SpringerLink
Log in

Fundamentals of Mathematical Modeling of Chemicals Through QSPR/QSAR

  • Chapter
  • First Online:
QSPR/QSAR Analysis Using SMILES and Quasi-SMILES

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((COCH,volume 33))

  • 270 Accesses

Abstract

The evolution of mathematical chemistry in its applications to establish the quantitative structure–property/activity relationships (QSPRs/QSARs) between molecular structure and the physicochemical and biochemical behavior of substances is discussed. The gradual improvement of molecular descriptors and the statistically validated methods developed for the above general task are described. The possible ways of applying and extending OECD principles are demonstrated via computational experiments to build QSPR/QSAR models. The leading role of validation in obtaining applicable models is noted. Stochastic procedures able to improve the reliability of QSPR/QSAR models are demonstrated.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
EUR 29.95
Price includes VAT (Germany)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
EUR 139.09
Price includes VAT (Germany)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
EUR 181.89
Price includes VAT (Germany)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
EUR 181.89
Price includes VAT (Germany)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Wiener H (1947) J Am Chem Soc 69(1):17–20. https://doi.org/10.1021/ja01193a005

    Article  CAS  PubMed  Google Scholar 

  2. Wiener H (1947) J Chem Phys 15(10):766. https://doi.org/10.1063/1.1746328

    Article  CAS  Google Scholar 

  3. Schindler D, Bensmann F, Dietze S, KrĂĽger F (2022) PeerJ Comput Sci 8:e835. https://doi.org/10.7717/PEERJ-CS.835

    Article  PubMed  PubMed Central  Google Scholar 

  4. Wiener H (1947) J Am Chem Soc 69(11):2636–2638. https://doi.org/10.1021/ja01203a022

    Article  CAS  Google Scholar 

  5. Bonchev D, Trinajstić N (1977) J Chem Phys 67:4517–4533. https://doi.org/10.1063/1.434593

    Article  CAS  Google Scholar 

  6. Balaban AT (1979) Theor Chim Acta 53(4):355–375. https://doi.org/10.1007/BF00555695

    Article  CAS  Google Scholar 

  7. Bonchev D, Mekenjan Ov, Protić G, Trinajstić N (1979) J Chromatogr A 176(2):149–156. https://doi.org/10.1016/S0021-9673(00)85645-9

  8. El-Basil S (1987) Chem Phys Lett 137(6):543–547. https://doi.org/10.1016/0009-2614(87)80626-7

    Article  CAS  Google Scholar 

  9. Gutman I, Miljković O, Caporossi G, Hansen P (1999) Chem Phys Lett 306(5–6):366–372. https://doi.org/10.1016/S0009-2614(99)00472-8

    Article  CAS  Google Scholar 

  10. Gutman I, Araujo O, Morales DA (2000) J Chem Inf Comput Sci 40(3):593–598. https://doi.org/10.1021/ci990095s

    Article  CAS  PubMed  Google Scholar 

  11. Hansch C, Fujita T (1964) J Am Chem Soc 86(24):5710. https://doi.org/10.1021/ja01078a623

    Article  Google Scholar 

  12. Dearden JC (2017) In: Leszczynski J (ed) Challenges and advances in computational chemistry and physics, vol 24, pp 57–88. https://doi.org/10.1007/978-3-319-56850-8_2

  13. Doweyko AM (2008) J Comput Aided Mol Des 22(2):81–89. https://doi.org/10.1007/s10822-007-9162-7

    Article  CAS  PubMed  Google Scholar 

  14. Tóth G, Bodai Z, Héberger K (2013) J Comput-Aided Mol Des 27(10):837–844. https://doi.org/10.1007/s10822-013-9680-4

    Article  CAS  PubMed  Google Scholar 

  15. Weininger D (1988) J Chem Inf Comput Sci 28(1):31–36. https://doi.org/10.1021/ci00057a005

    Article  CAS  Google Scholar 

  16. Mak K-K, Balijepalli MK, Pichika MR (2022) Expert Opin Drug Discov 17(1):79–92. https://doi.org/10.1080/17460441.2022.1985108

    Article  PubMed  Google Scholar 

  17. Segall MD, Beresford AP, Gola JMR, Hawksley D, Tarbit MH (2006) Expert Opin Drug Metab Toxicol 2(2):325–337. https://doi.org/10.1517/17425255.2.2.325

    Article  CAS  PubMed  Google Scholar 

  18. Giffin SA, Shah R, Soloff A, Vaysman AM, Oreper J, Gažo A, Gandhi P, Shah I, Malieckal T, Boulos D, Flowers T, Stevens CA, Rocco MS, Patel AS, Albano D (2019) Ther Innov Regul Sci 53(3):332–339. https://doi.org/10.1177/2168479018779920

