Novel macrocyclic antibiotic structure targeting BamA against gram-negative pathogens

Abstract

Discovery of antibiotics against Gram - negative species is uniquely challenging due to their restrictive penetration barrier. BamA, which assists in folding and insertion of proteins into the outer membrane, is an attractive target because of its surface location, exposed to the extracellular environment. In this study, we identify dynobactin A, a novel peptide antibiotic from Photorhabdus australis which targets BamA, and unveil two unique unlinked rings by cryogenic electron micros copy. a The novel compound is the fi rst natural product antibiotic of unknown structure solved de novo by this approach (PDB 7T3H). It is a decapeptide of sequence W1 N 2 S3N4 V5H6 S7Y 8 R 9F10, which has two closed rings: 1) a carbon-carbon bond formed between the Trp1 C 6 and the β -carbon of Asn 4 (green box) and 2) an unusual nitrogen-carbon linkage between the His6 imidazole Nε2 and the β - carbon of Tyr8 (orange box). These connections create unfused 4-and 3-constituent rings respectively, resulting in a fl exible peptide, contrasting the fused rings of darobactins. Dynobactin A is one example of natural -product antibiotics acting against the outer membrane protein of Gram - negative bacteria. This study demonstrates how electron microscope accelerates antibiotic discovery by providing unambiguous structures from submicron-sized crystals.