Molecular Insight into Affinities of Gallated and Nongallated Proanthocyanidins Dimers to Lipid Bilayers

Molecular Interactions Between Egg White Peptides and Giant Unilamellar Vesicle Membranes: Effect of Peptide Localization on Membrane Fluidity

Bioactive peptides have been shown to affect cell membrane fluidity, which is an important indicator of the cell membrane structure and function. However, the underlying mechanism of egg white-derived bioactive peptide regulation of cell membrane fluidity has not been elucidated yet. The cell membrane fluidity was investigated by giant unilamellar vesicles in the present study. The results showed that peptides TCNW, ADWAK, ESIINF, VPIEGII, LVEEY, and WKLC connect to membranes through intermolecular interactions, such as hydrogen bonding and regulated membrane fluidity, in a concentration-dependent way. In addition, peptides prefer to localize in the hydrophobic core of the bilayers. This study provides a theoretical basis for analyzing the localization of egg white bioactive peptides in specific cell membrane regions and their influence on the cell membrane fluidity.

Molecular insights into the structure destabilization effects of ECG and EC on the Aβ protofilament: An all-atom molecular dynamics simulation study

The formation of Aβ into amyloid fibrils was closely connected to AD, therefore, the Aβ aggregates were the primary therapeutic targets against AD. Previous studies demonstrated that epicatechin-3-gallate (ECG), which possessed a gallate moiety, exhibited a greater ability to disrupt the preformed Aβ amyloid fibrils than epicatechin (EC), indicating that the gallate moiety was crucial. In the present study, the molecular mechanisms were investigated. Our results demonstrated that ECG had more potent disruptive impacts on the β-sheet structure and K28-A42 salt bridges than EC. We found that ECG significantly interfered the interactions between Peptide-4 and Peptide-5. However, EC could not. The disruption of K28-A42 salt bridges by ECG was mainly due to the interactions between ECG and the hydrophobic residues located at C-terminus. Interestingly, EC disrupted the K28-A42 salt bridges by the interactions with C-terminal hydrophobic residues and the cation-π interactions with K28. Moreover, our results indicated that hydrophobic interactions, H-bonds, π-π interactions and cation-π interactions between ECG and the bend of L-shaped region caused the disaggregation of interactions between Peptide-4 and Peptide-5. Significantly, gallate moiety in ECG had contributed tremendously to the disaggregation. We believed that our findings could be useful for designing prospective drug candidates targeting AD.

Insights into the Surface Binding and Structural Interference of Polyphenols with the Membrane Raft Domains in Relation to Their Distinctive Ability to Inhibit Preadipocyte Differentiation in 3T3-L1 Cells

Polyphenols with different structures have shown distinct variations in their ability to inhibit the differentiation of 3T3-L1 preadipocytes. However, the underlying mechanisms for these differences remain unclear. In the present study, the surface binding of polyphenols to different membrane domains was explored using coarse-grained molecular dynamics simulation (CG-MDs). Subsequently, this surface binding was confirmed in the liposome system by microscale thermophoresis. Additionally, the interference of polyphenols on the membrane raft's structure was studied through atomic force microscopy and high-content screening fluorescence microscopy. The results indicated that polyphenols with a differentiation-inhibitory ability, such as epicatechin-3-gallate (ECG) and epicatechin-3-gallate-(4β → 8, 2β → O → 7)-epicatechin-3-gallate (A-type ECG dimer), exhibited strong binding to ordered domains enriched in sphingolipids and cholesterol. This binding led to the structural disruption of membrane rafts by altering their size and shape, with the binding constant of 3.8 μM for ECG and 0.3 μM for A-type ECG dimer, respectively. In contrast, epicatechin (EC) with little differentiation-inhibitory ability had no effects on membrane rafts, and its binding constant with the ordered domain was 380.6 μM. Overall, the surface binding of polyphenols to ordered domains and the resulting disruption of membrane rafts structure might be a fundamental mechanism by which polyphenols inhibited the differentiation of 3T3-L1 preadipocytes.