    Article  PubMed  Google Scholar 

  19. Varnek A, Fourches D, Hoonakker F, Solov’ev VP (2005) J Comput-Aided Mol Des 19(9–10):693–703. https://doi.org/10.1007/s10822-005-9008-0

    Article  CAS  PubMed  Google Scholar 

  20. Thurston BA, Ferguson AL (2018) Mol Simul 44(11):930–945. https://doi.org/10.1080/08927022.2018.1469754

    Article  CAS  Google Scholar 

  21. Rosandić M, Paar V (2022) BioSystems 218:104695. https://doi.org/10.1016/j.biosystems.2022.104695

    Article  CAS  PubMed  Google Scholar 

  22. Sanders J, Hoffmann SA, Green AP, Cai Y (2022) Curr Opin Biotechnol 75:102691. https://doi.org/10.1016/j.copbio.2022.102691

    Article  CAS  PubMed  Google Scholar 

  23. Kim S, Yi H, Kim YT, Lee HS (2022) J Mol Biol 434(8):167302. https://doi.org/10.1016/j.jmb.2021.167302

    Article  CAS  PubMed  Google Scholar 

  24. Kodama T, Ohtani H, Arakawa H, Ikai A (2005) Ultramicroscopy 105(1–4):189–195. https://doi.org/10.1016/j.ultramic.2005.06.035

    Article  CAS  Google Scholar 

  25. Blaurock B, Hippeli S, Metz N, Elstner EF (1992) Arch Toxicol 66(10):681–687. https://doi.org/10.1007/BF01972618

    Article  CAS  PubMed  Google Scholar 

  26. Gagarin SG (1979) J Struct Chem 19(4):620–621. https://doi.org/10.1007/BF00745694

    Article  Google Scholar 

  27. Fedorov VS (1975) J Struct Chem 15(5):794–797. https://doi.org/10.1007/BF00747289

    Article  Google Scholar 

  28. Bongrand P (2022) Curr Issues Mol Biol 44(2):505–525. https://doi.org/10.3390/cimb44020035

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Kampanarakis A, Farantos SC, Daskalakis V, Varotsis C (2012) Chem Phys 399:258–263. https://doi.org/10.1016/j.chemphys.2011.07.031

    Article  CAS  Google Scholar 

  30. Anikin NA, Bugaenko VL, Kuzminskii MB, Mendkovich AS (2012) Russ Chem Bull 61(1):12–16. https://doi.org/10.1007/s11172-012-0002-0

    Article  CAS  Google Scholar 

  31. Pramanik S, Roy K (2014) Environ Sci Pollut Res 21(4):2955–2965. https://doi.org/10.1007/s11356-013-2247-z

    Article  CAS  Google Scholar 

  32. Coi A, Massarelli I, Murgia L, Saraceno M, Calderone V, Bianucci AM (2006) Bioorg Med Chem 14(9):3153–3159. https://doi.org/10.1016/j.bmc.2005.12.030

    Article  CAS  PubMed  Google Scholar 

  33. Katritzky AR, Kulshyn OV, Stoyanova-Slavova I, Dobchev DA, Kuanar M, Fara DC, Karelson M (2006) Bioorg Med Chem 14(7):2333–2357. https://doi.org/10.1016/j.bmc.2005.11.015

    Article  CAS  PubMed  Google Scholar 

  34. Karelson M, Maran U, Wang Y, Katritzky AR (1999) Collect Czechoslov Chem Commun 64(1):1551–1571. https://doi.org/10.1135/cccc19991551

    Article  CAS  Google Scholar 

  35. Toropov AA, Toropova AP, Benfenati E, Salmona M (2018) Toxicol Mech Methods 28(5):321–327. https://doi.org/10.1080/15376516.2017.1422579

    Article  CAS  PubMed  Google Scholar 

  36. Toropova AP, Toropov AA, Begum S, Achary PGR (2018) Curr Neuropharmacol 16(6):769–785. https://doi.org/10.2174/1570159X15666171016163951

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Topliss JG, Costello RJ (1972) J Med Chem 15:1066–1068. https://doi.org/10.1021/jm00280a017

  38. Carbó-Dorca R (2021) Pure Appl Chem 93(10):1189–1196. https://doi.org/10.1515/pac-2021-0112

    Article  CAS  Google Scholar 

  39. Abdi H, Williams LJ (2010) Wiley Interdiscip Rev Comput Stat 2(4):433–459. https://doi.org/10.1002/wics.101

    Article  Google Scholar 

  40. Darnag R, Minaoui B, Fakir M (2017) Arab J Chem 10:S600–S608. https://doi.org/10.1016/j.arabjc.2012.10.021

    Article  CAS  Google Scholar 

  41. Cramer RD III (1993) Perspect Drug Discov Des 1(2):269–278. https://doi.org/10.1007/BF02174528

    Article  CAS  Google Scholar 

  42. Arian R, Hariri A, Mehridehnavi A, Fassihi A, Ghasemi F (2020) Comput Biol Chem 86:107269. https://doi.org/10.1016/j.compbiolchem.2020.107269

