Abstract
This chapter discusses the evolution of the so-called quasi-SMILES. The traditional simplified molecular-input line-entry system (SMILES) is a string of characters conveying information about the structure of molecules. Quasi-SMILES is a string of characters that can convey codes reflecting the structure of molecules and the conditions for conducting chemical or biochemical experiments. Several examples demonstrate the similarity in reporting data on individual nanomaterials and data on two or more nanomaterials subjected to the same type of experiment. The possibility of gradual expansion of the scope of application of quasi-SMILES, as well as the possibility of using quasi-SMILES as input information for the CORAL software (abbreviation CORrelation And Logic) when building models of physicochemical and biochemical phenomena for nanomaterials, is shown.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
GarcĂa-Hernndez DA, Iglesias-Groth S, Acosta-Pulido JA, Manchado A, GarcĂa-Lario P, Stanghellini L, Villaver E, Shaw RA, Cataldo F (2011) Astrophys J Lett 737(2):L30. https://doi.org/10.1088/2041-8205/737/2/L30
Iglesias-Groth S, Cataldo F, Manchado A (2011) Mon Not R Astron Soc 413(1):213–222. https://doi.org/10.1111/j.1365-2966.2011.18124.x
Cami J, Bernard-Salas J, Peeters E, Malek SE (2010) Science 329(5996):1180–1182. https://doi.org/10.1126/science.1192035
Barhoum A, GarcĂa-Betancourt ML, Jeevanandam J, Hussien EA, Mekkawy SA, Mostafa M, Omran MM, Abdalla MS, Bechelany M (2022) Nanomaterials 12(2):177. https://doi.org/10.3390/nano12020177
Pérez-Arantegui J, Larrea A (2003) TrAC Trends Anal Chem 22(5):327–329. https://doi.org/10.1016/S0165-9936(03)00502-8
Atlas of Sciences. https://atlasofscience.org/the-coral-software-as-spyglass-to-detect-coral-reefs-in-ocean-of-nanotechnologies/. Accessed 29 July 2022
Villaverde JJ, Sevilla-Morán B, LĂłpez-Goti C, Alonso-Prados JL, SandĂn-España P (2018) Sci Total Environ 634:1530–1539. https://doi.org/10.1016/j.scitotenv.2018.04.033s
Hellström T (2009) Technol Soc 31(3):325–331. https://doi.org/10.1016/j.techsoc.2009.06.002
OECD (2020) Guidance document for the testing of dissolution and dispersion stability of nanomaterials and the use of the data for further environmental testing and assessment strategies, No. 318. ENV/JM/MONO(2020)9
Mu Y, Wu F, Zhao Q, Ji R, Qie Y, Zhou Y, Hu Y, Pang C, Hristozov D, Giesy JP, **ng B (2016) Nanotoxicology 10(9):1207–1214. https://doi.org/10.1080/17435390.2016.1202352
Lubinski L, Urbaszek P, Gajewicz A, Cronin MTD, Enoch SJ, Madden JC, Leszczynska D, Leszczynski J, Puzyn T (2013) SAR QSAR Environ Res 24(12):995–1008. https://doi.org/10.1080/1062936X.2013.840679
Chugh H, Sood D, Chandra I, Tomar V, Dhawan G, Chandra R (2018) Artif Cells Nanomed Biotechnol 46(sup1):1210–1220. https://doi.org/10.1080/21691401.2018.1449118
Marchesan S, Prato M (2013) ACS Med Chem Lett 4(2):147–149. https://doi.org/10.1021/ml3003742
Yamakoshi Y, Umezawa N, Ryu A, Arakane K, Miyata N, Goda Y, Masumizu T, Nagano T (2003) J Am Chem Soc 125(42):12803–12809. https://doi.org/10.1021/ja0355574
