundation, Peterlee Place, Hebersham, NSW, 2770, Australia
| | - Salman Akhtar
- Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow, UP, 226026, India.
- Advanced Center of Bioengineering and Bioinformatics, Integral Information and Research Centre, Integral University, Lucknow, UP, 226026, India.
- Novel Global Community Educational Foundation, Peterlee Place, Hebersham, NSW, 2770, Australia.
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19
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Duskey JT, Baraldi C, Gamberini MC, Ottonelli I, Da Ros F, Tosi G, Forni F, Vandelli MA, Ruozi B. Investigating Novel Syntheses of a Series of Unique Hybrid PLGA-Chitosan Polymers for Potential Therapeutic Delivery Applications. Polymers (Basel) 2020; 12:polym12040823. [PMID: 32260469 PMCID: PMC7249265 DOI: 10.3390/polym12040823] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 01/23/2023] Open
Abstract
Discovering new materials to aid in the therapeutic delivery of drugs is in high demand. PLGA, a FDA approved polymer, is well known in the literature to form films or nanoparticles that can load, protect, and deliver drug molecules; however, its incompatibility with certain drugs (due to hydrophilicity or charge repulsion interactions) limits its use. Combining PLGA or other polymers such as polycaprolactone with other safe and positively-charged molecules, such as chitosan, has been sought after to make hybrid systems that are more flexible in terms of loading ability, but often the reactions for polymer coupling use harsh conditions, films, unpurified products, or create a single unoptimized product. In this work, we aimed to investigate possible innovative improvements regarding two synthetic procedures. Two methods were attempted and analytically compared using nuclear magnetic resonance (NMR), fourier-transform infrared spectroscopy (FT-IR), and dynamic scanning calorimetry (DSC) to furnish pure, homogenous, and tunable PLGA-chitosan hybrid polymers. These were fully characterized by analytical methods. A series of hybrids was produced that could be used to increase the suitability of PLGA with previously non-compatible drug molecules.
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Affiliation(s)
- Jason Thomas Duskey
- Te.Far.T.I.-Nanotech Lab, Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (J.T.D.); (I.O.); (F.D.R.); (G.T.); (F.F.); (M.A.V.)
- Umberto Veronesi Foundation, 20121 Milano, Italy
| | - Cecilia Baraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (C.B.); (M.C.G.)
| | - Maria Cristina Gamberini
- Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (C.B.); (M.C.G.)
| | - Ilaria Ottonelli
- Te.Far.T.I.-Nanotech Lab, Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (J.T.D.); (I.O.); (F.D.R.); (G.T.); (F.F.); (M.A.V.)
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Federica Da Ros
- Te.Far.T.I.-Nanotech Lab, Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (J.T.D.); (I.O.); (F.D.R.); (G.T.); (F.F.); (M.A.V.)
| | - Giovanni Tosi
- Te.Far.T.I.-Nanotech Lab, Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (J.T.D.); (I.O.); (F.D.R.); (G.T.); (F.F.); (M.A.V.)
| | - Flavio Forni
- Te.Far.T.I.-Nanotech Lab, Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (J.T.D.); (I.O.); (F.D.R.); (G.T.); (F.F.); (M.A.V.)
| | - Maria Angela Vandelli
- Te.Far.T.I.-Nanotech Lab, Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (J.T.D.); (I.O.); (F.D.R.); (G.T.); (F.F.); (M.A.V.)
| | - Barbara Ruozi
- Te.Far.T.I.-Nanotech Lab, Department of Life Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (J.T.D.); (I.O.); (F.D.R.); (G.T.); (F.F.); (M.A.V.)
- Correspondence:
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20
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Liu G, Yan X, Sedykh A, Pan X, Zhao X, Yan B, Zhu H. Analysis of model PM 2.5-induced inflammation and cytotoxicity by the combination of a virtual carbon nanoparticle library and computational modeling. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 191:110216. [PMID: 31972454 PMCID: PMC7018436 DOI: 10.1016/j.ecoenv.2020.110216] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/04/2019] [Accepted: 01/13/2020] [Indexed: 05/02/2023]
Abstract
Health risks induced by PM2.5 have become one of the major concerns among living populations, especially in regions facing serious pollution such as China and India. Furthermore, the composition of PM2.5 is complex and it also varies with time and locations. To facilitate our understanding of PM2.5-induced toxicity, a predictive modeling framework was developed in the present study. The core of this study was 1) to construct a virtual carbon nanoparticle library based on the experimental data to simulate the PM2.5 structures; 2) to quantify the nanoparticle structures by novel nanodescriptors; and 3) to perform computational modeling for critical toxicity endpoints. The virtual carbon nanoparticle library was developed to represent the nanostructures of 20 carbon nanoparticles, which were synthesized to simulate PM2.5 structures and tested for potential health risks. Based on the calculated nanodescriptors from virtual carbon nanoparticles, quantitative nanostructure-activity relationship (QNAR) models were developed to predict cytotoxicity and four different inflammatory responses induced by model PM2.5. The high predictability (R2 > 0.65 for leave-one-out validations) of the resulted consensus models indicated that this approach could be a universal tool to predict and analyze the potential toxicity of model PM2.5, ultimately understanding and evaluating the ambient PM2.5-induced toxicity.
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Affiliation(s)
- Guohong Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Xiliang Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China; The Rutgers Center for Computational and Integrative Biology, Camden, NJ, 08102, USA
| | - Alexander Sedykh
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ, 08102, USA; Sciome, Research Triangle Park, NC, 27709, USA
| | - Xiujiao Pan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Xiaoli Zhao
- Department of Physiological Science, Eastern Virginia Medical School, Norfolk, VA, 23507, USA
| | - Bing Yan
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou, 510006, China; School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China.
| | - Hao Zhu
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ, 08102, USA; Department of Chemistry, Rutgers University, Camden, NJ, 08102, USA.
