Bioactivity-driven fungal metabologenomics identifies antiproliferative stemphone analogs and their biosynthetic gene cluster

INTRODUCTION

Fungi biosynthesize chemically diverse secondary metabolites with a wide range of biological activities. Natural product scientists have increasingly turned towards bioinformatics approaches, combining metabolomics and genomics to target secondary metabolites and their biosynthetic machinery. We recently applied an integrated metabologenomics workflow to 110 fungi and identified more than 230 high-confidence linkages between metabolites and their biosynthetic pathways.

OBJECTIVES

To prioritize the discovery of bioactive natural products and their biosynthetic pathways from these hundreds of high-confidence linkages, we developed a bioactivity-driven metabologenomics workflow combining quantitative chemical information, antiproliferative bioactivity data, and genome sequences.

METHODS

The 110 fungi from our metabologenomics study were tested against multiple cancer cell lines to identify which strains produced antiproliferative natural products. Three strains were selected for further study, fractionated using flash chromatography, and subjected to an additional round of bioactivity testing and mass spectral analysis. Data were overlaid using biochemometrics analysis to predict active constituents early in the fractionation process following which their biosynthetic pathways were identified using metabologenomics.

RESULTS

We isolated three new-to-nature stemphone analogs, 19-acetylstemphones G (1), B (2) and E (3), that demonstrated antiproliferative activity ranging from 3 to 5 µM against human melanoma (MDA-MB-435) and ovarian cancer (OVACR3) cells. We proposed a rational biosynthetic pathway for these compounds, highlighting the potential of using bioactivity as a filter for the analysis of integrated-Omics datasets.

CONCLUSIONS

This work demonstrates how the incorporation of biochemometrics as a third dimension into the metabologenomics workflow can identify bioactive metabolites and link them to their biosynthetic machinery.

Expanding Chemical Frontiers: Approaches for Generating Diverse and Bioactive Natural Product-Like Compounds Libraries from Extracts

The realms of natural products and synthetic compounds exhibit distinct chemical spaces that not only differ but also complement each other. While the convergence of these two domains has been explored through semisynthesis and conventional pharmacomodulation endeavours applied to natural frameworks, a recent and innovative approach has emerged that involves the combinatorial generation of libraries of 'natural product-like compounds' (NPLCs) through the direct synthetic derivatization of natural extracts. This has led to the production of numerous NPLCs that incorporate structural elements from both their natural (multiple saturated rings, oxygen content, chiral centres) and synthetic (aromatic rings, nitrogen and halogen content, drug-like properties) precursors. Through careful selection of extracts and reagents, specific bioactivities have been achieved, and this strategy has been deployed in various ways, showing great promise without reaching its full potential to date. This review seeks to provide an overview of reported examples involving the chemical engineering of extracts, showcasing a spectrum of natural product alterations spanning from simple substitutions to complete scaffold remodelling. It also includes an analysis of the accomplishments, perspectives and technical challenges within this field.

Toward a More Sustainable Sample Preparation in Phytochemistry: Case Studies in Four Subclasses of Alkaloids

The fact that alkaloids are bases has been the most explored chemical feature of their extraction and purification procedures. The main drawback of these procedures is that they employ undesirable chemicals, with HCl and CH2Cl2 probably being the most commonly employed chemicals in their subsequent steps. This work tested the hypothesis that advantages in recovery efficiency support this common practice. Experiments were conducted in three laboratories, monitoring the alkaloids harmine (1), boldine (2), vincamine (3), and mescaline (4) extracted from Banisteriopsis caapi, Peumus boldus, Vinca minor, and Trichocereus macrogonus var. pachanoi, respectively. The research demonstrated that HCl could be replaced with citric acid (CA) without loss or even better extraction performance. The recommended EtOAc could completely replace CH2Cl2 in three out of four study cases and partially in the fourth case without harming the extraction efficiency. In addition, the alternative solvents tert-amyl methyl ether (TAME) and n-butyl acetate (BuOAc) could enhance the extraction of alkaloids. These results might incentivize natural products laboratories to consider sustainability more routinely, thus being closer to current practices in the pharmaceutical industry, which has been replacing solvents and processes with greener ones.

