Biophysical characterization of the SARS-CoV2 spike protein binding with the ACE2 receptor explains increased COVID-19 pathogenesis

Ratul Chowdhury; Costas D Maranas

We reported on the differences between three viral ACE2-RBD complexes and how they exploit the contact map of RBD-binding domain of human ACE2 receptor to facilitate binding. In an uninfected cell, through the action of the renin angiotensin system (RAS), ACE2 forms a complex with the angiotensin 2 receptor type I (ATR1) 4 . Due to the lack of an experimentally resolved structure for the ACE2-ATR1 complex, we used protein-protein docking and Rosetta-binding score screening to identify the most stable configuration of the complex. Analysis of the ACE2-ATR1 binding interface reveals 41 ACE2 residues and 26 ATR1 residues at the interface connected by five strong electrostatic contacts and several long range weak electrostatic contacts. We find that eleven SARS-CoV-2 RBD binding residues of ACE2 are shared by the ATR1 binding region. Moreover, SARS-CoV-2 RBD binds ACE2 with ~64% better binding score than ATR1. In contrast, SARS-CoV-1 show ~2.1% worse binding score with ACE2 compared to the ACE2-ATR1 complex while sharing only nine residues with the ATR1 binding interface of ACE2 (see Figure 6 ). These numbers indicate that SARS-CoV-2 (and OC43) outcompete the ATR1-ACE2 complex thus facilitating the formation of the ACE2-spike complex whereas SARS-CoV-1 cannot. This is in line with their respective viral infection rates. We computationally explored the potentially available margin of improvement for the binding affinity of SARS-CoV-2 with ACE2 using the IPRO 5 protein design software. We allowed all 21 contacting residues of the RBD of the spike protein to simultaneously mutate. We run two separate design trajectories and, in both cases the best design achieved an approximately 25% improvement in binding affinity using the Rosetta scoring function. This improvement is less than the difference between the calculated binding scores of SARS-CoV-1 and SARS-CoV-2 implying that SARS-CoV-2 has already achieved most of the theoretically possible binding affinity gain with ACE2 compared to SARS-CoV-1. Interestingly, the network of glycine residues in SARS-CoV-2 is conserved in all redesigned RBDs.