New Cytochalasins from the Marine-Derived Fungus Xylaria sp. SCSIO 156

Highly diverse endophytic fungi from Serra do Amolar-Pantanal (Brazil) producing bioactive secondary metabolites against phytopathogens

Introduction

The exploration of new bioactive compounds for agricultural applications is critical for sustainable development. Endophytic fungi, particularly those from underexplored biomes in Brazil, represent a promising source of natural compounds. This study focused on isolation and bioprospecting endophytic fungi from the medicinal plant Vochysia divergens (Pohl), grown in Serra do Amolar (Brazilian Pantanal Biome), with an additional emphasis on conserving microbial biodiversity.

Methods and results

Leaves and petioles were collected from 18 V. divergens specimens, from which 293 endophytes were isolated and grouped by morphological characteristics into 91 phenotypes. One representative of each phenotype was selected for secondary metabolite extraction and taxonomic identification. Fungi belonging to 27 families and 32 different genera were identified, with Diaporthe, Phyllosticta, and Pseudofusicoccum as the most predominant. We also introduce and describe a new endophytic species, Diaporthe amolarensis. Multiple extracts inhibited mycelial growth of the phytopathogenic fungus Colletotrichum abscissum, with a superior effect compared to the fungicide control. These extracts were produced by Diaporthe amolarensis, Xylaria arbuscula, and Nemania primolutea. Additionally, the extract from one X. arbuscula isolate displayed moderate activity against the phytopathogen Phyllosticta citricarpa. HPLC-UV and HPLC-MS analyses of these most inhibitory extracts revealed natural products with beneficial potential that need characterization and to have their modes of action elucidated.

Discussion

Finally, a very important contribution of this study was the ex situ conservation of the biodiversity of the Serra do Amolar, allowing future studies and biotechnological applications involving endophytes from this region.

Rosellichalasins A-H, cytotoxic cytochalasans from the endophytic fungus Rosellinia sp. Glinf021

Eight new cytochalasans rosellichalasins A-H (1-8), as well as two new shunt metabolites rosellinins A (9) and B (10) before intramolecular Diels-Alder cycloaddition reaction in cytochalasan biosynthesis, along with nine known cytochalsans (11-19) were isolated from the endophytic fungus Rosellinia sp. Glinf021, which was derived from the medicinal plant Glycyrrhiza inflata. Their structures were characterized by extensive analysis of 1D and 2D NMR as well as HRESIMS spectra and quantum chemical ECD calculations. The cytotoxic activities of these compounds were evaluated against four human cancer cell lines including HCT116, MDA-MB-231, BGC823, and PANC-1 with IC50 values ranging from 0.5 to 58.2 μM.

Cytotoxic Compounds from Marine Fungi: Sources, Structures, and Bioactivity

Marine fungi, such as species from the Penicillium and Aspergillus genera, are prolific producers of a diversity of natural products with cytotoxic properties. These fungi have been successfully isolated and identified from various marine sources, including sponges, coral, algae, mangroves, sediment, and seawater. The cytotoxic compounds derived from marine fungi can be categorized into five distinct classes: polyketides, peptides, terpenoids and sterols, hybrids, and other miscellaneous compounds. Notably, the pre-eminent group among these compounds comprises polyketides, accounting for 307 out of 642 identified compounds. Particularly, within this collection, 23 out of the 642 compounds exhibit remarkable cytotoxic potency, with IC50 values measured at the nanomolar (nM) or nanogram per milliliter (ng/mL) levels. This review elucidates the originating fungal strains, the sources of isolation, chemical structures, and the noteworthy antitumor activity of the 642 novel natural products isolated from marine fungi. The scope of this review encompasses the period from 1991 to 2023.

Progress in the Chemistry of Cytochalasans

Cytochalasans are a group of fungal-derived natural products characterized by a perhydro-isoindolone core fused with a macrocyclic ring, and they exhibit a high structural diversity and a broad spectrum of bioactivities. Cytochalasans have attracted significant attention from the chemical and pharmacological communities and have been reviewed previously from various perspectives in recent years. However, continued interest in the cytochalasans and the number of laboratory investigations on these compounds are both growing rapidly. This contribution provides a general overview of the isolation, structural determination, biological activities, biosynthesis, and total synthesis of cytochalasans. In total, 477 cytochalasans are covered, including "merocytochalasans" that arise by the dimerization or polymerization of one or more cytochalasan molecules with one or more other natural product units. This contribution provides a comprehensive treatment of the cytochalasans, and it is hoped that it may stimulate further work on these interesting natural products.

