7XAA image
Deposition Date 2022-03-17
Release Date 2023-02-22
Last Version Date 2023-11-29
Entry Detail
PDB ID:
7XAA
Keywords:
Title:
Crystal structure of PDE4D catalytic domain complexed with compound 21d
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.23
R-Value Work:
0.18
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
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
Discovery of novel PDE4 inhibitors targeting the M-pocket from natural mangostanin with improved safety for the treatment of Inflammatory Bowel Diseases.
Eur.J.Med.Chem. 242 114631 114631 (2022)
PMID: 35985255 DOI: 10.1016/j.ejmech.2022.114631

Abstact

Inflammatory Bowel Diseases (IBDs) are chronic disorders with iterative intestinal mucosal inflammation which remain unmet medical needs. PDE4 inhibitors were reported to be novel anti-IBD agents, but their clinical use was hampered by side effects such as emesis and nausea. Herein, structure-based discovery of natural mangostanin (1) targeting the M-pocket resulted in the novel and potent PDE4 inhibitor 22d (IC50 = 3.5 nM) and favorable physico-chemical properties. X-Ray study revealed that 22d interacted tightly with the M-pocket and maintained the key interactions between PDE4 and roflumilast. Worthy to note that compounds 22d and our previously reported 4e and 18a, originating from mangostanin, all caused no emesis on beagle dogs at the oral dose of 10 mg/kg, confirming the safety superiority of scaffold in mangostanin derivatives over that in positive roflumilast. Finally, administration of 22d (5.0 mg/kg, twice-daily) exhibited comparable anti-IBD effects to the positive control dipyridamole (25.0 mg/kg, twice-daily) in the dextran sulfate sodium (DSS)-induced IBD mice model, indicating its potential as a novel anti-IBD agent.

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Primary Citation of related structures