Broad-Spectrum Antimicrobial Peptides by Rational Combinatorial Design and High-Throughput Screening: The Importance of Interfacial Activity

TLDR

A 16,384-member combinatorial library was screened for peptides that permeabilize synthetic lipid vesicles, yielding ten candidates that lack common motifs but act via a mechanism similar to natural membrane‑permeabilizing antimicrobial peptides. The study aims to characterize these peptides and compare their in vivo and in vitro antimicrobial activity, proposing that in‑vitro screening for interfacial activity can guide the discovery of potent broad‑spectrum membrane‑active antibiotics. Peptides were selected based on vesicle permeabilization and were tested against bacteria, fungi, and mammalian cells, revealing that they disrupt membranes in a manner akin to natural.

Abstract

We recently described 10 peptides selected from a 16 384-member combinatorial library based on their ability to permeabilize synthetic lipid vesicles in vitro. (8) These peptides did not share a common sequence motif, length, or net charge; nonetheless, they shared a mechanism of action that is similar to the natural membrane permeabilizing antimicrobial peptides (AMP). To characterize the selected peptides and to compare the activity of AMPs in vivo and in vitro, we report on the biological activity of the same selected peptides in bacteria, fungi, and mammalian cells. Each of the peptides has sterilizing activity against all classes of microbes tested, at 2−8 μM peptide, with only slight hemolytic or cytotoxicity against mammalian cells. Similar to many natural AMPs, bacteria are killed within a few minutes of peptide addition, and the lethal step in vivo is membrane permeabilization. Single d-amino acid substitutions eliminated or diminished the secondary structure of the peptides, and yet, they retained activity against some microbes. Thus, secondary structure and biological activity are not coupled, consistent with the hypothesis that AMPs do not form pores of well-defined structure in membranes but rather destabilize membranes by partitioning into membrane interfaces and disturbing the organization of the lipids, a property that we have called "interfacial activity". The observation that broad-spectrum activity, but not all antimicrobial activity, is lost by small changes to the peptides suggests that the in vitro screen is specifically selecting for the rare peptides that have broad-spectrum activity. We put forth the hypothesis that methods focusing on screening peptide libraries in vitro for members with the appropriate interfacial activity can enable the design, selection, and discovery of novel, potent, and broad-spectrum membrane-active antibiotics.