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Peppers (Piper nigrum L.) are distinguished by their pungent flavor and aroma. Piperine is a major acid-amide alkaloid with a piperidine ring that gives pepper its flavor and scent. In plant metabolomics research, the accessibility of the chemical standards is critical for scientific credibility. We isolated and identified 10 novel dimers of acid amide alkaloids (9–15 and 20–22), along with 12 known monomers (1–6) and dimers (7 , 8 , 16 – 19) from black pepper. Subsequently, we found the distribution of monomers and dimers of acid amide alkaloids in black and white peppers by twenty-two acid amide alkaloids which we obtained using the molecular networking technique and multivariate analysis to reveal the molecular relationships between the acid amide alkaloids in black and white peppers. Our research delved into the chemical diversity of acid amide alkaloids in black and white peppers, which could help inform future culinary and potential medicinal utilization of pepper. [Display omitted] • Discovery of new dimeric acid amide alkaloids from pepper • Variations in acid amide alkaloids due to geographic and morphologic properties • More dimers with piperidine backbones are seen in white pepper. • The molecular networking predicts the undiscovered acid amide alkaloids in pepper. [ABSTRACT FROM AUTHOR]

The use of new psychoactive substances derived from ketamine is rarely reported in France. A chronic GHB, 3-MMC, and methoxetamine consumer presented a loss of consciousness in a chemsex context and was referred to the intensive care unit with a rapid and favorable outcome. To investigate the chemicals responsible for the intoxication, a comprehensive analysis was conducted on the ten plasma samples collected over a 29.5-hour period, urine obtained upon admission, a 2-cm hair strand sample, and a seized crystal. These analyses were performed using liquid chromatography hyphenated to high resolution tandem mass spectrometry operating in targeted and untargeted modes. Additionally, analyses using gas chromatography coupled to mass spectrometry and nuclear magnetic resonance were conducted to probe the composition of the seized crystal. The molecular network-based approach was employed for data processing in non-targeted analyses. It allowed to confirm a multidrug exposure encompassing GHB, methyl-(aminopropyl)benzofuran (MAPB), (aminopropyl)benzofuran (APB), methylmethcathinone, chloromethcathinone, and a new psychoactive substance belonging to the arylcyclohexylamine family namely deschloro-N-ethyl-ketamine (O-PCE). Molecular network analysis facilitated the annotation of 27 O-PCE metabolites, including phase II compounds not previously reported. Plasma kinetics of O-PCE allowed the estimation of the elimination half-life of ∼5 hours. Kinetics of O-PCE metabolites was additionally characterized, possibly useful as surrogate biomarkers of consumption. We also observed marked alterations in lipid metabolism related to poly consumption of drugs. In conclusion, this case report provides a comprehensive analysis of exposure to O-PCE in a multidrug user including kinetic and metabolism data in human. • First reported plasma kinetics of O-PCE and its main metabolites in humans. • First identification of plasma O-PCE metabolites in a poisoned patient using a molecular network approach. • Marked alteration in lipid metabolism after O-PCE use. • Multidrug user profile confirmed using hair analysis showing regular synthetic cathinone and recent O-PCE use. [ABSTRACT FROM AUTHOR]

• LC–Q–TOF–MS and molecular networking are combined to identify banned colorants. • Simultaneous quantitative analysis of the 26 banned colorants using LC–MS/MS. • Specific molecular network maps were formed based on the colorant's chemical structure. • Powerful technology to characterization and screening non-targeted colorants in cosmetics. Colorants have been a staple in the cosmetics industry for a considerable time, although certain varieties have been banned owing to health risks. Detecting and confirming these banned colorants simultaneously poses several challenges when employing LC–MS/MS. Molecular networking is a promising analytical technology that can be used to predict the structure of components and the correlation between them using structural and MS/MS spectral similarities. Molecular networking entails assessing the number of fragmented ions and the cosine score (the closer it is to one, the higher the similarity). In this study, we developed and verified a method for the simultaneous quantitative analysis of the 26 banned colorants in cosmetics using LC–MS/MS. Additionally, we propose a novel approach that combines LC–Q–TOF–MS and molecular networking technology to detect banned colorants in cosmetics. For successful molecular networking, a minimum of six fragment ions with cosine scores exceeding 0.5 is required. We developed a screening method for characterizing banned colorants using molecular networking based on LC–TOF–MS results for 26 banned colorants. Furthermore, we demonstrated that our established method can be used for screening by analyzing actual cosmetics (eyebrow tattoo, lipstick tattoo, and hair tint) spiked with three non-targeted banned colorants with similar structures (m/z 267.116, 315.149, and 345.157) in cosmetics. The combination of molecular networking techniques and LC–MS/MS proves highly advantageous for the swift characterization and screening of non-targeted colorants in cosmetics. [ABSTRACT FROM AUTHOR]

By co-culturing two endophytic fungi (Chaetomium virescens and Xylaria grammica) collected from the medicinal and edible plant Smilax glabra Roxb. and analyzing them with MolNetEnhancer module on GNPS platform, seven undescribed chromone-derived polyketides (chaetoxylariones A–G), including three pairs of enantiomer ones (2a / 2b , 4a / 4b and 6a / 6b) and four optical pure ones (1 , 3 , 5 and 7), as well as five known structural analogues (8 – 12), were obtained. The structures of these new compounds were characterized by NMR spectroscopy, single-crystal X-ray diffraction, 13C NMR calculation and DP4+ probability analyses, as well as the comparison of the experimental electronic circular dichroism (ECD) data. Structurally, compound 1 featured an unprecedented chromone-derived sulfonamide tailored by two isoleucine-derived δ -hydroxy-3-methylpentenoic acids via the acylamide and N O bonds, respectively; compound 2 represented the first example of enantiomeric chromone derivative bearing a unique spiro-[3.3]alkane ring system; compound 3 featured a decane alkyl side chain that formed an undescribed five-membered lactone ring between C-7′ and C-10′; compound 4 contained an unexpected highly oxidized five-membered carbocyclic system featuring rare adjacent keto groups; compound 7 featured a rare methylsulfonyl moiety. In addition, compound 10 showed a significant inhibition towards SW620/AD300 cells with an IC 50 value of PTX significantly decreased from 4.09 μM to 120 nM, and a further study uncovered that compound 10 could obviously reverse the MDR of SW620/AD300 cells. [Display omitted] • By co-culturing Chaetomium virescens and Xylaria grammica , seven new chromone-derived polyketides were obtained. • Compound 1 featured an unprecedented chromone-derived sulfonamide tailored by two isoleucine-derived δ -hydroxy-3-methylpentenoic acids. • Compound 2 represented the first example of enantiomeric chromone derivative bearing a unique spiro-[3.3]alkane ring. • Compound 3 featured a decane alkyl side chain form an undescribed five-membered lactone ring between C-7′ and C-10′. • Compound 4 contained an unexpected highly oxidized five-membered carbocyclic system featuring rare adjacent keto groups. • Compound 10 was a potential agent for MDR cancer as a P-gp inhibitor. By co-culturing two endophytic fungi (Chaetomium virescens and Xylaria grammica) collected from the medicinal and edible plant Smilax glabra Roxb. and analyzing them with MolNetEnhancer module on GNPS platform, seven undescribed chromone-derived polyketides (chaetoxylariones A–G), including three pairs of enantiomer ones (2a / 2b , 4a / 4b and 6a / 6b) and four optical pure ones (1 , 3 , 5 and 7), as well as five known structural analogues (8 – 12), were obtained. The structures of these new compounds were characterized by NMR spectroscopy, single-crystal X-ray diffraction, 13C NMR calculation and DP4+ probability analyses, as well as the comparison of the experimental electronic circular dichroism (ECD) data. Structurally, compound 1 featured an unprecedented chromone-derived sulfonamide tailored by two isoleucine-derived δ -hydroxy-3-methylpentenoic acids via the acylamide and N O bonds, respectively; compound 2 represented the first example of enantiomeric chromone derivative bearing a unique spiro-[3.3]alkane ring system; compound 3 featured a decane alkyl side chain that formed an undescribed five-membered lactone ring between C-7′ and C-10′; compound 4 contained an unexpected highly oxidized five-membered carbocyclic system featuring rare adjacent keto groups; compound 7 featured a rare methylsulfonyl moiety. In addition, compound 10 showed a significant inhibition towards SW620/AD300 cells with an IC 50 value of PTX significantly decreased from 4.09 μM to 120 nM, and a further study uncovered that compound 10 could obviously reverse the MDR of SW620/AD300 cells. [ABSTRACT FROM AUTHOR]

