Toward comprehension of multiple human cells uptake of engineered nano metal oxides: quantitative inter cell line uptake specificity (QICLUS) modeling

References

• Ambure, P., R. B. Aher, A. Gajewicz, T. Puzyn, and K. Roy. 2015. “NanoBRIDGES Software: Open Access Tools to Perform QSAR and nano-QSAR Modeling.” Chemometrics and Intelligent Laboratory Systems 147: 1–13. doi:10.1016/j.chemolab.2015.07.007.
   Web of Science ®Google Scholar
• Artemenko, A. G., E. N. Muratov, V. E. Kuz’Min, N. N. Muratov, E. V. Varlamova, A. V. Kuz’Mina, L. G. Gorb., et al. 2011. “QSAR Analysis of the Toxicity of Nitroaromatics in Tetrahymena pyriformis: Structural Factors and Possible Modes of Action.” SAR and QSAR in Environmental Research 22 (5–6): 575–601. doi:10.1080/1062936X.2011.569950.
   PubMed Web of Science ®Google Scholar
• Arvizo, R. R., O. R. Miranda, M. A. Thompson, C. M. Pabelick, R. Bhattacharya, J. D. Robertson, V. M. Rotello, Y. S. Prakash, and P. Mukherjee. 2010. “Effect of Nanoparticle Surface Charge at the Plasma Membrane and beyond.” Nano Letters 10 (7): 2543–2548. doi:10.1021/nl101140t.
   PubMed Web of Science ®Google Scholar
• Azhdarzadeh, M., A. A. Saei, S. Sharifi, M. J. Hajipour, A. M. Alkilany, M. Sharifzadeh, F. Ramazani, S. Laurent, A. Mashaghi, and M. Mahmoudi. 2015. “Nanotoxicology: Advances and Pitfalls in Research Methodology.” Nanomedicine 10 (18): 2931–2952. doi:10.2217/nnm.15.130.
   PubMed Web of Science ®Google Scholar
• Bañares, M. A., A. Haase, L. Tran, V. Lobaskin, G. Oberdörster, R. Rallo, J. Leszczynski., et al. 2017. “CompNanoTox2015: Novel Perspectives from a European Conference on Computational Nanotoxicology on Predictive Nanotoxicology.” Nanotoxicology 11 (7): 839–845. doi:10.1080/17435390.2017.1371351.
   PubMed Web of Science ®Google Scholar
• Basant, N., and S. Gupta. 2017. “Modeling Uptake of Nanoparticles in Multiple Human Cells Using Structure–Activity Relationships and Intercellular Uptake Correlations.” Nanotoxicology 11 (1): 20–30. doi:10.1080/17435390.2016.1257075.
   PubMed Web of Science ®Google Scholar
• Bayles, A. R., H. S. Chahal, D. S. Chahal, C. P. Goldbeck, B. E. Cohen, and B. A. Helms. 2010. “Rapid Cytosolic Delivery of Luminescent Nanocrystals in Live Cells with Endosome-Disrupting Polymer Colloids.” Nano Letters 10 (10): 4086–4092. doi:10.1021/nl102172j.
   PubMed Web of Science ®Google Scholar
• Behzadi, S., V. Serpooshan, W. Tao, M. A. Hamaly, M. Y. Alkawareek, E. C. Dreaden, D. Brown, A. M. Alkilany, O. C. Farokhzad, and M. Mahmoudi. 2017. “Cellular Uptake of Nanoparticles: journey inside the Cell.” Chemical Society Reviews 46 (14): 4218–4244. doi:10.1039/C6CS00636A.
   PubMed Web of Science ®Google Scholar
• Chau, Y. T., and C. W. Yap. 2012. “Quantitative Nanostructure–Activity Relationship Modelling of Nanoparticles.” RSC Advances 2 (22): 8489–8496. doi:10.1039/c2ra21489j.
   Web of Science ®Google Scholar
• Cho, E. C., J. Xie, P. A. Wurm, and Y. Xia. 2009. “Understanding the Role of Surface Charges in Cellular Adsorption versus Internalization by Selectively Removing Gold Nanoparticles on the Cell Surface with a I2/KI Etchant.” Nano Letters 9 (3): 1080–1084. doi:10.1021/nl803487r.
   PubMed Web of Science ®Google Scholar
• Das, S., P. K. Ojha, and K. Roy. 2017. “Multilayered Variable Selection in QSPR: A Case Study of Modeling Melting Point of Bromide Ionic Liquids.” International Journal of Quantitative Structure-Property Relationships 2 (1): 106–124. doi:10.4018/IJQSPR.2017010108.
