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Volumn 39, Issue 6, 2013, Pages 442-452

Inclusion complexes of β-cyclodextrine with organic ligands: Molecular dynamics simulation of the thermodynamic stability in gas phase and in water solution

Author keywords

binding affinity; cyclodextrine; inclusion complexes; molecular dynamics

Indexed keywords

BINDING AFFINITIES; BINDING FREE ENERGY; CYCLODEXTRINES; EQUILIBRIUM BINDING CONSTANT; EXPERIMENTAL DATUM; INCLUSION COMPLEX; MOLECULAR DYNAMICS SIMULATIONS; THERMODYNAMIC INTEGRATION;

EID: 84876282674     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927022.2012.740636     Document Type: Article
Times cited : (6)

References (58)
  • 2
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: A critical review
    • M.K. Gilson, J.A. Given, B.L. Bush, and J.A. McCammon, The statistical-thermodynamic basis for computation of binding affinities: A critical review, Biophys. J. 72 (1997), pp. 1047-1069.
    • (1997) Biophys. J. , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 3
    • 65249124122 scopus 로고    scopus 로고
    • Computations of standard binding free energies with molecular dynamics simulations
    • Y. Deng and B. Roux, Computations of standard binding free energies with molecular dynamics simulations, J. Phys. Chem. B 113 (2009), pp. 2234-2246.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 2234-2246
    • Deng, Y.1    Roux, B.2
  • 4
    • 5644287368 scopus 로고    scopus 로고
    • Free energy, entropy, and induced fit in host-guest recognition: Calculations with the second-generation mining minima algorithm
    • C.-E. Chang and M.K. Gilson, Free energy, entropy, and induced fit in host-guest recognition: Calculations with the second-generation mining minima algorithm, J. Am. Chem. Soc. 126 (2004), pp. 13156-13164.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 13156-13164
    • Chang, C.-E.1    Gilson, M.K.2
  • 5
    • 18744411546 scopus 로고    scopus 로고
    • Free energies of ligand binding for structurally diverse compounds
    • O. Oostenbrink and W. van Gunsteren, Free energies of ligand binding for structurally diverse compounds, Proc. Natl. Acad. Sci. USA 102 (2005), p. 6750.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 6750
    • Oostenbrink, O.1    Van Gunsteren, W.2
  • 6
    • 34249021392 scopus 로고    scopus 로고
    • Linear interaction energy (LIE) models for ligand binding in implicit solvent: Theory and application to the binding of NNRTIs to HIV-1 reverse transcriptase
    • Y. Su, E. Gallicchio, K. Das, E. Arnold, and R.M. Levy, Linear interaction energy (LIE) models for ligand binding in implicit solvent: Theory and application to the binding of NNRTIs to HIV-1 reverse transcriptase, J. Chem. Theor. Comput. 3 (2009), pp. 256-277.
    • (2009) J. Chem. Theor. Comput. , vol.3 , pp. 256-277
    • Su, Y.1    Gallicchio, E.2    Das, K.3    Arnold, E.4    Levy, R.M.5
  • 7
    • 33751344549 scopus 로고    scopus 로고
    • Calculations of solute and solvent entropies from molecular dynamics simulations
    • J. Carlsson and J. Aqvist, Calculations of solute and solvent entropies from molecular dynamics simulations, Phys. Chem. Chem. Phys. 8 (2006), p. 5385.
    • (2006) Phys. Chem. Chem. Phys. , vol.8 , pp. 5385
    • Carlsson, J.1    Aqvist, J.2
  • 9
    • 4243778369 scopus 로고    scopus 로고
    • Complexation thermodynamics of cyclodextrins
    • M.V. Rekharsky and Y. Inoue, Complexation thermodynamics of cyclodextrins, Chem. Rev. 98 (1998), pp. 1875-1917.
    • (1998) Chem. Rev. , vol.98 , pp. 1875-1917
    • Rekharsky, M.V.1    Inoue, Y.2
  • 10
    • 0029757992 scopus 로고    scopus 로고
    • Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: A molecular dynamics free energy perturbation study
    • B. Roux, M. Nina, R. Pomes, and J.C. Smith, Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: A molecular dynamics free energy perturbation study, Biophys. J. 71 (1996), pp. 670-681.