New anti-α-Glucosidase and Antioxidant Ingredients from Winery Byproducts: Contribution of Alkyl Gallates

Wine-making activity entails the production of solid and semisolid byproducts (grape stems and pomace and wine lees) that negatively impact the environment and industrial sustainability. Their features as sources of bioactive compounds support valorization procedures for functional and healthy ingredients. This work uncovers the quantitative alkyl gallates (gallic acid esters, C1-C12) profile of fresh (freeze-dried) materials and the effect of oven-drying on their stability by UHPLC-ESI-QqQ-MS/MS. The functionality was established concerning DPPH• scavenging and antihyperglycemic power. Wine lees exerted the highest high-free concentration of galloyl derivatives, ethyl gallate being the most abundant ester (3472.62 ng/g dw, on average). About the impact of the stabilization process, although as a general trend, the thermal treatment reduced the concentration, the reduction dimensions depended on the compound/matrix, remaining in valuable concentrations. Concerning radical scavenging, ze-dried stems and pomace displayed the highest capacity (24.11 and 18.46 mg TE/g dw, respectively), being correlated with propyl gallate (r2 = 0.690), butyl gallate (r2 = 0.686), and octyl gallate (r2 = 0.514). These two matrices exerted α-glucosidase inhibitory activity (1.58 and 1.46 units/L) equivalent to that of acarbose (a recognized α-glucosidase inhibitor). The newly described bioactive phytochemicals in winery residues (galloyl esters) and their correlation with functional traits allow for envisioning valorization alternatives.

Comparative metabolomic profiling of Cupriavidus necator B-4383 revealed production of cupriachelin siderophores, one with activity against Cryptococcus neoformans

Cupriavidus necator H16 is known to be a rich source of linear lipopeptide siderophores when grown under iron-depleted conditions; prior literature termed these compounds cupriachelins. These small molecules bear β-hydroxyaspartate moieties that contribute to a photoreduction of iron when bound as ferric cupriachelin. Here, we present structural assignment of cupriachelins from C. necator B-4383 grown under iron limitation. The characterization of B-4383 cupriachelins is based on MS/MS fragmentation analysis, which was confirmed by 1D- and 2D-NMR for the most abundant analog (1). The cupriachelin congeners distinguish these two strains with differences in the preferred lipid tail; however, our rigorous metabolomic investigation also revealed minor analogs with changes in the peptide core, hinting at a potential mechanism by which these siderophores may reduce biologically unavailable ferric iron (4-6). Antifungal screening of the C. necator B-4383 supernatant extract and the isolated cupriachelin analog (1) revealed inhibitory activity against Cryptococcus neoformans, with IC50 values of 16.6 and 3.2 μg/mL, respectively. This antifungal activity could be explained by the critical role of the iron acquisition pathway in the growth and pathogenesis of the C. neoformans fungal pathogen.

Alkaloids and Coumarins with Adiponectin-Secretion-Promoting Activities from the Leaves of Orixa japonica

Fractionation of a methanol extract of Orixa japonica leaves led to the identification of five new quinoline alkaloids (1, 2, 4, 8, and 9), three new coumarins (15, 17, and 19), and 20 known compounds. The structures were determined by analysis of 1D and 2D NMR spectroscopic data. The absolute configuration of 19 was proposed by electronic circular dichroism calculation. Among the compounds tested in the phenotypic screening to measure adiponectin secretion in human bone marrow mesenchymal stem cells, metabolites 4 and 12 stimulated adiponectin secretions with EC₅₀ values of 13.8 and 25.8 μM, respectively. Further PPARγ binding assay and molecular modeling suggested that compounds 4 and 12 are selective PPARγ agonists.

