Induction of EpRE-mediated gene expression by a series of mediterranean botanicals and their constituents

ETHNOPHARMACOLOGICAL RELEVANCE

A variety of Mediterranean plant species, traditionally used for the prevention and treatment of several health conditions, contain ingredients with potential biological activity of which many remain unexplored. Among the beneficial health effects of bioactive phytochemicals is the activation of cellular defense mechanisms involving the activation of EpRE (electrophile responsive element) - mediated changes in gene expression.

AIM OF THE STUDY

The present study aimed to identify botanicals and their active constituents able to activate the EpRE mediated gene expression within a series of Mediterranean plant species known for their hepatoprotective and/or cardioprotective properties.

MATERIALS AND METHODS

Methanolic extracts of 18 botanicals were prepared and tested for their ability to induce gene expression in EpRE-LUX reporter cells. Subsequently, LC-MS (Liquid Chromatography Mass Spectrometry) analysis combined with MAGMa (MS Annotation based on in silico Generated Metabolites) software for automated compound annotation was used to facilitate tentative identification of the active constituents within two of the active extracts. Selected annotated compounds were tested in the EpRE-LUX reporter gene assay followed by definite identification of the most active ones.

RESULTS

It appeared that 9 of the 18 extracts were able to activate EpRE-mediated gene expression. Many active ingredients of the methanolic extracts from Juglans regia and Rhamnus frangula were revealed. Among them, chrysophanol and aloe-emodin were confirmed to be active EpRE inducing ingredients and were definitely identified in the Rhamnus Frangula extract.

CONCLUSIONS

The protective effect of half of the tested botanical varieties via the activation of EpRE-mediated gene expression was confirmed. The study also provided an example of how in vitro bioassays can be combined with LC-MS and the automated chemical annotation software MAGMa, to identify biologically active constituents in complex botanical extracts.

Carbonization of Human Fingernails: Toward the Sustainable Production of Multifunctional Nitrogen and Sulfur Codoped Carbon Nanodots with Highly Luminescent Probing and Cell Proliferative/Migration Properties

A simple yet effective method is employed to prepare multifunctional fluorescent carbon nanodots (CNDs) from human fingernails. The results demonstrate that the CNDs have excellent optical properties and a quantum yield of 81%, which is attributed to the intrinsic composition of the precursor material itself. The CNDs are used to develop an ultrasensitive fluorescent probe for the detection of hexavalent chromium (limit of detection: 0.3 nM) via a combined inner-filter and static mechanism. Moreover, the toxicity of the CNDs over four epithelial cell lines is assessed. A negligible toxicity is induced on the three of the cell lines, whereas an increase in HEK-293 cell viability is demonstrated, granting cell proliferation properties to the as-synthesized CNDs. According to cell cycle analysis, cell proliferation is achieved by enhancing the transition of cells from the S phase to the G2/M one. Interestingly, CNDs are found to significantly promote cell migration, maybe because of their free-radical scavenging ability, making the CNDs suitable for wound healing applications. In addition, relevant experiments have revealed the blood compatibility of the CNDs. Finally, the CNDs were found suitable for cell imaging applications, and all of the aforementioned merits make it possible for them to be used for extraordinary, more advanced biological applications.

Biologically relevant conformational features of linear and cyclic proteolipid protein (PLP) peptide analogues obtained by high-resolution nuclear magnetic resonance and molecular dynamics

Proteolipid protein (PLP) is one of the main proteins of myelin sheath that are destroyed during the progress of multiple sclerosis (MS). The immunodominant PLP_139-151 epitope is known to induce experimental autoimmune encephalomyelitis (EAE, animal model of MS), wherein residues 144 and 147 are recognized by T cell receptor (TCR) during the formation of trimolecular complex with peptide-antigen and major histocompability complex. The conformational behavior of linear and cyclic peptide analogues of PLP, namely PLP_139-151 and cyclic (139-151) (L¹⁴⁴, R¹⁴⁷) PLP_139-151, have been studied in solution by means of nuclear magnetic resonance (NMR) methods in combination with unrestrained molecular dynamics simulations. The results indicate that the side chains of mutated amino acids in the cyclic analogue have different spatial orientation compared with the corresponding side chains of the linear analogue, which can lead to reduced affinity to TCR. NMR experiments combined with theoretical calculations pave the way for the design and synthesis of potent restricted peptides of immunodominant PLP_139-151 epitope as well as non peptide mimetics that rises as an ultimate goal.