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21
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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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Affiliation(s)
- Hagit Sason
- Faculty of Biomedical Engineering Technion – Israel Institute of Technology Haifa Israel
| | - Yosi Shamay
- Faculty of Biomedical Engineering Technion – Israel Institute of Technology Haifa Israel
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Yan X, Sedykh A, Wang W, Zhao X, Yan B, Zhu H. In silico profiling nanoparticles: predictive nanomodeling using universal nanodescriptors and various machine learning approaches. NANOSCALE 2019; 11:8352-8362. [PMID: 30984943 DOI: 10.1039/c9nr00844f] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Rational nanomaterial design is urgently demanded for new nanomaterial development with desired properties. However, computational nanomaterial modeling and virtual nanomaterial screening are not applicable for this purpose due to the complexity of nanomaterial structures. To address this challenge, a new computational workflow is established in this study to virtually profile nanoparticles by (1) constructing a structurally diverse virtual gold nanoparticle (GNP) library and (2) developing novel universal nanodescriptors. The emphasis of this study is the second task by developing geometrical nanodescriptors that are suitable for the quantitative modeling of GNPs and virtual screening purposes. The feasibility, rigor and applicability of this novel computational method are validated by testing seven GNP datasets consisting of 191 unique GNPs of various nano-bioactivities and physicochemical properties. The high predictability of the developed GNP models suggests that this workflow can be used as a universal tool for nanomaterial profiling and rational nanomaterial design.
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Affiliation(s)
- Xiliang Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
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24
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Piir G, Kahn I, García-Sosa AT, Sild S, Ahte P, Maran U. Best Practices for QSAR Model Reporting: Physical and Chemical Properties, Ecotoxicity, Environmental Fate, Human Health, and Toxicokinetics Endpoints. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:126001. [PMID: 30561225 PMCID: PMC6371683 DOI: 10.1289/ehp3264] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 10/19/2018] [Accepted: 11/07/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Quantitative and qualitative structure–activity relationships (QSARs) have been used to understand chemical behavior for almost a century. The main source of QSAR models is the scientific literature, but the open question is how well these models are documented. OBJECTIVES The main aim of this study was to critically analyze the publication practices of QSARs with regard to transparency, potential reproducibility, and independent verification. The focus was on the level of technical completeness of the published QSARs. METHODS A total of 1,533 QSAR articles reporting 79 individual endpoints, mostly in environmental and health science, were reviewed. The QSAR parameters required for technical completeness were grouped into five categories: chemical structures, experimental endpoint values, descriptor values, mathematical representation of the model, and predicted endpoint values. The data were summarized and discussed using Circos plots. RESULTS Altogether, 42.5% of the reviewed articles were found to be potentially reproducible. The potential reproducibility for different endpoint groups varied; the respective rates were 39% for physical and chemical properties, 52% for ecotoxicity, 56% for environmental fate, 30% for human health, and 32% for toxicokinetics. The reproducibility of QSARs is discussed and placed in the context of the reproducibility of the experimental methods. Included are 65 references to open QSAR datasets as examples of models restored from scientific articles. DISCUSSION Strikingly poor documentation of QSARs was observed, which reduces the transparency, availability, and consequently, the application of research results in scientific, industrial, and regulatory areas. A list of the components needed to ensure the best practices for QSAR reporting is provided, allowing long-term use and preservation of the models. This list also allows an assessment of the reproducibility of models by interested parties such as journal editors, reviewers, regulators, evaluators, and potential users. https://doi.org/10.1289/EHP3264.
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Affiliation(s)
- Geven Piir
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Iiris Kahn
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | | | - Sulev Sild
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Priit Ahte
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu, Estonia
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25
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Afantitis A, Melagraki G, Tsoumanis A, Valsami-Jones E, Lynch I. A nanoinformatics decision support tool for the virtual screening of gold nanoparticle cellular association using protein corona fingerprints. Nanotoxicology 2018; 12:1148-1165. [PMID: 30182778 DOI: 10.1080/17435390.2018.1504998] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The increasing use of nanoparticles (NPs) in a wide range of consumer and industrial applications has necessitated significant effort to address the challenge of characterizing and quantifying the underlying nanostructure - biological response relationships to ensure that these novel materials can be exploited responsibly and safely. Such efforts demand reliable experimental data not only in terms of the biological dose-response, but also regarding the physicochemical properties of the NPs and their interaction with the biological environment. The latter has not been extensively studied, as a large surface to bind biological macromolecules is a unique feature of NPs that is not relevant for chemicals or pharmaceuticals, and thus only limited data have been reported in the literature quantifying the protein corona formed when NPs interact with a biological medium and linking this with NP cellular association/uptake. In this work we report the development of a predictive model for the assessment of the biological response (cellular association, which can include both internalized NPs and those attached to the cell surface) of surface-modified gold NPs, based on their physicochemical properties and protein corona fingerprints, utilizing a dataset of 105 unique NPs. Cellular association was chosen as the end-point for the original experimental study due to its relevance to inflammatory responses, biodistribution, and toxicity in vivo. The validated predictive model is freely available online through the Enalos Cloud Platform ( http://enalos.insilicotox.com/NanoProteinCorona/ ) to be used as part of a regulatory or NP safe-by-design decision support system. This online tool will allow the virtual screening of NPs, based on a list of the significant NP descriptors, identifying those NPs that would warrant further toxicity testing on the basis of predicted NP cellular association.
