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QSAR study of the DPPH· radical scavenging activity of coumarin derivatives and xanthine oxidase inhibition by molecular docking

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Central European Journal of Chemistry

Abstract

A Quantitative Structure-Activity Relationship (QSAR) of coumarins by genetic algorithms employing physicochemical, topological, lipophilic and electronic descriptors was performed. We have used experimental antioxidant activities of specific coumarin derivatives against the DPPH· radical molecule. Molecular descriptors such as Randic Path/Walk, hydrophilic factor and chemical hardness were selected to propose a mathematical model. We obtained a linear correlation with R2 = 96.65 and Q 2 LOO = 93.14 values. The evaluation of the predictive ability of the model was performed by applying the Q 2 ASYM , \(\hat r^2 \) and Δr 2 m methods. Fukui functions were calculated here for coumarin derivatives in order to delve into the mechanics by which they work as primary antioxidants. We also investigated xanthine oxidase inhibition with these coumarins by molecular docking. Our results show that hydrophobic, electrostatic and hydrogen bond interactions are crucial in the inhibition of xanthine oxidase by coumarins.

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References

  1. I. Kostova, Curr. Med. Chem. 5, 29 (2005)

    CAS  Google Scholar 

  2. D. Berg, M.B.H. Youdim, P. Riederer, Cell Tissue Res. 318, 201 (2004)

    Article  Google Scholar 

  3. M. Garazd, O. Muzychka, A. Vovk, I. Nagorichna, A. Ogorodniichuk, Chem. Nat. Compd. 43, 19 (2007)

    Article  CAS  Google Scholar 

  4. A. Kotali, I. Lafazanis, P. Harris, Synthetic Communications 38, 3996 (2008)

    Article  CAS  Google Scholar 

  5. M. Traykova, I. Kostova, Int. J. Pharm. 1, 29 (2005)

    Article  CAS  Google Scholar 

  6. J.Z. Pedersen, C. Oliveira, S. Incerpi, V. Kumar, A.M. Fiore, P.D Vito, A.K. Prasad, S.V. Malhotra, V.S. Parmar, L. Saso, J. Pharm. Pharmacol. 59, 1721 (2007)

    Article  CAS  Google Scholar 

  7. K.C. Fylaktakidou, D.J. Hadjipavlou-Litina, K.E. Litinas, D.N. Nicolaides, Curr. Pharm. Design 10, 3813 (2004)

    Article  CAS  Google Scholar 

  8. A.A.H Kadhum, A.A. Al-Amiery, A.Y. Musa, A.B. Mohamad, Int. J. Mol. Sci. 12, 5747 (2011)

    Article  CAS  Google Scholar 

  9. J.D. Lambeth, Nat. Rev. Immun. 4, 181 (2004)

    Article  CAS  Google Scholar 

  10. T. Inoguchi, T. Sonta, H. Tsubouchi, T. Etoh, M. Kakimoto, N. Sonoda, N. Sato, N. Sekiguchi, K. Kobayashi, H. Sumimoto, H. Utsumi, H. Nawata, J. Am. Soc. Nephro. 14, S227 (2003)

    Article  CAS  Google Scholar 

  11. J.S. McNally, M.E. Davis, D.P. Giddens, A. Saha, J. Hwang, S. Dikalov, H. Jo, D.G. Harrison, Am. J. Physio I. 285, H2290 (2003)

    CAS  Google Scholar 

  12. Y.C. Chang, F.W. Lee, C.S. Chen, S.T. Huang, S.H. Tsai, S.H. Huang, C.M. Lin, FRBM 43, 1541 (2007)

    Article  CAS  Google Scholar 

  13. Jr. Merz, M. Kenneth, D. Ringe, C.H. Reynolds, Drug Design: Structure- and Ligand-Based Approaches (Cambridge University Press, New York, 2010)