Six 19,20-epoxycytochalasans from endophytic Diaporthe sp. RJ-47

Two new cytochalasins, deacetyl-19-epi-cytochalasin P1 (1), deacetyl-19,20-epoxycytochalasin D (2) were isolated from the endophytic fungus Diaporthe sp. RJ-47, along with four known compounds deacetyl-5,6-dihydro-7-oxo-19,20-epoxycytochalasin C (3), 19,20-epoxycytochalasin Q (4), 19,20-epoxycytochalasin C (5) and deacetyl-19,20-epoxy cytochalasin C (6). Their structures were unambiguously elucidated on the basis of the comprehensive analysis of extensive spectroscopic data. The antimicrobial effects of these compounds were evaluated.

Molecules derived from the extremes of life: a decade later

Covering: Early 2008 until the end of 2019Microorganisms which survive (extreme-tolerant) or even prefer (extremophilic) living at the limits of pH, temperature, salinity and pressure found on earth have proven to be a rich source of novel structures. In this update we summarise the wide variety of new molecules which have been isolated from extremophilic and extreme-tolerant microorganisms since our original 2009 review, highlighting the range of bioactivities these molecules have been reported to possess.

New curtachalasin from the Xylaria sp. DO 1801

One new cytochalasin, named curtachalasin Q (1), together with 8 known cytochalasins were isolated from the ethyl acetate extract of the Xylaria sp. DO1801. The structure of the new compound was elucidated on the basis of IR, UV, HR-ESI-MS, NMR spectra and X-ray diffraction. Compound 1 and 2 were not cytotoxic (IC₅₀>50uM) against four tumour cell lines (SW-1990, ASPC-1, HepG2 and Hep3B).

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

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

Mapping the Fungal Battlefield: Using in situ Chemistry and Deletion Mutants to Monitor Interspecific Chemical Interactions Between Fungi

Fungi grow in competitive environments, and to cope, they have evolved strategies, such as the ability to produce a wide range of secondary metabolites. This begs two related questions. First, how do secondary metabolites influence fungal ecology and interspecific interactions? Second, can these interspecific interactions provide a way to “see” how fungi respond, chemically, within a competitive environment? To evaluate these, and to gain insight into the secondary metabolic arsenal fungi possess, we co-cultured Aspergillus fischeri, a genetically tractable fungus that produces a suite of mycotoxins, with Xylaria cubensis, a fungus that produces the fungistatic compound and FDA-approved drug, griseofulvin. To monitor and characterize fungal chemistry in situ, we used the droplet-liquid microjunction-surface sampling probe (droplet probe). The droplet probe makes a microextraction at defined locations on the surface of the co-culture, followed by analysis of the secondary metabolite profile via liquid chromatography-mass spectrometry. Using this, we mapped and compared the spatial profiles of secondary metabolites from both fungi in monoculture versus co-culture. X. cubensis predominantly biosynthesized griseofulvin and dechlorogriseofulvin in monoculture. In contrast, under co-culture conditions a deadlock was formed between the two fungi, and X. cubensis biosynthesized the same two secondary metabolites, along with dechloro-5′-hydroxygriseofulvin and 5′-hydroxygriseofulvin, all of which have fungistatic properties, as well as mycotoxins like cytochalasin D and cytochalasin C. In contrast, in co-culture, A. fischeri increased the production of the mycotoxins fumitremorgin B and verruculogen, but otherwise remained unchanged relative to its monoculture. To evaluate that secondary metabolites play an important role in defense and territory establishment, we co-cultured A. fischeri lacking the master regulator of secondary metabolism laeA with X. cubensis. We found that the reduced secondary metabolite biosynthesis of the ΔlaeA strain of A. fischeri eliminated the organism’s ability to compete in co-culture and led to its displacement by X. cubensis. These results demonstrate the potential of in situ chemical analysis and deletion mutant approaches for shedding light on the ecological roles of secondary metabolites and how they influence fungal ecological strategies; co-culturing may also stimulate the biosynthesis of secondary metabolites that are not produced in monoculture in the laboratory.

Diagnostic fragmentation filtering for the discovery of new chaetoglobosins and cytochalasins

RATIONALE

Microbial natural products are often biosynthesized as classes of structurally related compounds that have similar tandem mass spectrometry (MS/MS) fragmentation patterns. Mining MS/MS datasets for precursor ions that share diagnostic or common features enables entire chemical classes to be identified, including novel derivatives that have previously been unreported. Analytical data analysis tools that can facilitate a class-targeted approach to rapidly dereplicate known compounds and identify structural variants within complex matrices would be useful for the discovery of new natural products.