Trivialities in metabolomics: Artifacts in extraction and analysis

The aim of this review is to show the risks of artifact formation in metabolomics analyses. Metabolomics has developed in a major tool in system biology approaches to unravel the metabolic networks that are the basis of life. Presently TLC, LC-MS, GC-MS, MS-MS and nuclear magnetic resonance are applied to analyze the metabolome of all kind of biomaterials. These analytical methods require robust preanalytical protocols to extract the small molecules from the biomatrix. The quality of the metabolomics analyses depends on protocols for collecting and processing of the biomaterial, including the methods for drying, grinding and extraction. Also the final preparation of the samples for instrumental analysis is crucial for highly reproducible analyses. The risks of artifact formation in these steps are reviewed from the point of view of the commonly used solvents. Examples of various artifacts formed through chemical reactions between solvents or contaminations with functional groups in the analytes are discussed. These reactions involve, for example, the formation of esters, trans-esterifications, hemiacetal and acetal formation, N-oxidations, and the formation of carbinolamines. It concerns chemical reactions with hydroxyl-, aldehyde-, keto-, carboxyl-, ester-, and amine functional groups. In the analytical steps, artifacts in LC may come from the stationary phase or reactions of the eluent with analytes. Differences between the solvent of the injected sample and the LC-mobile phase may cause distortions of the retention of analytes. In all analytical methods, poorly soluble compounds will be in all samples at saturation level, thus hiding a potential marker function. Finally a full identification of compounds remains a major hurdle in metabolomics, it requires a full set of spectral data, including methods for confirming the absolute stereochemistry. The putative identifications found in supplemental data of many studies, unfortunately, often become “truly” identified compounds in papers citing these results. Proper validation of the protocols for preanalytical and analytical procedures is essential for reproducible analyses in metabolomics.

Examples Showing the Utility of Doping Experiments in 1H NMR Analysis of Mixtures

Here we provide examples that demonstrate the value of using properly designed and easily performed doping experiments to give insights about the nature of the analyte(s) present in a ¹H NMR sample. Two mixtures, the first quite complex and the second far less so, have been chosen: (i) the crude pyrolysate from reaction of butyric acid in (supercritical) water at 600 °C and (ii) a mixture of two basic amines. In the former, 13 distinct carbonyl-containing compounds, ranging in relative concentration of nearly 2 orders of magnitude, were positively identified. The latter highlights the advantage of using a doping experiment as opposed to merely comparing the spectra from two separate samples containing the same analyte.

Synthesis of [2+2] Schiff base macrocycles by a solvent templating strategy and halogen bonding directed assembly

Schiff base imine condensations are a useful tool for macrocycle synthesis and applications within supramolecular chemistry. Here we address the mixtures of products that can arise from template free synthesis using dicarbonylheterocycles and diamines, and look to develop metal-free template methods for selective macrocycle formation. A range of alkyl α,ω-diamines were combined with phenanthroline and pyridine heterocyclic dicarbaldehydes under standard literature conditions. The reaction conditions were modified to demonstrate a relationship between choice of solvent and product equilibria. It was observed that benzene and toluene could shift a mixture of products and unreacted starting materials to form predominantly one imine product for a number of systems. Once the macrocyclic products had been characterized in selected solvents, iodinated halogen bonding guest molecules were added to direct macrocycle assemblies using non-covalent interactions. Studies to investigate host – guest suitability and halogen bond interactions were conducted, and it was found that tetraiodoethylene had an influence on the formation of a phenanthroline based macrocycle. Proof of concept experiments were performed to show the influence of the guest molecule, tetraiodoethylene, on the macrocyclic products formed under competitive dynamic combinatorial chemistry conditions.

TMS is Superior to Residual CHCl3 for Use as the Internal Reference for Routine 1H NMR Spectra Recorded in CDCl3

Tetramethylsilane was recommended for use as an internal reference compound in proton NMR spectroscopy over 60 years ago. However, it is a common practice that researchers reference the analyte chemical shifts to the residual proton resonance in the deuterated solvent in which the spectrum is recorded. Because CDCl₃ is the most commonly used NMR solvent for routine analysis of organic compounds, the effect of various functional groups on the CHCl₃ resonance is important. Described here are results that show why referencing spectra to TMS rather than CHCl₃ in CDCl₃ results in more accurate chemical shifts and should be the recommended practice. Simultaneous measurement of separate compartments of unperturbed CDCl₃/TMS vis-à-vis CDCl₃/TMS/solute solutions using a concentric tube arrangement was key. This study is reported in this venue because the audience/readership is quite appropriate and is, hopefully, both receptive to and appreciative of the guidance provided.

Recent Progress on Biological Activity of Amaryllidaceae and Further Isoquinoline Alkaloids in Connection with Alzheimer's Disease

Alzheimer’s disease (AD) is a progressive age-related neurodegenerative disease recognized as the most common form of dementia among elderly people. Due to the fact that the exact pathogenesis of AD still remains to be fully elucidated, the treatment is only symptomatic and available drugs are not able to modify AD progression. Considering the increase in life expectancy worldwide, AD rates are predicted to increase enormously, and thus the search for new AD drugs is urgently needed. Due to their complex nitrogen-containing structures, alkaloids are considered to be promising candidates for use in the treatment of AD. Since the introduction of galanthamine as an antidementia drug in 2001, Amaryllidaceae alkaloids (AAs) and further isoquinoline alkaloids (IAs) have been one of the most studied groups of alkaloids. In the last few years, several compounds of new structure types have been isolated and evaluated for their biological activity connected with AD. The present review aims to comprehensively summarize recent progress on AAs and IAs since 2010 up to June 2021 as potential drugs for the treatment of AD.

Species Prioritization Based on Spectral Dissimilarity: A Case Study of Polyporoid Fungal Species

Biological species collections are critical for natural product drug discovery programs. However, prioritization of target species in massive collections remains difficult. Here, we introduce an untargeted metabolomics-based prioritization workflow that uses MS/MS molecular networking to estimate scaffold-level distribution. As a demonstration, we applied the workflow to 40 polyporoid fungal species. Nine species were prioritized as candidates based on the chemical structural and compositional similarity (CSCS) metric. Most of the selected species showed relatively higher richness and uniqueness of metabolites than those of the others. Cryptoporus volvatus, one of the prioritized species, was investigated further. The chemical profiles of the extracts of C. volvatus culture and fruiting bodies were compared, and it was shown that derivative-level diversity was higher in the fruiting bodies; meanwhile, scaffold-level diversity was similar. This showed that the compounds found from a cultured fungus can also be isolated in wild mushrooms. Targeted isolation of the fruiting body extract yielded three unknown (1-3) and six known (4-9) cryptoporic acid derivatives, which are drimane-type sesquiterpenes with isocitric acid moieties that have been reported in this species. Cryptoporic acid T (1) is a trimeric cryptoporic acid reported for the first time. Compounds 2 and 5 exhibited cytotoxicity against HCT-116 cell lines with IC₅₀ values of 4.3 and 3.6 μM, respectively.

Virtual Screening for Reactive Natural Products and Their Probable Artifacts of Solvolysis and Oxidation

Chemically unstable natural products are prone to show their reactivity in the procedures of extraction, purification, or identification and turn into contaminants as so-called "artifacts". However, identification of artifacts requires considerable investments in technical equipment, time, and human resources. For revealing these reactive natural products and their artifacts by computational approaches, we set up a virtual screening system to seek cases in a biochemical database. The screening system is based on deep learning models of predicting the two main classifications of conversion reactions from natural products to artifacts, namely solvolysis and oxidation. A set of result data was reviewed for checking validity of the screening system, and we screened out a batch of reactive natural products and their probable artifacts. This work provides some insights into the formations of natural product artifacts, and the result data may act as warnings regarding the improper handling of biological matrixes in multicomponent extraction.

Chemical Composition and Antioxidant Activity of Thyme, Hemp and Coriander Extracts: A Comparison Study of Maceration, Soxhlet, UAE and RSLDE Techniques

