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4D-QSAR study of flavonoid derivatives with MCET method

Year 2017, Volume: 1 Issue: 1, 14 - 23, 19.10.2017
https://doi.org/10.32571/ijct.338920

Abstract

The Molecular Conformer Electron Topological (MCET) method was performed
for the identification of the pharmacophore (Pha) group and predicting
inhibitory activity of 42 flavonoid ligands on gamma-aminobutyric
acid/benzodiazepine receptor complex (GABAA/BZR). In this method, Electron
Topological Matrix (ETM) was used to visualize 3D structural descriptors.
Multiple comparisons of ETM matrices for all flavonoid compounds allow us to
define Pha-structure. Genetic algorithm (GA)- Partial
Least-Squares (
PLS) methods were performed to construct QSAR model and
to select most important descriptors of the training set (32 compounds) and
test set (10 compounds). The GA-PLS based model showed good results, q2 =
0.808 and r2test = 0.775 with high internal and external
validation. The developed model can help to understand the inhibitory
mechanism.

References

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  • 25. Karelson, M.; Lobanov, V.S.; Katritzky, A.R. Chem. Rev. 1996, 96, 1027-1044.
  • 26. Bersuker, I. B.; Dimoglo, A.S. In Reviews in Computational Chemistry, Lipkowitz, K. B.,Boyd, D.B., Eds.; VCH: New York,NY, U.S.A., 1991; Vol 2, pp 423-460.
  • 27. Bersuker, I.B.; Dimoglo, A.S.; Yu, M.; Gorbachov, P.; Vlad, F.; Pesaro, M. New J. Chem. 1991, 15, 307-320.
  • 28. Dimoglo, A.S.; Beda, A.A.; Shvets, N.M.; Gorvachov, M.Y.; Kheifits, L.A.; Aulchenko, I.S. New. J. Chem. 1995, 19, 149-154.
  • 29. Guzel, Y.; Saripinar, E.; Yildirim, I. J. Mol. Struct. 1997, 418, 83-91.
  • 30. Guzel, Y.; Ozturk, E. Bioorg. Med. Chem. 2003, 11, 4383-4388.
  • 31. Bersuker, I.B. J Comput. Aided Mol. Des. 2008, 22, 423–430.
  • 32. Bersuker, I.B.; Bahceci, S.; Boggs, E.J. The Electron Conformational Method of Identification of Pharmacophore and Anti-Pharmacophore Shielding. In Pharmacophore Perception. Development, and Use in Drug Design. Guner OF., Ed.; International University Line: La Jolla, 2000, 457-474.
  • 33. Bersuker, I.B.; Bahceci, S.; Boggs, E.J.; Pearlman, R.S. J. Comput. Aided Mol. Des. 1999, 13, 419-434.
  • 34. Bersuker, I.B.; Bahceci, S.; Boggs, E.J.; Pearlman, R.S. EnViron. Res. 1999, 10, 157-173.
Year 2017, Volume: 1 Issue: 1, 14 - 23, 19.10.2017
https://doi.org/10.32571/ijct.338920

