Folded Synthetic Peptides and Other Molecules Targeting Outer Membrane Protein Complexes in Gram-Negative Bacteria

Abstract

Conformationally constrained peptidomimetics have been developed to mimic interfacial epitopes and target a wide selection of protein-protein interactions. ß-Hairpin mimetics based on constrained macrocyclic peptides have provided access to excellent structural mimics of ß-hairpin epitopes and found applications as interaction inhibitors in many areas of biology and medicinal chemistry. Recently, ß-hairpin peptidomimetics and naturally occurring ß-hairpin-shaped peptides have also been discovered with potent antimicrobial activity and novel mechanisms of action, targeting essential outer membrane protein (OMP) complexes in Gram-negative bacteria. This includes the Lpt complex, required for transporting LPS to the cell surface during OM biogenesis and the BAM complex that folds OMPs and inserts them into the OM bilayer. The Lpt complex is a macromolecular superstructure comprising seven different proteins (LptA-LptG) that spans the entire bacterial cell envelope, whereas the BAM complex is a folding machine comprising a ß-barrel OMP (BamA) and four different lipoproteins (BamB-BamE). Folded synthetic and natural ß-hairpin-shaped peptides appear well-suited for interacting with proteins within the Lpt and BAM complexes that are rich in ß-structure. Recent progress in identifying antibiotics targeting these complexes are reviewed here. Already a clinical candidate has been developed (murepavadin) that targets LptD, with potent antimicrobial activity specifically against pseudmonads. The ability of folded synthetic ß-hairpin epitope mimetics to interact with ß-barrel and ß-jellyroll domains in the Lpt and Bam complexes represent new avenues for antibiotic discovery, which may lead to the development of much needed new antimicrobials to combat the rise of drug-resistant pathogenic Gram-negative bacteria.

Porins and small-molecule translocation across the outer membrane of Gram-negative bacteria

“…The regulation of porin expression involves several modes of regulation. In addition, the final assembly as functional trimers into the OM is tightly controlled by the BAM machinery but also requires LPS binding 26,[142][143][144] . These complex and partly redundant systems efficiently control the production of porins, which represent a prominent part of the OM protein landscape and are directly involved in OM permeability.…”

Thanatin Impairs Lipopolysaccharide Transport Complex Assembly by Targeting LptC–LptA Interaction and Decreasing LptA Stability

“…Previous in vitro data revealed that besides LptA, thanatin binds to the LptDE complex in the low nanomolar range and, furthermore, its binding site in LptA has been shown by modeling studies to be highly conserved in the periplasmic domain of LptD (Robinson, 2019). This suggests that thanatin can inhibit multiple protein-protein interactions required for the Lpt complex assembly.…”

Mutational analysis of the essential lipopolysaccharide-transport protein LptH of Pseudomonas aeruginosa to uncover critical oligomerization sites

“…This adds to the previously described peculiarities of the P. aeruginosa LptDE translocon, that differs from the E. coli counterpart for the presence of an additional domain of unknown function at the LptD N-terminus 14 , a larger lumen volume 26 , and the specific role of LptE, that is important as LptD chaperone and plug but is not directly involved in LPS transport 22 . The unique features of the P. aeruginosa LptD periplasmic domain have been proposed to justify the anti-pseudomonads specificity of recently identified peptidomimetics targeting LPS transport through interaction with LptD [27][28][29] . Since the cell envelope biogenesis pathways are nowadays considered attractive targets for novel antibacterial drugs [29][30][31] , this emphasizes the potential impact of investigating the conserved and divergent aspects of these systems in different human pathogens.…”

“…The unique features of the P. aeruginosa LptD periplasmic domain have been proposed to justify the anti-pseudomonads specificity of recently identified peptidomimetics targeting LPS transport through interaction with LptD [27][28][29] . Since the cell envelope biogenesis pathways are nowadays considered attractive targets for novel antibacterial drugs [29][30][31] , this emphasizes the potential impact of investigating the conserved and divergent aspects of these systems in different human pathogens. This information could indeed ultimately drive the rational design of new narrow-or broad-spectrum antibacterial agents.…”