Integrative open workflow for confident annotation and molecular networking of metabolomics MSE/DIA data.

Liquid chromatography coupled with high-resolution mass spectrometry data-independent acquisition (LC-HRMS/DIA), including MSE, enable comprehensive metabolomics analyses though they pose challenges for data processing with automatic annotation and molecular networking (MN) implementation. This motivated the present proposal, in which we introduce DIA-IntOpenStream, a new integrated workflow combining open-source software to streamline MSE data handling. It provides 'in-house' custom database construction, allows the conversion of raw MSE data to a universal format (.mzML) and leverages open software (MZmine 3 and MS-DIAL) all advantages for confident annotation and effective MN data interpretation. This pipeline significantly enhances the accessibility, reliability and reproducibility of complex MSE/DIA studies, overcoming previous limitations of proprietary software and non-universal MS data formats that restricted integrative analysis. We demonstrate the utility of DIA-IntOpenStream with two independent datasets: dataset 1 consists of new data from 60 plant extracts from the Ocotea genus; dataset 2 is a publicly available actinobacterial extract spiked with authentic standard for detailed comparative analysis with existing methods. This user-friendly pipeline enables broader adoption of cutting-edge MS tools and provides value to the scientific community. Overall, it holds promise for speeding up metabolite discoveries toward a more collaborative and open environment for research.

Age, gender, and 11 comorbidities as risk factors associated with COVID-19 mortality: A retrospective cohort including 1.8 million individuals.

The aim of this study was to investigate the risk factors age, gender, and 11 comorbidities for mortality attributed to COVID-19 among Brazilians. An observational, retrospective cohort study with 1,804,151 individuals was performed using the São Paulo State Statistics Portal database for COVID-19 monitoring. Multivariate binary logistic regression was conducted to estimate the influence of odds ratio (OR) for asthma, diabetes, obesity, Down's syndrome, puerperal, hematological, hepatic, neurological, pulmonary, immunological, kidney, and other diseases contributing to mortality attributed to COVID-19. An additional analysis was undertaken using age-stratified data including children, adults, and seniors. Our findings demonstrated that cardiac diseases (9.37%) and diabetes (6.26%) were the most prevalent disorders in therapeutically managed and deceased patients. Multivariate regression model found that male individuals (OR = 1.819, CI 1.783 to 1.856, p < 0.001), older age (OR per year = 1.081, CI 1.081 to 1.082, p < 0.001) and presenting comorbidities (OR varying from 1.84-5.47) were at a higher risk of death. The age-stratified analysis also indicates disparities in the impact of the comorbidities between children, adults, and seniors. Our comprehensive findings indicate the primary risk factors for mortality attributed to COVID-19 in the entire population examined, provide a broader perspective than investigations focused solely on hospitalized patients. This study may be utilized as a valuable tool for decision-making during the COVID-19 outbreak.

Chemical Composition, Anthelmintic Activity, and Mechanism of Action of Lippia dominguensis Mold. Essential Oil on Haemonchus contortus.

Gastrointestinal nematode parasitism is a major burden to small ruminant production globally, compounded by increasing anthelmintic resistance. Previous studies have identified essential oils (EOs) from the Lippia genus with antiprotozoal and anthelmintic effects. Lippia dominguensis Moldenke (Ld), an endemic specie from the Dominican Republic, has similar popular uses, however, is chemically and pharmacologically yet uncharacterized. Here, we investigated the in vitro anthelmintic activity of LdEO and its ultrastructural effects on eggs and adult nematodes of Haemonchus contortus multidrug-resistant isolated. The GC/MS analysis showed linalool (33.85 %), 1,8-cineole (30.88 %), and δ-terpineol (10.61 %) as the main EO constituents. The LdEO showed an IC50 =0.523 mg/mL in the egg hatch test, and the motility in the adult worm motility test was 95.8 % at 1 mg/mL. The confocal scanning laser microscopy of eggs indicated permeabilization or disruption of egg cell membranes as the possible mechanism of action of LdEO. The scanning electron microscopy of adult worms showed wrinkling, undulations, and cuticular disruptions. The LdEO displayed significant in vitro anthelmintic activity on eggs and adult worms of H. contortus. Additionally, the LdEO showed low oral toxicity in mice at 2,000 mg/kg. Thus, additional in vivo studies are justified to determine its anthelmintic efficacy in small ruminants.