Brucea javanica , a valued traditional medicinal plant in Malaysia, known for its fever-treating properties yet remains underexplored for its potential antiviral properties against dengue. This study aims to simultaneously identify chemical classes and metabolites within B. javanica using molecular networking (MN), by Global Natural Product Social (GNPS), and SIRIUS in silico annotation. Liquid chromatography-mass spectrometry (LC-MS2)-based MN explores chemical diversity across four plant parts (leaves, roots, fruits, and stem bark), revealing diverse metabolites such as tryptophan-derived alkaloids, terpenoids, and octadecadenoids. Simultaneous LC-MS2 and MN analyses reveal a discriminative capacity for individual plant components, with roots accumulating tryptophan alkaloids, fruits concentrating quassinoids, leaves containing fusidanes, and stem bark primarily characterised by simple indoles. Subsequently, extracts were evaluated for dengue antiviral activity using adenosine triphosphate (ATP) and plaque assays, indicates potent efficacy in the dichloromethane (DCM) extract from roots (EC 50 = 0.3 μg/mL, SI = 10). Molecular docking analysis of two major compounds; canthin-6-one (264) and 1-hydroxy-11-methoxycanthin-6-one (275) showed potential binding interactions with active sites of NS5 RNA-dependent RNA polymerase (RdRp) of dengue virus (DENV) protein. Subsequent in vitro evaluation revealed compounds 264 and 275 had a promising dengue antiviral activity with SI value of 63 and 1.85. These identified metabolites emerge as potential candidates for further evaluation in dengue antiviral activities. [Display omitted] • Brucea javanica highlights prominent alkaloids in root, quassinoids in fruit, indoles in stem bark, and fusidanes in leaves. • Molecular docking analysis annotated canthin-6-one derivatives as candidates for further evaluation in dengue assays. • Canthin-6-one showed potent EC 50 of 0.86 μM (SI = 63) and 1-hydroxy-11-methoxycanthin-6-one an EC 50 of 6.1 μM (SI = 1.85) [ABSTRACT FROM AUTHOR]

This study evaluates the reno-protective effect of Beta vulgaris subspecies maritima lyophilized 70% ethanolic extract (BVLE) in renal ischemia/reperfusion (I/R) induced injury model in rats. Detailed investigation of the effects of its oral administration was checked. serum blood urea nitrogen (BUN), which was reduced to 0.7 ± 0.04mmol/L at a dose of 200 mg/kg of BVLE compared to 1.9 ± 0.08 mmol/L for the I/R group. And creatinine levels were reduced to 1.2 ± 0.06 nmol/L at a dose of 200 mg/kg of BVLE compared to 4.7 ± 0.12 nmol/L for the I/R group. Oxidative stress biomarkers including MDA (reduced to 0.4 ± 0.03 compared to 1.7 ± 0.05 nmol/mg protein of I/R a dose of 200 mg/kg) and GSH levels (increased to 1.3 ± 0.03 compared to 0.3 ± 0.02 nmol/mg protein of I/R a dose of 200 mg/kg). Meanwhile, inflammatory mediators including TNF-α and IL-6 levels were lowered to 46.7 ± 0.60 and 32.1 ± 1.78 pg/mg protein, respectively. Oxidative stress genetic pathways including Nrf2/HO-1 signaling pathway via testing Nrf2 and its dependent HO-1 mRNA expression levels were studied as well. Metabolomic profiling of BVLE was achieved by UPLC-HR-ESIMS coupled with molecular networking. BVLE significantly improved renal inflammatory markers, oxidative stress biomarkers and renal functions test, in dose dependent manner. Thirty-nine compounds were tentatively identified in BVLE by UPLC-MS/MS. Mainly flavonoid glycosides, triterpenoidal saponins and fatty acids. Among identified saponins five unreported betavulgaroside derivatives were tentatively described for the first time. [Display omitted] • Lyophilized Beta vulgaris subspecies maritima extract had reno-protective effect. • It reduced BUN and serum creatinine compared to non-treated and disease controls. • It alleviated oxidative stress by reducing MDA and increasing GSH. • It reduced TNF-α and IL-6, and upregulated Nrf2 and HO-1 mRNA expression. • LC-MS/MS and molecular networking revealed 5 new saponins. [ABSTRACT FROM AUTHOR]

Two linear proline-rich peptides (1–2), bearing an N-terminal pyroglutamate, were isolated from the marine bacterium Microbacterium sp. V1, associated with the marine sponge Petrosia ficiformis, collected in the volcanic CO2 vents in Ischia Island (South Italy). Peptide production was triggered at low temperature following the one strain many compounds (OSMAC) method. Both peptides were detected together with other peptides (3–8) via an integrated, untargeted MS/MS-based molecular networking and cheminformatic approach. The planar structure of the peptides was determined by extensive 1D and 2D NMR and HR-MS analysis, and the stereochemistry of the aminoacyl residues was inferred by Marfey’s analysis. Peptides 1–8 are likely to arise from Microbacterium V1 tailor-made proteolysis of tryptone. Peptides 1 and 2 were shown to display antioxidant properties in the ferric-reducing antioxidant power (FRAP) assay.

Alternaria fungi are widely distributed plant pathogens that invade crop products, causing significant economic damage. In addition, toxic secondary metabolites produced by the fungi can also endanger consumers. Many of these secondary metabolites are chemically characterized as mycotoxins. In this study, Q Exactive Orbitrap mass spectrometry was used for the non-targeted analysis of the metabolome of seven Alternaria isolates cultured on Potato Carrot Agar (PCA), Potato Dextrose Agar (PDA) and Potato Sucrose Agar (PSA) medium. Due to the difficulty of detecting modified toxins, an analytical strategy with multiple visual analysis tools was also used to determine the presence of sulfate conjugated toxins, as well as to visualize the molecular network of Alternaria toxins. The results show that PSA medium exhibits more advantageous properties for the culture of Alternaria, with more toxigenic species and quantities and more obvious metabolic pathways. Based on high-resolution tandem mass spectrometry (MS/MS) data, the mycotoxins and their metabolites were mainly clustered into four groups: alternariol (AOH)/alternariol monomethyl ether (AME)/altenusin (ALU)/altenuene (ALT)/dehydroaltenusin (DHA)/Desmethyldehydroaltenusin (DMDA) families, Altertoxin-I (ATX-I) family, tentoxin (TEN) family and tenuazonic acid (TeA) family. Moreover, the PSA medium is more suitable for the accumulation of AOH, AME, ALU, ALT, DHA and DMDA, while the PDA medium is more suitable for the accumulation of ATX-I, TEN and TeA. This research may provide theoretical support for the metabolomics study of Alternaria.

In this interdisciplinary study, we selected two compounds, namely, smenamide A, a peptide–polyketide, and smenolactone D, a polyketide, as models because they are representative of two different classes of molecules isolated from the marine sponge Smenospongia aurea. The organic extract of Smenospongia aurea was analyzed using a combination of high-resolution LC-MS/MS and molecular networking, a recently developed method for automated LC-MS data analysis. The analyses were targeted to highlight clusters made by chlorinated compounds present in the extracts. Then, the two model compounds were analyzed for their bioactivity. Data reported here show that smenamide A did not exhibit a cytotoxic effect, while smenolactone D was cytotoxic on different tumor cell lines and was able to induce different types of cell death, including ferroptosis and apoptosis.

Prunus mume (Maesil) is used in health foods and alternative medicine in Korea. In the present study, the anti-inflammatory and antioxidant effects of phenolics from P. mume seed extracts were examined. First, the biological activities of various P. mume extracts were evaluated, and the profiles of their chemical compounds were investigated by Global Natural Products Social (GNPS)-molecular networking. Among these extracts, fermented Maesil seed extract (FMSE) showed potent anti-inflammatory and antioxidant activity, and demonstrated the presence of phenolic clusters in GNPS-based studies. Thus, the chemical constituents of this extract were further investigated. Subsequently, the chemical composition of the active CH2Cl2 fraction of FMSE was explored using an advanced GNPS analysis tool, MolNetEnhancer. In addition, the molecular structure of compound 1 from the CH2Cl2 fraction was similarly predicted with Network Annotation Propagation (NAP). Finally, the anti-inflammatory and antioxidant effects of compound 1 were confirmed by lipopolysaccharide (LPS)-induced nitric oxide production and DPPH assay. Western blot analysis revealed that compound 1 downregulated the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) proteins. The molecular docking simulation additionally confirmed significant interactions of 1 with iNOS and COX-2 proteins. Our findings suggested that an integrated GNPS-based approach could prioritize samples in the early fractionation process and improve the accuracy of target compound prediction.