METHODS

A diagnostic fragmentation filtering (DFF) module was developed for MZmine to enable the efficient screening of MS/MS datasets for class-specific product ions(s) and/or neutral loss(es). This approach was applied to series of the structurally related chaetoglobosin and cytochalasin classes of compounds. These were identified from the culture filtrates of three fungal genera: Chaetomium globosum, a putative new species of Penicillium (called here P. cf. discolor: closely related to P. discolor), and Xylaria sp. Extracts were subjected to LC/MS/MS analysis under positive electrospray ionization and operating in a data-dependent acquisition mode, performed using a Thermo Q-Exactive mass spectrometer. All MS/MS datasets were processed using the DFF module and screened for diagnostic product ions at m/z 130.0648 and 185.0704 for chaetoglobosins, and m/z 120.0808 and 146.0598 for cytochalasins.

RESULTS

Extracts of C. globosum and P. cf. discolor strains revealed different mixtures of chaetoglobosins, whereas the Xylaria sp. produced only cytochalasins; none of the strains studied produced both classes of compounds. The dominant chaetoglobosins produced by both C. globosum and P. cf. discolor were chaetoglobosins A, C, and F. Tetrahydrochaetoglobosin A was identified from P. cf. discolor extracts and is reported here for the first time as a natural product. The major cytochalasins produced by the Xylaria sp. were cytochalasin D and epoxy cytochalasin D. A larger unknown "cytochalasin-like" molecule with the molecular formula C₃₈ H₄₇ NO₁₀ was detected from Xylaria sp. culture filtrate extracts and is a current target for isolation and structural characterization.

CONCLUSIONS

DFF is an effective LC/MS data analysis approach for rapidly identifying entire classes of compounds from complex mixtures. DFF has proved useful in the identification of new natural products and allowing for their partial characterization without the need for isolation.

Chemical constituents and cytotoxic activity from the wood-decaying fungus Xylaria sp. SWUF08-37

A new cyclic pentapeptide, pentaminolarin (1), and a new cytochalasin, xylochalasin (2), along with thirteen known compounds (3-15) were isolated from the wood-decaying fungus Xylaria sp. SWUF08-37. The absolute configurations of 1 were determined by a combination of Marfey's method and TDDFT ECD calculation and the absolute configurations of 2 were established by TDDFT ECD calculation. Compound 12 showed moderate cytotoxicity against HeLa (IC₅₀ = 19.60 µg/mL), HT29 (IC₅₀ = 17.31 µg/mL), HCT116 (IC₅₀ = 14.28 µg/mL), MCF-7 (IC₅₀ = 15.38 µg/mL), and Vero (IC₅₀ = 24.97 µg/mL) cell lines by MTT assay. Compounds 1 and 2 showed slight cytotoxicity against all tested cancer cell lines.

The potential of compounds isolated from Xylaria spp. as antifungal agents against anthracnose

Anthracnose is a crop disease usually caused by fungi in the genus Colletotrichum or Gloeosporium. These are considered one of the main pathogens, causing significant economic losses, such as in peppers and guarana. The current forms of control include the use of resistant cultivars, sanitary pruning and fungicides. However, even with the use of some methods of controlling these cultures, the crops are not free of anthracnose. Additionally, excessive application of fungicides increases the resistance of pathogens to agrochemicals and cause harm to human health and the environment. In order to find natural antifungal agents against guarana anthracnose, endophytic fungi were isolated from Amazon guarana. The compounds piliformic acid and cytochalasin D were isolated by chromatographic techniques from two Xylaria spp., guided by assays with Colletotrichum gloeosporioides. The isolated compounds were identified by spectrometric techniques, as NMR and mass spectrometry. This is the first report that piliformic acid and cytochalasin D have antifungal activity against C. gloeosporioides with MIC 2.92 and 2.46 μmol mL⁻¹ respectively. Captan and difenoconazole were included as positive controls (MIC 16.63 and 0.02 μmol mL⁻¹, respectively). Thus, Xylaria species presented a biotechnological potential and production of different active compounds which might be promising against anthracnose disease.

Cytochalasin P1, a new cytochalasin from the marine-derived fungus Xylaria sp. SOF11

A new cytochalasin, named cytochalasin P1 (1), together with four known analogs (2-5) was isolated from marine-derived fungus Xylaria sp. SOF11 from the South China Sea. The structure of the new compound was elucidated on the basis of MS and NMR (1H, 13C, HSQC, HMBC, and NOESY) data analyses. Compounds 1-5 were tested for their cytotoxicities against four tumor cell lines (SF-268, MCF-7, NCI-H460, and HepG-2). Compounds 1-5 showed significant cytotoxicity against two tumor cell lines MCF-7 and SF-268, with the IC50 values varying between 0.33 and 4.17 μM.

