Unexpected free fatty acid binding pocket in the cryo-EM structure of SARS-CoV-2 spike protein

Abstract

COVID-19, caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), represents a global crisis. Key to SARS-CoV-2 therapeutic development is unraveling the mechanisms driving high infectivity, broad tissue tropism and severe pathology. Our cryo-EM structure of SARS-CoV-2 spike (S) glycoprotein reveals that the receptor binding domains 5 (RBDs) tightly and specifically bind the essential free fatty acid (FFA) linoleic acid (LA) in three composite binding pockets. The pocket also appears to be present in the highly pathogenic coronaviruses SARS-CoV and MERS-CoV. Lipid metabolome remodeling is a key feature of coronavirus infection, with LA at its core. LA metabolic pathways are central to inflammation, immune modulation and membrane fluidity. Our structure directly links LA and S, setting the 10 stage for interventions targeting LA binding and metabolic remodeling by SARS-CoV-2. One Sentence Summary:A direct structural link between SARS-CoV-2 spike and linoleic acid, a key molecule in inflammation, immune modulation and membrane fluidity. 15 20

Structures, conformations and distributions of SARS-CoV-2 spike protein trimers on intact virions

“…3D). We did not observe any additional density that would correspond to bound lipids such as those described in a recent preprint (19), or other bound co-factors. These may be present sub-stoichiometrically or in rare conformations but are not a general feature of the S trimer in situ.…”

“…The prefusion structure of S from coronaviruses including SARS-CoV-2 has been extensively studied using ectopic expression of a soluble, secreted form of S, followed by purification combined with cryo-EM and single particle reconstruction (7,8,(18)(19)(20). In the prefusion form, the receptor binding domain (RBD) sits at the top of a broad, trimeric spike, above the fusion core.…”

“…Three copies of the RBD are surrounded by three copies of the N-terminal domain (NTD) which show some mobility (7,8,12,18). In the closed prefusion conformation all three copies of the RBD lay flat on the spike surface, largely occluding the receptor binding site, while in the open prefusion conformation one or multiple RBDs can lift up to expose the receptor binding site (7,8,18,19). The surface of the trimer is extensively glycosylated with 22 potential N-linked glycosylation sites on each monomer (7,8,21).…”

Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate

“…Linoleic acid, an essential free fatty acid, was buried within a hydrophobic pocket in the CTD with its main chain carboxyl group making contacts with the adjacent RBD in closed conformation. A recent report by Toelzer et al also identified this density and attributed it to the presence of linoleic acid (34). The second large density occupied by PS 80 is situated in the NTD and is relatively more surface exposed.…”

“…state (34). Recent reports by Henderson et al have revealed that mutations at certain positions can alter the propensity toward 'up' and 'down' states of the RBD (36,37).…”