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Affiliation(s)
| | | | | | - Eugenia Valsami-Jones
- b School of Geography Earth and Environmental Sciences , University of Birmingham , Birmingham , United Kingdom
| | - Iseult Lynch
- b School of Geography Earth and Environmental Sciences , University of Birmingham , Birmingham , United Kingdom
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26
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Toropov AA, Sizochenko N, Toropova AP, Leszczynski J. Towards the Development of Global Nano-Quantitative Structure-Property Relationship Models: Zeta Potentials of Metal Oxide Nanoparticles. NANOMATERIALS 2018; 8:nano8040243. [PMID: 29662037 PMCID: PMC5923573 DOI: 10.3390/nano8040243] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/12/2018] [Accepted: 04/12/2018] [Indexed: 11/25/2022]
Abstract
Zeta potential indirectly reflects a charge of the surface of nanoparticles in solutions and could be used to represent the stability of the colloidal solution. As processes of synthesis, testing and evaluation of new nanomaterials are expensive and time-consuming, so it would be helpful to estimate an approximate range of properties for untested nanomaterials using computational modeling. We collected the largest dataset of zeta potential measurements of bare metal oxide nanoparticles in water (87 data points). The dataset was used to develop quantitative structure–property relationship (QSPR) models. Essential features of nanoparticles were represented using a modified simplified molecular input line entry system (SMILES). SMILES strings reflected the size-dependent behavior of zeta potentials, as the considered quasi-SMILES modification included information about both chemical composition and the size of the nanoparticles. Three mathematical models were generated using the Monte Carlo method, and their statistical quality was evaluated (R2 for the training set varied from 0.71 to 0.87; for the validation set, from 0.67 to 0.82; root mean square errors for both training and validation sets ranged from 11.3 to 17.2 mV). The developed models were analyzed and linked to aggregation effects in aqueous solutions.
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Affiliation(s)
- Andrey A Toropov
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Science, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milano, Italy.
| | - Natalia Sizochenko
- Interdisciplinary Center for Nanotoxicity, Jackson State University, Jackson, MS 39217, USA.
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA.
| | - Alla P Toropova
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Science, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milano, Italy.
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Jackson State University, Jackson, MS 39217, USA.
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27
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Sizochenko N, Mikolajczyk A, Jagiello K, Puzyn T, Leszczynski J, Rasulev B. How the toxicity of nanomaterials towards different species could be simultaneously evaluated: a novel multi-nano-read-across approach. NANOSCALE 2018; 10:582-591. [PMID: 29168526 DOI: 10.1039/c7nr05618d] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Application of predictive modeling approaches can solve the problem of missing data. Numerous studies have investigated the effects of missing values on qualitative or quantitative modeling, but only a few studies have discussed it for the case of applications in nanotechnology-related data. The present study is aimed at the development of a multi-nano-read-across modeling technique that helps in predicting the toxicity of different species such as bacteria, algae, protozoa, and mammalian cell lines. Herein, the experimental toxicity of 184 metal and silica oxide (30 unique chemical types) nanoparticles from 15 datasets is analyzed. A hybrid quantitative multi-nano-read-across approach that combines interspecies correlation analysis and self-organizing map analysis is developed. In the first step, hidden patterns of toxicity among nanoparticles are identified using a combination of methods. Subsequently, the developed model based on categorization of the toxicity of the metal oxide nanoparticle outcomes is evaluated via the combination of supervised and unsupervised machine learning techniques to determine the underlying factors responsible for the toxicity.
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Affiliation(s)
- Natalia Sizochenko
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
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28
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Noventa S, Hacker C, Rowe D, Elgy C, Galloway T. Dissolution and bandgap paradigms for predicting the toxicity of metal oxide nanoparticles in the marine environment: an in vivo study with oyster embryos. Nanotoxicology 2017; 12:63-78. [DOI: 10.1080/17435390.2017.1418920] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Seta Noventa
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Christian Hacker
- College of Life and Environmental Sciences, Bioimaging Centre, University of Exeter, Exeter, UK
| | - Darren Rowe
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Christine Elgy
- Department of Geography, Earth and Environmental Sciences, Facility for Environmental Nanoscience Analysis and Characterization, University of Birmingham, Birmingham, UK
| | - Tamara Galloway
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
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29
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Aligning nanotoxicology with the 3Rs: What is needed to realise the short, medium and long-term opportunities? Regul Toxicol Pharmacol 2017; 91:257-266. [DOI: 10.1016/j.yrtph.2017.10.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 09/24/2017] [Accepted: 10/19/2017] [Indexed: 11/20/2022]
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30
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Li Y, Wang J, Zhao F, Bai B, Nie G, Nel AE, Zhao Y. Nanomaterial libraries and model organisms for rapid high-content analysis of nanosafety. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nwx120] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Abstract
Safety analysis of engineered nanomaterials (ENMs) presents a formidable challenge regarding environmental health and safety, due to their complicated and diverse physicochemical properties. Although large amounts of data have been published regarding the potential hazards of these materials, we still lack a comprehensive strategy for their safety assessment, which generates a huge workload in decision-making. Thus, an integrated approach is urgently required by government, industry, academia and all others who deal with the safe implementation of nanomaterials on their way to the marketplace. The rapid emergence and sheer number of new nanomaterials with novel properties demands rapid and high-content screening (HCS), which could be performed on multiple materials to assess their safety and generate large data sets for integrated decision-making. With this approach, we have to consider reducing and replacing the commonly used rodent models, which are expensive, time-consuming, and not amenable to high-throughput screening and analysis. In this review, we present a ‘Library Integration Approach’ for high-content safety analysis relevant to the ENMs. We propose the integration of compositional and property-based ENM libraries for HCS of cells and biologically relevant organisms to be screened for mechanistic biomarkers that can be used to generate data for HCS and decision analysis. This systematic approach integrates the use of material and biological libraries, automated HCS and high-content data analysis to provide predictions about the environmental impact of large numbers of ENMs in various categories. This integrated approach also allows the safer design of ENMs, which is relevant to the implementation of nanotechnology solutions in the pharmaceutical industry.