Anti-Inflammatory Markers of Hops Cultivars (Humulus lupulus L.) Evaluated by Untargeted Metabolomics Strategy.

Hops (Humulus lupulus L.) are edible flowers commonly used to add flavour and aroma to beer, besides they have rich chemical diversity and medicinal potential. In this work, an ex vivo anti-inflammatory assay via the LPS-induced signalling pathway and metabolomics approaches were performed to evaluate the ability of hops to inhibit the production of prostaglandin E2 (PGE2) inflammatory mediator and analyze which metabolites produced by the nine different hop cultivars are potential anti-inflammatory markers. Columbus, Chinook and Hallertau Mittelfrüh hop cultivars yielded extracts with PGE2 release inhibition rates of 86.7, 92.5 and 73.5 %, respectively. According to the multivariate statistical analysis, the majority of the metabolites correlated with the activity were prenylated phloroglucinol and phenolic homologs. These results suggest promissory anti-inflammatory hop metabolites.

Immunological Modulation and Control of Parasitaemia by Ayahuasca Compounds: Therapeutic Potential for Chagas's Disease.

Ayahuasca is a psychoactive and psychedelic decoct composed mainly of Banisteriopsis caapi and Psychotria viridis plant species. The beverage is rich in alkaloids and it is ritualistically used by several indigenous communities of South America as a natural medicine. There are also reports in the literature indicating the prophylaxis potential of Ayahuasca alkaloids against internal parasites. In the present study, Ayahuasca exhibited moderate in vitro activity against Trypanosoma cruzi trypomastigotes (IC50 95.78 µg/mL) compared to the reference drug benznidazole (IC50 2.03 µg/mL). The ß-carboline alkaloid harmine (HRE), isolated from B. caapi, was considered active against the trypomastigotes forms (IC50 6.37), and the tryptamine N, N-dimethyltryptamine (DMT), isolated from P. viridis was also moderately active with IC50 of 21.02 µg/mL. Regarding the in vivo evaluations, no collateral effects were observed. The HRE alone demonstrated the highest trypanocidal activity in a dose-responsive manner (10 and 100 mg/kg). The Ayahuasca and the association between HRE and DMT worsened the parasitaemia, suggesting a modulation of the immunological response during the T. cruzi infection, especially by increasing total Immunoglobulin (IgG) and IgG1 antibody levels. The in silico molecular docking revealed HRE binding with low energy at two sites of the Trypanothione reductase enzyme (TR), which are absent in humans, and thus considered a promissory target for drug discovery. In conclusion, Ayahuasca compounds seem to not be toxic at the concentrations of the in vivo evaluations and can promote trypanocidal effect in multi targets, including control of parasitaemia, immunological modulation and TR enzymatic inhibition, which might benefit the treatments of patients with Chagas' disease. Moreover, the present study also provides scientific information to support the prophylactic potential of Ayahuasca against internal parasites.

Phytochemical investigation of Nigrospora zimmermanii isolated from Poincianella pluviosa (Sibipiruna): metabolites characterisation and screening for anti-inflammatory activity.

Endophytic fungi residing symbiotically in plant tissues are promising sources of bioactive natural products. This study explored the anti-inflammatory potential of an endophytic fungus isolated from the Brazilian medicinal plant Poincianella pluviosa (Sibipiruna). The extract from the endophyte FPD13 exhibited potential ex vivo anti-inflammatory effects by inhibiting prostaglandin E2 (PGE2) release by 75.22%. Phytochemical analysis using High-Performance Liquid Chromatography (HPLC), Nuclear Magnetic Resonance (NMR), and Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) enabled the isolation and identification of three compounds, including the macrolide Nigrosporolide, the phenyl-propanol Tyrosol, and the terpene Decarestrictine A. Morphological characteristics and Internal Transcribed Spacers region (ITS) sequencing classified fungus FPD13 as Nigrospora zimmermanii. The results reveal the anti-inflammatory potential and chemical diversity of P. pluviosa endophytes, warranting further investigation into the bioactivity and structure elucidation of their bioactive metabolites.

