Miniaturized fungal cultures and metabolomics for assessing halogenated tryptophan incorporation aimed at structural diversification of bioactive scaffolds

We recently developed a high-throughput 96-well plate platform [ 1 ] integrating parallelized miniaturized cultures and SPE to transform fungal strains into extracts compatible for antimicrobial screening and metabolomic profiling. Screening with this platform identified 102 strains active against Gram-positive and Gram-negative bacteria. Our study aimed to identify strains utilizing tryptophan in their specialized metabolites biosynthesis and assess their potential to incorporate halogenated derivatives for unnatural natural products biosynthesis. Indeed, it has been interestingly demonstrated [ 2 ] that species of the genus Verticillium can incorporate fluorinated tryptophan in their metabolites by precursor-directed biosynthesis. Molecular network analysis of untargeted LC-HRMS/MS metabolite profiling data of all active strains identified tryptophan-derived alkaloids in multiple extracts. Among them, we selected one strain of Chaetomium globosum (known to be active against Staphylococcus aureus [ 3 ]) and cultured it with chlorinated/brominated tryptophan. Metabolomic analysis of this strain grown with halogenated tryptophan revealed several metabolites incorporating chlorine and bromine. Based on this proof of concept, we are now identifying their structures via large-scale production for targeted isolation and full de novo NMR elucidation. We also are evaluating whether the 96-well platform enables rapid metabolomics-based screening of other strains’ capacity to incorporate modified tryptophan (halogenated or modified differently). Acknowledgements : AA, AB, NL, AL, SS, TK, KG, EFQ and J-LW are thankful to the Swiss National Science Foundation for the funding of the project (SNF Bridge Discovery N° 40B2-0_211759) Publication History Article published online: 05 March 2026 © 2026. Thieme. All rights reserved. Georg Thieme Verlag KG Oswald-Hesse-Straße 50, 70469 Stuttgart, Germany