6I55

Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) co-crystallized with N-(2,2-Diphenylethyl)-4-hydroxy-1,2,5-thiadiazole-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Hydroxyazole scaffold-based Plasmodium falciparum dihydroorotate dehydrogenase inhibitors: Synthesis, biological evaluation and X-ray structural studies.

Pippione, A.C.Sainas, S.Goyal, P.Fritzson, I.Cassiano, G.C.Giraudo, A.Giorgis, M.Tavella, T.A.Bagnati, R.Rolando, B.Caing-Carlsson, R.Costa, F.T.M.Andrade, C.H.Al-Karadaghi, S.Boschi, D.Friemann, R.Lolli, M.L.

(2018) Eur J Med Chem 163: 266-280

  • DOI: https://doi.org/10.1016/j.ejmech.2018.11.044
  • Primary Citation of Related Structures:  
    6I4B, 6I55

  • PubMed Abstract: 

    Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) has been clinically validated as a target for antimalarial drug discovery, as a triazolopyrimidine class inhibitor (DSM265) is currently undergoing clinical development. Here, we have identified new hydroxyazole scaffold-based PfDHODH inhibitors belonging to two different chemical series. The first series was designed by a scaffold hopping strategy that exploits the use of hydroxylated azoles. Within this series, the hydroxythiadiazole 3 was identified as the best selective PfDHODH inhibitor (IC 50 12.0 μM). The second series was designed by modulating four different positions of the hydroxypyrazole scaffold. In particular, hydroxypyrazoles 7e and 7f were shown to be active in the low μM range (IC 50 2.8 and 5.3 μM, respectively). All three compounds, 3, 7e and 7f showed clear selectivity over human DHODH (IC 50  > 200 μM), low cytotoxicity, and retained micromolar activity in P. falciparum-infected erythrocytes. The crystallographic structures of PfDHODH in complex with compounds 3 and 7e proved their binding mode, supplying essential data for future optimization of these scaffolds.


  • Organizational Affiliation

    Department of Science and Drug Technology, University of Turin, via Pietro Giuria 9, 10125, Turin, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase
A, B
405Plasmodium falciparumMutation(s): 0 
Gene Names: dhod
UniProt
Find proteins for Q54A96 (Plasmodium falciparum)
Explore Q54A96 
Go to UniProtKB:  Q54A96
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54A96
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.842α = 90
b = 158.422β = 106.56
c = 62.252γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release