Castro E, Garcia AH, Zavala G, Echegoyen L (2017) J Mater Chem B 5(32):6523–6535. https://doi.org/10.1039/c7tb00855d
Anilkumar P, Lu F, Cao L, Luo PG, Liu J-H, Sahu S, Tackett KN, Wang Y, Sun Y-P (2011) Curr Med Chem 18(14):2045–2059. https://doi.org/10.2174/092986711795656225
Sacchetti C, Motamedchaboki K, Magrini A, Palmieri G, Mattei M, Bernardini S, Rosato N, Bottini N, Bottini M (2013) ACS Nano 7(3):1974–1989. https://doi.org/10.1021/nn400409h
Bhirde AA, Patel S, Sousa AA, Patel V, Molinolo AA, Ji Y, Leapman RD, Gutkind JS, Rusling JF (2010) Nanomedicine 5(10):1535–1546. https://doi.org/10.2217/nnm.10.90
Benjamin SR, Vilela RS, de Camargo HS, Guedes MIF, Fernandes KF, Colmati F (2018) Int J Electrochem Sci 13(1):563–586. https://doi.org/10.20964/2018.01.51
Wagay JA, Nayik GA, Wani SA, Mir RA, Ahmad MA, Rahman QI, Vyas D (2019) J Food Meas Charact 13(3):1805–1819. https://doi.org/10.1007/s11694-019-00099-3
Schwaminger SP, Fraga-GarcĂa P, Selbach F, Hein FG, FuĂź EC, Surya R, Roth H-C, Blank-Shim SA, Wagner FE, Heissler S, Berensmeier S (2017) Adsorption 23(2–3):281–292. https://doi.org/10.1007/s10450-016-9849-y
Zhong L, Yu Y, Lian H-Z, Hu X, Fu H, Chen Y-J (2017) J Nanopart Res 19(11):375. https://doi.org/10.1007/s11051-017-4064-7
Yong K-T, Law W-C, Hu R, Ye L, Liu L, Swihart MT, Prasad PN (2013) Chem Soc Rev 42(3):1236–1250. https://doi.org/10.1039/c2cs35392j
Zhang H, Yee D, Wang C (2008) Nanomedicine 3(1):83–91. https://doi.org/10.2217/17435889.3.1.83
Raj S, Jose S, Sumod US, Sabitha M (2012) J Pharm Bioallied Sci 4(3):186–193. https://doi.org/10.4103/0975-7406.99016
Nohynek GJ, Dufour EK, Roberts MS (2008) Skin Pharmacol Physiol 21(3):136–149. https://doi.org/10.1159/000131078
Lu P-J, Huang S-C, Chen Y-P, Chiueh L-C, Shih DY-C (2015) J Food Drug Anal 23(3):587–594. https://doi.org/10.1016/j.jfda.2015.02.009
Auffan M, Pedeutour M, Rose J, Masion A, Ziarelli F, Borschneck D, Chaneac C, Botta C, Chaurand P, Labille J, Bottero J-Y (2010) Environ Sci Technol 44(7):2689–2694. https://doi.org/10.1021/es903757q
Mihranyan A, Ferraz N, Strømme M (2012) Prog Mater Sci 57(5):875–910. https://doi.org/10.1016/j.pmatsci.2011.10.001
Benn TM, Westerhoff P, Herckes P (2011) Environ Pollut 159(5):1334–1342. https://doi.org/10.1016/j.envpol.2011.01.018
Fytianos G, Rahdar A, Kyzas GZ (2020) Nanomaterials 10(5):979. https://doi.org/10.3390/nano10050979
Jiang T, Song X, Mu X, Cheang UK (2022) Sci Rep 12(1):13080. https://doi.org/10.1038/s41598-022-17053-x
Puzyn T, Leszczynska D, Leszczynski J (2009) Small 5(22):2494–2509. https://doi.org/10.1002/smll.200900179
Marchese Robinson RL, Cronin MTD, Richarz A-N, Rallo R (2015) Beilstein J Nanotechnol 6(1):1978–1999. https://doi.org/10.3762/bjnano.6.202
Panneerselvam S, Choi S (2014) Int J Mol Sci 15(5):7158–7182. https://doi.org/10.3390/ijms15057158
Melagraki G, Afantitis A (2014) RSC Adv 4(92):50713–50725. https://doi.org/10.1039/c4ra07756c
Puzyn T, Rasulev B, Gajewicz A, Hu X, Dasari TP, Michalkova A, Hwang H-M, Toropov A, Leszczynska D, Leszczynski J (2011) Nat Nanotechnol 6(3):175–178. https://doi.org/10.1038/nnano.2011.10
