Identification of Mortalin as the Main Interactor of Mycalin A, a Poly-Brominated C-15 Acetogenin Sponge Metabolite, by MS-Based Proteomics

Mycalin A (MA) is a polybrominated C-15 acetogenin isolated from the marine sponge Mycale rotalis. Since this substance displays a strong antiproliferative bioactivity towards some tumour cells, we have now directed our studies towards the elucidation of the MA interactome through functional proteomic approaches, (DARTS and t-LIP-MS). DARTS experiments were performed on Hela cell lysates with the purpose of identifying MA main target protein(s); t-LiP-MS was then applied for an in-depth investigation of the MA-target protein interaction. Both these techniques exploit limited proteolysis coupled with MS analysis. To corroborate LiP data, molecular docking studies were performed on the complexes. Finally, biological and SPR analysis were conducted to explore the effect of the binding. Mortalin (GRP75) was identified as the MA's main interactor. This protein belongs to the Hsp70 family and has garnered significant attention due to its involvement in certain forms of cancer. Specifically, its overexpression in cancer cells appears to hinder the pro-apoptotic function of p53, one of its client proteins, because it becomes sequestered in the cytoplasm. Our research, therefore, has been focused on the possibility that MA might prevent this sequestration, promoting the re-localization of p53 to the nucleus and facilitating the apoptosis of tumor cells.

Analysis of the Fecal Metabolomic Profile in Breast vs. Different Formula Milk Feeding in Late Preterm Infants

Human milk is the gold standard for infant nutrition, but when it is not available or insufficient to satisfy the needs of the infant, formula milk is proposed as an effective substitute. A prospective observational cohort study was conducted on late preterm infants fed with breast and two different formula milks. On this basis, they were divided into three groups: group FMPB (fed with formula + postbiotic), group FM (fed with standard formula), and group BM (breastfed). Stool samples for a metabolomic study were collected at T0 (5-7 days after birth), T1 (30 days of life), and T2 (90 days of life), giving rise to 74 samples analyzed via liquid chromatography coupled with high-resolution mass spectrometry. The T0, T1, and T2 LC-MS raw data were processed for Partial Least Square Discriminant Analysis (PLS-DA), followed by a statistical analysis. This preliminary study highlighted a good overlapping between the fecal metabolome of breast and substitute feeding systems, confirming the efficacy of the formula preparations as breast milk substitutes. Moreover, several similarities were also detected between the FMPB and BM metabolome, highlighting that the addition of a postbiotic to standard formula milk could be more effective and considered a better alternative to breast milk.

NMR Metabolomics and Chemometrics of Commercial Varieties of Phaseolus vulgaris L. Seeds from Italy and In Vitro Antioxidant and Antifungal Activity

The metabolite fingerprinting of four Italian commercial bean seed cultivars, i.e., Phaseolus Cannellino (PCANN), Controne (PCON), Vellutina (PVEL), and Occhio Nero (PON), were investigated by Nuclear Magnetic Resonance (NMR) spectroscopy and multivariate data analysis. The hydroalcoholic and organic extract analysis disclosed more than 32 metabolites from various classes, i.e., carbohydrates, amino acids, organic acids, nucleosides, alkaloids, and fatty acids. PVEL, PCON, and PCANN varieties displayed similar chemical profiles, albeit with somewhat different quantitative results. The PON metabolite composition was slightly different from the others; it lacked GABA and pipecolic acid, featured a higher percentage of malic acid than the other samples, and showed quantitative variations of several metabolites. The lipophilic extracts from all four cultivars demonstrated the presence of omega-3 and omega-6 unsaturated fatty acids. After the determination of the total phenolic, flavonoids, and condensed tannins content, in vitro antioxidant activity was then assessed using the DPPH scavenging activity, the ABTS scavenging assay, and ferric-reducing antioxidant power (FRAP). Compared to non-dark seeds (PCON, PCANN), brown seeds (PVEL, PON) featured a higher antioxidant capacity. Lastly, only PON extract showed in vitro antifungal activity against the sclerotia growth of S. rolfsii, by inhibiting halo growth by 75%.

