Application of SMILES to Cheminformatics and Generation of Optimum SMILES Descriptors Using CORAL Software

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QSPR/QSAR Analysis Using SMILES and Quasi-SMILES

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

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Abstract

This chapter uses a simplified molecular input-line entry system (SMILES) to solve diverse problems in science, technology, and medicine. SMILES can be useful to model quantitative structure–property/activity relationships (QSPRs/QSARs). The evolution of the applications of SMILES and the evolution of SMILES descriptors are discussed. The construction of so-called optimal descriptors based on SMILES using the CORAL software is described. These optimal descriptors are useful for training QSPR/QSAR models for a wide range of diverse properties.

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References

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

    Article  CAS  Google Scholar 

  2. Weininger D, Weininger A, Weininger JL (1989) J Chem Inf Comput Sci 29:97–101. https://doi.org/10.1021/ci00062a008

    Article  CAS  Google Scholar 

  3. Weininger D (1990) J Chem Inf Comput Sci 30:237–243. https://doi.org/10.1021/ci00067a005

    Article  CAS  Google Scholar 

  4. Toropov AA, Toropova AP, Mukhamedzhanova DV, Gutman I (2005) Indian J Chem Inorg Phys Theor Anal Chem 44(8):1545–1552

    Google Scholar 

  5. Toropov AA, Toropova AP, Benfenati E, Leszczynska D, Leszczynski J (2010) J Comput Chem 31(2):381–392. https://doi.org/10.1002/jcc.21333

    Article  CAS  PubMed  Google Scholar 

  6. Enoch SJ, Madden JC, Cronin MTD (2008) SAR QSAR Environ Res 19(5–6):555–578. https://doi.org/10.1080/10629360802348985

    Article  CAS  PubMed  Google Scholar 

  7. Toropov AA, Toropova AP, Benfenati E, Manganaro A (2009) J Comput Chem 30:2576–2582. https://doi.org/10.1002/jcc.21263

    Article  CAS  PubMed  Google Scholar 

  8. 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

    Article  CAS  Google Scholar 

  9. Toropova AP, Toropov AA, Benfenati E, Gini G (2011) Chem Biol Drug Des 77:343–360. https://doi.org/10.1111/j.1747-0285.2011.01109.x

    Article  CAS  PubMed  Google Scholar 

  10. Toropov AA, Toropova AP, Benfenati E, Leszczynska D, Leszczynski J (2010) Eur J Med Chem 45:1387–1394. https://doi.org/10.1016/j.ejmech.2009.12.037

    Article  CAS  PubMed  Google Scholar 

  11. Toropov AA, Toropova AP, Benfenati E (2010) Mol Divers 14:183–192. https://doi.org/10.1007/s11030-009-9156-6

    Article  CAS  PubMed  Google Scholar 

  12. Toropov AA, Toropova AP, Benfenati E (2009) J Math Chem 46:1060–1073. https://doi.org/10.1007/s10910-008-9491-3

    Article  CAS  Google Scholar 

  13. Toropov AA, Toropova AP, Benfenati E, Leszczynska D, Leszczynski J (2009) J Math Chem 47:355–369. https://doi.org/10.1007/s10910-009-9574-9

    Article  CAS  Google Scholar 

  14. Olah M, Bologa C, Oprea TI (2004) J Comput Aided Mol Des 18(7–9):437–449. https://doi.org/10.1007/s10822-004-4060-8

    Article  CAS  PubMed  Google Scholar 

  15. Thalheim T, Vollmer A, Ebert R-U, Kühne R, Schüürmann G (2010) J Chem Inf Model 50(7):1223–1232. https://doi.org/10.1021/ci1001179

    Article  CAS  PubMed  Google Scholar 

  16. Ma EYT, Kremer SC (2009) In: IEEE international conference on bioinformatics and biomedicine (BIBM), vol 5341870, pp 37–42. https://doi.org/10.1109/BIBM.2009.60

