Discovery of Novel Antimicrobial Agents Targeting the Bacterial RNA Polymerase by High-Throughput Virtual Screening

Abstract

Bacterial RNA polymerase (RNAP) is the least popular target for antibiotics, and currently Rifampicin is only an approved drug for clinical use. However, RNAP is essential for bacterial growth and survival, and it can be a promising target for antimicrobial agents. Thus, we decided to search new antimicrobial agents for RNAP by virtual screening. When virtual screenings are performed, certain compounds repeatedly appears on hits covering a wide range of targets (frequently hitters). Also, the performance of hit generation is important factor in success of the virtual screening. Since we previously developed the optimized docking scores, we examined our scoring methods with rigorous removals of frequent hitters. We used two complex structures for RNAP, and also used two unrelated structures as negative controls to remove frequent hitters. Finally, we selected seven high-scored candidates from hits, and two of them showed the inhibition of Gram-positive bacteria by paper disk agar diffusion assay in vivo.

Discovery of a capuramycin analog that kills nonreplicating Mycobacterium tuberculosis and its synergistic effects with translocase I inhibitors

“… 35 In preliminary assay screening of UT-01320 ( 3 ) against the potential drug targets for non-replicating Mtb, it was observed that 3 inhibited E. coli, S. aureus, and M. smegmatis RNA polymerases with the IC 50 values of the 100-150 nM range (vs IC 50 120 nM for rifampicin against E. coli RNA polymerase) ( Figure 5B ), whereas, 3 did not inhibit electron transport systems, menaquinone biosynthesis, Mtb serine/threonine kinases (PKnA and B), and DNA gyrase. 36 , 37 , 38 , 39 Capuramycin ( 1 ) and SQ 641 ( 2 ) did not inhibit bacterial RNA polymerases even at 100 μM concentrations. Figure 5 summaries MurX and RNA polymerase inhibitory activities of Capuramycin ( 1 ), SQ 641 ( 2 ), and UT-01320 ( 3 ).…”