Rational design of structurally rigidified ketone-peptide deformylase inhibitors with enhanced membrane permeability for combating gram-negative bacterial infections.

Gram-negative bacterial infections remain a critical global health challenge due to their complex membrane structure and limited treatment options. While peptide deformylase (PDF) inhibitors demonstrate potent activity against Gram-positive pathogens, their efficacy against Gram-negative species is constrained by poor outer membrane permeability. To address this, we rationally designed a novel series of ketone-incorporated compounds with enhanced structural rigidity to improve membrane penetration. Our lead compounds (10a, 10f, 12b) exhibited exceptional activity against Acinetobacter baumannii (MIC₅₀ < 2 μg/mL) and clinically isolated strains (MIC₅₀ < 8 μg/mL), with compound 6 showing particularly potent PDF inhibition (IC₅₀ = 70.8 ± 8.0 nM). The lead compound demonstrated no significant cytotoxicity toward human hepatic stellate cells (LX-2) at the tested concentrations. Molecular docking confirmed their mechanism of action through competitive PDF binding. This work establishes a strategic framework for developing next-generation antibiotics against Gram-negative infections by optimizing membrane permeability while maintaining target inhibition.