Optimizing production and evaluating biosynthesis in situ of a herbicidal compound, mevalocidin, from Coniolariella sp

Phytotoxic fungal secondary metabolites as herbicides

Among the alternatives to synthetic plant protection products, biocontrol appears as a promising method. This review reports on the diversity of fungal secondary metabolites phytotoxic to weeds and on the approach generally used to extract, characterize, identify and exploit them for weed management. The 183 phytotoxic fungal secondary metabolites discussed in this review fall into five main classes of molecules: 61 polyketides, 53 terpenoids, 36 nitrogenous metabolites, 18 phenols and phenolic acids, and 15 miscellaneous. They are mainly produced by the genera Drechslera, Fusarium and Alternaria. The phytotoxic effects, more often described by the symptoms they produce on plants than by their mode of action, range from inhibition of germination to inhibition of root and vegetative growth, including tissue and organ alterations. The biochemical characterization of fungal secondary metabolites requires expertise and tools to carry out fungal cultivation and metabolite extraction, phytotoxicity tests, purification and fractionation of the extracts, and chemical identification procedures. Phytotoxicity tests are mainly carried out under controlled laboratory conditions (not always on whole plants), while effectiveness against targeted weeds and environmental impacts must be assessed in greenhouses and open fields. These steps are necessary for the formulation of effective, environment-friendly fungal secondary metabolites-derived bioherbicides using new technologies such as nanomaterials. © 2023 Society of Chemical Industry.

Discovery of Anticancer Agents of Diverse Natural Origin

Research progress from mainly over the last five years is described for a multidisciplinary collaborative program project directed toward the discovery of potential anticancer agents from a broad range of taxonomically defined organisms. Selected lead compounds with potential as new antitumor agents that are representative of considerable structural diversity have continued to be obtained from each of tropical plants, terrestrial and aquatic cyanobacteria, and filamentous fungi. Recently, a new focus has been on the investigation of the constituents of U.S. lichens and their fungal mycobionts. A medicinal chemistry and pharmacokinetics component of the project has optimized structurally selected lead natural products, leading to enhanced cytotoxic potencies against selected cancer cell lines. Biological testing has shown several compounds to have in vivo activity, and relevant preliminary structure-activity relationship and mechanism of action studies have been performed. Several promising lead compounds worthy of further investigation have been identified from the most recent collaborative work performed.

Pathogenic potential and phytotoxic effects of Coniolariella gamsii Iran 2506C on Iranian knapweed (Centaurea depressa)

Application of fungal phytotoxins is one of the possible solutions to reduce the use of chemical products in agricultural fields. Phytotoxic compounds isolated from phytopathogenic fungi provide a promising source of environmentally friendly herbicides. This paper focuses on the phytotoxic fungus Coniolariella gamsii Iran 2506C as a fungal pathogen against Iranian knapweed (Centaurea depressa) in the western Iran and investigate its phytotoxic constituents. The fungal pathogen was identified on the basis of morphological characteristics and confirmed by sequencing of the internal transcribed spacer (ITS) region and partial LSU rDNA gene. Pathogenicity tests were conducted on the weed seedlings and C. gamsii Iran 2506C isolate with high disease severity was selected for phytotoxin studies. Phytotoxic activity of the isolate was checked by screening the production of phytotoxins, which interestingly inhibited seed germination and seedling growth of Iranian knapweed as compared to wheat in the bioassays. The active metabolites were extracted from cell-free culture filtrate (CFCF) by ethyl acetate and separated by thin layer chromatography (TLC). The results indicated that two out of four spots had phytotoxicity with R_f values of 0.43 and 0.82 on the weed, whereas wheat was not sensitive in the bioassays. Using Gas Chromatography-Mass spectrometry (GC-MS), 3-Carene and Oleic acid were identified as the main constituents and quantified by a gas chromatographic method with 12.7 ± 0.03 and 2.9 ± 0.01 μg ml^-1 respectively. This is the first finding presented on the phytotoxic effects of the active metabolites of C. gamsii Iran 2506C and highlights its herbicidal potential which can be used as a biocontrol agent of C. depressa.

