Mechanism of inhibition of SARS-CoV-2 infection by the interaction of the spike glycoprotein with heparin

Heparin is administered intravenously as an anticoagulant to COVID-19 patients and via aerosol to treat other lung diseases. It has recently been found to have antiviral activity against SARS-CoV-2 as it hinders attachment of the virus to the host cell by binding to the virus spike glycoprotein. Here, we describe molecular dynamics simulations to investigate how heparin binds to the spike and the mechanism by which it exerts its antiviral activity. The simulations show that heparin polyanionic chains can bind at long, mostly positively charged patches on the spike, preventing the binding of host cell heparan sulphate proteoglycans to the spike. Heparin can mask both the S1/S2 basic motif, thereby inhibiting furin cleavage and the formation of the prefusion conformation, and the basic residues of the receptor binding domain (RBD), thus acting on the hinge region responsible for the motion of the RBD between inactive closed and active open conformations of the spike. In simulations of the closed spike, heparin binds the RBD and the N-terminal domain of two adjacent spike subunits and hinders the opening. In simulations of the open spike, heparin binds similarly but induces stabilization of the hinge region and a change in RBD motion. Heparin is therefore able to inhibit host cell attachment directly and by two allosteric mechanisms. Furthermore, the simulations provide insights into how heparan sulphate proteoglycans on the host cell can facilitate viral infection. Our results will aid the rational optimization of heparin derivatives for SARS-CoV-2 antiviral therapy.