Appropriate and standardized techniques for the extraction of secondary metabolites with interesting biological activity from plants are required. In this work, a comparison of different conventional and unconventional extraction techniques (maceration—M, Soxhlet—S, ultrasound assisted extraction—UAE, and rapid solid-liquid dynamic extraction—RSLDE) was investigated. Bioactive compounds were extracted from Thymus vulgaris L. (thyme), Cannabis sativa L. (industrial hemp) and Coriandrum sativum L. (coriander) and chemically characterized for their volatile fraction and polyphenolic content by means of gas chromatography-mass spectrometry (GC-MS) and high performance liquid chromatography-ultraviolet (HPLC-UV). Linalool (48.19%, RSLDE) and carvacrol (21.30%, M) for thyme, caryophyllene (54.78%, S) and humulene (14.13%, S) for hemp, and linalool (84.16%, RSLDE) for coriander seeds were the main compounds among terpenes, while thyme was the richest source of polyphenols with rosmarinic acid (51.7 mg/g dry extract-S), apigenin (7.6 mg/g dry extract-S), and luteolin (4.1 mg/g dry extract-UAE) being the most abundant. In order to shed light on their potential as natural food preservatives, the biological activity of the extracts was assessed in terms of antioxidant activity (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid—ABTS˙⁺, ferric reducing antioxidant power—FRAP, 2,2-diphenyl-1-picrylhydrazyl—DPPH˙ assays) and phenolic content (Folin–Ciocâlteu method). For thyme, Soxhlet extracts showed best performances in FRAP and ABTS˙⁺ assays (74 mg TE/g dry extract and 134 mg TE/g dry extract, respectively), while Soxhlet and RSLDE extracts recorded similar activity in DPPH˙ (107–109 mg TE/g dry extract). For hemp and coriander, indeed, RSLDE extracts accounted for higher antioxidant activity as evidenced by FRAP (80 mg TE/g dry extract and 18 mg TE/g dry extract, respectively) and ABTS˙⁺ (557 mg TE/g dry extract and 48 mg TE/g dry extract, respectively) assays. With respect to DPPH˙, the best results were observed for UAE extracts (45 mg TE/g dry extract and 220 mg TE/g dry extract, respectively). Our findings suggest that all the investigated techniques are valid extraction methods to retain bioactive compounds and preserve their activity for application in food and pharmaceutical formulations. Among them, the innovative RSLDE stands out for the slightly higher antioxidant performances of the extracts, coupled with the facility of use and standardization of the extraction process.

Caution: Chemical Instability of Natural Biomolecules During Routine Analysis

Natural products (NPs) constitute a significant source of active biomolecules widely used in medicine, pharmacology and cosmetics. However, NPs structural characterization has the drawback of their chemical instability during the extraction steps and their likely transformation during the analytical protocol. In particular, tamariscol and conocephalenol are two compounds largely used in the cosmetic industry for their odorant properties. Thus, in the present study, we focused on the evolution of these two metabolites (extracted from Frullania tamarisci and Conocephalum conicum, respectively), as followed by NMR. Interestingly, we found that, once dissolved in deuterated chloroform, these two tertiary alcohols are both subjected to transformation processes, leading to degradation compounds with altered structures. Accordingly, these detected degradation compounds have been fully characterized by NMR and the experimental findings were supported by computational chemistry data.

Volatiles from the Mandibular Gland Reservoir Content of Colobopsis explodens Laciny and Zettel, 2018, Worker Ants (Hymenoptera: Formicidae)

Forty-five volatile organic compounds (VOCs) were identified or annotated in the mandibular gland reservoir content (MGRC) of the Southeast Asian ant Colobopsis explodens Laciny and Zettel, 2018 (Hymenoptera: Formicidae), using headspace solid-phase microextraction (HS-SPME) coupled to gas chromatography-mass spectrometry (GC-MS) and liquid extraction combined with GC-MS. In extension of previous reports on VOCs of C. explodens, members of different compound classes, such as alkanes, aliphatic and aromatic carboxylic acids, and phenolics, were detected. The ketone 2-heptanone and the biochemically related phenolics benzene-1,3,5-triol (phloroglucinol, PG), 1-(2,4,6-trihydroxyphenyl)ethanone (monoacetylphloroglucinol, MAPG), 5,7-dihydroxy-2-methylchromen-4-one (noreugenin), and 1-(3-Acetyl-2,4,6-trihydroxyphenyl)ethanone (2,4-diacetylphloroglucinol, DAPG) dominated the GC-MS chromatograms. The identities of the main phenolics MAPG and noreugenin were further verified by liquid chromatography-high resolution-tandem mass spectrometry (LC-HRMS/MS). A comparative study of MGRC samples originating from three distinct field expeditions revealed differences in the VOC profiles, but the presence and relative abundances of the dominating constituents were largely consistent in all samples. Our study considerably extends the knowledge about the number and type of VOCs occurring in the MGRC of C. explodens. Based on the type of the detected compounds, we propose that the likely irritant and antibiotic phenolic constituents play a role in defense against arthropod opponents or in protection against microbial pathogens.