Time-related multivariate strategy for the comprehensive evaluation of microbial chemical data.

INTRODUCTION: In microbial metabolomics, the use of multivariate data analysis (MDVA) has not been comprehensively explored regarding the different techniques available and the information that each gives about the metabolome. To overcome these limitations, here we show the use of Fusarium oxysporum cultured in the presence of exogenous alkaloids as a model system to demonstrate a comprehensive strategy for metabolic profiling. MATHERIALS AND METHODS: F. oxysporum was harvested on different days of incubation after alkaloidal addition, and the chemical profiles were compared using LC-MS data and MDVA. We show significant innovation to evaluate the chemical production of microbes during their life cycle by utilizing the full capabilities of Partial Least Square (PLS) with microbial-specific modeling that considers incubation days, media culture availability, and growth rate in solid media. RESULTS AND DISCUSSCION: Results showed that the treatment of the Y-data and the use of both PLS regression and discrimination (PLSr and PLS-DA) inferred complemental chemical information. PLSr revealed the metabolites that are produced/consumed during fungal growth, whereas PLS-DA focused on metabolites that are only consumed/produced at a specific period. Both regression and classificatory analysis were equally important to identify compounds that are regulated and/or selectively produced as a response to the presence of the alkaloids. Lastly, we report the annotation of analogs from the piperidine alkaloids biotransformed by F. oxysporum as a defense response to the toxic plant metabolites. These molecules do not show the antimicrobial potential of their precursors in the fungal extracts and were rapidly produced and consumed within 4 days of microbial growth.

Induction of metabolic variability of the endophytic fungus Xylaria sp. by OSMAC approach and experimental design.

This work has as the main focus, to analyze the behavior of physic-chemical variations from the fungus Xylaria sp., through the OSMAC (One Strain, Many Compounds) approach as an efficient way of obtaining new compounds. To perform such inductions and to explore the variability of the metabolic network of this microorganism, a factorial design was designed to induce variability (or enhancement) of metabolites. In view of chemometric insights, the planned inductions were imposed on the microorganism and variations in the chemical profile were observed in the crude extracts. Through mass spectrometry (HR-ESI-MS) and nuclear magnetic resonance-based profiles, combined with multivariate analysis through Principal Component Analysis (PCA), it was observed a marked variability of signals, confirming the efficacy in the metabolic alteration, defining the culture medium and agitation as the most important variables in the metabolic variability of the fungus. However, the extract mass is more significant for the agitation variable, and there is no relationship between the mass of crude extract and the amount of molecular signals of the complex matrices studied.

Characterization of aporphine alkaloids by electrospray ionization tandem mass spectrometry and density functional theory calculations.

RATIONALE: Aporphine alkaloids represent a large group of isoquinoline natural products with important roles in biological and biomedical areas. Their characterization by electrospray ionization tandem mass spectrometry (ESI-MS/MS) can contribute to their rapid identification in complex biological matrices. METHODS: We report the fragmentation of protonated 7,7-dimethylaporphine alkaloids by ESI-MS/MS, and the putative annotation of aporphine alkaloids in plant extracts. We used low- and high-resolution MS/MS analyses to rationalize the fragmentation pathways, and employed the B3LYP/6-31 + G(d,p) density functional theory (DFT) model to provide thermochemical parameters and to obtain the reactive sites. RESULTS: DFT calculations of a set of 7,7-dimethylaporphine alkaloids suggested the heterocyclic amino group as the most basic site due to the proton affinity of the nitrogen atom. Collision-induced dissociation experiments promoted • OCH3 elimination instead of the expected neutral loss of the heterocyclic amino group, pointing to the [M - 15 + H]•+ ion as the diagnostic fragment for 7,7-dimethylaporphine alkaloids. The analysis of plant extracts led to the annotation of 25 aporphine alkaloids. Their fragmentation initiated with the loss of the amino group followed by formation of a cyclic carbocation. Further reactions derived from consecutive charge-remote and/or charge-induced fragmentations of the substituents attached to the aromatic system. The mechanisms were re-examined based on plausible gas-phase ion chemistry reactions. CONCLUSIONS: Taken together, the diagnostic product ions and the series of radical and neutral eliminations provided information about the location of methylenedioxy, aromatic methoxy, and vicinal methoxy and hydroxy groups in aporphine alkaloids, assisting their characterization via MS/MS.

Mass Spectral Similarity Networking and Gas-Phase Fragmentation Reactions in the Structural Analysis of Flavonoid Glycoconjugates.

Flavonoids represent an important class of natural products with a central role in plant physiology and human health. Their accurate annotation using untargeted mass spectrometry analysis still relies on differentiating similar chemical scaffolds through spectral matching to reference library spectra. In this work, we combined molecular network analysis with rules for fragment reactions and chemotaxonomy to enhance the annotation of similar flavonoid glyconjugates. Molecular network topology progressively propagated the flavonoid chemical functionalization according to collision-induced dissociation (CID) reactions, as the following chemical attributes: aglycone nature, saccharide type and number, and presence of methoxy substituents. This structure-based distribution across the spectral networks revealed the chemical composition of flavonoids across intra- and interspecies and guided the putatively assignment of 64 isomers and isobars in the Chrysobalanaceae plant species, most of which are not accurately annotated by automated untargeted MS2 matching. These proof of concept results demonstrate how molecular networking progressively grouped structurally related molecules according to their product ion scans, abundances, and ratios. The approach can be extrapolated to other classes of metabolites sharing similar structures and diagnostic fragments from tandem mass spectrometry.

Oxidative functionalization of a halimane diterpenoid achieved by fungal transformation.

Regio and stereoselective activation of sp3 CH bonds remain one of the major advantages of biocatalysis over traditional chemocatalytic methods. Herein, we describe the oxy-functionalization of halimane diterpenoid 1 by whole cells of three filamentous fungi, aiming to obtain derivatives with desirable biological properties. After incubating 1 with Fusarium oxysporum, Myrothecium verrucaria, and Rhinocladiella similis at different concentrations and incubation times, four known (3, 5, 6, and 7) and three new (2, 4, and 8) halimane derivatives were obtained and characterized. F. oxysporum catalyzed the hydroxylation of positions C-2 (2) and C-7 (4), while R. similis simultaneously mediated the 2-oxo-functionalization and the hydration of 13,14-(CC)double bond belonging to an α,ß-unsaturated carbonyl system (8). Compounds 1-7 were non-cytotoxic against HCT-116 and MCF-7 cancer cell lines at tested concentrations. However, substrate 1 displayed moderate reduction ability against biofilm produced by Staphylococcus epidermidis ATCC35984 (84% at 1.6 mM), and this effect was retained to some extent by derivatives 4 and 7. These results emphasize the prominent potential of filamentous fungi associated with the microbiota of medicinal plants as versatile catalysts for singularly useful reactions through their complex enzymatic machinery, as well as the high susceptibility of halimane-diterpenoid substrates.

Improvement of bioactive metabolite production in microbial cultures-A systems approach by OSMAC and deconvolution-based 1 HNMR quantification.

Traditionally, the screening of metabolites in microbial matrices is performed by monocultures. Nonetheless, the absence of biotic and abiotic interactions generally observed in nature still limit the chemical diversity and leads to "poorer" chemical profiles. Nowadays, several methods have been developed to determine the conditions under which cryptic genes are activated, in an attempt to induce these silenced biosynthetic pathways. Among those, the one strain, many compounds (OSMAC) strategy has been applied to enhance metabolic production by a systematic variation of growth parameters. The complexity of the chemical profiles from OSMAC experiments has required increasingly robust and accurate techniques. In this sense, deconvolution-based 1 HNMR quantification have emerged as a promising methodology to decrease complexity and provide a comprehensive perspective for metabolomics studies. Our present work shows an integrated strategy for the increased production and rapid quantification of compounds from microbial sources. Specifically, an OSMAC design of experiments (DoE) was used to optimize the microbial production of bioactive fusaric acid, cytochalasin D and 3-nitropropionic acid, and Global Spectral Deconvolution (GSD)-based 1 HNMR quantification was carried out for their measurement. The results showed that OSMAC increased the production of the metabolites by up to 33% and that GSD was able to extract accurate NMR integrals even in heavily coalescence spectral regions. Moreover, GSD-1 HNMR quantification was reproducible for all species and exhibited validated results that were more selective and accurate than comparative methods. Overall, this strategy up-regulated important metabolites using a reduced number of experiments and provided fast analyte monitor directly in raw extracts.

