Role of peptide primary sequence in polyphenol–protein recognition: An example with neurotensin

Polyphenols are known for their impact on health and one of their major properties is the formation of complexes with proteins. To investigate the involvement of polyphenol–protein complexes in health, the interactions between bioactive polyphenols and neurotensin were examined by structural NMR and molecular modeling. Neurotensin is a linear bioactive tridecapeptide and polyphenols seem to affect the NT metabolism. We studied the polyphenols resveratrol and its glucoside the piceid in order to observe the possible role of glucose group and the penta-O-galloyl-d-glucopyranose (PGG). NMR data and molecular modeling showed that interaction occurred with the three polyphenols involving hydrophobic stacking and hydrogen bonds. Moreover, the peptide primary sequence plays a role in the specificity of complex formation.     

Recognition characters in peptide–polyphenol complex formation

Dietary polyphenols have received attention for their anti-oxidative, anti-carcinogenic and anti-neurodegenerative effects. Polyphenols bind to proteins leading to the formation of soluble or insoluble protein–polyphenol complexes which could significantly influence their biological activities. NMR and molecular modeling studies were performed to investigate the influence of the bulk, flexibility and hydrophobicity of polyphenols on the association with bradykinin, the peptide model. Our results show that the strength of the interactions could be positively correlated with polyphenol hydrophobicity and a comparison between pentagalloylglucose and vescalagin indicated that flexibility might play a positive role in the interaction with peptides and proteins.     

Recognition characters in peptide-polyphenol complex formation

Dietary polyphenols have received attention for their anti-oxidative, anti-carcinogenic and anti-neurodegenerative effects. Polyphenols bind to proteins leading to the formation of soluble or insoluble protein-polyphenol complexes which could significantly influence their biological activities. NMR and molecular modeling studies were performed to investigate the influence of the bulk, flexibility and hydrophobicity of polyphenols on the association with bradykinin, the peptide model. Our results show that the strength of the interactions could be positively correlated with polyphenol hydrophobicity and a comparison between pentagalloylglucose and vescalagin indicated that flexibility might play a positive role in the interaction with peptides and proteins.     

NMR and simulated annealing investigations of bradykinin in presence of polyphenols

Epidemiological studies have shown that the incidence of some cardiovascular degenerative diseases appears to be lower in populations with regular but moderate drinking of red wine rich in polyphenols. One of the most important properties of polyphenols is to form complexes with proteins. The linear nonapeptide hormone bradykinin (H-Arg1-Pro2-Pro3-Gly4-Phe5-Ser6-Pro7-Phe8-Arg9-OH) is involved in a variety of physiological processes such as the cardiovascular processes. Thus, the goal of this work was to study the effects of tannins on the peptide structure by NMR investigations and molecular modeling. The results of these investigations show that in the presence of catechin, the peptide conformation is not affected and is in a random coil structure. On the contrary, the peptide structure is modified by the addition of dimeric proanthocyanidin B3 (catechin 4alpha-->8 catechin). The dimer leads to the formation of a large flexible turn between the 6-9 residues. Thus, the biological activities of bradykinin in the presence of polyphenols could be affected.     

NMR spectroscopic and molecular modeling studies of protein-carbohydrate and protein-peptide interactions

Investigations of the conformations of carbohydrates, their analogues and their molecular mimics are described, with emphasis on structural and functional information that can be gained by NMR spectroscopic techniques in combination with molecular modeling. The transferred nuclear Overhauser effect (trNOE) has been employed to determine the bound conformations of carbohydrates and other bioactive molecules in complex with protein receptors. The corresponding experiments in the rotating frame (trROE) and selective editing experiments (e.g., QUIET-NOESY) are used to eliminate indirect cross-relaxation pathways (spin diffusion), thereby minimizing errors in the data used for calculation of conformations. Saturation transfer difference NMR experiments reveal detailed information about intermolecular contacts between ligand and protein. Computational techniques are integrated with NMR-derived information to construct structural models of these bioactive molecules and of their complexes with proteins. Recent investigations into the nature of molecular mimicry with regard to protein-ligand interactions are described, along with applications in determining the mode of action of enzyme inhibitors. The results are relevant for the design of the next generation of drug and vaccine candidates.     

