7P3S

Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Synthesis, structure-activity relationships, cocrystallization and cellular characterization of novel smHDAC8 inhibitors for the treatment of schistosomiasis.

Ghazy, E.Heimburg, T.Lancelot, J.Zeyen, P.Schmidtkunz, K.Truhn, A.Darwish, S.Simoben, C.V.Shaik, T.B.Erdmann, F.Schmidt, M.Robaa, D.Romier, C.Jung, M.Pierce, R.Sippl, W.

(2021) Eur J Med Chem 225: 113745-113745

  • DOI: https://doi.org/10.1016/j.ejmech.2021.113745
  • Primary Citation of Related Structures:  
    7P3S

  • PubMed Abstract: 

    Schistosomiasis is a major neglected parasitic disease that affects more than 265 million people worldwide and for which the control strategy consists of mass treatment with the only available drug, praziquantel. In this study, we chemically optimized our previously reported benzhydroxamate-based inhibitors of Schistosoma mansoni histone deacetylase 8 (smHDAC8). Crystallographic analysis provided insights into the inhibition mode of smHDAC8 activity by the highly potent inhibitor 5o. Structure-based optimization of the novel inhibitors was carried out using the available crystal structures as well as docking studies on smHDAC8. The compounds were evaluated in screens for inhibitory activity against schistosome and human HDACs (hHDAC). The in vitro and docking results were used for detailed structure activity relationships. The synthesized compounds were further investigated for their lethality against the schistosome larval stage using a fluorescence-based assay. The most promising inhibitor 5o showed significant dose-dependent killing of the schistosome larvae and markedly impaired egg laying of adult worm pairs maintained in culture.


  • Organizational Affiliation

    Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120, Halle/Saale, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase
A, B, C, D
447Schistosoma mansoniMutation(s): 0 
Gene Names: HDAC8
UniProt
Find proteins for A5H660 (Schistosoma mansoni)
Explore A5H660 
Go to UniProtKB:  A5H660
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5H660
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5IB (Subject of Investigation/LOI)
Query on 5IB

Download Ideal Coordinates CCD File 
K [auth A],
L [auth B],
Q [auth C],
W [auth D]
~{N}-[2-methoxy-5-(oxidanylcarbamoyl)phenyl]dibenzofuran-4-carboxamide
C21 H16 N2 O5
RFROQVRGDKTHLN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
H [auth A]
I [auth A]
J [auth A]
AA [auth D],
BA [auth D],
H [auth A],
I [auth A],
J [auth A],
P [auth B],
U [auth C],
V [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
M [auth B],
R [auth C],
X [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
N [auth B]
O [auth B]
S [auth C]
F [auth A],
G [auth A],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
Y [auth D],
Z [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.39α = 78.05
b = 70.39β = 75.57
c = 97.94γ = 85.69
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Communitys Seventh Framework ProgrammeEuropean Union241865
European Communitys Seventh Framework ProgrammeEuropean Union602080

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description