   Google Scholar
• Epa, V. C., F. R. Burden, C. Tassa, R. Weissleder, S. Shaw, and D. A. Winkler. 2012. “Modeling Biological Activities of Nanoparticles.” Nano Letters 12 (11): 5808–5812. doi:10.1021/nl303144k.
   PubMed Web of Science ®Google Scholar
• Farrés, M., S. Platikanov, S. Tsakovski, and R. Tauler. 2015. “Comparison of the Variable Importance in Projection (VIP) and of the Selectivity Ratio (SR) Methods for Variable Selection and Interpretation.” Journal of Chemometrics 29(10): 528–536. doi:10.1002/cem.2736.
   Web of Science ®Google Scholar
• Fourches, D., D. Pu, and A. Tropsha. 2011. “Exploring Quantitative Nanostructure-Activity Relationships (QNAR) Modeling as a Tool for Predicting Biological Effects of Manufactured Nanoparticles.” Combinatorial Chemistry & High Throughput Screening 14 (3): 217–225. doi:10.2174/138620711794728743.
   PubMed Web of Science ®Google Scholar
• Fourches, D., D. Pu, C. Tassa, R. Weissleder, S. Y. Shaw, R. J. Mumper, and A. Tropsha. 2010. “Quantitative Nanostructure − Activity Relationship Modeling.” ACS Nano 4 (10): 5703–5712. doi:10.1021/nn1013484.
   PubMed Web of Science ®Google Scholar
• Gajewicz, A. 2017. “Development of Valuable Predictive Read-across Models Based on “Real-Life”(Sparse) Nanotoxicity Data.” Environmental Science: Nano 4 (6): 1389–13403. doi:10.1039/C7EN00102A.
   Web of Science ®Google Scholar
• Gajewicz, A., T. Puzyn, B. Rasulev, D. Leszczynska, and J. Leszczynski. 2011. “Metal Oxide Nanoparticles: Size-Dependence of Quantum-Mechanical Properties.” Nanoscience and Nanotechnology-Asia 1 (1): 53–58. doi: 10.2174/2210681211101010053.
   Google Scholar
• Gajewicz, A., B. Rasulev, T. C. Dinadayalane, P. Urbaszek, T. Puzyn, D. Leszczynska, and J. Leszczynski. 2012. “Advancing Risk Assessment of Engineered Nanomaterials: application of Computational Approaches.” Advanced Drug Delivery Reviews 64 (15): 1663–1693. doi:10.1016/j.addr.2012.05.014.
   PubMed Web of Science ®Google Scholar
• Gao, H., W. Shi, and L. B. Freund. 2005. “Mechanics of Receptor-Mediated Endocytosis.” Proceedings of the National Academy of Sciences 102 (27): 9469–9474. doi:10.1073/pnas.0503879102.
   PubMed Web of Science ®Google Scholar
• Ge, C., J. Du, L. Zhao, L. Wang, Y. Liu, D. Li, Y. Yang., et al. 2011. “Binding of Blood Proteins to Carbon Nanotubes Reduces Cytotoxicity.” Proceedings of the National Academy of Sciences 108 (41): 16968–16973. doi:10.1073/pnas.1105270108.
   PubMed Web of Science ®Google Scholar
• Geys, J., A. Nemmar, E. Verbeken, E. Smolders, M. Ratoi, M. F. Hoylaerts, B. Nemery, and P. H. Hoet. 2008. “Acute Toxicity and Prothrombotic Effects of Quantum Dots: Impact of Surface Charge.” Environmental Health Perspectives 116 (12): 1607. doi:10.1289/ehp.11566.
   PubMed Web of Science ®Google Scholar
• Ghorbanzadeh, M., M. H. Fatemi, and M. Karimpour. 2012. “Modeling the Cellular Uptake of Magnetofluorescent Nanoparticles in Pancreatic Cancer Cells: A Quantitative Structure Activity Relationship Study.” Industrial & Engineering Chemistry Research 51 (32): 10712–10718. doi:10.1021/ie3006947.
   Web of Science ®Google Scholar
• Golbraikh, A., and A. Tropsha. 2002. “Beware of q2!.” Journal of Molecular Graphics and Modelling 20 (4): 269–276. doi:10.1016/S1093-3263(01)00123-1.
