Discovery of Novel Antibiotics as Covalent Inhibitors of Fatty Acid Synthesis.

The steady increase in the prevalence of multidrug-resistant Staphylococcus aureus has urged the search for novel antibiotics to combat this clinically important pathogen. In an effort to discover antibacterials with new chemical structures and mechanisms, we performed a growth inhibition screen of a synthetic library against Staphylococcus aureus and discovered a promising scaffold with 1,3,5-oxadiazin-2-one core. These compounds are potent against both methicillin-sensitive and methicillin-resistant Staphylococcus aureus strains. Isolation of compound resistant strains followed by whole genome sequencing revealed its cellular target as FabH, a key enzyme in bacterial fatty acid synthesis. Detailed mechanism of action studies suggested the compounds inhibit FabH activity by covalently modifying its active site cysteine residue with high selectivity. A crystal structure of FabH protein modified by a selected compound Oxa1 further confirmed covalency and suggested a possible mechanism for reaction. Moreover, the structural snapshot provided an explanation for compound selectivity. Based on the structure, we designed and synthesized Oxa1 derivatives and evaluated their antibacterial activity. The structure-activity rela-tionship supports the hypothesis that non-covalent recognition between compounds and FabH is critical for the activity of these covalent inhibitors. We believe further optimization of the current scaffold could lead to antibacterial with potentials to treat drug resistant bacteria in the clinic.