6QBS image
Deposition Date 2018-12-21
Release Date 2019-02-06
Last Version Date 2024-10-09
Entry Detail
PDB ID:
6QBS
Keywords:
Title:
The Alkyne Moiety as a Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
1.70 Å
R-Value Free:
0.21
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 61 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Cathepsin K
Gene (Uniprot):CTSK
Chain IDs:A, B
Chain Length:215
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
The Alkyne Moiety as a Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K.
J. Am. Chem. Soc. 141 3507 3514 (2019)
PMID: 30689386 DOI: 10.1021/jacs.8b11027

Abstact

Irreversible covalent inhibitors can have a beneficial pharmacokinetic/pharmacodynamics profile but are still often avoided due to the risk of indiscriminate covalent reactivity and the resulting adverse effects. To overcome this potential liability, we introduced an alkyne moiety as a latent electrophile into small molecule inhibitors of cathepsin K (CatK). Alkyne-based inhibitors do not show indiscriminate thiol reactivity but potently inhibit CatK protease activity by formation of an irreversible covalent bond with the catalytic cysteine residue, confirmed by crystal structure analysis. The rate of covalent bond formation (kinact) does not correlate with electrophilicity of the alkyne moiety, indicative of a proximity-driven reactivity. Inhibition of CatK-mediated bone resorption is validated in human osteoclasts. Together, this work illustrates the potential of alkynes as latent electrophiles in small molecule inhibitors, enabling the development of irreversible covalent inhibitors with an improved safety profile.

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