Beauveria bassiana is a globally distributed entomopathogenic fungus that produces various secondary metabolites to support its pathogenesis in insects. Two polyketide synthase genes, pks14 and pks15, are highly conserved in entomopathogenic fungi and are important for insect virulence. However, understanding of their mechanisms in insect pathogenicity is still limited. Here, we overexpressed these two genes in B. bassiana and compared the metabolite profiles of pks14 and pks15 overexpression strains to those of their respective knockout strains in culture and in vivo using tandem liquid chromatography-mass spectrometry (LC-MS/MS) with Global Natural Products Social Molecular Networking (GNPS). The pks14 and pks15 clusters exhibited crosstalk with biosynthetic clusters encoding insect-virulent metabolites, including beauvericins, bassianolide, enniatin A, and the intracellular siderophore ferricrocin under certain conditions. These secondary metabolites were upregulated in the pks14-overexpressing strain in culture and the pks15-overexpressing strain in vivo. These data suggest that pks14 and pks15, their proteins or their cluster components might be directly or indirectly associated with key pathways in insect pathogenesis of B. bassiana, particularly those related to secondary metabolism. Information about interactions between the polyketide clusters and other biosynthetic clusters improves scientific understanding about crosstalk among biosynthetic pathways and mechanisms of pathogenesis.

Alzheimer’s disease poses a global health concern with unmet demand requiring creative approaches to discover new medications. In this study, we investigated the chemical composition and the anticholinesterase activity of Aspergillus niveus Fv-er401 isolated from Foeniculum vulgare (Apiaceae) roots. Fifty-eight metabolites were identified using UHPLC-MS/MS analysis of the crude extract. The fungal extract showed acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibitory effects with IC50 53.44 ± 1.57 and 48.46 ± 0.41 µg/mL, respectively. Two known metabolites were isolated, terrequinone A and citrinin, showing moderate AChE and BuChE inhibitory activity using the Ellman’s method (IC50 = 11.10 ± 0.38 µg/mL and 5.06 ± 0.15 µg/mL, respectively for AChE, and IC50 15.63 ± 1.27 µg/mL and 8.02 ± 0.08 µg/mL, respectively for BuChE). As evidenced by molecular docking, the isolated compounds and other structurally related metabolites identified by molecular networking had the required structural features for AChE and BuChE inhibition. Where varioxiranol G (−9.76 and −10.36 kcal/mol), penicitrinol B (−9.50 and −8.02 kcal/mol), dicitrinol A (−8.53 and −7.98 kcal/mol) and asterriquinone CT5 (−8.02 and −8.25 kcal/mol) showed better binding scores as AChE and BuChE inhibitors than the co-crystallized inhibitor (between −7.89 and 7.82 kcal/mol) making them promising candidates for the development of new drugs to treat Alzheimer’s.

With the increasingly serious antimicrobial resistance, discovering novel antibiotics has grown impendency. The Antarctic abundant microbial resources, especially fungi, can produce unique bioactive compounds for adapting to the hostile environment. In this study, three Antarctic fungi, Chrysosporium sp. HSXSD-11-1, Cladosporium sp. HSXSD-12 and Acrostalagmus luteoalbus CH-6, were found to have the potential to produce antimicrobial compounds. Furthermore, the crude extracts of CH-6 displayed the strongest antimicrobial activities with 72.3–84.8% growth inhibition against C. albicans and Aeromonas salmonicida. The secondary metabolites of CH-6 were researched by bioactivity tracking combined with molecular networking and led to the isolation of two new α-pyrones, acrostalapyrones A (1) and B (2), along with one known analog (3), and three known indole diketopiperazines (4–6). The absolute configurations of 1 and 2 were identified through modified Mosher's method. Compounds 4 and 6 showed strong antimicrobial activities. Remarkably, the antibacterial activity of 6 against A. salmonicida displayed two times higher than that of the positive drug Ciprofloxacin. This is the first report to discover α-pyrones from the genus Acrostalagmus, and the significant antimicrobial activities of 4 and 6 against C. albicans and A. salmonicida. This study further demonstrates the great potential of Antarctic fungi in the development of new compounds and antibiotics. [ABSTRACT FROM AUTHOR]

Clitoria ternatea Linn. (CT), or butterfly pea, is an Ayurvedic plant traditionally used as a brain tonic. Recently, it was reported to be of use in treating central nervous system (CNS) disorders, i.e., as an antistress treatment and antidepressant. In the present study, we report a detailed phytochemical profile of the ethyl acetate fraction of the flower of CT (CTF_EA) with significant neuroprotective and anti-neuroinflammatory properties in both LPS-activated BV-2 and SK-N-SH cells. Concurrently, the molecular network (MN) derived from the CTF_EA metabolome allows putative identification of flavonol 3-O-glycosides, hydrocinnamic acids, and primary metabolites. Molecular docking studies suggest that CTF_EA preferentially targets iNOS, resulting in a decrease in nitric oxide (NO). Furthermore, no toxic effects on normal embryonic development, blood vessel formation, and apoptosis are observed when CTF_EA is tested for in vivo toxicity in zebrafish models. The overall preliminary results suggest the anti-neuroinflammatory and neuroprotective effects of CT and provide scientific support for the efficacy of this medicinal plant at local and traditional levels. However, studies on the targeted isolation of bioactive metabolites, in-depth pharmacological efficacy, and safety in mammalian models are urgently needed to expand our understanding of this plant before it is developed into a promising therapeutic agent for brain-related diseases. [ABSTRACT FROM AUTHOR]

The proliferation of new psychoactive substances (NPS) has necessitated the development and improvement of current practices for the detection and identification of known NPS and newly emerging derivatives. High-resolution mass spectrometry (HRMS) is quickly becoming the industry standard for these analyses due to its ability to be operated in data-independent acquisition (DIA) modes, allowing for the collection of large amounts of data and enabling retrospective data interrogation as new information becomes available. The increasing popularity of HRMS has also prompted the exploration of new ways to screen for NPS, including broad-spectrum wastewater analysis to identify usage trends in the community and metabolomic-based approaches to examine the effects of drugs of abuse on endogenous compounds. In this paper, the novel applications of HRMS techniques to the analysis of NPS is reviewed. In particular, the development of innovative data analysis and interpretation approaches is discussed, including the application of machine learning and molecular networking to toxicological analyses. [ABSTRACT FROM AUTHOR]

Chemical investigation of Lessingianthus brevifolius (Less.) H.Rob. aerial parts resulted in the isolation of the hirsutinolide-type sesquiterpene lactones piptocarphol, spicatolide D, piptocarphin D and 8α-acetoxy-10α-hydroxy-13-O-methylhirsutinolide, and also of a cadinanolide identified as 13-O-methylvernojalcanolide 8-O-acetate. Flavonoids, triterpenes and chlorogenic acids were also isolated. In addition, a dereplication study was carried out using UHPLC-HRMS and molecular networking, resulting in the identification of fifteen known compounds, being two sesquiterpene lactones and thirteen flavonoids. Some of the compounds are being described for the first time in L. brevifolius, and also in the Lessingianthus genus. [ABSTRACT FROM AUTHOR]

In this study, a strain of Anabaena flos-aquae UTEX 1444 was cultivated in six different concentrations of iron (III). Cultures were extracted with organic solvents and analyzed using our dereplication strategy, based on the combined use of high-resolution tandem mass spectrometry and molecular networking. The analysis showed the presence of the siderophores' family, named synechobactins, only in the zero iron (III) treatment culture. Seven unknown synechobactin variants were present in the extract, and their structures have been determined by a careful HRMS/MS analysis. This study unveils the capability of Anabaena flos-aquae UTEX 1444 to produce a large array of siderophores and may be a suitable model organism for a sustainable scale-up exploitation of such bioactive molecules, for the bioremediation of contaminated ecosystems, as well as in drug discovery. [ABSTRACT FROM AUTHOR]

