Metabolomics insights into the polyketide-lactones produced by Diaporthe caliensis sp. nov., an endophyte of the medicinal plant Otoba gracilipes

Abstract

Plants of the genus Otoba have been the basis for the treatment of tropical diseases in indigenous communities of countries like Colombia. Despite the lack of knowledge about their bioactive principles, endophytic fungi derived from medicinal plants are a prolific source of innovative chemistry. We systematically investigated the secondary metabolite production of a previously undescribed species of Diaporthe , herein introduced as Diaporthe caliensis sp. nov., using different metabolomics approaches together with classical chemical screening. To get an outline of the chemical space produced by this fungus, an exploratory molecular networking (MN) analysis was undertaken. A major molecular family was found to contain the known 10-membered lactone phomol ( 1 ), together with other putative congeners as compound 3 . After isolation by preparative high-performance liquid chromatography, we confirmed phomol ( 1 ) as the main reason for the antimicrobial activity of the crude extract. The unknown absolute configuration of 1 was determined by the synthesis of α-methoxy-α-trifluoromethylphenylacetyl (MTPA)-esters and chemical degradation experiments. Moreover, caliensolides A ( 2 ) and B ( 3 ) were isolated, and their structures were elucidated as novel butenolides structurally unrelated to 1 . Overall, the initial MN analysis incorrectly clustered compounds 1 and 3 within a single molecular family, despite evident differences in chemical structures and biosynthetic origin. Contrariwise, the unsupervised substructure discovery algorithm MS2LDA provided a deeper understanding of the fragmentation patterns and correctly clustered the polyketide-lactones produced by D. caliensis sp. nov. Our findings encourage the exploration of Colombian fungal diversity, which as demonstrated here could result in the discovery of new natural products. IMPORTANCE The integration of metabolomics-based approaches into the discovery pipeline has enabled improved mining and prioritization of prolific secondary metabolite producers such as endophytic fungi. However, relying on automated untargeted analysis tools might lead to misestimation of the chemical complexity harbored in these organisms. Our study emphasizes the importance of isolation and structure elucidation of the respective metabolites in addition to deep metabolome analysis for the correct interpretation of untargeted metabolomics approaches such as molecular networking. Additionally, it encourages the further exploration of endophytic fungi from traditional medicinal plants for the discovery of natural products.

Depicting the Chemical Diversity of Bioactive Meroterpenoids Produced by the Largest Organism on Earth

“…In metabolomics analyses, a common challenge arises from structurally similar metabolites exhibiting distinct MS/MS spectra due to minor chemical modifications. For a comprehensive understanding of this phenomenon, a meticulous examination and the accessibility of pure standards are imperative [35] . On the other hand, the melleolide linoleate MF was represented by only three nodes, suggesting that the number of dimeric melleolides is much higher than the one of analogs with a substituted fatty acid chain.…”

“…For a comprehensive understanding of this phenomenon, a meticulous examination and the accessibility of pure standards are imperative. [35] On the other hand, the melleolide linoleate MF was represented by only three nodes, suggesting that the number of dimeric melleolides is much higher than the one of analogs with a substituted fatty acid chain. To show the effect of cultivation under different media on metabolite abundance, compounds 1-5, 6-9, 11-16, and 6'dechloroarnamial annotated within the FBMN were grouped by hierarchical clustering, as shown by the heat map in Figure 6C.…”

Darstellung der chemischen Diversität bioaktiver Meroterpenoide, die vom größten Organismus der Erde produziert werden

“…Bei Metabolomik‐Analysen stellt sich häufig die Herausforderung, dass strukturell ähnliche Metaboliten aufgrund geringfügiger chemischer Veränderungen unterschiedliche MS/MS‐Spektren aufweisen. Für ein umfassendes Verständnis dieses Phänomens sind eine sorgfältige Untersuchung und der Zugang zu reinen Standards unerlässlich [35] . Andererseits war die Melleolid‐Linoleat‐MF durch nur drei Knotenpunkte vertreten, was darauf hindeutet, dass die Anzahl der dimeren Melleolide viel höher ist als die der analogen Substanzen mit einer substituierten Fettsäurekette.…”

Priming of ash saplings with a low virulent Hymenoscyphus fraxineus strain as a possible disease control approach for reducing symptoms of ash dieback

“…MS spectra were acquired in positive ion mode. Raw data were pre-processed with MetaboScape 2022 (Bruker Daltonics, Bremen, Germany) in the retention time range of 1.0 to 20 min (Charria-Girón et al 2023b). The obtained features were dereplicated based on their accurate molecular weight and MS/MS spectra against the compounds as previously reported for H. fraxineus in the Natural Product Atlas (NP Atlas) database (van Santen et al 2019).…”