Fourches D, Pu D, Tassa C, Weissleder R, Shaw SY, Mumper RJ, Tropsha A (2010) ACS Nano 4(10):5703–5712. https://doi.org/10.1021/nn1013484
Doweyko AM (2008) J Comput Aided Mol Des 22(2):81–89. https://doi.org/10.1007/s10822-007-9162-7
Maggiora GM (2006) J Chem Inf Model 46(4):1535. https://doi.org/10.1021/ci060117s
Doweyko AM (2004) J Comput Aided Mol Des 18(7–9):587–596. https://doi.org/10.1007/s10822-004-4068-0
Johnson SR (2008) J Chem Inf Model 48(1):25–26. https://doi.org/10.1021/ci700332k
Dearden JC, Cronin MTD, Kaiser KLE (2009) SAR QSAR Environ Res 20(3–4):241–266. https://doi.org/10.1080/10629360902949567
Scior T, Medina-Franco JL, Do Q-T, MartĂnez-Mayorga K, Yunes Rojas JA, Bernard P (2009) Curr Med Chem 16(32):4297–4313. https://doi.org/10.2174/092986709789578213
Lee Y, von Gunten U (2012) Water Res 46(19):6177–6195. https://doi.org/10.1016/j.watres.2012.06.006
Papa E, Villa F, Gramatica P (2005) J Chem Inf Model 45(5):1256–1266. https://doi.org/10.1021/ci0502121
Toropova AP, Toropov AA, Martyanov SE, Benfenati E, Gini G, Leszczynska D, Leszczynski J (2012) Chemom Intell Lab Syst 110(1):177–181. https://doi.org/10.1016/j.chemolab.2011.10.005
Toropova AP, Toropov AA, Benfenati E, Gini G (2011) Chemom Intell Lab Syst 105(2):215–219. https://doi.org/10.1016/j.chemolab.2010.12.007
Toropov AA, Toropova AP, Benfenati E (2010) Mol Divers 14(1):183–192. https://doi.org/10.1007/s11030-009-9156-6
Toropov AA, Toropova AP, Kudyshkin VO (2022) Struct Chem 33(2):617–624. https://doi.org/10.1007/s11224-021-01875-y
Sivaraman N, Srinivasan TG, Vasudeva Rao PR, Natarajan R (2001) J Chem Inf Comput Sci 41(4):1067–1074. https://doi.org/10.1021/ci010003a
Toropov AA, Rasulev BF, Leszczynska D, Leszczynski J (2008) Chem Phys Lett 457(4–6):332–336. https://doi.org/10.1016/j.cplett.2008.04.013
Villaverde JJ, Sevilla-Morán B, LĂłpez-Goti C, Alonso-Prados JL, SandĂn-España P (2020) In: Shukla V, Kumar N (eds) Environmental concerns and sustainable development, air, water and energy resources, vol 1. Springer, Singapore, pp 1–27
Stoudmann N, Nowack B, Som C (2019) Environ Sci Nano 6(8):2520–2531. https://doi.org/10.1039/c9en00472f
Chopra SS, Bi Y, Brown FC, Theis TL, Hristovski KD, Westerhoff P (2019) Environ Sci Nano 6(11):3256–3267. https://doi.org/10.1039/c9en00603f
Organization for Economic Co-operation and Development (OECD) (2014) Ecotoxicology and environmental fate of manufactured nanomaterials. In: Series on the safety of manufactured nanomaterials, ENV/JM/MONO(2014)1, No. 40. OECD, Paris. Accessed 12 Aug 2022
Organization for Economic Co-operation and Development (OECD) (2020) Guidance document for the testing of dissolution and dispersion stability of nanomaterials and the use of the data for further environmental testing and assessment strategies. In: OECD guidelines for the testing of chemicals, ENV/JM/MONO(2020)9, No. 318. OECD, Paris. Accessed 12 Aug 2022
Camacho J, Smilde AK, Saccenti E, Westerhuis JA (2020) Chemom Intell Lab Syst 196:103907. https://doi.org/10.1016/j.chemolab.2019.103907
Siao MD, Shen WC, Chen RS, Chang ZW, Shih MC, Chiu YP, Cheng C-M (2018) Nat Commun 9(1):1442. https://doi.org/10.1038/s41467-018-03824-6