Chemoproteomics Reveals USP5 (Ubiquitin Carboxyl-Terminal Hydrolase 5) as Promising Target of the Marine Polyketide Gracilioether A

Mass spectrometry-based chemical proteomic approaches using limited proteolysis have become a powerful tool for the identification and analysis of the interactions between a small molecule (SM) and its protein target(s). Gracilioether A (GeA) is a polyketide isolated from a marine sponge, for which we aimed to trace the interactome using this strategy. DARTS (Drug Affinity Responsive Target Stability) and t-LiP-MS (targeted-Limited Proteolysis-Mass Spectrometry) represented the main techniques used in this study. DARTS was applied on HeLa cell lysate for the identification of the GeA target proteins, and t-LiP-MS was employed to investigate the protein's regions involved in the binding with GeA. The results were complemented through the use of binding studies using Surface Plasmon Resonance (SPR) and in silico molecular docking experiments. Ubiquitin carboxyl-terminal hydrolase 5 (USP5) was identified as a promising target of GeA, and the interaction profile of the USP5-GeA complex was explained. USP5 is an enzyme involved in the pathway of protein metabolism through the disassembly of the polyubiquitin chains on degraded proteins into ubiquitin monomers. This activity is connected to different cellular functions concerning the maintenance of chromatin structure and receptors and the degradation of abnormal proteins and cancerogenic progression. On this basis, this structural information opens the way to following studies focused on the definition of the biological potential of Gracilioether A and the rational development of novel USP5 inhibitors based on a new structural skeleton.

Phytochemical Investigation and Biofilm-Inhibitory Activity of Bachtiari Savory (Satureja bachtiarica Bunge) Aerial Parts

Satureja bachtiarica is an endemic plant from the Lamiaceae family, growing in the Zagros mountain range in Iran. Even if S. bachtiarica is reported to possess many biological activities, little is known about its chemical composition. For this reason, in the present research, a phytochemical investigation of this species was carried out. To have a preliminary metabolite profile of S. bachtiarica, the n-BuOH extract was analyzed using LC-ESI/LTQOrbitrap/MS/MS in negative ion mode, allowing the identification of specialized metabolites belonging to flavonoid, monoterpene, indol, phenylpropanoid, phenolic, lignan, coumarin, biphenyl, and triterpene classes. The LC-MS/MS analysis guided the isolation of compounds, and their structures were characterized using spectroscopic methods including 1D- and 2D-NMR experiments and HRMSn analysis. In this way, a compound never reported before belonging to the biphenyl class was identified. Total flavonoid content of the extract along with the antioxidant activity were assessed. Based on the traditional uses of S. bachtiarica suggesting potential antibacterial properties, an evaluation of the biofilm inhibitory activity of the extract and isolated compounds against mature biofilms of Acinetobacter baumannii, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, and Staphylococcus aureus, as well as their influence on the metabolism of sessile bacterial cells, was conducted. The results evidenced that some compounds including parmentin B, biphenyls, and 1-(1H-indole-3-carboxylate)-β-D-glucopyranoside might inhibit some changes occurring in the bacterial cells, which increases their virulence. In particular, biphenyl derivatives at a concentration of 80 μg/mL were capable of limiting remarkably the mature biofilms of A. baumannii and L. monocytogenes remarkably at a percentage ranging between 52.76% and 75.02%, and they reached an inhibition percentage of 69.28 % against E. coli. Biphenyl derivatives were also effective in exerting an inhibitory action against the mature biofilm of P. aeruginosa (inhibition ranging from 59.38% to 81.08%) and Staphylococcus aureus (inhibition percentage reached 82.94%). Of note, the biphenyl derivatives resulted in being capable of acting on the metabolism of the cells within the biofilm of all five pathogens.

LC-MS and NMR Based Plant Metabolomics: A Comprehensive Phytochemical Investigation of Symphytum anatolicum

The application of metabolomics to the study of plants is growing because of the current development of analytical techniques. The most commonly used analytical technology driving plant metabolomics studies is Mass Spectrometry (MS) coupled to liquid chromatography (LC). In recent years, Nuclear Magnetic Resonance (NMR) spectroscopy, not requiring a previous chromatographic separation, has been receiving growing attention for metabolite fingerprinting of natural extracts. Herein, an integrated LC-MS and 1H NMR metabolomic approach provided a comprehensive phytochemical characterization of Symphytum anatolicum whole plant, taking into account both primary and specialized metabolites. Moreover, the NMR analyses provided direct quantitative information. Species belonging to the Symphytum genus, known as comfrey, have shown several biological activities including anti-inflammatory, analgesic, hepatoprotective, antifungal, and antibacterial. The LC-MS profile showed the presence of 21 main specialized metabolites, belonging to the classes of flavonoids, phenylpropanoids, salvianols, and oxylipins. The 1H NMR spectrum revealed the occurrence of metabolites including organic acids, phenolics, flavonoids, sugars, and amino acids. A quantitative analysis of these metabolites was performed and their concentration was obtained with respect to the known concentration of TSP, by means of the software package Chenomx which allows quantification of individual components in the NMR spectra. Furthermore, the phenolic content, antioxidant activity, glucosidase, and tyrosinase inhibitory activity of S. anatolicum extract were evaluated. The resulting bioactivity profile suggests how S. anatolicum represents a source of metabolites with health-promoting activity.