The synergistic ramification of insoluble dietary fiber and associated non-extractable polyphenols on gut microbial population escorting alleviation of lifestyle diseases

Most of the pertinent research which aims at exploring the therapeutic effects of polyphenols usually misapprehends a large fraction of non-extractable polyphenols due to their poor aqueous-organic solvent extractability. These polymeric polyphenols (i.e., proanthocyanins, hydrolysable tannins and phenolic acids) possess a unique property to adhere to the food matrix polysaccharides and protein sowing to their structural complexity with high glycosylation, degree of polymerization, and plenty of hydroxyl groups. Surprisingly resistance to intestinal absorption does not hinder its bioactivity but accelerates its functionality manifolds due to the colonic microbial catabolism in the gastrointestinal tract, thereby protecting the body from local and systemic inflammatory diseases. This review highlights not only the chemistry, digestion, colonic metabolism of non-extractable polyphenols (NEPP) but also summarises the synergistic effect of matrix-bound NEPP exerting local as well as systemic health benefits.

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

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.

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

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.

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

Because of the negative side-effects of synthetic preservatives, the naturally-occurring polyphenols aroused intense interest of researchers. It has been suggested that chlorogenic acid (CA) and isochlorogenic acid A (iso-CAA) were good candidates to replace the synthetic preservatives. Moreover, the bactericidal activity of iso-CAA was stronger than CA, and the anti-bacterial activities of iso-CAA and CA were highly membrane-dependent. However, the mechanisms were still unclear. Therefore, in the present study, we investigated the mechanisms of the interactions between the two polyphenols and lipid bilayers through molecular dynamics simulations. The results revealed that iso-CAA could be inserted much deeper into POPG lipid bilayer than CA. We also found that hydrophobic interactions and hydrogen bonds both contributed to the insertion of iso-CAA into the POPG lipid bilayer, and the quinic acid moiety was the key structure in iso-CAA to form hydrogen bonds with POPG lipid bilayer. We believed that these findings would provide more useful information to explain the stronger bactericidal activity of iso-CAA than CA at the atomic level.

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

Previous studies suggested that naturally occurring EGCG primarily acted on the bacterial cell membrane then damaged the membrane and the gallate moiety in EGCG was very important to its anti-bacterial activity. However, the detailed mechanisms were still poorly understood. In this paper, EGCG and EGC were selected to study the great contribution of gallate moiety on the anti-bacterial activities of polyphenols. The results indicated that EGCG could penetrate deeper into the POPG lipid bilayer and possess more potent structure-perturbing potency on the POPG lipid bilayer than EGC. We also found that EGCG had the ability to form hydrogen bonds with the deeper inside oxygen atoms in the POPG lipid bilayer and the gallate moiety was the key functional group for EGCG forming hydrogen bonds with the POPG lipid bilayer. Moreover, results from the binding free energy analysis demonstrated that the gallate moiety made great contribution to the high affinity between EGCG and the POPG lipid bilayer. We believed that these findings could yield useful insights into the influence mechanisms of gallate moiety on the anti-bacterial activities of polyphenols.

Health-Promoting Properties of Proanthocyanidins for Intestinal Dysfunction

The intestinal barrier is constantly exposed to potentially harmful environmental factors, including food components and bacterial endotoxins. When intestinal barrier function and immune homeostasis are compromised (intestinal dysfunction), inflammatory conditions may develop and impact overall health. Evidence from experimental animal and cell culture studies suggests that exposure of intestinal mucosa to proanthocyanidin (PAC)-rich plant products, such as grape seeds, may contribute to maintaining the barrier function and to ameliorating the pathological inflammation present in diet-induced obesity and inflammatory bowel disease. In this review, we aim to update the current knowledge on the bioactivity of PACs in experimental models of intestinal dysfunction and in humans, and to provide insights into the underlying biochemical and molecular mechanisms.

