Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators

Shaoyong Lu; Yingyi Chen; Jiacheng Wei; Mingzhu Zhao; Duan Ni; Xinheng He; Jian Zhang

doi:10.1016/j.apsb.2020.09.010

Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators

Acta Pharm Sin B. 2021 May;11(5):1355-1361. doi: 10.1016/j.apsb.2020.09.010. Epub 2020 Sep 19.

Authors

Shaoyong Lu^{1

2}, Yingyi Chen¹, Jiacheng Wei¹, Mingzhu Zhao², Duan Ni³, Xinheng He¹, Jian Zhang^{1

2}

Affiliations

¹ Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.
² State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200127, China.
³ The Charles Perkins Centre, University of Sydney, Sydney NSW 2006, Australia.

Abstract

The recent discovery of activator compounds binding to an allosteric site on the NAD⁺-dependent protein lysine deacetylase, sirtuin 6 (SIRT6) has attracted interest and presents a pharmaceutical target for aging-related and cancer diseases. However, the mechanism underlying allosteric activation of SIRT6 by the activator MDL-801 remains largely elusive because no major conformational changes are observed upon activator binding. By combining molecular dynamics simulations with biochemical and kinetic analyses of wild-type SIRT6 and its variant M136A, we show that conformational rotation of 2-methyl-4-fluoro-5-bromo substituent on the right phenyl ring (R-ring) of MDL-801, which uncovers previously unseen hydrophobic interactions, contributes to increased activating deacetylation activity of SIRT6. This hypothesis is further supported by the two newly synthesized MDL-801 derivatives through the removal of the 5-Br atom on the R-ring (MDL-801-D1) or the restraint of the rotation of the R-ring (MDL-801-D2). We further propose that the 5-Br atom serves as an allosteric driver that controls the ligand allosteric efficacy. Our study highlights the effect of allosteric enzyme catalytic activity by activator binding and provides a rational approach for enhancing deacetylation activity.

Keywords: ADPR, ADP-ribose; Allosteric driver; Allosteric mechanisms; Allosteric sites; Drug design; EC50, Effective concentration; Enzyme catalysis; FDL, Fluor de Lys; H3K56, histone 3 lysine 56; H3K9, histone 3 lysine 9; HPLC, high-performance liquid chromatography; MD, molecular dynamics; MST, microscale thermophoresis; Myr-H3K9, myristoyl H3K9; NAM, nicotinamide; PCA, principal component analysis; Protein dynamics; RMSD, root-mean-square deviation; SIRT6, sirtuin 6.