journal article·2014-02

QSAR model for cytotoxicity of SiO2 nanoparticles on human lung fibroblasts

Alla P. Toropova, Andrey A. Toropov, Emilio Benfenati, Rafi Korenstein

Journal of Nanoparticle Research· Volume 16· Issue 2
Publisher page

Abstract

The possibility of building up predictive model for cytotoxicity of SiO2-nanoparticles (SiO2-NPs) by means of so-called optimal descriptors which are mathematical functions of size and concentration of SiO2-NPs is demonstrated with data on sixteen systems’ “size–concentration.” The calculation has been carried out by means of the CORAL software (http://www.insilico.eu/coral/). The statistical quality of the best model for the cytotoxic inhibition ratio (%) of human lung fibroblasts cultured in the media containing different concentrations of SiO2‐NPs which is measured by MTT assay is the following: n = 10, r2 = 0.9837, s = 2.53 %, F = 483 (training set) and n = 6, r2 = 0.9269, s = 7.94 % (test set). The perspectives of this approach are discussed.
Source: openaire · Quality: candidate unverified · Source record ↗

Research context

OpenAlex topics: Computational Drug Discovery Methods · Nanoparticles: synthesis and applications · thermodynamics and calorimetric analyses

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

References (49)

Show source-provided references
1. Afantitis A, Melagraki G, Sarimveis H, Igglessi-Markopoulou O, Kollias G (2009) A novel QSAR model for predicting the inhibition of CXCR3 receptor by 4-N-aryl-[1,4] diazepane ureas. Eur J Med Chem 44:877–88410.1016/j.ejmech.2008.05.028 ↗
2. Afantitis A, Melagraki G, Koutentis PA, Sarimveis H, Kollias G (2011) Ligand-based virtual screening procedure for the prediction and the identification of novel β-amyloid aggregation inhibitors using Kohonen maps and Counterpropagation Artificial Neural Networks. Eur J Med Chem 46:497–50810.1016/j.ejmech.2010.11.029 ↗
3. Cattaneo AG, Gornati R, Sabbioni E, Chiriva-Internati M, Cobos E, Jenkins MR, Bernardini G (2010) Nanotechnology and human health: risks and benefits. J Appl Toxicol 30:730–74410.1002/jat.1609 ↗
4. Deng Y, Qi D, Deng C, Zhang X, Zhao D (2008) Superparamagnetic highmagnetization microspheres with an Fe3O4@SiO2 core and perpendicularly aligned mesoporous SiO2 shell for removal of microcystins. J Am Chem Soc 130:28–2910.1021/ja0777584 ↗
5. Fourches D, Pu D, Tassa C, Weissleder R, Shaw SY, Mumper RJ, Tropsha A (2010) Quantitative nanostructure–activity relationship modeling. ACS Nano 4:5703–571210.1021/nn1013484 ↗
6. Furtula B, Gutman I (2011) Relation between second and third geometric-arithmetic indices of trees. J Chemometr 25:87–9110.1002/cem.1342 ↗
7. Gajewicz A, Rasulev B, Dinadayalane TC, Urbaszek P, Puzyn T, Leszczynska D, Leszczynski J (2012) Advancing risk assessment of engineered nanomaterials: application of computational approaches. Adv Drug Deliv Rev 64:1663–169310.1016/j.addr.2012.05.014 ↗
8. García J, Duchowicz PR, Rozas MF, Caram JA, Mirífico MV, Fernández FM, Castro EA (2011) A comparative QSAR on 1,2,5-thiadiazolidin-3-one 1,1-dioxide compounds as selective inhibitors of human serine proteinases. J Mol Graph Model 31:10–1910.1016/j.jmgm.2011.07.007 ↗
9. Garro Martinez JC, Duchowicz PR, Estrada MR, Zamarbide GN, Castro EA (2011) QSAR study, molecular design of open-chain enaminones as anticonvulsant agents. Int J Mol Sci 12:9354–936810.3390/ijms12129354 ↗
10. González MP, Toropov AA, Duchowicz PR, Castro EA (2004) QSPR calculation of normal boiling points of organic molecules based on the use of correlation weighting of atomic orbitals with extended connectivity of zero- and first-order graphs of atomic orbitals. Molecules 9:1019–103310.3390/91201019 ↗
11. Hollas B, Gutman I, Trinajstić N (2005) On reducing correlations between topological indices. Croat Chem Acta 78:489–492
12. Ibezim E, Duchowicz PR, Ortiz EV, Castro EA (2012) QSAR on aryl-piperazine derivatives with activity on malaria. Chemometr Intell Lab Syst 110:81–8810.1016/j.chemolab.2011.10.002 ↗