Metabolomics Unveils Disrupted Pathways in Parkinson's Disease: Toward Biomarker-Based Diagnosis.

Parkinson's disease (PD) is a neurodegenerative disorder characterized by diverse symptoms, where accurate diagnosis remains challenging. Traditional clinical observation methods often result in misdiagnosis, highlighting the need for biomarker-based diagnostic approaches. This study utilizes ultraperformance liquid chromatography coupled to an electrospray ionization source and quadrupole time-of-flight untargeted metabolomics combined with biochemometrics to identify novel serum biomarkers for PD. Analyzing a Brazilian cohort of serum samples from 39 PD patients and 15 healthy controls, we identified 15 metabolites significantly associated with PD, with 11 reported as potential biomarkers for the first time. Key disrupted metabolic pathways include caffeine metabolism, arachidonic acid metabolism, and primary bile acid biosynthesis. Our machine learning model demonstrated high accuracy, with the Rotation Forest boosting model achieving 94.1% accuracy in distinguishing PD patients from controls. It is based on three new PD biomarkers (downregulated: 1-lyso-2-arachidonoyl-phosphatidate and hypoxanthine and upregulated: ferulic acid) and surpasses the general 80% diagnostic accuracy obtained from initial clinical evaluations conducted by specialists. Besides, this machine learning model based on a decision tree allowed for visual and easy interpretability of affected metabolites in PD patients. These findings could improve the detection and monitoring of PD, paving the way for more precise diagnostics and therapeutic interventions. Our research emphasizes the critical role of metabolomics and machine learning in advancing our understanding of the chemical profile of neurodegenerative diseases.

Effects of geographical origin and post-harvesting processing on the bioactive compounds and sensory quality of Brazilian specialty coffee beans.

Specialty coffee beans are those produced, processed, and characterized following the highest quality standards, toward delivering a superior final product. Environmental, climatic, genetic, and processing factors greatly influence the green beans' chemical profile, which reflects on the quality and pricing. The present study focuses on the assessment of eight major health-beneficial bioactive compounds in green coffee beans aiming to underscore the influence of the geographical origin and post-harvesting processing on the quality of the final beverage. For that, we examined the non-volatile chemical profile of specialty Coffea arabica beans from Minas Gerais state, Brazil. It included samples from Cerrado (Savannah), and Matas de Minas and Sul de Minas (Atlantic Forest) regions, produced by two post-harvesting processing practices. Trigonelline, theobromine, theophylline, chlorogenic acid derivatives, caffeine, caffeic acid, ferulic acid, and p-coumaric acid were quantified in the green beans by high-performance liquid chromatography with diode array detection. Additionally, all samples were roasted and subjected to sensory analysis for coffee grading. Principal component analysis suggested that Cerrado samples tended to set apart from the other geographical locations. Those samples also exhibited higher levels of trigonelline as confirmed by two-way ANOVA analysis. Samples subjected to de-pulping processing showed improved chemical composition and sensory score. Those pulped coffees displayed 5.8% more chlorogenic acid derivatives, with an enhancement of 1.5% in the sensory score compared to unprocessed counterparts. Multivariate logistic regression analysis pointed out altitude, ferulic acid, p-coumaric acid, sweetness, and acidity as predictors distinguishing specialty coffee beans obtained by the two post-harvest processing. These findings demonstrate the influence of regional growth conditions and post-harvest treatments on the chemical and sensory quality of coffee. In summary, the present study underscores the value of integrating target metabolite analysis with statistical tools to augment the characterization of specialty coffee beans, offering novel insights for quality assessment with a focus on their bioactive compounds.

