3WD9 image
Entry Detail
PDB ID:
3WD9
Title:
Crystal structure of phosphodiesterase 4B in complex with compound 10f
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2013-06-11
Release Date:
2013-10-23
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.26
R-Value Work:
0.17
R-Value Observed:
0.18
Space Group:
P 21 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:cAMP-specific 3',5'-cyclic phosphodiesterase 4B
Chain IDs:A, B
Chain Length:377
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Synthesis and biological evaluation of 5-carbamoyl-2-phenylpyrimidine derivatives as novel and potent PDE4 inhibitors
Bioorg.Med.Chem. 21 7025 7037 (2013)
PMID: 24094436 DOI: 10.1016/j.bmc.2013.09.013

Abstact

5-Carbamoyl-2-phenylpyrimidine derivative 2 has been identified as a phosphodiesterase 4 (PDE4) inhibitor with moderate PDE4B inhibitory activity (IC50=200 nM). Modification of the carboxylic acid moiety of 2 gave N-neopentylacetamide derivative 10f, which had high in vitro PDE4B inhibitory activity (IC50=8.3 nM) and in vivo efficacy against lipopolysaccharide (LPS)-induced pulmonary neutrophilia in mice (ID50=16 mg/kg, ip). Furthermore, based on the X-ray crystallography of 10f bound to the human PDE4B catalytic domain, we designed 7,8-dihydro-6H-pyrido[4,3-d]pyrimidin-5-one derivative 39 which has a fused bicyclic lactam scaffold. Compound 39 exhibited excellent inhibitory activity against LPS-induced tumor necrosis factor alpha (TNF-α) production in mouse splenocytes (IC50=0.21 nM) and in vivo anti-inflammatory activity against LPS-induced pulmonary neutrophilia in mice (41% inhibition at a dose of 1.0 mg/kg, i.t.).

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