Molecular dynamic simulation reveals E484K mutation enhances spike RBD-ACE2 affinity and the combination of E484K, K417N and N501Y mutations (501Y.V2 variant) induces conformational change greater than N501Y mutant alone, potentially resulting in an escape mutant

Abstract

Rapidly spreading SARS-CoV-2 variants present not only an increased threat to human health due to the confirmed greater transmissibility of several of these new strains but, due to conformational changes induced by the mutations, may render first-wave SARS-CoV-2 convalescent sera, vaccine-induced antibodies, or recombinant neutralizing antibodies (nAbs) ineffective. To be able to assess the risk of viral escape from neutralization by first-wave antibodies, we leveraged our capability for Molecular Dynamic (MD) simulation of the spike receptor binding domain (S RBD) and its binding to human angiotensin-converting enzyme 2 (hACE2) to predict alterations in molecular interactions resulting from the presence of the E484K, K417N, and N501Y variants found in the South African 501Y.V2 strain – alone and in combination. We report here the combination of E484K, K417N and N501Y results in the highest degree of conformational alterations of S RBD when bound to hACE2, compared to either E484K or N501Y alone. Both E484K and N501Y increase affinity of S RBD for hACE2 and E484K in particular switches the charge on the flexible loop region of RBD which leads to the formation of novel favorable contacts. Enhanced affinity of S RBD for hACE2 very likely underpins the greater transmissibility conferred by the presence of either E484K or N501Y; while the induction of conformational changes may provide an explanation for evidence that the 501Y.V2 variant, distinguished from the B.1.1.7 UK variant by the presence of E484K, is able to escape neutralization by existing first-wave anti-SARS-CoV-2 antibodies and re-infect COVID-19 convalescent individuals.

E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies

“…It is found that the residue Glu484 is located on a flexible loop of RBD, and the substitution of Glu484 by Lys leads to obvious conformational movements of the flexible loop towards the receptor hACE2, which results in the more tight binding between RBD and hACE2. Our simulation results are consistent with the simulation results of Nelson [33]. Therefore, the conformational rearrangements of the binding interface caused by the mutation result in the decrease of the van der Waals and the polar desolvation energies.…”

“…Fortunately, the sera neutralization assay showed that the N501Y mutation has little effect on the neutralization of the human sera elicited by the BNT162b2 mRNA vaccine [25]. In the 501Y.V2 and 501Y.V3 variants, besides the N501Y mutation, two other mutations E484K and K417N (or K417T) were occurred in RBD of the S protein, and it is revealed that the E484K mutation obviously enhances the binding affinity between RBD and hACE2 [33].…”

E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil

“…It creates a new site for the amino acid 75 hACE-2 binding. This interaction seems even stronger than the binding between hACE-2 and the original main site located at position 501 (at RBD and hACE-2 interface) (Nelson et al, 2021) . We speculate that the consequent neutralization escape due to E484K alone or as a part of a larger array of distinct mutations might act as a common evolutionary solution for several different viral lineages.…”

“…To the best of our knowledge, the impact of E484K in different lineages have not been deeply explored. It was structurally demonstrated that, at least in combination with K417N and N501Y, the substitution has profound impact in shifting the main site of contact between viral RBD and hACE-2 residues (Nelson et al, 2021) . However, we still do not know if this holds true for other sets of mutations associated with E484K.…”

“…The presence of E484K and N501Y substitutions in the same SARS-CoV-2 genome may be particularly relevant for viral evolution. This combination was shown to induce more conformational changes than the N501Y mutant alone, potentially altering antibodies' complementarity to this region resulting in the above mentioned immune escape phenomena (Nelson et al, 2021) .…”