    Book  Google Scholar 

  14. R. Benigni, C. Bossa, J. Chem. Inf. Model 48, 971 (2008)

    Article  CAS  Google Scholar 

  15. F.A. Pasha, S.J. Cho, Y. Beg, Y.B. Tripathi, Med. Chem. Res. 16, 408 (2007)

    Article  CAS  Google Scholar 

  16. Y. Xue, Y. Zheng, L. An, L. Zhang, Y. Qian, D. Yu, X. Gong, Y. Liu, Comp. Theor. Chem. 982, 74 (2012)

    Article  CAS  Google Scholar 

  17. R.G. Parr, W.T. Yang, J. Am. Chem. Soc. 106(14), 4049 (1984)

    Article  CAS  Google Scholar 

  18. P. Fuentealba, E. Florez, W. Tiznado, J. Chem. Theor. Comp. 6, 1470 (2010)

    Article  CAS  Google Scholar 

  19. C. Cardenas, W. Tiznado, P.W. Ayers, P. Fuentealba, J. Phys. Chem. A 115, 2325 (2011)

    Article  CAS  Google Scholar 

  20. P. Geerlings, F.D. Proft, W. Langenaeker, Chem. Rev. 103, 1793 (2003)

    Article  CAS  Google Scholar 

  21. P.W. Ayers, J. Math. Chem. 43, 285 (2008)

    Article  CAS  Google Scholar 

  22. J.P. Perdew, R.G. Parr, M. Levy, J.L.J. Balduz, Phys. Rev. Lett. 49, 1691 (1982)

    Article  CAS  Google Scholar 

  23. P.W. Ayers, M. Levy, Theor. Chem. Acc. 103, 353 (2000)

    Article  CAS  Google Scholar 

  24. P.W. Ayers, W.T. Yang, L.J. Bartolotti, P.K. Chattaraj, Fukui function chemical reactivity theory: A density functional. Boca Raton: CRC Press, 255 (2009)

    Google Scholar 

  25. W. Kohn, L.J. Sham, Phys. Rev. 140, A1133 (1965)

    Article  Google Scholar 

  26. P. Hohenberg, W. Kohn, Phys. Rev. 136, B864 (1964)

    Article  Google Scholar 

  27. R.G. Parr, W. Yang, Density functional theory of atoms and molecules (Oxford University Press, New York, 1989)

    Google Scholar 

  28. W. Yang, R.G. Parr, R. Pucci, J. Chem. Phys. 81, 2862 (1984)

    Article  CAS  Google Scholar 

  29. A. Michalak, F. De Proft, P. Geerlings, R.F. Nalewajski, J. Phys. Chem. A 103(6), 762 (1999)

    Article  CAS  Google Scholar 

  30. R. Balawender, P. Geerlings, J. Chem. Phys. 123(12), 124103 (2005)

    Article  Google Scholar 

  31. R. Flores-Moreno, A.M. Köster, J. Chem. Phys. 128(13), 134105 (2008)

    Article  Google Scholar 

  32. R. Flores-Moreno, J. Melin, J.V. Ortiz, G. Merino, J. Chem. Phys. 129(22), 224105 (2008)

    Article  Google Scholar 

  33. R. Flores-Moreno, J. Chem. Theor. Comp. 6(1), 48 (2010)

    Article  CAS  Google Scholar 

  34. W. Yang, A.J. Cohen, F. De Proft, P. Geerlings, J. Chem. Phys. 136(14), 144110 (2012)

    Article  Google Scholar 

  35. H.C. Lin, S.H. Tsai, C.S. Chen, Y.C. Chang, C.M. Lee, Z.Y. Lai, C.M. Lin, Biochem. Pharm. 75, 1416 (2008)

    Article  CAS  Google Scholar 

  36. F.J. Martinez-Martinez, R.S. Razo-Hernandez, A.L. Peraza-Campos, M. Villanueva-Garcia, M.T. Sumaya-Martinez, D. Jaramillo-Cano, Z. Gomez-Sandoval, Molecules 17, 14882 (2012)

    Article  CAS  Google Scholar 

  37. J.J.P. Stewart, J. Comput. Chem. 10, 209 (1989)

    Article  CAS  Google Scholar 

  38. W.J. Hehre, Guide to Molecular Mechanics and Quantum Chemical Calculations, (Wavefunction Inc. Irvine, California, 2003)

    Google Scholar 

  39. A.D. Becke, J. Chem. Phys. 98, 5648 (1993)

    Article  CAS  Google Scholar 

  40. G.A. Petersson, M.A. Al-Laham, J. Chem. Phys. 94, 6081 (1991)

    Article  CAS  Google Scholar 

  41. Gaussian 09, Revision A.1, M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.A. Montgomery, Jr., J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, D.J. Fox (Gaussian, Inc., Wallingford CT, 2009)

  42. F.A. Pasha, S.J. Cho, Y. Beg, Y.B. Tripathi, Med. Chem. Res. 408 (2007)

    Google Scholar 

  43. R. Todeschini, M. Vighi, A. Finizio and P. Gramatica, SAR QSAR Envir. Res. 7(1–4) 173 (1997)

    Article  CAS  Google Scholar 

  44. R.G. Parr, W. Yang, Chemical potential derivatives. Density-Functional Theory of Atoms and Molecules (Oxford University Press, New York, 1989) 87–95

    Google Scholar 

  45. P.K. Chattaraj, D.R. Roy, Chem. Rev. 107(9), PR46 (2007)

    Article  CAS  Google Scholar 

  46. A. Sakar, T.R. Middya, A.D. Jana, J. Mol. Model 18, 2621 (2012)

    Article  Google Scholar 

  47. M. Randic, J. Chem. Inf. Model 41, 607 (2001)

    Article  CAS  Google Scholar 

  48. A.K. Ghose, V.N. Viswanadhan, J.J. Wendoloski, J. Phys. Chem. A 102, 3762 (1998)

    Article  CAS  Google Scholar 

  49. A.K. Ghose, G.M. Crippen, J. Chem. Infor. Comp. Sci. 27, 21 (1987)

    Article  CAS  Google Scholar 

  50. DRAGON for Windows, Version 5.4. (TALETE srl, Milano, Italy, 2006)

    Google Scholar 

  51. R. Thomsen, M.H. Christensen, J. Med. Chem. 49, 3315 (2006)

    Article  CAS  Google Scholar 

  52. A.M. Köster, G. Geudtner, P. Calaminici, M.E. Casida, V.D. Dominguez, R. Flores-Moreno, G.U. Gamboa, A. Goursot, T. Heine, A. Ipatov, F. Janetzko, J.M. del Campo, J.U. Reveles, A. Vela, B. Zuñiga-Gutierrez, D.R. Salahub, deMon2k version 3. [Online] Cinvestav, (2011), http://www.demon-software.com