    Article  CAS  PubMed  Google Scholar 

  43. Niculescu SP (2003) J Mol Struct: THEOCHEM 622(1–2):71–83. https://doi.org/10.1016/S0166-1280(02)00619-X

    Article  CAS  Google Scholar 

  44. Andrada MF, Vega-Hissi EG, Estrada MR, Garro Martinez JC (2015) Chemom Intell Lab Syst 143:122–129. https://doi.org/10.1016/j.chemolab.2015.03.001

    Article  CAS  Google Scholar 

  45. Seifi A, Riahi-Madvar H (2019) Environ Sci Pollut Res 26(1):867–885. https://doi.org/10.1007/s11356-018-3613-7

    Article  Google Scholar 

  46. Sun M, Zheng Y, Wei H, Chen J, Cai J, ** M (2009) QSAR Comb Sci 28(3):312–324. https://doi.org/10.1002/qsar.200860107

    Article  CAS  Google Scholar 

  47. Teixeira AL, Leal JP, Falcao AO (2013) J Cheminform 5(2):9. https://doi.org/10.1186/1758-2946-5-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Ambure P, Cordeiro MNDS (2020) In: Roy K (ed) Ecotoxicological QSARs. Methods in pharmacology and toxicology. Humana, New York, NY, pp 97–109. https://doi.org/10.1007/978-1-0716-0150-1_5

  49. Patel M, Chilton ML, Sartini A, Gibson L, Barber C, Covey-Crump L, Przybylak KR, Cronin MTD, Madden JC (2018) J Chem Inf Model 58(3):673–682. https://doi.org/10.1021/acs.jcim.7b00523

    Article  CAS  PubMed  Google Scholar 

  50. Schultz TW, Hewitt M, Netzeva TI, Cronin MTD (2007) QSAR Comb Sci 26(2):238–254. https://doi.org/10.1002/qsar.200630020

    Article  CAS  Google Scholar 

  51. Jaworska J, Nikolova-Jeliazkova N, Aldenberg T (2005) ATLA Altern Lab Anim 33(5):445–459. https://doi.org/10.1177/026119290503300508

    Article  CAS  PubMed  Google Scholar 

  52. Gramatica P (2007) QSAR Comb Sci 26(5):694–701. https://doi.org/10.1002/qsar.200610151

    Article  CAS  Google Scholar 

  53. Tropsha A, Gramatica P, Gombar VK (2003) QSAR Comb Sci 22(1):69–77. https://doi.org/10.1002/qsar.200390007

    Article  CAS  Google Scholar 

  54. Tropsha A (2010) Mol Inform 29(6–7):476–488. https://doi.org/10.1002/minf.201000061

    Article  CAS  PubMed  Google Scholar 

  55. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Toropov AA, Toropova AP, Benfenati E (2010) Eur J Med Chem 45(9):3581–3587. https://doi.org/10.1016/j.ejmech.2010.05.002

    Article  CAS  PubMed  Google Scholar 

  57. Toropov AA, Toropova AP, Puzyn T, Benfenati E, Gini G, Leszczynska D, Leszczynski J (2013) Chemosphere 92(1):31–37. https://doi.org/10.1016/j.chemosphere.2013.03.012

    Article  CAS  PubMed  Google Scholar 

  58. 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

    Article  CAS  PubMed  Google Scholar 

  59. Toropov AA, Toropova AP (2015) Chemosphere 124(1):40–46. https://doi.org/10.1016/j.chemosphere.2014.10.067

    Article  CAS  PubMed  Google Scholar 

  60. Trinh TX, Choi J-S, Jeon H, Byun H-G, Yoon T-H, Kim J (2018) Chem Res Toxicol 31(3):183–190. https://doi.org/10.1021/acs.chemrestox.7b00303

    Article  CAS  PubMed  Google Scholar 

  61. Veselinović AM, Milosavljević JB, Toropov AA, Nikolić GM (2013) Eur J Pharm Sci 48(3):532–541. https://doi.org/10.1016/j.ejps.2012.12.021

    Article  CAS  PubMed  Google Scholar 

  62. Worachartcheewan A, Mandi P, Prachayasittikul V, Toropova AP, Toropov AA, Nantasenamat C (2014) Chemom Intell Lab Syst 138:120–126. https://doi.org/10.1016/j.chemolab.2014.07.017