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Affiliation(s)
- Yiye Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Bai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - André E Nel
- Division of NanoMedicine, Department of Medicine, and California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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31
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Mikolajczyk A, Sizochenko N, Mulkiewicz E, Malankowska A, Nischk M, Jurczak P, Hirano S, Nowaczyk G, Zaleska-Medynska A, Leszczynski J, Gajewicz A, Puzyn T. Evaluating the toxicity of TiO 2-based nanoparticles to Chinese hamster ovary cells and Escherichia coli: a complementary experimental and computational approach. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:2171-2180. [PMID: 29114443 PMCID: PMC5669235 DOI: 10.3762/bjnano.8.216] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/18/2017] [Indexed: 05/25/2023]
Abstract
Titania-supported palladium, gold and bimetallic nanoparticles (second-generation nanoparticles) demonstrate promising photocatalytic properties. However, due to unusual reactivity, second-generation nanoparticles can be hazardous for living organisms. Considering the ever-growing number of new types of nanoparticles that can potentially contaminate the environment, a determination of their toxicity is extremely important. The main aim of presented study was to investigate the cytotoxic effect of surface modified TiO2-based nanoparticles, to model their quantitative nanostructure-toxicity relationships and to reveal the toxicity mechanism. In this context, toxicity tests for surface-modified TiO2-based nanoparticles were performed in vitro, using Gram-negative bacteria Escherichia coli and Chinese hamster ovary (CHO-K1) cells. The obtained cytotoxicity data were analyzed by means of computational methods (quantitative structure-activity relationships, QSAR approach). Based on a combined experimental and computational approach, predictive models were developed, and relationships between cytotoxicity, size, and specific surface area (Brunauer-Emmett-Teller surface, BET) of nanoparticles were discussed.
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Affiliation(s)
- Alicja Mikolajczyk
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Natalia Sizochenko
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
- Interdisciplinary Center for Nanotoxicity, Jackson State University, 39217, Jackson, MS, USA
| | - Ewa Mulkiewicz
- Department of Environmental Analytics, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Anna Malankowska
- Department of Environmental Technology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Michal Nischk
- Department of Environmental Technology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Przemyslaw Jurczak
- Department of Biomedical Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Seishiro Hirano
- Center for Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, 16-2 Onogawa, Ibaraki 305-8506, Japan
| | - Grzegorz Nowaczyk
- NanoBioMedical Centre, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland
| | - Adriana Zaleska-Medynska
- Department of Environmental Technology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Jackson State University, 39217, Jackson, MS, USA
| | - Agnieszka Gajewicz
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Tomasz Puzyn
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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Sizochenko N, Leszczynska D, Leszczynski J. Modeling of Interactions between the Zebrafish Hatching Enzyme ZHE1 and A Series of Metal Oxide Nanoparticles: Nano-QSAR and Causal Analysis of Inactivation Mechanisms. NANOMATERIALS 2017; 7:nano7100330. [PMID: 29035311 PMCID: PMC5666495 DOI: 10.3390/nano7100330] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/12/2017] [Accepted: 10/12/2017] [Indexed: 12/14/2022]
Abstract
The quantitative relationships between the activity of zebrafish ZHE1 enzyme and a series of experimental and physicochemical features of 24 metal oxide nanoparticles were revealed. Vital characteristics of the nanoparticles’ structure were reflected using both experimental and theoretical descriptors. The developed quantitative structure–activity relationship model for nanoparticles (nano-QSAR) was capable of predicting the enzyme inactivation based on four descriptors: the hydrodynamic radius, mass density, the Wigner–Seitz radius, and the covalent index. The nano-QSAR model was calculated using the non-linear regression tree M5P algorithm. The developed model is characterized by high robustness R2bagging = 0.90 and external predictivity Q2EXT = 0.93. This model is in agreement with modern theories of aquatic toxicity. Dissolution and size-dependent characteristics are among the key driving forces for enzyme inactivation. It was proven that ZnO, CuO, Cr2O3, and NiO nanoparticles demonstrated strong inhibitory effects because of their solubility. The proposed approach could be used as a non-experimental alternative to animal testing. Additionally, methods of causal discovery were applied to shed light on the mechanisms and modes of action.
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Affiliation(s)
- Natalia Sizochenko
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, USA.
| | - Danuta Leszczynska
- Department of Civil and Environmental Engineering, Jackson State University, Jackson, MS 39217, USA.
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, USA.
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Perspectives from the NanoSafety Modelling Cluster on the validation criteria for (Q)SAR models used in nanotechnology. Food Chem Toxicol 2017; 112:478-494. [PMID: 28943385 DOI: 10.1016/j.fct.2017.09.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 08/31/2017] [Accepted: 09/19/2017] [Indexed: 11/20/2022]
Abstract
Nanotechnology and the production of nanomaterials have been expanding rapidly in recent years. Since many types of engineered nanoparticles are suspected to be toxic to living organisms and to have a negative impact on the environment, the process of designing new nanoparticles and their applications must be accompanied by a thorough risk analysis. (Quantitative) Structure-Activity Relationship ([Q]SAR) modelling creates promising options among the available methods for the risk assessment. These in silico models can be used to predict a variety of properties, including the toxicity of newly designed nanoparticles. However, (Q)SAR models must be appropriately validated to ensure the clarity, consistency and reliability of predictions. This paper is a joint initiative from recently completed European research projects focused on developing (Q)SAR methodology for nanomaterials. The aim was to interpret and expand the guidance for the well-known "OECD Principles for the Validation, for Regulatory Purposes, of (Q)SAR Models", with reference to nano-(Q)SAR, and present our opinions on the criteria to be fulfilled for models developed for nanoparticles.