   PubMed Web of Science ®Google Scholar
• Guadagnini, R., B. Halamoda Kenzaoui, L. Walker, G. Pojana, Z. Magdolenova, D. Bilanicova, M. Saunders., et al. 2015. “Toxicity Screenings of Nanomaterials: Challenges Due to Interference with Assay Processes and Components of Classic in Vitro Tests.” Nanotoxicology 9 (supp1): 13–24. doi:10.3109/17435390.2013.829590.
   PubMedGoogle Scholar
• He, C., Y. Hu, L. Yin, C. Tang, and C. Yin. 2010. “Effects of Particle Size and Surface Charge on Cellular Uptake and Biodistribution of Polymeric Nanoparticles.” Biomaterials 31 (13): 3657–3666. http://qsar4u.com/pages/sirms.php. http://www.talete.mi.it/products/dragondescription.htm. doi:10.1016/j.biomaterials.2010.01.065.
   PubMed Web of Science ®Google Scholar
• Hühn, D., K. Kantner, C. Geidel, S. Brandholt, I. De Cock, S. J. H. Soenen, P. Rivera_Gil., et al. 2013. “Polymer-Coated Nanoparticles Interacting with Proteins and Cells: Focusing on the Sign of the Net Charge.” ACS Nano 7 (4): 3253–3263. doi:10.1021/nn3059295.
   PubMed Web of Science ®Google Scholar
• Jing, B., and Y. Zhu. 2011. “Disruption of Supported Lipid Bilayers by Semihydrophobic Nanoparticles.” Journal of the American Chemical Society 133 (28): 10983–10989. doi:10.1021/ja2040305.
   PubMed Web of Science ®Google Scholar
• Kar, S., R. N. Das, K. Roy, and J. Leszczynski. 2016. “Can Toxicity for Different Species Be Correlated?: The Concept and Emerging Applications of Interspecies Quantitative Structure-Toxicity Relationship (i-QSTR) Modeling.” International Journal of Quantitative Structure-Property Relationships 1 (2): 23–51. doi:10.4018/IJQSPR.2016070102.
   Google Scholar
• Kar, S., O. Deeb, and K. Roy. 2012. “Development of Classification and Regression Based QSAR Models to Predict Rodent Carcinogenic Potency Using Oral Slope Factor.” Ecotoxicology and Environmental Safety 82: 85–95. doi:10.1016/j.ecoenv.2012.05.013.
   PubMed Web of Science ®Google Scholar
• Kar, S., A. Gajewicz, T. Puzyn, and K. Roy. 2014. “Nano-Quantitative Structure–Activity Relationship Modeling Using Easily Computable and Interpretable Descriptors for Uptake of Magnetofluorescent Engineered Nanoparticles in Pancreatic Cancer Cells.” Toxicology in Vitro 28 (4): 600–606. doi:10.1016/j.tiv.2013.12.018.
   PubMed Web of Science ®Google Scholar
• Kar, S., A. Gajewicz, K. Roy, J. Leszczynski, and T. Puzyn. 2016. “Extrapolating between Toxicity Endpoints of Metal Oxide Nanoparticles: Predicting Toxicity to Escherichia coli and Human Keratinocyte Cell Line (HaCaT) with Nano-QTTR.” Ecotoxicology and Environmental Safety 126: 238–244. doi:10.1016/j.ecoenv.2015.12.033.
   PubMed Web of Science ®Google Scholar
• Lee, H. Y., S. H. R. Shin, L. L. Abezgauz, S. A. Lewis, A. M. Chirsan, D. D. Danino, and K. J. Bishop. 2013. “Integration of Gold Nanoparticles into Bilayer Structures via Adaptive Surface Chemistry.” Journal of the American Chemical Society 135 (16): 5950–5953. doi:10.1021/ja400225n.
   PubMed Web of Science ®Google Scholar
• Li, S., and N. Malmstadt. 2013. “Deformation and Poration of Lipid Bilayer Membranes by Cationic Nanoparticles.” Soft Matter 9 (20): 4969–4976. doi:10.1039/c3sm27578g.
   Web of Science ®Google Scholar
• Li, Y., and N. Gu. 2010. “Thermodynamics of Charged Nanoparticle Adsorption on Charge-Neutral Membranes: A Simulation Study.” The Journal of Physical Chemistry B 114 (8): 2749–2754. doi:10.1021/jp904550b.
