8QJI

Crystal structure of GSK3b in complex with N-(4-(5-(1,2,4-oxadiazol-3-yl)thiophen-2-yl)pyridin-2-yl)cyclopropanecarboxamide inhibitor (TW362)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.253 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Exploring Novel GSK-3 beta Inhibitors for Anti-Neuroinflammatory and Neuroprotective Effects: Synthesis, Crystallography, Computational Analysis, and Biological Evaluation.

Goral, I.Wichur, T.Slugocka, E.Grygier, P.Gluch-Lutwin, M.Mordyl, B.Honkisz-Orzechowska, E.Szalaj, N.Godyn, J.Panek, D.Zareba, P.Sarka, A.Zmudzki, P.Latacz, G.Pustelny, K.Bucki, A.Czarna, A.Menezes, F.Wieckowska, A.

(2024) ACS Chem Neurosci 15: 3181-3201

  • DOI: https://doi.org/10.1021/acschemneuro.4c00365
  • Primary Citation of Related Structures:  
    8QJI

  • PubMed Abstract: 

    In the pathogenesis of Alzheimer's disease, the overexpression of glycogen synthase kinase-3β (GSK-3β) stands out due to its multifaced nature, as it contributes to the promotion of amyloid β and tau protein accumulation, as well as neuroinflammatory processes. Therefore, in the present study, we have designed, synthesized, and evaluated a new series of GSK-3β inhibitors based on the N -(pyridin-2-yl)cyclopropanecarboxamide scaffold. We identified compound 36 , demonstrating an IC 50 of 70 nM against GSK-3β. Subsequently, through crystallography studies and quantum mechanical analysis, we elucidated its binding mode and identified the structural features crucial for interactions with the active site of GSK-3β, thereby understanding its inhibitory potency. Compound 36 was effective in the cellular model of hyperphosphorylated tau-induced neurodegeneration, where it restored cell viability after okadaic acid treatment and showed anti-inflammatory activity in the LPS model, significantly reducing NO, IL-6, and TNF-α release. In ADME-tox in vitro studies, we confirmed the beneficial profile of 36, including high permeability in PAMPA ( Pe equals 9.4) and high metabolic stability in HLMs as well as lack of significant interactions with isoforms of the CYP enzymes and lack of considerable cytotoxicity on selected cell lines (IC 50 > 100 μM on HT-22 cells and 89.3 μM on BV-2 cells). Based on promising pharmacological activities and favorable ADME-tox properties, compound 36 may be considered a promising candidate for in vivo research as well as constitute a reliable starting point for further studies.


  • Organizational Affiliation

    Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., Krakow 30-688, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen synthase kinase-3 beta364Homo sapiensMutation(s): 0 
Gene Names: GSK3B
EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens)
Explore P49841 
Go to UniProtKB:  P49841
PHAROS:  P49841
GTEx:  ENSG00000082701 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49841
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VNG
Query on VNG

Download Ideal Coordinates CCD File 
B [auth A]N-[4-[5-(1,2,4-oxadiazol-3-yl)thiophen-2-yl]pyridin-2-yl]cyclopropanecarboxamide
C15 H12 N4 O2 S
MRPLZYZSVZVELT-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.253 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.188α = 90
b = 103.379β = 90
c = 94.702γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2019/34/E/NZ7/00090
Polish National Science CentrePoland2019/34/E/NZ1/00467

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Structure summary