LC-MS/DIA-based strategy for comprehensive flavonoid profiling: an Ocotea spp. applicability case.

We introduce a liquid chromatography - mass spectrometry with data-independent acquisition (LC-MS/DIA)-based strategy, specifically tailored to achieve comprehensive and reliable glycosylated flavonoid profiling. This approach facilitates in-depth and simultaneous exploration of all detected precursors and fragments during data processing, employing the widely-used open-source MZmine 3 software. It was applied to a dataset of six Ocotea plant species. This framework suggested 49 flavonoids potentially newly described for these plant species, alongside 45 known features within the genus. Flavonols kaempferol and quercetin, both exhibiting O-glycosylation patterns, were particularly prevalent. Gas-phase fragmentation reactions further supported these findings. For the first time, the apigenin flavone backbone was also annotated in most of the examined Ocotea species. Apigenin derivatives were found mainly in the C-glycoside form, with O. porosa displaying the highest flavone : flavonol ratio. The approach also allowed an unprecedented detection of kaempferol and quercetin in O. porosa species, and it has underscored the untapped potential of LC-MS/DIA data for broad and reliable flavonoid profiling. Our study annotated more than 50 flavonoid backbones in each species, surpassing the current literature.

Bioprospecting-based untargeted metabolomics identifies alkaloids as potential anti-inflammatory bioactive markers of Ocotea species (Lauraceae).

BACKGROUND: Species within the Ocotea genus (Lauraceae), have demonstrated an interesting profile of bioactivities. Renowned for their diverse morphology and intricate specialized metabolite composition, Ocotea species have re-emerged as compelling candidates for bioprospecting in drug discovery research. However, it is a genus insufficiently studied, particularly regarding anti-inflammatory activity. PURPOSE: To investigate the anti-inflammatory activity of Ocotea spp. extracts and determine the major markers in this genus. METHODS: Extracts of 60 different Ocotea spp. were analysed by an ex vivo anti-inflammatory assay in human whole blood. The experiment estimates the prostaglandin E2 levels, which is one of the main mediators of the inflammatory cascade, responsible for the classical symptoms of fever, pain, and other common effects of the inflammatory process. Untargeted metabolomics analysis through liquid chromatography coupled with high-resolution mass spectrometry was performed, along with statistical analysis, to investigate which Ocotea metabolites are correlated with their anti-inflammatory activity. RESULTS: The anti-inflammatory screening indicated that 49 out of 60 Ocotea spp. extracts exhibited significant inhibition of PGE2 release compared to the vehicle (p < 0.05). Furthermore, 10 of these extracts showed statistical similarity to the reference drugs. The bioactive markers were accurately identified using multivariate statistics combined with a fold change (> 1.5) and adjusted false discovery rate analysis as unknown compounds and alkaloids, with a majority of aporphine and benzylisoquinolines. These alkaloids were annotated with an increased level of confidence since MSE spectra were compared with comprehensive databases. CONCLUSION: This study represents the first bioprospecting report revealing the anti-inflammatory potential of several Ocotea spp. The determination of their anti-inflammatory markers could contribute to drug discovery and the chemical knowledge of the Ocotea genus.

Insecticidal activity of extracts of handroanthus impetiginosus on Plutella xylostella (Lepidoptera: plutellidae) larvae.

Plutella xylostella is considered the main pest of cabbage in Brazil and the world, causing damage of up to 100%. Thus, this study evaluated the insecticidal activity of extracts obtained from the fruits, seeds, bark, leaves, and flowers of Handroanthus impetiginosus against the diamondback moth, P. xylostella larvae. The seed extract showed the highest mortality (97.0%) compared to the control treatment. The LC50 values indicated that the seed and flower extracts (0.01003 and 0.01288 mg/L respectively) assumed the highest toxicity to P. xylostella larvae after 24 h of exposure. The results of this study indicated that the seeds extract is the most promising toxic extract, with measured mortality of approximately 97.0% for P. xylostella larvae after 144 h of exposure in kale plants. Seed extract showed the best insecticidal activity. Thus, this extract can be applied to develop an insecticide based on H. impetiginosus seed.