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Boyes WK, Thornton BLM, Al-Abed SR, Andersen CP, Bouchard DC, Burgess RM, Hubal EAC, Ho KT, Hughes MF, Kitchin K, Reichman JR, Rogers KR, Ross JA, Rygiewicz PT, Scheckel KG, Thai SF, Zepp RG, Zucker RM. A comprehensive framework for evaluating the environmental health and safety implications of engineered nanomaterials. Crit Rev Toxicol 2017; 47:767-810. [DOI: 10.1080/10408444.2017.1328400] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- William K. Boyes
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Brittany Lila M. Thornton
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Souhail R. Al-Abed
- National Risk Management Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, USA
| | - Christian P. Andersen
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Corvallis, OR, USA
| | - Dermont C. Bouchard
- National Exposure Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Athens, GA, USA
| | - Robert M. Burgess
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Narragansett, RI, USA
| | - Elaine A. Cohen Hubal
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Kay T. Ho
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Narragansett, RI, USA
| | - Michael F. Hughes
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Kirk Kitchin
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Jay R. Reichman
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Corvallis, OR, USA
| | - Kim R. Rogers
- National Exposure Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Jeffrey A. Ross
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Paul T. Rygiewicz
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Corvallis, OR, USA
| | - Kirk G. Scheckel
- National Risk Management Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, USA
| | - Sheau-Fung Thai
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Richard G. Zepp
- National Exposure Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Athens, GA, USA
| | - Robert M. Zucker
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
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Gajewicz A. What if the number of nanotoxicity data is too small for developing predictive Nano-QSAR models? An alternative read-across based approach for filling data gaps. NANOSCALE 2017; 9:8435-8448. [PMID: 28604902 DOI: 10.1039/c7nr02211e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Over the past decade, computational nanotoxicology, in particular Quantitative Structure-Activity Relationship models (Nano-QSAR) that help in assessing the biological effects of nanomaterials, have received much attention. In effect, a solid basis for uncovering the relationships between the structure and property/activity of nanoparticles has been created. Nonetheless, six years after the first pioneering computational studies focusing on the investigation of nanotoxicity were commenced, these computational methods still suffer from many limitations. These are mainly related to the paucity of widely available, systematically varied, libraries of experimental data necessary for the development and validation of such models. This results in the still-low acceptance of these methods as valuable research tools for nanosafety and raises the query as to whether these methods could gain wide acceptance of regulatory bodies as alternatives for traditional in vitro methods. This study aimed to give an answer to the following question: How to remedy the paucity of experimental nanotoxicity data and thereby, overcome key roadblock that hinders the development of approaches for data-driven modeling of nanoparticle properties and toxicities? Here, a simple and transparent read-across algorithm for a pre-screening hazard assessment of nanomaterials that provides reasonably accurate results by making the best use of existing limited set of observations will be introduced.
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Affiliation(s)
- Agnieszka Gajewicz
- University of Gdansk, Faculty of Chemistry, Laboratory of Environmental Chemometrics, Gdansk, Poland.
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González-Durruthy M, Alberici LC, Curti C, Naal Z, Atique-Sawazaki DT, Vázquez-Naya JM, González-Díaz H, Munteanu CR. Experimental-Computational Study of Carbon Nanotube Effects on Mitochondrial Respiration: In Silico Nano-QSPR Machine Learning Models Based on New Raman Spectra Transform with Markov-Shannon Entropy Invariants. J Chem Inf Model 2017; 57:1029-1044. [PMID: 28414908 DOI: 10.1021/acs.jcim.6b00458] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The study of selective toxicity of carbon nanotubes (CNTs) on mitochondria (CNT-mitotoxicity) is of major interest for future biomedical applications. In the current work, the mitochondrial oxygen consumption (E3) is measured under three experimental conditions by exposure to pristine and oxidized CNTs (hydroxylated and carboxylated). Respiratory functional assays showed that the information on the CNT Raman spectroscopy could be useful to predict structural parameters of mitotoxicity induced by CNTs. The in vitro functional assays show that the mitochondrial oxidative phosphorylation by ATP-synthase (or state V3 of respiration) was not perturbed in isolated rat-liver mitochondria. For the first time a star graph (SG) transform of the CNT Raman spectra is proposed in order to obtain the raw information for a nano-QSPR model. Box-Jenkins and perturbation theory operators are used for the SG Shannon entropies. A modified RRegrs methodology is employed to test four regression methods such as multiple linear regression (LM), partial least squares regression (PLS), neural networks regression (NN), and random forest (RF). RF provides the best models to predict the mitochondrial oxygen consumption in the presence of specific CNTs with R2 of 0.998-0.999 and RMSE of 0.0068-0.0133 (training and test subsets). This work is aimed at demonstrating that the SG transform of Raman spectra is useful to encode CNT information, similarly to the SG transform of the blood proteome spectra in cancer or electroencephalograms in epilepsy and also as a prospective chemoinformatics tool for nanorisk assessment. All data files and R object models are available at https://dx.doi.org/10.6084/m9.figshare.3472349 .
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Affiliation(s)
| | | | | | | | | | - José M Vázquez-Naya
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna , Campus de Elviña s/n, 15071 A Coruña, Spain
| | - Humberto González-Díaz
- Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country UPV/EHU , 48940, Leioa, Bizkaia, Spain.,IKERBASQUE, Basque Foundation for Science , 48011, Bilbao, Bizkaia, Spain
| | - Cristian R Munteanu
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna , Campus de Elviña s/n, 15071 A Coruña, Spain.,Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC) , A Coruña, 15006, Spain
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37
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Hjorth R, van Hove L, Wickson F. What can nanosafety learn from drug development? The feasibility of "safety by design". Nanotoxicology 2017; 11:305-312. [PMID: 28303735 DOI: 10.1080/17435390.2017.1299891] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
"Safety by design" (SbD) is an intuitively appealing concept that is on the rise within nanotoxicology and nanosafety research, as well as within nanotechnology research policy. It leans on principles established within drug discovery and development (DDD) and seeks to address safety early, as well as throughout product development. However, it remains unclear what the concept of SbD exactly entails for engineered nanomaterials (ENMs) or how it is envisioned to be implemented. Here, we review the concept as it is emerging in European research and compare its resemblance with the safety testing and assessment practices in DDD. From this comparison, it is clear that "safety" is not obtained through DDD, and that SbD should be considered a starting point rather than an end, meaning that products will still need to progress through thorough safety evaluations and regulation. We conclude that although risk reduction is clearly desirable, the way SbD is currently communicated tends to treat safety as an inherent material property and that this is fundamentally problematic as it represents a recasting and reduction of societal issues into technical problems. SbD therefore faces a multitude of challenges, from practical implementation to unrealistic stakeholder expectations.