    • (1996) Biophys. J. , vol.71 , pp. 670-681
    • Roux, B.1    Nina, M.2    Pomes, R.3    Smith, J.C.4
  • 15
    • 0000795938 scopus 로고
    • Free energies of hydration and pure liquid properties of hydrocarbonsfrom the OPLS all-atom model
    • G. Kaminski, E.M. Duffy, T. Matsui, and W.L. Jorgensen, Free energies of hydration and pure liquid properties of hydrocarbonsfrom the OPLS all-atom model, J. Phys. Chem. 98 (1994), pp. 13077-13082.
    • (1994) J. Phys. Chem. , vol.98 , pp. 13077-13082
    • Kaminski, G.1    Duffy, E.M.2    Matsui, T.3    Jorgensen, W.L.4
  • 18
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular dynamics simulations
    • I. Tironi, R. Sperb, P. Smith, and W. van Gunsteren, A generalized reaction field method for molecular dynamics simulations, J. Chem. Phys. 102 (1995), p. 5451.
    • (1995) J. Chem. Phys. , vol.102 , pp. 5451
    • Tironi, I.1    Sperb, R.2    Smith, P.3    Van Gunsteren, W.4
  • 19
    • 84961980477 scopus 로고    scopus 로고
    • Quantum mechanical continuum solvation models
    • J. Tomasi, B. Mennucci, and R. Cammi, Quantum mechanical continuum solvation models, Chem. Rev. 105 (2005), p. 2999.
    • (2005) Chem. Rev. , vol.105 , pp. 2999
    • Tomasi, J.1    Mennucci, B.2    Cammi, R.3
  • 20
    • 0242321249 scopus 로고    scopus 로고
    • Computations of solvation free energies for polyatomic ions in water in terms of a combined molecular-continuum approach
    • M. Vener, I. Leontyev, and M. Basilevsky, Computations of solvation free energies for polyatomic ions in water in terms of a combined molecular-continuum approach, J. Chem. Phys. 119 (2003), p. 8038.
    • (2003) J. Chem. Phys. , vol.119 , pp. 8038
    • Vener, M.1    Leontyev, I.2    Basilevsky, M.3
  • 21
    • 0032233055 scopus 로고    scopus 로고
    • Computer simulations with explicit solvent: Recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects
    • R.M. Levy and E. Gallicchio, Computer simulations with explicit solvent: Recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects, Annu. Rev. Phys. Chem. 49 (1998), pp. 531-567.
    • (1998) Annu. Rev. Phys. Chem. , vol.49 , pp. 531-567
    • Levy, R.M.1    Gallicchio, E.2
  • 24
    • 7044260905 scopus 로고    scopus 로고
    • Free energies of hydration from a generalized born model and an allatom force field
    • W.L. Jorgensen, J.P. Ulmschneider, and J. Tirado-Rives, Free energies of hydration from a generalized born model and an allatom force field, J. Phys. Chem. B 108 (2004), pp. 16264-16270.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 16264-16270
    • Jorgensen, W.L.1    Ulmschneider, J.P.2    Tirado-Rives, J.3
  • 25
    • 0000975320 scopus 로고
    • Free energies of hydration of solute molecules. 4. Revised treatment of the hydration shell model
    • Y.K. Kang, K.D. Gibson, G. Nemethy, and H.A. Scheraga, Free energies of hydration of solute molecules. 4. Revised treatment of the hydration shell model, J. Phys. Chem. 92 (1988), pp. 4739-4742.
    • (1988) J. Phys. Chem. , vol.92 , pp. 4739-4742
    • Kang, Y.K.1    Gibson, K.D.2    Nemethy, G.3    Scheraga, H.A.4
  • 26
    • 33947397110 scopus 로고    scopus 로고
    • Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent
    • D.L. Mobley, E. Dumont, J.D. Chodera, and K.A. Dill, Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent, J. Phys. Chem. B 111 (2007), pp. 2242-2254.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 2242-2254
    • Mobley, D.L.1    Dumont, E.2    Chodera, J.D.3    Dill, K.A.4
  • 27
    • 37049110045 scopus 로고
    • Adamantan-1-ylamine and adamantan-1-ylamine hydrochloride complexes with cycloamyloses
    • R.I. Gelb, L.M. Schwartz, and D.A. Laufer, Adamantan-1-ylamine and adamantan-1-ylamine hydrochloride complexes with cycloamyloses, J. Chem. Soc. Perkin Trans. II (1984), pp. 15-21.
