Molecular dynamics simulations of cyclodextrin-cumene hydroperoxide complexes in water

Computational and Theoretical Chemistry

Volumn 1013, Issue , 2013, Pages 1-6

  Jiao, Aiquan ^a   Zhou, Xing ^a   Xu, Xueming ^a   Jin, Zhengyu ^a  

^a JIANGNAN UNIVERSITY   (China)

Author keywords

Cumene hydroperoxide; Cyclodextrins; Host guest supramolecular complexes; Molecular dynamics simulations

Indexed keywords

EID: 84875831471     PISSN: 2210271X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.comptc.2013.02.023     Document Type: Article

References (35)

1. Szejtli J. Introduction and general overview of cyclodextrin chemistry. Chem. Rev. 1998, 98:1743-1753.
2. Hapiot F., Tilloy S., Monflier E. Cyclodextrins as supramolecular hosts for organometallic complexes. Chem. Rev. 2007, 106:767-780.
3. van der Veen B.A., Uitdehaag J.C.M., Dijkstra B.W., Dijkhuizen L. Engineering of cyclodextrin glycosyltransferase reaction and product specificity. Biochim. Biophys. Acta 2000, 1543:336-360.
4. Breslow R., Chung S. Strong binding of ditopic substrates by a doubly linked occlusive C1 clamshell as distinguished from an aversive C2 loveseat cyclodextrin dimer. J. Am. Chem. Soc. 1990, 112:9659-9660.
5. Breslow R., Dong S.D. Biomimetic reactions catalyzed by cyclodextrins and their derivatives. Chem. Rev. 1998, 98:1997-2011.
6. Bhabak K.P., Mugesh G. Functional mimics of glutathione peroxidase: bioinspired synthetic antioxidants. Accounts Chem. Res. 2010, 43:1408-1419.
7. Luo G.M., Ren X.J., Liu J.Q., Mu Y., Shen J.C. Towards more efficient glutathione peroxidase mimics: substrate recognition and catalytic group assembly. Curr. Med. Chem. 2003, 10:1151-1183.
8. Ren X.J., Xue Y., Liu J.Q., Zhang K., Zheng J., Luo G., Guo C.H., Mu Y., Shen J.C. A novel cyclodextrin-derived tellurium compound with glutathione peroxidase activity. Chembiochem 2002, 3:356-363.
9. McNaughton M., Engman L., Birmingham A., Powis G., Cotgreave I.A. Cyclodextrin-derived diorganyl tellurides as glutathione peroxidase mimics and inhibitors of thioredoxin reductase and cancer cell growth. J. Med. Chem. 2004, 47:233-239.
10. Dong Z.Y., Huang X., Mao S.Z., Liang K., Liu J.Q., Luo G.M., Shen J.C. Cyclodextrin-derived mimic of glutathione peroxidase exhibiting enzymatic specificity and high catalytic efficiency. Chem. - Eur. J. 2006, 12:3575-3579.
11. Brocos P., Diaz-Vergara N., Banquy X., Perez-Casas S., Costas M., Pineiro A. Similarities and differences between cyclodextrin-sodium dodecyl sulfate host-guest complexes of different stoichiometries: molecular dynamics simulations at several temperatures. J. Phys. Chem. B 2010, 114:12455-12467.
12. Lv S.W., Zheng Q.C., Mu Y., Wang X.G., Ji Y.T., Luo G.M., Liu J.Q., Shen J.C. Evaluating substrate specificity of glutathione peroxidase mimic by molecular dynamics simulations and kinetics. J. Incl. Phenom. Macro. 2008, 60:139-144.
13. Lv S.W., Wang X.G., Mu Y., Zang T.Z., Ji Y.T., Liu J.Q., Shen J.C., Luo G.M. A novel dicyclodextrinyl diselenide compound with glutathione peroxidase activity. FEBS J. 2007, 274:3846-3854.
14. Dong Z.Y., Liang K., Wang C.Y., Huang X., Mao S., Li X.Z., Xu J.Q., Liu J.Q., Luo G.M., Shen J.C. A study of biomimetic system: exploration of factors modulating the catalytic capacity of glutathione peroxidase mimics. J. Mol. Catal. A - Chem. 2007, 277:193-201.
15. Dong Z.Y., Liu J.Q., Mao S.Z., Huang X., Luo G.M., Shen J.C. A glutathione peroxidase mimic 6,6'-ditellurobis (6-deoxy-beta-cyclodextrin) with high substrate specificity. J. Incl. Phenom. Macro. 2006, 56:179-182.
