Coupled Hydrogen-Bond–Electrostatic Recognition of Phosphatidylglycerol Drives the Design of Resistance-Suppressing Miniature Peptidomimetics

The
emergence of multidrug-resistant (MDR) pathogens has urged
us to find new antimicrobial strategies. Phosphatidylglycerol (PG)
is an attractive bacterial-specific lipid target but is targeted by
only one clinical agent, daptomycin. Yet daptomycin, like most reported
PG binders, binds PG through an imprecise hydrophobic–electrostatic
mode, necessitating a relatively large molecular size. This requirement,
together with its strict Ca2+ dependence, significantly
limits its efficacy. Here, we report bis-pyridinium
amides (BisPAs), a rationally designed class of small
molecules capable of precisely recognizing PG through amide–diol
hydrogen bonding coupled with pyridinium–phosphate anionic–π
interaction, independent of environmental conditions such as Ca2+. The lead compound, BisPA14, with ∼one-third
the molecular weight of daptomycin, exhibits comparable PG-binding
affinity, with Kd(BisPA14) = 1.4 × 10–6 M versus Kd(daptomycin-Ca2+) = 0.9 × 10–6 M. BisPA14 disrupts PG self-assembly and membrane integrity
and simultaneously engages bacterial DNA as a secondary intracellular
target. This dual-targeting mechanism enables BisPA14 to eradicate proliferating, tolerant, and persister bacterial populations
while suppressing resistance evolution. It remains active in serum-containing
environments, protects host cells from bacterial damage, and demonstrates
excellent biocompatibility and strong therapeutic efficacy in intraperitoneal,
pulmonary, and bloodstream methicillin-resistant Staphylococcus
aureus infection models. As a synthetically accessible
small molecule that functionally mimics and improves upon daptomycin’s
lipid-targeting mechanism, this work establishes a secondary-bonding-driven
PG-recognition paradigm for combating MDR bacterial infections.