Evaluation of the herbicidal potential of some fungal species against Bidens pilosa, the coffee farming weeds

Weeds are the most productive limiting factor, especially in organic farming systems where the uses of synthetic herbicides are not allowed due to their negative impacts. Hence, synthetic herbicides need to be replaced with biological herbicides for weed management. Thus, the present study was designed to evaluate the herbicidal activity of conidia suspensions from Aspergillus niger, Trichoderma asperlium, Trichoderma atroviride, Trichoderma hamatum, Trichoderma harzanium, Trichoderma longibrachatum and Trichoderma viride against Bidens pilosa weed via a series of laboratory and lath-house conditions that laid out in a CRD and RCBD, respectively, with three replications for each bioassay. The results revealed that all fungi, except T. longibrachatum, had significantly reduced seed germination as well as early growth of the target weed compared to the untreated control. The inhibitory effects were measured to be varied among the types of conidia suspensions of fungal species and their level of concentration. The highest rate of inhibition was observed for conidia suspension from A. niger which suppressed with the maximum seed germination inhibitory level (65%) over control. Likewise, the plumule and radicle growth length of the target weed also significantly inhibited by the tested fungi (ranging from 10 to 85% and 34 to 97%) compared to the control, respectively. Based on their efficacy in the laboratory bioassay, the herbicidal potential of selected fungi was further evaluated in pot experiments. In contrarily to laboratory observations, the effect of different fungal conidia suspensions on various growth parameters of the targeted weed was insignificant in the lath-house experiments. In conclusion, the application of A. niger displayed some potential green light to be investigated as a biocontrol agent with promising retarding in the germination and early growth of B. pilosa. Hence, we recommend further investigation of those fungi under field conditions on different coffee weed species.

The liquid micro junction-surface sampling probe (LMJ-SSP); a versatile ambient mass spectrometry interface

Ambient ionization methods have become important tools in mass spectrometry. The LMJ-SSP can significantly simplify/reduce lengthy sample preparation requirements associated with mass spectrometry analysis. Samples may be introduced through direct contact, insertion and droplet injection, enabling applications from drug discovery and surface analysis to tissue profiling and metabolic mapping. This review examines the underlying principles associated with the LMJ-SSP interface and highlights modifications of the original design that have extended its capability. We summarize different application areas that have exploited the method and describe potential future directions for the adaptable ambient ionization source.

Fungal Guttation, a Source of Bioactive Compounds, and Its Ecological Role-A Review

Guttation is a common phenomenon in the fungal kingdom. Its occurrence and intensity depend largely on culture conditions, such as growth medium composition or incubation temperature. As filamentous fungi are a rich source of compounds, possessing various biological activities, guttation exudates could also contain bioactive substances. Among such molecules, researchers have already found numerous mycotoxins, antimicrobials, insecticides, bioherbicides, antiviral, and anticancer agents in exudate droplets. They belong to either secondary metabolites (SMs) or proteins and are secreted with different intensities. The background of guttation, in terms of its biological role, in vivo, and promoting factors, has been explored only partially. In this review, we describe the metabolites present in fungal exudates, their diversity, and bioactivities. Pointing to the significance of fungal ecology and natural products discovery, selected aspects of guttation in the fungi are discussed.

Polyphasic Approach Utilized for the Identification of Two New Toxigenic Members of Penicillium Section Exilicaulis, P. krskae and P. silybi spp. nov

Two new species, Penicillium krskae (isolated from the air as a lab contaminant in Tulln (Austria, EU)) and Penicillium silybi (isolated as an endophyte from asymptomatic milk thistle (Silybum marianum) stems from Josephine County (Oregon, USA)) are described. The new taxa are well supported by phenotypic (especially conidial ornamentation under SEM, production of red exudate and red pigments), physiological (growth at 37 °C, response to cycloheximide and CREA), chemotaxonomic (production of specific extrolites), and multilocus phylogenetic analysis using RNA-polymerase II second largest subunit (RPB2), partial tubulin (benA), and calmodulin (CaM). Both new taxa are resolved within the section Exilicaulis in series Restricta and show phylogenetic affiliation to P. restrictum sensu stricto. They produce a large spectrum of toxic anthraquinoid pigments, namely, monomeric anthraquinones related to emodic and chloremodic acids and other interesting bioactive extrolites (i.e., endocrocin, paxilline, pestalotin, and 7-hydroxypestalotin). Of note, two bianthraquinones (i.e., skyrin and oxyskyrin) were detected in a culture extract of P. silybi. Two new chloroemodic acid derivatives (2-chloro-isorhodoptilometrin and 2-chloro-desmethyldermoquinone) isolated from the exudate of P. krskae ex-type culture were analyzed by nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LC-MS).