Effects of White and Blue-Red Light on Growth and Metabolism of Basil Grown under Microcosm Conditions

Indoor farming of basil (Ocimum basilicum L.) under artificial lighting to support year-round produce demand is an area of increasing interest. Literature data indicate that diverse light regimes differently affect downstream metabolic pathways which influence basil growth, development and metabolism. In this study, basil was grown from seedlings to fully developed plants in a microcosm, an innovative device aimed at growing plants indoor as in natural conditions. Specifically, the effects of white (W) and blue-red (BR) light under a photosynthetic photon flux density of 255 μmol m^-2 s^-1 on plant growth, photochemistry, soluble nutrient concentration and secondary metabolism were investigated. Plants grew taller (41.8 ± 5.0 vs. 28.4 ± 2.5 cm) and produced greater biomass (150.3 ± 24.2/14.7 ± 2.0 g vs. 116.2 ± 28.3/12.3 ± 2.5 g fresh/dry biomass) under W light compared to BR light. The two lighting conditions differently influenced the soluble nutrient concentration and the translocation rate. No photosynthetic stress was observed under the two lighting regimes, but leaves grown under W light displayed higher levels of maximum quantum yield of PSII and electron transport rate. Sharp differences in metabolic patterns under the two lighting regimes were detected with higher concentrations of phenolic compounds under the BR light.

A Comparative UHPLC-Q-Trap-MS/MS-Based Metabolomics Analysis to Distinguish Foeniculum vulgare Cultivars' Antioxidant Extracts

Among the environmental factors, seasonality is the one which most affects the metabolome of a plant. Depending on the harvest season, the plant may have a variable content of certain metabolites and thus may have different biological properties. Foeniculum vulgare is an annual plant whose cultivation creates large amounts of waste rich in bioactive compounds. The present investigation was performed with the aim of determining the amount of biologically active compounds in F. vulgare wastes obtained from varieties of different seasonality. Ten polyphenolic compounds were quantified in the little stems and leaves of Tiziano, Pegaso, and Preludio cultivars by ultra performance liquid chromatography (UPLC) hyphenated to QTRAP mass spectrometry by using the MRM (multiple reaction monitoring) method. The antioxidant activity of hydroalcoholic extracts was then evaluated using TEAC and DPPH spectrophotometric assays, followed by a multivariate statistical analysis to determine the correlation between metabolite expression and antioxidant activity. The Preludio variety, grown in summer, showed a higher content of bioactive compounds, which guarantees it a better antioxidant power; kaempferol 3-O-glucuronide, quercetin 3-O-glucuronide, and quercetin 3-O-glucoside are the polyphenolic compounds that could be mainly responsible for the antioxidant effect of fennel. The PLS chemometric model, which correlated quantitative data obtained by a sensitive and selective LC-ESI-QTrap-MS/MS analysis of antioxidant activity, resulted in a selective tool to detect the compounds responsible for the activity shown by the extracts in chemical tests.

Sustainable Extraction Methods Affect Metabolomics and Oxidative Stability of Myrtle Seed Oils Obtained from Myrtle Liqueur By-Products: An Electron Paramagnetic Resonance and Mass Spectrometry Approach

Myrtle liqueur production generates high amounts of by-products that can be employed for the extraction of bioactive compounds. Bio-based, non-toxic and biodegradable solvents (ethyl acetate and 2-methyltetrahydrofuran), and a mechanical extraction were applied to myrtle seeds, by-products of the liqueur production, to extract oils rich in phenolic compounds. The oils obtained were characterized for yield, peroxide value (PV), lipid composition, and total phenolic concentration (TPC). The phenolic profile of the oils, determined by LC-MS, the antioxidant activity, and the oxidative stability were also analyzed. A validated UHPLC-ESI-QTRAP-MS/MS analytical method in multiple reaction monitoring (MRM) mode was applied to quantify myricetin and its main derivatives in myrtle oils. The results pointed out clear differences among extraction methods on myricetin concentration. The oxidative stability of myrtle oils was studied with electron paramagnetic resonance (EPR) spectroscopy highlighting the effect of the extraction method on the oxidation status of the oils and the role of phenolic compounds in the evolution of radical species over time. A principal component analysis applied to LC-MS data highlighted strong differences among phenolic profiles of the oils and highlighted the role of myricetin in the oxidative stability of myrtle oils. Myrtle oil, obtained from the by-products of myrtle liqueur processing industry, extracted with sustainable and green methods might have potential application in food or cosmetic industries.

