Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin Complexes

Mazurek, Anna; Szeleszczuk, Łukasz; Gubica, Tomasz

doi:10.3390/ijms22179422

Cited by 40 publications

(23 citation statements)

References 159 publications

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“…Solely for the DFT-based works in this topic, the number of published articles has already exceeded 300. While this number is still relatively low, when compared to the amount of reported molecular dynamics simulations at the molecular mechanics level [12], the reviewed works reveal that the application of QC calculations in the studies of CD complexes can be essential, providing the results unobtainable by any other method, both experimental and computational.…”

Section: Discussionmentioning

confidence: 99%

“…In terms of the sizes of the modeled objects, CD complexes are somewhere in between. While geometry optimization calculations on the static structures of CD complexes are, nowadays, performed mostly at the QM level, usually by the means of DFT, the MD simulations are still being performed at the MM level [12].…”

Section: • Molecular Dynamicsmentioning

confidence: 99%

“…This is why a lot of the molecular modelling studies devoted to those complexes utilize molecular dynamics simulation at the molecular mechanics level. Those works have been recently reviewed by us [12]. However, the types of intermolecular forces that stabilize such complexes such as hydrogen bonding, van der Waals, and hydrophobic and dipole-dipole interactions, usually cannot be modeled with the required accuracy using the molecular mechanics methods.…”

Section: Introductionmentioning

confidence: 99%

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Current Status of Quantum Chemical Studies of Cyclodextrin Host–Guest Complexes

Mazurek

Szeleszczuk

2022

Molecules

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This article aims to review the application of various quantum chemical methods (semi-empirical, density functional theory (DFT), second order Møller–Plesset perturbation theory (MP2)) in the studies of cyclodextrin host–guest complexes. The details of applied approaches such as functionals, basis sets, dispersion corrections or solvent treatment methods are analyzed, pointing to the best possible options for such theoretical studies. Apart from reviewing the ways that the computations are usually performed, the reasons for such studies are presented and discussed. The successful applications of theoretical calculations are not limited to the determination of stable conformations but also include the prediction of thermodynamic properties as well as UV–Vis, IR, and NMR spectra. It has been shown that quantum chemical calculations, when applied to the studies of CD complexes, can provide results unobtainable by any other methods, both experimental and computational.

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Section: Discussionmentioning

confidence: 99%

Section: • Molecular Dynamicsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Current Status of Quantum Chemical Studies of Cyclodextrin Host–Guest Complexes

Mazurek

Szeleszczuk

2022

Molecules

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“…The commonly used universal force fields are UFF, ESFF, and Dreiding . Specifically, GAFF, GROMOS96, and CHARMM are the most popular force field in the CD–guest simulations . Because CDs are often modified by functional groups, using a validated dedicated force field can improve the accuracy of simulations.…”

Section: Methodsmentioning

confidence: 99%

Computational Methods for the Interaction between Cyclodextrins and Natural Compounds: Technology, Benefits, Limitations, and Trends

Ding

Geng

et al. 2022

J. Agric. Food Chem.

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Cyclodextrins (CDs) have a hollow structure with a hydrophobic interior and hydrophilic exterior. Forming inclusion complexes with CDs will maximize the bioavailability of natural compounds and enable active components to be processed into functional foods, medicines, additives, and so forth. However, experimental methods cannot explain CD−guest binding at the atomic level. Different models have been recently developed to simulate the interaction between CDs and guests to study the binding conformation and analyze noncovalent forces. This review paper summarizes modeling methods of CD-natural compound complexes. The methods include quantitative structure−activity relationships, molecular docking, molecular dynamics simulations, and quantum-chemical calculations. The applications of these methods to enhance the solubility and bioactivities of guest molecules, assist material transportation, and promote compound extraction are also discussed. The purpose of this review is to explore interaction mechanisms of CDs and guests and to help expand new applications of CDs.

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“…Molecular modeling methods are commonly applied to study the host-guest behavior of CD complexes [22]. A molecular docking study was conducted to predict the interaction of 6-G and its orientation within the cavities of βCD and HPβCD.…”

Section: Docking Studymentioning

confidence: 99%

Development of Cyclodextrin-Functionalized Transethoniosomes of 6-Gingerol: Statistical Optimization, In Vitro Characterization and Assessment of Cytotoxic and Anti-Inflammatory Effects

et al. 2022

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The poor solubility and stability of 6-gingerol (6-G) could hamper its clinical applications. The aim of the current study was to develop a novel ultra-deformable cyclodextrin-functionalized transethoniosomes (CD-TENs) as a promising delivery system for 6-G. Transethoniosomes (TENs) are flexible niosomes (NVs) due to their content of ethanol and edge activators (EAs). CD-functionalized nanoparticles could improve drug solubility and stability compared to the corresponding nanovesicles. 6-G-loaded ethoniosomes (ENs) were formulated by the ethanol injection technique in the presence and absence of EA and CD to explore the impact of the studied independent variables on entrapment efficiency (EE%) and % 6-G released after 24 h (Q24h). According to the desirability criteria, F8 (CD-functionalized transethoniosomal formula) was selected as the optimized formulation. F8 demonstrated higher EE%, permeation, deformability and stability than the corresponding TENs, ENs and NVs. Additionally, F8 showed higher cytotoxic and anti-inflammatory activity than pure 6-G. The synergism between complexation with CD and novel ultra-deformable nanovesicles (TENs) in the form of CD-TENs can be a promising drug delivery carrier for 6-G.

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Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin Complexes

Cited by 40 publications

References 159 publications

Current Status of Quantum Chemical Studies of Cyclodextrin Host–Guest Complexes

Current Status of Quantum Chemical Studies of Cyclodextrin Host–Guest Complexes

Computational Methods for the Interaction between Cyclodextrins and Natural Compounds: Technology, Benefits, Limitations, and Trends

Development of Cyclodextrin-Functionalized Transethoniosomes of 6-Gingerol: Statistical Optimization, In Vitro Characterization and Assessment of Cytotoxic and Anti-Inflammatory Effects

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