Streptomyces sp. BRA-346 is an Actinobacteria isolated from the Brazilian endemic tunicate Euherdmania sp. We have reported that this strain produces epoxyketone peptides, as dihydroeponemycin (DHE) and structurally related analogs. This cocktail of epoxyketone peptides inhibits the proteasome chymotrypsin-like activity and shows high cytotoxicity to glioma cells. However, low yields and poor reproducibility of epoxyketone peptides production by BRA-346 under laboratory cultivation have limited the isolation of epoxyketone peptides for additional studies. Here, we evaluated several cultivation methods using different culture media and chemical elicitors to increase the repertoire of peptide epoxyketone production by this bacterium. Furthermore, BRA-346 genome was sequenced, revealing its broad genetic potential, which is mostly hidden under laboratory conditions. By using specific growth conditions, we were able to evidence different classes of secondary metabolites produced by BRA-346. In addition, by combining genome mining with untargeted metabolomics, we could link the metabolites produced by BRA-346 to its genetic capacity and potential regulators. A single biosynthetic gene cluster (BGC) was related to the production of the target epoxyketone peptides by BRA-346. The candidate BGC displays conserved biosynthetic enzymes with the reported eponemycin (EPN) and TMC-86A (TMC) BGCs. The core of the putative epoxyketone peptide BGC (ORFs A-L), in which ORF A is a LuxR-like transcription factor, was cloned into a heterologous host. The recombinant organism was capable to produce TMC and EPN natural products, along with the biosynthetic intermediates DH-TMC and DHE, and additional congeners. A phylogenetic analysis of the epn/tmc BGC revealed related BGCs in public databases. Most of them carry a proteasome beta-subunit, however, lacking an assigned specialized metabolite. The retrieved BGCs also display a diversity of regulatory genes and TTA codons, indicating tight regulation of this BGC at the transcription and translational levels. These results demonstrate the plasticity of the epn/tmc BGC of BRA-346 in producing epoxyketone peptides and the feasibility of their production in a heterologous host. This work also highlights the capacity of BRA-346 to tightly regulate its secondary metabolism and shed light on how to awake silent gene clusters of Streptomyces sp. BRA-346 to allow the production of pharmacologically important biosynthetic products. [ABSTRACT FROM AUTHOR]

Drug powder composition analysis is of particular interest in forensic investigations to identify illicit substance content, cutting agents and impurities. Powder profiling is difficult to implement due to multiple analytical methods requirement and remains a challenge for forensic toxicology laboratories. Furthermore, visualization tools allowing seizure products identification appear to be under-used to date. The aim of this study is to present the utility of molecular networking for the composition establishment of natural origin drugs. A powder suspected to contain heroin and three powders suspected to contain cocaine obtained from law enforcement agency seizures were analyzed using untargeted screening by liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS/MS). Molecular networking and metabolite annotation applied to suspected heroin sample allowed rapid confirmation of its illicit content (heroin), the identification of structurally related major impurities (6-monoacetylmorphine, 6-monoacetylcodeine, noscapine, and papaverine), as well as cutting agents (acetaminophen and caffeine). The cocaine powder profiling allowed the comparison of its constituents in a semi-quantitative manner (cocaine, benzoylecgonine, trans/cis-cinnamoylcocaine, trimethoxycocaine, hexanoylecgonine methylester, caffeine, hydroxyzine, levamisole, and phenacetin), bringing additional information for their identification, including geographically sourcing of natural product and their putative place in the supply chain. Although this approach does not replace the profiling techniques used by forensic laboratories, the use of molecular networks provides a visual overview of structurally related constituents which aids the comparison and investigation of seizure powders. Molecular networks offers here an ideal way to depict structurally related and unrelated compounds in these often complex mixtures of chemicals. [ABSTRACT FROM AUTHOR]

The biological screening of 44 marine sponge extracts for the research of bioactive molecules, with potential application in the treatment of age-related diseases (cancer and Alzheimer's disease) and skin aging, resulted in the selection of Scopalina hapalia extract for chemical study. As no reports of secondary metabolites of S. hapalia were found in the literature, we undertook this research to further extend current knowledge of Scopalina chemistry. The investigation of this species led to the discovery of four new compounds: two butenolides sinularone J (1) and sinularone K (2), one phospholipid 1-O-octadecyl-2-pentanoyl-sn-glycero-3-phosphocholine (3) and one lysophospholipid 1-O-(3-methoxy-tetradecanoyl)-sn-glycero-3-phosphocholine (4) alongside with known lysophospholipids (5 and 6), alkylglycerols (7–10), epidioxysterols (11 and 12) and diketopiperazines (13 and 14). The structure elucidation of the new metabolites (1–4) was determined by detailed spectroscopic analysis, including 1D and 2D NMR as well as mass spectrometry. Molecular networking was also explored to complement classical investigation and unravel the chemical classes within this species. GNPS analysis provided further information on potential metabolites with additional bioactive natural compounds predicted. [ABSTRACT FROM AUTHOR]

In this study, the pharmacokinetic profiles of the bioactive components in the leaf extract of the medicinal herb, Cudrania tricuspidate, were investigated using an MS/MS-based molecular networking system. To identify the major active components of the C. tricuspidate leaf extract (CLE), HPLC-DAD analysis was conducted with a standard mixture of six flavonoids (rutin, isoquercitrin, nicotiflorin, kaempferol 3-O-glucoside, quercetin, and kaempferol). The unknown peaks were determined via molecular networking analysis using the mass dataset obtained by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF/MS). For the subsequent pharmacokinetic study, CLE (1 g/kg) was orally administered to rats, and plasma samples were collected. The product ion mass data of plasma samples using LC-QTOF/MS were obtained and subjected to molecular networking analysis. The resulting molecular networking map indicated that the glucuronide metabolites of quercetin and kaempferol were the major circulating species. Accordingly, quercetin and kaempferol were determined following β-glucuronidase treatment, and their pharmacokinetic parameters were calculated. These findings indicate that the proposed molecular network-based approaches are potential and efficient methods for the pharmacokinetic study of herbal medicines.

Untargeted metabolomics is a powerful tool for profiling the biochemical phenotypes of organisms and discovering new metabolites that drive biological function and might be exploited as pharmaceutical leads. Yet, connecting physiological processes to metabolites detected remains a challenge due to the lack of structural and activity annotations and the underlying complexity of mixed samples (e.g., multiple microorganisms, organelles, etc.). To simplify this biological complexity, we separated coral holobionts into host mitochondria and their algal symbionts prior to LC-MS/MS-based untargeted metabolomic analysis followed by molecular networking. We found distinct metabolomic profiles between tissue fractions. Notably, 14% of metabolites detected were only observed in the mitochondria and algal symbionts, not in the holobiont, and thus were masked when the bulk (holobiont) sample was analyzed. The utility of tissue separation for hypothesis testing was assessed using a simple temperature experiment. We tested the hypothesis that membrane lipids of the coral mitochondria and algal symbionts become more saturated at higher temperatures to maintain membrane rigidity. While the holobiont metabolite profiles showed little change in response to elevated temperature, there was a change in lipid saturation of both fractions through time. The fatty acid saturation of both the coral mitochondria and the algal symbionts shifted upon exposure to higher temperatures (1 h) then returned to ambient saturation levels by 4 h, indicating rapid acclimatization to warmer water. Surprisingly, the fractions deviated in opposite directions: during the first hour of the experiment, the mitochondria showed an increase in saturated lipid concentrations, while the algal symbionts showed an increase in unsaturated lipids. Partitioning the holobiont prior to untargeted metabolomic analysis revealed disparate responses to environmental stress that would have gone undetected if only the holobiont/bulk tissue was analyzed. This work illustrates rapid physiological acclimatization to environmental changes in specific host organelles and symbionts, though via different paths.

Atractylodes macrocephala rhizome (called Bái-zhú in China) has a long history as a functional food and herbal medicine in East Asia, especially China. Sesquiterpenoids are one of the main active compounds of Atractylodes macrocephala rhizome. This study aimed to explore the unknown sesquiterpenoids of A. macrocephala rhizome using a molecular networking strategy. Two new nitrogen-containing sesquiterpenoids, atractylenolactam A (1) and atractylenolactam B (2), and 2 new sesquiterpene lactones, 8-methoxy-atractylenolide V (6) and 15-acetoxyl atractylenolide III (7), along with 12 known analogs (3-5 and 8-16) were discovered and isolated. All the structures were assigned based on detailed spectroscopic analyses. The absolute configurations of 1, 2, 6, and 7 were established by time-dependent density functional theory ECD (TDDFT-ECD) calculations. All these compounds had different degrees of concentration-dependent activating effects on nuclear-factor-E2-related factor-2 (Nrf2).

