9VCI
Crystal structure of Escherichia coli tryptophanyl-tRNA synthetase in complex with an inhibitor
This is a non-PDB format compatible entry.
Summary for 9VCI
| Entry DOI | 10.2210/pdb9vci/pdb |
| Descriptor | Tryptophan--tRNA ligase, ~{N}-[[5-[4-(6-azanyl-8-oxidanylidene-9-piperidin-4-yl-purin-7-yl)phenoxy]-2-fluoranyl-4-oxidanyl-phenyl]methyl]ethanamide, SULFATE ION, ... (6 entities in total) |
| Functional Keywords | tryptophanyl-trna synthetase, an inhibitor, complex, lyase |
| Biological source | Escherichia coli |
| Total number of polymer chains | 2 |
| Total formula weight | 78438.30 |
| Authors | |
| Primary citation | Xia, K.,Peng, X.,Xiao, L.,Huang, Q.,Xu, J.,Chen, B.,Zhou, H. Structure-based design of tirabrutinib derivatives as inhibitors of bacterial tryptophanyl-tRNA synthetase. Bioorg.Chem., 165:108978-108978, 2025 Cited by PubMed Abstract: The escalating threat of antibiotic resistance poses a critical challenge to global public health, necessitating the urgent development of novel therapeutic agents with distinct mechanisms of action and unique structural scaffolds. Tryptophanyl-tRNA synthetase (TrpRS) has emerged as a promising antibacterial target. Our previous study demonstrated that the clinically utilized Bruton's tyrosine kinase (BTK) inhibitor tirabrutinib, along with several of its analogues, can simultaneously occupy both the substrates l-Trp and tRNA A76 binding sites of Escherichia coli tryptophanyl-tRNA synthetase (EcTrpRS), thereby effectively inhibiting its catalytic activity. Building on this finding, we employed structure-based drug design to systematically optimize the interactions of tirabrutinib analogues with the l-Trp and tRNA binding sites, as well as to further extend the structure to the adjacent ATP binding site within the catalytic pocket of EcTrpRS to establish additional interactions, leading to the design and synthesis of 22 new derivatives. Among these, WRS22 (a racemic mixture) demonstrated the best binding to EcTrpRS, with a ΔT value of 33.2 °C and 90 % inhibition rate at 10 μM concentration. Its binding affinity for EcTrpRS (K = 0.33 ± 0.03 μM) is superior to that of the positive control, indolmycin (K = 0.71 ± 0.1 μM). Notably, WRS22 displayed no affinity to human cytoplasmic TrpRS (HcTrpRS) and its interaction with human BTK is likely to be disrupted, indicating high degree of target selectivity. Therefore, the structure-guided design successfully developed new tirabrutinib analogues as inhibitors of bacterial TrpRS, presenting a promising lead compound for the development of AARS-based antibacterial agents. PubMed: 40945024DOI: 10.1016/j.bioorg.2025.108978 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.88 Å) |
Structure validation
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