Bacterial Transcription Inhibitor of RNA Polymerase Holoenzyme Formation by Structure-Based Drug Design: From in Silico Screening to Validation.
Bacterial transcription is a proven target for antibacterial research. However, most of the known inhibitors targeting transcription are from natural extracts or are hits from screens where the binding site remains unidentified. Using an RNA polymerase holoenzyme homology structure from the model Gram-positive organism Bacillus subtilis, we created a pharmacophore model and used it for in silico screening of a publicly available library for compounds able to inhibit holoenzyme formation. The hits demonstrated specific affinity to bacterial RNA polymerase and excellent activity using in vitro assays and showed no binding to the equivalent structure from human RNA polymerase II. The target specificity in live cells and antibacterial activity was demonstrated in microscopy and growth inhibition experiments. This is the first example of targeted inhibitor development for a bacterial RNA polymerase, outlining a complete discovery process from virtual screening to biochemical validation. This approach could serve as an appropriate platform for the future identification of inhibitors of bacterial transcription.
School of Environmental and Life Sciences, University of Newcastle , Callaghan, New South Wales 2308, Australia.
Cong
C
Ma
School of Environmental and Life Sciences, University of Newcastle , Callaghan, New South Wales 2308, Australia.
Xiao
X
Yang
School of Environmental and Life Sciences, University of Newcastle , Callaghan, New South Wales 2308, Australia.
Peter J
PJ
Lewis
D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001412:Bacillus subtilis / Q000187:drug effects*; D019295:Computational Biology / Q000639:trends; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D015195:Drug Design; D015964:Gene Expression Regulation, Bacterial; D020035:Holoenzymes / Q000378:metabolism; D006801:Humans; D008826:Microbial Sensitivity Tests; D011485:Protein Binding / Q000187:drug effects; D015203:Reproducibility of Results; D040681:Structural Homology, Protein; D013329:Structure-Activity Relationship; D014158:Transcription, Genetic; D015533:Transcriptional Activation
D000900:Anti-Bacterial Agents; D020035:Holoenzymes; D012321:DNA-Directed RNA Polymerases
antibiotic discovery; bacteria; in silico screening; protein−protein interaction; target validation; transcription