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Monatshefte für Chemie - Chemical Monthly

, Volume 142, Issue 9, pp 949–959 | Cite as

QSAR study on the interactions between antibiotic compounds and DNA by a hybrid genetic-based support vector machine

  • Xi Bin Zhou
  • Wen Jing Han
  • Jing Chen
  • Xiao Quan LuEmail author
Original Paper

Abstract

Studies on the interactions of antibiotic compounds with DNA can provide useful suggestions and guidance for the design of new and more efficient DNA-binding drugs. A quantitative structure–activity relationship (QSAR) study of the binding modes and binding affinities of the interactions between 30 antibiotic compounds and DNA was performed. A large number of descriptors that encode hydrophobic, topological, geometrical, and electronic properties were calculated to represent the structures of the antibiotic compounds. Aiming at a system with small, multidimensional samples, we utilized the genetic algorithm-support vector machine (GA-SVM) method to develop the QSAR, which can select an optimized feature subset and optimize SVM parameters simultaneously. A binary QSAR model for predicting binding mode and conventional QSAR models for predicting binding affinity were built based on the GA-SVM approach. The descriptors selected using GA-SVM represented the overall descriptor space and can account well for the binding nature of the considered dataset. The descriptors selected using the GA-SVM method were then used for developing conventional QSAR models by the artificial neural network (ANN) approach. A comparison between the conventional QSAR models using GA-SVM with those using ANN revealed that the former were much better. GA-SVM models can be useful for predicting binding modes and binding activities of the interactions of new antibiotic compounds with DNA.

Graphical abstract

Keywords

Antibiotic compound DNA Genetic algorithm-support vector machine Binary QSAR Regression 

Notes

Acknowledgments

This work was supported by the National Natural Science Foundation of China (Nos. 20945003, 21005063), and the Natural Science Foundation of Gansu (No. 096RJZA121).

