3.1.4  SARS-CoV2 receptor binding domain contains cyclic regions that can make interaction with cell-surface GRP78
Pep42 is a cyclic oligopeptide that, with its hydrophobic character, can selectively interact with cell surface glucose‐regulated protein 78 (GRP78), a member of 70 kDa heat shock proteins. GRP78, also known as BiP or HSPA5, under endoplasmic reticulum stress, can be translocated from the endoplasmic reticulum to the membrane and helps to maintain cellular integrity under physiologic and pathological stress. It critically contributes to various functions ranging from protein folding, transportation, and degradation to cell-signaling, proliferation, survival, apoptosis, inflammation, and immunity. The expression of GRP78 decreases with age.
On the 2019-nCoV spike protein, 13 disulfide bonds are corresponding to 13 different cyclic regions thought to be similar to the cyclic form of Pep42 [8]. Among these, four regions I-IV take place in the outer surface of a putative receptor-binding domain (RBD) on the viral spike., including C361, C379, C391, and C480. These regions share sequence similarity with Pep42, ranging from 15.38% to 46.15%. However, only one of them, i.e., region IV (GRAVY = 0.08), is a hydrophobic region, like Pep42 (GRAVY = 1.1). Structural models evaluate the energy contribution for region IV as a part of region III to the GRP78 to be about (−9.8 out of −14.0 kcal/mol), and the docking platform proposes region IV as the best region binding to GRP78. The region IV can be linked to the substrate-binding domain β (SBDB) of GRP78 using five H-bonds (through P479, N481, E484, and N487) and four hydrophobic interactions (through T478, E484, and F486).