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Binding mode and free energy prediction of fisetin/beta-cyclodextrin inclusion complexes
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Metadata
Document Title
Binding mode and free energy prediction of fisetin/beta-cyclodextrin inclusion complexes
Author
Nutho B, Khuntawee W, Rungnim C, Pongsawasdi P, Wolschann P, Karpfen A, Kungwan N, Rungrotmongkol T
Name from Authors Collection
Affiliations
Chulalongkorn University; Chulalongkorn University; National Science & Technology Development Agency - Thailand; National Nanotechnology Center (NANOTEC); University of Vienna; University of Vienna; Chiang Mai University
Type
Article
Source Title
BEILSTEIN JOURNAL OF ORGANIC CHEMISTRY
Year
2014
Volume
10
Page
2789-2799
Open Access
Green Published, gold, Green Submitted
Publisher
BEILSTEIN-INSTITUT
DOI
10.3762/bjoc.10.296
Format
Abstract
In the present study, our aim is to investigate the preferential binding mode and encapsulation of the flavonoid fisetin in the nanopore of beta-cyclodextrin (beta-CD) at the molecular level using various theoretical approaches: molecular docking, molecular dynamics (MD) simulations and binding free energy calculations. The molecular docking suggested four possible fisetin orientations in the cavity through its chromone or phenyl ring with two different geometries of fisetin due to the rotatable bond between the two rings. From the multiple MD results, the phenyl ring of fisetin favours its inclusion into the beta-CD cavity, whilst less binding or even unbinding preference was observed in the complexes where the larger chromone ring is located in the cavity. All MM- and QM-PBSA/GBSA free energy predictions supported the more stable fisetin/beta-CD complex of the bound phenyl ring. Van der Waals interaction is the key force in forming the 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.
Keyword
Cyclodextrin | Fisetin | Flavonoid | MM-PBSA | Molecular dynamics simulation | QM-PBSA
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
Funding Sponsor
TRF-CHE Research Grant for New Scholars [MRG5580223]; Ratchadapiseksomphot Endowment Fund of Chulalongkorn University [RES560530176-FW]
Publication Source
WOS