Molecular dynamics simulation on the role of CL5D in accelerating the product dissociation of SIRT6

Abstract

SIRT6 is a member of the NAD⁺-dependent histone deacetylase family and is integral to maintaining genome stability and regulating metabolic transcription. SIRT6 transfers acetyl groups from the lysine side chains of protein substrates to the cofactor NAD⁺, generating nicotinamide, 2′-O-acyl-ADP-ribose (ADPr), and a deacetylated substrate. SIRT6 has been found to be activated by small molecule activators, such as CL5D. However, the process of dissociation of the SIRT6 product and the mechanism of activation by small molecule activators are unknown. In this work, we elucidated these activation mechanisms by performing extensive molecular dynamics simulations. The results of random acceleration molecular dynamics and umbrella sampling demonstrated that the dissociation sequence involves the exit of the deacetylated substrate first, followed by ADPr. The binding of CL5D does not alter the dissociation pathway of the products, but it increases the catalytic activity of SIRT6 by facilitating the dissociation of products within SIRT6. Our results suggest a mechanism of SIRT6 activation, which highlights the importance of product dissociation in enzyme catalysis. This result may help facilitate the development of new SIRT6 activators.