5BRH

Crystal structure of Trypanosoma cruzi glucokinase in complex with inhibitor DBT-GlcN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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This is version 1.5 of the entry. See complete history


Literature

Structure-based approach to the identification of a novel group of selective glucosamine analogue inhibitors of Trypanosoma cruzi glucokinase.

D'Antonio, E.L.Deinema, M.S.Kearns, S.P.Frey, T.A.Tanghe, S.Perry, K.Roy, T.A.Gracz, H.S.Rodriguez, A.D'Antonio, J.

(2016) Mol Biochem Parasitol 204: 64-76

  • DOI: 10.1016/j.molbiopara.2015.12.004
  • Primary Citation of Related Structures:  
    5BRD, 5BRE, 5BRF, 5BRH

  • PubMed Abstract: 
  • Glucokinase and hexokinase from pathogenic protozoa Trypanosoma cruzi are potential drug targets for antiparasitic chemotherapy of Chagas' disease. These glucose kinases phosphorylate d-glucose with co-substrate ATP and yield glucose 6-phosphate and are involved in essential metabolic pathways, such as glycolysis and the pentose phosphate pathway ...

    Glucokinase and hexokinase from pathogenic protozoa Trypanosoma cruzi are potential drug targets for antiparasitic chemotherapy of Chagas' disease. These glucose kinases phosphorylate d-glucose with co-substrate ATP and yield glucose 6-phosphate and are involved in essential metabolic pathways, such as glycolysis and the pentose phosphate pathway. An inhibitor class was conceived that is selective for T. cruzi glucokinase (TcGlcK) using structure-based drug design involving glucosamine having a linker from the C2 amino that terminates with a hydrophobic group either being phenyl, p-hydroxyphenyl, or dioxobenzo[b]thiophenyl groups. The synthesis and characterization for two of the four compounds are presented while the other two compounds were commercially available. Four high-resolution X-ray crystal structures of TcGlcK inhibitor complexes are reported along with enzyme inhibition constants (Ki) for TcGlcK and Homo sapiens hexokinase IV (HsHxKIV). These glucosamine analogue inhibitors include three strongly selective TcGlcK inhibitors and a fourth inhibitor, benzoyl glucosamine (BENZ-GlcN), which is a similar variant exhibiting a shorter linker. Carboxybenzyl glucosamine (CBZ-GlcN) was found to be the strongest glucokinase inhibitor known to date, having a Ki of 0.71±0.05μM. Also reported are two biologically active inhibitors against in vitro T. cruzi culture that were BENZ-GlcN and CBZ-GlcN, with intracellular amastigote growth inhibition IC50 values of 16.08±0.16μM and 48.73±0.69μM, respectively. These compounds revealed little to no toxicity against mammalian NIH-3T3 fibroblasts and provide a key starting point for further drug development with this class of compound.


    Organizational Affiliation

    Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucokinase 1, putativeA, B381Trypanosoma cruzi strain CL BrenerMutation(s): 0 
Gene Names: Tc00.1047053510187.100
EC: 2.7.1.2
UniProt
Find proteins for Q4E4E1 (Trypanosoma cruzi (strain CL Brener))
Explore Q4E4E1 
Go to UniProtKB:  Q4E4E1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4V3 (Subject of Investigation/LOI)
Query on 4V3

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]2-deoxy-2-({[(1,1-dioxido-1-benzothiophen-2-yl)methoxy]carbonyl}amino)-beta-D-glucopyranose
C16 H19 N O9 S
ACIPDYFLRJNHEW-DIAXPKBXSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4V3 Binding MOAD:  5BRH Ki: 4100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.245α = 90
b = 78.744β = 94.8
c = 75.389γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103499
University of South Carolina Office of the Vice President for ResearchUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-12-23
    Changes: Database references
  • Version 1.2: 2016-02-03
    Changes: Database references
  • Version 1.3: 2016-02-10
    Changes: Database references
  • Version 1.4: 2017-09-27
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Refinement description
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence