Interfacing medicinal chemistry with structural bioinformatics: implications for T box riboswitch RNA drug discovery

BACKGROUND: The T box riboswitch controls bacterial transcription by structurally responding to tRNA aminoacylation charging ratios. Knowledge of the thermodynamic stability difference between two competing structural elements within the riboswitch, the terminator and the antiterminator, is critical for effective T box-targeted drug discovery. METHODS: The ΔG of aminoacyl tRNA synthetase (aaRS) T box riboswitch terminators and antiterminators was predicted using DINAMelt and the resulting ΔΔG (ΔG(Terminator )- ΔG(Antiterminator)) values were compared. RESULTS: Average ΔΔG values did not differ significantly between the bacterial species analyzed, but there were significant differences based on the type of aaRS. CONCLUSIONS: The data indicate that, of the bacteria studied, there is little potential for drug targeting based on overall bacteria-specific thermodynamic differences of the T box antiterminator vs. terminator stability, but that aaRS-specific thermodynamic differences could possibly be exploited for designing drug specificity.