Antimicrobial peptoid TM1 rapidly permeabilizes E. coli membranes and flocculates ribosomes/DNA faster than LL-37

The escalating threat of antimicrobial resistance (AMR), particularly in Gram-negative bacteria, necessitates novel therapeutic strategies. Host-defense peptides (HDPs), like LL-37, offer broad-spectrum antimicrobial activity but often face challenges in clinical translation due to cytotoxicity and protease susceptibility. Peptoids, synthetic mimics of HDPs, overcome protease degradation and show promise, but their dynamic mechanisms of action, especially regarding membrane translocation and intracellular target engagement, have remained largely unexplored, hindering rational design efforts.

Researchers investigated the dynamic effects of the 12mer peptoid TM1 and its shorter alkylated/brominated analogues on Escherichia coli using single-bacterial-cell, time-resolved fluorescence microscopy and single-particle tracking. The study focused on cytoplasmic membrane permeabilization and the rigidification of intracellular DNA and ribosomes. Peptoid solutions were flowed over cells, and their effects were compared against the known human antimicrobial peptide LL-37, serving as a positive control for both membrane disruption and nucleic acid binding.

TM1 and several of its analogues demonstrated rapid permeabilization of the E. coli cytoplasmic membrane within five minutes of exposure, a rate notably faster than observed for the human antimicrobial peptide LL-37. Concurrently, these peptoids rigidified both bacterial DNA and ribosomes as effectively as LL-37. Biophysical studies further revealed that TM1 binds to both double-stranded and single-stranded DNA, as well as single-stranded RNA, in a manner similar to LL-37, which is recognized for its strong nucleic acid binding properties.

TM1 displayed a higher affinity for RNA compared to DNA, suggesting a preferential binding to bacterial ribosomes in vivo, supporting the hypothesis that its antimicrobial effects stem from intracellular aggregation of biomacromolecules like ribosomes, RNA, and DNA.