Media and strain studies for the scaled production of cis-enone resorcylic acid lactones as feedstocks for semisynthesis

Resorcylic acid lactones (RALs) with a cis-enone moiety, represented by hypothemycin (1) and (5Z)-7-oxozeaenol (2), are fungal secondary metabolites with irreversible inhibitory activity against protein kinases, with particularly selective activity for inhibition of TAK1 (transforming growth factor beta-activated kinase 1). Gram-scale quantities of these compounds were needed as feedstock for semi-synthesizing RAL-analogues in a step-economical fashion. To do so, this study had three primary goals: identifying fungi that biosynthesized 1 and 2, enhancing their production by optimizing the fermentation conditions on the lab scale, and developing straight forward purification processes. After evaluating 536 fungal extracts via an in-house dereplication protocol, three strains were identified as producing cis-enone RALs (i.e., MSX78495, MSX63935, MSX45109). Screening these fungal strains on three grain-based media revealed enhanced production of 1 by strain MSX78495 on oatmeal medium, while rice medium increased the biosynthesis of 2 by strain MSX63935. Furthermore, the purification processes were improved, moving away from HPLC purification to utilizing two to four cycles of resuspension and centrifugation in small volumes of organic solvents, generating gram-scale quantities of these metabolites readily. In addition, studying the chemistry profiles of strains MSX78495 and MSX63935 resulted in the isolation of ten other RALs (3-12), two radicinin analogues (13-14), and six benzopyranones (15-20), with 19 and 20 being newly described chlorinated benzopyranones.

Bioherbicidal potential of different species of Phoma: opportunities and challenges

Modern agriculture has been facing new challenges and fostering innovations to establish sustainable plant production. An integral part of these strategies is implementing new eco-friendly technologies in plant protection for better human health and a safer environment by minimizing the use of hazardous chemicals and also encouraging innovations such as the use of bio-based strategies for weed control. This specific strategy addresses the need to reduce the use and risk of pesticides, replacing conventional chemical herbicides with new bio-based solutions. In response to these issues, biocontrol strategies are gaining increased attention from stakeholders such as farmers, seed companies, agronomists, breeders, and consumers. Among these, bioherbicides have huge potential for the management of harmful weeds without affecting the natural quality of the environment and human health. In this context, this review is devoted to present an overview of the mycoherbicidal potential of Phoma sensu lato group of fungi, examining the advances in this field, including technological and scientific challenges and outcomes achieved in recent years. The mycoherbicides are eco-friendly and economically viable. KEY POINTS: • Some Phoma species have demonstrated herbicide activity. • These species secrete secondary metabolites responsible for the control of weeds. • They can be used as non-chemical, cost-effective, and eco-friendly bioherbicides.

Cytotoxic Naphthoquinone Analogues, Including Heterodimers, and Their Structure Elucidation Using LR-HSQMBC NMR Experiments

Approximately 1700 naphthoquinones have been reported from a range of natural product source materials, but only 283 have been isolated from fungi, fewer than 75 of those were dimers, and only 2 were heterodimers with a head-to-tail linkage. During a search for anticancer leads from fungi, a series of new naphthoquinones (1-4), including two heterodimers (3 and 4), were isolated from Pyrenochaetopsis sp. (strain MSX63693). In addition, the previously reported 5-hydroxy-6-(1-hydroxyethyl)-2,7-dimethoxy-1,4-naphthalenedione (5), misakimycin (6), 5-hydroxy-6-[1-(acetyloxy)ethyl]-2,7-dimethoxy-1,4-naphthalenedione (7), 6-ethyl-2,7-dimethoxyjuglone (8), and kirschsteinin (9) were isolated. While the structure elucidation of 1-9 was achieved using procedures common for natural products chemistry studies (high-resolution electrospray ionization mass spectrometry (HRESIMS), 1D and 2D NMR), the elucidation of the heterodimers was facilitated substantially by data from the long-range heteronuclear single quantum multiple bond correlation (LR-HSQMBC) experiment. The absolute configuration of 1 was established by analysis of the measured vs calculated ECD data. The racemic mixture of 4 was established via X-ray crystallography of an analogue that incorporated a heavy atom. All compounds were evaluated for cytotoxicity against the human cancer cells lines MDA-MB-435 (melanoma), MDA-MB-231 (breast), and OVCAR3 (ovarian), where the IC50 values ranged between 1 and 20 μM.

