Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex

Abstract

SARS-CoV-2 entry in human cells is mediated by the interaction between the viral Spike protein and the human ACE2 receptor. This mechanism evolved from the ancestor bat coronavirus and is currently one of the main targets for antiviral strategies. However, there currently exist several Spike protein variants in the SARS-CoV-2 population as the result of mutations, and it is unclear if these variants may exert a specific effect on the affinity with ACE2 which, in turn, is also characterized by multiple alleles in the human population. In the current study, the GBPM analysis, originally developed for highlighting host-guest interaction features, has been applied to define the key amino acids responsible for the Spike/ACE2 molecular recognition, using four different crystallographic structures. Then, we intersected these structural results with the current mutational status, based on more than 295,000 sequenced cases, in the SARS-CoV-2 population. We identified several Spike mutations interacting with ACE2 and mutated in at least 20 distinct patients: S477N, N439K, N501Y, Y453F, E484K, K417N, S477I and G476S. Among these, mutation N501Y in particular is one of the events characterizing SARS-CoV-2 lineage B.1.1.7, which has recently risen in frequency in Europe. We also identified five ACE2 rare variants that may affect interaction with Spike and susceptibility to infection: S19P, E37K, M82I, E329G and G352V.Communicated by Ramaswamy H. Sarma.

Keywords: ACE2; COVID-19; SARS-CoV-2; mutations; spike.

Figure 1.

Conformational comparison of Spike-ACE2 PDB complexes: (A) alignment of PDB entries, Spike and ACE2 are respectively surrounded by cyan and orange fog, and (B) bar graph showing RMSd (in Å) computed on protein atoms.

Figure 2.

Summary of the pipeline adopted by GBPM to identify key residues contributing to the SARS-CoV-2 Spike/Human ACE2 interface. Spike is depicted in cyan, and ACE2 in orange, based on the 6LZG PDB model (Wang et al., 2020). Residues highlighted by GBPM are then tested for mutation frequency in the worldwide SARS-CoV-2 population.

Figure 3.

3 D ribbon representation of the interaction domains of SARS-CoV-2 Spike (left, orange) and human ACE2 (right, green), based on the crystal structure 6LZG deposited on Protein Data Bank and produced by Wang et al. (2020). The positions of the three most frequent Spike mutations in the interacting region (AA 350-550) with a non-zero GBPM score are indicated: N439K, N501Y and S477N.

Figure 4.

(A) Occurrence of AA-changing variants on SARS-CoV-2 Spike protein. X-axis indicates the position of the affected AA. Y-axis indicates the log10 of the number of occurrences of the variant in the SARS-CoV-2 dataset. Labels indicate variants affecting ACE2/Spike binding and detected in at least five SARS-CoV-2 sequences. Vertical dashed lines indicate crystalized region analyzed (aa 330 – 530). The D614G variant, located outside the RBD, is also indicated. (B) Scatter plot indicating the occurrence of the variant in the population (x-axis) and the GBPM score of the reference AA in the model (y-axis). Mutations with non-zero GBPM score are indicated. CC indicates the Pearson correlation coefficient and p indicates the p-value of the CC.

Figure 5.

Frequency of mutations on ACE2. X-axis indicates the AA position in isoform 1 (UniProt id Q9BYF1-1). Y-axis indicates the allele frequency in the global population according to the GNOMAD v3 database. Labels indicate AA changes observed in the human population with non-zero GBPM average score in the ACE2/Spike interaction models. Vertical dashed lines indicate the crystalized region analyzed in this study (aa 15 – 615).