9WP5 image
Deposition Date 2025-09-08
Release Date 2026-02-11
Last Version Date 2026-02-11
Entry Detail
PDB ID:
9WP5
Keywords:
Title:
The crystal structure of PDE4D with Pinoresinol Dimethyl Ether
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Expression System(s):
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:3',5'-cyclic-AMP phosphodiesterase 4D
Gene (Uniprot):PDE4D
Chain IDs:A, B
Chain Length:327
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Discovery of pinoresinol dimethyl ether as a natural PDE4 inhibitor with anti-psoriatic effects.
Bioorg.Chem. 169 109414 109414 (2026)
PMID: 41453305 DOI: 10.1016/j.bioorg.2025.109414

Abstact

Psoriasis is a complex chronic inflammatory disease that severely impairs patients' quality of life. However, current medications could only control the symptoms but not cure psoriasis with unmet medical needs. Targeting phosphodiesterase 4 (PDE4) represents a validated therapeutic strategy for psoriasis, though the clinical application of existing PDE4 inhibitors is often hampered by systemic side effects. In this study, we identified pinoresinol dimethyl ether (PDME), a natural furanoid lignan previously reported to be isolated from the stem bark of Magnolia Kobus, as a novel PDE4 inhibitor (IC50 = 0.90 μM) through an integrated virtual screening approach. The binding mode of PDME to PDE4 was clearly elucidated through molecular dynamics simulations, isothermal titration calorimetry, and co-crystal structure analysis, revealing an enthalpy-driven interaction involving key hydrogen bonds with Gln369 and π-π stacking within the hydrophobic clamp. In vitro, PDME significantly suppressed the expression of pro-inflammatory cytokines in keratinocytes. In a murine imiquimod-induced psoriasis model, PDME treatment markedly alleviated psoriatic lesions, reduced skin thickening, and suppressed inflammatory responses. These findings highlight PDME as a promising natural PDE4 inhibitor with significant potential for the treatment of psoriasis.

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Primary Citation of related structures
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