Exploring the Fatty Acid Binding Pocket in the SARS-CoV‑2 Spike Protein – Confirmed and Potential Ligands

Severe Acute Respiratory syndrome 2 (SARS-CoV-2) is a
respiratory
virus responsible for coronavirus disease 19 (COVID-19) and the still
ongoing and unprecedented global pandemic. The key viral protein for
cell infection is the spike glycoprotein, a surface-exposed fusion
protein that both recognizes and mediates entry into host cells. Within
the spike glycoprotein, a fatty acid binding pocket (FABP) was confirmed,
with the crystallization of linoleic acid (LA) occupying a well-defined
site. Importantly, when the pocket is occupied by a fatty acid, an
inactive conformation is stabilized, and cell recognition is hindered.
In this review, we discuss ligands reported so far for this site,
correlating their activity predicted through in silico studies with antispike experimental activity, assessed by either
binding assays or cell-infection assays. LA was the first confirmed
ligand, cocrystallized in a cryo-EM structure of the spike protein,
resulting in increased stability of the inactive conformation of the
spike protein. The next identified ligand, lifitegrast, was also experimentally
confirmed as a ligand with antiviral activity, suggesting the potential
for diverse chemical scaffolds to bind this site. Finally, SPC-14
was also confirmed as a ligand, although no inhibition assays were
performed. In this review, we identified 20 studies describing small-molecule
compounds predicted to bind the pocket in in silico studies and with confirmed binding or in vitro activity,
either inhibitory activity against the spike-ACE2 interaction or antiviral
activity in cell-based assays. When considering all ligands confirmed
with in vitro assays, a good overall occupation of
the pocket should be complemented with the ability to make direct
interactions, both hydrophilic and hydrophobic, with key amino acid
residues defining the pocket surface. Among the active compounds,
long flexible carbon chains are recurrent, with retinoids capable
of binding the FABP, although bulkier systems are also capable of
affecting viral fitness. Compounds able to bind this site with high
affinity have the potential to stabilize the inactive conformation
of the SARS-CoV-2 spike protein and therefore reduce the virus’s
ability to infect new cells. Since this pocket is conserved in highly
pathogenic human coronaviruses, including MERS-CoV and SARS-CoV, this
effect could be exploited for the development of new antiviral agents,
with broad-spectrum anticoronavirus activity.