Utility of dry load injection for an efficient natural products isolation at the semi-preparative chromatographic scale

Comprehensive comparative metabolome study of a large collection of Corsican bryophytes

Introduction

Bryophytes are non-vascular plants that appeared on Earth before vascular plants. More than 24,000 species are reported worldwide, and only a small proportion have been studied. However, part of their biosynthetic potential has been unveiled and more than 1,600 terpenoids have been detected and identified. The study of bryophytes faces challenges due to their small size, and sociology, making it difficult to collect large amounts of uncontaminated samples. Additionally, their chemical specificity and the scarcity of chemical data specific to this branch further complicate their study. Traditionally, research on bryophytes has focused only on specific species or classes of compounds.

Methods

In contrast, our work proposes the first untargeted metabolite profiling investigation of a large collection of bryophytes (63 species) mainly issued from Corsican biodiversity. Metabolite profiling was performed by UHPLC-HRMS/MS and the data was extensively annotated using computational tools and molecular networking. This allowed us to describe in detail the chemical space covered by our collection and to establish comparisons between all the moss and liverwort species available. To validate some of the structural annotations, 3 liverworts (Frullania tamarisci, Pellia epiphylla, Plagiochila porelloides) and 2 mosses (Antitrichia curtipendula and Dicranum scoparium), available in larger quantities were fractionated using high-resolution semi-preparative HPLC, yielding 20 pure compounds. Five of them were newly discovered.

Results and discussion

This study highlights the main compositional differences between mosses and liverworts at the chemical class level. By analyzing given molecular network clusters, specific biosynthetic features or compounds that are characteristic of certain species are highlighted and discussed in detail.

High-Resolution Isolation of Natural Products: Efficient Combination of Dryload Injection and HPLC Gradient Transfer

The isolation of pure compounds from complex extracts is a crucial step in natural products (NPs) research. Historically, this process has been recognized to be slow and laborious. However, significant advancements have been made in isolation methods. Efficient separation conditions can now be efficiently determined at the analytical scale using high- or ultra-high-performance liquid chromatography and transferred to the preparative scale by chromatographic calculations. This ensures consistent selectivity at both scales, offering precise separation predictions. High-resolution chromatographic conditions at the preparative scale can be achieved through optimized sample preparation and dry load sample introduction. Monitoring chromatographic traces issued from ultraviolet (UV), mass spectrometry (MS), and/or universal detectors such as evaporative light-scattering detectors (ELSD) can precisely guide the isolation or trigger the collection of specific NPs with diverse structural scaffolds. These approaches can be applied across different scales depending on the amounts of NPs targeted for isolation. This chapter presents a detailed description of an isolation protocol, using the aforementioned methodologies.

Study of phenoxy radical couplings using the enzymatic secretome of Botrytis cinerea

Phenoxy radical coupling reactions are widely used in nature for the synthesis of complex molecules such as lignin. Their use in the laboratory has great potential for the production of high value compounds from the polyphenol family. While the enzymes responsible for the generation of the radicals are well known, the behavior of the latter is still enigmatic and difficult to control in a reaction flask. Previous work in our laboratory using the enzymatic secretome of B. cinerea containing laccases has shown that incubation of stilbenes leads to dimers, while incubation of phenylpropanoids leads to dimers as well as larger coupling products. Building on these previous studies, this paper investigates the role of different structural features in phenoxy radical couplings. We first demonstrate that the presence of an exocyclic conjugated double bond plays a role in the generation of efficient reactions. In addition, we show that the formation of phenylpropanoid trimers and tetramers can proceed via a decarboxylation reaction that regenerates this reactive moiety. Lastly, this study investigates the reactivity of other phenolic compounds: stilbene dimers, a dihydro-stilbene, a 4-O-methyl-stilbene and a simple phenol with the enzymatic secretome of B. cinerea. The observed efficient dimerization reactions consistently correlate with the presence of a para-phenol conjugated to an exocyclic double bond. The absence of this structural feature leads to variable results, with some compounds showing low conversion or no reaction at all. This research has allowed the development of a controlled method for the synthesis of specific dimers and tetramers of phenylpropanoid derivatives and novel stilbene derivatives, as well as an understanding of features that can promote efficient radical coupling reactions.