Ecological Insights to Track Cytotoxic Compounds among Maytenus ilicifolia Living Individuals and Clones of an Ex Situ Collection.

Biodiversity is key for maintenance of life and source of richness. Nevertheless, concepts such as phenotype expression are also pivotal to understand how chemical diversity varies in a living organism. Sesquiterpene pyridine alkaloids (SPAs) and quinonemethide triterpenes (QMTs) accumulate in root bark of Celastraceae plants. However, despite their known bioactive traits, there is still a lack of evidence regarding their ecological functions. Our present contribution combines analytical tools to study clones and individuals of Maytenus ilicifolia (Celastraceae) kept alive in an ex situ collection and determine whether or not these two major biosynthetic pathways could be switched on simultaneously. The relative concentration of the QMTs maytenin (1) and pristimerin (2), and the SPA aquifoliunin E1 (3) were tracked in raw extracts by HPLC-DAD and ¹H-NMR. Hierarchical Clustering Analysis (HCA) was used to group individuals according their ability to accumulate these metabolites. Semi-quantitative analysis showed an extensive occurrence of QMT in most individuals, whereas SPA was only detected in minor abundance in five samples. Contrary to QMTs, SPAs did not accumulate extensively, contradicting the hypothesis of two different biosynthetic pathways operating simultaneously. Moreover, the production of QMT varied significantly among samples of the same ex situ collection, suggesting that the terpene contents in root bark extracts were not dependent on abiotic effects. HCA results showed that QMT occurrence was high regardless of the plant age. This data disproves the hypothesis that QMT biosynthesis was age-dependent. Furthermore, clustering analysis did not group clones nor same-age samples together, which might reinforce the hypothesis over gene regulation of the biosynthesis pathways. Indeed, plants from the ex situ collection produced bioactive compounds in a singular manner, which postulates that rhizosphere environment could offer ecological triggers for phenotypical plasticity.

Dereplication by HPLC-DAD-ESI-MS/MS and Screening for Biological Activities of Byrsonima Species (Malpighiaceae).

INTRODUCTION: Byrsonima species have been used in the treatment of gastrointestinal and gynecological inflammations, skin infections and snakebites. Based on their biological activities, it is important to study other organisms from this genus and to identify their metabolites. OBJECTIVES: To determine the metabolic fingerprinting of methanol and ethyl acetate extracts of four Byrsonima species (B. intermedia, B. coccolobifolia, B. verbascifolia and B. sericea) by HPLC-DAD-ESI-MS/MS and evaluate their in vitro antioxidant, anti-glycation, anti-inflammatory and cytotoxic activities. MATERIALS AND METHODS: Antioxidant activity was determined by DPPH˙, ABTS˙+ and ROO˙ scavenging assays. Anti-glycation activity was evaluated by the ability to inhibit the formation of advanced glycation endproducts (AGEs). Anti-inflammatory activity was evaluated using a murine macrophage cell line (RAW 264-7) in the presence of lipopolysaccharide (LPS). Tumour necrosis factor alpha (TNF-α) and nitrite (NO2- ) production were measured by ELISA and the Griess reaction, respectively. The compounds present in the extracts were tentatively identified by HPLC-DAD-ESI-MS/MS. RESULTS: The evaluation of the biological activities showed the potential of the extracts. The activities were assigned to the presence of glycoside flavonoids mainly derived from quercetin, quinic acid derivatives, gallic acid derivatives, galloylquinic acids and proanthocyanidins. Two isomers of sinapic acid-O-hexoside were described for the first time in a Byrsonima species. CONCLUSION: This research contributes to the study of the genus, it is the first report of the chemical composition of B. sericea and demonstrates the importance of the dereplication process, allowing the identification of known compounds without time-consuming procedures. Copyright © 2017 John Wiley & Sons, Ltd.