Antimicrobial peptide ROAD-1 triggers phase change in local membrane environment to execute its activity

Emergence of antibiotic-resistant pathogens has paved way for development of newer class of drugs that would not be susceptible to resistance. Antimicrobial peptides such as defensins that target the microbial membrane are promising candidates. ROAD-1 is an alpha-defensin present in the oral cavity of rhesus macaque and shares very high sequence similarity to human enteric defensin 5. In this study we have performed microsecond long all atom molecular dynamic simulations to understand the mechanism of action of ROAD-1. We find that ROAD-1 is able to adopt an energetically stable conformation predominantly stabilized by electrostatic interactions only in presence of bacterial membranes. In mammalian membrane even though it gets absorbed onto the bilayer, it is unable to adopt an equilibrium conformation. Binding of ROAD-1 to bilayer induces clustering of POPG molecules up to 15 Å around the peptide. POPG molecules show higher order parameters than the neighboring POPE implying coexistence of different phases. Analysis of binding free energy of ROAD-1-membrane complex indicates Arg1, Arg2, Arg7, and Arg25 to play key role in its antimicrobial activity. Unlike its homolog HD5, ROAD-1 is not observed to form a dimer. Our study gives insight into the membrane-bound conformation of ROAD-1 and its mechanism of action that can aid in designing defensin-based therapeutics. Graphical abstract Antimicrobial peptide ROAD-1 adopts a different membrane-bound conformation as compared with HD5 even though they belong to the same family implying a different mechanism of action.

Evaluation of EGCG Loading Capacity in DMPC Membranes

Catechins are molecules with potential use in different pathologies such as diabetes and cancer, but their pharmaceutical applications are often hindered by their instability in the bloodstream. This issue can be circumvented using liposomes as their nanocarriers for in vivo delivery. In this work, we studied the molecular details of (-)-epigallocatechin-3-gallate (EGCG) interacting with 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) monolayer/bilayer systems to understand the catechin loading ability and liposome stability, using experimental and computational techniques. The molecular dynamics simulations show the EGCG molecules deep inside the lipid bilayer, positioned below the lipid ester groups, generating a concentration-dependent lipid condensation. This effect was also inferred from the surface pressure isotherms of DMPC monolayers. In the polarization-modulated infrared reflection absorption spectra assays, the predominant effect at higher concentrations of EGCG (e.g., 20 mol %) was an increase in lipid tail disorder. The steady-state fluorescence data confirmed this disordered state, indicating that the catechin-induced liposome aggregation outweighs the condensation effects. Therefore, by adding more than 10 mol % EGCG to the liposomes, a destabilization of the vesicles occurs with the ensuing release of entrapped catechins. The loading capacity for DMPC seems to be limited by its disordered lipid arrangements, typical of a fluid phase. To further increase the clinical usefulness of liposomes, lipid bilayers with more stable and organized assemblies should be employed to avoid aggregation at large concentrations of catechin.

Penta-O-galloyl-β-d-glucose, a hydrolysable tannin from Radix Paeoniae Alba, inhibits adipogenesis and TNF-α-mediated inflammation in 3T3-L1 cells

Penta-O-galloyl-β-d-glucose (PGG) was purified and identified from Radix Paeoniae Alba by HSCCC and HPLC/ESI-MS, and its inhibitory effects on adipogenesis and TNF-α-induced inflammation were assessed in 3T3-L1 cell line. The results showed that PGG dose-dependently reduced intracellular lipids accumulation, and this involved decrease the expression levels of major adipogenic markers, PPARγ, C/EBP α, through MAPKs inhibition. This was accompanied by a reduction of lipogenic genes, ACC, FAS, and SCD-1, involved in fatty acid synthesis. Furthermore, PGG also inhibited TNF-α-induced expression of inflammatory cytokines including IL-6 and MCP-1 in the matured 3T3-L1 adipocytes. The inhibitions were likely mediated by blocking the MAPKs and NF-κB activation. These findings highlighted that PGG could serve as a potent therapeutic agent for controlling obesity and obesity-related chronic inflammation.