Advanced high-resolution chromatographic strategies for efficient isolation of natural products from complex biological matrices: from metabolite profiling to pure chemical entities

The isolation of pure compounds from extracts represents a key step common to all investigations of natural product (NP) research. Isolation methods have gone through a remarkable evolution. Current approaches combine powerful metabolite profiling methods for compounds annotation with omics mining results and/or bioassay for bioactive NPs/biomarkers priorisation. Targeted isolation of prioritized NPs is performed using high-resolution chromatographic methods that closely match those used for analytical profiling. Considerable progress has been made by the introduction of innovative stationary phases providing remarkable selectivity for efficient NPs isolation. Today, efficient separation conditions determined at the analytical scale using high- or ultra-high-performance liquid chromatography can be optimized via HPLC modelling software and efficiently transferred to the semi-preparative scale by chromatographic calculation. This ensures similar selectivity at both the analytical and preparative scales and provides a precise separation prediction. High-resolution conditions at the preparative scale can notably be granted using optimized sample preparation and dry load sample introduction. Monitoring by ultraviolet, mass spectrometry, and or universal systems such as evaporative light scattering detectors and nuclear magnetic resonance allows to precisely guide the isolation or trigger the collection of specific NPs with different structural scaffolds. Such approaches can be applied at different scales depending on the amounts of NPs to be isolated. This review will showcase recent research to highlight both the potential and constraints of using these cutting-edge technologies for the isolation of plant and microorganism metabolites. Several strategies involving their application will be examined and critically discussed.

Graphical abstract

Integration of Wnt-inhibitory activity and structural novelty scoring results to uncover novel bioactive natural products: new Bicyclo[3.3.1]non-3-ene-2,9-diones from the leaves of Hymenocardia punctata

In natural products (NPs) research, methods for the efficient prioritization of natural extracts (NEs) are key for discovering novel bioactive NPs. In this study a biodiverse collection of 1,600 NEs, previously analyzed by UHPLC-HRMS2 metabolite profiling was screened for Wnt pathway regulation. The results of the biological screening drove the selection of a subset of 30 non-toxic NEs with an inhibitory IC50 ≤ 5 μg/mL. To increase the chance of finding structurally novel bioactive NPs, Inventa, a computational tool for automated scoring of NEs based on structural novelty was used to mine the HRMS2 analysis and dereplication results. After this, four out of the 30 bioactive NEs were shortlisted by this approach. The most promising sample was the ethyl acetate extract of the leaves of Hymenocardia punctata (Phyllanthaceae). Further phytochemical investigations of this species resulted in the isolation of three known prenylated flavones (3, 5, 7) and ten novel bicyclo[3.3.1]non-3-ene-2,9-diones (1, 2, 4, 6, 8-13), named Hymenotamayonins. Assessment of the Wnt inhibitory activity of these compounds revealed that two prenylated flavones and three novel bicyclic compounds showed interesting activity without apparent cytotoxicity. This study highlights the potential of combining Inventa's structural novelty scores with biological screening results to effectively discover novel bioactive NPs in large NE collections.

A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery

The ENPKG framework organizes large heterogeneous metabolomics data sets as a knowledge graph, offering exciting opportunities for drug discovery and chemodiversity characterization.

One-step Bio-guided Isolation of Secondary Metabolites from the Endophytic Fungus Penicillium crustosum Using High-resolution Semi-preparative HPLC

BACKGROUND

An endophytic fungal strain Penicillium crustosum was isolated from the seagrass Posidonia oceanica and investigated to identify its antimicrobial constituents and characterize its metabolome composition. The ethyl acetate extract of this fungus exhibited antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA) as well as an anti-quorum sensing effect against Pseudomonas aeruginosa.

METHODS

The crude extract was profiled by UHPLC-HRMS/MS, and the dereplication was assisted by feature-based molecular networking. As a result, more than twenty compounds were annotated in this fungus. To rapidly identify the active compounds, the enriched extract was fractionated by semipreparative HPLC-UV applying a chromatographic gradient transfer and dry load sample introduction to maximise resolution. The collected fractions were profiled by 1H-NMR and UHPLC-HRMS.

RESULTS

The use of molecular networking-assisted UHPLC-HRMS/MS dereplication allowed preliminary identification of over 20 compounds present in the ethyl acetate extract of P. crustosum. The chromatographic approach significantly accelerated the isolation of the majority of compounds present in the active extract. The one-step fractionation allowed the isolation and identification of eight compounds (1-8).

CONCLUSION

This study led to the unambiguous identification of eight known secondary metabolites as well as the determination of their antibacterial properties.

Generation of potent antibacterial compounds through enzymatic and chemical modifications of the trans-δ-viniferin scaffold

Stilbene dimers are well-known for their diverse biological activities. In particular, previous studies have demonstrated the high antibacterial potential of a series of trans-δ-viniferin-related compounds against gram-positive bacteria such as Staphylococcus aureus. The trans-δ-viniferin scaffold has multiple chemical functions and can therefore be modified in various ways to generate derivatives. Here we report the synthesis of 40 derivatives obtained by light isomerization, O-methylation, halogenation and dimerization of other stilbene monomers. The antibacterial activities of all generated trans-δ-viniferin derivatives were evaluated against S. aureus and information on their structure-activity relationships (SAR) was obtained using a linear regression model. Our results show how several parameters, such as the O-methylation pattern and the presence of halogen atoms at specific positions, can determine the antibacterial activity. Taken together, these results can serve as a starting point for further SAR investigations.