References

  1. 1.
    Haq I (2002) Arch Biochem Biophys 403:1CrossRefGoogle Scholar
  2. 2.
    Wan KX, Shibue T, Gross ML (2000) J Am Chem Soc 122:300CrossRefGoogle Scholar
  3. 3.
    Chaires JB (2006) Arch Biochem Biophys 453:26CrossRefGoogle Scholar
  4. 4.
    Lerman LS (1961) J Mol Biol 3:18CrossRefGoogle Scholar
  5. 5.
    Waring M (1970) J Mol Biol 54:247CrossRefGoogle Scholar
  6. 6.
    Wartell RM, Larson JE, Wells RD (1974) J Biol Chem 249:6719Google Scholar
  7. 7.
    Kumar GS, He QY, Behr-Ventura D, Tomasz M (1995) Biochemistry 34:2662CrossRefGoogle Scholar
  8. 8.
    Qu XG, Chaires JB (2001) J Am Chem Soc 123:1CrossRefGoogle Scholar
  9. 9.
    Gopal M, Shenoy S (2003) J Photochem Photobiol B 72:69CrossRefGoogle Scholar
  10. 10.
    Ibrahim MS (2001) Anal Chim Acta 443:63CrossRefGoogle Scholar
  11. 11.
    Leng FF, Priebe W, Chaires JB (1998) Biochemistry 37:1743CrossRefGoogle Scholar
  12. 12.
    Wang SF, Peng TZ, Yang CF (2003) J Biochem Biophys Methods 55:191CrossRefGoogle Scholar
  13. 13.
    Wang J, Ozsoz M, Cai XH, Rivas G, Shiraishi H, Grant DH, Chicharro M, Fernandes J, Palecek E (1998) Bioelectrochem Bioenerg 45:33CrossRefGoogle Scholar
  14. 14.
    Agrawal P, Barthwal SK, Barthwal R (2009) Eur J Med Chem 44:1437CrossRefGoogle Scholar
  15. 15.
    Evstigneev MP, Mykhina VY, Davies DB (2005) Biophys Chem 118:118CrossRefGoogle Scholar
  16. 16.
    Barthwal R, Sharma U, Srivastava N, Jain M, Awasthi P, Kaur M, Barthwal SK, Govil G (2006) Eur J Med Chem 41:27CrossRefGoogle Scholar
  17. 17.
    Mallena S, Lee MPH, Bailly C, Neidle S, Kumar A, Boykin DW, Wilson WD (2004) J Am Chem Soc 126:13659CrossRefGoogle Scholar
  18. 18.
    Haj HTB, Salerno M, Priebe W, Kozlowski H, Garnier-Suillerot A (2003) Chem Biol Interact 145:349CrossRefGoogle Scholar
  19. 19.
    Miao Y, Lee MPH, Parkinson GN, Batista-Parra A, Ismail MA, Neidle S, Boykin DW, Wilson DW (2005) Biochemistry 44:14701CrossRefGoogle Scholar
  20. 20.
    Teulade-Fichou MP, Carrasco C, Guittat L, Bailly C, Alberti P, Mergny GL, David A, Lehn JM, Wilson WD (2003) J Am Chem Soc 125:4732CrossRefGoogle Scholar
  21. 21.
    Li VS, Choi D, Wang Z, Jimenez LS, Tang MS, Kohn H (1996) J Am Chem Soc 118:2326CrossRefGoogle Scholar
  22. 22.
    Guan Y, Shi R, Li XM, Zhao MP, Li YZ (2007) J Phys Chem B 111:7336CrossRefGoogle Scholar
  23. 23.
    Tian L, Wei WZ, Mao Y (2004) Clin Biochem 37:120CrossRefGoogle Scholar
  24. 24.
    Lu XQ, Wang L, Liu HD, Chen J (2007) Talanta 73:444CrossRefGoogle Scholar
  25. 25.
    Chen J, Lu XQ (2009) Talanta 79:129CrossRefGoogle Scholar
  26. 26.
    Ismail I, Francois P, Elodie D, Olivier B, Andre M (2007) Bioorg Med Chem 15:4256CrossRefGoogle Scholar
  27. 27.
    Menard PR, Lewis RA, Mason JS (1998) J Chem Inf Comput Sci 38:497Google Scholar
  28. 28.
    Menard PR, Mason JS, Morize I, Bauerschmidt S (1998) J Chem Inf Comput Sci 38:1204Google Scholar
  29. 29.
    Todeschini R, Consonni V (2000) Handbook of molecular descriptors. Wiley-VCH, WeinheimGoogle Scholar
  30. 30.
    Consonni C, Todeschini R, Pavan M (2002) J Chem Inf Comput Sci 42:682Google Scholar
  31. 31.
    Consonni V, Todeschini R, Pavan M, Gramatica P (2002) J Chem Inf Comput Sci 42:693Google Scholar
  32. 32.
    Kumar CV, Asuncion EH (1993) J Am Chem Soc 115:8541Google Scholar
  33. 33.
    Mazur S, Tanious FA, Ding D, Kumar A, Boykin DW, Simpson IJ, Neidle S, Wilson WD (2000) J Mol Biol 300:321CrossRefGoogle Scholar
  34. 34.
    Rahimian M, Kumar A, Say M, Bakunov SA, Boykin DW, Tidwell RR, Wilson WD (2009) Biochemistry 48:1573CrossRefGoogle Scholar
  35. 35.
    Banerjee D, Pal SK (2008) J Phys Chem B 112:1016CrossRefGoogle Scholar
  36. 36.
    Athri P, Wilson WD (2009) J Am Chem Soc 131:7618CrossRefGoogle Scholar
  37. 37.
    HyperChem Release 7, HyperCube Inc. (2002), http://www.hyper.com
  38. 38.
    Long W, Liu P, Li X, Xu Y, Yu J, Ma S, Yu L, Zou Z (2009) J Chemom 23:304CrossRefGoogle Scholar
  39. 39.
    Li ZR, Han LY, Xue Y, Yap CW, Li H, Jiang L, Chen YZ (2007) Biotechnol Bioeng 97:389CrossRefGoogle Scholar
  40. 40.
    Cortes C, Vapnik V (1995) Mach Learn 20:273Google Scholar
  41. 41.
    Wang WJ, Xu ZB, Lu WZ, Zhang XY (2003) Neurocomputing 55:643CrossRefGoogle Scholar
  42. 42.
  43. 43.
    Fang SF, Wang MP, Qi WH, Zheng F (2008) Comput Mater Sci 44:647CrossRefGoogle Scholar
  44. 44.
    Pai PF, Hong WC (2005) Electric Power Syst Res 74:417CrossRefGoogle Scholar
  45. 45.
    Pourbasheer E, Riahi S, Ganjali MR, Norouzi P (2009) Eur J Med Chem 44:5023CrossRefGoogle Scholar
  46. 46.
    Dolatabadi M, Nekoei M, Banaei A (2010) Monatsh Chem 141:577CrossRefGoogle Scholar
  47. 47.
    Goodarzi M, Freitas MP, Wu CH, Duchowicz PR (2010) Chemometr Intell Lab Syst 101:102CrossRefGoogle Scholar
  48. 48.
    Li ZC, Zhou XB, Lin YR, Zou XY (2008) Amino Acids 35:581CrossRefGoogle Scholar
  49. 49.
    Li TH, Mei H, Cong PS (1999) Chemometr Intell Lab Syst 45:177CrossRefGoogle Scholar
  50. 50.
    Habibi-Yangjeh A (2009) Monatsh Chem 140:523CrossRefGoogle Scholar
  51. 51.
    Corwin H, Rajeshwar PV (2009) Mol Pharmaceutics 6:3849Google Scholar
  52. 52.
    Eduardo BM, Marcia MCF (2009) Eur J Med Chem 44:3577CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Xi Bin Zhou
    • 1
  • Wen Jing Han
    • 1
  • Jing Chen
    • 1
  • Xiao Quan Lu
    • 1
    Email author
  1. 1.Key Laboratory of Bioelectrochemistry and Environmental Analysis of Gansu Province, College of Chemistry and Chemical EngineeringNorthwest Normal UniversityLanzhouChina

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