In silico analysis of neutral sphingomyelinase 2

Abstract

Neutral sphingomyelinase 2 (nSMase2) is an important sphingolipid metabolism enzyme that generates ceramide through the hydrolysis of sphingomyelin (SM) present in the plasma membrane. It has been suggested as a therapeutic target for many diseases from Alzheimer’s disease to cancer because of its possible role in several cel lular processes including exosome secretion and inflammation. Mammalian nSMases comprise catalytic and membrane domains, and the crystal structure of the catalytic domain of human nSMase2 was recently resolved facilitating detailed structural anal ysis of this enzyme. The aim of this current study was to investigate the structure and dynamics of human nSMase2 by comparison with bacterial sphingomyelinase (Bc SMase) structures to unveil its catalytic mechanism. Docking and MD simulations were performed on apo and SM-bound bacterial and human nSMase catalytic domains. The simulations suggested that the membrane-associated N-terminal domain of human nS Mase2 may be important for the stability of this enzyme. SM interacted with Glu53 and Mg2+ in Bc-SMases and with the corresponding Glu364 and Ca2+ in human nS Mase2 highlighting the importance of these residues and ions in SM binding. The possible binding site and binding mode of the experimentally determined nSMase2 in hibitor GW4869 were identified through SiteMap and molecular docking analysis, and MD simulations were carried out on GW4869-bound structures to further investigate the catalytic mechanism of human nSMase2.