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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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Borowska M, Jankowski K. Basic and advanced spectrometric methods for complete nanoparticles characterization in bio/eco systems: current status and future prospects. Anal Bioanal Chem 2023:10.1007/s00216-023-04641-7. [PMID: 36949345 PMCID: PMC10329056 DOI: 10.1007/s00216-023-04641-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/27/2023] [Accepted: 03/03/2023] [Indexed: 03/24/2023]
Abstract
The use of engineered nanoparticles in the environment and human life has increased in the last 20 years. The risk assessment concerning application of nanomaterials in biological systems requires their thorough characterization. Understanding the correlations between physicochemical properties of nanoparticles concerning not only the size, particle size distribution, number concentration, degree of aggregation, or agglomeration but also solubility, stability, binding affinity, surface activity, chemical composition, and nanoparticle synthesis yield allows their reliable characterization. Thus, to find the structure-function/property relationship of nanoparticles, multifaceted characterization approach based on more than one analytical technique is required. On the other hand, the increasing demand for identification and characterization of nanomaterials has contributed to the continuous development of spectrometric techniques which enables for their qualitative and quantitative analysis in complex matrices giving reproducible and reliable results. This review is aimed at providing a discussion concerning four main aspects of nanoparticle characterization: nanoparticle synthesis yield, particle size and number concentration, elemental and isotopic composition of nanoparticles, and their surface properties. The conventional and non-conventional spectrometric techniques such as spectrophotometry UV-Vis, mass spectrometric techniques working in conventional and single-particle mode, or those based on optical emission detection systems are described with special emphasis paid on their advantages and drawbacks. The application and recent advances of these methods are also comprehensively reviewed and critically discussed.
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Affiliation(s)
- Magdalena Borowska
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw, 00-664, Poland.
| | - Krzysztof Jankowski
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw, 00-664, Poland
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Svadlakova T, Holmannova D, Kolackova M, Malkova A, Krejsek J, Fiala Z. Immunotoxicity of Carbon-Based Nanomaterials, Starring Phagocytes. Int J Mol Sci 2022; 23:ijms23168889. [PMID: 36012161 PMCID: PMC9408998 DOI: 10.3390/ijms23168889] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
In the field of science, technology and medicine, carbon-based nanomaterials and nanoparticles (CNMs) are becoming attractive nanomaterials that are increasingly used. However, it is important to acknowledge the risk of nanotoxicity that comes with the widespread use of CNMs. CNMs can enter the body via inhalation, ingestion, intravenously or by any other route, spread through the bloodstream and penetrate tissues where (in both compartments) they interact with components of the immune system. Like invading pathogens, CNMs can be recognized by large numbers of receptors that are present on the surface of innate immune cells, notably monocytes and macrophages. Depending on the physicochemical properties of CNMs, i.e., shape, size, or adsorbed contamination, phagocytes try to engulf and process CNMs, which might induce pro/anti-inflammatory response or lead to modulation and disruption of basic immune activity. This review focuses on existing data on the immunotoxic potential of CNMs, particularly in professional phagocytes, as they play a central role in processing and eliminating foreign particles. The results of immunotoxic studies are also described in the context of the entry routes, impacts of contamination and means of possible elimination. Mechanisms of proinflammatory effect depending on endocytosis and intracellular distribution of CNMs are highlighted as well.