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Affiliation(s)
- Rune Hjorth
- a Department of Environmental Engineering , Technical University of Denmark , Kgs. Lyngby , Denmark
| | - Lilian van Hove
- b Department of Society, Ecology and Ethics , GenØk Centre for Biosafety , Tromsø , Norway
| | - Fern Wickson
- b Department of Society, Ecology and Ethics , GenØk Centre for Biosafety , Tromsø , Norway
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38
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Skjolding LM, Sørensen SN, Hartmann NB, Hjorth R, Hansen SF, Baun A. Aquatic Ecotoxicity Testing of Nanoparticles-The Quest To Disclose Nanoparticle Effects. Angew Chem Int Ed Engl 2016; 55:15224-15239. [PMID: 27564250 PMCID: PMC5132032 DOI: 10.1002/anie.201604964] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Indexed: 01/09/2023]
Abstract
The number of products on the market containing engineered nanoparticles (ENPs) has increased significantly, and concerns have been raised regarding their ecotoxicological effects. Environmental safety assessments as well as relevant and reliable ecotoxicological data are required for the safe and sustainable use of ENPs. Although the number of publications on the ecotoxicological effects and uptake of ENPs is rapidly expanding, the applicability of the reported data for hazard assessment is questionable. A major knowledge gap is whether nanoparticle effects occur when test organisms are exposed to ENPs in aquatic test systems. Filling this gap is not straightforward, because of the broad range of ENPs and the different behavior of ENPs compared to "ordinary" (dissolved) chemicals in the ecotoxicity test systems. The risk of generating false negatives, and false positives, in the currently used tests is high, and in most cases difficult to assess. This Review outlines some of the pitfalls in the aquatic toxicity testing of ENPs which may lead to misinterpretation of test results. Response types are also proposed to reveal potential nanoparticle effects in the aquatic test organisms.
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Affiliation(s)
- Lars Michael Skjolding
- Department of Environmental EngineeringTechnical University of DenmarkBygningstorvet B115DK-2800Kgs. LyngbyDenmark
| | - Sara Nørgaard Sørensen
- Department of Environmental EngineeringTechnical University of DenmarkBygningstorvet B115DK-2800Kgs. LyngbyDenmark
| | - Nanna Bloch Hartmann
- Department of Environmental EngineeringTechnical University of DenmarkBygningstorvet B115DK-2800Kgs. LyngbyDenmark
| | - Rune Hjorth
- Department of Environmental EngineeringTechnical University of DenmarkBygningstorvet B115DK-2800Kgs. LyngbyDenmark
| | - Steffen Foss Hansen
- Department of Environmental EngineeringTechnical University of DenmarkBygningstorvet B115DK-2800Kgs. LyngbyDenmark
| | - Anders Baun
- Department of Environmental EngineeringTechnical University of DenmarkBygningstorvet B115DK-2800Kgs. LyngbyDenmark
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39
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Skjolding LM, Sørensen SN, Hartmann NB, Hjorth R, Hansen SF, Baun A. Aquatische Ökotoxizität von Nanopartikeln - Versuche zur Aufklärung von Nanopartikeleffekten. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604964] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Lars Michael Skjolding
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet B115 DK-2800 Kgs. Lyngby Dänemark
| | - Sara Nørgaard Sørensen
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet B115 DK-2800 Kgs. Lyngby Dänemark
| | - Nanna Bloch Hartmann
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet B115 DK-2800 Kgs. Lyngby Dänemark
| | - Rune Hjorth
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet B115 DK-2800 Kgs. Lyngby Dänemark
| | - Steffen Foss Hansen
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet B115 DK-2800 Kgs. Lyngby Dänemark
| | - Anders Baun
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet B115 DK-2800 Kgs. Lyngby Dänemark
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40
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Altman RB, Khuri N, Salit M, Giacomini KM. Unmet needs: Research helps regulators do their jobs. Sci Transl Med 2016; 7:315ps22. [PMID: 26606966 DOI: 10.1126/scitranslmed.aac4369] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A plethora of innovative new medical products along with the need to apply modern technologies to medical-product evaluation has spurred seminal opportunities in regulatory sciences. Here, we provide eight examples of regulatory science research for diverse products. Opportunities abound, particularly in data science and precision health.
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Affiliation(s)
- Russ B Altman
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Natalia Khuri
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA 94305, USA. Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, CA 94143-2911, USA
| | - Marc Salit
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA 94305, USA. Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, CA 94143-2911, USA. Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA.
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41
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Shatkin JA, Ong KJ. Alternative Testing Strategies for Nanomaterials: State of the Science and Considerations for Risk Analysis. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2016; 36:1564-1580. [PMID: 27273523 DOI: 10.1111/risa.12642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 03/02/2016] [Accepted: 04/19/2016] [Indexed: 06/06/2023]
Abstract
The rapid growth of the nanotechnology industry has warranted equal progress in the nanotoxicology and risk assessment fields. In vivo models have traditionally been used to determine human and environmental risk for chemicals; however, the use of these tests has limitations, and there are global appeals to develop reliable alternatives to animal testing. Many have investigated the use of alternative (nonanimal) testing methods and strategies have quickly developed and resulted in the generation of large toxicological data sets for numerous nanomaterials (NMs). Due to the novel physicochemical properties of NMs that are related to surface characteristics, the approach toward toxicity test development has distinct considerations from traditional chemicals, bringing new requirements for adapting these approaches for NMs. The methodical development of strategies that combine multiple alternative tests can be useful for predictive NM risk assessment and help screening-level decision making. This article provides an overview of the main developments in alternative methods and strategies for reducing uncertainty in NM risk assessment, including advantages and disadvantages of in vitro, ex vivo, and in silico methods, and examples of existing comprehensive strategies. In addition, knowledge gaps are identified toward improvements for experimental and strategy design, specifically highlighting the need to represent realistic exposure scenarios and to consider NM-specific concerns such as characterization, assay interferences, and standardization. Overall, this article aims to improve the reliability and utility of alternative testing methods and strategies for risk assessment of manufactured NMs.
