Exploring rare coumarins biosynthesis by Gloeophyllum trabeum: an integrated computational genomics, molecular docking and spectroscopic approach

Abstract

Abstract The sustained rise of antibiotics resistance demands the discovery of novel compounds to enhance current treatment efficiency and decrease the spread of resistant pathogens. Gloeophyllum trabeum is a common wood-decaying basidiomycete fungus, however its capability for production of specialised metabolites remains poorly understood. We integrated spectroscopic analysis, computational genomic, and molecular docking to explore isocoumarin biosynthesis of this mushroom. Using plate-based overlay bioassays we showed that G. trabeum is antagonistic against three microbes: Escherichia coli , Saccharomyces cerevisiae , and Bacillus subtilis , with most effect against B. subtilis . The culture filtrates of G. trabeum were analysed by LCMS, with four products being further characterised by 2-D NMR, leading to the characterization of four rare coumarin-based polyketides: compound 1(tentatively, hydroxylated naphthoquinone derivative), compound 2 (oospoglycol), compound 3 (oosponol), and compound 4 (Naphthazarin-6,7-dihydrodiol (FD48)). Notably, both oospoglycol and oosponol exhibited antimicrobial activity against B. subtilis . Genome mining and annotation of G. trabeum predicted several biosynthetic gene clusters (BGCs), including clusters associated with isocoumarin-derived compounds, which likely corresponds to the newly identified metabolites. The docking analysis in its turn identified oosponol as the most promising lead compound, exhibiting exceptional affinity for UspA1 of Moraxella catarrhalis , while oospoglycol showed broader antimicrobial potential through interactions with multiple targets, highlighting UspA1 as a key candidate for further future validation. Given that oosponol derivatives are commercially unavailable, due to the high costs associated with their production and purification, therefore characterising these compounds in G. trabeum considered an important scientific progress, as G. trabeum represents the only species from the Gloeophyllales order with available whole-genome sequences. Characterizing these unique compounds and their putative BGCs in G. trabeum boost the potential for high-yield, rapid cost effect production and development of novel antibiotics through synthetic biology and pharmacophore modelling.