  17. Saracci R (2006) Int J Epidemiol 35(3):513–514. https://doi.org/10.1093/ije/dyl101

    Article  PubMed  Google Scholar 

  18. Gutman I, Trinajstić N (1972) Chem Phys Lett 17(4):535–538. https://doi.org/10.1016/0009-2614(72)85099-1

    Article  CAS  Google Scholar 

  19. Randić M (1974) J Chem Phys 60:3920–3928. https://doi.org/10.1063/1.1680839

    Article  Google Scholar 

  20. Gutman I, Ruščić B, Trinajstić N, Wilcox CF Jr (1975) J Chem Phys 62(9):3399–3405. https://doi.org/10.1063/1.430994

    Article  CAS  Google Scholar 

  21. Balaban AT (1983) Pure Appl Chem 55(2):199–206. https://doi.org/10.1351/pac198855020199

    Article  CAS  Google Scholar 

  22. Kier LB (1985) Quant Struct-Act Relat 4(3):109–116. https://doi.org/10.1002/qsar.19850040303

    Article  CAS  Google Scholar 

  23. Mekenyan O, Bonchev D, Balaban A (1988) J Math Chem 2(4):347–375. https://doi.org/10.1007/BF01166300

    Article  CAS  Google Scholar 

  24. Diudea MV (1994) J Chem Inf Comput Sci 34(5):1064–1071. https://doi.org/10.1021/ci00021a005

    Article  CAS  Google Scholar 

  25. Basak SC, Bertelsen S, Grunwald GD (1994) J Chem Inf Comput Sci 34(2):270–276. https://doi.org/10.1021/ci00018a007

    Article  CAS  Google Scholar 

  26. Bonchev D, Balaban AT, Liu X, Klein DJ (1994) Int J Quantum Chem 50(1):1–20. https://doi.org/10.1002/qua.560500102

    Article  CAS  Google Scholar 

  27. Estrada E (1997) J Chem Inf Comput Sci 37(2):320–328. https://doi.org/10.1021/ci960113v

    Article  CAS  Google Scholar 

  28. Ivanciuc O (2000) J Chem Inf Comput Sci 40(6):1412–1422. https://doi.org/10.1021/ci000068y

    Article  CAS  PubMed  Google Scholar 

  29. Pogliani L (2000) Chem Rev 100(10):3827–3858. https://doi.org/10.1021/cr0004456

    Article  CAS  PubMed  Google Scholar 

  30. Fujita S, Karasawa Y, Fujii M, Hironaka K-I, Uda S, Kubota H, Inoue H, Sumitomo Y, Hirayama A, Soga T, Kuroda S (2022) NPJ Syst Biol Appl 8(1):6. https://doi.org/10.1038/s41540-022-00213-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Sheng C, Zhang W, Ji H, Zhang M, Song Y, Xu H, Zhu J, Miao Z, Jiang Q, Yao J, Zhou Y, Zhu J, Lü J (2006) J Med Chem 49(8):2512–2525. https://doi.org/10.1021/jm051211n

    Article  CAS  PubMed  Google Scholar 

  32. Klimisch H-J, Andreae M, Tillmann U (1997) Regul Toxicol Pharmacol 25(1):1–5. https://doi.org/10.1006/rtph.1996.1076

    Article  CAS  PubMed  Google Scholar 

  33. Taniguchi T, Tanaka K, Wang HO (2000) IEEE Trans Fuzzy Syst 8(4):442–452. https://doi.org/10.1109/91.868950

    Article  Google Scholar 

  34. Guha R, Jurs PC (2005) J Chem Inf Model 45(3):800–806. https://doi.org/10.1021/ci050022a

    Article  CAS  PubMed  Google Scholar 

  35. Casañola-Martín GM, Marrero-Ponce Y, Khan MTH, Ather A, Sultan S, Torrens F, Rotondo R (2007) Bioorg Med Chem 15(3):1483–1503. https://doi.org/10.1016/j.bmc.2006.10.067

