8BRN image
Deposition Date 2022-11-23
Release Date 2023-08-02
Last Version Date 2024-10-16
Entry Detail
PDB ID:
8BRN
Title:
Crystal structure of red kidney bean purple acid phosphatase in complex with an alpha-aminonaphthylmethylphosphonic acid inhibitor
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.20
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 31 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Fe(3+)-Zn(2+) purple acid phosphatase
Chain IDs:A, B, C, D
Chain Length:428
Number of Molecules:4
Biological Source:Phaseolus vulgaris
Primary Citation
Optimization of an alpha-aminonaphthylmethylphosphonic acid inhibitor of purple acid phosphatase using rational structure-based design approaches.
Eur.J.Med.Chem. 254 115383 115383 (2023)
PMID: 37087894 DOI: 10.1016/j.ejmech.2023.115383

Abstact

Purple acid phosphatases (PAPs) are ubiquitous binuclear metallohydrolases that have been isolated from various animals, plants and some types of fungi. In humans and mice, elevated PAP activity in osteoclasts is associated with osteoporosis, making human PAP an attractive target for the development of anti-osteoporotic drugs. Based on previous studies focusing on phosphonate scaffolds, as well as a new crystal structure of a PAP in complex with a derivative of a previously synthesized α-aminonaphthylmethylphosphonic acid, phosphonates 24-40 were designed as new PAP inhibitor candidates. Subsequent docking studies predicted that all of these compounds are likely to interact strongly with the active site of human PAP and most are likely to interact strongly with the active site of pig PAP. The seventeen candidates were synthesized with good yields and nine of them (26-28, 30, 33-36 and 38) inhibit in the sub-micromolar to nanomolar range against pig PAP, with 28 and 35 being the most potent mammalian PAP inhibitors reported with Ki values of 168 nM and 186 nM, respectively. This study thus paves the way for the next stage of drug development for phosphonate inhibitors of PAPs as anti-osteoporotic agents.

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