We Work Hard but Our Bacteria Work Harder: An Investigation into Fludarabine Metabolism by the Gut Microbiome

Abstract

The many microbes comprising the human gut microbiome play an important role in the metabolism of several drugs. Fludarabine is a chemotherapeutic whose function may rely on reactions carried out in the microbiome environment. Previous studies have suggested that Escherichia coli breaks this drug down to a purine base and that a purine nucleoside phosphorylase encoded by this bacteria enhances fludarabine’s antitumor activity. However, despite this drug’s common use in cancer treatment, the direct role of Escherichia coli in fludarabine metabolism is not well defined and the specific bacterial enzyme-drug interaction occurring has not been concretely demonstrated. The present study sought to clarify the details of fludarabine’s metabolic pathway in the body by testing common gut microbiome components for their ability to metabolize this drug and using mutant Escherichia coli strains with specific gene knockouts to identify the enzyme driving the conversion of fludarabine to its purine base. Compounds that are structurally and functionally analogous to fludarabine were also examined to determine whether the mechanisms of gut microbiome-based metabolism were conserved among fludarabine’s drug class. These experiments revealed that the Escherichia coli purine nucleoside phosphorylase deoD-type, encoded by the deoD gene, catalyzes a phosphorylation and subsequent deglycosylation reaction to liberate fludarabine’s purine base. This implicated gene was then used to detect other bacteria with deoD homologs that may interact with fludarabine as well. Tests with fludarabine analogs also exhibited similar gut microbiome-derived metabolic steps, suggesting that fludarabine may serve as a proxy for studying the metabolism of the purine nucleoside drug class. These findings provide a better understanding of fludarabine metabolism that further illuminates the importance of the gut microbiome in an individual’s response to oral drugs. Such comprehension is beneficial to developing safer and more effective drug use within the personalized medicine field.