The Human Gut Microbiome Metabolizes Diverse Bioactive Coumarins via α,β-Unsaturated Lactone Reduction

The gut microbiome can influence drug efficacy through the direct metabolism of bioactive molecules. Despite numerous high-throughput screens for drug-microbiome interactions, the gut microbial metabolism of many bioactive compounds and its impact on treatment efficacy remain uncharacterized. We chose to investigate coumarins, which are a large class of bioactive natural products and chemical scaffolds for synthetic drugs. The core of the class, 1,2-benzopyrone, is metabolized by the microbiome to yield 3,4-dihydrocoumarin and melilotic acid via α,β-unsaturated lactone reduction. To explore the scope of this pathway, we screened a structurally diverse group of 12 bioactive coumarins using semitargeted LC-MS/MS metabolomics and ex vivo cultures of human feces. The culturable gut microbiome can reduce the α,β-unsaturated lactone of isocoumarin, simple, furano, pyrano, and prenylated coumarins with an unsubstituted 3,4-alkene bond. In a monoculture screen of microbiome isolates, we determined that 11 species could metabolize multiple coumarins through this pathway. Further, we demonstrate the direct coumarin-reducing capability of N-ethylmaleimide reductase from Escherichia coli. Finally, gut microbial metabolites of methoxsalen had diminished cytotoxicity against melanoma cancer cells compared to the parent drug. In summary, the human gut microbiome utilizes a single metabolic pathway to modulate the bioactivities of many coumarins.