The use of mass-spectrometry-based chemical proteomics approaches in bioactivity annotation of natural products and biocatalyst discovery : Applications to the natural product Zelkovamycin and fungi

Bioactive natural compounds are a widely underexplored source of potential drugs and inhibitors. To investigate and characterize these compounds, mass spectrometry is a valuable tool. As mass spectrometry is nowadays well-configured for high throughput analysis, it is an appropriate tool for characterization of the almost indefinite number of bioactive natural compounds.
Zelkovamycin is a bioactive natural compound of the argyrin family whose bioactivity in humans is not investigated so far. This stands in contrast to its reported antibiotic effects against bacteria. On the contrary, most other reported argyrins also show promising anti-cancer effects in humans. In this work, mass spectrometric analysis in conjunction with biochemical and biological assays were used to identify an argyrin-unique OXPHOS inhibitory bioactivity of Zelkovamycin. Moreover, this PhD work revealed that Zelkovamycin is able to significantly decrease cell viability of OXPHOS-dependent skin cancer cells. Two unusual, non-canonical amino acids, a 4-methoxy tryptophan and a 2-methyl dehydrothreonine residue, are thereby essential for Zelkovamycin’s bioactivity. The results highlight the potential scope of Zelkovamycin and suggests further approaches for optimizing its bioactivity.
Dead plant material is an almost indefinite feedstock of organic matter for energy production. However, its recalcitrant nature towards controlled and directed degradation severely hampers its large scale industrial use. Several fungi are however known as efficient dead plant material degraders. To this end, they secrete a huge arsenal of lignocellulolytic and accessory enzymes. Among them, Phanerochaete chrysosporium overtakes a prominent role as a model organism with the capacity for a complete break-down of dead plant material via secretion of ligninases, (hemi)cellulases and several accessory enzymes – the complete repertoire of lignocellulolytic enzymes. This PhD work shows that activity-based protein-profiling (ABPP) can be used to identify and characterize such degradation enzymes. To this end, two types of activity based probes (ABPs) were used: For the identification of plant-material degrading esterases, a fluorophosphonate-based ABP, while glycosidases were identified by a cyclophellitol-inspired ABP. Accordingly, this work points out the use of ABPP for enzymatic profiling of fungi.


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