Structural dynamics and binding free energy of neral-cyclodextrins inclusion complexes: molecular dynamics simulation

References

• Leimann FV, Gonçalves OH, Machado RAF, et al. Antimicrobial activity of microencapsulated lemongrass essential oil and the effect of experimental parameters on microcapsules size and morphology. Mater Sci Eng C. 2009;29:430–436.10.1016/j.msec.2008.08.025
   Web of Science ®Google Scholar
• Nguefack J, Dongmo JBL, Dakole CD, et al. Food preservative potential of essential oils and fractions from Cymbopogon citratus, Ocimum gratissimum and Thymus vulgaris against mycotoxigenic fungi. Int J Food Microbiol. 2009;131:151–156.10.1016/j.ijfoodmicro.2009.02.009
   PubMed Web of Science ®Google Scholar
• Oyedele AO, Gbolade AA, Sosan MB, et al. Formulation of an effective mosquito-repellent topical product from Lemongrass oil. Phytomedicine. 2002;9:259–262.10.1078/0944-7113-00120
   PubMed Web of Science ®Google Scholar
• Ming CL, Figueiredo RO, Machado SR, et al. In yield of essential oil of and citral content in different parts of lemongrass leaves (cymbopogon citratus (D.C) stape) poaceae. Int Soc Hort Sci. 1996:555–559.
   Google Scholar
• Rauber CS, Guterres SS, Schapoval EES. LC determination of citral in Cymbopogon citratus volatile oil. J Pharm Biomed Anal. 2005;37:597–601.10.1016/j.jpba.2004.10.042
   PubMed Web of Science ®Google Scholar
• Maswal M, Dar AA. Formulation challenges in encapsulation and delivery of citral for improved food quality. Food Hydrocolloids. 2014;37:182–195.10.1016/j.foodhyd.2013.10.035
   Web of Science ®Google Scholar
• Onawunmi GO, Yisak WA, Ogunlana EO. Antibacterial constituents in the essential oil of Cymbopogon citratus (DC.) Stapf. J Ethnopharmacol. 1984;12:279–286.10.1016/0378-8741(84)90057-6
   PubMed Web of Science ®Google Scholar
• Kimura K, Nishimura H, Iwata I, et al. Deterioration mechanism of lemon flavor. 2. Formation mechanism of off-odor substances arising from citral. J Agric Food Chem. 1983;31:801–804.10.1021/jf00118a030
   Web of Science ®Google Scholar
• Ueno T, Masuda H, Ho CT. Formation Mechanism of p-Methylacetophenone from Citral via a tert-Alkoxy Radical Intermediate. J Agric Food Chem. 2004;52:5677–5684.10.1021/jf035517j
   PubMed Web of Science ®Google Scholar
• Liu XD, Furuta T, Yoshii H, et al. Cyclodextrin encapsulation to prevent the loss of l-menthol and its retention during drying. Biosci Biotechnol Biochem. 2000;64:1608–1613.10.1271/bbb.64.1608
   PubMed Web of Science ®Google Scholar
• Astray G, Gonzalez-Barreiro C, Mejuto JC, et al. A review on the use of cyclodextrins in foods. Food Hydrocolloids. 2009;23:1631–1640.10.1016/j.foodhyd.2009.01.001
   Web of Science ®Google Scholar
• Szente L, Szejtli J. Cyclodextrins as food ingredients. Trends Food Sci Technol. 2004;15:137–142.10.1016/j.tifs.2003.09.019
   Web of Science ®Google Scholar
• Li Z, Wang M, Wang F, et al. γ-Cyclodextrin: a review on enzymatic production and applications. Appl Microbiol Biotechnol. 2007;77:245–255.10.1007/s00253-007-1166-7
   PubMed Web of Science ®Google Scholar
• Del Valle EM. Cyclodextrins and their uses: a review. Process Biochem. 2004; 39:1033–1046.10.1016/S0032-9592(03)00258-9
   Web of Science ®Google Scholar
• Gidwani B, Vyas A. A comprehensive review on cyclodextrin-based carriers for delivery of chemotherapeutic cytotoxic anticancer drugs. BioMed Res Int. 2015;2015:198268.