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Affiliation(s)
- Tereza Svadlakova
- Department of Clinical Immunology and Allergology, University Hospital Hradec Kralove and Faculty of Medicine in Hradec Kralove, Charles University, 50005 Hradec Kralove, Czech Republic
- Department of Preventive Medicine, Faculty of Medicine in Hradec Kralove, Charles University, 50003 Hradec Kralove, Czech Republic
- Correspondence:
| | - Drahomira Holmannova
- Department of Preventive Medicine, Faculty of Medicine in Hradec Kralove, Charles University, 50003 Hradec Kralove, Czech Republic
| | - Martina Kolackova
- Department of Clinical Immunology and Allergology, University Hospital Hradec Kralove and Faculty of Medicine in Hradec Kralove, Charles University, 50005 Hradec Kralove, Czech Republic
| | - Andrea Malkova
- Department of Preventive Medicine, Faculty of Medicine in Hradec Kralove, Charles University, 50003 Hradec Kralove, Czech Republic
- Department of Pathological Physiology, Faculty of Medicine in Hradec Kralove, Charles University, 50003 Hradec Kralove, Czech Republic
| | - Jan Krejsek
- Department of Clinical Immunology and Allergology, University Hospital Hradec Kralove and Faculty of Medicine in Hradec Kralove, Charles University, 50005 Hradec Kralove, Czech Republic
| | - Zdenek Fiala
- Department of Preventive Medicine, Faculty of Medicine in Hradec Kralove, Charles University, 50003 Hradec Kralove, Czech Republic
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Saeedimasine M, Brandt EG, Lyubartsev AP. Atomistic Perspective on Biomolecular Adsorption on Functionalized Carbon Nanomaterials under Ambient Conditions. J Phys Chem B 2021; 125:416-430. [PMID: 33373230 PMCID: PMC7871326 DOI: 10.1021/acs.jpcb.0c08622] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/03/2020] [Indexed: 01/23/2023]
Abstract
The use of carbon-based nanomaterials is tremendously increasing in various areas of technological, bioengineering, and biomedical applications. The functionality of carbon-based nanomaterials can be further broadened via chemical functionalization of carbon nanomaterial surfaces. On the other hand, concern is rising on possible adverse effects when nanomaterials are taken up by biological organisms. In order to contribute into understanding of interactions of carbon-based nanomaterials with biological matter, we have investigated adsorption of small biomolecules on nanomaterials using enhanced sampling molecular dynamics. The biomolecules included amino acid side chain analogues, fragments of lipids, and sugar monomers. The adsorption behavior on unstructured amorphous carbon, pristine graphene and its derivatives (such as few-layer graphene, graphene oxide, and reduced graphene oxide) as well as pristine carbon nanotubes, and those functionalized with OH-, COOH-, COO-, NH2-, and NH3+ groups was investigated with respect to surface concentration. An adsorption profile, that is, the free energy as a function of distance from the nanomaterial surfaces, was determined for each molecule and surface using the Metadynamics approach. The results were analyzed in terms of chemical specificity, surface charge, and surface concentration. It was shown that although morphology of the nanomaterial has a limited effect on the adsorption properties, functionalization of the surface by various molecular groups can drastically change the adsorption behavior that can be used in the design of nanosurfaces with highly selective adsorption properties and safe for human health and environment.
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Affiliation(s)
- Marzieh Saeedimasine
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Erik G. Brandt
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Alexander P. Lyubartsev
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm 10691, Sweden
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Fadeel B, Bussy C, Merino S, Vázquez E, Flahaut E, Mouchet F, Evariste L, Gauthier L, Koivisto AJ, Vogel U, Martín C, Delogu LG, Buerki-Thurnherr T, Wick P, Beloin-Saint-Pierre D, Hischier R, Pelin M, Candotto Carniel F, Tretiach M, Cesca F, Benfenati F, Scaini D, Ballerini L, Kostarelos K, Prato M, Bianco A. Safety Assessment of Graphene-Based Materials: Focus on Human Health and the Environment. ACS NANO 2018; 12:10582-10620. [PMID: 30387986 DOI: 10.1021/acsnano.8b04758] [Citation(s) in RCA: 313] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Graphene and its derivatives are heralded as "miracle" materials with manifold applications in different sectors of society from electronics to energy storage to medicine. The increasing exploitation of graphene-based materials (GBMs) necessitates a comprehensive evaluation of the potential impact of these materials on human health and the environment. Here, we discuss synthesis and characterization of GBMs as well as human and environmental hazard assessment of GBMs using in vitro and in vivo model systems with the aim to understand the properties that underlie the biological effects of these materials; not all GBMs are alike, and it is essential that we disentangle the structure-activity relationships for this class of materials.