    Article  CAS  PubMed  Google Scholar 

  36. Tseng YJ, Hopfinger AJ, Esposito EX (2012) J Comput Aided Mol Des 26(1):39–43. https://doi.org/10.1007/s10822-011-9511-4

    Article  CAS  PubMed  Google Scholar 

  37. Parthasarathi R, Subramanian V, Roy DR, Chattaraj PK (2004) Bioorg Med Chem 12(21):5533–5543. https://doi.org/10.1016/j.bmc.2004.08.013

    Article  CAS  PubMed  Google Scholar 

  38. Hall LH, Kier LB (2001) J Mol Graph Model 20(1):4–18. https://doi.org/10.1016/S1093-3263(01)00097-3

    Article  CAS  PubMed  Google Scholar 

  39. Feng G-S (2012) Cancer Cell 21(2):150–154. https://doi.org/10.1016/j.ccr.2012.01.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Joshi CP, Mansfield SD (2007) Curr Opin Plant Biol 10(3):220–226. https://doi.org/10.1016/j.pbi.2007.04.013

    Article  CAS  PubMed  Google Scholar 

  41. 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 

  42. Box GEP (1976) J Am Stat Assoc 71(356):791–799. https://doi.org/10.1080/01621459.1976.10480949

    Article  Google Scholar 

  43. Box GEP, Tiao GC (1976) J Appl Stat 25(3):195–200. https://doi.org/10.2307/2347226

    Article  Google Scholar 

  44. 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 

  45. Ellison CM, Sherhod R, Cronin MTD, Enoch SJ, Madden JC, Judson PN (2011) J Chem Inf Model 51(5):975–985. https://doi.org/10.1021/ci1000967

    Article  CAS  PubMed  Google Scholar 

  46. Sahigara F, Mansouri K, Ballabio D, Mauri A, Consonni V, Todeschini R (2012) Molecules 17(5):4791–4810. https://doi.org/10.3390/molecules17054791

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Li T, Zhao X, Li L (2021) IEEE Trans Pattern Anal Mach Intell (in press). https://doi.org/10.1109/TPAMI.2021.3120428

  48. Gomari DP, Schweickart A, Cerchietti L, Paietta E, Fernandez H, Al-Amin H, Suhre K, Krumsiek J (2022) Commun Biol 5(1):645. https://doi.org/10.1038/s42003-022-03579-3

    Article  PubMed  PubMed Central  Google Scholar 

  49. Fuhr AS, Sumpter BG (2022) Front Mater 9:865270. https://doi.org/10.3389/fmats.2022.865270

    Article  Google Scholar 

  50. Sridharan B, Goel M, Priyakumar UD (2022) ChemComm 58(35):5316–5331. https://doi.org/10.1039/d1cc07035e

    Article  CAS  Google Scholar 

  51. Monroe JI, Shen VK (2022) J Chem Theory Comput 18(6):3622–3636. https://doi.org/10.1021/acs.jctc.2c00110

    Article  CAS  PubMed  Google Scholar 

  52. Aoto S, Hangai M, Ueno-Yokohata H, Ueda A, Igarashi M, Ito Y, Tsukamoto M, **no T, Sakamoto M, Okazaki Y, Hasegawa F, Ogata-Kawata H, Namura S, Kojima K, Kikuya M, Matsubara K, Taniguchi K, Okamura K (2022) Sci Rep 12(1):3730. https://doi.org/10.1038/s41598-022-07560-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Kumar R, Sharma A, Alexiou A, Bilgrami AL, Kamal MA, Ashraf GM (2022) Front Neurosci 16:858126. https://doi.org/10.3389/fnins.2022.858126

    Article  PubMed  PubMed Central  Google Scholar 

  54. Zhang X-C, Yi J-C, Yang G-P, Wu C-K, Hou T-J, Cao D-S (2022) Brief Bioinform 23(2): bbac033. https://doi.org/10.1093/bib/bbac033

