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This article is part of the supplement: Proceedings from the Great Lakes Bioinformatics Conference 2011

Open Access Proceedings

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

Franziska Jentzsch12 and Jennifer V Hines2*

Author Affiliations

1 Department of Chemistry, Leipzig University, Leipzig, Germany

2 Department of Chemistry & Biochemistry, Ohio University, Athens, OH, USA

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BMC Bioinformatics 2012, 13(Suppl 2):S5  doi:10.1186/1471-2105-13-S2-S5

Published: 13 March 2012

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 (ΔGTerminator - ΔGAntiterminator) 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.