Masking of Hydrophobicity through Macromolecular Nanoaggregation Ameliorates Toxicity while Retaining Excellent Antibacterial Efficacy

The activity–toxicity trade-off remains a central challenge for developing membrane-active antimicrobial peptide-mimicking macromolecules. Increasing hydrophobicity enhances bactericidal potency but often leads to elevated host–cell toxicity and loss of selectivity, as hydrophobic moieties indiscriminately interact with both bacterial and mammalian lipid membranes. Here, we introduce a polarity-induced stable aggregation strategy that effectively decouples hydrophobicity from toxicity, establishing a new design principle for selective macromolecular antibacterials. We engineered maleimide-based cationic macromolecules bearing hydrophobic alkyl chains of varying lengths (decyl to docosyl). Increasing the alkyl chain length promotes nanoaggregation, with the longest chain bearing (docosyl) macromolecule undergoing a structural transition in which the nonselective hydrophobic segments are masked within a stable aggregate core while cationic functionalities remain surface-exposed, facilitating strong electrostatic interactions with negatively charged bacterial membranes. This topological segregation diminishes the nonspecific interactions with zwitterionic mammalian membranes, leading to significantly lower toxicity. The optimized stable nanoaggregate (QNpt-22) exhibits potent antibacterial activity, including eradication of stationary-phase bacteria and preformed biofilms, which are the challenges for conventional antibiotics. The nanoaggregate exhibits excellent biocompatibility across multiple routes of administration in mice and displays significant therapeutic efficacy in an Acinetobacter baumannii superficial skin infection model. Our findings recommend that the spatial segregation of hydrophobic domains via nanoaggregation is a robust strategy to achieve selectivity, offering a new paradigm in membrane-targeting antibacterial design.