9HUL | pdb_00009hul

Crystal structure of human GSK3b in complex with ARN25423


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.244 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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Literature

Rational optimization of D3R/GSK-3 beta dual target-directed ligands as potential treatment for bipolar disorder: Design, synthesis, X-ray crystallography, molecular dynamics simulations, in vitro ADME, and in vivo pharmacokinetic studies.

Di Martino, R.M.C.Russo, D.Penna, I.Demuro, S.Dalle Vedove, A.Spagnuolo, R.Ottonello, G.Bertozzi, S.M.Summa, M.Desantis, J.Valeri, A.Pruccoli, L.Tripathi, S.K.Tarozzi, A.Storici, P.Girotto, S.Bertorelli, R.Armirotti, A.Cruciani, G.Bandiera, T.Cavalli, A.Bottegoni, G.

(2025) Eur J Med Chem 297: 117899-117899

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117899
  • Primary Citation of Related Structures:  
    9HUK, 9HUL, 9HV3

  • PubMed Abstract: 

    Bipolar disorder is a complex neuropsychiatric condition with a significant unmet medical need, as current treatments lack disease-modifying properties and multimodal therapeutic effects. To overcome the limitations of single-target drugs, we designed dual-target ligands that combine partial agonism at the dopamine D3 receptor (D3R) with inhibition of glycogen synthase kinase-3β (GSK-3β). We previously identified ARN24161 (1) as a promising prototype, demonstrating partial agonism at D3R (EC 50  = 10.1 nM, % Eff. = 26.3) and GSK-3β inhibition (IC 50  = 561 nM). However, its drug-like properties remained suboptimal. To optimize this compound, we initiated a multidisciplinary refinement campaign, leveraging computational modeling and crystallographic data to fine-tune the balance between D3R and GSK-3β activity, reduce P-glycoprotein (P-gp) affinity, and improve the pharmacokinetic profile. This effort led to the identification of ARN25297 (5), a moderately balanced dual-target ligand that exhibits partial agonism at D3R (EC 50  = 13.1 nM, % Eff. = 17.1) and potent GSK-3β inhibition (IC 50  = 47.0 nM). Notably, ARN25657 (16) emerged as the most well-balanced candidate, demonstrating enhanced D3R partial agonism (EC 50  = 15.2 nM, % Eff. = 37.7) alongside strong GSK-3β inhibition (IC 50  = 19.3 nM). Compound 16 also exhibited the lowest P-gp inhibition and significant improvements in in vitro ADME properties compared to prototype 1, while maintaining a balanced dual target profile. Although the PK profile of 16 remained comparable to that of prototype 1, these findings lay the groundwork for further lead optimization and structural refinement, driving future in vivo proof-of-concept toward innovative therapeutic strategies for bipolar disorder and related neuropsychiatric conditions.


  • Organizational Affiliation
    • Computational and Chemical Biology, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genova (GE), Italy. Electronic address: rita.dimartino@uniupo.it.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen synthase kinase-3 beta
A, B
442Homo 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
A1IXM (Subject of Investigation/LOI)
Query on A1IXM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
~{N}-[3-[4-[2,3-bis(chloranyl)phenyl]piperazin-1-yl]propyl]-2-oxidanylidene-6-pyridin-3-yl-3~{H}-benzimidazole-1-carboxamide
C26 H26 Cl2 N6 O2
QSLKMFIYZMLKJC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.244 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.44α = 90
b = 85.86β = 90
c = 178.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release