Discovery of small molecule protease inhibitors by investigating a widespread human gut bacterial biosynthetic pathway

Abstract

Natural products from the human microbiota may mediate host health and disease. However, discovery of the biosynthetic gene clusters that generate these metabolites has far outpaced identification of the molecules themselves. Here, we used an isolation-independent approach to access the probable products of a nonribosomal peptide synthetase-encoding gene cluster from Ruminococcus bromii, an abundant gut commensal bacterium. By combining bioinformatics with in vitro biochemical characterization of biosynthetic enzymes, we predicted that this pathway likely generates an N-acylated dipeptide aldehyde (ruminopeptin). We then used chemical synthesis to access putative ruminopeptin scaffolds. Several of these compounds inhibited Staphylococcus aureus endoproteinase GluC (SspA/V8 protease). Homologs of this protease are found in gut commensals and opportunistic pathogens as well as human gut metagenomes. Overall, this work reveals the utility of isolation-independent approaches for rapidly accessing bioactive compounds and highlights a potential role for gut microbial natural products in targeting gut microbial proteases.