Engineering Fluorine into Verticillins (Epipolythiodioxopiperazine Alkaloids) via Precursor-Directed Biosynthesis

Precursor-directed biosynthesis was used to generate a series of fluorinated verticillins. The biosynthesis of these epipolythiodioxopiperazine alkaloids was monitored in situ via the droplet liquid microjunction surface sampling probe (droplet probe), and a suite of NMR and mass spectrometry data were used for their characterization. All analogues demonstrated nanomolar IC50 values vs a panel of cancer cell lines. This approach yielded new compounds that would be difficult to generate via synthesis.

Natural products: a strategic lead generation approach in crop protection discovery

With the anticipated population growth in the coming decades, the changing regulatory environment, and the continued emergence of resistance to commercial pesticides, there is a constant need to discover new lead chemistries with novel modes of action. We have established a portfolio of approaches to accelerate lead generation. One of these approaches capitalizes on the rich bioactivity of natural products (NPs), highlighted by the numerous examples of NP-based crop protection compounds. Within Corteva Agriscience and the affiliated preceding companies, NPs have been a fruitful approach, for nearly three decades, to identifying and bringing to the market crop protection products inspired by or originating from NPs, . Included in these NP-based crop protection products are the spinosyns family of insecticides, and those from more recent areas of NP-based fungicidal chemistry, as highlighted in this perspective. © 2019 Society of Chemical Industry.

Droplet probe: coupling chromatography to the in situ evaluation of the chemistry of nature

Covering: up to 2019The chemistry of nature can be beautiful, inspiring, beneficial and poisonous, depending on perspective. Since the isolation of the first secondary metabolites roughly two centuries ago, much of the chemical research on natural products has been both reductionist and static. Typically, compounds were isolated and characterized from the extract of an entire organism from a single time point. While there could be subtexts to that approach, the general premise has been to determine the chemistry with very little in the way of tools to differentiate spatial and/or temporal changes in secondary metabolite profiles. However, the past decade has seen exponential advances in our ability to observe, measure, and visualize the chemistry of nature in situ. Many of those techniques have been reviewed in this journal, and most are tapping into the power of mass spectrometry to analyze a plethora of sample types. In nearly all of the other techniques used to study chemistry in situ, the element of chromatography has been eliminated, instead using various ionization sources to coax ions of the secondary metabolites directly into the mass spectrometer as a mixture. Much of that science has been driven by the great advances in ambient ionization techniques used with a suite of mass spectrometry platforms, including the alphabet soup from DESI to LAESI to MALDI. This review discusses the one in situ analysis technique that incorporates chromatography, being the droplet-liquid microjunction-surface sampling probe, which is more easily termed "droplet probe". In addition to comparing and contrasting the droplet probe with other techniques, we provide perspective on why scientists, particularly those steeped in natural products chemistry training, may want to include chromatography in in situ analyses. Moreover, we provide justification for droplet sampling, especially for samples with delicate and/or non-uniform topographies. Furthermore, while the droplet probe has been used the most in the analysis of fungal cultures, we digest a variety of other applications, ranging from cyanobacteria, to plant parts, and even delicate documents, such as herbarium specimens.

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.

Non-Destructive Chemical Analysis of a Garcinia mangostana L. (Mangosteen) Herbarium Voucher Specimen

Herbarium voucher specimens are used primarily for taxonomic confirmation. However, they also afford a record of the metabolic profile of a plant, potentially at the time it was collected, or at the very least, at the time of analysis. Even with the enhanced sensitivity of modern analytical techniques, analysis of the metabolites of a herbarium voucher requires removal and consumption of at least part of an entire specimen. We present herein a non-destructive method to analyze the metabolites of herbarium voucher specimens with the droplet-liquid microjunction-surface sampling probe (droplet probe) coupled to ultra-performance liquid chromatography and highresolution mass spectrometry. As proof of concept, a herbarium voucher specimen of Garcinia mangostana (mangosteen) was utilized due to the well-characterized xanthones biosynthesized by this plant, which are of interest as potential anticancer agents. Also, the juice of the fruits of this plant is used widely in the United States and in other countries as a botanical dietary supplement. Metabolite profiles of the sampled surfaces were compared to a subset of xanthone standards. Using this innovative method on the herbarium voucher specimen, we were able to readily identify cytotoxic prenylated xanthones while maintaining the integrity of the entire specimen.

