Mechanism of inhibition of bacterial RNA helicases by diazo dyes and implications for antimicrobial drug development

RNA helicases represent attractive drug targets as their activity is linked to several human diseases and impacts microbial infectious processes. While some inhibitors of human RNA helicases demonstrated therapeutic po-tential as anticancer and antiviral drugs in preclinical trials, chemical inhibition of microbial RNA helicases is less investigated. Here, we address this matter by focusing on the RhlE proteobacterial group of RNA helicases. Having previously shown that the RhlE2 RNA helicase is important for the virulence of the opportunistic pathogen Pseudomonas aeruginosa, we screened a library of 1280 molecules for inhibitors of RhlE2 RNA -dependent ATP hydrolytic activity. The most potent inhibitor is the diazo compound Chicago Sky Blue (CSB). Using hydrogen-deuterium exchange mass spectrometry and biochemical assays, we mapped CSB binding to RhlE2 catalytic core and defined its inhibitory mechanism. Targeting microbial RNA helicases as therapeutic strategy is challenging due to potential side-effects linked to protein conservation across life kingdoms. Inter-estingly, our structure-activity relationship analysis delineates other diazo dyes closely related to CSB differ-entially affecting RhlE homologs. Our work could thus be exploited for future drug development studies, which are extremely timely considering the increasing spread of antibiotic resistance among bacterial pathogens.

Automated summary

RNA helicases, including microbial RNA helicases, can be potential drug targets. In this study, the researchers screened a library of molecules and identified a potent inhibitor, CSB, for RhlE2 RNA helicase. They also investigated the inhibitory mechanism and found other diazo dyes that affect RhlE homologs differently. This research provides valuable insights for future drug development.