In silico comparison of SARS-CoV-2 spike protein-ACE2 binding affinities across species and implications for virus origin

Abstract

The devastating impact of the COVID-19 pandemic caused by SARS-coronavirus 2 (SARS-CoV-2) has raised important questions about its origins and the mechanism of its transfer to humans. A further question was whether companion or commercial animals could act as SARS-CoV-2 vectors, with early data suggesting susceptibility is species specific. To better understand SARS-CoV-2 species susceptibility, we undertook an in silico structural homology modelling, protein-protein docking, and molecular dynamics simulation study of SARS-CoV-2 spike protein's ability to bind angiotensin converting enzyme 2 (ACE2) from relevant species. Spike protein exhibited the highest binding to human (h)ACE2 of all the species tested, forming the highest number of hydrogen bonds with hACE2. Interestingly, pangolin ACE2 showed the next highest binding affinity despite having a relatively low sequence homology, whereas the affinity of monkey ACE2 was much lower despite its high sequence similarity to hACE2. These differences highlight the power of a structural versus a sequence-based approach to cross-species analyses. ACE2 species in the upper half of the predicted affinity range (monkey, hamster, dog, ferret, cat) have been shown to be permissive to SARS-CoV-2 infection, supporting a correlation between binding affinity and infection susceptibility. These findings show that the earliest known SARS-CoV-2 isolates were surprisingly well adapted to bind strongly to human ACE2, helping explain its efficient human to human respiratory transmission. This study highlights how in silico structural modelling methods can be used to rapidly generate information on novel viruses to help predict their behaviour and aid in countermeasure development.

Figure 1

Upper panel: Picture of the complex formed by SARS-CoV-2 S protein and human ACE2 (CC-BY-NC-ND 4.0 International license; adapted from Taka et al.). Lower panel: Sequence alignment of S1 subunit of four closely related spike proteins (sequence commences 60 residues before RBD). Coloured differences in spike protein sequences from pangolin CoV (green), bat RATG13 CoV (cyan) SARS CoV (red) when compared to sequence of SARS-CoV-2. The spike protein receptor binding domain (RBD) is denoted by the red bar in the sequence alignments.

Figure 2

RMSD of overlay of S protein RBD (pink = with pangolin and turquoise = with human) complex with human ACE2 (red) or pangolin ACE2 (blue) after MD simulation showing different geometry of the two complexes.

Figure 3

RMSD of overlay of S protein RBD (pink = monkey and turquoise = human) complex with human (red) or monkey (blue) ACE2 after MD simulations showing different geometry of the two complexes.

Figure 4

3D structure of SARS-CoV-2 S protein (PDB ID 6M0J (open form) and the homology modelled structure from Modeller. This demonstrates the very high structural similarity of our homology modelled spike protein structure with the EM structures (PDB ID 6M0J (RBD)), with an RMSD of 0.36 Å.