In vivo evaluation of analgesic and anti-inflammatory activity of hydroalcoholic extracts from Handroanthus impetiginosus and their chemical composition by UPLC/MS analysis.

This study demonstrates in vivo analgesic and anti-inflammatory properties of hydroalcoholic extracts of leaves, bark and flowers from the Handroanthus impetiginosus (Bignoniaceae) plant, recognized as 'Ipê roxo' in Brazil. The extracts were evaluated in male Swiss albino mice via oral administration. Moreover, results of the in vivo paw oedema test induced by carrageenan revealed that extracts of leaves and bark displayed relevant anti-inflammatory activity potential at the dosage of 100 mg/kg, 300 mg/kg, and 500 mg/kg. Likewise, the results obtained for leaves and flowers extracts suggested potent analgesic action in the conventional hot plate test. UPLC/MS analysis of the hydroalcoholic extracts samples identified metabolites belonging to several classes, mainly naphthoquinones and iridoids derivatives as well as flavonoids. Thus, the obtained results indicate that the extracts of H. impetiginosus plant parts could be considered as a complementary herbal medicine for the treatment of pain and inflammation disorders.

Ex vivo inhibition of PGE2 formation in human blood by four bicyclico [3.2.1] octane neolignans isolated from Aniba firmula bark, two with unusual structural pattern.

The phytochemical investigation of the stem bark crude extract of Aniba firmula (Lauraceae) led to the isolation of undescribed bicyclic [3.2.1] octane neolignans, 1 and 2, characterized by unusual bicyclic patterns and two other known bicyclic neolignans 3 and 4. Anti-inflammatory bicyclic [3.2.1] octane neolignans metabolites were previously reported in the literature, and the A. firmula stands out in the Lauraceae family as a source of potentially bioactive compounds. Thus, herein the anti-inflammatory potential of four isolated compounds from A. firmula was accessed via an ex vivo anti-inflammatory model that included plasmatic quantification of the prostaglandin E2 (PGE2) inflammatory mediator. Compounds 2 and 3 exhibited significant anti-inflammatory activity by inhibiting the production of PGE2 in plasma samples, thus by interference with the cyclooxygenase (COX) inflammatory pathway. Therefore, these findings demonstrate that the bicyclic octane neolignan classes [3.2.1] can present anti-inflammatory potential.

Confirmation of ethnopharmacological anti-inflammatory properties of Ocotea odorifera and determination of its main active compounds.

ETHNOPHARMACOLOGICAL RELEVANCE: Ocotea odorifera (Vell.) Rohwer has been used in traditional medicine in the south of Brazil for the treatment of inflammatory-related conditions, such as rheumatism. However, there is not any scientific evidence for popular use. AIMS OF THE STUDY: To investigate the O. odorifera anti-inflammatory potential and identification of the main active compounds through metabolomic approaches. MATERIALS AND METHODS: In order to in vivo evaluate the inhibition of the main inflammatory pathways, the leaf decoction, leaf extract, its fractions and the essential oils from leaves and branches were submitted to the ear oedema and the neutrophils recruitment assays. The samples were chemically investigated by UHPLC-HRMS or GC-MS. The multivariate statistical analysis (PLS-DA) was used to determine the substances correlated with the anti-inflammatory properties. RESULTS: The in vivo studies indicated a promissory anti-inflammatory effect on both oedema and neutrophil recruitment for some samples including the decoction; hydroethanolic, ethyl acetate, and chloroform fractions; and the essential oils. According to the PLS-DA, the S-(+)-reticuline was evidenced as one of the three compounds of the plant most correlated with both anti-inflammatory mechanisms. Thus, S-(+)-reticuline was isolated and the anti-inflammatory activity was confirmed. Moreover, for the first time, the dual inhibition of oedema and neutrophil recruitment was uncovered and reported. Another compound positively correlated with the anti-inflammatory activity is likely to be a new compound since zero hit on the comprehensive mass database were encountered. The compounds found in the essential oils also showed significant anti-inflammatory activity, and thus indeed the plant has different classes of active substances. CONCLUSIONS: The decoction of O. odorifera and different fractions from its ethanolic extract demonstrated anti-inflammatory activity through dual inhibition of oedema and neutrophil recruitment. Thus, corroborating the popular medicinal use of the decoction of leaves from O. odorifera as an anti-inflammatory medicine. Besides, reticuline, one of the main active compounds, was isolated and proved to display the dual mechanism of action, indicating the O. odorifera as a promising source of active compounds for the treatment of inflammatory conditions.

