Computational design of a soluble mimic of the outer membrane LPS transport protein LptD suitable for screening of antibiotics.

Lipopolysaccharides (LPS) are the principal chemical component of the outer leaflet of Gram-negative bacteria and constitute the first barrier of defense against foreign molecules. Inhibition of LPS transport presents a novel concept for antibiotic discovery, and components of the transport bridge are targets of antimicrobial peptides. LptD, a β-barrel outer membrane protein, the terminal module of the Lpt transport bridge, however, remains largely unexplored as a drug target as its biosynthesis is complicated and screens against membrane proteins are challenging. Herein, we report a computationally designed, soluble E. coli LptD periplasmic epitope mimic, LptDm. We describe an efficient in silico design pipeline that includes verification of interactions of LptD mimics with the cognate ligands LptA and thanatin using nuclear magnetic resonance (NMR) and size-exclusions chromatography (SEC) techniques. A small peptide library demonstrates that LptDm allows for selection of high-affinity binders against LptD, rendering LptD accessible to modern drug discovery approaches.