Amino Acid Conjugated Anthraquinones from the Marine-Derived Fungus Penicillium sp. SCSIO sof101

Emodacidamides A-H (1-8), natural products featuring anthraquinone-amino acid conjugates, have been isolated from a marine-derived fungus, Penicillium sp. SCSIO sof101, together with known anthraquinones 9 and 10. The planar structures of 1-8 were elucidated using a combination of NMR spectroscopy and mass spectrometry. The absolute configurations of the amino acid residues were confirmed using Marfey's method and chiral-phase HPLC analyses. Additionally, isolates were evaluated for possible immunomodulatory and cytotoxic activities. Emodacidamides A (1), C (3), D (4), and E (5) inhibited interleukin-2 secretion from Jurkat cells with IC₅₀ values of 4.1, 5.1, 12, and 5.4 μM, respectively.

Cold-water marine natural products, 2006 to 2016

This is an update report on marine natural products isolated from cold-water organisms in the last decade, following the previous review that covered the literature up to 2005. Emphasis is on structural assignments and biological activity.

Enantioselective synthesis of chiral α,β-unsaturated γ-substituted butyrolactams by organocatalyzed direct asymmetric vinylogous Michael addition of α,β-unsaturated γ-butyrolactam to 2-enoylpyridines

Approach providing a series of optically active α,β-unsaturated γ-substituted butyrolactams in high yields with excellent diastereo- and enantioselectivities.

Cytochalasins from cultures of endophytic fungus Phoma multirostrata EA-12

Two new cytochalsians, multirostratin A (1) and 20-oxo-deoxaphomin (2), together with five known analogues (3-7), were obtained from the endophytic fungus Phoma multirostrata EA-12. The structures of 1 and 2 were elucidated by MS and 1D- and 2D-NMR spectroscopic data analyses, as well as by comparison of data with those of analogues reported in the literature. Compounds 1 and 2 showed moderate cytotoxicity against five tumor cell lines (HL-60, A-549, SMMC-7721, MCF-7 and SW-480).

Natural products chemistry research: progress in China in 2011

This article reviews the progress made by Chinese scientists in the field of natural products chemistry in 2011. Selected compounds with unique structural features and/or promising bioactivities are described herein on the basis of structural types.

Marine natural products

This review covers the literature published in 2011 for marine natural products, with 870 citations (558 for the period January to December 2011) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1152 for 2011), together with the relevant biological activities, source organisms and country of origin. Biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.

Halogenated anthraquinones from the marine-derived fungus Aspergillus sp. SCSIO F063

Metabolomic investigations focusing on the marine-derived fungus Aspergillus sp. SCSIO F063 have unveiled seven new chlorinated anthraquinones (1-7) related to averantin, together with five known analogues (11-15) when the fungus was fermented using sea salt-containing potato dextrose broth. Through the addition of sodium bromide to the broth, two new brominated anthraquinones (8, 9) and one new nonhalogenated anthraquinone (10) were obtained from the fungal mycelia. Their structures were elucidated by extensive spectroscopic analyses including MS and 1D and 2D NMR data. One metabolite, 6-O-methyl-7-chloroaveratin (2), displayed inhibition activity against three human tumor cell lines, SF-268, MCF-7, and NCI-H460, with IC(50) values of 7.11, 6.64, and 7.42 μM, respectively.

Cyclic heptapeptides, cordyheptapeptides C-E, from the marine-derived fungus Acremonium persicinum SCSIO 115 and their cytotoxic activities

Three new cycloheptapeptides, cordyheptapeptides C-E (1-3), were isolated from the fermentation extract of the marine-derived fungus Acremonium persicinum SCSIO 115. Their planar structures were elucidated on the basis of extensive MS, as well as 1D and 2D (COSY, HMQC, and HMBC) NMR spectroscopic data analyses. The absolute configurations of the amino acid residues were determined by single-crystal X-ray diffraction, Marfey's method, and chiral-phase HPLC analysis. Compounds 1 and 3 displayed cytotoxicity against SF-268, MCF-7, and NCI-H460 tumor cell lines with IC(50) values ranging from 2.5 to 12.1 μM.

Four eremophilane sesquiterpenes from the mangrove endophytic fungus Xylaria sp. BL321

Three new eremophilane sesquiterpenes (1–3) were isolated from the mangrove endophytic fungus Xylaria sp. BL321 together with 07H239-A (4), a known analogue of the new compounds. The structures of these compounds were elucidated by analysis of their MS, 1D and 2D NMR spectroscopic data. Compound 4 showed activation activity on α-glucosidase at 0.15 μM (146%), and then, 4 gradually produced inhibitory activity on α-glucosidase with increasing concentration, and the IC₅₀ value is 6.54 μM.