Influence of the gallate moiety on the interactions between green tea polyphenols and lipid membranes elucidated by molecular dynamics simulations

Nie, Rongzu; Dang, Meizhu; Zhang, Ge; Huo, Yinqiang; Yu, Bo; Tang, Shang-wen

doi:10.1016/j.bpc.2021.106592

Cited by 13 publications

(24 citation statements)

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“…This progress is supported by developments in the computing hardware, algorithms and software that allow for longer and cheaper simulations [ 105 ]. In general, the molecular dynamics simulations are powerful tools for elucidating the mechanisms of interactions at the atomic level, complementing the experimental methods such as X-ray crystallography, cryo-electron microscope, NMR, paramagnetic resonance and Förster resonance energy transfer (FRET) [ 33 , 103 , 106 ]. Molecular dynamics simulations can be used in stand-alone research or to interpret experimental results or guide the experiments, for example, for structural and dynamic studies (to study conformational flexibility and stability), perturbations (to observe response after a controlled change to a system) and processes (to observe a dynamic process over time) [ 105 ].…”

Section: Methodsmentioning

confidence: 99%

“…Molecular dynamics simulations can be used in stand-alone research or to interpret experimental results or guide the experiments, for example, for structural and dynamic studies (to study conformational flexibility and stability), perturbations (to observe response after a controlled change to a system) and processes (to observe a dynamic process over time) [ 105 ]. For polyphenol–lipid interactions, these studies have included the penetration, location and orientation of polyphenols in the lipid bilayer [ 107 , 108 , 109 ] and the effects of the structural features of polyphenols on these interactions [ 106 , 110 ].…”

Section: Methodsmentioning

confidence: 99%

“…The forces in molecular dynamics simulation are calculated using a model called a molecular mechanics force field, which is fitted to the results of quantum mechanical calculations and typically also to particular experimental data [ 105 ]. The common choices are AMBER (assisted model building with energy refinement), CHARMM (Chemistry at HARvard Macromolecular Mechanics) and OPLS (optimized potentials for liquid simulations), and for phospholipid systems, the Gromacs 2019.1 software with the GROMOS G53A6 force field has been used [ 106 , 111 ]. Community-driven GROMACS [ 112 ] is one of the most widely used free and open-source software in chemistry [ 111 ] and it is primarily used for high-performance molecular dynamics simulations of biomolecules.…”

Section: Methodsmentioning

confidence: 99%

“…Community-driven GROMACS [ 112 ] is one of the most widely used free and open-source software in chemistry [ 111 ] and it is primarily used for high-performance molecular dynamics simulations of biomolecules. The GROMOS G53A6 force field has been commonly used for the molecular dynamics simulation of lipid membranes with sufficient accuracy [ 106 , 113 ], and Zhu et al used the GROMOS53a6 force field and Berger lipid parameters in studies on the penetration of galloylated and nongalloylated PAs into POPC:1-palmitoyl-2-oleoyl phosphatidylethanolamine (POPE) (1:1) lipid bilayers [ 110 ]. However, it has to be remembered that the force fields are approximations even though they have developed significantly in recent years [ 105 ].…”

Section: Methodsmentioning

confidence: 99%

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Insights into Polyphenol–Lipid Interactions: Chemical Methods, Molecular Aspects and Their Effects on Membrane Structures

Karonen

2022

Plants

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Plant polyphenols have many potential applications, for example, in the fields of chemical ecology and human and animal health and nutrition. These biological benefits are related to their bioavailability, bioaccessibility and interactions with other biomolecules, such as proteins, lipids, fibers and amino acids. Polyphenol–protein interactions are well-studied, but less is known about their interactions with lipids and cell membranes. However, the affinity of polyphenols for lipid bilayers partially determines their biological activity and is also important from the usability perspective. The polyphenol–lipid interactions can be studied with several chemical tools including, among others, partition coefficient measurements, calorimetric methods, spectroscopic techniques and molecular dynamics simulation. Polyphenols can variably interact with and penetrate lipid bilayers depending on the structures and concentrations of the polyphenols, the compositions of the lipids and the ambient conditions and factors. Polyphenol penetrating the lipid bilayer can perturb and cause changes in its structure and biophysical properties. The current studies have used structurally different polyphenols, diverse model lipids and various measuring techniques. This approach provides detailed information on polyphenol–lipid interactions, but there is much variability, and the results may even be contradictory, for example, in relation to the locations and orientations of the polyphenols in the lipid bilayers. Nevertheless, by using well-characterized model polyphenols and lipids systematically and combining the results obtained with several techniques within a study, it is possible to create a good overall picture of these fascinating interactions.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Insights into Polyphenol–Lipid Interactions: Chemical Methods, Molecular Aspects and Their Effects on Membrane Structures

Karonen

2022

Plants

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“…PBN [354], Quinones [145,355], Menaquinone [356,357], Lutein [358], Glutathione [359], Flavonoids [360][361][362][363][364][365][366][367][368][369][370], Liponitroxides [371] Amino acids L-phenylalanine [372][373][374][375], L-Tyrosine [374], L-Phenylglycine, Phenylacetic acid [374,376],…”

Section: Antioxidantsmentioning

confidence: 99%

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

2021

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We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard “lock and key” paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.

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Interactions of chlorogenic acid and isochlorogenic acid A with model lipid bilayer membranes: Insights from molecular dynamics simulations

Nie

Dang

Zhang

et al. 2021

Chemistry and Physics of Lipids

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Influence of the gallate moiety on the interactions between green tea polyphenols and lipid membranes elucidated by molecular dynamics simulations

Cited by 13 publications

References 50 publications

Insights into Polyphenol–Lipid Interactions: Chemical Methods, Molecular Aspects and Their Effects on Membrane Structures

Insights into Polyphenol–Lipid Interactions: Chemical Methods, Molecular Aspects and Their Effects on Membrane Structures

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

Interactions of chlorogenic acid and isochlorogenic acid A with model lipid bilayer membranes: Insights from molecular dynamics simulations

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