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Affiliation(s)
| | - K J Ong
- Vireo Advisors, LLC, Boston, MA, USA
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Stone V, Johnston HJ, Balharry D, Gernand JM, Gulumian M. Approaches to Develop Alternative Testing Strategies to Inform Human Health Risk Assessment of Nanomaterials. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2016; 36:1538-1550. [PMID: 27285586 DOI: 10.1111/risa.12645] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 02/11/2016] [Accepted: 04/12/2016] [Indexed: 06/06/2023]
Abstract
The development of alternative testing strategies (ATS) for hazard assessment of new and emerging materials is high on the agenda of scientists, funders, and regulators. The relatively large number of nanomaterials on the market and under development means that an increasing emphasis will be placed on the use of reliable, predictive ATS when assessing their safety. We have provided recommendations as to how ATS development for assessment of nanomaterial hazard may be accelerated. Predefined search terms were used to identify the quantity and distribution of peer-reviewed publications for nanomaterial hazard assessment following inhalation, ingestion, or dermal absorption. A summary of knowledge gaps relating to nanomaterial hazard is provided to identify future research priorities and areas in which a rich data set might exist to allow ATS identification. Consultation with stakeholders (e.g., academia, industry, regulators) was critical to ensure that current expert opinion was reflected. The gap analysis revealed an abundance of studies that assessed the local and systemic impacts of inhaled particles, and so ATS are available for immediate use. Development of ATS for assessment of the dermal toxicity of chemicals is already relatively advanced, and these models should be applied to nanomaterials as relatively few studies have assessed the dermal toxicity of nanomaterials to date. Limited studies have investigated the local and systemic impacts of ingested nanomaterials. If the recommendations for research prioritization proposed are adopted, it is envisioned that a comprehensive battery of ATS can be developed to support the risk assessment process for nanomaterials. Some alternative models are available for immediate implementation, while others require more developmental work to become widely adopted. Case studies are included that can be used to inform the selection of alternative models and end points when assessing the pathogenicity of fibers and mode of action of nanomaterial toxicity.
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Affiliation(s)
- Vicki Stone
- School of Life Sciences, Nano Safety Research Group, Heriot-Watt University, Edinburgh, UK
| | - Helinor J Johnston
- School of Life Sciences, Nano Safety Research Group, Heriot-Watt University, Edinburgh, UK
| | - Dominique Balharry
- School of Life Sciences, Nano Safety Research Group, Heriot-Watt University, Edinburgh, UK
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jeremy M Gernand
- Department of Energy and Mineral Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Mary Gulumian
- Toxicology and Biochemistry Section NIOH, Johannesburg, South Africa
- Haematology and Molecular Medicine Department School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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43
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Jones DE, Ghandehari H, Facelli JC. A review of the applications of data mining and machine learning for the prediction of biomedical properties of nanoparticles. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2016; 132:93-103. [PMID: 27282231 PMCID: PMC4902872 DOI: 10.1016/j.cmpb.2016.04.025] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/11/2016] [Accepted: 04/22/2016] [Indexed: 05/08/2023]
Abstract
This article presents a comprehensive review of applications of data mining and machine learning for the prediction of biomedical properties of nanoparticles of medical interest. The papers reviewed here present the results of research using these techniques to predict the biological fate and properties of a variety of nanoparticles relevant to their biomedical applications. These include the influence of particle physicochemical properties on cellular uptake, cytotoxicity, molecular loading, and molecular release in addition to manufacturing properties like nanoparticle size, and polydispersity. Overall, the results are encouraging and suggest that as more systematic data from nanoparticles becomes available, machine learning and data mining would become a powerful aid in the design of nanoparticles for biomedical applications. There is however the challenge of great heterogeneity in nanoparticles, which will make these discoveries more challenging than for traditional small molecule drug design.
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Affiliation(s)
- David E Jones
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA
| | - Hamidreza Ghandehari
- Departments of Bioengineering and Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112, USA; Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT 84112, USA
| | - Julio C Facelli
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA; Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT 84112, USA.
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44
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Chen G, Peijnenburg WJGM, Kovalishyn V, Vijver MG. Development of nanostructure–activity relationships assisting the nanomaterial hazard categorization for risk assessment and regulatory decision-making. RSC Adv 2016. [DOI: 10.1039/c6ra06159a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Developed nano-SARs based on the state-of-art of ecotoxicity testing of metallic nanomaterials.
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Affiliation(s)
- Guangchao Chen
- Institute of Environmental Sciences CML
- Leiden University
- Leiden
- The Netherlands
| | - Willie J. G. M. Peijnenburg
- Institute of Environmental Sciences CML
- Leiden University
- Leiden
- The Netherlands
- National Institute of Public Health and the Environment-RIVM
| | - Vasyl Kovalishyn
- Department of Medical and Biological Research
- Institute of Bioorganic Chemistry & Petrochemistry
- Kyiv 02660
- Ukraine
| | - Martina G. Vijver
- Institute of Environmental Sciences CML
- Leiden University
- Leiden
- The Netherlands
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45
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Bos PMJ, Gottardo S, Scott-Fordsmand JJ, van Tongeren M, Semenzin E, Fernandes TF, Hristozov D, Hund-Rinke K, Hunt N, Irfan MA, Landsiedel R, Peijnenburg WJGM, Sánchez Jiménez A, van Kesteren PCE, Oomen AG. The MARINA Risk Assessment Strategy: A Flexible Strategy for Efficient Information Collection and Risk Assessment of Nanomaterials. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:15007-21. [PMID: 26633430 PMCID: PMC4690897 DOI: 10.3390/ijerph121214961] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/10/2015] [Accepted: 11/12/2015] [Indexed: 11/26/2022]
Abstract
An engineered nanomaterial (ENM) may actually consist of a population of primary particles, aggregates and agglomerates of various sizes. Furthermore, their physico-chemical characteristics may change during the various life-cycle stages. It will probably not be feasible to test all varieties of all ENMs for possible health and environmental risks. There is therefore a need to further develop the approaches for risk assessment of ENMs. Within the EU FP7 project Managing Risks of Nanoparticles (MARINA) a two-phase risk assessment strategy has been developed. In Phase 1 (Problem framing) a base set of information is considered, relevant exposure scenarios (RESs) are identified and the scope for Phase 2 (Risk assessment) is established. The relevance of an RES is indicated by information on exposure, fate/kinetics and/or hazard; these three domains are included as separate pillars that contain specific tools. Phase 2 consists of an iterative process of risk characterization, identification of data needs and integrated collection and evaluation of data on the three domains, until sufficient information is obtained to conclude on possible risks in a RES. Only data are generated that are considered to be needed for the purpose of risk assessment. A fourth pillar, risk characterization, is defined and it contains risk assessment tools. This strategy describes a flexible and efficient approach for data collection and risk assessment which is essential to ensure safety of ENMs. Further developments are needed to provide guidance and make the MARINA Risk Assessment Strategy operational. Case studies will be needed to refine the strategy.