  55. Lim S, Lee YO, Yoon J, Kim YJ (2022) J Comput-Aided Mol Des 36(3):225–235. https://doi.org/10.1007/s10822-022-00448-3

    Article  CAS  PubMed  Google Scholar 

  56. Wang S, Liu J, Ding M, Gao Y, Liu D, Tian Q, Zhu J (2022) Comb Chem High Throughput Screen 25(4):642–650. https://doi.org/10.2174/1386207324666210219102728

    Article  CAS  PubMed  Google Scholar 

  57. Han X, **e R, Li X, Li J (2022) Life 12(2):319. https://doi.org/10.3390/life12020319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Hung C, Gini G (2021) Mol Divers 25(3):1283–1299. https://doi.org/10.1007/s11030-021-10250-2

    Article  CAS  PubMed  Google Scholar 

  59. Probst D, Reymond J-L (2018) J Chem Inf Model 58(1):1–7. https://doi.org/10.1021/acs.jcim.7b00425

    Article  CAS  PubMed  Google Scholar 

  60. Přívratský J, Novák J (2021) J Cheminform 13(1):51. https://doi.org/10.1186/s13321-021-00530-2

    Article  PubMed  PubMed Central  Google Scholar 

  61. Berenger F, Tsuda K (2021) J Cheminform 13(1):88. https://doi.org/10.1186/s13321-021-00566-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Rajan K, Zielesny A, Steinbeck C (2020) J Cheminform 12(1):65. https://doi.org/10.1186/s13321-020-00469-w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. ArĂşs-Pous J, Johansson SV, Prykhodko O, Bjerrum EJ, Tyrchan C, Reymond J-L, Chen H, Engkvist O (2019) J Cheminform 11(1):71. https://doi.org/10.1186/s13321-019-0393-0

    Article  PubMed  PubMed Central  Google Scholar 

  64. Drefahl A (2011) J Cheminform 3:1. https://doi.org/10.1186/1758-2946-3-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Toropova AP, Toropov AA, Benfenati E, Leszczynska D, Leszczynski J (2018) BioSystems 169–170:5–12. https://doi.org/10.1016/j.biosystems.2018.05.003

    Article  CAS  PubMed  Google Scholar 

  66. Toropov AA, Toropova AP (2015) Chemosphere 139:18–22. https://doi.org/10.1016/j.chemosphere.2015.05.042

    Article  CAS  PubMed  Google Scholar 

  67. 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

    Article  Google Scholar 

  68. Toropova AP, Toropov AA (2022) Sci Total Environ 823:153747. https://doi.org/10.1016/j.scitotenv.2022.153747

    Article  CAS  PubMed  Google Scholar 

  69. Toropova AP, Toropov AA (2021) Int J Environ Res 15(4):709–722. https://doi.org/10.1007/s41742-021-00346-w

    Article  CAS  Google Scholar 

  70. Toropov AA, Kjeldsen F, Toropova AP (2022) Chemosphere 303:135086. https://doi.org/10.1016/j.chemosphere.2022.135086

    Article  CAS  PubMed  Google Scholar 

  71. Weisgerber DW (1997) J Am Soc Inf Sci 48(4):349–360. https://doi.org/10.1002/(SICI)1097-4571(199704)48:4%3c349::AID-ASI8%3e3.0.CO;2-W

    Article  CAS  Google Scholar 

  72. O’Boyle NM (2012) J Cheminform 4(9):22. https://doi.org/10.1186/1758-2946-4-22

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Österberg T, Norinder U (2001) Eur J Pharm Sci 12(3):327–337. https://doi.org/10.1016/S0928-0987(00)00189-5

