6GOU

Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

Starting Model: experimental
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Literature

Development of alkyl glycerone phosphate synthase inhibitors: Structure-activity relationship and effects on ether lipids and epithelial-mesenchymal transition in cancer cells.

Stazi, G.Battistelli, C.Piano, V.Mazzone, R.Marrocco, B.Marchese, S.Louie, S.M.Zwergel, C.Antonini, L.Patsilinakos, A.Ragno, R.Viviano, M.Sbardella, G.Ciogli, A.Fabrizi, G.Cirilli, R.Strippoli, R.Marchetti, A.Tripodi, M.Nomura, D.K.Mattevi, A.Mai, A.Valente, S.

(2018) Eur J Med Chem 163: 722-735

  • DOI: https://doi.org/10.1016/j.ejmech.2018.11.050
  • Primary Citation of Related Structures:  
    6GOU

  • PubMed Abstract: 

    In aggressive tumors, alkylglyceronephosphate synthase (AGPS) controls cellular ether phospholipid utilization and metabolism to promote cancer cell proliferation and motility. SAR studies on the first-in-class AGPS inhibitor 1, discovered by our group, led to the 2,6-difluoro analog 2i which showed higher binding affinity than 1in vitro. In 231MFP cancer cells, 2i reduced ether lipids levels and cell migration rate. When tested in PC-3 and MDA-MB-231 cancer cells, 2i specifically impaired epithelial to mesenchymal transition (EMT) by modulating E-cadherin, Snail and MMP2 expression levels. Moreover, the combination of siRNAs against AGPS and 2i provided no additive effect, confirming that the modulation of 2i on EMT specifically relies on AGPS inhibition. Finally, this compound also affected cancer cell proliferation especially in MDA-MB-231 cells expressing higher AGPS level, whereas it provided negligible effects on MeT5A, a non-tumorigenic cell line, thus showing cancer specificity.


  • Organizational Affiliation

    Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alkyldihydroxyacetonephosphate synthase, peroxisomalA [auth D],
B [auth A],
C [auth B],
D [auth C]
658Cavia porcellusMutation(s): 0 
Gene Names: AGPS
EC: 2.5.1.26
UniProt
Find proteins for P97275 (Cavia porcellus)
Explore P97275 
Go to UniProtKB:  P97275
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97275
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.958α = 90
b = 120.644β = 95.27
c = 148.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyFellowship 18022

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description