8QIC

Structure-based identification of salicylic acid derivatives as malarial threonyl tRNA-synthetase inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 


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Literature

Structure-based identification of salicylic acid derivatives as malarial threonyl tRNA-synthetase inhibitors.

Bobrovs, R.Bolsakova, J.Buitrago, J.A.R.Varaceva, L.Skvorcova, M.Kanepe, I.Rudnickiha, A.Parisini, E.Jirgensons, A.

(2024) PLoS One 19: e0296995-e0296995

  • DOI: https://doi.org/10.1371/journal.pone.0296995
  • Primary Citation of Related Structures:  
    8QIC

  • PubMed Abstract: 

    Emerging resistance to existing antimalarial drugs drives the search for new antimalarials, and protein translation is a promising pathway to target. Threonyl t-RNA synthetase (ThrRS) is one of the enzymes involved in this pathway, and it has been validated as an anti-malarial drug target. Here, we present 9 structurally diverse low micromolar Plasmodium falciparum ThrRS inhibitors that were identified using high-throughput virtual screening (HTVS) and were verified in a FRET enzymatic assay. Salicylic acid-based compound (LE = 0.34) was selected as a most perspective hit and was subjected to hit-to-lead optimisation. A total of 146 hit analogues were synthesised or obtained from commercial vendors and were tested. Structure-activity relationship study was supported by the crystal structure of the complex of a salicylic acid analogue with a close homologue of the plasmodium target, E. coli ThrRS (EcThrRS). Despite the availability of structural information, the hit identified via virtual screening remained one of the most potent PfThrRS inhibitors within this series. However, the compounds presented herein provide novel scaffolds for ThrRS inhibitors, which could serve as starting points for further medicinal chemistry projects targeting ThrRSs or structurally similar enzymes.


  • Organizational Affiliation

    Latvian Institute of Organic Synthesis, Riga, Latvia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Threonine--tRNA ligaseA,
B [auth D]
400Escherichia coli IAI1Mutation(s): 0 
Gene Names: thrS
UniProt
Find proteins for P0A8M3 (Escherichia coli (strain K12))
Explore P0A8M3 
Go to UniProtKB:  P0A8M3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8M3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VL0 (Subject of Investigation/LOI)
Query on VL0

Download Ideal Coordinates CCD File 
C [auth A],
F [auth D]
2-oxidanyl-5-[[4-(phenylmethyl)phenyl]sulfamoyl]benzoic acid
C20 H17 N O5 S
RLHVRGDXIJZLQC-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
G [auth D],
H [auth D],
I [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
J [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.78α = 90
b = 110.5β = 90
c = 113.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Regional Development FundEuropean Union1.1.1.1/19/A/019

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release