Neuroprotective potential of Ayahuasca and untargeted metabolomics analyses: applicability to Parkinson's disease.

ETHNOPHARMACOLOGY RELEVANCE: Ayahuasca is a tea produced through decoction of Amazonian plants. It has been used for centuries by indigenous people of South America. The beverage is considered to be an ethnomedicine, and it is traditionally used for the treatment of a wide range of diseases, including neurological illness. Besides, some scientific evidence suggests it may be applicable to Parkinson's disease (PD) treatment. Thus, Ayahuasca deserves in depth studies to clarify its potential role in this disease. AIM OF THE STUDY: This study aimed to use an untargeted metabolomics approach to evaluate the neuroprotective potential of the Ayahuasca beverage, the extracts from its matrix plants (Banisteriopsis caapi and Psychotria viridis), its fractions and its main alkaloids on the viability of SH-SY5Y neuroblastoma cells in an in vitro PD model. MATERIAL AND METHODS: The cytotoxicity of Ayahuasca, crude extracts, and fractions of B. caapi and P. viridis, as well as neuroprotection promoted by these samples in a 6-hydroxydopamine (6-OHDA)-induced neurodegeneration model, were evaluated by the MTT assay at two time-points: 48 h (T1) and 72 h (T2). The main alkaloids from Ayahuasca matrix plants, harmine (HRE) and N,N-dimethyltryptamine (DMT), were also isolated and evaluated. An untargeted metabolomics approach was developed to explore the chemical composition of samples with neuroprotective activity. Ultra-Performance Liquid Chromatography coupled to Electrospray Ionisation and Time-of-Flight (UPLC-ESI-TOF) metabolome data was treated and further analysed using multivariate statistical analyses (MSA): principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA). The metabolites were dereplicated using the Dictionary of Natural Products and an in house database. The main alkaloids were also quantified by UPLC-MS/MS. RESULTS: The samples did not cause cytotoxicity in vitro and three of samples intensely increased cell viability at T1. The crude extracts, alkaloid fractions and HRE demonstrated remarkable neuroprotective effect at T2 while the hydroalcoholic fractions demonstrated this neuroprotective effect at T1 and T2. Several compounds from different classes, such as ß-carbolines and monoterpene indole alkaloids (MIAs) were revealed correlated with this property by MSA. Additionally, a total of 2419 compounds were detected in both ionisation modes. HRE showed potent neuroprotective action at 72 h, but it was not among the metabolites positively correlated with the most efficacious neuroprotective profile at either time (T1 and T2). Furthermore, DMT was statistically important to differentiate the dataset (VIP value > 1), although it did not exhibit sufficient neuroprotective activity by in vitro assay, neither a positive correlation with T1 and T2 neuroprotective profile, which corroborated the MSA results. CONCLUSION: The lower doses of the active samples stimulated neuronal cell proliferation and/or displayed the most efficacious neuroprotection profile, namely by preventing neuronal damage and improving cell viability against 6-OHDA-induced toxicity. Intriguingly, the hydroalcoholic fractions exhibited enhanced neuroprotective effects when compared to other samples and isolated alkaloids. This finding corroborates the significance of a holistic approach. The results demonstrate that Ayahuasca and its base plants have potential applicability for PD treatment and to prevent its progression differently from current drugs to treat PD.