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

Jentzsch, Franziska; Hines, Jennifer V.

doi:10.1186/1471-2105-13-s2-s5

Cited by 9 publications

(4 citation statements)

References 23 publications

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“…Neomycin B and a series oxazolidinone derivatives had been found to bind a 29‐nucleotide anti‐terminator model of the B. subtilis glyS T‐box . Binding at this site may impede proper transcription control by taking advantage of the stability (free energy) differences between the anti‐terminator and terminator T‐box elements . However, development of this binding site as a drug target remains challenging due to the lack of a binding pocket and the fact that the complementary UGG sequence is ubiquitous to RNAs, mammalian and bacterial cells alike.…”

Section: Discussionmentioning

confidence: 99%

Discovery of Small‐Molecule Antibiotics against a Unique tRNA‐Mediated Regulation of Transcription in Gram‐Positive Bacteria

et al. 2019

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The emergence of multidrug‐resistant bacteria necessitates the identification of unique targets of intervention and compounds that inhibit their function. Gram‐positive bacteria use a well‐conserved tRNA‐responsive transcriptional regulatory element in mRNAs, known as the T‐box, to regulate the transcription of multiple operons that control amino acid metabolism. T‐box regulatory elements are found only in the 5′‐untranslated region (UTR) of mRNAs of Gram‐positive bacteria, not Gram‐negative bacteria or the human host. Using the structure of the 5′UTR sequence of the Bacillus subtilis tyrosyl‐tRNA synthetase mRNA T‐box as a model, in silico docking of 305 000 small compounds initially yielded 700 as potential binders that could inhibit the binding of the tRNA ligand. A single family of compounds inhibited the growth of Gram‐positive bacteria, but not Gram‐negative bacteria, including drug‐resistant clinical isolates at minimum inhibitory concentrations (MIC 16–64 μg mL−1). Resistance developed at an extremely low mutational frequency (1.21×10−10). At 4 μg mL−1, the parent compound PKZ18 significantly inhibited in vivo transcription of glycyl‐tRNA synthetase mRNA. PKZ18 also inhibited in vivo translation of the S. aureus threonyl‐tRNA synthetase protein. PKZ18 bound to the Specifier Loop in vitro (Kd≈24 μm). Its core chemistry necessary for antibacterial activity has been identified. These findings support the T‐box regulatory mechanism as a new target for antibiotic discovery that may impede the emergence of resistance.

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Section: Discussionmentioning

confidence: 99%

Discovery of Small‐Molecule Antibiotics against a Unique tRNA‐Mediated Regulation of Transcription in Gram‐Positive Bacteria

et al. 2019

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“…This element must be stabilized by interaction with the acceptor end of the tRNA. The structure of this domain [31–32] was therefore used as the basis for design of families of compounds that were predicted to bind to the antiterminator, and the resulting compounds were tested for effects on tRNA binding, tRNA-dependent stabilization of the antiterminator and antitermination [38–43]. Further development of these compounds holds promise for development of useful new antimicrobial compounds that are predicted to be specific for Gram-positive organisms, avoiding more general effects on the commensal flora.…”

Section: Targeting Of the T Box Riboswitch With Novel Antimicrobiamentioning

confidence: 99%

The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand

Henkin

2014

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

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The T box riboswitch is a cis-acting regulatory RNA that controls expression of amino acid-related genes in response to the aminoacylation state of a specific tRNA. Multiple genes in the same organism can utilize this mechanism, with each gene responding independently to its cognate tRNA. The uncharged tRNA interacts directly with the regulatory RNA element, and this interaction promotes readthrough of an intrinsic transcriptional termination site upstream of the regulated coding sequence. A second class of T box elements uses a similar tRNA-dependent response to regulate translation initiation. This review will describe the current state of our knowledge about this regulatory system.

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“…As part of a comprehensive drug discovery effort, we have been investigating the highly conserved antiterminator element as a specific RNA target within the T box riboswitch [19-26]. Using a fluorescence-based binding assay we determined that T box antiterminator model RNA binds aminoglycosides in a structure-specific manner primarily through electrostatic interactions [27,28].…”

Section: Introductionmentioning

confidence: 99%

Factors that influence T box riboswitch efficacy and tRNA affinity

Zeng¹,

Zhou²,

Bergmeier³

et al. 2015

Bioorganic & Medicinal Chemistry

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The T box riboswitch is an intriguing potential target for antibacterial drug discovery. Found primarily in Gram-positive bacteria, the riboswitch regulates gene expression by selectively responding to uncharged tRNA to control transcription readthrough. Polyamines and molecular crowding are known to specifically affect RNA function, but their effect on T box riboswitch efficacy and tRNA affinity have not been fully characterized. A fluorescence-monitored in vitro transcription assay was developed to readily quantify these molecular interactions and to provide a moderate-throughput functional assay for a comprehensive drug discovery screening cascade. The polyamine spermidine specifically enhanced T box riboswitch readthrough efficacy with an EC50 = 0.58 mM independent of tRNA binding. Molecular crowding, simulated by the addition of polyethylene glycol, had no effect on tRNA affinity for the riboswitch, but did reduce the efficacy of tRNA-induced readthrough. These results indicate that the T box riboswitch tRNA affinity and readthrough efficacy are intricately modulated by environmental factors.

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

Cited by 9 publications

References 23 publications

Discovery of Small‐Molecule Antibiotics against a Unique tRNA‐Mediated Regulation of Transcription in Gram‐Positive Bacteria

Discovery of Small‐Molecule Antibiotics against a Unique tRNA‐Mediated Regulation of Transcription in Gram‐Positive Bacteria

The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand

Factors that influence T box riboswitch efficacy and tRNA affinity

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