Enzymatic carbon-fluorine bond cleavage by human gut microbes

Abstract

SummaryThe human gut microbiota is known for its pharmaceutical biotransformation capabilities. Many pharmaceuticals are fluorinated; however, it was previously unknown whether gut microbial enzymes cleave carbon-fluorine bonds. Here we show that dehalogenases encoded by human gut microbes, includingClostridia, Bacilli,andCoriobacteriia, can hydrolyze fluorinated amino and organic acids. Through the development of a rapid, miniaturized fluoride detection assay, we characterized five new microbial gut defluorinases. Using alanine scanning and chimeric protein design, we identified a disordered 41-amino acid carboxyl-terminal region which is necessary and sufficient to enable weak defluorination when fused to a non-defluorinating dehalogenase. Based on features of the carboxyl-terminus alone, we were able to predict the defluorination activity of microbial dehalogenases with >83% classification accuracy (compared to 95% based on the entire protein). By uncovering the hidden potential of human gut microbes to catalyze defluorination reactions, our findings lay the foundation for therapeutic interventions relevant to human and gut microbiome health.