9LRO image
Deposition Date 2025-02-01
Release Date 2026-03-11
Last Version Date 2026-03-11
Entry Detail
PDB ID:
9LRO
Keywords:
Title:
The crystal structure of PDE4D with T3700
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Expression System(s):
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.24
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 phosphodiest
Gene (Uniprot):PDE4D
Chain IDs:A, B
Chain Length:335
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Artificial Intelligence-Driven Discovery of Pyrazolo[1,5- a ]pyrimidine Derivatives as Novel Phosphodiesterase 4 Inhibitors for Treating Idiopathic Pulmonary Fibrosis.
J. Med. Chem. 68 24436 24455 (2025)
PMID: 41252469 DOI: 10.1021/acs.jmedchem.5c02407

Abstact

Phosphodiesterase 4 (PDE4) has been validated as a promising therapeutic target for idiopathic pulmonary fibrosis (IPF), a devastating interstitial lung disease lacking really effective therapeutic drugs, particularly exacerbated in the post-COVID-19 era. Herein, we reported the discovery of 13c, a novel pyrazolo[1,5-a]pyrimidine-based PDE4 inhibitor, via an innovative artificial intelligence (AI)-driven virtual screening approach integrated with structure-based design. The cocrystal analysis of PDE4-13c elucidated the structural basis of its high affinity, revealing that the unique "halogen-binding and metal-coordination" synergistic network significantly influenced PDE4 inhibitory activity, which resulted in a 268-fold potency enhancement (IC(50) = 2.7 nM) over hit T3700 (IC(50) = 725 nM). Notably, 13c exhibited remarkable hepatic microsomal stability (RLM(1/2) = 141.4 min). Furthermore, 13c exhibited remarkable antifibrotic activity in vitro and significantly attenuated bleomycin-induced pulmonary fibrosis in vivo, highlighting its potential as a novel PDE4 inhibitor for IPF.

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Primary Citation of related structures
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