Partial least squares model and design of experiments toward the analysis of the metabolome of Jatropha gossypifolia leaves: Extraction and chromatographic fingerprint optimization.

A major challenge in metabolomic studies is how to extract and analyze an entire metabolome. So far, no single method was able to clearly complete this task in an efficient and reproducible way. In this work we proposed a sequential strategy for the extraction and chromatographic separation of metabolites from leaves Jatropha gossypifolia using a design of experiments and partial least square model. The effect of 14 different solvents on extraction process was evaluated and an optimized separation condition on liquid chromatography was estimated considering mobile phase composition and analysis time. The initial conditions of extraction using methanol and separation in 30 min between 5 and 100% water/methanol (1:1 v/v) with 0.1% of acetic acid, 20 µL sample volume, 3.0 mL min(-1) flow rate and 25°C column temperature led to 107 chromatographic peaks. After the optimization strategy using i-propanol/chloroform (1:1 v/v) for extraction, linear gradient elution of 60 min between 5 and 100% water/(acetonitrile/methanol 68:32 v/v with 0.1% of acetic acid), 30 µL sample volume, 2.0 mL min(-1) flow rate, and 30°C column temperature, we detected 140 chromatographic peaks, 30.84% more peaks compared to initial method. This is a reliable strategy using a limited number of experiments for metabolomics protocols.

Chemical composition of the bark of Tetrapterys mucronata and identification of acetylcholinesterase inhibitory constituents.

The secondary metabolite content of Tetrapterys mucronata, a poorly studied plant that is used occasionally in Brazil for the preparation of a psychotropic plant decoction called "Ayahuasca", was determined to establish its chemical composition and to search for acetylcholinesterase (AChE) inhibitors. The ethanolic extract of the bark of T. mucronata exhibited in vitro AChE inhibition in a TLC bioautography assay. To localize the active compounds, biological profiling for AChE inhibition was performed using at-line HPLC-microfractionation in 96-well plates and subsequent AChE inhibition bioautography. The analytical HPLC-PDA conditions were transferred geometrically to a preparative medium-pressure liquid chromatography column using chromatographic calculations for the efficient isolation of the active compounds at the milligram scale. Twenty-two compounds were isolated, of which six are new natural products. The structures of the new compounds (9, 10, 16-18, and 20) were elucidated by spectroscopic data interpretation. Compounds 1, 5, 6, 9, and 10 inhibited AChE with IC50 values below 15 µM.

Development of a natural products database from the biodiversity of Brazil.

We describe herein the design and development of an innovative tool called the NuBBE database (NuBBEDB), a new Web-based database, which incorporates several classes of secondary metabolites and derivatives from the biodiversity of Brazil. This natural product database incorporates botanical, chemical, pharmacological, and toxicological compound information. The NuBBEDB provides specialized information to the worldwide scientific community and can serve as a useful tool for studies on the multidisciplinary interfaces related to chemistry and biology, including virtual screening, dereplication, metabolomics, and medicinal chemistry. The NuBBEDB site is at http://nubbe.iq.unesp.br/nubbeDB.html .

Enhancing chemical and biological diversity by co-cultivation.

In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.

Application of feature-based molecular networking and MassQL for the MS/MS fragmentation study of depsipeptides.