Abstract

References

  • 1. Martens, S.; Mithöfer A. Phytochem. 2005, 66, 2399-2407.
  • 2. Harborne, J.B.; Williams C.A. Phytochem. 2000, 55, 481–504.
  • 3. Treutter, D. Environ. Chem. Lett. 2006, 4: 147–157.
  • 4. Medina, J.H.; Viola, H.; Wolfman, C.; Marder, M.; Wasowski, C.; Calvo, D. Paladini AC. Neurochem. Res. 1997, 22, 419-425.
  • 5. Marder, M.; Viola, H.; Wasowski, C.; Wolfman, C.; Waterman, P.G.; Cassels, B.K.; Medina, J.H.; Paladini, A.C. Biochem. Biophy. Res. Commun. 1996, 223, 384-389.
  • 6. Marder, M.; Zinczuk, J.; Colombo, M.I.; Wasowski, C.; Viola, H.; Wolfman, C.; Medina, J.H.; Ruveda, E.A.; Paladini, A.C. Bioorg. Med. Chem. Lett. 1997, 7, 2003-2008.
  • 7. Marder, M.; Viola, H.; Bacigaluppo, J.A.; Colombo, M.I.; Wasowski, C.; Wolfman, C.; Medina, J.H.; Ruveda, E.A.; Paladini, A.C. Biochem. Biophy. Res. Commun. 1998, 249, 481-485.
  • 8. Teuber, L.; Watjen, F.; Jensen, L.H. Curr. Pharm. Des. 1999, 5, 317- 343.
  • 9. Argyropoulos, S.V.; Nutt, D. Eur. Neuropsychopharharmacol. 1999, 6, 407-412.
  • 10. Tija, C.J.; Stephen, J.M.; Rachel, J. Nat. Rev. Neurosci. 2008, 9, 331-343.
  • 11. Amić, D.; Davidović-Amić, D.; Jurić, A.; Lučić, B.; Trinajstić, N. J. Chem. Inf. Comput. Sci. 1995, 35, 1034-1038.
  • 12. Costantino, L.; Rastelli, G.; Albasini, A. Eur. J. Med. Chem. 1996, 31, 693–699.
  • 13. Li, G.; Mian, Z.; Song, W.; Ai-Lin, L.; Guan-Hua, D. Bioorg. Med. Chem. Lett. 2011, 21, 5964-5970.
  • 14. Duchowicz, P.R.; Vitale, M.G.; Castro, E.A.; Autino, J.C.; Romanelli, G.P.; Bennardi, D.O. Eur. J. Med. Chem. 2008, 43, 1593-1602.
  • 15. Yilmaz, H.; Güzel, Y.; Önal, Z.; Altiparmak, G.; Özhan-Kocakaya, Ş. Bull. Korean Chem. Soc. 2012, 32, 4352-4360.
  • 16. Yilmaz, H.; Güzel, Y.; Boz, M.; Türkmenoğlu, B. Trop. J. Pharm. Res. 2014, 13,117-129.
  • 17. Hopfinger, A.J.; Wang, S.; Tokarski, J.S.; Jin, B.; Albuquerque, M.; Madhav, P.J.; Duraiswami, C. J Am Chem Soc. 1997, 119, 10509-10524.
  • 18. Hopfinger, A.J.; Reaka, A.; Venkatarangan, P.; Duca, J.S.; Wang, S. J. Chem Inf Comput Sci. 1999, 39: 1151-1160.
  • 19. Senese, C.L.; Duca, J.; Pan, D.; Hopfinger, A.J.; Tseng, Y.J. J. Chem. Inf. Comput. Sci. 2004, 44: 1526-1539.
  • 20. Huang, X.; Liu, T.; Gu, J.; Luo, X.; Ji, R.; Cao, Y.; Xue, H.; Wong, J.T.; Wong, B.L.; Pei, G.; Jiang, H.; Chen, K. J. Med. Chem. 2001, 44, 1883-1891.
  • 21. Bernardino, A.M.R.; Castro, H.C.; Frugulhetti, L.C. P.P.; Loureiro, N.I.V.; Azevedo, A.R.; Pinheiro, L.C.S.; Souza, T.M.L.; Giongo, V.; Passamani, F.; Magalhaes, U.O.; Albuquerque, M.G.; Cabral, L.M.; Rodrigues, C.R. Bioorg. Med. Chem. 2008, 16, 8670-8675.
  • 22. Bernardino, A.M.R.; Pinheiro, L.C.S.; Rodrigues, C.R.; Loureiro, N.I.V.; Castro, H.C.; Lanfredi-Rangel, A.; Sabatini-Lopes, J.; Borges, J.C.; Carvalho, J.M.; Romeiro, G.A.; Ferreira, V.F.; Frugulhetti, I.C.P.P.; Vannier-Santos, M.A. Bioorg. Med. Chem. 2006, 14, 5765-5770.
  • 23. Bharatam, P.V. Modeling and Informatics in Drug Design. Precilinical Development Handbook. 2008, 1-47.
  • 24. Hopfinger, A.J.; Wang, S.; Tokarski, J.S.; Jin, B.; Albuquerque, M.; Madhav, P.J.; Duraiswami, C. J. Am. Chem. Soc. 1997, 119, 10509-10524.
  • 25. Karelson, M.; Lobanov, V.S.; Katritzky, A.R. Chem. Rev. 1996, 96, 1027-1044.
  • 26. Bersuker, I. B.; Dimoglo, A.S. In Reviews in Computational Chemistry, Lipkowitz, K. B.,Boyd, D.B., Eds.; VCH: New York,NY, U.S.A., 1991; Vol 2, pp 423-460.
  • 27. Bersuker, I.B.; Dimoglo, A.S.; Yu, M.; Gorbachov, P.; Vlad, F.; Pesaro, M. New J. Chem. 1991, 15, 307-320.
  • 28. Dimoglo, A.S.; Beda, A.A.; Shvets, N.M.; Gorvachov, M.Y.; Kheifits, L.A.; Aulchenko, I.S. New. J. Chem. 1995, 19, 149-154.
  • 29. Guzel, Y.; Saripinar, E.; Yildirim, I. J. Mol. Struct. 1997, 418, 83-91.
  • 30. Guzel, Y.; Ozturk, E. Bioorg. Med. Chem. 2003, 11, 4383-4388.
  • 31. Bersuker, I.B. J Comput. Aided Mol. Des. 2008, 22, 423–430.
  • 32. Bersuker, I.B.; Bahceci, S.; Boggs, E.J. The Electron Conformational Method of Identification of Pharmacophore and Anti-Pharmacophore Shielding. In Pharmacophore Perception. Development, and Use in Drug Design. Guner OF., Ed.; International University Line: La Jolla, 2000, 457-474.
  • 33. Bersuker, I.B.; Bahceci, S.; Boggs, E.J.; Pearlman, R.S. J. Comput. Aided Mol. Des. 1999, 13, 419-434.
  • 34. Bersuker, I.B.; Bahceci, S.; Boggs, E.J.; Pearlman, R.S. EnViron. Res. 1999, 10, 157-173.
There are 34 citations in total.

