Simple graph-theoretical model for flavonoid binding to P-glycoprotein / Jednostavan graf-teorijski model vezivanja flavonoida za P-glikoprotein / Jednostavan graf-teorijski model vezivanja flavonoida za P-glikoprotein

Open access

Abstract

Three sets of flavonoid derivatives (N=32, 40, and 74) and logarithms of their dissociation constants (log Kd) that describe flavonoid affinity toward P-glycoprotein were modelled using six connectivity indices. The best results were obtained with the zero-order valence molecular connectivity index (0χv) for all three sets. Standard errors of the calibration models were around 0.3, and of the constants from the test sets even a little lower, 0.22 and 0.24. Despite using only one descriptor, our model proved better in internal (cross-validation) and especially in external (test set) statistics than much more demanding methods used in previous 3D QSAR modelling.

1. Formica JV, Regelson W. Review of the biology of quercetin and related bioflavonoids. Food Chem Toxicol 1995;33:1061-80. doi: 10.1016/0278-6915(95)00077-1

2. Scott BC, Butler J, Halliwell B, Aruoma OI. Evaluation of the antioxidant actions of ferulic acid and catechins. Free Radic Res Commun 1993;19:241-53. PMID: 7507456

3. Teixeira S, Siquet C, Alves C, Boal I, Marques MP, Borges F, Lima JLFC, Reis S, Structure-property studies on the antioxidant activity of flavonoids present in diet. Free Radic Biol Medic 2005;39:1099-108. doi: 10.1016/j.freeradbiomed. 2005.05.028

4. Cohen SD, Kennedy JA. Plant metabolism and the environment: Implications for managing phenolics. Crit Rev Food Sci Nutr 2010;50:620-43. doi: 10.1080/1040839 0802603441

5. Vinson JA. Flavonoids in foods as in vitro and in vivo antioxidants. Adv Exp Med Biol 1998;439:151-64. doi: 10.1007/978-1-4615-5335-9_11

6. Johnson J, de Mejia EG. Dietary factors and pancreatic cancer: The role of food bioactive compounds. Mol Nutr Food Res 2011;55:58-73. doi: 10.1002/mnfr.201000420

7. Perron NR, Brumaghin JL. A review of the antioxidant mechanisms of polyphenol Compounds related to iron binding. Cell Biochem Biophys 2009;53:75-100. doi: 10.1007/s12013-009-9043-x

8. Xiao J, Chen T, Cao H, Chen L, Yang F. Molecular propertyaffinity relationship of flavonoids and flavonoids for HSA in vitro. Mol Nutr Food Res 2011;55:310-7. doi: 10.1002/ mnfr.201000208

9. Shi J, Cao H. Molecular structure-affinity relationship of dietary flavonoids for bovine serum albumin. Rev Bras Farmacogn 2011;21:594-600. doi: 10.1590/S0102-695X 2011005000118

10. Xiao J, Cao H, Chen T, Yang F, Liu C, Xu X. Molecular property-binding affinity relationship of flavonoids for common rat plasma proteins in vitro. Biochemie 2011;93:134-40. doi: 10.1016/j.biochi.2010.08.013

11. Xiao J, Mao F, Yang F, Zhao Y, Zhang C, Yamamoto K. Interaction of dietary polyphenols with bovine milk proteins: Molecular structure-affinity relationship and influencing bioactivity aspects. Mol Nutr Food Res 2011;55:1637-45. doi: 10.1002/mnfr.201100280

12. Leveille-Webster CR, Arias IM. The biology of the P-glycoproteins. J Membr Biol 1995;143:89-102. doi: 10.1007/BF00234655

13. Simon SM, Schindler M. Cell biological mechanisms of multidrug resistance in tumors. Proc Natl Acad Sci USA 1994;91:3497-504. PMID: 7909602

14. Gottesman MM, Pastan I. Biochemistry of multidrug resistance mediated by the multidrug transporter. Annu Rev Biochem 1993;62:385-427. doi: 10.1146/annurev.bi.62. 070193.002125

15. Cordon-Cardo C, O’Brien JP, Boccia J, Casals D, Bertino JR, Melamed MR. Expression of the multidrug resistance gene product (P-glycoprotein) in human normal and tumor tissues. J Histochem Cytochem 1990;38:1277-87. PMID: 1974900

16. Li Y, Wang Y, Yang L, Zhang S, Liu C. Structural determinants of flavones interacting with the C-terminal nucleotidebinding domain as P-glycoprotein inhibitors. Internet Electron J Mol Des 2006;5:1-12.