Purification,structural elucidation,antioxidant capacity and neuroprotective potential of the main polyphenolic compounds contained in Achyrocline satureioides (Lam) D.C. (Compositae)

Achyrocline satureioides (Lam) D.C (Compositae) is a native medicinal plant of South America traditionally utilized for its anti-inflammatory, sedative and anti-atherosclerotic properties among others. Neuroprotective effects have been reported in vivo and could be associated to its elevated content of flavonoid aglycones. In the present study we performed the isolation and structure elucidation of the major individual flavonoids of A. satureioides along with the in vitro characterization of their individual antioxidant and neuroprotective properties in order to see their putative relevance for treating neurodegeneration.Exact mass, HPLC-MS/MS and ¹H NMR identified dicaffeoyl quinic acid isomers, quercetin, luteolin, isoquercitrin, and 3-O-methylquercetin as the mayor polyphenols. Flavonoids intrinsic redox properties were evaluated in the presence of the endogenous antioxidants GSH and Ascorbate. Density Functional Theory (DFT) molecular modeling and electron density studies showed a theoretical basis for their different redox properties. Finally, in vitro neuroprotective effect of each isolated flavonoid was evaluated against hydrogen peroxide-induced toxicity in a primary neuronal culture paradigm. Our results showed that quercetin was more efficacious than luteolin and isoquercitrin, while 3-O-methylquercetin was unable to afford neuroprotection significantly. This was in accordance with the susceptibility of each flavonoid to be oxidized and to react with GSH. Overall our results shed light on chemical and molecular mechanisms underlying bioactive actions of A. satureioides main flavonoids that could contribute to its neuroprotective effects and support the positive association between the consumption of A. satureioides as a natural dietary source of polyphenols, and beneficial health effect.     

The metabolic fate of dietary polyphenols in humans

Dietary polyphenols are widely considered to contribute to health benefits in humans. However, little is yet known concerning their bioactive forms in vivo and the mechanisms by which they may contribute toward disease prevention. Although many studies are focusing on the bioavailability of polyphenols through studying their uptake and the excretion of their conjugated forms, few are emphasizing the occurrence of metabolites in vivo formed via degradation by the enzymes of colonic bacteria and subsequent absorption. The purpose of this research was to investigate the relationship between biomarkers of the colonic biotransformation of ingested dietary polyphenols and the absorbed conjugated polyphenols. The results show that the majority of the in vivo forms derive from cleavage products of the action of colonic bacterial enzymes and subsequent metabolism in the liver. Those include the glucuronides of 3-hydroxyphenylacetic, homovanillic, vanillic and isoferulic acid as well as 3-(3-methoxy-4-hydroxyphenyl)-propionic, 3-(3-hydroxyphenyl)-propionic acid, and 3-hydroxyhippuric acid. In contrast, intact conjugated polyphenols themselves, such as the glucuronides of quercetin, naringenin and ferulic, p-coumaric, and sinapic acid were detected at much lower levels. The results suggest that consideration should be given to the cleavage products as having a putative role as physiologically relevant bioactive components in vivo.     

Lactobacillus acidophilus—Rutin Interplay Investigated by Proteomics

Dietary polyphenols are bioactive molecules that beneficially affect human health, due to their anti-oxidant, anti-inflammatory, cardio-protective and chemopreventive properties. They are absorbed in a very low percentage in the small intestine and reach intact the colon, where they are metabolized by the gut microbiota. Although it is well documented a key role of microbial metabolism in the absorption of polyphenols and modulation of their biological activity, molecular mechanisms at the basis of the bacteria-polyphenols interplay are still poorly understood. In this context, differential proteomics was applied to reveal adaptive response mechanisms that enabled a potential probiotic Lactobacillus acidophilus strain to survive in the presence of the dietary polyphenol rutin. The response to rutin mainly modulated the expression level of proteins involved in general stress response mechanisms and, in particular, induced the activation of protein quality control systems, and affected carbohydrate and amino acid metabolism, protein synthesis and cell wall integrity. Moreover, rutin triggered the expression of proteins involved in oxidation-reduction processes.This study provides a first general view of the impact of dietary polyphenols on metabolic and biological processes of L. acidophilus.     

Enzymatic assays and molecular modeling studies of Schisandra chinensis lignans and phenolics from fruit and leaf extracts

Abstract

Considerable interest has been shown in natural sources and their compounds in developing new therapeutically agents for different diseases. In this framework, investigations performed on this topic play a central role for human health and drug development process. Schisandra chinensis (Turcz.) Baill is a medicinal and edible plant showing highly advantageous bioactivity and nutritional value. The main bioactive compounds from its fruits are lignans, derivatives of dibenzocyclooctadiene whereas concerning its leaves, phenolic acids, and flavonoids are dominant. The purpose of this study was to investigate the enzyme inhibitory potential on selected carbohydrate hydrolases, cholinesterases, and tyrosinase of extracts from fruits and leaves of Schisandra in relation with their main bioactive compounds. Furthermore, the interactions between dominant compounds (schisandrol A, schisandrol B, schisandrin B, and cinnamic acid) from extracts and selected enzymes were investigated by molecular modeling and molecular dynamic studies in order to explain at a molecular level our findings.     