Toropov AA, Toropova AP, Benfenati E, Leszczynska D, Leszczynski J (2009) J Math Chem 46(4):1232–1251. https://doi.org/10.1007/s10910-008-9514-0
Toropova AP, Toropov AA, Benfenati E, Gini G, Leszczynska D, Leszczynski J (2011) Mol Divers 15(1):249–256. https://doi.org/10.1007/s11030-010-9245-6
Toropova AP, Toropov AA (2019) J Mol Struct 1182:141–149. https://doi.org/10.1016/j.molstruc.2019.01.040
Mashino T, Shimotohno K, Ikegami N, Nishikawa D, Okuda K, Takahashi K, Nakamura S, Mochizuki M (2005) Bioorg Med Chem Lett 15(4):1107–1109. https://doi.org/10.1016/j.bmcl.2004.12.030
Toropova AP, Toropov AA, Benfenati E (2019) Fuller Nanotub Carbon Nanostruct 27(10):816–821. https://doi.org/10.1080/1536383X.2019.1649659
Marchesan S, Da Ros T, Spalluto G, Balzarini J, Prato M (2005) Bioorg Med Chem Lett 15(15):3615–3618. https://doi.org/10.1016/j.bmcl.2005.05.069
Salahinejad M, Zolfonoun E (2013) J Nanopart Res 15(11):2028. https://doi.org/10.1007/s11051-013-2028-0
Yilmaz H, Rasulev B, Leszczynski J (2015) Nanomaterials 5(2):778–791. https://doi.org/10.3390/nano5020778
Salahinejad M (2015) Curr Top Med Chem 15(18):1868–1886. https://doi.org/10.2174/1568026615666150506145017
Toropov AA, Toropova AP (2015) Chemosphere 124(1):40–46. https://doi.org/10.1016/j.chemosphere.2014.10.067
Toropov AA, Toropova AP (2015) Chemosphere 139:18–22. https://doi.org/10.1016/j.chemosphere.2015.05.042
Toropova AP, Toropov AA (2015) Mini Rev Med Chem 15(8):608–621. https://doi.org/10.2174/1389557515666150219121652
Toropova AP, Toropov AA, Benfenati E, Leszczynska D, Leszczynski J (2010) J Math Chem 48(4):959–987. https://doi.org/10.1007/s10910-010-9719-x
Toropov AA, Toropova AP (2014) Chemosphere 104:262–264. https://doi.org/10.1016/j.chemosphere.2013.10.079
Toropov AA, Toropova AP, Veselinović AM, Veselinović JB, Nesmerak K, Raska I Jr, Duchowicz PR, Castro EA, Kudyshkin VO, Leszczynska D, Leszczynski J (2015) Comb Chem High Throughput Screen 18(4):376–386. https://doi.org/10.2174/1386207318666150305125044
Toropov AA, Rallo R, Toropova AP (2015) Curr Top Med Chem 15(18):1837–1844. https://doi.org/10.2174/1568026615666150506152000
Fjodorova N, Novič M, Venko K, Drgan V, Rasulev B, Türker Saçan M, Sağ Erdem S, Tugcu G, Toropova AP, Toropov AA (2022) Comput Struct Biotechnol J 20:913–924. https://doi.org/10.1016/j.csbj.2022.02.006
Weininger D (1988) J Chem Inf Comput Sci 28(1):31–36. https://doi.org/10.1021/ci00057a005
Lotfi S, Ahmadi S, Zohrabi P (2020) Struct Chem 31(6):2257–2270. https://doi.org/10.1007/s11224-020-01568-y
Chopdar KS, Dash GC, Mohapatra PK, Nayak B, Raval MK (2020) J Biomol Struct Dyn. https://doi.org/10.1080/07391102.2020.1867643
Achary PGR, Toropova AP, Toropov AA (2019) Int Food Res J 122:40–46. https://doi.org/10.1016/j.foodres.2019.03.067
Pogány P, Arad N, Genway S, Pickett SD (2019) J Chem Inf Model 59(3):1136–1146. https://doi.org/10.1021/acs.jcim.8b00626
Fatemi MH, Malekzadeh H (2015) J Iran Chem Soc 12(3):405–412. https://doi.org/10.1007/s13738-014-0497-4
Toropova AP, Toropov AA, Rasulev BF, Benfenati E, Gini G, Leszczynska D, Leszczynski J (2012) Struct Chem 23(6):1873–1878. https://doi.org/10.1007/s11224-012-9996-z