Unscrambling micro-solvation of –COOH and –NH groups in neat dimethyl sulfoxide: insights from 1H-NMR spectroscopy and computational studies

This study investigates the interactions of –COOH and –NH groups in neat DMSO solutions, with special focus on their thermodynamics and kinetics.

1H-NMR based metabolomics study for the detection of the human urine metabolic profile effects of Origanum dictamnus tea ingestion

NMR based metabolomics clarify theOriganum dictamnustea effect upon the human urine metabolome.

Exploring the "forgotten"-OH NMR spectral region in natural products

Significantly enhanced resolution in the -OH NMR spectral region was observed which, in combination with 2D (1)H-(13)C HMBC techniques, will open new avenues in structure analysis of natural products with phenol type -OH groups in complex natural extracts without the need of laborious isolation of the individual compounds.

PBOND: web server for the prediction of proline and non-proline cis/trans isomerization

PBOND is a web server that predicts the conformation of the peptide bond between any two amino acids. PBOND classifies the peptide bonds into one out of four classes, namely cis imide (cis-Pro), cis amide (cis-nonPro), trans imide (trans-Pro) and trans amide (trans-nonPro). Moreover, for every prediction a reliability index is computed. The underlying structure of the server consists of three stages: (1) feature extraction, (2) feature selection and (3) peptide bond classification. PBOND can handle both single sequences as well as multiple sequences for batch processing. The predictions can either be directly downloaded from the web site or returned via e-mail. The PBOND web server is freely available at http://195.251.198.21/pbond.html.

Phytochemicals in olive-leaf extracts and their antiproliferative activity against cancer and endothelial cells

Olive oil compounds is a dynamic research area because Mediterranean diet has been shown to protect against cardiovascular disease and cancer. Olive leaves, an easily available natural material of low cost, share possibly a similar wealth of health benefiting bioactive phytochemicals. In this work, we investigated the antioxidant potency and antiproliferative activity against cancer and endothelial cells of water and methanol olive leaves extracts and analyzed their content in phytochemicals using LC-MS and LC-UV-SPE-NMR hyphenated techniques. Olive-leaf crude extracts were found to inhibit cell proliferation of human breast adenocarcinoma (MCF-7), human urinary bladder carcinoma (T-24) and bovine brain capillary endothelial (BBCE). The dominant compound of the extracts was oleuropein; phenols and flavonoids were also identified. These phytochemicals demonstrated strong antioxidant potency and inhibited cancer and endothelial cell proliferation at low micromolar concentrations, which is significant considering their high abundance in fruits and vegetables. The antiproliferative activity of crude extracts and phytochemicals against the cell lines used in this study is demonstrated for the first time.

Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation

Background

Polypeptides are composed of amino acids covalently bonded via a peptide bond. The majority of peptide bonds in proteins is found to occur in the trans conformation. In spite of their infrequent occurrence, cis peptide bonds play a key role in the protein structure and function, as well as in many significant biological processes.

Results

We perform a systematic analysis of regions in protein sequences that contain a proline cis peptide bond in order to discover non-random associations between the primary sequence and the nature of proline cis/trans isomerization. For this purpose an efficient pattern discovery algorithm is employed which discovers regular expression-type patterns that are overrepresented (i.e. appear frequently repeated) in a set of sequences. Four types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, iii) pattern discovery using a structural equivalency set and iv) pattern discovery using certain amino acids' physicochemical properties. The extracted patterns are carefully validated using a specially implemented scoring function and a significance measure (i.e. log-probability estimate) indicative of their specificity. The score threshold for the first three types of pattern discovery is 0.90 while for the last type of pattern discovery 0.80. Regarding the significance measure, all patterns yielded values in the range [-9, -31] which ensure that the derived patterns are highly unlikely to have emerged by chance. Among the highest scoring patterns, most of them are consistent with previous investigations concerning the neighborhood of cis proline peptide bonds, and many new ones are identified. Finally, the extracted patterns are systematically compared against the PROSITE database, in order to gain insight into the functional implications of cis prolyl bonds.

