Identification of Bacteria-Selective Threonyl-tRNA Synthetase Substrate Inhibitors by Structure-Based Design

Teng, Maikun; Hilgers, M.T.; Cunningham, Mark L.; Borchardt, Allen; Locke, Jeffrey B.; Abraham, Sunny; Haley, Gregory; Kwan, Bryan; Hall, Courtney D.; Hough, Grayson W.; Shaw, Karen Joy; Finn, John M.

doi:10.1021/jm301756m

Cited by 45 publications

(53 citation statements)

References 33 publications

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“…Having established the experimental system, we then used it to investigate target specificity of a series of compounds derived from the synthetic Thr-RS inhibitor 5′- O -[ N -(threonyl)sulfamoyl] adenosine, a mimic of the threonyl adenosine monophosphate intermediate and a known competitive inhibitor of Thr-RS (8,25). These compounds were part of a structure-based drug design program to identify substrate analogs that inhibit Thr-RS (8,25).…”

Section: Resultsmentioning

confidence: 99%

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Identifying the targets of aminoacyl-tRNA synthetase inhibitors by primer extension inhibition

Orelle¹,

Szal²,

Klepacki³

et al. 2013

Nucleic Acids Research

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Aminoacyl-transfer RNA (tRNA) synthetases (RS) are essential components of the cellular translation machinery and can be exploited for antibiotic discovery. Because cells have many different RS, usually one for each amino acid, identification of the specific enzyme targeted by a new natural or synthetic inhibitor can be cumbersome. We describe the use of the primer extension technique in conjunction with specifically designed synthetic genes to identify the RS targeted by an inhibitor. Suppression of a synthetase activity reduces the amount of the cognate aminoacyl-tRNA in a cell-free translation system resulting in arrest of translation when the corresponding codon enters the decoding center of the ribosome. The utility of the technique is demonstrated by identifying a switch in target specificity of some synthetic inhibitors of threonyl-tRNA synthetase.

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Section: Resultsmentioning

confidence: 99%

“…These compounds were part of a structure-based drug design program to identify substrate analogs that inhibit Thr-RS (8,25). As anticipated, most of the tested compounds stalled the ribosome at the Thr codon of the RST1 template, confirming that these derivatives inhibited the activity of Thr-RS (Figure 2).…”

Section: Resultsmentioning

confidence: 99%

Identifying the targets of aminoacyl-tRNA synthetase inhibitors by primer extension inhibition

Orelle¹,

Szal²,

Klepacki³

et al. 2013

Nucleic Acids Research

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“…Because of the inherent specific recognition of amino acid by aaRSs, amino acid binding site in aaRS active center is often considered to be critical for developing aaRS specific inhibitors (Pope et al, 1998; Teng et al, 2013), with ATP site used for further binding stabilization (Keller et al, 2012; Zhou et al, 2013). The binding of natural substrate in one sub-site could also affect the binding of the inhibitor in other sub-sites.…”

Section: Discussionmentioning

confidence: 99%

Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor

Fang

Han

Wang

et al. 2015

Chemistry & Biology

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Summary Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits P. falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves the specificity is unknown. Here we report 3 crystal structures of cladosporin with human LysRS, PfLysRS, and a Pf-like human LysRS mutant. In all 3 structures, cladosporin occupies the class defining ATP-binding pocket, replacing the adenosine portion of ATP. Three residues holding the methyltetrahydro-pyran moiety of cladosporin are critical for cladosporin's specificity against LysRS over other class II tRNA synthetase families. The species-exclusive inhibition of PfLysRS is linked to a structural divergence beyond the active site that mounts a lysine-specific stabilizing response to binding cladosporin. These analyses reveal that inherent divergence of tRNA synthetase structural assembly may allow for highly specific inhibition even through the otherwise universal substrate binding pocket and highlight the potential for structure driven drug development.

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“…It is worth noting that inhibitors targeting multiple substrate binding pockets in aaRS are common. For example, naturally occurring LeuRS inhibitor mupiricin [50] or synthetic inhibitors of ThrRS [51] bind to both amino acid and ATP pockets to derive high binding affinity, and could serve as inspiration to develop HisRS inhibitors.…”

Section: Resultsmentioning

confidence: 99%

Comparison of histidine recognition in human and trypanosomatid histidyl-tRNA synthetases

et al. 2014

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As part of a project aimed at obtaining selective inhibitors and drug-like compounds targeting tRNA synthetases from trypanosomatids, we have elucidated the crystal structure of human cytosolic histidyl-tRNA synthetase (Hs-cHisRS) in complex with histidine in order to be able to compare human and parasite enzymes. The resultant structure of Hs-cHisRS·His represents the substrate-bound state (H-state) of the enzyme. It provides an interesting opportunity to compare with ligand-free and imidazole-bound structures Hs-cHisRS published recently, both of which represent the ligand-free state (F-state) of the enzyme. The H-state Hs-cHisRS undergoes conformational changes in active site residues and several conserved motif of HisRS, compared to F-state structures. The histidine forms eight hydrogen bonds with HisRS of which six engage the amino and carboxylate groups of this amino acid. The availability of published imidazole-bound structure provides a unique opportunity to dissect the structural roles of individual chemical groups of histidine. Remarkably, the analysis revealed the importance of the amino and carboxylate groups, of the histidine in leading to these dramatic conformational changes of the H-state. Further, comparison with previously published trypanosomatid HisRS structures reveals a pocket in the F-state of the parasite enzyme that may provide opportunities for developing specific inhibitors of Trypanosoma brucei HisRS.

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Identification of Bacteria-Selective Threonyl-tRNA Synthetase Substrate Inhibitors by Structure-Based Design

Cited by 45 publications

References 33 publications

Identifying the targets of aminoacyl-tRNA synthetase inhibitors by primer extension inhibition

Identifying the targets of aminoacyl-tRNA synthetase inhibitors by primer extension inhibition

Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor

Comparison of histidine recognition in human and trypanosomatid histidyl-tRNA synthetases

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