   PubMed Web of Science ®Google Scholar
• Li, Y., X. Chen, and N. Gu. 2008. “Computational Investigation of Interaction Between Nanoparticles and Membranes: Hydrophobic/Hydrophilic Effect.” The Journal of Physical Chemistry B 112 (51): 16647–16653. doi:10.1021/jp8051906.
   PubMed Web of Science ®Google Scholar
• Mahmoudi, M.,. S. E. Lohse, C. J. Murphy, A. Fathizadeh, A. Montazeri, and K. S. Suslick. 2014. “Variation of Protein Corona Composition of Gold Nanoparticles following Plasmonic Heating.” Nano Letters 14 (1): 6–12. doi:10.1021/nl403419e.
   PubMed Web of Science ®Google Scholar
• Mahmoudi, M., A. Tachibana, A. B. Goldstone, Y. J. Woo, P. Chakraborty, K. R. Lee, C. S. Foote., et al. 2016. “Novel MRI Contrast Agent from Magnetotactic Bacteria Enables in Vivo Tracking of iPSC-Derived Cardiomyocytes.” Scientific Reports 6: 26960. doi:10.1038/srep26960.
   PubMed Web of Science ®Google Scholar
• The Math Works, Inc. 2012. MATLAB and statistics toolbox release,. The Math Works, Inc., Natick, Massachusetts, United States,
   Google Scholar
• Melagraki, G., and A. Afantitis. 2013. “Enalos KNIME Nodes: exploring Corrosion Inhibition of Steel in Acidic Medium.” Chemometrics and Intelligent Laboratory Systems 123: 9–14. doi:10.1016/j.chemolab.2013.02.003.
   Web of Science ®Google Scholar
• Mikolajczyk, A., A. Gajewicz, B. Rasulev, N. Schaeublin, E. Maurer-Gardner, S. Hussain, J. Leszczynski, and T. Puzyn. 2015. “Zeta Potential for Metal Oxide Nanoparticles: A Predictive Model Developed by a Nano-Quantitative Structure–Property Relationship Approach.” Chemistry of Materials 27 (7): 2400–2407. doi:10.1021/cm504406a.
   Web of Science ®Google Scholar
• Moghadam, B. Y., W. C. Hou, C. Corredor, P. Westerhoff, and J. D. Posner. 2012. “Role of Nanoparticle Surface Functionality in the Disruption of Model Cell Membranes.” Langmuir: The Acs Journal of Surfaces and Colloids 28 (47): 16318–16326. doi:10.1021/la302654s.
   PubMed Web of Science ®Google Scholar
• Oberdörster, G., A. Maynard, K. Donaldson, V. Castranova, J. Fitzpatrick, K. Ausman, J. Carter., et al. 2005. “Principles for Characterizing the Potential Human Health Effects from Exposure to Nanomaterials: elements of a Screening Strategy.” Particle and Fibre Toxicology 2 (1): 1. doi:10.1186/1743-8977-2-8
   PubMedGoogle Scholar
• Ojha, P. K., and K. Roy. 2018a. “Chemometric Modeling of Odor Threshold Property of Diverse Aroma Components of Wine.” RSC Advances 8 (9): 4750–4760. doi:10.1039/C7RA12295K.
   Web of Science ®Google Scholar
• Ojha, P. K., and K. Roy. 2018b. “PLS Regression-Based Chemometric Modeling of Odorant Properties of Diverse Chemical Constituents of Black Tea and Coffee.” RSC Advances 8 (5): 2293–22304. doi:10.1039/C7RA12914A.
   Web of Science ®Google Scholar
• Papa, E., J. P. Doucet, and A. Doucet-Panaye. 2016. “Computational Approaches for the Prediction of the Selective Uptake of Magnetofluorescent Nanoparticles into Human Cells.” RSC Advances 6 (73): 68806–68818. doi:10.1039/C6RA07898B.
   Web of Science ®Google Scholar
• Roy, K., S. Kar, and R. N. Das. 2015. Understanding the basics of QSAR for applications in pharmaceutical sciences and risk assessment. New York: Academic Press.
   Google Scholar
• Schu¨u¨rmann, G., R. U. Ebert, and, and R. Ku¨Hne, 2011. “Quantitative Read-across for Predicting the Acute Fish Toxicity of Organic Compounds.” Environmental Science & Technology 45 (10): 4616–4622. doi:10.1021/es200361r.
