Solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase

Abstract

Due to its potential as an antibiotic target, E. coli peptide deformylase (PDF Ec) serves as a model enzyme system for inhibitor design. While investigating the structural–functional and inhibitory features of this enzyme, we unexpectedly discovered that 2-amino-5-mercapto-1,3,4-thiadiazole (AMT) served as a slow-binding inhibitor of PDF Ec when the above compound was dissolved only in dimethylformamide (DMF), but not in any other solvent, and allowed to age. The time dependent inhibitory potency of the DMF-dissolved AMT was correlated with the broadening of the inhibitor's 295 nm spectral band toward the visible region, concomitant with the increase in the mass of the parent compound by about 2-fold. These data led to the suggestion that DMF facilitated the slow dimerization of AMT (via the formation of a disulfide bond), and that the dimeric form of AMT served as an inhibitor for PDF Ec. The latter is not caused by the simple oxidation of sulfhydryl groups by oxidizing agents such as H 2O 2. Newly synthesized dimeric/dithiolated form of AMT (“bis-AMT”) exhibited similar spectral and inhibitory features as given by the parent compound when incubated with DMF. The computer graphic modeling data revealed that bis-AMT could be reliably accommodated within the active site pocket of PDF Ec, and the above enzyme–ligand interaction involves coordination with the enzyme resident Ni 2+ cofactor. The mechanism of the DMF-assisted activation of AMT (generating bis-AMT), the overall microscopic pathway for the slow-binding inhibition of PDF Ec by bis-AMT, and the potential of bis-AMT to serve as a new class of antibiotic agent are presented.