Extraction and analysis of polyphenols: recent trends

In recent years, there has been an increasing interest in diets rich in fruits and vegetables and this is mostly due to their presumed role in the prevention of various degenerative diseases, such as cancer and cardiovascular diseases. This is mainly due to the presence of bioactive compounds, such as polyphenols, carotenoids, among others. Polyphenols are one of the main classes of secondary metabolites derived from plants offering several health benefits resulting in their use as functional foods. Prior to the use of these polyphenols in specific applications, such as food, pharmaceutical, and the cosmetic industries, they need to be extracted from the natural matrices, then analyzed and characterized. The development of an efficient procedure for the extraction, proper analysis, and characterization of phenolic compounds from different sources is a challenging task due to the structural diversity of phenolic compounds, a complex matrix, and their interaction with other cellular components. In this light, this review discusses different methods of extraction, analysis, and the structural characterization of polyphenolic compounds.     

Cyclomaltooligosaccharide-assisted spectroscopic discrimination of phthalimido-derived amino acids through the formation of molecular aggregates

Spectroscopic evidence was used to demonstrate the formation of molecular associates in an aqueous solution of phthalimido tryptophan. These molecular associates are loosely formed through pi-pi aromatic stacking, properties that are not sufficient to cause NMR spectroscopic enantiomeric discrimination. A cyclomaltooligosaccharide with a larger cavity, such as cyclomaltooctaose (gamma-cyclodextrin), is capable of forming a ternary complex with these molecular associates and enhances pi-pi aromatic stacking interactions, resulting in NMR enantiomeric discrimination. Electrospray-ionization mass spectroscopy (ESIMS) and NOESY two-dimensional NMR spectroscopic methods were used to study these complexes. Association constants and thermodynamic data for these cyclomaltooligosaccharide complexes were also estimated.     

Encapsulation systems for the delivery of hydrophilic nutraceuticals: Food application

Increased health risk associated with the sedentary life style is forcing the food manufacturers to look for food products with specific or general health benefits e.g. beverages enriched with nutraceuticals like catechin, curcumin rutin. Compounds like polyphenols, flavonoids, vitamins are the good choice of bioactive compounds that can be used to fortify the food products to enhance their functionality. However due to low stability and bioavailability of these bioactives (both hydrophobic and hydrophilic) within the heterogeneous food microstructure and in the Gastro Intestinal Tract (GIT), it becomes extremely difficult to pass on the real health benefits to the consumers.Recent developments in the application of nano-delivery systems for food product development is proving to be a game changer which has raised the expectations of the researchers, food manufacturers and consumers regarding possibility of enhancing the functionality of bioactives within the fortified food products. In this direction, nano/micro delivery systems using lipids, surfactants and other materials (carbohydrates, polymers, complexes, protein) have been fabricated to stabilize and enhance the biological activity of the bioactive compounds.In the present review, current status of the various delivery systems that are used for the delivery of hydrophilic bioactives and future prospects for using other delivery systems that have been not completely explored for the delivery of hydrophilic bioactives e.g. niosomes; bilosomes, cubosomes are discussed.     

Proposed criteria for assessing the efficacy of cancer reduction by plant foods enriched in carotenoids, glucosinolates, polyphenols and selenocompounds

