Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin

• Waratchada Sangpheak,
• Jintawee Kicuntod,
• Roswitha Schuster,
• Thanyada Rungrotmongkol,
• Peter Wolschann,
• Nawee Kungwan,
• Helmut Viernstein,
• Monika Mueller and
• Piamsook Pongsawasdi

Beilstein J. Org. Chem. 2015, 11, 2763–2773, doi:10.3762/bjoc.11.297

• binding free energies, or calculate the free energies of molecules in solution (∆Gbind) using the MM-PBSA/GBSA method. The free energy decomposition of each complex in terms of gas phase energy (∆EMM) including ∆Eele and ∆Evdw energies, solvation free energy (∆Gsol) and entropic term (T∆S) is shown in

• information was in good agreement with previous studies in which the hydrophobic interaction was found to be the main driving force for flavanones–CD inclusion complexes [40][41]. For the summation of entropic and solvation terms, both MM/PBSA and MM/GBSA methods predicted that the binding free energy of

• hesperetin/DM-β-CD was by ≈7.6 kcal·mol−1 lower than that of hesperetin/β-CD, and a better binding of naringenin in the cavity of DM-β-CD than in that of β-CD by ≈4.6 kcal·mol−1 was suggested [40]. Nevertheless, the MM-PBSA/GBSA binding free energies of the two inclusion complexes might be overestimated due

Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

• Chompoonut Rungnim,
• Sarunya Phunpee,
• Manaschai Kunaseth,
• Supawadee Namuangruk,
• Kanin Rungsardthong,
• Thanyada Rungrotmongkol and
• Uracha Ruktanonchai

Beilstein J. Org. Chem. 2015, 11, 2306–2317, doi:10.3762/bjoc.11.251

• key factor controlling the formation of inclusion complexes; van der Waals interactions could be more important. The MM-PBSA result in Table S2, Supporting Information File 1, confirmed this assumption; the main contribution for α-MGS inclusion arises from van der Waals interactions (ΔEvdW) 7–8 fold

• water and ethanol molecules always solvate around 2 Å from O3, compared to other oxygen atoms in α-MGS. Binding energy analysis Based on the MM-PBSA approach, the binding free energies of the α-MGS/β-CD complexes at various EtOH concentrations were predicted. The decomposition of free energy into

• -CD), in six inclusion complexes. MM-PBSA binding free energies (kcal/mol) and their energy components for α-MGS/β-CD complexes at different EtOH concentrations. Supporting Information Supporting Information File 484: Additional data. Acknowledgements The authors thank the National Nanotechnology

Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes

• Bodee Nutho,
• Wasinee Khuntawee,
• Chompoonut Rungnim,
• Piamsook Pongsawasdi,
• Peter Wolschann,
• Alfred Karpfen,
• Nawee Kungwan and
• Thanyada Rungrotmongkol

Beilstein J. Org. Chem. 2014, 10, 2789–2799, doi:10.3762/bjoc.10.296

• complexes. In addition, the quantum mechanics calculations with M06-2X/6-31G(d,p) clearly showed that both solvation effect and BSSE correction cannot be neglected for the energy determination of the chosen system. Keywords: cyclodextrin; fisetin; flavonoid; MM-PBSA; molecular dynamics simulation; QM-PBSA

• inclusion complex. The ligand binding mode and water accessibility, host–guest interaction, and binding free energy of the inclusion complex were analyzed. The MM-PBSA/GBSA and M06-2X/6-31G(d,p)//MM-PBSA/GBSA approaches were used to predict the binding affinity of fisetin/β-CD complexes. The M06-2X/6-31G(d

• radial distribution function (RDF). The calculations of MM-PBSA/GBSA binding free energies (∆GMM-PBSA and ∆GMM-GBSA) and their energy components were analyzed using the mm_pbsa module. Free energy prediction The MM-PBSA and MM-GBSA methods have been widely used to estimate the binding free energies of