Separation and purification of glycosides from medicinal plants based on strong polar separation medium with online closed-loop mode

Natural glycosides widely distributed in medicinal plants are valuable sources of therapeutic agents, showing various pharmacological effects. The separation and purification of natural glycosides are meaningful for their pharmacological research, which face with great challenges due to the complex of medicinal plants samples. In this work, two kinds of functional monolithic separation mediums A and S were fabricated and fully applied in the online extraction, separation and purification of active glycoside components from medicinal plants with a simple-procedure closed-loop mode. Chrysophanol glucoside and physcion glucoside were detected and separated from Rhei Radix et Rhizoma using separation medium A as a solid-phase extraction adsorbent. Rhapontin was isolated and purified from Rheum hotaoense C. Y. Cheng et Kao using separation medium S as the stationary phase of high-performance liquid chromatography. Compared to the reported literatures, high yield of 5.68, 1.20 and 4.76 mg g-1 of these three products were obtained with high purity. These two online closed-loop mode methods were carried out using high-performance liquid chromatography system, in which the sample injection, isolation and purification procedures are all online mode, and reduced loss compared to offline extraction and purification procedures, thus achieving high recovery and high purity.

Advances in extraction and purification of citrus flavonoids

Flavonoids are the representative active substances of citrus with various biological activities and high nutritional value. In order to evaluate and utilize citrus flavonoids, isolation and purification are necessary steps. This manuscript reviewed the research advances in the extraction and purification of citrus flavonoids. The structure classification, the plant and nutritional functions, and the biosynthesis of citrus flavonoids were summarized. The characteristics of citrus flavonoids and the selection of separation strategies were explained. The technical system of extraction and purification of citrus flavonoids was systematically described. Finally, outlook and research directions were proposed.

Reaction of the Phytochemistry Community to Green Chemistry: Insights Obtained Since 1990

This review article aims to study how phytochemists have reacted to green chemistry insights since 1990, the year when the U.S. Environmental Protection Agency launched the "Pollution Prevention Act". For each year in the period 1990 to 2019, three highly cited phytochemistry papers that provided enough information about the experimental procedures utilized were sampled. The "greenness" of these procedures was assessed, particularly for the use of solvents. The highly hazardous diethyl ether, benzene, and carbon tetrachloride did not appear in the papers sampled after 2010. Advances in terms of sustainability were observed mainly in the extraction stage. Similar progress was not observed in purification procedures, where chloroform, dichloromethane, and hexane regularly have been employed. Since replacing such solvents in purification procedures should be a major goal, potential alternative approaches are discussed. Moreover, some current initiatives toward a more sustainable phytochemical research considering aspects other than only solvents are highlighted. Although some advances have been achieved, it is believed that natural products chemists can play a major role in developing a novel ecological paradigm in chemistry. To contribute to this objective, six principles for performing natural products chemistry consistent with the guidelines of green chemistry are proposed.

Shallow- and Deep-Water Ophiura Species Produce a Panel of Chlorin Compounds with Potent Photodynamic Anticancer Activities

A Pacific brittle star Ophiura sarsii has previously been shown to produce a chlorin (3S,4S)-14-Ethyl-9-(hydroxymethyl)-4,8,13,18-tetramethyl-20-oxo-3-phorbinepropanoic acid (ETPA) (1) with potent phototoxic activities, making it applicable to photodynamic therapy. Using extensive LC-MS metabolite profiling, molecular network analysis, and targeted isolation with de novo NMR structure elucidation, we herein identify five additional chlorin compounds from O. sarsii and its deep-sea relative O. ooplax: 10S-Hydroxypheophorbide a (2), Pheophorbide a (3), Pyropheophorbide a (4), (3S,4S,21R)-14-Ethyl-9-(hydroxymethyl)-21-(methoxycarbonyl)-4,8,13,18-tetramethyl-20-oxo-3-phorbinepropanoic acid (5), and (3S,4S,21R)-14-Ethyl-21-hydroxy-9-(hydroxymethyl)-4,8,13,18-tetramethyl-20-oxo-3-phorbinepropanoic acid (6). Chlorins 5 and 6 have not been previously reported in natural sources. Interestingly, low amounts of chlorins 1-4 and 6 could also be identified in a distant species, the basket star Gorgonocephalus cf. eucnemis, demonstrating that chlorins are produced by a wide spectrum of marine invertebrates of the class Ophiuroidea. Following the purification of these major Ophiura chlorin metabolites, we discovered the significant singlet oxygen quantum yield upon their photoinduction and the resulting phototoxicity against triple-negative breast cancer BT-20 cells. These studies identify an arsenal of brittle star chlorins as natural photosensitizers with potential photodynamic therapy applications.

