Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin Complexes

Abstract

Cyclodextrins (CDs) are highly respected for their ability to form inclusion complexes via host–guest noncovalent interactions and, thus, ensofance other molecular properties. Various molecular modeling methods have found their applications in the analysis of those complexes. However, as showed in this review, molecular dynamics (MD) simulations could provide the information unobtainable by any other means. It is therefore not surprising that published works on MD simulations used in this field have rapidly increased since the early 2010s. This review provides an overview of the successful applications of MD simulations in the studies on CD complexes. Information that is crucial for MD simulations, such as application of force fields, the length of the simulation, or solvent treatment method, are thoroughly discussed. Therefore, this work can serve as a guide to properly set up such calculations and analyze their results.

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

“…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.…”

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

“…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.…”

“…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].…”

“…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.…”

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

“…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.…”