    • (1984) J. Chem. Soc. Perkin Trans. , vol.2 , pp. 15-21
    • Gelb, R.I.1    Schwartz, L.M.2    Laufer, D.A.3
  • 28
    • 33645955001 scopus 로고
    • Cyclodextrin inclusion complexes: Studies of the variation in the size of alicyclic guests
    • M.R. Eftink, M.L. Andy, K. Bystrom, H.D. Perlmutter, and D.S. Kristol, Cyclodextrin inclusion complexes: Studies of the variation in the size of alicyclic guests, J. Am. Chem. Soc. 111 (1989), pp. 6765-6772.
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 6765-6772
    • Eftink, M.R.1    Andy, M.L.2    Bystrom, K.3    Perlmutter, H.D.4    Kristol, D.S.5
  • 29
    • 84876290544 scopus 로고    scopus 로고
    • Complexation of adamantyl compounds by b-cyclodextrin and monoaminoderivatives
    • J. Carrazana, A. Jover, F. Meijide, V.H. Soto, and J.V. Tato, Complexation of adamantyl compounds by b-cyclodextrin and monoaminoderivatives, J. Chem. Phys. B 109 (2005), pp. 9717-9726.
    • (2005) J. Chem. Phys. B , vol.109 , pp. 9717-9726
    • Carrazana, J.1    Jover, A.2    Meijide, F.3    Soto, V.H.4    Tato, J.V.5
  • 30
  • 31
    • 65249112693 scopus 로고    scopus 로고
    • Predictions of hydration free energies from all-atom molecular dynamics simulations
    • D.L. Mobley, C.I. Bayly, M.D. Cooper, and K.A. Dill, Predictions of hydration free energies from all-atom molecular dynamics simulations, J. Phys. Chem. B 113 (2009), pp. 4533-4537.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 4533-4537
    • Mobley, D.L.1    Bayly, C.I.2    Cooper, M.D.3    Dill, K.A.4
  • 32
    • 33749223814 scopus 로고
    • Reevaluation of the born model of ion hydration
    • A.A. Rashin and B. Honig, Reevaluation of the born model of ion hydration, J. Phys. Chem. 89 (1985), p. 5588.
    • (1985) J. Phys. Chem. , vol.89 , pp. 5588
    • Rashin, A.A.1    Honig, B.2
  • 33
    • 0000763912 scopus 로고
    • Molecular basis for the born model of ion solvation
    • B. Roux, H. Yu, and M. Karplus, Molecular basis for the born model of ion solvation, J. Phys. Chem. 94 (1990), p. 4683.
    • (1990) J. Phys. Chem. , vol.94 , pp. 4683
    • Roux, B.1    Yu, H.2    Karplus, M.3
  • 34
    • 39349099179 scopus 로고    scopus 로고
    • Hydration free energy of a model lennard-jones solute particle: Microscopic monte carlo simulation studies and interpretation based on mesoscopic models
    • M. Gruziel, W.R. Rudnicki, and B. Lesyng, Hydration free energy of a model lennard-jones solute particle: Microscopic monte carlo simulation studies, and interpretation based on mesoscopic models, J. Chem. Phys. 128 (2008), 064503.
    • (2008) J. Chem. Phys. , vol.128 , pp. 064503
    • Gruziel, M.1    Rudnicki, W.R.2    Lesyng, B.3
  • 35
    • 33847296148 scopus 로고    scopus 로고
    • Unravelling the solvent response to neutral and charged solutes
    • M.V. Fedorov and A.A. Kornyshev, Unravelling the solvent response to neutral and charged solutes, Mol. Phys. 105 (2007), p. 1.
    • (2007) Mol. Phys. , vol.105 , pp. 1
    • Fedorov, M.V.1    Kornyshev, A.A.2
  • 36
    • 33751143432 scopus 로고    scopus 로고
    • Free energy of ionic hydration
    • G. Hummer, R.P. Pratt, and A.E. Garcia, Free energy of ionic hydration, J. Phys. Chem. 100 (1996), pp. 1206-1215.