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Affiliation(s)
- Bengt Fadeel
- Nanosafety & Nanomedicine Laboratory, Institute of Environmental Medicine , Karolinska Institutet , 17777 Stockholm , Sweden
| | - Cyrill Bussy
- Nanomedicine Laboratory, Faculty of Biology, Medicine & Health , University of Manchester , Manchester M13 9PL , United Kingdom
| | - Sonia Merino
- Faculty of Chemical Science and Technology , University of Castilla-La Mancha , 13071 Ciudad Real , Spain
| | - Ester Vázquez
- Faculty of Chemical Science and Technology , University of Castilla-La Mancha , 13071 Ciudad Real , Spain
| | | | | | | | - Laury Gauthier
- CNRS, Université Paul Sabatier , 31062 Toulouse , France
| | - Antti J Koivisto
- National Research Centre for the Working Environment , 2100 Copenhagen , Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment , 2100 Copenhagen , Denmark
| | - Cristina Martín
- University of Strasbourg, CNRS , Immunology, Immunopathology and Therapeutic Chemistry , 67000 Strasbourg , France
| | - Lucia G Delogu
- Department of Chemistry and Pharmacy University of Sassari , Sassari 7100 , Italy
- Istituto di Ricerca Pediatrica , Fondazione Città della Speranza , 35129 Padova , Italy
| | - Tina Buerki-Thurnherr
- Swiss Federal Laboratories for Materials Science and Technology (EMPA) , 9014 St. Gallen , Switzerland
| | - Peter Wick
- Swiss Federal Laboratories for Materials Science and Technology (EMPA) , 9014 St. Gallen , Switzerland
| | | | - Roland Hischier
- Swiss Federal Laboratories for Materials Science and Technology (EMPA) , 9014 St. Gallen , Switzerland
| | - Marco Pelin
- Department of Life Sciences , University of Trieste , 34127 Trieste , Italy
| | | | - Mauro Tretiach
- Department of Life Sciences , University of Trieste , 34127 Trieste , Italy
| | - Fabrizia Cesca
- Center for Synaptic Neuroscience and Technology , Istituto Italiano di Tecnologia , 16132 Genova , Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology , Istituto Italiano di Tecnologia , 16132 Genova , Italy
| | - Denis Scaini
- Scuola Internazionale Superiore di Studi Avanzati (SISSA) , 34136 Trieste , Italy
| | - Laura Ballerini
- Scuola Internazionale Superiore di Studi Avanzati (SISSA) , 34136 Trieste , Italy
| | - Kostas Kostarelos
- Nanomedicine Laboratory, Faculty of Biology, Medicine & Health , University of Manchester , Manchester M13 9PL , United Kingdom
| | - Maurizio Prato
- Department of Chemical and Pharmaceutical Sciences , University of Trieste , 34127 Trieste , Italy
- Carbon Nanobiotechnology Laboratory , CIC BiomaGUNE , 20009 San Sebastian , Spain
- Basque Foundation for Science, Ikerbasque , 48013 Bilbao , Spain
| | - Alberto Bianco
- University of Strasbourg, CNRS , Immunology, Immunopathology and Therapeutic Chemistry , 67000 Strasbourg , France
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Louro H. Relevance of Physicochemical Characterization of Nanomaterials for Understanding Nano-cellular Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1048:123-142. [PMID: 29453536 DOI: 10.1007/978-3-319-72041-8_8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The manufactured nanomaterials (NMs) have specific physicochemical properties that confer unique mechanical, optical, electrical and magnetic characteristics that are beneficial for biomedical and industrial applications. However, recent studies have suggested that such specific physicochemical properties of the NMs may define nano-bio interactions thereby determining their toxic potential.One of the major concerns about NMs is the potential to induce cancer, suggested by some experimental studies, as seen for titanium dioxide nanomaterials or carbon nanotubes. To analyze in a short term the carcinogenic properties of a compound, genotoxicity assays in mammalian cell lines or animal models are frequently used. However, the investigation of the genotoxic properties of NMs has been inconclusive, up to date, since divergent results have been reported throughout the literature. While trying to understand how the NMs' characteristics may encompass increased toxicological effects that harbor uncertainties for public health, the use of correlation analysis highlights some physicochemical properties that influence the genotoxic potential of these NM.In this chapter, it is hypothesized that the different genotoxicity observed in closely related NMs may be due to subtle differences in their physicochemical characteristics. The present work provides an overview of the studies exploring the correlation between physicochemical properties of nanomaterials and their genotoxic effects in human cells, with focus on the toxicity of two groups of NMs, titanium dioxide nanomaterials and multiwalled-carbon nanotubes. It is suggested that, for tackling NMs' uncertainties, the in-depth investigation of the nano-bio interactions must be foreseen, where in vitro research must be integrated with in vivo and biomonitoring approaches, to cope with the complex dynamic behaviour of nanoscale materials.
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Affiliation(s)
- Henriqueta Louro
- Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal.
- Toxicogenomics and Human Health (ToxOmics), Nova Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal.
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