5YQO

Crystal structure of Sirt2 in complex with selective inhibitor L5C

Summary for 5YQO

• Entry DOI: 10.2210/pdb5yqo/pdb
• Descriptor: NAD-dependent protein deacetylase sirtuin-2, ZINC ION, N-[4-[[3-[2-(4,6-dimethylpyrimidin-2-yl)sulfanylethanoylamino]phenyl]methoxy]phenyl]-1-methyl-pyrazole-4-carboxamide, ... (4 entities in total)
• Functional Keywords: nad-dependent deacetylase sirtuin-2, inhibitor, complex, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 35017.67

Authors

Wang, H.,Yu, Y.,Li, G.,Chen, Q. (deposition date: 2017-11-07, release date: 2018-10-17, Last modification date: 2023-11-22)

Primary citation

Yang, L.L.,Wang, H.L.,Zhong, L.,Yuan, C.,Liu, S.Y.,Yu, Z.J.,Liu, S.,Yan, Y.H.,Wu, C.,Wang, Y.,Wang, Z.,Yu, Y.,Chen, Q.,Li, G.B.
X-ray crystal structure guided discovery of new selective, substrate-mimicking sirtuin 2 inhibitors that exhibit activities against non-small cell lung cancer cells.
Eur J Med Chem, 155:806-823, 2018

PubMed Abstract: Human sirtuin 2 (SIRT2) is a nicotinamide adenine dinucleotide (NAD)-dependent deacylase, and is implicated in human diseases including cancer. Selective small-molecule inhibitors for SIRT2 are sought as chemical tools and potential therapeutics. Here we report the X-ray crystal structure guided structure-activity relationship studies of new N-(3-(phenoxymethyl)phenyl)acetamide derivatives with SIRT2, which led to the identification of potent, selective SIRT2 inhibitors. Crystallographic analyses reveal that the new inhibitors act via inducing the formation of an enlarged hydrophobic pocket and particularly mimicking the interactions made by myristoylated-lysine substrates. The most potent inhibitor 24a could dose-dependently elevate the acetylation level of α-tubulin in the non-small cell lung cancer H441 cells, which have a high expression level of SIRT2 as determinated by Western blotting analyses. Further cellular assays reveal that 24a restrains cell growth mainly through inhibiting cellular proliferation rather than inducing apoptosis. Moreover, 24a could suppress the migration and invasion of H441 cells. These results provide an excellent basis for further development of new potent, selective, and cell active SIRT2 inhibitors as chemical tools and potential therapeutics for SIRT2-driven non-small cell lung cancers.

PubMed: 29957526
DOI: 10.1016/j.ejmech.2018.06.041

Experimental method

X-RAY DIFFRACTION (1.483 Å)