    • (1996) J. Phys. Chem. , vol.100 , pp. 1206-1215
    • Hummer, G.1    Pratt, R.P.2    Garcia, A.E.3
  • 37
    • 34547854183 scopus 로고    scopus 로고
    • Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids
    • M.A. Kastenholz and H. Hunenberger, Computation of methodology- independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids, J. Chem. Phys. 124 (2006), 124106.
    • (2006) J. Chem. Phys. , vol.124 , pp. 124106
    • Kastenholz, M.A.1    Hunenberger, H.2
  • 38
    • 33745155379 scopus 로고    scopus 로고
    • Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation
    • M.A. Kastenholz and H. Hunenberger, Computation of methodology- independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation, J. Chem. Phys. 124 (2006), 224501.
    • (2006) J. Chem. Phys. , vol.124 , pp. 224501
    • Kastenholz, M.A.1    Hunenberger, H.2
  • 39
    • 79954589281 scopus 로고    scopus 로고
    • Computation of methodologyindependent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions
    • M.M. Reif and H. Hunenberger, Computation of methodologyindependent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions, J. Chem. Phys. 134 (2011), 144103.
    • (2011) J. Chem. Phys. , vol.134 , pp. 144103
    • Reif, M.M.1    Hunenberger, H.2
  • 40
    • 34547889165 scopus 로고    scopus 로고
    • Hydration free energies of monovalent ions in transferable intermolecular potential four point fluctuating charge water: An assessment of simulation methodology and force field performance and transferability
    • G.L. Warren and S. Patel, Hydration free energies of monovalent ions in transferable intermolecular potential four point fluctuating charge water: An assessment of simulation methodology and force field performance and transferability, J. Chem. Phys. 127 (2007), 064509.
    • (2007) J. Chem. Phys. , vol.127 , pp. 064509
    • Warren, G.L.1    Patel, S.2
  • 41
    • 63649153582 scopus 로고    scopus 로고
    • Rational design of ion force fields based on thermodynamic solvation properties
    • D. Horinek, S.I. Mamatkulov, and R.R. Netz, Rational design of ion force fields based on thermodynamic solvation properties, J. Chem. Phys. 130 (2009), 124507.
    • (2009) J. Chem. Phys. , vol.130 , pp. 124507
    • Horinek, D.1    Mamatkulov, S.I.2    Netz, R.R.3
  • 43
    • 0034227795 scopus 로고    scopus 로고
    • Enthalpy-entropy and cavity decomposition of alkane hydration free energies: Numerical results and implications for theories of hydrophobic solvation
    • E. Gallicchio, M.M. Kubo, and R.M. Levy, Enthalpy-entropy and cavity decomposition of alkane hydration free energies: Numerical results and implications for theories of hydrophobic solvation, J. Phys. Chem. B 104 (2000), pp. 6271-6285.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 6271-6285
    • Gallicchio, E.1    Kubo, M.M.2    Levy, R.M.3
  • 44
    • 7544232432 scopus 로고    scopus 로고
    • Hydration of amino acid side chains: Nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules
    • Y. Deng and B. Roux, Hydration of amino acid side chains: Nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules, J. Phys. Chem. B 108 (2004), pp. 16567-16576.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 16567-16576
    • Deng, Y.1    Roux, B.2
  • 45
    • 33244497652 scopus 로고    scopus 로고
    • Scaled particle theory and the length scales of hydrophobicity
    • H.S. Ashbaugh and L.R. Pratt, Scaled particle theory and the length scales of hydrophobicity, Rev. Mod. Phys. 78 (2006), pp. 159-178.
    • (2006) Rev. Mod. Phys. , vol.78 , pp. 159-178
    • Ashbaugh, H.S.1    Pratt, L.R.2
  • 46
    • 33645831413 scopus 로고    scopus 로고
    • Entropy-enthalpy compensation: Perturbation and relaxation in thermodynamic systems
    • H. Qian, and J.J. Hopfield, Entropy-enthalpy compensation: Perturbation and relaxation in thermodynamic systems, J. Chem. Phys. 105 (1996), pp. 9292-9298.