    Article  PubMed  Google Scholar 

  74. Toropova AP, Toropov AA (2019) J Mol Struct 1182:141–149. https://doi.org/10.1016/j.molstruc.2019.01.040

    Article  CAS  Google Scholar 

  75. Mukhopadhyay SK, Ahmad MO, Swamy MNS (2017) Biomed Signal Process Control 31:470–482. https://doi.org/10.1016/j.bspc.2016.09.021

    Article  Google Scholar 

  76. Toropov A, Toropova A (2004) J Mol Struct THEOCHEM 711(1–3):173–183. https://doi.org/10.1016/j.theochem.2004.10.003

    Article  CAS  Google Scholar 

  77. Toropova AP, Toropov AA, Benfenati E (2021) Struct Chem 32(3):967–971. https://doi.org/10.1007/s11224-021-01778-y

    Article  CAS  Google Scholar 

  78. Toropov AA, Rasulev BF, Leszczynski J (2008) Bioorg Med Chem 16(11):5999–6008. https://doi.org/10.1016/j.bmc.2008.04.055

    Article  CAS  PubMed  Google Scholar 

  79. Achary PGR (2014) SAR QSAR Environ Res 25(6):507–526. https://doi.org/10.1080/1062936X.2014.899267

    Article  CAS  PubMed  Google Scholar 

  80. Toropov AA, Toropova AP, Benfenati E, Leszczynska D, Leszczynski J (2010) Eur J Med Chem 45(4):1387–1394. https://doi.org/10.1016/j.ejmech.2009.12.037

    Article  CAS  PubMed  Google Scholar 

  81. Kumar P, Kumar A (2018) Drug Res 68(4):189–195. https://doi.org/10.1055/s-0043-119288

    Article  CAS  Google Scholar 

  82. Kumar P, Kumar A (2020) Chemometr Intell Lab Syst 200:103982. https://doi.org/10.1016/j.chemolab.2020.103982

    Article  CAS  Google Scholar 

  83. 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 

  84. 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 

  85. Ahmadi S (2020) Chemosphere 242:125192. https://doi.org/10.1016/j.chemosphere.2019.125192

    Article  CAS  PubMed  Google Scholar 

  86. Kumar P, Kumar A, Sindhu J, Lal S (2019) Drug Res 69(3):159–167. https://doi.org/10.1055/a-0652-5290

    Article  CAS  Google Scholar 

  87. Jain S, Amin SA, Adhikari N, Jha T, Gayen S (2020) J Biomol Struct Dyn 38(1):66–77. https://doi.org/10.1080/07391102.2019.1566093

    Article  CAS  PubMed  Google Scholar 

  88. Golubović M, Lazarević M, Zlatanović D, Krtinić D, Stoičkov V, Mladenović B, Milić DJ, Sokolović D, Veselinović AM (2018) Comput Biol Chem 75:32–38. https://doi.org/10.1016/j.compbiolchem.2018.04.009

    Article  CAS  PubMed  Google Scholar 

  89. Duhan M, Sindhu J, Kumar P, Devi M, Singh R, Kumar R, Lal S, Kumar A, Kumar S, Hussain K (2022) J Biomol Struct Dyn 40(11):4933–4953. https://doi.org/10.1080/07391102.2020.1863861

    Article  CAS  PubMed  Google Scholar 

  90. Toropov AA, Toropova AP (2020) Sci Total Environ 737:139720. https://doi.org/10.1016/j.scitotenv.2020.139720

    Article  CAS  PubMed  Google Scholar 

  91. Kumar P, Kumar A (2021) J Mol Struct 1246:131205. https://doi.org/10.1016/j.molstruc.2021.131205

    Article  CAS  Google Scholar 

  92. Kumar P, Kumar A, Singh D (2022) Environ Toxicol Pharm 93:103893. https://doi.org/10.1016/j.etap.2022.103893

    Article  CAS  Google Scholar 

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Toropov, A.A., Toropova, A.P. (2023). Application of SMILES to Cheminformatics and Generation of Optimum SMILES Descriptors Using CORAL Software. 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_3

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