The Feature-based Molecular Networking (FBMN) is a well-known approach for mapping and identifying structures and analogues. However, in the absence of prior knowledge about the molecular class, assessing specific fragments and clusters requires time-consuming manual validation. This study demonstrates that combining FBMN and Mass Spec Query Language (MassQL) is an effective strategy for accelerating the decoding mass fragmentation pathways and identifying molecules with comparable fragmentation patterns, such as beauvericin and its analogues. To accomplish this objective, a spectral similarity network was built from ESI-MS/MS experiments of Fusarium oxysporum at various collision energies (CIDs) and paired with a MassQL search query for conserved beauvericin ions. FBMN analysis revealed that sodiated and protonated ions clustered differently, with sodiated adducts needing more collision energy and exhibiting a distinct fragmentation pattern. Based on this distinction, two sets of particular fragments were discovered for the identification of these hexadepsipeptides: ([M + H]+) m/z 134, 244, 262, and 362 and ([M + Na]+) m/z 266, 284 and 384. By using these fragments, MassQL accurately found other analogues of the same molecular class and annotated beauvericins that were not classified by FBMN alone. Furthermore, FBMN analysis of sodiated beauvericins at 70 eV revealed subclasses with distinct amino acid residues, allowing distinction between beauvericins (beauvericin and beauvericin D) and two previously unknown structural isomers with an unusual methionine sulfoxide residue. In summary, our integrated method revealed correlations between adduct types and fragmentation patterns, facilitated the detection of beauvericin clusters, including known and novel analogues, and allowed for the differentiation between structural isomers.

Untargeted metabolomics approach and molecular networking analysis reveal changes in chemical composition under the influence of altitudinal variation in bamboo species.

Bamboo species have traditionally been used as building material and potential source of bioactive substances, as they produce a wide variety of phenolic compounds, including flavonoids and cinnamic acid derivatives that are considered biologically active. However, the effects of growth conditions such as location, altitude, climate, and soil on the metabolome of these species still need to be fully understood. This study aimed to evaluate variations in chemical composition induced by altitudinal gradient (0-3000 m) by utilizing an untargeted metabolomics approach and mapping chemical space using molecular networking analysis. We analyzed 111 samples from 12 bamboo species collected from different altitudinal ranges using liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (LC-QTOF-MS). We used multivariate and univariate statistical analyses to identify the metabolites that showed significant differences in the altitude environments. Additionally, we used the Global Natural Products Social Molecular Networking (GNPS) web platform to perform chemical mapping by comparing the metabolome among the studied species and the reference spectra from its database. The results showed 89 differential metabolites between the altitudinal ranges investigated, wherein high altitude environments significantly increased the profile of flavonoids. While, low altitude environments significantly boosted the profile of cinnamic acid derivatives, particularly caffeoylquinic acids (CQAs). MolNetEnhancer networks confirmed the same differential molecular families already found, revealing metabolic diversity. Overall, this study provides the first report of variations induced by altitude in the chemical profile of bamboo species. The findings may possess fascinating active biological properties, thus offering an alternative use for bamboo.

An unprecedented neolignan skeleton from Chimarrhis turbinata.

A lignan with a new skeleton named chimarrhinin (1) was isolated from an extract of the leaves of Chimarrhis turbinata, a Rubiaceae plant species. (13)C NMR spectrometric techniques including 1D and 2D experiments and HRESIMS provided unequivocal structural confirmation of this new C(6).C(3) skeleton type. The relative configuration of 1 was established by 2D (1)H-H analysis and J couplings, while its conformation was evaluated through molecular modeling using the RM1 semiempirical method, with the aid of coupling constants obtained by NMR analysis. The antioxidant activity of the new derivative 1 and two known and previously isolated phenolic derivatives (2 and 3) was investigated. An IC(50) value of 7.50 ± 0.5 µmol L(-1) was obtained for the new derivative 1, while 2 and 3 showed IC(50) values of 18.60 ± 0.4 and 18.50 ± 0.6 µmol, respectively.

Evaluation of antioxidant capacity and synergistic associations of quinonemethide triterpenes and phenolic substances from Maytenus ilicifolia (Celastraceae).