13. Ivanciuc T, Ivanciuc O, Klein DJ (2006) Modeling the bioconcentration factors and bioaccumulation factors of polychlorinated biphenyls with posetic quantitative super-structure/activity relationships (QSSAR). Mol Divers 10:133–14510.1007/s11030-005-9003-3 ↗
14. Leszczynski J (2010) Bionanoscience: Nano meets bio at the interface. Nat Nanotech 5:633–63410.1038/nnano.2010.182 ↗
15. Li W, Samra DA, Merzaban J, Khashab NM (2013) P-glycoprotein targeted nanoscale drug carriers. J Nanosci Nanotech 13:1399–140210.1166/jnn.2013.6084 ↗
16. Marinescu G, Patron L, Culita DC, Neagoe C, Lepadatu CI, Balint I, Bessais L, Cizmas CB (2006) Synthesis of magnetite nanoparticles in the presence of aminoacids. J Nanopart Res 8:1045–105110.1007/s11051-006-9134-1 ↗
17. Melagraki G, Afantitis A (2011) Ligand and structure based virtual screening strategies for hit-finding and optimization of Hepatitis C virus (HCV) inhibitors. Curr Med Chem 18:2612–261910.2174/092986711795933759 ↗
18. Melagraki G, Afantitis A, Sarimveis H, Igglessi-Markopoulou O, Koutentis PA, Kollias G (2010) In silico exploration for identifying structure-activity relationship of MEK inhibition and oral bioavailability for isothiazole derivatives. Chem Biol Drug Des 76:397–40610.1111/j.1747-0285.2010.01029.x ↗
19. Mullen LMA, Duchowicz PR, Castro EA (2011) QSAR treatment on a new class of triphenylmethyl-containing compounds as potent anticancer agents. Chemometr Intell Lab Syst 107:269–27510.1016/j.chemolab.2011.04.011 ↗
20. Nurgaliev IN, Toropov AA, Kudyshkin VO, Ruban IN, Voropaeva NL, Rashidova SSh (2006) QSPR-modeling of oligophenylene melting points. J Struct Chem 47:362–36610.1007/s10947-006-0307-7 ↗
21. Ojha PK, Mitra I, Das RN, Roy K (2011) Further exploring rm 2 metrics for validation of QSPR models. Chemometr Intell Lab Syst 107:194–20510.1016/j.chemolab.2011.03.011 ↗
22. Olson MA, Braunschweig AB, Ikeda T, Fang L, Trabolsi A, Slawin AMZ, Khan SI, Stoddart JF (2009) Thermodynamic forecasting of mechanically interlocked switches. Organ Biomol Chem 7:4391–440510.1039/b911874h ↗
23. Petrova T, Rasulev BF, Toropov AA, Leszczynska D, Leszczynski J (2011) Improved model for fullerene C 60 solubility in organic solvents based on quantum-chemical and topological descriptors. J Nanopart Res 13:3235–324710.1007/s11051-011-0238-x ↗
24. Puzyn T, Leszczynska D, Leszczynski J (2009) Toward the development of “Nano-QSARs”: advances and challenges. Small 5:2494–250910.1002/smll.200900179 ↗
25. Puzyn T, Rasulev B, Gajewicz A, Hu X, Dasari TP, Michalkova A, Hwang H-M, Toropov A, Leszczynska D, Leszczynski J (2011) Using nano-QSAR to predict the cytotoxicity of metal oxide nanoparticles. Nat Nanotech 6:175–17810.1038/nnano.2011.10 ↗
26. Roy K, Toropov AA (2005) QSPR modeling of the water solubility of diverse functional aliphatic compounds by optimization of correlation weights of local graph invariants. J Mol Model 11:89–9610.1007/s00894-004-0224-7 ↗
27. Sayes C, Ivanov I (2010) Comparative study of predictive computational models for nanoparticle-induced cytotoxicity. Risk Anal 30:1723–173410.1111/j.1539-6924.2010.01438.x ↗
28. Thomas DG, Gaheen S, Harper SL, Fritts M, Klaessig F, Hahn-Dantona E, Paik D, Pan S, Stafford GA, Freund ET, Klemm JD, Baker NA (2013) ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format. BMC Biotechnol 13: art. no. 210.1186/1472-6750-13-2 ↗
29. Toropov AA, Benfenati E (2007) SMILES in QSPR/QSAR modeling: results and perspectives. Curr Drug Discov Technol 4:77–11610.2174/157016307781483432 ↗
30. Toropov AA, Leszczynski J (2006) A new approach to the characterization of nanomaterials: predicting Young’s modulus by correlation weighting of nanomaterials codes. Chem Phys Lett 433:125–12910.1016/j.cplett.2006.11.010 ↗
31. Toropov AA, Voropaeva NL, Ruban IN, Rashidova SSh (1999) Quantitative structure–property relationships for binary polymer-solvent systems: Correlation weighing of the local invariants of molecular graphs. Polymer Sci A 41:975–985