Toropov AA, Toropova AP, Martyanov SE, Benfenati E, Gini G, Leszczynska D, Leszczynski J (2012) Chemom Intell Lab Syst 112:65–70. https://doi.org/10.1016/j.chemolab.2011.12.003
Toropov AA, Toropova AP, Martyanov SE, Benfenati E, Gini G, Leszczynska D, Leszczynski J (2011) Chemom Intell Lab Syst 109(1):94–100. https://doi.org/10.1016/j.chemolab.2011.07.008
Toropov AA, Benfenati E (2007) Comput Biol Chem 31(1):57–60. https://doi.org/10.1016/j.compbiolchem.2007.01.003
Toropova AP, Toropov AA, Veselinović AM, Veselinović JB, Benfenati E, Leszczynska D, Leszczynski J (2016) Ecotoxicol Environ Saf 124:32–36. https://doi.org/10.1016/j.ecoenv.2015.09.038
Toropova AP, Toropov AA, Rallo R, Leszczynska D, Leszczynski J (2016) Int J Environ Res 10(1):59–64
Ahmadi S (2020) Chemosphere 242:125192. https://doi.org/10.1016/j.chemosphere.2019.125192
Cassano A, Robinson RLM, Palczewska A, Puzyn T, Gajewicz A, Tran L, Manganelli S, Cronin MTD (2016) ATLA Altern Lab Anim 44(6):533–556. https://doi.org/10.1177/026119291604400603
Toropov AA, Toropova AP, Leszczynska D, Leszczynski J (2019) BioSystems 181:51–57. https://doi.org/10.1016/j.biosystems.2019.04.008
Toropova AP, Toropov AA, Rallo R, Leszczynska D, Leszczynski J (2015) Ecotoxicol Environ Saf 112:39–45. https://doi.org/10.1016/j.ecoenv.2014.10.003
Toropova AP, Toropov AA, Manganelli S, Leone C, Baderna D, Benfenati E, Fanelli R (2016) NanoImpact 1:60–64. https://doi.org/10.1016/j.impact.2016.04.003
Achary PGR, Begum S, Toropova AP, Toropov AA (2016) Mater Discov 5:22–28. https://doi.org/10.1016/j.md.2016.12.003
Toropov AA, Achary PGR, Toropova AP (2016) Chem Phys Lett 660:107–110. https://doi.org/10.1016/j.cplett.2016.08.018
Toropov AA, Kjeldsen F, Toropova AP (2022) Chemosphere 303:135086. https://doi.org/10.1016/j.chemosphere.2022.135086
Ahmadi S, Aghabeygi S, Farahmandjou M, Azimi N (2021) Struct Chem 32(5):1893–1905. https://doi.org/10.1007/s11224-021-01748-4
Toropova AP, Toropov AA, Leszczynski J, Sizochenko N (2021) Environ Toxicol Pharmacol 86:103665. https://doi.org/10.1016/j.etap.2021.103665
Toropov AA, Toropova AP (2021) Sci Total Environ 772:145532. https://doi.org/10.1016/j.scitotenv.2021.145532
Toropova AP, Toropov AA, Leszczynska D, Leszczynski J (2021) Comput Biol Med 136:104720. https://doi.org/10.1016/j.compbiomed.2021.104720
Acknowledgements
This work was supported by ONTOX, grant agreement 963845 of the European Commission under the Horizon 2020 research and innovation framework program.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this chapter
Cite this chapter
Toropova, A.P., Toropov, A.A. (2023). The CORAL Software as a Tool to Develop Models for Nanomaterials’ Endpoints. In: Toropova, A.P., Toropov, A.A. (eds) QSPR/QSAR Analysis Using SMILES and Quasi-SMILES. Challenges and Advances in Computational Chemistry and Physics, vol 33. Springer, Cham. https://doi.org/10.1007/978-3-031-28401-4_14
Download citation
DOI: https://doi.org/10.1007/978-3-031-28401-4_14
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-031-28400-7
Online ISBN: 978-3-031-28401-4
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)