Inventa: A computational tool to discover structural novelty in natural extracts libraries

Collections of natural extracts hold potential for the discovery of novel natural products with original modes of action. The prioritization of extracts from collections remains challenging due to the lack of a workflow that combines multiple-source information to facilitate the data interpretation. Results from different analytical techniques and literature reports need to be organized, processed, and interpreted to enable optimal decision-making for extracts prioritization. Here, we introduce Inventa, a computational tool that highlights the structural novelty potential within extracts, considering untargeted mass spectrometry data, spectral annotation, and literature reports. Based on this information, Inventa calculates multiple scores that inform their structural potential. Thus, Inventa has the potential to accelerate new natural products discovery. Inventa was applied to a set of plants from the Celastraceae family as a proof of concept. The Pristimera indica (Willd.) A.C.Sm roots extract was highlighted as a promising source of potentially novel compounds. Its phytochemical investigation resulted in the isolation and de novo characterization of thirteen new dihydro-β-agarofuran sesquiterpenes, five of them presenting a new 9-oxodihydro-β-agarofuran base scaffold.

Chiral Separation of Stilbene Dimers Generated by Biotransformation for Absolute Configuration Determination and Antibacterial Evaluation

A series of complex stilbene dimers have been generated through biotransformation of resveratrol, pterostilbene, and the mixture of both using the enzymatic secretome of Botrytis cinerea Pers. The process starts with achiral molecules and results in the generation of complex molecules with multiple chiral carbons. So far, we have been studying these compounds in the form of enantiomeric mixtures. In the present study, we isolated the enantiomers to determine their absolute configuration and assess if the stereochemistry could impact their biological properties. Eight compounds were selected for this study, corresponding to the main scaffolds generated (pallidol, leachianol, restrytisol and acyclic dimers) and the most active compounds (trans-δ-viniferin derivatives) against a methicillin-resistant strain of Staphylococcus aureus (MRSA). To isolate these enantiomers and determine their absolute configuration, a chiral HPLC-PDA analysis was performed. The analysis was achieved on a high-performance liquid chromatography system equipped with a chiral column. For each compound, the corresponding enantiomeric pair was obtained with high purity. The absolute configuration of each enantiomer was determined by comparison of experimental and calculated electronic circular dichroism (ECD). The antibacterial activities of the four trans-δ-viniferin derivatives against two S. aureus strains were evaluated.

Chemoenzymatic Synthesis of Original Stilbene Dimers Possessing Wnt Inhibition Activity in Triple-Negative Breast Cancer Cells Using the Enzymatic Secretome of Botrytis cinerea Pers

The Wnt signaling pathway controls multiple events during embryonic development of multicellular animals and is carcinogenic when aberrantly activated in adults. Breast cancer and triple-negative breast cancer (TNBC) in particular depend upon Wnt pathway overactivation. Despite this importance, no Wnt pathway-targeting drugs are currently available, which necessitates novel approaches to search for therapeutically relevant compounds targeting this oncogenic pathway. Stilbene analogs represent an under-explored field of therapeutic natural products research. In the present work, a library of complex stilbene derivatives was obtained through biotransformation of a mixture of resveratrol and pterostilbene using the enzymatic secretome of Botrytis cinerea. To improve the chemodiversity, the reactions were performed using i-PrOH, n-BuOH, i-BuOH, EtOH, or MeOH as cosolvents. Using this strategy, a series of 73 unusual derivatives was generated distributed among 6 scaffolds; 55 derivatives represent novel compounds. The structure of each compound isolated was determined by nuclear magnetic resonance and high-resolution mass spectrometry. The inhibitory activity of the isolated compounds against the oncogenic Wnt pathway was comprehensively quantified and correlated with their capacity to inhibit the growth of the cancer cells, leading to insights into structure-activity relationships of the derivatives. Finally, we have dissected mechanistic details of the stilbene derivatives activity within the pathway.

Chemoenzymatic Synthesis of Complex Phenylpropanoid Derivatives by the Botrytis cinerea Secretome and Evaluation of Their Wnt Inhibition Activity

In this study, a series of complex phenylpropanoid derivatives were obtained by chemoenzymatic biotransformation of ferulic acid, caffeic acid, and a mixture of both acids using the enzymatic secretome of Botrytis cinerea. These substrates were incubated with fungal enzymes, and the reactions were monitored using state-of-the-art analytical methods. Under such conditions, a series of dimers, trimers, and tetramers were generated. The reactions were optimized and scaled up. The resulting mixtures were purified by high-resolution semi-preparative HPLC combined with dry load introduction. This approach generated a series of 23 phenylpropanoid derivatives, 11 of which are described here for the first time. These compounds are divided into 12 dimers, 9 trimers (including a completely new structural scaffold), and 2 tetramers. Elucidation of their structures was performed with classical spectroscopic methods such as NMR and HRESIMS analyses. The resulting compound series were analyzed for anti-Wnt activity in TNBC cells, with several derivatives demonstrating specific inhibition.