This work describes the isolation of the secondary metabolites identified as the quinonemethides maytenin (1) and pristimerin (2) from Maytenus ilicifolia extracts obtained from root barks of adult plants and roots of seedlings and their quantification by high performance liquid chromatography coupled to a diode array detector. The electrochemical profiles obtained from cyclic voltammetry and a coulometric detector coupled to high-performance liquid chromatography contributed to the evaluation of their antioxidant capacity. The antioxidant properties of individual components and the crude extracts of the root barks of Maytenus ilicifolia were compared and the possible synergistic associations of quinonemethide triterpenes and phenolic substances were investigated by using rutin as a model phenolic compound.

Rapid qualitative profiling of metabolites present in Fusarium solani, a rhizospheric fungus derived from Senna spectabilis, using GC/MS and UPLC-QTOF/MSE techniques assisted by UNIFI information system.

Fungi are an important source of natural products found in a variety of plant species. A wide range of methods for the detection of metabolites present in fungi have been reported in the literature. The search for methodologies that allow the rapid detection of compounds present in crude extracts is crucial to enable the metabolite annotation doing a qualitative analysis of the complex matrix. Mass spectrometry is an important ally when it comes to in silico detection of previously reported metabolites. In this work, the ethyl acetate extract of Fusarium solani was analyzed by gas chromatography coupled to mass spectrometry (GC/MS) after derivatization process. The ethyl acetate extract was also investigated by liquid chromatography coupled with high-resolution tandem mass spectrometry assisted by the UNIFI software system. A library containing previously reported metabolites from the Fusarium genus was added to the UNIFI platform. Simultaneously, the extract was analyzed through anticholinesterase and antifungal assays. The analysis of the derivatized extract by GC/MS led to the putative identification of five metabolites, and the investigation using Ultra-High Performance Liquid Chromatography - Quadrupole Time-of-Flight Mass Spectrometry (UPLC-QTOF) analysis in data-independent acquisition mode (mass spectrometry) led to the annotation of 15 compounds present in the built-in Fusarium library added to the UNIFI system. The Fusarium solani extract showed potential anticholinesterase and in vitro antifungal activity supported by the detection of bioactive metabolites.

Peanut skin polyphenols inhibit toxicity induced by advanced glycation end-products in RAW264.7 macrophages.

This is the first work to use a polyphenolic fraction derived from peanut skin to attenuate the toxicity induced by advanced glycation-end products (AGEs) in RAW264.7 macrophages. The RAW264.7 cells were stimulated by AGEs using the bovine serum albumin-fructose (BSA-FRU), bovine serum albumin-methylglyoxal (BSA-MGO) and arginine-methylglyoxal (ARG-MGO) models. The AGEs increased considerably the levels of reactive oxygen species and the gene expression of proinflammatory cytokines interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and nitric oxide. Twenty-eight polyphenols, including catechin, phenolic acids, and resveratrol were annotated in peanut skin extract (PSE) with the use of ultra-performance liquid chromatography coupled to quadrupole time of flight mass spectrometry (UPLC-QTOF/MSE) and to the UNIFI Scientific Information System. The administration of PSE at 100 and 150 µg/mL significantly inhibited oxidative stress, by suppressing the production of reactive oxygen species up to 70% and reducing the production of nitric oxide, IL-6 and TNF-α up to 1.7-, 10- and 107-fold, respectively.

Cytotoxic guanidine alkaloids from Pterogyne nitens.

As part of a bioprospecting program aimed at the discovery of potential anticancer drugs, two new guanidine-type alkaloids, nitensidines D and E (1, 2), and the known pterogynine (3), pterogynidine (4), and galegine (5), were isolated from the leaves of Pterogyne nitens. The structures of 1 and 2 were established on the basis of spectroscopic data interpretation. These compounds were tested against a small panel of human cancer cell lines. Compound 2 exhibited cytotoxicity for HL-60 (human myeloblastic leukemia) and SF-245 (human glioblastoma) cells.