Molecular Basis of Selectivity and Activity for the Antimicrobial Peptide Lynronne‐1 Informs Rational Design of Peptide with Improved Activity

Abstract

Antibiotic resistance is a significant threat to human health, with natural products remaining the best source for new antimicrobial compounds. Antimicrobial peptides (AMPs) are natural products with great potential for clinical use as they are small, amenable to customization, and show broad-spectrum activities. Lynronne-1 is a promising AMP identified in the rumen microbiome that shows broad-spectrum activity against pathogens such as methicillin-resistant Staphylococcus aureus and Acinetobacter baumannii. Here we investigated the structure of Lynronne-1 using solution NMR spectroscopy and identified a 13-residue amphipathic helix containing all six cationic residues. We used biophysical approaches to observe folding, membrane partitioning and membrane lysis selective to the presence of anionic lipids. We translated our understanding of Lynronne-1 structure to design peptides which varied in the size of their hydrophobic helical face. These peptides displayed the predicted continuum of membrane-lysis activities in vitro and in vivo, and yielded a new AMP with 4-fold improved activity against A. baumannii and 32-fold improved activity against S. aureus.

Microbiome-derived antimicrobial peptides show therapeutic activity against the critically important priority pathogen, Acinetobacter baumannii

“…Structural examination using circular dichroism indicates that Lynronne-1, -2 and -3 all demonstrated alpha helical structures when in the presence of SDS detergent micelles, based on the observed peaks at 195 nm, and low dips at 208 nm and 220 nm 27 , suggesting that this conformation is also adopted during bacterial lipid binding corroborating with previous findings for Lynronne-1 25 . The difference in spectra peak height indicates that Lynronne-3 structures in SDS may contain less α-helical content than Lynronne-1 or -2.…”

“…Numerous AMPs identified from the rumen microbiome, including Lynronne peptides, have shown proven efficacy against a variety of bacterial species, including Gram-positive and negative isolates [20][21][22][23][24] . These studies suggest that they work as membrane disruptors against S. aureus 23,25 and Pseudomonas aeruginosa, and possess low mammalian cell cytotoxicity 22 . Lynronne-1 has also undergone structural investigations, which concluded that it displayed an alpha-helical conformation in the presence of bacterial lipids 25 .…”

“…These studies suggest that they work as membrane disruptors against S. aureus 23,25 and Pseudomonas aeruginosa, and possess low mammalian cell cytotoxicity 22 . Lynronne-1 has also undergone structural investigations, which concluded that it displayed an alpha-helical conformation in the presence of bacterial lipids 25 . In addition, these AMPs have been observed to have antibiofilm activity against methicillin-resistant S. aureus (MRSA) at 2x minimum inhibitory concentration (MIC) 23 .…”

Microbiome-derived antimicrobial peptides offer therapeutic solutions for the treatment of Pseudomonas aeruginosa infections

“…Lynronne 1–3 have been shown to adopt α-helical conformations 2 . A more detailed structural analysis of Lynronne 1 including solution NMR spectroscopy, confirmed a 13-residue amphipathic helix containing all six cationic residues, positively associated with increased peptide selectivity 17 . Structural modelling using PEP-FOLD, revealed an antiparallel β-sheet turn structure for P15s, which is distinct from the α-helical conformations adopted Lynronne 1–3 (Fig.…”

Antifungal Activity of ToAP2D Peptide Against Sporothrix globosa

“…In addition, non-membranolytic cytotoxicity is also involved in antimicrobial activity, such as genetic material damage, immune regulation, and apoptosis ( Wassing et al, 2015 ; Struyfs et al, 2021b ). Unlike traditional antibiotics, antimicrobial peptides have many advantages such as quick killing effect and low tendency to induce resistance ( Guilhelmelli et al, 2016 ; Xu et al, 2020 ; Jayawant et al, 2021 ). However, natural antimicrobial peptides are usually longer peptides with relatively low activity, high cytotoxicity, and strong antigenicity, and these drawbacks limit their applications ( Kreling et al, 2016 ).…”