Recovery and purification of bikaverin produced by Fusarium oxysporum CCT7620

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Ethyl acetate extraction resulted in the highest bikaverin yield.

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Kinetic study revealed a saturation of bikaverin extraction after 256 min.

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Three sequential ethyl acetate extractions was the most economical to recover bikaverin.

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Open column chromatography or nanofiltration were not suitable to purify bikaverin.

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Bikaverin was successfully purified on semi-preparative HPLC.

Microbial pigments have a distinguished potential for applications in food and pharmaceutical industries, stimulating the research in this field. The present study evaluated the ideal conditions for extracting bikaverin (red pigment) from the biomass of Fusarium oxysporum CCT7620. Among the solvents tested, ethyl acetate extraction resulted in the highest bikaverin concentration and the kinetic study revealed a saturation in bikaverin concentration from 256 min on. Based on a preliminary economic study, three sequential extractions with ethyl acetate was considered the ideal protocol to recover bikaverin. After extraction, chromatographic methods were tested to purify bikaverin. The use of silica gel or Sephadex (open column) could not successfully purify bikaverin, but the semi-preparative HPLC resulted in a bikaverin-enriched fraction with a purity degree equivalent to the commercial analytical standard. This work provides relevant information regarding the extraction and purification of bikaverin, which may be useful for other downstraming processes.

Preparative separation of 1,1-diphenyl-2-picrylhydrazyl inhibitors originating from Saxifraga sinomontana employing medium-pressure liquid chromatography in combination with reversed-phase liquid chromatography

Traditional Tibetan medicines elaborately document the health benefits of Saxifraga sinomontana. However, there have been limited reports on its chemical make-up, presumably because of the complicated separation and purification process. In this work, a methanolic extract of Saxifraga sinomontana was utilized for targeted separation of 4 key 1,1-diphenyl-2-picrylhydrazyl inhibitors employing the medium-pressure liquid chromatography, reversed-phase liquid chromatography in combination with on-line reversed-phase liquid chromatography-1,1-diphenyl-2-picrylhydrazyl detection. Pre-treatment of the sample was carried out by employing medium-pressure liquid chromatography using MCI GEL® CHP20P as the stationary phase, furnishing 2.4 g of fraction Fr3 and 3.4 g of fraction Fr4 (the percentage retrieval was 32.7%). The 1,1-diphenyl-2-picrylhydrazyl inhibitors contained in fractions Fr3 and Fr4 were subjected to additional separation using a C18 (ReproSil-Pur C18 AQ) column and yielded 106.2 mg of Fr3-1, 246.9 mg of Fr3-2, 248.5 mg of Fr4-1 and 41.8 mg of Fr4-2. The degree of purity, structures and 1,1-diphenyl-2-picrylhydrazyl inhibition activity of the isolated DPPH inhibitors were determined, and four 1,1-diphenyl-2-picrylhydrazyl inhibitors including two new diarylnonanoids (3-methoxy-4-hydroxyphenol-(6'-O-galloyl)-1-O-β-d-glucopyrano side with IC₅₀ of 39.6 μM, 3,4,5-trimethoxyphenyl-(6'-O-galloyl)-1-O-β-d-glucopyranoside with IC₅₀ of 46.9 μM, saximonsin A with IC₅₀ of 11.4 μM, and saximonsin B with IC₅₀ of 20.6 μM) were isolated with a percentage purity above 95%. The methodology thus evolved has good efficacy for preparatively isolating high-purity 1,1-diphenyl-2-picrylhydrazyl inhibitors from extracts of Saxifraga sinomontana and could be efficiently utilized for rapidly isolating 1,1-diphenyl-2-picrylhydrazyl inhibitors from other natural products.

Combination of Pseudo-LC-NMR and HRMS/MS-Based Molecular Networking for the Rapid Identification of Antimicrobial Metabolites From Fusarium petroliphilum

An endophytic fungal strain isolated from a seagrass endemic to the Mediterranean Sea (Posidonia oceanica) was studied in order to identify its antimicrobial constituents and further characterize the composition of its metabolome. It was identified as Fusarium petroliphilum by in-depth phylogenetic analyses. The ethyl acetate extract of that strain exhibited antimicrobial activities and an ability to inhibit quorum sensing of Staphylococcus aureus. To perform this study with a few tens of mg of extract, an innovative one-step generic strategy was devised. On one side, the extract was analyzed by UHPLC-HRMS/MS molecular networking for dereplication. On the other side, semi-preparative HPLC using a similar gradient profile was used for a single-step high-resolution fractionation. All fractions were systematically profiled by ¹H-NMR. The data were assembled into a 2D contour map, which we call “pseudo-LC-NMR,” and combined with those of UHPLC-HRMS/MS. This further highlighted the connection within structurally related compounds, facilitated data interpretation, and provided an unbiased quantitative profiling of the main extract constituents. This innovative strategy led to an unambiguous characterization of all major specialized metabolites of that extract and to the localization of its bioactive compounds. Altogether, this approach identified 22 compounds, 13 of them being new natural products and six being inhibitors of the quorum sensing mechanism of S. aureus and Pseudomonas aeruginosa. Minor analogues were also identified by annotation propagation through the corresponding HRMS/MS molecular network, which enabled a consistent annotation of 27 additional metabolites. This approach was designed to be generic and applicable to natural extracts of the same polarity range.

