8D22

Crystal structure of Plasmodium falciparum GRP78-NBD in complex with Piclidenoson


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A non-traditional crystal-based compound screening method targeting the ATP binding site of Plasmodium falciparum GRP78 for identification of novel nucleoside analogues.

Mrozek, A.Antoshchenko, T.Chen, Y.Zepeda-Velazquez, C.Smil, D.Kumar, N.Lu, H.Park, H.W.

(2022) Front Mol Biosci 9: 956095-956095

  • DOI: https://doi.org/10.3389/fmolb.2022.956095
  • Primary Citation of Related Structures:  
    8D1P, 8D1Q, 8D1S, 8D1Y, 8D20, 8D22, 8D24

  • PubMed Abstract: 

    Drug resistance to front-line malarial treatments represents an ongoing threat to control malaria, a vector borne infectious disease. The malarial parasite, Plasmodium falciparum has developed genetic variants, conferring resistance to the current standard therapeutic artemisinin and its derivatives commonly referred to as artemisinin-combination therapies (ACTs). Emergence of multi-drug resistance parasite genotypes is a warning of potential treatment failure, reaffirming the urgent and critical need to find and validate alternate drug targets to prevent the spread of disease. An attractive and novel drug target includes glucose-regulated protein 78 kDa (GRP78, or BiP), an essential molecular chaperone protein involved in the unfolded protein response that is upregulated in ACT treated P. falciparum parasites. We have shown that both sequence and structure are closely related to human GRP78 (hGRP78), a chaperone belonging to the HSP70 class of ATPase proteins, which is often upregulated in cellular stress responses and cancer. By screening a library of nucleoside analogues, we identified eight 'hit' compounds binding at the active site of the ATP binding domain of P. falciparum GRP78 using a high-throughput ligand soaking screen using x-ray crystallography. These compounds were further evaluated using protein thermal shift assays to assess target binding activity. The nucleoside analogues identified from our screen provide a starting point for the development of more potent and selective antimalarial inhibitors. In addition, we have established a well-defined, high-throughput crystal-based screening approach that can be applied to many crystallizable P. falciparum proteins for generating anti- Plasmodium specific compounds.


  • Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperone DnaK397Plasmodium falciparum Palo Alto/UgandaMutation(s): 0 
Gene Names: PFUGPA_02944
UniProt
Find proteins for W4J0F1 (Plasmodium falciparum (isolate Palo Alto / Uganda))
Explore W4J0F1 
Go to UniProtKB:  W4J0F1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW4J0F1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.277α = 90
b = 84.277β = 90
c = 292.195γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-12-13
    Changes: Database references