   PubMed Web of Science ®Google Scholar
• Schu¨u¨rmann, G., R. U. Ebert, J. Chen, B. Wang, and, and R. Ku¨Hne, 2008. “External Validation and Prediction Employing the Predictive Squared Correlation Coefficient Test Set Activity Mean vs Training Set Activity Mean.” Journal of Chemical Information and Modeling 48 (11): 2140–2145. pp. doi:10.1021/ci800253u.
   PubMed Web of Science ®Google Scholar
• Seel, M., D. B. Turner, and P. Willett. 1999. “Effect of Parameter Variations on the Effectiveness of HQSAR Analyses.” Quantitative Structure-Activity Relationships 18 (3): 245–252. doi:10.1002/(SICI)1521-3838(199907)18:3<245::AID-QSAR245>3.0.CO;2-O.
   Google Scholar
• Shang, L., K. Nienhaus, and G. U. Nienhaus. 2014. “Engineered Nanoparticles Interacting with Cells: Size Matters.” Journal of Nanobiotechnology 12 (1): 5. doi:10.1186/1477-3155-12-5.
   PubMed Web of Science ®Google Scholar
• Singh, K. P., and S. Gupta. 2014. “Nano-QSAR Modeling for Predicting Biological Activity of Diverse Nanomaterials.” RSC Advances 4 (26): 13215–13230. doi:10.1039/C4RA01274G.
   Web of Science ®Google Scholar
• Singh, R. P., and P. Ramarao. 2013. “Accumulated Polymer Degradation Products as Effector Molecules in Cytotoxicity of Polymeric Nanoparticles.” Toxicological Sciences 136 (1): 131–143. doi:10.1093/toxsci/kft179.
   PubMed Web of Science ®Google Scholar
• Sizochenko, N., D. Leszczynska, and J. Leszczynski. 2017. “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 7 (10): 330. doi:10.3390/nano7100330.
   Web of Science ®Google Scholar
• Toropov, A. A., A. P. Toropova, T. Puzyn, E. Benfenati, G. Gini, D. Leszczynska, and J. Leszczynski. 2013. “QSAR as a Random Event: Modeling of Nanoparticles Uptake in PaCa2 Cancer Cells.” Chemosphere 92 (1): 31–37. doi:10.1016/j.chemosphere.2013.03.012.
   PubMed Web of Science ®Google Scholar
• UMETRICS 2002. UMETRICS SIMCA-P 10.0, Umea, Sweden, [email protected], www.umetrics.com. Accessed on October 7, 2018
   Google Scholar
• Wang, B., L. Zhang, S. C. Bae, and S. Granick. 2008. “Nanoparticle-Induced Surface Reconstruction of Phospholipid Membranes.” Proceedings of the National Academy of Sciences 105 (47): 18171–18175. doi:10.1073/pnas.0807296105.
   PubMed Web of Science ®Google Scholar
• Wang, L., Y. Liu, W. Li, X. Jiang, Y. Ji, X. Wu, L. Xu., et al. 2011. “Selective Targeting of Gold Nanorods at the Mitochondria of Cancer Cells: Implications for Cancer Therapy.” Nano Letters 11 (2): 772–780. doi:10.1021/nl103992v.
   PubMed Web of Science ®Google Scholar
• Weissleder, R., K. Kelly, E. Y. Sun, T. Shtatland, and L. Josephson. 2005. “Cell-Specific Targeting of Nanoparticles by Multivalent Attachment of Small Molecules.” Nature Biotechnology 23 (11): 1418–1423. doi:10.1038/nbt1159.
   PubMed Web of Science ®Google Scholar
• Winkler, D. A., F. R. Burden, B. Yan, R. Weissleder, C. Tassa, S. Shaw, and V. C. Epa. 2014. “Modelling and Predicting the Biological Effects of Nanomaterials.” SAR and QSAR in Environmental Research 25 (2): 161–172. doi:10.1080/1062936X.2013.874367.
   PubMed Web of Science ®Google Scholar
• Wold, S., M. Sjöström, and L. Eriksson. 2001. “PLS-Regression: A Basic Tool of Chemometrics.” Chemometrics and Intelligent Laboratory Systems 58 (2): 109–130. doi:10.1016/S0169-7439(01)00155-1.
   Web of Science ®Google Scholar
• Zanganeh, S., R. Spitler, M. Erfanzadeh, A. M. Alkilany, and M. Mahmoudi. 2016. “Protein Corona: Opportunities and Challenges.” The International Journal of Biochemistry & Cell Biology 75: 143–147. doi:10.1016/j.biocel.2016.01.005.
   PubMed Web of Science ®Google Scholar