   PubMed Web of Science ®Google Scholar
• Miranda JC, Martins TEA, Veiga F, et al. Cyclodextrins and ternary complexes: technology to improve solubility of poorly soluble drugs. Braz J Pharm Sci. 2011;47:665–681.10.1590/S1984-82502011000400003
   Web of Science ®Google Scholar
• Bekers O, Uijtendaal EV, Beijnen JH, et al. Cyclodextrins in the pharmaceutical field. Drug Dev Ind Pharm. 1991;17:1503–1549.10.3109/03639049109026630
   Web of Science ®Google Scholar
• Szejtli J. The properties and potential uses of cyclodextrin derivatives. J Inclusion Phenom Mol Recognit Chem. 1992;14:25–36.10.1007/BF01041363
   Web of Science ®Google Scholar
• Decock G, Landy D, Surpateanu G, et al. Study of the retention of aroma components by cyclodextrins by static headspace gas chromatography. J Incl Phenom Macrocycl Chem. 2008;62:297–302.10.1007/s10847-008-9471-z
   Web of Science ®Google Scholar
• Astray G, Mejuto JC, Morales J, et al. Factors controlling flavors binding constants to cyclodextrins and their applications in foods. Food Res Int. 2010;43:1212–1218.10.1016/j.foodres.2010.02.017
   Web of Science ®Google Scholar
• Liao P, Yang T, Chou J, et al. Anti-inflammatory activity of neral and geranial isolated from fruits of Litsea cubeba Lour. J Funct Foods. 2015;19:248–258.10.1016/j.jff.2015.09.034
   Web of Science ®Google Scholar
• Nutho B, Khuntawee W, Rungnim C, et al. Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes. Beilstein J Org Chem. 2014;10:2789–2799.10.3762/bjoc.10.296
   PubMed Web of Science ®Google Scholar
• Sangpheak W, Khuntawee W, Wolschann P, et al. Enhanced stability of a naringenin/2,6-dimethyl β-cyclodextrin inclusion complex: Molecular dynamics and free energy calculations based on MM- and QM-PBSA/GBSA. J Mol Graph Model. 2014;50:10–15.10.1016/j.jmgm.2014.03.001
   PubMed Web of Science ®Google Scholar
• Kicuntod J, Khuntawee W, Wolschann P, et al. Inclusion complexation of pinostrobin with various cyclodextrin derivatives. J Mol Graph Model. 2016;63:91–98.10.1016/j.jmgm.2015.11.005
   PubMed Web of Science ®Google Scholar
• Ikeda Y, Motoune S, Matsuoka T, et al. Inclusion complex formation of captopril with α‐ and β‐cyclodextrins in aqueous solution: NMR spectroscopic and molecular dynamic studies. J Pharm Sci. 2002;91:2390–2398.10.1002/jps.10232
   PubMed Web of Science ®Google Scholar
• Frisch MJ, Trucks,GW, Schlegel HB, et al. Gaussian 09. Wallingford (CT): Gaussian, Inc. 2009.
   Google Scholar
• Snor W, Liedl E, Weiss-Greiler P, et al. On the structure of anhydrous β-cyclodextrin. Chem Phys Lett. 2007;441:159–162.10.1016/j.cplett.2007.05.007
   Web of Science ®Google Scholar
• Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. J Comput Chem. 2010;31:455–461.
   PubMed Web of Science ®Google Scholar
• Morris GM, Huey R, Lindstrom W, et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30:2785–2791.10.1002/jcc.v30:16
   PubMed Web of Science ®Google Scholar
• Weiner SJ, Kollman PA, Nguyen DT, et al. An all atom force field for simulations of proteins and nucleic acids. J Comput Chem. 1986;7:230–252.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron. 1980;36:3219–3228.10.1016/0040-4020(80)80168-2
   Web of Science ®Google Scholar
• Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera–A visualization system for exploratory research and analysis. J Comput Chem. 2004;25:1605–1612.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Case DA, Darden TA, Cheatham TE, et al. AMBER 14 University of California, San Francisco. 2014.
