The accomplices: Heparan sulfates and N-glycans foster SARS-CoV-2 spike:ACE2 receptor binding and virus priming

Although it is well established that the SARS-CoV-2spike glycoprotein binds to the host
cell ACE2 receptor to initiate infection, far less is known about the tissue tropism and host
cell susceptibility to the virus. Differential expression across different cell types of heparan
sulfate (HS) proteoglycans, with variably sulfated glycosaminoglycans (GAGs), and their synergistic interactions with host and viral N-glycans may contribute to tissue tropism
and host cell susceptibility. Nevertheless, their contribution remains unclear since HS and
N-glycans evade experimental characterization. We, therefore, carried out microsecond-long
all-atom molecular dynamics simulations, followed by random acceleration molecular
dynamics simulations, of the fully glycosylated spike:ACE2 complex with and without
highly sulfated GAG chains bound. By considering the model GAGs as surrogates for
the highly sulfated HS expressed in lung cells, we identified key cell entry mechanisms of
spike SARS-CoV-2. We find that HS promotes structural and energetic stabilization of
the active conformation of the spike receptor-binding domain (RBD) and reorientation
of ACE2 toward the N-terminaldomain in the same spike subunit as the RBD. Spike
and ACE2 N-glycansexert synergistic effects, promoting better packing, strengthening
the protein:protein interaction, and prolonging the residence time of the complex. ACE2
and HS binding trigger rearrangement of the S2’ functional protease cleavage site through
allosteric interdomain communication. These results thus show that HS has a multifaceted
role in facilitating SARS-CoV-2 infection, and they provide a mechanistic basis for the
development of GAG derivatives with anti-SARS-CoV-2 potential.