Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism

Abstract

The spread of COVID-19 caused by the SARS-CoV-2 outbreak has been growing since its first identification in December 2019. The publishing of the first SARS-CoV-2 genome made a valuable source of data to study the details about its phylogeny, evolution, and interaction with the host. Protein-protein binding assays have confirmed that Angiotensin-converting enzyme 2 (ACE2) is more likely to be the cell receptor through which the virus invades the host cell. In the present work, we provide an insight into the interaction of the viral spike Receptor Binding Domain (RBD) from different coronavirus isolates with host ACE2 protein. By calculating the binding energy score between RBD and ACE2, we highlighted the putative jump in the affinity from a progenitor form of SARS-CoV-2 to the current virus responsible for COVID-19 outbreak. Our result was consistent with previously reported phylogenetic analysis and corroborates the opinion that the interface segment of the spike protein RBD might be acquired by SARS-CoV-2 via a complex evolutionary process rather than a progressive accumulation of mutations. We also highlighted the relevance of Q493 and P499 amino acid residues of SARS-CoV-2 RBD for binding to human ACE2 and maintaining the stability of the interface. Moreover, we show from the structural analysis that it is unlikely for the interface residues to be the result of genetic engineering. Finally, we studied the impact of eight different variants located at the interaction surface of ACE2, on the complex formation with SARS-CoV-2 RBD. We found that none of them is likely to disrupt the interaction with the viral RBD of SARS-CoV-2.

Keywords: ACE2; COVID-19; Homology-based protein-protein docking; Variants; Viral spike receptor binding domain.

Fig. 1

Phylogenetic and sequence analysis based on full genomes and RBDs from the different isolates included in this study. (A) Phylogeny trees are opposed to each other to show the clade discrepancies and discontinuous lines shows the equivalent taxon between each tree. (B) Multiple sequence alignment of the interface residues of RBD. Blocks in red color indicate the residues with similar biochemical properties to the positions in SARS-CoV-2. Conserved residues are colored in blue. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2

Homology based protein-protein docking of RBD/ACE2 and binding energy score analysis of spike RBD with ACE2 receptor. (A) Homology based protein-protein docking complex of SARS-CoV-2 RBD with hACE2. The red spheres are the interface residues of the RBD. (B) Binding energy scores calculated with PRODIGY, MM-GBSA and FoldX methods for RBDs from different coronaviruses forms with hACE2. (C) Binding energy scores of RBDs from SARS-CoV-2 and SARS-CoV interacting with ACE2 orthologues. Asterisks indicate the putative overlap of a glycosylation site with the protein-protein interface. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3

Analysis of the interaction between RBD and hACE2. Decomposition of the MM-GBSA energy for each amino acid of the binding surface from SARS-CoV-2 (A) and SARS-CoV Sino1-11 isolate (B). Position of the hotspot residues of the complexes RBD-SARS-CoV-2/hACE2 (C) and RBD-SARS-CoV/hACE2 (D). (E) Similarity matrix in network representation calculated from the free energy decomposition profiles of complexes involving SARS-CoV-2 and SARS-CoV RBDs interacting with different orthologous sequences of ACE2. (F) Flexibility of RBD interface residue expressed as Root Mean Square Fluctuation (RMSF) for two forms of RBD-SARS-CoV-2, T499 and P499.

Fig. 4

Analyzing the interaction of SARS-CoV-2 RBD with different variants of hACE2. (A) Localization of the variants, labeled by the amino acid change and the dbSNP ID, on the interaction surface of hACE2 and RBD from SARS-CoV-2. Estimation of the changing upon mutation for hACE2 variants calculated for enthalpy (ddG) and entropy (ddS) terms of the folding energy calculated with DynaMut (B) and the interaction energy calculated with PRODIGY (D).