ABSTRACT Streptomyces bacteria are a key source of microbial specialized metabolites with useful applications in medicine and agriculture. In addition, some species are important plant pathogens and cause diseases such as potato scab, which reduces the quality and market value of affected potato crops. Most scab-associated Streptomyces spp. produce the phytotoxic metabolite thaxtomin A as the principal pathogenicity factor. However, recent reports have described scab-causing strains that do not produce thaxtomin A, but instead produce other phytotoxins that are thought to contribute to plant host infection and symptom development. Streptomyces sp. 11-1-2 is a highly pathogenic strain that was originally isolated from a scab symptomatic potato tuber in Newfoundland, Canada. The strain secretes one or more phytotoxic compounds of unknown identity, and it is hypothesized that these compounds serve as virulence factors for this organism. We analyzed the genome sequence of Streptomyces sp. 11-1-2 and found biosynthetic gene clusters for producing the known herbicidal compounds nigericin and geldanamycin. Phytotoxic culture extracts were analyzed using liquid chromatography-coupled tandem mass spectrometry and molecular networking, and this confirmed the production of both compounds by Streptomyces sp. 11-1-2 along with other, potentially related metabolites. The biosynthesis of both metabolites was found to be suppressed by the addition of N-acetylglucosamine to the culture medium, and pure nigericin and geldanamycin were able to exhibit phytotoxic effects against both radish seedlings and potato tuber tissue. Furthermore, the coadministration of the two compounds produced greater phytotoxic effects against potato tuber tissue than administration of each compound alone. IMPORTANCE Plant pathogens use a variety of mechanisms, including the production of phytotoxic specialized metabolites, to establish an infection of host tissue. Although thaxtomin A is considered the key phytotoxin involved in the development of potato scab disease, there is increasing evidence that other phytotoxins can play a role in disease development in some instances. In this study, we show that the highly pathogenic Streptomyces sp. 11-1-2 is capable of producing nigericin and geldanamycin, which individually and combined can cause significant damage to potato tuber tissue and radish seedlings. Our results suggest that the pathogenic phenotype of Streptomyces sp. 11-1-2 is due in part to the production of these specialized metabolites. As the biological activity of nigericin and geldanamycin is vastly different from the proposed activity of thaxtomin A against plants, the secretion of these compounds may represent a novel mechanism of plant pathogenicity exhibited by some Streptomyces species.

Human-mediated dispersal of alien species in new biogeographic realms is one of the major drivers of biodiversity change in marine ecosystems. Among others, ascidians are invasive species spreading worldwide, thus causing ecological and economic harms in the recipient environments. An integrated taxonomic approach on selected samples allowed the identification of Botrylloides niger Herdman 1886 as a non-indigenous ascidian forming large aggregates and outcompeting native species in the Fusaro Lake (central-western Mediterranean Sea). This led to the opportunity to investigate in deep its metabolome for the first time. Untargeted mass spectrometry-based metabolomics unveiled B. niger to be a source of nutraceuticals and bioactive natural products, such as lysophospholipids, sulfonolipids, polyunsaturated fatty acids, sphingolipids, monoacylglycerols, and alkaloids. Even if causing ecosystem alterations, our results suggest that B. niger could be exploited for nutritional and/or pharmaceutical purposes, thereby turning a treat in a resource.

Context: Dayuanyin decoction is a traditional Chinese medicine formulation that is commonly used in modern clinical practice to treat viral infections such as viral pneumonia, viral fever, influenza, and hepatitis. Although the usage rate of Dayuanyin decoction is gradually increasing in clinical practice, its pharmacological constituents are still unclear., Objective: This study comprehensively characterized the chemical constituents in Dayuanyin decoction using ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) and molecular networking., Materials and Methods: The overall strategy involved retrieving structural information, such as fragment ions and precursor ion masses, from self-built databases to identify the target constituents of the Dayuanyin decoction extract. The identification of non-targeted constituents was achieved by analyzing different categories, fragment pathways, mass spectrometry data, and the relationships between clusters of structures in molecular networking. Unannotated constituents were inferred from secondary mass spectrometry similarity and molecular weight differences and annotated constituents in the same constituent cluster. A few predicted constituents were selected and validated by comparing them to reference standards under identical mass spectrometry conditions., Results: This study preliminarily identified 216 constituents, including flavonoids, amino acids, alkaloids, triterpenes, steroidal saponins, phenylpropanoids, and other constituents., Conclusions: This integrated strategy using UPLC-QTOF-MS and molecular networking lays the foundation for clinical research on pharmacologically active substances in Dayuanyin decoction and could be popularized for the comprehensive profiling of chemical constituents of other traditional Chinese medicines.

Natural products from culture collections have enormous impact in advancing discovery programs for metabolites of biotechnological importance. These discovery efforts rely on the metabolomic characterization of strain collections. Many emerging approaches compare metabolomic profiles of such collections, but few enable the analysis and prioritization of thousands of samples from diverse organisms while delivering chemistry specific read outs. In this work we utilize untargeted LC-MS/MS based metabolomics together with molecular networking to. This approach annotated 76 molecular families (a spectral match rate of 28 %), including clinically and biotechnologically important molecules such as valinomycin, actinomycin D, and desferrioxamine E. Targeting a molecular family produced primarily by one microorganism led to the isolation and structure elucidation of two new molecules designated maridric acids A and B. Molecular networking guided exploration of large culture collections allows for rapid dereplication of know molecules and can highlight producers of uniques metabolites. These methods, together with large culture collections and growing databases, allow for data driven strain prioritization with a focus on novel chemistries.

Multi-omics methods have greatly advanced our understanding of the biological organism and its microbial associates. However, they are not routinely used in clinical or industrial applications, due to the length of time required to generate and analyze omics data. Here, we applied a novel integrated omics pipeline for the analysis of human and environmental samples in under 48 h. Human subjects that ferment their own foods provided swab samples from skin, feces, oral cavity, fermented foods, and household surfaces to assess the impact of home food fermentation on their microbial and chemical ecology. These samples were analyzed with 16S rRNA gene sequencing, inferred gene function profiles, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics through the Qiita, PICRUSt, and GNPS pipelines, respectively. The human sample microbiomes clustered with the corresponding sample types in the American Gut Project (http://www.americangut.org), and the fermented food samples produced a separate cluster. The microbial communities of the household surfaces were primarily sourced from the fermented foods, and their consumption was associated with increased gut microbial diversity. Untargeted metabolomics revealed that human skin and fermented food samples had separate chemical ecologies and that stool was more similar to fermented foods than to other sample types. Metabolites from the fermented foods, including plant products such as procyanidin and pheophytin, were present in the skin and stool samples of the individuals consuming the foods. Some food metabolites were modified during digestion, and others were detected in stool intact. This study represents a first-of-its-kind analysis of multi-omics data that achieved time intervals matching those of classic microbiological culturing. IMPORTANCE Polymicrobial infections are difficult to diagnose due to the challenge in comprehensively cultivating the microbes present. Omics methods, such as 16S rRNA sequencing, metagenomics, and metabolomics, can provide a more complete picture of a microbial community and its metabolite production, without the biases and selectivity of microbial culture. However, these advanced methods have not been applied to clinical or industrial microbiology or other areas where complex microbial dysbioses require immediate intervention. The reason for this is the length of time required to generate and analyze omics data. Here, we describe the development and application of a pipeline for multi-omics data analysis in time frames matching those of the culture-based approaches often used for these applications. This study applied multi-omics methods effectively in clinically relevant time frames and sets a precedent toward their implementation in clinical medicine and industrial microbiology.

Trace amounts of components in traditional Chinese medicine are considered pharmacological active substances used for treating many serious diseases. However, purifying all the trace substances and making clear their structures are not easy. In this context, high‐performance liquid chromatography coupled with quadrupole time‐of‐flight tandem mass spectrometry based molecular networking was applied to investigate the chemical constituents of the roots of Aconitum kusnezoffii Reichb., which led to the identification of 33 nodes in different groups (N1–N33). Based on the excremental fragmentation pathway of known diterpenoid alkaloids (1–9) and comparisons of characteristic ions and characteristic loss of analogs in literature, the structures of unknown ions were deduced. This work lays a foundation for the evaluation of the clinical basis and mechanism of traditional Chinese medicine from the aspects of chemistry. In this paper, the method speculation of unknown natural products by means of molecular network method is expected to be applied in the discovery and change law of relevant active components in clinical pharmacology and the change of complex systems caused by trace active compounds. [ABSTRACT FROM AUTHOR]