Isolation and Identification of Isocoumarin Derivatives With Specific Inhibitory Activity Against Wnt Pathway and Metabolome Characterization of Lasiodiplodia venezuelensis

The Wnt signaling pathway controls multiple events during embryonic development of multicellular animals and is carcinogenic when aberrantly activated in adults. Breast cancers are dependent on Wnt pathway overactivation mostly through dysregulation of pathway component protein expression, which necessitates the search for therapeutically relevant compounds targeting them. Highly diverse microorganisms as endophytes represent an underexplored field in the therapeutic natural products research. In the present work, the objective was to explore the chemical diversity and presence of selective Wnt inhibitors within a unique collection of fungi isolated as foliar endophytes from the long-lived tropical palm Astrocaryum sciophilum. The fungi were cultured, extracted with ethyl acetate, and screened for their effects on the Wnt pathway and cell proliferation. The endophytic strain Lasiodiplodia venezuelensis was prioritized for scaled-up fractionation based on its selective activity. Application of geometric transfer from analytical HPLC conditions to semi-preparative scale and use of dry load sample introduction enabled the isolation of 15 pure compounds in a single step. Among the molecules identified, five are original natural products described for the first time, and six are new to this species. An active fraction obtained by semi-preparative HPLC was re-purified by UHPLC-PDA using a 1.7 µm phenyl column. 75 injections of 8 µg were necessary to obtain sufficient amounts of each compound for structure elucidation and bioassays. Using this original approach, in addition to the two major compounds, a third minor compound identified as (R)-(-)-5-hydroxymellein (18) was obtained, which was found to be responsible for the significant Wnt inhibition activity recorded. Further studies of this compound and its structural analogs showed that only 18 acts in a highly specific manner, with no acute cytotoxicity. This compound is notably selective for upstream components of the Wnt pathway and is able to inhibit the proliferation of three triple negative breast cancer cell lines. In addition to the discovery of Wnt inhibitors of interest, this study contributes to better characterize the biosynthetic potential of L. venezuelensis.

Characterization of Pseudomonas aeruginosa Quorum Sensing Inhibitors from the Endophyte Lasiodiplodia venezuelensis and Evaluation of Their Antivirulence Effects by Metabolomics

The opportunistic pathogen Pseudomonas aeruginosa is one of the "critical priority pathogens" due to its multidrug resistance to a wide range of antibiotics. Its ability to invade and damage host tissues is due to the use of quorum sensing (QS) to collectively produce a plethora of virulence factors. Inhibition of QS is an attractive strategy for new antimicrobial agents because it disrupts the initial events of infection without killing the pathogen. Highly diverse microorganisms as endophytes represent an under-explored source of bioactive natural products, offering opportunities for the discovery of novel QS inhibitors (QSI). In the present work, the objective was to explore selective QSIs within a unique collection of fungal endophytes isolated from the tropical palm Astrocaryum sciophilum. The fungi were cultured, extracted, and screened for their antibacterial and specific anti-QS activities against P. aeruginosa. The endophytic strain Lasiodiplodia venezuelensis was prioritized for scaled-up fractionation for its selective activity, leading to the isolation of eight compounds in a single step. Among them, two pyran-derivatives were found to be responsible for the QSI activity, with an effect on some QS-regulated virulence factors. Additional non-targeted metabolomic studies on P. aeruginosa documented their effects on the production of various virulence-related metabolites.

Metabolite profile of Nectandra oppositifolia Nees & Mart. and assessment of antitrypanosomal activity of bioactive compounds through efficiency analyses

EtOH extracts from the leaves and twigs of Nectandra oppositifolia Nees & Mart. shown activity against amastigote forms of Trypanosoma cruzi. These extracts were subjected to successive liquid-liquid partitioning to afford bioactive CH2Cl2 fractions. UHPLC-TOF-HRMS/MS and molecular networking were used to obtain an overview of the phytochemical composition of these active fractions. Aiming to isolate the active compounds, both CH2Cl2 fractions were subjected to fractionation using medium pressure chromatography combined with semi-preparative HPLC-UV. Using this approach, twelve compounds (1-12) were isolated and identified by NMR and HRMS analysis. Several isolated compounds displayed activity against the amastigote forms of T. cruzi, especially ethyl protocatechuate (7) with EC50 value of 18.1 μM, similar to positive control benznidazole (18.7 μM). Considering the potential of compound 7, protocatechuic acid and its respective methyl (7a), n-propyl (7b), n-butyl (7c), n-pentyl (7d), and n-hexyl (7e) esters were tested. Regarding antitrypanosomal activity, protocatechuic acid and compound 7a were inactive, while 7b-7e exhibited EC50 values from 20.4 to 11.7 μM, without cytotoxicity to mammalian cells. These results suggest that lipophilicity and molecular complexity play an important role in the activity while efficiency analysis indicates that the natural compound 7 is a promising prototype for further modifications to obtain compounds effective against the intracellular forms of T. cruzi.