Details

Subjects Chemical Engineering
Journal Section Research Articles
Authors

Burçin Türkmenoğlu 0000-0002-5770-0847

Hayriye Yilmaz This is me 0000-0001-9305-8364

Ekrem Mesut Su This is me 0000-0002-4519-9143

Tuğba Alp Tokat 0000-0003-2713-7093

Yahya Güzel 0000-0002-4698-1866

Publication Date October 19, 2017
Published in Issue Year 2017 Volume: 1 Issue: 1

Cite

APA Türkmenoğlu, B., Yilmaz, H., Su, E. M., Alp Tokat, T., et al. (2017). 4D-QSAR study of flavonoid derivatives with MCET method. International Journal of Chemistry and Technology, 1(1), 14-23. https://doi.org/10.32571/ijct.338920
AMA Türkmenoğlu B, Yilmaz H, Su EM, Alp Tokat T, Güzel Y. 4D-QSAR study of flavonoid derivatives with MCET method. Int. J. Chem. Technol. December 2017;1(1):14-23. doi:10.32571/ijct.338920
Chicago Türkmenoğlu, Burçin, Hayriye Yilmaz, Ekrem Mesut Su, Tuğba Alp Tokat, and Yahya Güzel. “4D-QSAR Study of Flavonoid Derivatives With MCET Method”. International Journal of Chemistry and Technology 1, no. 1 (December 2017): 14-23. https://doi.org/10.32571/ijct.338920.
EndNote Türkmenoğlu B, Yilmaz H, Su EM, Alp Tokat T, Güzel Y (December 1, 2017) 4D-QSAR study of flavonoid derivatives with MCET method. International Journal of Chemistry and Technology 1 1 14–23.
IEEE B. Türkmenoğlu, H. Yilmaz, E. M. Su, T. Alp Tokat, and Y. Güzel, “4D-QSAR study of flavonoid derivatives with MCET method”, Int. J. Chem. Technol., vol. 1, no. 1, pp. 14–23, 2017, doi: 10.32571/ijct.338920.
ISNAD Türkmenoğlu, Burçin et al. “4D-QSAR Study of Flavonoid Derivatives With MCET Method”. International Journal of Chemistry and Technology 1/1 (December 2017), 14-23. https://doi.org/10.32571/ijct.338920.
JAMA Türkmenoğlu B, Yilmaz H, Su EM, Alp Tokat T, Güzel Y. 4D-QSAR study of flavonoid derivatives with MCET method. Int. J. Chem. Technol. 2017;1:14–23.
MLA Türkmenoğlu, Burçin et al. “4D-QSAR Study of Flavonoid Derivatives With MCET Method”. International Journal of Chemistry and Technology, vol. 1, no. 1, 2017, pp. 14-23, doi:10.32571/ijct.338920.
Vancouver Türkmenoğlu B, Yilmaz H, Su EM, Alp Tokat T, Güzel Y. 4D-QSAR study of flavonoid derivatives with MCET method. Int. J. Chem. Technol. 2017;1(1):14-23.