6M0T image
Entry Detail
PDB ID:
6M0T
Title:
Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Cladosporin derivative (CL-2)
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2020-02-22
Release Date:
2021-04-21
Method Details:
Experimental Method:
Resolution:
2.68 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Lysine--tRNA ligase
Chain IDs:A, B, C, D
Chain Length:507
Number of Molecules:4
Biological Source:Plasmodium falciparum 3D7
Primary Citation
Design, Synthesis, and Structural Analysis of Cladosporin-Based Inhibitors of Malaria Parasites.
Acs Infect Dis. 7 1777 1794 (2021)
PMID: 33843204 DOI: 10.1021/acsinfecdis.1c00092

Abstact

Here we have described a systematic structure activity relationship (SAR) of a set of compounds inspired from cladosporin, a tool compound that targets parasite (Plasmodium falciparum) lysyl tRNA synthetase (KRS). Four sets of analogues, synthesized based on point changes in the chemical scaffold of cladosporin and other logical modifications and hybridizations, were assessed using high throughput enzymatic and parasitic assays along with in vitro pharmacokinetics. Co-crystallization of the most potent compound in our series (CL-2) with PfKRS revealed its structural basis of enzymatic binding and potency. Further, we report that CL-2 has performed better than cladosporin in terms of metabolic stability. It thus represents a new lead for further optimization toward the development of antimalarial drugs. Collectively, along with a lead compound, the series offers insights on how even the slightest chemical modification might play an important role in enhancing or decreasing the potency of a chemical scaffold.

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