   Google Scholar
• Chompoonut Rungnim C, Phunpee S, Kunaseth M, et al. Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex. Beilstein J Org Chem. 2015;11:2306–2317.10.3762/bjoc.11.251
   PubMed Web of Science ®Google Scholar
• Sangpheak W, Kicuntod J, Schuster R, et al. Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin. Beilstein J Org Chem. 2015;11:2763–2773.10.3762/bjoc.11.297
   PubMed Web of Science ®Google Scholar
• Phanich J, Rungrotmongkol T, Sindhikara D, et al. A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase. Protein Sci. 2016;25:147–158.10.1002/pro.2718
   PubMed Web of Science ®Google Scholar
• Kirschner KN, Yongye AB, Tschampel SM, et al. GLYCAM06: A generalizable biomolecular force field. Carbohydrates. J Comput Chem. 2008;29:622–655.10.1002/jcc.20820
   PubMed Web of Science ®Google Scholar
• Meeprasert A, Khuntawee W, Kamlungsua K, et al. Binding pattern of the long acting neuraminidase inhibitor laninamivir towards influenza A subtypes H5N1 and pandemic H1N1. J Mol Graph Model. 2012;38:148–154.10.1016/j.jmgm.2012.06.007
   PubMed Web of Science ®Google Scholar
• Meeprasert A, Hannongbua S, Rungrotmongkol T. Key binding and susceptibility of NS3/4A serine protease inhibitors against hepatitis C Virus. J Chem Inf Model. 2014;54:1208–1217.10.1021/ci400605a
   PubMed Web of Science ®Google Scholar
• Kaiyawet N, Rungrotmongkol T, Hannongbua S. Effect of halogen substitutions on dUMP to stability of thymidylate synthase/dUMP/mTHF ternary complex using molecular dynamics simulation. J Chem Inf Model. 2013;53:1315–1323.10.1021/ci400131y
   PubMed Web of Science ®Google Scholar
• Bayly CI, Cieplak P, Cornell W, et al. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem. 1993;97:10269–10280.10.1021/j100142a004
   Web of Science ®Google Scholar
• Wang J, Wolf RM, Caldwell JW, et al. Development and testing of a general amber force field. J Comput Chem. 2004;25:1157–1174.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Luty BA, van Gunsteren WF. Calculating electrostatic interactions using the particle−particle particle−mesh method with nonperiodic long-range interactions. J Phys Chem. 1996;100:2581–2587.10.1021/jp9518623
   Web of Science ®Google Scholar
• Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977;23:327–341.10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Berendsen HJC, Postma JPM, van Gunsteren WF, et al. Molecular dynamics with coupling to an external bath. J Chem Phys. 1984;81:3684–3690.10.1063/1.448118
   Web of Science ®Google Scholar
• Kollman PA, Massova I, Reyes C, et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res. 2000;33:889–897.10.1021/ar000033j
   PubMed Web of Science ®Google Scholar
• Rastelli G, Rio AD, Degliesposti G, et al. Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. J Comput Chem. 2010;31:797–810.
   PubMed Web of Science ®Google Scholar
• Ghatee MH, Sedghamiz T. Chiral recognition of Propranolol enantiomers by β-Cyclodextrin: quantum chemical calculation and molecular dynamics simulation studies. Chem Phys. 2014;445:5–13.10.1016/j.chemphys.2014.10.008
   Web of Science ®Google Scholar
• El-Barghouthia MI, Jaimeb C, Al-Sakhena NA, et al. Molecular dynamics simulations and MM–PBSA calculations of the cyclodextrin inclusion complexes with 1-alkanols, para-substituted phenols and substituted imidazoles. J Mol Struc-Theochem. 2008;853:45–52.10.1016/j.theochem.2007.12.005
   Web of Science ®Google Scholar
• Bounab MM, djameleddine K, Stephane H, et al. Molecular dynamics and quantum mechanics study of the [2-oxo-N-phenyl-3-oxazolidinesulfonamide@β-cyclodextrin] complex. J Mol Liq. 2016;222:777–782.10.1016/j.molliq.2016.07.121
   Web of Science ®Google Scholar