7BT5

Crystal structure of plasmodium LysRS complexing with an antitumor compound

Summary for 7BT5

• Entry DOI: 10.2210/pdb7bt5/pdb
• Descriptor: Lysine--tRNA ligase, LYSINE, N4-[2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]-N2-(2-propan-2-ylsulfonylphenyl)-1,3,5-triazine-2,4-diamine, ... (4 entities in total)
• Functional Keywords: protein translation, lysyl-trna synthetase, ligase
• Biological source: Plasmodium falciparum
• Total number of polymer chains: 2
• Total formula weight: 121018.15

Authors

Zhou, J.,Wang, J.,Fang, P. (deposition date: 2020-03-31, release date: 2020-09-30, Last modification date: 2024-11-20)

Primary citation

Zhou, J.,Huang, Z.,Zheng, L.,Hei, Z.,Wang, Z.,Yu, B.,Jiang, L.,Wang, J.,Fang, P.
Inhibition of Plasmodium falciparum Lysyl-tRNA synthetase via an anaplastic lymphoma kinase inhibitor.
Nucleic Acids Res., 48:11566-11576, 2020

PubMed Abstract: Aminoacyl-tRNA synthetases are attractive targets for the development of antibacterial, antifungal, antiparasitic agents and for the treatment of other human diseases. Lysyl-tRNA synthetase (LysRS) from this family has been validated as a promising target for the development of antimalarial drugs. Here, we developed a high-throughput compatible assay and screened 1215 bioactive compounds to identify Plasmodium falciparum cytoplasmic LysRS (PfLysRS) inhibitor. ASP3026, an anaplastic lymphoma kinase inhibitor that was used in clinical trials for the treatment of B-cell lymphoma and solid tumors, was identified as a novel PfLysRS inhibitor. ASP3026 suppresses the enzymatic activity of PfLysRS at nanomolar potency, which is >380-fold more effective than inhibition of the human counterpart. In addition, the compound suppressed blood-stage P. falciparum growth. To understand the molecular mechanism of inhibition by ASP3026, we further solved the cocrystal structure of PfLysRS-ASP3026 at a resolution of 2.49 Å, providing clues for further optimization of the compound. Finally, primary structure-activity relationship analyses indicated that the inhibition of PfLysRS by ASP3026 is highly structure specific. This work not only provides a new chemical scaffold with good druggability for antimalarial development but also highlights the potential for repurposing kinase-inhibiting drugs to tRNA synthetase inhibitors to treat human diseases.

PubMed: 33053158
DOI: 10.1093/nar/gkaa862

Experimental method

X-RAY DIFFRACTION (2.493 Å)