Genome Mining-Based Discovery and Engineering of Trojan Horse Peptide Antibiotics Against Gram-Negative Pathogens

Objective

Antimicrobial resistance (AMR) is a growing global threat, with the World Health Organization highlighting Gram-negative pathogens as a critical priority. New antibiotics with innovative modes of action are urgently needed. This project aims to discover and characterize a previously unexplored biosynthetic gene cluster predicted to encode a hybrid natural product that links two major peptide classes: ribosomally synthesized and post-translationally modified peptides (RiPPs) and nonribosomal peptides (NRPs). Such hybrid pathways are extremely rare and represent a promising but uncharted area for antibiotic discovery. The first objective is to identify and structurally characterize the natural product encoded by this pathway. This will be achieved using genome mining, bioinformatics, and heterologous expression of candidate genes, followed by isolation and advanced qualitative organic analysis methods such as NMR and MS. The second objective is to investigate the structural basis of the encoded RiPP, which is predicted to form a β-helix through an alternating L/D residue pattern. Biophysical methods will test whether this fold contributes to antibacterial activity, for example through ion channel formation. The third objective is to characterize the unique enzyme responsible for attaching the NRP to the RiPP scaffold, which represents a new enzymatic function at the interface of two biosynthetic classes. This enzyme will be studied using biochemical assays and engineered through directed evolution to assess its potential for generating “mix-and-match” antibiotics. By combining natural product discovery, structural biology, and enzyme engineering, this interdisciplinary project will provide new insights into peptide biosynthesis and resistance-evading antibiotic mechanisms. The outcomes will include fundamental advances in understanding RiPP–NRP hybrid biosynthesis, along with identification of new antibiotic drug leads to target Gram-negative infections.