Conclusion

Cis patterns with matches in the PROSITE database fell mostly into two main functional clusters: family signatures and protein signatures. However considerable propensity was also observed for targeting signals, active and phosphorylation sites as well as domain signatures.

Prediction of cis/trans isomerization using feature selection and support vector machines

In protein structures the peptide bond is found to be in trans conformation in the majority of the cases. Only a small fraction of peptide bonds in proteins is reported to be in cis conformation. Most of these instances (>90%) occur when the peptide bond is an imide (X-Pro) rather than an amide bond (X-nonPro). Due to the implication of cis/trans isomerization in many biologically significant processes, the accurate prediction of the peptide bond conformation is of high interest. In this study, we evaluate the effect of a wide range of features, towards the reliable prediction of both proline and non-proline cis/trans isomerization. We use evolutionary profiles, secondary structure information, real-valued solvent accessibility predictions for each amino acid and the physicochemical properties of the surrounding residues. We also explore the predictive impact of a modified feature vector, which consists of condensed position-specific scoring matrices (PSSMX), secondary structure and solvent accessibility. The best discriminating ability is achieved using the first feature vector combined with a wrapper feature selection algorithm and a support vector machine (SVM). The proposed method results in 70% accuracy, 75% sensitivity and 71% positive predictive value (PPV) in the prediction of the peptide bond conformation between any two amino acids. The output of the feature selection stage is investigated in order to identify discriminatory features as well as the contribution of each neighboring residue in the formation of the peptide bond, thus, advancing our knowledge towards cis/trans isomerization.

Predicting peptide bond conformation using feature selection and the Naïve Bayes approach

Distinguishing cis peptide bonds from trans isomers in protein sequences facilitates the exploration of protein structures and functions. In this study, we evaluated the effect of a large and informative feature vector, towards the reliable prediction of peptide bond conformation between any two amino acids. We used multiple sequence alignment, secondary structure information, real valued solvent accessibility predictions for each amino acid and physicochemical properties of the surrounding residues. A three stage schema was developed, comprising of feature extraction, feature selection and peptide bond classification between any two amino acids. We also explored the performance achieved when using the full feature vector without performing feature selection. The best discriminating ability was achieved using a Naïve Bayes classifier, combined with wrapper feature selection. The proposed approach yielded prediction accuracy 86%, sensitivity 82% and specificity 90% in discriminating cis and trans peptide bond conformations.

Identification of the major constituents of Hypericum perforatum by LC/SPE/NMR and/or LC/MS

The newly established hyphenated instrumentation of LC/DAD/SPE/NMR and LC/UV/(ESI)MS techniques have been applied for separation and structure verification of the major known constituents present in Greek Hypericum perforatum extracts. The chromatographic separation was performed on a C18 column. Acetonitrile-water was used as a mobile phase. For the on-line NMR detection, the analytes eluted from column were trapped one by one onto separate SPE cartridges, and hereafter transported into the NMR flow-cell. LC/DAD/SPE/NMR and LC/UV/MS allowed the characterization of constituents of Greek H. perforatum, mainly naphtodianthrones (hypericin, pseudohypericin, protohypericin, protopseudohypericin), phloroglucinols (hyperforin, adhyperforin), flavonoids (quercetin, quercitrin, isoquercitrin, hyperoside, astilbin, miquelianin, I3,II8-biapigenin) and phenolic acids (chlorogenic acid, 3-O-coumaroylquinic acid). Two phloroglucinols (hyperfirin and adhyperfirin) were detected for the first time, which have been previously reported to be precursors in the biosynthesis of hyperforin and adhyperforin.