    • (1996) J. Chem. Phys. , vol.105 , pp. 9292-9298
    • Qian, H.1    Hopfield, J.J.2
  • 47
    • 0001594721 scopus 로고    scopus 로고
    • Entropy-enthalpy compensation in solvation and ligand binding revisited
    • E. Gallicchio, M.M. Kubo, and R.M. Levy, Entropy-enthalpy compensation in solvation and ligand binding revisited, J. Am. Chem. Soc. 120 (1998), pp. 4526-4527.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 4526-4527
    • Gallicchio, E.1    Kubo, M.M.2    Levy, R.M.3
  • 49
    • 0028204490 scopus 로고
    • Do salt bridges stabilize proteins? A continuum electrostatic analysis
    • Z.S. Hendsch and B. Tidor, Do salt bridges stabilize proteins? A continuum electrostatic analysis, Prot. Sci. 3 (1994), pp. 211-226.
    • (1994) Prot. Sci. , vol.3 , pp. 211-226
    • Hendsch, Z.S.1    Tidor, B.2
  • 50
    • 33646062293 scopus 로고    scopus 로고
    • Concepts in receptor optimization: Targeting the RGD peptide
    • W. Chen, C. Chang, and M.K. Gilson, Concepts in receptor optimization: Targeting the RGD peptide, J. Am. Chem. Soc. 128 (2006), pp. 4675-4684.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 4675-4684
    • Chen, W.1    Chang, C.2    Gilson, M.K.3
  • 51
    • 0037117480 scopus 로고    scopus 로고
    • Supramolecular chemistry and self-assembly
    • F.M. Menger, Supramolecular chemistry and self-assembly, Proc. Natl. Acad. Sci. USA 99 (2002), pp. 4818-4822.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 4818-4822
    • Menger, F.M.1
  • 52
    • 84961976132 scopus 로고    scopus 로고
    • Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton
    • C.P. Kelly, C.J. Cramer, and D.G. Truhlar, Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton, J. Phys. Chem. B 110 (2006), pp. 16066-16081.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 16066-16081
    • Kelly, C.P.1    Cramer, C.J.2    Truhlar, D.G.3
  • 54
    • 0037123079 scopus 로고    scopus 로고
    • Molecular mechanism of ion binding to the liquid/vapor interface of water
    • L.X. Dang and T.-M. Chang, Molecular mechanism of ion binding to the liquid/vapor interface of water, J. Phys. Chem. B 106 (2002), pp. 235-238.
    • (2002) J. Phys. Chem. B , vol.106 , pp. 235-238
    • Dang, L.X.1    Chang, T.-M.2
  • 55
    • 0001060901 scopus 로고    scopus 로고
    • Surface tension of water droplets: A molecular dynamics study of model and size dependencies
    • V.V. Zakharov, E.N. Brodskaya, and A. Laaksonen, Surface tension of water droplets: A molecular dynamics study of model and size dependencies, J. Chem. Phys. 107 (1997), pp. 10675-10682.
    • (1997) J. Chem. Phys. , vol.107 , pp. 10675-10682
    • Zakharov, V.V.1    Brodskaya, E.N.2    Laaksonen, A.3
  • 56
    • 0242290834 scopus 로고    scopus 로고
    • Mixed bilayer containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine: Lipid complexation
    • S.A. Pandit, D. Bosick, and M.L. Berkowitz, Mixed bilayer containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine: Lipid complexation, ion binding, and electrostatics, Biophys. J. 85 (2003), pp. 3120-3131.
    • (2003) Ion Binding, and Electrostatics, Biophys. J. , vol.85 , pp. 3120-3131
    • Pandit, S.A.1    Bosick, D.2    Berkowitz, M.L.3
  • 57
    • 0033984826 scopus 로고    scopus 로고
    • A new table of the thermodynamic quantities of ionic hydration: Values and some applications (enthalpy-entropy compensation and Born radii)
    • R. Schmid, A.M. Miah, and V.N. Sapunov, A new table of the thermodynamic quantities of ionic hydration: Values and some applications (enthalpy-entropy compensation and Born radii), Phys. Chem. Chem. Phys. 2 (2000), pp. 97-102.
    • (2000) Phys. Chem. Chem. Phys. , vol.2 , pp. 97-102
    • Schmid, R.1    Miah, A.M.2    Sapunov, V.N.3
  • 58
    • 33644879448 scopus 로고    scopus 로고
    • Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field
    • G. Lamoureux and B. Roux, Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field, J. Phys. Chem. B 110 (2006), pp. 3308-3322.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 3308-3322
    • Lamoureux, G.1    Roux, B.2


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