7WMI image
Entry Detail
PDB ID:
7WMI
Title:
Threonyl-tRNA synthetase from Salmonella enterica in complex with an inhibitor
Biological Source:
PDB Version:
Deposition Date:
2022-01-14
Release Date:
2022-04-27
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Threonine--tRNA ligase
Chain IDs:A, B
Chain Length:411
Number of Molecules:2
Biological Source:Salmonella enterica subsp. enterica serovar Cubana str. 76814
Primary Citation
Design, Synthesis, and Proof-of-Concept of Triple-Site Inhibitors against Aminoacyl-tRNA Synthetases.
J.Med.Chem. 65 5800 5820 (2022)
PMID: 35363470 DOI: 10.1021/acs.jmedchem.2c00134

Abstact

Aminoacyl-tRNA synthetases (aaRSs) are promising drug targets due to their essential roles in protein translation. Although current inhibitors primarily occupy one or two of the three substrate binding sites on aaRSs, we report here the structure-based design of the first class of triple-site aaRS inhibitors by targeting Salmonella enterica threonyl-tRNA synthetase (SeThrRS). Competition of our compounds with all three substrates on SeThrRS binding was confirmed via isothermal titration calorimetry assays. Cocrystal structures of three compounds bound to SeThrRS unambiguously confirmed their substrate-mimicking triple-site binding mode. Compound 36j exhibited the best enzyme activity against SeThrRS with IC50 = 19 nM and Kd = 35.4 nM. Compounds 36b, 36k, and 36l exhibited antibacterial activities with minimum inhibitory concentration values of 2-8 μg/mL against the tested bacteria, which are superior to those of the reported dual-site ThrRS inhibitors. Our study provides the first proof-of-concept for developing triple-site inhibitors against aaRSs, inspiring future aaRS-based drug discoveries.

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