Solvation Properties of N-Substituted Cis and Trans Amides Are Not Identical: Significant Enthalpy and Entropy Changes Are Revealed by the Use of Variable Temperature 1H NMR in Aqueous and Chloroform Solutions and ab Initio Calculations

The cis/trans conformational equilibrium of N-methyl formamide (NMF) and the sterically hindered tert-butylformamide (TBF) was investigated by the use of variable temperature gradient 1H NMR in aqueous solution and in the low dielectric constant and solvation ability solvent CDCl3 and various levels of first principles calculations. The trans isomer of NMF in aqueous solution is enthalpically favored relative to the cis (deltaH(o) = -5.79 +/- 0.18 kJ mol(-1)) with entropy differences at 298 K (298 x deltaS(o) = -0.23 +/- 0.17 kJ mol(-1)) playing a minor role. The experimental value of the enthalpy difference strongly decreases (deltaH(o) = -1.72 +/- 0.06 kJ mol(-1)), and the contribution of entropy at 298 K (298 x deltaS(o) = -1.87 +/- 0.06 kJ mol(-1)) increases in the case of the sterically hindered tert-butylformamide. The trans isomer of NMF in CDCl3 solution is enthalpically favored relative to the cis (deltaH(o) = -3.71 +/- 0.17 kJ mol(-1)) with entropy differences at 298 K (298 x deltaS(o) = 1.02 +/- 0.19 kJ mol(-1)) playing a minor role. In the sterically hindered tert-butylformamide, the trans isomer is enthalpically disfavored (deltaH(o) = 1.60 +/- 0.09 kJ mol(-1)) but is entropically favored (298 x deltaS(o) = 1.71 +/- 0.10 kJ mol(-1)). The results are compared with literature data of model peptides. It is concluded that, in amide bonds at 298 K and in the absence of strongly stabilizing sequence-specific inter-residue interactions involving side chains, the free energy difference of the cis/trans isomers and both the enthalpy and entropy contributions are strongly dependent on the N-alkyl substitution and the solvent. The significant decreasing enthalpic benefit of the trans isomer in CDCl3 compared to that in H2O, in the case of NMF and TBF, is partially offset by an adverse entropy contribution. This is in agreement with the general phenomenon of enthalpy versus entropy compensation. B3LY/6-311++G** and MP2/6-311++G** quantum chemical calculations confirm the stability orders of isomers and the deltaG decrease in going from water to CHCl3 as solvent. However, the absolute calculated values, especially for TBF, deviate significantly from the experimental values. Consideration of the solvent effects via the PCM approach on NMF x H2O and TBF x H2O supermolecules improves the agreement with the experimental results for TBF isomers, but not for NMF.

On the Structural Basis of the Hypertensive Properties of Angiotensin II: A Solved Mystery or a Controversial Issue?

Angiotensin II (AII), Asp1-Arg2-Val3-Tyr4-Ile5-His6-Pro7-Phe8, the primary active hormone of the Renin-Angiotensin-System (RAS), is a major vasoconstrictor implicated in the cause of hypertension. To unravel the question of the biologically active conformation(s) of this flexible peptide hormone and to better understand the stereoelectronic requirements that lead to the molecular basis of hypertension, we will analyze research efforts in the identification of pharmacophoric groups of AII and three general approaches for structural characterisation: the free peptide-ligand approach, the receptor based approach, and approaches that target the peptide-receptor complex. The free peptide-ligand based approach can be further categorized to: (a) conformational analysis of AII and linear peptide analogues in aqueous solution; (b) the use of solvents of medium dielectric constants; (c) conformationally restricted analogues, with emphasis to cyclic analogues; (d) the use of receptor-simulating environments, and (e) non-peptide mimetics. The receptor and peptide-receptor based approaches can be categorised to: (a) The use of monoclonal antibodies and (b) the generic description of AII receptor sites through homology modelling and mutagenesis studies. These investigations, with particular emphasis to recent developments, have greatly assisted in the identification of pharmacophoric groups for receptor activation and the development of several models of AII-receptor complexes.

