5MVC

Crystal structure of potent human Dihydroorotate Dehydrogenase inhibitors based on hydroxylated azole scaffolds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Design, synthesis, biological evaluation and X-ray structural studies of potent human dihydroorotate dehydrogenase inhibitors based on hydroxylated azole scaffolds.

Sainas, S.Pippione, A.C.Giorgis, M.Lupino, E.Goyal, P.Ramondetti, C.Buccinna, B.Piccinini, M.Braga, R.C.Andrade, C.H.Andersson, M.Moritzer, A.C.Friemann, R.Mensa, S.Al-Kadaraghi, S.Boschi, D.Lolli, M.L.

(2017) Eur J Med Chem 129: 287-302

  • DOI: 10.1016/j.ejmech.2017.02.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A new generation of potent hDHODH inhibitors designed by a scaffold-hopping replacement of the quinolinecarboxylate moiety of brequinar, one of the most potent known hDHODH inhibitors, is presented here. Their general structure is characterized by a ...

    A new generation of potent hDHODH inhibitors designed by a scaffold-hopping replacement of the quinolinecarboxylate moiety of brequinar, one of the most potent known hDHODH inhibitors, is presented here. Their general structure is characterized by a biphenyl moiety joined through an amide bridge with an acidic hydroxyazole scaffold (hydroxylated thiadiazole, pyrazole and triazole). Molecular modelling suggested that these structures should adopt a brequinar-like binding mode involving interactions with subsites 1, 2 and 4 of the hDHODH binding site. Initially, the inhibitory activity of the compounds was studied on recombinant hDHODH. The most potent compound of the series in the enzymatic assays was the thiadiazole analogue 4 (IC 50 16 nM). The activity was found to be dependent on the fluoro substitution pattern at the biphenyl moiety as well as on the choice/substitution of the heterocyclic ring. Structure determination of hDHODH co-crystallized with one representative compound from each series (4, 5 and 6) confirmed the brequinar-like binding mode as suggested by modelling. The specificity of the observed effects of the compound series was tested in cell-based assays for antiproliferation activity using Jurkat cells and PHA-stimulated PBMC. These tests were also verified by addition of exogenous uridine to the culture medium. In particular, the triazole analogue 6 (IC 50 against hDHODH: 45 nM) exerted potent in vitro antiproliferative and immunosuppressive activity without affecting cell survival.


    Organizational Affiliation

    LabMol, Faculty of Pharmacy, Federal University of Goias, 74605-170 Goiania, Brazil.,Department of Science and Drug Technology, University of Torino, via Pietro Giuria 9, 10125 Torino, Italy. Electronic address: marco.lolli@unito.it.,Department of Science and Drug Technology, University of Torino, via Pietro Giuria 9, 10125 Torino, Italy.,Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Gothenburg Sweden; Department of Structural Biology, Stanford University School of Medicine, 299 Campus Drive West Stanford, CA 94305-5126, USA.,Department of Oncology, University of Torino, via Michelangelo 27/B, 10126 Torino, Italy.,Stephenson Institute for Renewable Energy, Department of Chemistry, University of Liverpool, L69 7ZF Liverpool, UK.,Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Gothenburg Sweden; Department of Chemistry, Biochemistry, University of Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany.,Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Gothenburg Sweden.,Department of Biochemistry and Structural Biology, Lund University, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase (quinone), mitochondrial
A
390Homo sapiensMutation(s): 0 
Gene Names: DHODH
EC: 1.3.5.2
Find proteins for Q02127 (Homo sapiens)
Go to Gene View: DHODH
Go to UniProtKB:  Q02127
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y9B
Query on Y9B

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A
4-oxidanyl-~{N}-[2,3,5,6-tetrakis(fluoranyl)-4-phenyl-phenyl]-1,2,5-thiadiazole-3-carboxamide
C15 H7 F4 N3 O2 S
UCKLLJALHASQDA-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN

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A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ORO
Query on ORO

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A
OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Y9BIC50: 16 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.162 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.190α = 90.00
b = 91.190β = 90.00
c = 122.645γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release