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Affiliation(s)
- Peter M J Bos
- National Institute for Public Health and the Environment (RIVM), PO Box 1, Bilthoven 3720 BA, The Netherlands.
| | - Stefania Gottardo
- European Commission, Joint Research Centre, Via E. Fermi 2749, Ispra (VA) 21027, Italy.
| | | | - Martie van Tongeren
- Institute of Occupational Medicine, Centre for Human Exposure Science (CHES), Research Avenue North, Riccarton, Edinburgh EH14 4AP, UK.
| | - Elena Semenzin
- Department of Environmental Sciences, Informatics and Statistics, University Ca' Foscari of Venice, c/o VEGApark, Via delle Industrie 21/8, Marghera (VE) 30175, Italy.
| | - Teresa F Fernandes
- School of Life Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK.
| | - Danail Hristozov
- Department of Environmental Sciences, Informatics and Statistics, University Ca' Foscari of Venice, c/o VEGApark, Via delle Industrie 21/8, Marghera (VE) 30175, Italy.
| | - Kerstin Hund-Rinke
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Auf dem Aberg 1, Schmallenberg 57392, Germany.
| | - Neil Hunt
- The REACH Centre, Gordon Manley Building, Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK.
| | - Muhammad-Adeel Irfan
- Experimental Toxicology and Ecology, BASF SE, GB/TB-Z470, Ludwigshafen 67056, Germany.
| | - Robert Landsiedel
- Experimental Toxicology and Ecology, BASF SE, GB/TB-Z470, Ludwigshafen 67056, Germany.
| | - Willie J G M Peijnenburg
- National Institute for Public Health and the Environment (RIVM), PO Box 1, Bilthoven 3720 BA, The Netherlands.
- Centre for Environmental Sciences, University Leiden, PO Box 9518, 2300 RA Leiden, The Netherlands.
| | - Araceli Sánchez Jiménez
- Institute of Occupational Medicine, Centre for Human Exposure Science (CHES), Research Avenue North, Riccarton, Edinburgh EH14 4AP, UK.
| | - Petra C E van Kesteren
- National Institute for Public Health and the Environment (RIVM), PO Box 1, Bilthoven 3720 BA, The Netherlands.
| | - Agnes G Oomen
- National Institute for Public Health and the Environment (RIVM), PO Box 1, Bilthoven 3720 BA, The Netherlands.
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46
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Metal Oxide Nanomaterial QNAR Models: Available Structural Descriptors and Understanding of Toxicity Mechanisms. NANOMATERIALS 2015; 5:1620-1637. [PMID: 28347085 PMCID: PMC5304772 DOI: 10.3390/nano5041620] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/03/2015] [Accepted: 10/03/2015] [Indexed: 11/17/2022]
Abstract
Metal oxide nanomaterials are widely used in various areas; however, the divergent published toxicology data makes it difficult to determine whether there is a risk associated with exposure to metal oxide nanomaterials. The application of quantitative structure activity relationship (QSAR) modeling in metal oxide nanomaterials toxicity studies can reduce the need for time-consuming and resource-intensive nanotoxicity tests. The nanostructure and inorganic composition of metal oxide nanomaterials makes this approach different from classical QSAR study; this review lists and classifies some structural descriptors, such as size, cation charge, and band gap energy, in recent metal oxide nanomaterials quantitative nanostructure activity relationship (QNAR) studies and discusses the mechanism of metal oxide nanomaterials toxicity based on these descriptors and traditional nanotoxicity tests.
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Oksel C, Ma CY, Wang XZ. Current situation on the availability of nanostructure-biological activity data. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:79-94. [PMID: 25608859 DOI: 10.1080/1062936x.2014.993702] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recent developments in nanotechnology have not only increased the number of nanoproducts on the market, but also raised concerns about the safety of engineered nanomaterials (ENMs) for human health and the environment. As the production and use of ENMs increase, we are approaching the point at which it is impossible to individually assess the toxicity of a vast number of ENMs. Therefore, it is desirable to use time-effective computational methods, such as the quantitative structure-activity relationship (QSAR) models, to predict the toxicity of ENMs. However, the accuracy of the nano-(Q)SARs is directly tied to the quality of the data from which the model is estimated. Although the amount of available nanotoxicity data is insufficient for generating robust nano-(Q)SAR models in most cases, there are a handful of studies that provide appropriate experimental data for (Q)SAR-like modelling investigations. The aim of this study is to review the available literature data that are particularly suitable for nano-(Q)SAR modelling. We hope that this paper can serve as a starting point for those who would like to know more about the current availability of experimental data on the health effects of ENMs for future modelling purposes.
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Affiliation(s)
- C Oksel
- a Institute of Particle Science and Engineering, School of Chemical and Process Engineering , University of Leeds , Leeds , LS2 9JT , UK
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