BACKGROUND AND AIMS: The cancer-protective properties of vegetable consumption are most likely mediated through 'bioactive compounds' that induce a variety of physiologic functions including acting as direct or indirect antioxidants, regulating enzymes and controlling apoptosis and the cell cycle. The 'functional food' industry has produced and marketed foods enriched with bioactive compounds, but there are no universally accepted criteria for judging efficacy of the compounds or enriched foods. SCOPE: Carotenoids, glucosinolates, polyphenols and selenocompounds are families of bioactive compounds common to vegetables. Although numerous studies have investigated the agricultural and human health implications of enriching foods with one or more of these compounds, inadequate chemical identification of compounds, lack of relevant endpoints and inconsistencies in mechanistic hypotheses and experimental methodologies leave many critical gaps in our understanding of the benefits of such compounds. This review proposes a decision-making process for determining whether there is reasonable evidence of efficacy for the both the compound and the enriched food. These criteria have been used to judge the evidence of efficacy for cancer prevention by carotenoids, polyphenols, glucosinolates and selenocompounds. CONCLUSIONS: The evidence of efficacy is weak for carotenoids and polyphenols; the evidence is stronger for glucosinolates and lycopene, but production of enriched foods still is premature. Additionally there is unacceptable variability in the amount and chemical form of these compounds in plants. The evidence of efficacy for selenocompounds is strong, but the clinical study that is potentially the most convincing is still in progress; also the variability in amount and chemical form of Se in plants is a problem. These gaps in understanding bioactive compounds and their health benefits should not serve to reduce research interest but should, instead, encourage plant and nutritional scientists to work together to develop strategies for improvement of health through food.     

Solvated protein–DNA docking using HADDOCK

Interfacial water molecules play an important role in many aspects of protein–DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein–DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein–DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein–DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein–DNA complexes.     

Comparative analysis of phenolic acids and flavonoids in shoot cultures of Eryngium alpinum L.: an endangered and protected species with medicinal value

Plant Cell, Tissue and Organ Culture (PCTOC) - Phenolic acids and flavonoids, important bioactive compounds of polyphenols, play a significant role in plants; their impact, mainly as antioxidants,...     

Conformational analysis of N,N-disubstituted-1,4-diazepane orexin receptor antagonists and implications for receptor binding

NMR spectroscopy, X-ray crystallography, and molecular modeling studies indicate that N,N-disubstituted-1,4-diazepane orexin receptor antagonists exist in an unexpected low-energy conformation that is characterized by an intramolecular π-stacking interaction and a twist-boat ring conformation. Synthesis and evaluation of a macrocycle that enforces a similar conformation suggest that this geometry mimics the bioactive conformation.     

Anatomy of a successful imprint: analysing the recognition mechanisms of a molecularly imprinted polymer for quercetin

This study comprises a retrospective analysis of a successful molecular imprint for quercetin with the main aim of deriving rational design strategies for more effective molecularly imprinted polymers. Hence, polymers of varying composition were synthesised and chromatographically characterised to examine the effects of monomer-template ratios. (1)H NMR analysis of the pre-polymerisation mixture yielded further information on the nature of the complexes formed prior to the polymerisation step. A direct correlation between the optimum monomer-template ratio derived from the chromatographic studies and the monomer-template ratio providing the most stable pre-polymerisation complexes observed via (1)H NMR T(1) relaxation time measurements, suggests that the formation of particularly stable pre-polymerisation complexes is responsible for an increased formation of selective binding sites during the polymerisation step. Furthermore, physical aspects of the polymerisation, such as the MIP surface area and macroscopic phase partitioning of the mixture during the polymerisation are investigated. The observed effects and their analytical assessment offer insight into the mechanisms governing MIP selectivity at a molecular level.     

Characterization of the interaction of interleukin-8 with hyaluronan, chondroitin sulfate, dermatan sulfate and their sulfated derivatives by spectroscopy and molecular modeling

The interactions between glycosaminoglycans (GAGs), important components of the extracellular matrix, and proteins such as growth factors and chemokines play critical roles in cellular regulation processes. Therefore, the design of GAG derivatives for the development of innovative materials with bio-like properties in terms of their interaction with regulatory proteins is of great interest for tissue engineering and regenerative medicine. Previous work on the chemokine interleukin-8 (IL-8) has focused on its interaction with heparin and heparan sulfate, which regulate chemokine function. However, the extracellular matrix contains other GAGs, such as hyaluronic acid (HA), dermatan sulfate (DS) and chondroitin sulfate (CS), which have so far not been characterized in terms of their distinct molecular recognition properties towards IL-8 in relation to their length and sulfation patterns. NMR and molecular modeling have been in great part the methods of choice to study the structural and recognition properties of GAGs and their protein complexes. However, separately these methods have challenges to cope with the high degree of similarity and flexibility that GAGs exhibit. In this work, we combine fluorescence spectroscopy, NMR experiments, docking and molecular dynamics simulations to study the configurational and recognition properties of IL-8 towards a series of HA and CS derivatives and DS. We analyze the effects of GAG length and sulfation patterns in binding strength and specificity, and the influence of GAG binding on IL-8 dimer formation. Our results highlight the importance of combining experimental and theoretical approaches to obtain a better understanding of the molecular recognition properties of GAG-protein systems.