Computational Insights into the Conformational Accessibility and Binding Strength of SARS-CoV-2 Spike Protein to Human Angiotensin-Converting Enzyme 2

Abstract

The spike protein of SARS-CoV-2 (CoV-2-S) mediates the virus entry into human cells. Experimental studies have shown the stronger binding affinity of the RBD (receptor binding domain) of CoV-2-S to angiotensin-converting enzyme 2 (ACE2) as compared to that of SARS-CoV spike (CoV-S). However, a similar or weaker binding affinity of CoV-2-S compared to that of CoV-S is observed if entire spikes are used in the bioassay. To explore the underlying mechanism, we calculated the binding affinities of the RBDs to ACE2 and simulated the transitions between ACE2-inaccessible and -accessible conformations. We found that the ACE2-accessible angle of CoV-2-S is 52.2° and that the ACE2 binding strength of CoV-2-S RBD is much stronger than that of CoV-S RBD. However, CoV-2-S has much less of an ACE2-accessible conformation and is much more difficult to shift from ACE2-inaccessible to -accessible than CoV-S, making the binding affinity of the entire protein decrease. Further analysis revealed key interactional residues for strong binding and five potential ligand-binding pockets for drug research.