Calothrixamides A and B from the Cultured Cyanobacterium Calothrix sp. UIC 10520

Cyanobacteria are a source of chemically diverse metabolites with potential medicinal and biotechnological applications. Rapid identification of compounds is central to expedite the natural product discovery process. Mass spectrometry has been shown to be an important tool for dereplication of complex natural product samples. In addition, chromatographic separation and complementary spectroscopic analysis (e.g., UV) can enhance the confidence of the dereplication process. Here, we applied a droplet-liquid microjunction-surface sampling probe (droplet probe) coupled with UPLC-PDA-HRMS-MS/MS to identify two new natural products in situ from the freshwater strain Calothrix sp. UIC 10520. This allowed us to prioritize this strain for chemical investigation based on the presence of new metabolites very early in our discovery process, saving both time and resources. Subsequently, calothrixamides A (1) and B (2) were isolated from large-scale cultures, and the structures were elucidated by 1D and 2D NMR spectroscopy and mass spectrometry. The absolute configurations were determined by a combination of chemical degradation reactions, derivatization methods (Mosher's, Marfey's, and phenylglycine methyl ester), and J-based configurational analysis. Calothrixamides showed no cytotoxic activity against the MDA-MB-435, MDA-MB-231, and OVCAR3 cancer cell lines. They represent the first functionalized long-chain fatty acid amides reported from the Calothrix genus and from a freshwater cyanobacterium.

Media studies to enhance the production of verticillins facilitated by in situ chemical analysis

Abstract

Verticillins are a group of epipolythiodioxopiperazine alkaloids that have displayed potent cytotoxicity. To evaluate their potential further, a larger supply of these compounds was needed for both in vivo studies and analogue development via semisynthesis. To optimize the biosynthesis of these secondary metabolites, their production was analyzed in two different fungal strains (MSX59553 and MSX79542) under a suite of fermentation conditions. These studies were facilitated by the use of the droplet-liquid microjunction-surface sampling probe (droplet probe), which enables chemical analysis in situ directly from the surface of the cultures. These experiments showed that the production of verticillins was greatly affected by growth conditions; a significantly higher quantity of these alkaloids was noted when the fungal strains were grown on an oatmeal-based medium. Using these technologies to select the best among the tested growth conditions, the production of the verticillin analogues was increased while concomitantly decreasing the time required for fermentations from 5 weeks to about 11 days. Importantly, where we could previously supply 5–10 mg every 6 weeks, we are now able to supply 50–150 mg quantities of key analogues per month via laboratory scale fermentation.

Graphical abstract

Electronic supplementary material

The online version of this article (10.1007/s10295-018-2083-8) contains supplementary material, which is available to authorized users.

In situ mass spectrometry monitoring of fungal cultures led to the identification of four peptaibols with a rare threonine residue

Peptaibols are an intriguing class of fungal metabolites due both to their wide range of reported bioactivities and to the structural variability that can be generated by the exchange of variable amino acid building blocks. In an effort to streamline the discovery of structurally diverse peptaibols, a mass spectrometry surface sampling technique was applied to screen the chemistry of fungal cultures in situ. Four previously undescribed peptaibols, all containing a rare threonine residue, were identified from a fungal culture (MSX53554), which was identified as Nectriopsis Maire (Bionectriaceae, Hypocreales, Ascomycota). These compounds not only increased the known threonine-containing peptaibols by nearly 20%, but also, the threonine residue was situated in a unique place compared to the other reported threonine-containing peptaibols. After the initial in situ detection and characterization, a large-scale solid fermentation culture was grown. The four peptaibols were isolated and characterized by mass spectrometry. In addition, one of the peptaibols was fully characterized by NMR and amino acid analysis using Marfey's reagent and exhibited moderate in vitro anticancer activity.