The recreational use of new psychoactive substances (NPS) is increasing worldwide. Among them, the arylcyclohexylamine family including phencyclidine (PCP) and ketamine derivatives is increasing. We report a non-fatal intoxication mainly due to arylcyclohexylamine compounds illustrated by molecular networking (MN). A 37-year-old man with a history of drug abuse was discovered with several bags labeled as research chemicals around him and traces of powder on his nose. He was rehydrated, intubated, and admitted to the intensive care unit (ICU). Urine and drug were analyzed by liquid chromatography-mass spectrometry for NPS identification. Several NPS were quantified in urine: 3-OH-PCP at 12,085 mg/L, 3-MeO-PCP at 1100 mg/L, 2F-DCK at 147 mg/L, N-ethylhexedrone at 165 mg/L and CMC at 48 mg/L. Using a bioinformatic approach, a molecular network was built to confirm the consumption of powders contained in the bags by comparison with patient's urine. This case illustrates the interest of MN to (i) perform sample-to-sample comparison, (ii) target quantification methods, and (iii) allow proper management to confirm the relevance of the treatment. [ABSTRACT FROM AUTHOR]

The deadliest insect, Culex pipiens, plays a critical role in the transmission of multiple diseases to livestock, animals, and humans. In the current work, the waste of Mangifera indica (Mango) seed kernels was extracted with ethyl acetate to profile the gallotannins components. Moreover, the major compounds pentagalloyl glucose (PGG) and mangiferin were isolated and their larvicidal activity against C. pipiens was determined. A total of 20 secondary metabolites were annotated based on high-performance liquid chromatography with photodiode array (PDA) detector and mass spectrometry (MS) detection. PGG and mangiferin were isolated and identified depending on different chromatographic and spectroscopic techniques. The extract exhibited good larvicidal activity against the 3rd larval instar of C. pipiens with LC50 value of 64.02 µg/ml, whereas those of pentagalloyl glucose and mangiferin were 169.38 and 232.15 µg/ml, respectively. The tested extract and the two isolated secondary metabolites exploited significant alterations for the tested enzymes (acetylcholinesterase, carboxylesterase, α-esterases, glutathione S-transferase, and cytochrome P-450 monooxygenase) compared to the untreated larvae with p < 0.01. The GST, carboxylesterase, and α-esterase have the main role in the detoxification of PGG and mangiferin. In conclusion, Mango waste could provide a cheap, available, and important source for tackling an environmental problem as an ecofriendly alternative to the currently used chemical insecticides. The strategy of our study using M. indica kernel against C. pipiens larvae. [ABSTRACT FROM AUTHOR]

This work first aims to investigate metabolites of 2‐fluoro‐deschloroketamine (2F‐DCK), a new arylcyclohexylamine derivatives (a group of dissociative ketamine‐based substances) using two in vitro experimental approaches, and to compare obtained results by means of molecular networking. Metabolites of 2F‐DCK were investigated using both human liver microsomes (HLMs) and hepatic (HepaRG) cell line incubates using molecular networking approach: 2F‐DCK pure substance was incubated with HLMs for up to 1 h at two concentrations (100 and 500 μM) and with HepaRG cells for two time periods (8 and 24 h) at one concentration (20 μM). In vitro obtained results were subsequently applied to a 2F‐DCK‐related fatality case. In vitro‐produced metabolites were investigated using high‐resolution accurate mass spectrometry using Orbitrap mass analyzer technology. Thirteen metabolites were in vitro produced and several metabolic pathways can be postulated. Seven additional metabolites were found in post‐mortem samples (bile and urine) of the case, comprising three Phase II metabolites, which appear to be minor in vivo metabolites. HLMs and HepaRG cell models appear to be complementary and obtained data allowed the identification of several specific 2F‐DCK metabolites in biological samples. In practical terms, observed metabolic ratios suggested that nor‐2F‐DCK (208.1137 m/z) and a hydrogenated metabolite (224.1443 m/z) could be proposed as reliable metabolites to be recorded in HRMS libraries in order to improve detection of 2F‐DCK use. [ABSTRACT FROM AUTHOR]

In the present study, the efficiency of three different solvents (H2O, acidified H2O, and 70% Methanol) for metabolites extraction from the leaves of sugar beet (Beta vulgaris subsp. vulgaris var. rubra) was investigated along with their inhibitory activity on pancreatic α-amylase and lipase for obesity management. The metabolic profile of the three extracts was analyzed by ultra-performance liquid chromatography (UPLC) coupled with electrospray ionization high-resolution mass spectrometric (ESI-HRMS-MS). Mass spectrometry-based molecular networking was employed to aid in metabolites annotation and for the visual investigation of the known metabolites and their analogues. The study led to the tentative identification of 45 metabolites including amino acids, purine derivatives, phenolic acids, flavonoids, fatty acids, and an alkaloid, articulating 24 compounds as a first time report from beet leaves along with 2 new putatively identified compounds: a flavone feruloyl conjugate (39) and a malonylated acacetin diglycoside (40). The three extracting systems exhibited comparable efficiency for pulling out the secondary metabolites from the beet leaves. The in vitro study supported this finding and demonstrated that the three extracts inhibited the activity of both pancreatic α-amylase and lipase enzymes with no significant difference observed regarding the percentage of the inhibition of the enzymes. Conclusively, the extraction protocol has a minimal effect on the anti-obesity properties of beet leaves.

Abstract The neuronal ceroid lipofuscinoses (NCLs), commonly known as Batten disease, belong to a family of neurological disorders that cause blindness, seizures, loss of motor function and cognitive ability, and premature death. There are 13 different subtypes of NCL that are associated with mutations in 13 genetically distinct genes (CLN1-CLN8, CLN10-CLN14). Similar clinical and pathological profiles of the different NCL subtypes suggest that common disease mechanisms may be involved. As a result, there have been many efforts to determine how NCL proteins are connected at the cellular level. A main driving force for NCL research has been the utilization of mammalian and non-mammalian cellular models to study the mechanisms underlying the disease. One non-mammalian model that has provided significant insight into NCL protein function is the social amoeba Dictyostelium discoideum. Accumulated data from Dictyostelium and mammalian cells show that NCL proteins display similar localizations, have common binding partners, and regulate the expression and activities of one another. In addition, genetic models of NCL display similar phenotypes. This review integrates findings from Dictyostelium and mammalian models of NCL to highlight our understanding of the molecular networking of NCL proteins. The goal here is to help set the stage for future work to reveal the cellular mechanisms underlying the NCLs.

Background: Bromelia laciniosa Mart. ex Schult. & Schult.f. is a Bromeliaceae plant species from the Brazilian Caatinga, popularly used for the treatment of childhood colic, diarrhea, fever, jaundice, dandruff and hepatitis. The objective of this work was to evaluate the chemical composition and antimicrobial activity of the species B. laciniosa. Method: In this study, we evaluated the antimicrobial activity of ethanolic extract from the leaves of B. laciniosa by microdilution MIC method, and provided a comprehensive panel of B. laciniosa’s metabolite composition through mass spectrometry (MS) coupled to gas chromatography (GC–MS) and liquid chromatography (LC-MS). Results: B. laciniosa ethanolic extract inhibited Staphylococcus aureus growth at the lowest concentration tested. The GC–MS analysis revealed 45 non-polar metabolites, including campesterol, palmitic acid, oleic acid and α-tocopherol. Isolation and structural elucidation by NMR experiments supported the identification of cirsilineol (1), and the mixture of steroids β-sitosterol (2) and stigmasterol (3). The LC-MS metabolite profiling was assisted by Global Natural Product Social Molecular Networking (GNPS) and led to the putative annotation of 22 metabolites, consisting of phenylpropanoids, C- and O-glycosyl-flavonoids and fatty acids. In total, 39 chemical constituents are being described for the first time in B. laciniosa. Conclusions: The results show the diversity of secondary metabolites in the species B. laciniosa as well as antibacterial activity against S. aureus.

Excisional wounds are considered one of the most common physical injuries. This study aims to test the effect of a nanophytosomal formulation loaded with a dried hydroalcoholic extract of S. platensis on promoting excisional wound healing. The Spirulina platensis nanophytosomal formulation (SPNP) containing 100 mg PC and 50 mg CH exhibited optimum physicochemical characteristics regarding particle size (598.40 ± 9.68 nm), zeta potential (−19.8 ± 0.49 mV), entrapment efficiency (62.76 ± 1.75%), and Q6h (74.00 ± 1.90%). It was selected to prepare an HPMC gel (SPNP-gel). Through metabolomic profiling of the algal extract, thirteen compounds were identified. Molecular docking of the identified compounds on the active site of the HMGB-1 protein revealed that 12,13-DiHome had the highest docking score of −7.130 kcal/mol. SPNP-gel showed higher wound closure potential and enhanced histopathological alterations as compared to standard (MEBO® ointment) and S. platensis gel in wounded Sprague-Dawley rats. Collectively, NPS promoted the wound healing process by enhancing the autophagy process (LC3B/Beclin-1) and the NRF-2/HO-1antioxidant pathway and halting the inflammatory (TNF-, NF-κB, TlR-4 and VEGF), apoptotic processes (AIF, Caspase-3), and the downregulation of HGMB-1 protein expression. The present study’s findings suggest that the topical application of SPNP-gel possesses a potential therapeutic effect in excisional wound healing, chiefly by downregulating HGMB-1 protein expression.