A Cytotoxic Porphyrin from North Pacific Brittle Star Ophiura sarsii

Triple-negative breast cancer (TNBC) represents the deadliest form of gynecological tumors currently lacking targeted therapies. The ethanol extract of the North Pacific brittle star Ophiura sarsii presented promising anti-TNBC activities. After elimination of the inert material, the active extract was submitted to a bioguided isolation approach using high-resolution semipreparative HPLC-UV, resulting in one-step isolation of an unusual porphyrin derivative possessing strong cytotoxic activity. HRMS and 2D NMR resulted in the structure elucidation of the compound as (3S,4S)-14-Ethyl-9-(hydroxymethyl)-4,8,13,18-tetramethyl-20-oxo-3-phorbinepropanoic acid. Never identified before in Ophiuroidea, porphyrins have found broad applications as photosensitizers in the anticancer photodynamic therapy. The simple isolation of a cytotoxic porphyrin from an abundant brittle star species we describe here may pave the way for novel natural-based developments of targeted anti-cancer therapies.

Targeted isolation of 1,1-diphenyl-2-picrylhydrazyl inhibitors from Saxifraga atrata using medium- and high- pressure liquid chromatography combined with online high performance liquid chromatography-1,1-diphenyl-2- picrylhydrazyl detection

Traditional Tibetan medicine (TTM) is a valuable source of novel therapeutic lead molecules inspired by natural products (NPs). The health benefits of Saxifraga atrata are well documented in TTM, but reports on its chemical composition are limited, most likely due to the complicated purification process. Herein, target separation and identification of 4 main radical scavenging compounds from the methanolic extract of S. atrata was were performed using medium- and high-pressure liquid chromatography coupled with online HPLC-DPPH detection. The sample was pretreated using medium pressure liquid chromatography with MCI GELⓇ CHP20P styrene-divinylbenzene beads as a stationary phase, yielding 1.4 g of the target DPPH inhibitors (Fr4, 11.9% recovery). The compounds were further purified and isolated using HPLC on RP-C18 (ReproSil-Pur C18 AQ) followed by HILIC (Click XIon) column separation, resulting in 2.8 mg of fraction Fr4-1-1, 6.8 mg of fraction Fr4-2, 244.9 mg of the Fr4-3-1 sample, and 38.3 mg of Fr4-4-1. The structure and purity of the target compounds were determined, and four compounds (ethyl gallate, 11-O-galloylbergenin, rutin and isoquercitrin) were isolated with >95% purity. The developed methodology is efficient for targeted isolation of high-purity radical scavengers from NP extracts and could be used for rapid identification and isolation of DPPH inhibitors from various NPs.

Production of Highly Active Antiparasitic Compounds from the Controlled Halogenation of the Arrabidaea brachypoda Crude Plant Extract

Direct halogenation of phenolic compounds present in the CH₂Cl₂ extract of the roots of Arrabidaea brachypoda was investigated to enhance chemodiversity. The approach is based on eco-friendly reactions using NaBr, NaI, and NaCl in aqueous media to generate multiple "unnatural" halogenated natural products from crude extracts. The halogenation reactions, monitored by UHPLC-PDA-ELSD-MS, were optimized to generate mono-, di-, or trihalogenated derivatives. To isolate these compounds, the reactions were scaled up and the halogenated analogues were isolated by semipreparative HPLC-UV and fully characterized by NMR and HR-MS data. All of the original 16 halogenated derivatives were evaluated for their antiparasitic activities against the parasites Leishmania amazonensis and Trypanosoma cruzi. Compounds presenting selective antiparasitic activities against one or both parasites with IC₅₀ values comparable to the reference were identified.

Generation of Stilbene Antimicrobials against Multiresistant Strains of Staphylococcus aureus through Biotransformation by the Enzymatic Secretome of Botrytis cinerea

The biotransformation of a mixture of resveratrol and pterostilbene was performed by the protein secretome of Botrytis cinerea. Several reaction conditions were tested to overcome solubility issues and to improve enzymatic activity. Using MeOH as cosolvent, a series of unusual methoxylated compounds was generated. The reaction was scaled-up, and the resulting mixture purified by semipreparative HPLC-PDA-ELSD-MS. Using this approach, 15 analogues were isolated in one step. Upon full characterization by NMR and HRMS analyses, eight of the compounds were new. The antibacterial activities of the isolated compounds were evaluated in vitro against the opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus. The selectivity index was calculated based on cytotoxic assays performed against human liver carcinoma cells (HepG2) and the human breast epithelial cell line (MCF10A). Some compounds revealed remarkable antibacterial activity against multidrug-resistant strains of S. aureus with moderate human cell line cytotoxicity.

