7XBB image
Deposition Date 2022-03-21
Release Date 2022-07-06
Last Version Date 2023-11-29
Entry Detail
PDB ID:
7XBB
Keywords:
Title:
Crystal structure of PDE4D catalytic domain complexed with compound 23a
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Isoform 3 of cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Gene (Uniprot):PDE4D
Chain IDs:A, B
Chain Length:507
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Structure-based optimization of Toddacoumalone as highly potent and selective PDE4 inhibitors with anti-inflammatory effects.
Biochem Pharmacol 202 115123 115123 (2022)
PMID: 35688178 DOI: 10.1016/j.bcp.2022.115123

Abstact

Phosphodiesterase-4 (PDE4) is an important drug target for inflammatory diseases. Previously, we identified a series of novel PDE4 inhibitors derived from the natural Toddacoumalone, among which the hit compound 2 with a naphthyridine scaffold showed moderate potency with the IC50 value of 400 nM. Based on the co-crystal structure of PDE4D-2, further structural optimizations and structure-activity relationship studies led to a highly potent PDE4 inhibitor 23a with the IC50 value of 0.25 nM and excellent selectivity profiles over other PDEs (>4000-fold). The co-crystal structure of PDE4D-23a elucidated that 23a has strong interactions with the M and Q pocket of PDE4D. Importantly, compound 23a significantly inhibits the release of inflammatory cytokines TNF-α and IL-6 in lipopolysaccharide-stimulated RAW264.7 cells. Thus, compound 23a with a naphthyridine scaffold is a promising PDE4 inhibitor for the treatment of inflammatory diseases.

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Primary Citation of related structures