7Y1H image
Entry Detail
PDB ID:
7Y1H
Title:
Controlling fibrosis using compound with novel binding mode to prolyl-tRNA synthetase 1
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2022-06-08
Release Date:
2023-07-05
Method Details:
Experimental Method:
Resolution:
1.99 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Bifunctional glutamate/proline--tRNA ligase
Chain IDs:A, B
Chain Length:512
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Control of fibrosis with enhanced safety via asymmetric inhibition of prolyl-tRNA synthetase 1.
Embo Mol Med 15 e16940 e16940 (2023)
PMID: 37212275 DOI: 10.15252/emmm.202216940

Abstact

Prolyl-tRNA synthetase 1 (PARS1) has attracted much interest in controlling pathologic accumulation of collagen containing high amounts of proline in fibrotic diseases. However, there are concerns about its catalytic inhibition for potential adverse effects on global protein synthesis. We developed a novel compound, DWN12088, whose safety was validated by clinical phase 1 studies, and therapeutic efficacy was shown in idiopathic pulmonary fibrosis model. Structural and kinetic analyses revealed that DWN12088 binds to catalytic site of each protomer of PARS1 dimer in an asymmetric mode with different affinity, resulting in decreased responsiveness at higher doses, thereby expanding safety window. The mutations disrupting PARS1 homodimerization restored the sensitivity to DWN12088, validating negative communication between PARS1 promoters for the DWN12088 binding. Thus, this work suggests that DWN12088, an asymmetric catalytic inhibitor of PARS1 as a novel therapeutic agent against fibrosis with enhanced safety.

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