Innovative omics-based approaches for prioritisation and targeted isolation of natural products - new strategies for drug discovery

Covering: 2013 to 2019 The exploration of the chemical diversity of extracts from various biological sources has led to major drug discoveries. Over the past two decades, despite the introduction of advanced methodologies for natural product (NP) research (e.g., dereplication and high content screening), successful accounts of the validation of NPs as lead therapeutic candidates have been limited. In this context, one of the main challenges faced is related to working with crude natural extracts because of their complex composition and the inadequacies of classical bioguided isolation studies given the pace of high-throughput screening campaigns. In line with the development of metabolomics, genomics and chemometrics, significant advances in metabolite profiling have been achieved and have generated high-quality massive genome and metabolome data on natural extracts. The unambiguous identification of each individual NP in an extract using generic methods remains challenging. However, the establishment of structural links among NPs via molecular network analysis and the determination of common features of extract composition have provided invaluable information to the scientific community. In this context, new multi-informational-based profiling approaches integrating taxonomic and/or bioactivity data can hold promise for the discovery and development of new bioactive compounds and return NPs back to an exciting era of development. In this article, we examine recent studies that have the potential to improve the efficiency of NP prioritisation and to accelerate the targeted isolation of key NPs. Perspectives on the field's evolution are discussed.

Discovery of Lipid Peroxidation Inhibitors from Bacopa Species Prioritized through Multivariate Data Analysis and Multi-Informative Molecular Networking

A major goal in the discovery of bioactive natural products is to rapidly identify active compound(s) and dereplicate known molecules from complex biological extracts. The conventional bioassay-guided fractionation process can be time consuming and often requires multi-step procedures. Herein, we apply a metabolomic strategy merging multivariate data analysis and multi-informative molecular maps to rapidly prioritize bioactive molecules directly from crude plant extracts. The strategy was applied to 59 extracts of three Bacopa species (B. monnieri, B. caroliniana and B. floribunda), which were profiled by UHPLC-HRMS² and screened for anti-lipid peroxidation activity. Using this approach, six lipid peroxidation inhibitors 1–6 of three Bacopa spp. were discovered, three of them being new compounds: monnieraside IV (4), monnieraside V (5) and monnieraside VI (6). The results demonstrate that this combined approach could efficiently guide the discovery of new bioactive natural products. Furthermore, the approach allowed to evidence that main semi-quantitative changes in composition linked to the anti-lipid peroxidation activity were also correlated to seasonal effects notably for B. monnieri.

Identification of chemotypes in bitter melon by metabolomics: a plant with potential benefit for management of diabetes in traditional Chinese medicine

INTRODUCTION

Bitter melon (Momordica charantia, Cucurbitaceae) is a popular edible medicinal plant, which has been used as a botanical dietary supplement for the treatment of diabetes and obesity in Chinese folk medicine. Previously, our team has proved that cucurbitanes triterpenoid were involved in bitter melon's anti-diabetic effects as well as on increasing energy expenditure. The triterpenoids composition can however be influenced by changes of varieties or habitats.

OBJECTIVES

To clarify the significance of bioactive metabolites diversity among different bitter melons and to provide a guideline for selection of bitter melon varieties, an exploratory study was carried out using a UHPLC-HRMS based metabolomic study to identify chemotypes.

METHODS

Metabolites of 55 seed samples of bitter melon collected in different parts of China were profiled by UHPLC-HRMS. The profiling data were analysed with multivariate (MVA) statistical methods. Principle component analysis (PCA) and hierarchical cluster analysis (HCA) were applied for sample differentiation. Marker compounds were identified by comparing spectroscopic data with isolated compounds, and additional triterpenes were putatively identified by propagating annotations through a molecular network (MN) generated from UHPLC-HRMS & MS/MS metabolite profiling.

RESULTS

PCA and HCA provided a good discrimination between bitter melon samples from various origins in China. This study revealed for the first time the existence of two chemotypes of bitter melon. Marker compounds of those two chemotypes were identified at different MSI levels. The combined results of MN and MVA demonstrated that the two chemotypes mainly differ in their richness in cucurbitane versus oleanane triterpenoid glycosides (CTGs vs. OTGs).

CONCLUSION

Our finding revealed a clear chemotype distribution of bioactive components across bitter melon varieties. While bioactivities of individual CTGs and OTGs still need to be investigated in more depth, our results could help in future the selection of bitter melon varieties with optimised metabolites profile for an improved management of diabetes with this popular edible Chinese folk medicine.