Antarctic krill (Euphausia superba) of the Euphausiidae family comprise one of the largest biomasses in the world and play a key role in the Antarctic marine ecosystem. However, the study of E. superba-derived microbes and their secondary metabolites has been limited. Chemical investigation of the secondary metabolites of the actinomycetes Nocardiopsis sp. LX-1 (in the family of Nocardiopsaceae), isolated from E. superba, combined with molecular networking, led to the identification of 16 compounds a–p (purple nodes in the molecular network) and the isolation of one new pyrroline, nocarpyrroline A (1), along with 11 known compounds 2–12. The structure of the new compound 1 was elucidated by extensive spectroscopic investigation. Compound 2 exhibited broad-spectrum antibacterial activities against A. hydrophila, D. chrysanthemi, C. terrigena, X. citri pv. malvacearum and antifungal activity against C. albicans in a conventional broth dilution assay. The positive control was ciprofloxacin with the MIC values of 1 and compounds 7, 10, and 11 displayed antifungal activities against F. fujikuroi and D. citri, respectively, in modified agar diffusion test. Prochloraz was used as positive control and showed the inhibition zone radius of 17 mm and 15 mm against F. fujikuroi and D. citri, respectively. All the annotated compounds a–p by molecular networking were first discovered from the genus Nocardiopsis. Nocarpyrroline A (1) features an unprecedented 4,5-dihydro-pyrrole-2-carbonitrile substructure, and it is the first pyrroline isolated from the genus Nocardiopsis. This study further demonstrated the guiding significance of molecular networking in the research of microbial secondary metabolites.

Trichoderma is recognized as a prolific producer of nonribosomal peptides (NRPs) known as peptaibols, which have remarkable biological properties, such as antimicrobial and anticancer activities, as well as the ability to promote systemic resistance in plants against pathogens. In this study, the sequencing of 11-, 14- and 15-res peptaibols produced by a marine strain of Trichoderma isolated from the ascidian Botrylloides giganteus was performed via liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-MS/MS). Identification, based on multilocus phylogeny, revealed that our isolate belongs to the species T. endophyticum, which has never been reported in marine environments. Through genome sequencing and genome mining, 53 biosynthetic gene clusters (BGCs) were identified as being related to bioactive natural products, including two NRP-synthetases: one responsible for the biosynthesis of 11- and 14-res peptaibols, and another for the biosynthesis of 15-res. Substrate prediction, based on phylogeny of the adenylation domains in combination with molecular networking, permitted extensive annotation of the mass spectra related to two new series of 15-res peptaibols, which are referred to herein as “endophytins”. The analyses of synteny revealed that the origin of the 15-module peptaibol synthetase is related to 18, 19 and 20-module peptaibol synthetases, and suggests that the loss of modules may be a mechanism used by Trichoderma species for peptaibol diversification. This study demonstrates the importance of combining genome mining techniques, mass spectrometry analysis and molecular networks for the discovery of new natural products.

Metabolomics strategies are important tools to get holistic chemical information from a system, but they are scarcely applied to endophytic fungi to understand their chemical profiles of biosynthesized metabolites. Here Penicillium sp. was cultured using One Strain Many Compounds (OSMAC) conditions as a model system to demonstrate how this strategy can help in understanding metabolic profiles and determining bioactive metabolites with the application of metabolomics and statistical analyses, as well as molecular networking. Penicillium sp. was fermented in different culture media and the crude extracts from mycelial biomass (CEm) and broth (CEb) were obtained, evaluated against bacterial strains (Staphylococcus aureus and Pseudomonas aeruginosa), and the metabolomic profiles by LC-DAD-MS were obtained and chemometrics statistical analyses were applied. The CEm and CEb extracts presented different chemical profiles and antibacterial activities; the highest activities observed were against S. aureus from CEm (MIC = 16, 64, and 128 µg/mL). The antibacterial properties from the extracts were impacted for culture media from which the strain was fermented. From the Volcano plot analysis, it was possible to determine statistically the most relevant features for the antibacterial activity, which were also confirmed from biplots of PCA as strong features for the bioactive extracts. These compounds included 75 (13-oxoverruculogen isomer), 78 (austalide P acid), 87 (austalide L or W), 88 (helvamide), 92 (viridicatumtoxin A), 96 (austalide P), 101 (dihydroaustalide K), 106 (austalide k), 110 (spirohexaline), and 112 (pre-viridicatumtoxin). Thus, these features included diketopiperazines, meroterpenoids, and polyketides, such as indole alkaloids, austalides, and viridicatumtoxin A, a rare tetracycline.

In addition to having different biological activities of interest, corn silks play a role in the defense of plants. While benzoxamines and flavonoids have already been identified as molecules of plant defense and growth mechanisms, knowledge on the phytochemical composition of corn silk is lacking. Such knowledge would make it possible to better select the most effective varieties to improve resistance or bioactive properties. In this article, an approach was implemented to map a corn silk extract in two complementary ways. The first one involved working with UHPLC/HRMS data and Kendrick and van Krevelen plots to highlight a homologous series of compounds, such as lipids from 17 to 23 carbons, monoglycosylated flavonoids from 21 to 24 carbons, diglycosylated flavonoids of 26 to 28 carbons and organic acids of 14 to 19 carbons. The second way was to analyze the sample in UHPLC/HRMS2 and to plot mass spectral similarity networks with the GNPS platform and Cytoscape software to refine identification. By combining the information obtained, we were able to propose an identification for 104 detected molecules, including 7 nitrogenous, 28 lipidic and 67 phenolic compounds, leading to the first detailed phytochemical analysis of corn silk extract.

Myrica gale is an aromatic peatland shrub that has reported traditional use as an insect repellent. Different extraction methodologies were used in this study to isolate the essential oil of Myrica gale L., including Clevenger hydrodistillation (CH) and microwave-assisted hydrodistillation (MAH). The oils, isolated from different plant parts (leaves, fruit and branches) collected in summer and autumn, were analysed by GC-MS and the volatiles from plant tissue were directly analysed by headspace-GC-MS. A total of 58 components were identified, including 15 monoterpene hydrocarbons (22.78–98.98%), 14 oxygenated monoterpenes (0.91–43.02%), 13 sesquiterpene hydrocarbons (0.05–24.98%), 3 oxygenated sesquiterpenes (0.07–13.16%) and 13 other compounds (0.05–5.21%). Headspace sampling furnished monoterpenes, while CH and MAH extracted monoterpenes and sesquiterpenes, with α-pinene (6.04–70.45%), eucalyptol (0.61–33.80%), limonene (2.27–20.73%) and α-phellandrene (2.33–15.61%) as major components in all plant parts. Quantitative differences occurred between extraction methodologies, with MAH yielding higher quantities of monoterpene and sesquiterpene hydrocarbons and CH targeting oxygenated counterparts. Leaves gave more complex chemical fingerprints than branches and fruit, and the summer collection yielded more components than the autumn collections. An OPLS-DA model was applied to the GC-MS data to compare the chemical profiles based on the extraction techniques and plant parts, and molecular networks were obtained for monoterpenes and sesquiterpenes connected via biosynthetic pathways. The essential oil profile of Myrica gale was influenced by the season of collection, plant part and extraction method.

Azaphilones are microbial specialized metabolites employed as yellow, orange, red or purple pigments. In particular, yellow azaphilones react spontaneously with functionalized nitrogen groups, leading to red azaphilones. In this study, a new two-step solid-state cultivation process to produce specific red azaphilones pigments was implemented, and their chemical diversity was explored based on liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and a molecular network. This two-step procedure first implies a cellophane membrane allowing accumulating yellow and orange azaphilones from a Penicillium sclerotiorum SNB-CN111 strain, and second involves the incorporation of the desired functionalized nitrogen by shifting the culture medium. The potential of this solid-state cultivation method was finally demonstrated by overproducing an azaphilone with a propargylamine side chain, representing 16% of the metabolic crude extract mass.