32. Toropov AA, Kudyshkin VO, Voropaeva NL, Ruban IN, Rashidova SSh (2001) Modeling of activity of monomers in radical copolymerization by optimization of correlation weights of local graph invariants. Polymer Sci B 43:116–119
33. Toropov AA, Kudyshkin VO, Voropaeva NL, Ruban IN, Rashidova SSh (2004) QSPR modeling of the reactivity parameters of monomers in radical copolymerizations. J Struct Chem 45:945–95010.1007/s10947-005-0084-8 ↗
34. Toropov AA, Toropova AP, Mukhamedzhanova DV, Gutman I (2005) Simplified molecular input line entry system (SMILES) as an alternative for constructing quantitative structure–property relationships (QSPR). Indian J Chem A 44:1545–1552
35. Toropov AA, Rasulev BF, Leszczynski J (2007a) QSAR modeling of acute toxicity for nitrobenzene derivatives towards rats: comparative analysis by MLRA and optimal descriptors. QSAR Comb Sci 26:686–69310.1002/qsar.200610135 ↗
36. Toropov AA, Leszczynska D, Leszczynski J (2007b) Predicting thermal conductivity of nanomaterials by correlation weighting technological attributes codes. Mater Lett 61:4777–478010.1016/j.matlet.2007.03.026 ↗
37. Toropov AA, Toropova AP, Raska I Jr (2008a) QSPR modeling of octanol/water partition coefficient for vitamins by optimal descriptors calculated with SMILES. Eur J Med Chem 43:714–74010.1016/j.ejmech.2007.05.007 ↗
38. Toropov AA, Toropova AP, Benfenati E (2008b) QSPR modeling for enthalpies of formation of organometallic compounds by means of SMILES-based optimal descriptors. Chem Phys Lett 461:343–34710.1016/j.cplett.2008.07.027 ↗
39. Toropov AA, Rasulev BF, Leszczynski J (2008c) QSAR modeling of acute toxicity by balance of correlations. Bioorg Med Chem 16:5999–600810.1016/j.bmc.2008.04.055 ↗
40. Toropov AA, Toropova AP, Benfenati E, Manganaro A (2009a) QSAR modelling of carcinogenicity by balance of correlations. Mol Divers 13:367–37310.1007/s11030-009-9113-4 ↗
41. Toropov AA, Toropova AP, Benfenati E, Leszczynska D, Leszczynski J (2009b) Additive InChI-based optimal descriptors: QSPR modeling of fullerene C 60 solubility in organic solvents. J Math Chem 46:1232–125110.1007/s10910-008-9514-0 ↗
42. Toropov AA, Toropova AP, Benfenati E (2009c) QSPR modeling of octanol water partition coefficient of platinum complexes by InChI-based optimal descriptors. J Math Chem 46:1060–107310.1007/s10910-008-9491-3 ↗
43. Toropov AA, Toropova AP, Benfenati E, Leszczynska D, Leszczynski J (2010a) InChI-based optimal descriptors: QSAR analysis of fullerene[C60]-based HIV-1 PR inhibitors by correlation balance. Eur J Med Chem 45:1387–139410.1016/j.ejmech.2009.12.037 ↗
44. Toropov AA, Toropova AP, Benfenati E (2010b) QSAR-modeling of toxicity of organometallic compounds by means of the balance of correlations for InChI-based optimal descriptors. Mol Divers 14:183–19210.1007/s11030-009-9156-6 ↗
45. Toropov AA, Toropova AP, Benfenati E, Leszczynska D, Leszczynski J (2010c) SMILES-based optimal descriptors: QSAR analysis of fullerene-based HIV-1 PR inhibitors by means of balance of correlations. J Comput Chem 31:381–39210.1002/jcc.21333 ↗
46. Toropova AP, Toropov AA, Benfenati E, Gini G (2011a) Co-evolutions of correlations for QSAR of toxicity of organometallic and inorganic substances: an unexpected good prediction based on a model that seems untrustworthy. Chemometr Intell Lab Syst 105:215–21910.1016/j.chemolab.2010.12.007 ↗
47. Toropova AP, Toropov AA, Benfenati E, Gini G (2011b) QSAR modelling toxicity toward rats of inorganic substances by means of CORAL Cent Eur J Chem 9:75–85
48. Toropova AP, Toropov AA, Puzyn T, Benfenati E, Leszczynska D, Leszczynski J (2013) Optimal descriptor as a translator of eclectic information into the prediction of thermal conductivity of micro-electro-mechanical systems. J Math Chem 51:2230–223710.1007/s10910-013-0211-2 ↗
49. Xu Z, Chou L, Sun J (2012) Effects of SiO2 nanoparticles on HFL-I activating ROS-mediated apoptosis via p53 pathway. J Appl Toxicol 32:358–36410.1002/jat.1710 ↗