14N NMR relaxation times of several protein amino acids in aqueous solution--comparison with 17O NMR data and estimation of the relative hydration numbers in the cationic and zwitterionic forms

The 14N nuclear magnetic resonance (NMR) linewidths of the alpha-amino groups of several protein amino acids were measured in aqueous solution, with and without composite proton decoupling, to estimate the effect of proton exchange and molecular weight on the linewidths. It is shown that, contrary to earlier claims, the increase in the linewidth at low pH is not exclusively due to the effect of proton exchange broadening. The 14N linewidths, under composite proton decoupling, increase with the bulk of the amino acid, and increase at low pH. Statistical treatment of the experimental 14N and literature 17O NMR data was performed assuming two models: (i) an isotropic molecular reorientation of a rigid sphere in a medium of viscosity eta, (ii) a stochastic diffusion of the amino and carboxyl groups comprising contributions from internal (tauint) and overall (taumol) motions. Assuming a single correlation time from overall molecular reorientation (taumol), then, a linear correlation was found between the linewidths and the molecular weights of the protein amino acids at the pH values 0.5 and 6.0, which are characteristic of the cationic and zwitterionic forms, respectively. The slopes of the straight-lines were found to be dependent of pH for 14N, contrary to the 17O linear correlations whose slopes were found to be independent of pH. Assuming effective correlation times of the amino and carboxyl groups, which comprise contributions from the internal (tauint) and overall (taumol) motions, then, a significant improvement of the statistics of the regression analysis was observed. The 14N relaxation data, in conjunction with 17O NMR linewidths, can be interpreted by assuming that the 14N quadrupole coupling constants (NQCCs) are influenced by the protonation state of the carboxyl group, the 17O NQCCs remain constant, and the cationic form of the amino acids is hydrated by an excess of 1-3 molecules of water relative to the zwitterionic state.

Synthetic analogs for oxovanadium(IV/V)-glutathione interaction: an NMR, EPR, synthetic and structural study of oxovanadium(IV/V) compounds with sulfhydryl-containing pseudopeptides and dipeptides

The reaction of [VO(CH3COO)2(phen)] (phen = 1,10-phenanthroline) with the sulfhydryl-containing pseudopeptides (scp), N-(2-mercaptopropionyl)glycine (H3mpg), N-(2-mercaptopropionyl)cysteine (H4m2pc), N-(3-mercaptopropionyl)cysteine (H4m3pc) and the dipeptides glycylglycine (H2glygly) and glycyl-L-alanine (H2glyala), in the presence of triethylamine, results in the formation of the compounds Et3NH[VO(mpg)(phen)] (1), (Et3NH)2[VO(m2pc)] (4), [(Et3NH)2[VO(m3pc) (5), [VO(glygly)(phen)] x 2CH3OH (2 x 2CH3OH) and [VO(glyala)(phen)] x CH3OH (3 x CH3OH). Evidence for the molecular connectivity in 2 x CH3OH was established by X-ray crystallography, showing the vanadium(IV) atom ligated to a tridentate glygly2- ligand at the N(amine), N(peptide) and O(carboxylato) atoms. Combination of the correlation plot of the EPR parameters gz versus Az, together with the additivity relationship supported the prediction of the equatorial donor atom sets of the V(IV)O2+ center at various pH values for the V(IV)O2+-glutathione system considered in this study. Model NMR studies (interaction of vanadium(V) with the scp H3mpg) showed that there is a possibility of vanadium(V) ligation to glutathione.

Involvement of phospholipids in apolipoprotein B modification during low density lipoprotein oxidation

An increased amount of phospholipids remained attached on delipidated apolipoprotein B originated from oxidized low density lipoprotein (LDL). 31P nuclear magnetic resonance analysis of such apolipoprotein showed an organic phosphorus peak at -0.55 ppm, which suggests the formation of adducts (most probably Schiff bases) of oxidized phospholipids with apolipoprotein B. The above reaction occurs in parallel with the hydrolysis of oxidized phospholipids, catalyzed by the LDL-attached platelet-activating factor acetylhydrolase, and may contribute to the proatherogenic effect of oxidatively modified low density lipoprotein.