title: Interfacing medicinal chemistry with structural bioinformatics: implications for T box riboswitch RNA drug discovery.
abstract: 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.
authors.affiliation: Department of Chemistry, Leipzig University, Leipzig, Germany.
authors.forename: Franziska
authors.initials: F
authors.lastname: Jentzsch
authors.forename: Jennifer V
authors.initials: JV
authors.lastname: Hines
mesh_terms: D000604:Amino Acyl-tRNA Synthetases / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D055808:Drug Discovery; D012329:RNA, Bacterial / Q000737:chemistry; D058928:Riboswitch; D013728:Terminator Regions, Genetic
chemical_list: D012329:RNA, Bacterial; D058928:Riboswitch; D000604:Amino Acyl-tRNA Synthetases