16. Ren X.J., Yang L.Q., Liu J.Q., Su D., You D.L., Liu C.P., Zhang K., Luo G.M., Mu Y., Yan G.L., Shen J.C. A novel glutathione peroxidase mimic with antioxidant activity. Arch. Biochem. Biophys. 2001, 387:250-256.
17. Hao Y., Wu Y., Liu J., Luo G., Yang G. 1H NMR Study on the Inclusion Complex of Glutathione with a Glutathione Peroxidase Mimic, 2,2'-ditelluro-bridged β-cyclodextrins. J. Incl. Phenom. Macro. 2006, 171-175.
18. Hao Y., Liu X., Liu J., Wu Y. Association mechanism of S-dinitrophenyl glutathione with two glutathione peroxidase mimics: 2, 2'-ditelluro- and 2, 2'-diseleno-bridged β-cyclodextrins. Molecules 2009, 904-916.
19. Lv S., Zheng Q., Mu Y., Wang X., Ji Y., Luo G., Liu J., Shen J. Evaluating substrate specificity of glutathione peroxidase mimic by molecular dynamics simulations and kinetics. J. Incl. Phenom. Macro. 2008, 139-144.
20. Lipkowitz K.B. Applications of computational chemistry to the study of cyclodextrins. Chem. Rev. 1998, 1829-1873.
21. Cai W.S., Wang T., Liu Y.Z., Liu P., Chipot C., Shao X.G. Free energy calculations for cyclodextrin inclusion complexes. Curr. Org. Chem. 2011, 15:839-847.
22. Lino A.C.S., Jaime C. Theoretical and experimental methods applied to development of new medicines. The arise of new era of drug delivery systems based upon cyclodextrins molecular structure. Adv. Comput. Methods Sci. Eng. 2005, 334-336. (Lecture Series on Computer and Computational Sciences 4 A).
23. Harata K. Structure of the cyclodextrin complex. I. Crystal and molecular structure of the α-cyclodextrin-p-iodoaniline complex. Bull. Chem. Soc. Jpn. 1975, 48:2409-2413.
24. Lindner K., Saenger W. Topography of cyclodextrin complexes. Part XVII. Crystal and molecular structure of cycloheptaamylose dodecahydrate. Carbohyd. Res. 1982, 99:103-115.
25. Harata K. The structure of the cyclodextrin complex. XX. Crystal structure of uncomplexed hydrated γ-cyclodextrin. Bull. Chem. Soc. Jpn. 1987, 60:2763-2767.
26. Sun Y., Mu Y., Ma S.M., Gong P.S., Yan G.L., Liu J.Q., Shen J.C., Luo G.M. The molecular mechanism of protecting cells against oxidative stress by 2-selenium-bridged beta-cyclodextrin with glutathione peroxidase activity. Bba-Mol. Cell Res. 2005, 1743:199-204.
27. Berendsen H.J.C., van der Spoel D., van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 1995, 91:43-56.
28. Lindahl E., Hess B., van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 2001, 7:306-317.
29. Schuler L.D., van Gunsteren W.F. On the choice of dihedral angle potential energy functions for n-alkanes. Mol. Simulat. 2000, 25:301-319.
30. Miyamoto S., Kollman P.A. Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. Rev. 1992, 13:952-962.
31. Hess B., Bekker H., Berendsen H.J.C., Fraaije J.G.E.M. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. Rev. 1997, 18:1463-1472.
32. Yu Y.M., Chipot C., Cai W.S., Shao X.G. Molecular dynamics study of the inclusion of cholesterol into cyclodextrins. J. Phys. Chem. B 2006, 110:6372-6378.
33. Rodriguez-Gomez D., Darve E., Pohorille A. Assessing the efficiency of free energy calculation methods. J. Chem. Phys. 2004, 120:3563-3578.
34. Shoup D., Szabo A. Role of diffusion in ligand binding to macromolecules and cell-bound receptors. Biophys. J. 1982, 40:33-39.
35. Rekharsky M.V., Inoue Y. Complexation thermodynamics of cyclodextrins. Chem. Rev. 1998, 98:1875-1917.