Design, Syntheses, and Evaluations of Bicyclomycin-Based Rho Inactivators

The commercial antibiotic bicyclomycin (1) has been shown to target the essential transcriptional termination factor rho in Escherichia coli. Little is known, however, about the bicyclomycin binding site in rho. A recent structure−activity relationship study permitted us to design modified bicyclomycins that may irreversibly inactivate rho. The four compounds selected were C(5a)-(4-azidoanilino)dihydrobicyclomycin (3), C(5a)-(3-formylanilino)dihydrobicyclomycin (4), C(5)−norbicyclomycin C(5)-O-(4-azidobenzoate) (5), and C(5)-norbicyclomycin C(5)-O-(3-formylbenzoate) (6). In each of these compounds the inactivating unit was placed at the C(5)−C(5a) site in bicyclomycin. In compounds 3 and 5 an aryl azide moiety was used as a photoaffinity label whereas in 4 and 6 an aryl aldehyde group was employed as a reductive amination probe. The synthesis and spectral properties of 3−6 are described. Chemical studies demonstrated that 3 and 4 were stable in D₂O and CD₃OD (room temperature, 7 d), while 5 and 6 underwent significant change within 1 d. Biochemical investigations showed that 3 and 4 retained appreciable inhibitory activities in rho-dependent ATPase and transcription termination assays. In the ATPase assay, I₅₀ values for 1, 3, and 4 were 60, 135, and 70 μM, respectively. Correspondingly, the I₅₀ values for 5 and 6 were >400 and 225 μM, respectively. In the transcription termination assay, compounds 1, 3, and 4 all prevented (≥97%) the production of rho-dependent transcripts at 40 μM, whereas little (≤15%) inhibition of transcription termination was observed for 5 and 6 at this concentration. Antimicrobial evaluation of 3−6 showed that none of the four compounds exhibited antibiotic activity at 32 mg/mL or less against W3350 E. coli. The combined chemical and biochemical studies led to our further evaluation of 3 and 4. Photochemical irradiation (254 nm) of 3 in the presence of rho led to a 29−32% loss of rho ATPase activity. Attempts to confirm the irreversible adduction of 3 to rho by electrospray mass spectrometry were unsuccessful. No higher molecular weight adducts were detected. Incubation of rho with 4 at room temperature (4 h) followed by the addition of NaBH₄ led to significant losses (>62%) of rho ATPase activity. Analyses of the 4−rho modified adduct showed appreciable levels of adduction (∼40%). Mass spectrometric analyses indicated a molecular weight for the adduct of approximately 47 410, consistent with a modification of a rho lysine residue by 4. Compound 4 was selected for additional studies.