7QRC

X-ray structure of Trypanosoma cruzi PEX14 in complex with a PEX5-PEX14 PPI inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.272 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-based design, synthesis and evaluation of a novel family of PEX5-PEX14 interaction inhibitors against Trypanosoma.

Napolitano, V.Mroz, P.Marciniak, M.Kalel, V.C.Softley, C.A.Janna Olmos, J.D.Tippler, B.G.Schorpp, K.Rioton, S.Frohlich, T.Plettenburg, O.Hadian, K.Erdmann, R.Sattler, M.Popowicz, G.M.Dawidowski, M.Dubin, G.

(2022) Eur J Med Chem 243: 114778-114778

  • DOI: https://doi.org/10.1016/j.ejmech.2022.114778
  • Primary Citation of Related Structures:  
    7QRC

  • PubMed Abstract: 

    Trypanosomiases are neglected tropical diseases caused by Trypanosoma (sub)species. Available treatments are limited and have considerable adverse effects and questionable efficacy in the chronic stage of the disease, urgently calling for the identification of new targets and drug candidates. Recently, we have shown that impairment of glycosomal protein import by the inhibition of the PEX5-PEX14 protein-protein interaction (PPI) is lethal to Trypanosoma. Here, we report the development of a novel dibenzo[b,f][1,4]oxazepin-11(10H)-one scaffold for small molecule inhibitors of PEX5-PEX14 PPI. The initial hit was identified by a high throughput screening (HTS) of a library of compounds. A bioisosteric replacement approach allowed to replace the metabolically unstable sulphur atom from the initial dibenzo[b,f][1,4]thiazepin-11(10H)-one HTS hit with oxygen. A crystal structure of the hit compound bound to PEX14 surface facilitated the rational design of the compound series accessible by a straightforward chemistry for the initial structure-activity relationship (SAR) analysis. This guided the design of compounds with trypanocidal activity in cell-based assays providing a promising starting point for the development of new drug candidates to tackle trypanosomiases.


  • Organizational Affiliation

    Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland. Electronic address: valeria.napolitano@helmholtz-muenchen.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxin-14A [auth B],
B [auth A]
66Trypanosoma cruziMutation(s): 0 
Gene Names: C3747_80g13
UniProt
Find proteins for Q4D1H5 (Trypanosoma cruzi (strain CL Brener))
Explore Q4D1H5 
Go to UniProtKB:  Q4D1H5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4D1H5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ET7 (Subject of Investigation/LOI)
Query on ET7

Download Ideal Coordinates CCD File 
D [auth B],
E [auth A]
~{N}-(5-ethyl-6-oxidanylidene-benzo[b][1,4]benzothiazepin-2-yl)-2-(4-fluorophenyl)ethanamide
C23 H19 F N2 O2 S
HMFFZASNCXIJTL-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.272 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.538α = 90
b = 25.416β = 105.56
c = 56.031γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Accelerated Early staGe drug dIScovery (AEGIS)European Union675555

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description