Chemotype- and Target-Driven Genome Mining for a New Natural Product Inhibitor of Bacterial Peptide Deformylase

Antibiotics are essential for modern medicine, but their use drives the evolution of antimicrobial resistance (AMR) that limits the long-term efficacy of any one drug. To keep pace with AMR and preserve our ability to treat bacterial infections, it is essential that we identify antibiotics with new structures and targets that are not affected by clinical resistance. Historically, most developmental candidates for antibiotics have come from microbial natural products, as they feature chemical structures and biological activities that have been honed over millions of years of evolution. Unfortunately, as classical bioactivity screens for natural product discovery are blind to the pharmacological properties of their hits, they often identify molecules with functional groups that limit their utility as drugs. One prominent example is actinonin, an inhibitor of bacterial peptide deformylase (PDF) whose activity is dependent on a hydroxamate moiety associated with toxicity in vivo. The abundance of bacterial genomes now presents an opportunity for target-based natural product discovery, where biosynthetic pathways can be mined for molecules that possess desired activities but lack known pharmacophores. Here, we use bioinformatics to lead a chemotype-sensitive, target-based search for natural product inhibitors of bacterial PDF that lack the conserved metal chelating group. We describe the discovery, heterologous expression, biosynthesis, total synthesis, and activity of the gammanonins: actinonin homologues from Gammaproteobacteria. Moving forward, we hope this chemotype- and target-driven approach will help to expedite the discovery of new leads for antibiotic development.