LC-ESI/LTQOrbitrap/MS Metabolomic Analysis of Fennel Waste (Foeniculum vulgare Mill.) as a Byproduct Rich in Bioactive Compounds

Food industries produce a high amount of waste every year. These wastes represent a source of bioactive compounds to be used to produce cosmetic and nutraceutical products. In this study, the possibility to retrain food waste as a potential source of bioactive metabolites is evaluated. In particular, metabolite profiles of different parts (bulb, leaves, stems and little stems) of fennel waste were investigated by liquid chromatography coupled with mass spectrometry (LC-ESI/LTQ Orbitrap MS). To discriminate the different plant parts, a Multivariate Data Analysis approach was developed. Metabolomic analysis allowed the identification of different metabolites mainly belonging to hydroxycinnamic acid derivatives, flavonoid glycosides, flavonoid aglycons, phenolic acids, iridoid derivatives and lignans. The identification of compounds was based on retention times, accurate mass measurements, MS/MS data, exploration on specific metabolites database and comparison with data reported in the literature for F. vulgare. Moreover, the presence of different oxylipins was relieved; these metabolites for the first time were identified in fennel. Most of the metabolites identified in F. vulgare possess anti-inflammatory, antioxidant and/or immunomodulatory properties. Considering that polyphenols are described to possess antioxidant activity, spectrophotometric tests were performed to evaluate the antioxidant activity of each part of the fennel.

LC-ESI/LTQ-Orbitrap-MS Based Metabolomics in Evaluation of Bitter Taste of Arbutus unedo Honey

Strawberry tree honey is a high-value honey from the Mediterranean area and it is characterised by a typical bitter taste. To possibly identify the secondary metabolites responsible for the bitter taste, the honey was fractionated on a C18 column and the individual fractions were subjected to sensory analysis and then analysed by liquid chromatography coupled with high-resolution tandem mass spectrometry in negative ion mode, using a mass spectrometer with an electrospray source coupled to a hybrid high resolution mass analyser (LC-ESI/LTQ-Orbitrap-MS). A chemometric model obtained by preliminary principal component analysis (PCA) of LC-ESI/LTQ-Orbitrap-MS data allowed the identification of the fractions that caused the perception of bitterness. Subsequently, a partial least squares (PLS) regression model was built. The studies carried out with multivariate analysis showed that unedone (2-(1,2-dihydroxypropyl)-4,4,8-trimethyl-1-oxaspiro [2.5] oct-7-en-6-one) can be considered responsible for the bitter taste of strawberry tree honey. Confirmation of the bitter taste of unedone was obtained by sensory evaluation of a pure standard, allowing it to be added to the list of natural compounds responsible for giving the sensation of bitterness to humans.

Identification of Bioactive Phytochemicals in Mulberries

Mulberries are consumed either freshly or as processed fruits and are traditionally used to tackle several diseases, especially type II diabetes. Here, we investigated the metabolite compositions of ripe fruits of both white (Morus alba) and black (Morus nigra) mulberries, using reversed-phase HPLC coupled to high resolution mass spectrometry (LC-MS), and related these to their in vitro antioxidant and α-glucosidase inhibitory activities. Based on accurate masses, fragmentation data, UV/Vis light absorbance spectra and retention times, 35 metabolites, mainly comprising phenolic compounds and amino sugar acids, were identified. While the antioxidant activity was highest in M. nigra, the α-glucosidase inhibitory activities were similar between species. Both bioactivities were mostly resistant to in vitro gastrointestinal digestion. To identify the bioactive compounds, we combined LC-MS with 96-well-format fractionation followed by testing the individual fractions for α-glucosidase inhibition, while compounds responsible for the antioxidant activity were identified using HPLC with an online antioxidant detection system. We thus determined iminosugars and phenolic compounds in both M. alba and M. nigra, and anthocyanins in M. nigra as being the key α-glucosidase inhibitors, while anthocyanins in M. nigra and both phenylpropanoids and flavonols in M. alba were identified as key antioxidants in their ripe berries.