Leveraging Protein Dynamics for Selective Inhibition of Threonyl-tRNA Synthetase by Obafluorin Analogs

The widespread emergence of antibiotic resistance necessitates the development of novel agents with unique mechanisms of action. Obafluorin (OB), a natural β-lactone antibiotic, is a covalent inhibitor of threonyl-tRNA synthetase (ThrRS), but the high conservation of the active site between prokaryote and eukaryote ThrRSs results in minimal selectivity, hindering the therapeutic potential of OB. Here, we report a structure dynamics-based design strategy that transforms OB into a selective antibacterial agent. OB inhibits human and bacterial ThrRSs with nearly equal potency due to identical binding modes. The nitrophenyl moiety of OB is proposed as a 'kinetic sensor' that discriminates between sensitive and resistant ThrRS paralogs. Guided by this insight, we designed a series of OB analogs through rational modification of this moiety. Among them, OB-D4 bearing a para-methoxyphenyl group in place of the nitrophenyl group, exhibited a 241-fold selectivity for bacterial over human ThrRS, along with a markedly improved safety profile with minimal cytotoxicity. In a murine skin infection model, OB-D4 effectively eradicated pathogens, resolving inflammation, and promoting wound healing. Together, this work establishes a 'kinetic sensor' strategy for achieving species selectivity, turning a fundamental challenge in drug discovery-high active-site conservation-into an exploitable opportunity based on dynamic differences.