6I4B

Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) co-crystallized with 3-Hydroxy-1-methyl-5-((3-(trifluoromethyl)phenoxy)methyl)-1H-pyrazole-4-carboxylic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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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: 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 ...

    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. Electronic address: marco.lolli@unito.it.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenaseA, B405Plasmodium falciparumMutation(s): 0 
Gene Names: dhod
EC: 1.3.5.2
Membrane Entity: Yes 
UniProt
Find proteins for Q08210 (Plasmodium falciparum (isolate 3D7))
Explore Q08210 
Go to UniProtKB:  Q08210
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08210
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
E2N (Subject of Investigation/LOI)
Query on E2N
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]		1-methyl-3-oxidanyl-5-[[3-(trifluoromethyl)phenoxy]methyl]pyrazole-4-carboxylic acid
C13 H11 F3 N2 O4
ZOSMQYUVHWSYCZ-UHFFFAOYSA-N		 Ligand Interaction
ORO
Query on ORO
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]		OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
E2N Binding MOAD:  6I4B IC50: 2800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.607α = 90
b = 158.121β = 105.67
c = 61.753γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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