Analysis of extracts of the marine sponge Clathria faviformis by high-resolution LC-MS2 and molecular networking resulted in the discovery of a new family of potentially UV-protecting phospholipids, the favilipids. One of them, favilipid A (1), was isolated and its structure determined by mass and tandem mass spectrometry, NMR, electronic circular dichroism (ECD), and computational studies. Favilipid A, which has no close analogues among natural products, possesses an unprecedented structure characterized by a 4-aminodihydropiridinium core, resulting in UV-absorbing properties that are very unusual for a phospholipid. Consequently, favilipid A could inspire the development of a new class of molecules to be used as sunscreen ingredients. In addition, favilipid A inhibited by 58–48% three kinases (JAK3, IKKβ, and SYK) involved in the regulation of the immune system, suggesting a potential use for treatment of autoimmune diseases, hematologic cancers, and other inflammatory states.

Ophiopogonis Radix, also known as “Maidong” (MD) in China, is frequently sulfur-fumigated (SF) in the pretreatment process of MD to improve the appearance and facilitate preservation. However, the process leads to changes in chemical composition, so it is essential to develop an approach to identify the chemical characteristics between nonfumigated and sulfur-fumigated products. This paper provided a practical method based on UPLC-QTOF-MS combined Global Natural Products Social Molecular Networking (GNPS) with multivariate statistical analysis for the characterization and discrimination of MD with different levels of sulfur fumigation, high concentration sulfur fumigation (HS), low concentration sulfur fumigation (LS) and without sulfur fumigation (WS). First, a number of 98 compounds were identified in those MD samples. Additionally, the results of Principal component analysis (PCA) and Orthogonal partial least-squares-discriminant analysis (OPLS-DA) demonstrated that there were significant chemical differences in the chemical composition of MD with different degrees of SF. Finally, fourteen and sixteen chemical markers were identified upon the comparison between HS and WS, LS and WS, respectively. Overall, these results can be able to discriminate MD with different levels of SF as well as establish a solid foundation for further quality control and pharmacological research.

Phytochemical investigation of the dichloromethane crude extract from the bark of Ochreinauclea maingayi with the aid of LCMS/MS-based molecular networking guided the isolation and accelerated the elucidation of known and new indole alkaloids. The molecular networking analysis produces two main clusters, along with 41 non-prioritized clusters and self-loop nodes. Each cluster has several nodes which depict the fractions contained within those nodes. An implementation of a fraction mapping for each node represents the molecular weight and key fragment data of each compound. From the analysis of each cluster and node, we can deduce the indole alkaloids are the scaffold of interest. Indole scaffold can be found between F5 and F10 that contain several types of indole alkaloids. In total, we have successfully purified nine indole alkaloids, including 9H-β-carboline-4-carboxylate 2, norharmane 3, harmane 4, naucledine 10, neonaucline 15, 1,2,3,4-tetranorharmane-1-one 16, naulafine 19, cadambine 9, and a new monoterpene indole alkaloid dihyrodeglycocadambine 7 from F5 to F10 using a chromatographic technique. Their structures were confirmed by 1D-NMR, 2D-NMR, UV, IR, LCMS, and MS2LDA. Several clusters and nodes contain ions that could not be annotated, suggesting that they may possess novel compounds that are yet to be discovered.

Centaurea is a genus compromising over 250 herbaceous flowering species and is used traditionally to treat several ailments. Among the Egyptian Centaurea species, C. lipii was reported to be cytotoxic against multidrug-resistant cancer cells. In this context, we aimed to explore the metabolome of C. lipii and compare it to other members of the genus in pursuance of identifying its bioactive principles. An LC-MS/MS analysis approach synchronized with feature-based molecular networks was adopted to offer a holistic overview of the metabolome diversity of the Egyptian Centaurea species. The studied plants included C. alexandrina, C. calcitrapa, C. eryngioides, C. glomerata, C. lipii, C. pallescens, C. pumilio, and C. scoparia. Their constitutive metabolome showed diverse chemical classes such as cinnamic acids, sesquiterpene lactones, flavonoids, and lignans. Linking the recorded metabolome to the previously reported cytotoxicity identified sesquiterpene lactones as the major contributors to this activity. To confirm our findings, bioassay-guided fractionation of C. lipii was adopted and led to the isolation of the sesquiterpene lactone cynaropicrin with an IC50 of 1.817 µM against the CCRF-CEM leukemia cell line. The adopted methodology highlighted the uniqueness of the constitutive metabolome of C. lipii and determined the sesquiterpene lactones to be the responsible cytotoxic metabolites.

LC-HRMS/MS-based molecular networking was applied to investigate the bioactive sesquiterpene lactones and their analogs contained in Inula helenium, enabling the isolation of four undescribed eudesmane-eudesmane sesquiterpene dimers (1-4), a sesquiterpene-amino acid adduct (5), and 17 known sesquiterpenes (6-22). The structures were determined based on 1D, 2D NMR, and HRESIMS data analysis, as well as DP4+ probability analyses and ECD calculations. The biosynthetic pathway of the sesquiterpene dimers is postulated to proceed via the Diels-Alder reaction as the key step. The inhibitory activity of all isolates on LPS-induced nitric oxide (NO) production in RAW 264.7 macrophages was evaluated. Compounds 4, 17, and 20 exhibited significant inhibitory activity against NO production, with IC 50 values of 8.4, 5.5, and 9.1 μM, respectively., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

In this study, we report the metabolic profiling of several previously uncharacterized Passiflora species native to Brazil, employing molecular networks to delve deeper into chemical constituents. Using the GNPS platform, in silico tools, and substructure annotation techniques, we expanded the chemical annotations. Principal Coordinate Analysis (PCoA) revealed significant metabolic similarities between several species, including P. incarnata, suggesting shared pharmacological potential. Our identification of metabolic compounds facilitated comparisons between understudied species with medicinal properties. Notably, we documented 25 previously uncharacterized species, paving the way for the development of novel products aimed at improving human well-being. This research focused on several native Passiflora species from Brazil, highlighting their unexplored therapeutic potential., (© 2024 Wiley-VHCA AG, Zurich, Switzerland.)

Understanding the chemical nature of soil organic carbon (SOC) with great potential to bind iron (Fe) minerals is critical for predicting the stability of SOC. Organic ligands of Fe are among the top candidates for SOCs able to strongly sorb on Fe minerals, but most of them are still molecularly uncharacterized. To shed insights into the chemical nature of organic ligands in soil and their fate, this study developed a protocol for identifying organic ligands using ultrahigh-performance liquid chromatography-high-resolution tandem mass spectrometry (UHPLC-HRMS/MS) and metabolomic tools. The protocol was used for investigating the Fe complexes formed by model compounds of lignin-derived organic ligands, namely, caffeic acid (CA), p -coumaric acid (CMA), vanillin (VNL), and cinnamic acid (CNA). Isotopologue analysis of 54/56 Fe was used to screen out the potential UHPLC-HRMS ( m / z ) features for complexes formed between organic ligands and Fe, with multiple features captured for CA, CMA, VNL, and CNA when 35/37 Cl isotopologue analysis was used as supplementary evidence for the complexes with Cl. MS/MS spectra, fragment analysis, and structure prediction with SIRIUS were used to annotate the structures of mono/bidentate mono/biligand complexes. The analysis determined the structures of monodentate and bidentate complexes of FeL x Cl y (L: organic ligand, x = 1-4, y = 0-3) formed by model compounds. The protocol developed in this study can be used to identify unknown organic ligands occurring in complex environmental samples and shed light on the molecular-level processes governing the stability of the SOC.

The fungus Talaromyces hainanensis , isolated from the mangrove soil, was characterized as a novel species by morphology observation and phylogenetic analyses. Four new γ -lactam alkaloids talaroilactams A-D ( 1 - 4 ) and two reported compounds harzianic acid ( 5 ) and isoharzianic acid ( 6 ) were identified from the fungus T. hainanensis WHUF0341, assisted by OSMAC along with molecular networking approaches. Their structures were determined through ECD calculations and spectroscopic analyses. Moreover, the biosynthetic route of 1 - 4 was also proposed. Compound 1 displayed potent cytotoxicity against HepG2 cell lines, with an IC 50 value of 10.75 ± 1.11 μM. In addition, network pharmacology was employed to dissect the probable mechanisms contributing to the antihepatocellular carcinoma effects of compound 1 , revealing that cytotoxicity was mainly associated with proteolysis, negative regulation of autophagy, inflammatory response, and the renin-angiotensin system. These results not only expanded the chemical space of natural products from the mangrove associated fungi but also afforded promising lead compounds for developing the antihepatocellular carcinoma agents.