  53. P.A.M. Dirac, P. Roy, Soc. London A 117, 610 (1928)

    Article  Google Scholar 

  54. S.H. Vosko, L. Wilk, M. Nusair, Can. J. Phys. 58, 1200 (1980)

    Article  CAS  Google Scholar 

  55. N. Godbout, D.R. Salahub, J. Andzelm, E. Wimmer, Can. J. Phys. 70, 560 (1992)

    CAS  Google Scholar 

  56. J. Andzelm, E. Radzio, D.R. Salahub, J. Comput. Chem. 6, 520 (1985)

    Article  CAS  Google Scholar 

  57. J. Andzelm, N. Russo, D.R. Salahub, J. Chem. Phys. 87, 6562 (1987)

    Article  CAS  Google Scholar 

  58. R. Flores-Moreno, K. Pineda-Urbina, Z. Gomez-Sandoval, Sinapsis Version XII-V. Sinapsis developers. [Online] http://sinapsis.sourceforge.net.

  59. R. Leardi, in: R. Todeschini, V. Consonni, A. Mauri, M. Pavan (Eds.), MobyDigs: software for regression and classification models by genetic algorithms. Nature-inspired Methods in Chemometrics: Genetic Algorithms and Artificial Neural Networks (Elsevier, Amsterdam, 2003) 141–167

  60. R. Todeschini, D. Ballabio, V. Consonni, A. Mauri, M. Pavan, MobyDigs-Version 1.0. s.l: TALETE srl, (2004)

    Google Scholar 

  61. I.E. Frank, R. Todeschini, The Data Analysis Handbook (Elsevier, Amsterdam, Netherlands, 1994)

    Google Scholar 

  62. R. Todeschini, V. Consonni, A. Maiocchi, Chemometrics Intell. Lab. Sys. 46(1), 13 (1999)

    Article  CAS  Google Scholar 

  63. R. Todeschini, Anal. Chim. Acta 348, 419 (1997)

    Article  CAS  Google Scholar 

  64. R. Todeschini, V. Consonni, A. Mauri, M. Pavan, Anal. Chim. Acta 515, 199 (2004)

    Article  CAS  Google Scholar 

  65. G. Cruciani, M. Baroni, S. Clementi, G. Costantino, D. Riganelli, B. Skagerberg, J. Chemometr. 6, 347 (1992).

    Article  Google Scholar 

  66. U. Wählby, E.N. Jonsson, M.O. Karlsson, J. Am. Assoc. Pharm. Sci. 4, 68 (2002)

    Google Scholar 

  67. P. K. Ojha, I. Mitra, R.N. Das, K. Roy, Chemometrics Intell. Lab. Sys. 107(1), 194 (2011)

    Article  CAS  Google Scholar 

  68. K. Roy, I. Mitra, S. Kar, P.K. Ojha, R.N. Das, H. Kabir, J. Chem. Inf. Model. 52(2), 396 (2012)

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Faculty of Chemical Sciences, University of Colima, Mexico, C.P. 28400, Mexico

    Rodrigo S. Razo-Hernández, Kayim Pineda-Urbina, Marlene A. Velazco-Medel, Francisco J. Martínez-Martínez & Zeferino Gómez-Sandoval

  2. Association of Retired at the University of Guanajuato, Guanajuato, Gto., Mexico, C.P. 36000, Mexico

    Manuel Villanueva-García

  3. Research and Graduate Studies, Autonomous University of Nayarit, City of Culture “Amado Nervo”, Tepic, Nayarit, CP 63190, Mexico

    M. Teresa Sumaya-Martínez

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  1. Rodrigo S. Razo-Hernández
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  2. Kayim Pineda-Urbina
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  3. Marlene A. Velazco-Medel
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  6. Francisco J. Martínez-Martínez
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  7. Zeferino Gómez-Sandoval
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Correspondence to Zeferino Gómez-Sandoval.

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Razo-Hernández, R.S., Pineda-Urbina, K., Velazco-Medel, M.A. et al. QSAR study of the DPPH· radical scavenging activity of coumarin derivatives and xanthine oxidase inhibition by molecular docking. cent.eur.j.chem. 12, 1067–1080 (2014). https://doi.org/10.2478/s11532-014-0555-x

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