    Article  CAS  Google Scholar 

  63. Kumar P, Kumar A, Sindhu J (2019) SAR QSAR Environ Res 30(2):63–80. https://doi.org/10.1080/1062936X.2018.1564067

    Article  CAS  PubMed  Google Scholar 

  64. Toropov AA, Toropova AP, Marzo M, Dorne JL, Georgiadis N, Benfenati E (2017) Environ Toxicol Pharmacol 53:158–163. https://doi.org/10.1016/j.etap.2017.05.011

    Article  CAS  PubMed  Google Scholar 

  65. Manisha, Chauhan S, Kumar P, Kumar A (2019) SAR QSAR Environ Res 30(3):145–159. https://doi.org/10.1080/1062936X.2019.1568299

  66. Kumar A, Chauhan S (2017) Drug Res 67(3):156–162. https://doi.org/10.1055/s-0042-119725

    Article  CAS  Google Scholar 

  67. Achary PGR (2014) SAR QSAR Environ Res 25(1):73–90. https://doi.org/10.1080/1062936X.2013.842930

    Article  CAS  PubMed  Google Scholar 

  68. Stoičkov V, Stojanović D, Tasić I, Šarić S, Radenković D, Babović P, Sokolović D, Veselinović AM (2018) Struct Chem 29(2):441–449. https://doi.org/10.1007/s11224-017-1041-9

    Article  CAS  Google Scholar 

  69. Ahmadi S, Akbari A (2018) SAR QSAR Environ Res 29(11):895–909. https://doi.org/10.1080/1062936X.2018.1526821

    Article  CAS  PubMed  Google Scholar 

  70. Islam MA, Pillay TS (2016) Chemom Intell Lab Syst 153:67–74. https://doi.org/10.1016/j.chemolab.2016.02.008

    Article  CAS  Google Scholar 

  71. Ahmadi S, Mehrabi M, Rezaei S, Mardafkan N (2019) J Mol Struct 1191:165–174. https://doi.org/10.1016/j.molstruc.2019.04.103

    Article  CAS  Google Scholar 

  72. Toropov AA, Toropova AP (2002) J Mol Struct: THEOCHEM 581(1–3):11–15. https://doi.org/10.1016/S0166-1280(01)00733-3

    Article  CAS  Google Scholar 

  73. Kurashov EA, Fedorova EV, Krylova JV, Mitrukova GG (2016) Scientifica 2016:1205680. https://doi.org/10.1155/2016/1205680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Crippen GM (2008) Curr Comput-Aided Drug Des 4(4):259–264. https://doi.org/10.2174/157340908786786001

    Article  CAS  Google Scholar 

  75. Toropov AA, Toropova AP, Benfenati E (2020) Aquat Toxicol 227:105589. https://doi.org/10.1016/j.aquatox.2020.105589

    Article  CAS  PubMed  Google Scholar 

  76. Toropov AA, Toropova AP (2017) Mutat Res-Genet Toxicol Environ Mutagen 819:31–37. https://doi.org/10.1016/j.mrgentox.2017.05.008

    Article  CAS  PubMed  Google Scholar 

  77. Toropova AP, Toropov AA (2017) Sci Total Environ 586:466–472. https://doi.org/10.1016/j.scitotenv.2017.01.198

    Article  CAS  PubMed  Google Scholar 

  78. Majumdar S, Basak SC (2018) Curr Comput-Aided Drug Des 14(1):5–6. https://doi.org/10.2174/157340991401180321112006

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

AAT and APT are grateful to the project LIFE-CONCERT (LIFE17 GIE/IT/000461) for their support.

Author information

Authors and Affiliations

  1. Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Science, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milano, Italy

    Andrey A. Toropov & Alla P. Toropova

  2. 3rd Medical Department, 1st Faculty of Medicine, Charles University in Prague, U Nemocnice 1, 12808, Prague 2, Czech Republic

    Maria Raskova & Ivan Raska Jr.

Authors
  1. Andrey A. Toropov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Maria Raskova
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ivan Raska Jr.
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Alla P. Toropova
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Andrey A. Toropov .

Editor information

Editors and Affiliations

  1. Department of Environmental Health Science, Institute of Pharmacological Research Mario Negri IRCCS, Milan, Italy

    Alla P. Toropova

  2. Department of Environmental Health Science, Institute of Pharmacological Research Mario Negri IRCCS, Milan, Italy

    Andrey A. Toropov

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Toropov, A.A., Raskova, M., Raska, I., Toropova, A.P. (2023). Fundamentals of Mathematical Modeling of Chemicals Through QSPR/QSAR. 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_1

Download citation

Publish with us

Policies and ethics

Search

Navigation