17. Kothandan G, Gadhe CG, Madhaven T, Choi CH, Cho SJ. Docking and 3D-QSAR (quantitative structure activity relationship) studies of flavones, the potent inhibitors of p-glycoprotein targeting the nucleotide binding domain. Eur J Med Chem 2011;46:4078-88. doi: 10.1016/j.ejmech. 2011.06.008

18. Boccard J, Bajot F, Di Pietro A, Rudaz S, Boumendjel A, Nicolle E, Carrupt P-A. A 3D linear solvation energy model to quantify the affinity of flavonoid derivatives toward P-glycoprotein. Eur J Pharm Sci 2009;36:254-64. doi: 10.1016/j.ejps.2008.09.009

19. Raos N, Miličević A. Estimation of stability constants of coordination compounds using models based on topological indices. Arh Hig Rada Toksikol 2009;60:123-8. doi: 10.2478/10004-1254-60-2009-1923

20. Miličević A, Raos N. Prediction of stability constants for copper(II) binding to tetrapeptides containing histidyl residue with graph-theoretical method. Int J Chem Model 2014;6:301-9.

21. Miličević A, Raos N. Graph-theoretical modelling of stability constants of copper(II) complexes with tripeptides containing glycine, glutamic acid, and histidine. Bull Chem Soc Jpn 2015;88:490-5. doi: 10.1246/bcsj.20140358

22. Miličević A, Raos N. Modelling of copper(II) binding to pentapeptides related to atrial natriuretic factor using the 3χv connectivity index. Arh Hig Rada Toksikol 2015;66:165-70. doi: 10.1515/aiht-2015-66-2631

23. Kier LB, Hall LH. Molecular Connectivity in Chemistry and Drug Research. New York: Academic Press; 1976.

24. Hall LH, Kier LB. The relation of molecular connectivity to molecular volume and biological activity. Eur J Med Chem 1981;16:399-407.

25. Miličević A, Nikolić S, Trinajstić N. Toxicity of aliphatic ethers: A comparative study. Mol Diversity 2006;10:95-9. doi: 10.1007/s11030-005-9006-0

26. Medić-Šarić M, Maleš Ž, Šarić S, Brantner A. Quantitative modeling of flavonoid glycosides isolated from Paliurus spina-christi Mill. Croat Chem Acta 1996;69:1603-16.

27. Tetko IV, Gasteiger J, Todeschini R, Mauri A, Livingstone D, Ertl P, Palyulin VA, Radchenko EV, Zefirov NS, Makarenko AS, Tanchuk VY, Prokopenko VV. Virtual computational chemistry laboratory-design and description. J Comput Aided Mol Des 2005;19:453-63. doi: 10.1007/ s10822-005-8694-y

28. Virtual Computational Chemistry Laboratory [display 14 March 2016]. Available at http://www.vcclab.org

29. Enhanced NCI Database Browser 2.2 [displayed 14 March 2016]. Available at http://cactus.nci.nih.gov/ncidb2.2/

30. Kier LB, Hall LH. Molecular connectivity VII: Specific treatment to heteroatoms. J Pharm Sci 1976;65:1806-9. doi: 10.1002/jps.2600651228

31. Kier LB, Hall LH. Molecular Connectivity in Structure- Activity Analysis. New York: Willey; 1986.

32. Randić M. On history of the Randic index and emerging hostility toward chemical graph theory. MATCH Commun Math Comput Chem 2008;59:5-124.

33. Lučić B, Trinajstić N. Multivariate regression outperforms several robust architectures of neural networks in QSAR modeling. J Chem Inf Comput Sci 1999;39:121-32. doi: 10.1021/ci980090f

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