The Increased Amyloidogenicity of Spike RBD and pH-Dependent Binding to ACE2 May Contribute to the Transmissibility and Pathogenic Properties of SARS-CoV-2 Omicron as Suggested by In Silico Study

Abstract

SARS-CoV-2 is a rapidly evolving pathogen that has caused a global pandemic characterized by several consecutive waves. Based on epidemiological and NGS data, many different variants of SARS-CoV-2 were described and characterized since the original variant emerged in Wuhan in 2019. Notably, SARS-CoV-2 variants differ in transmissibility and pathogenicity in the human population, although the molecular basis for this difference is still debatable. A significant role is attributed to amino acid changes in the binding surface of the Spike protein to the ACE2 receptor, which may facilitate virus entry into the cell or contribute to immune evasion. We modeled in silico the interaction between Spike RBDs of Wuhan-Hu-1, Delta, and Omicron BA.1 variants and ACE2 at different pHs (pH 5 and pH 7) and showed that the strength of this interaction was higher for the Omicron BA.1 RBD compared to Wuhan-Hu-1 or Delta RBDs and that the effect was more profound at pH 5. This finding is strikingly related to the increased ability of Omicron variants to spread in the population. We also noted that during its spread in the population, SARS-CoV-2 evolved to a more charged, basic composition. We hypothesize that the more basic surface of the Omicron variant may facilitate its spread in the upper respiratory tract but not in the lower respiratory tract, where pH estimates are different. We calculated the amyloidogenic properties of Spike RBDs in different SARS-CoV-2 variants and found eight amyloidogenic regions in the Spike RBDs for each of the variants predicted by the FoldAmyloid program. Although all eight regions were almost identical in the Wuhan to Gamma variants, two of them were significantly longer in both Omicron variants, making the Omicron RBD more amyloidogenic. We discuss how the increased predicted amyloidogenicity of the Omicron variants RBDs may be important for protein stability, influence its interaction with ACE2 and contribute to immune evasion.

Omicron Coronavirus: pH-Dependent Electrostatic Potential and Energy of Association of Spike Protein to ACE2 Receptor

“…The conclusions about the effect of mutations in the omicron variant are made employing different methods and using different protein structures: our results for the binding energy Δ G assoc and the isoelectric point pI were obtained by the method of protein electrostatics for the S-trimer [ 79 ], but those in the studies of Barroso da Silva et al [ 35 ] and Aksenova et al [ 36 ] by molecular dynamics of RBD. The main difference is that we find out that, at pH 7.4, the omicron variant binds less strongly to ACE2 than the wild-type strain, which we attribute to its lower pathogenicity ( Section 3.2 and Section 4.6 ).…”

“…The main difference is that we find out that, at pH 7.4, the omicron variant binds less strongly to ACE2 than the wild-type strain, which we attribute to its lower pathogenicity ( Section 3.2 and Section 4.6 ). Possibly, the difference stems from the fact that we calculated the binding energy of the almost-whole S-protein (except for the three short intramembrane segments) in its trimeric form (S-trimer), whereas in [ 35 , 36 ], only single RBD, which is a small segment (about two hundred amino acid residues) of the polypeptide chain of one of the three S-monomers, was used.…”

“…In particular, a linear correlation of the binding affinity of the RBD to the ACE2 on the pH-dependent net electric charge of RBD of 15 S mutants is established by electrostatic simulations, which allows for predicting the contagiousness of new coronavirus variants [ 35 ]. Some stronger RBD–ACE2 binding is found at pH 5.5 more than pH 7.5 by molecular dynamics simulations of the RBD–ACE2 binding, which predicts higher infectivity of both wild-type strain and omicron and delta variants in the upper respiratory tract than in the lung; the binding affinity of the omicron variant is higher in comparison to the delta variant and the wild-type strain [ 36 ]. However, it is shown experimentally by surface plasmonic resonance (SPR) that the binding of ACE2 to the S-trimer, S-monomer and RBD is different; after the formation of the ACE2–S-trimer complex, a secondary state in the S-protein emerges, which increases the complex’s stability approximately two hundred times, but this new state appears only when the S-protein is in its trimeric form, it does not occur in the case of the isolated S-monomer and RBD fragment; the authors’ conclusion is that the whole extramembrane domain (including the S1 and S2 subunits) is needed for the formation of a stable complex of the S-protein with the ACE2 receptor [ 37 ].…”

Impacts of the SARS-CoV-2 Spike Protein on the Innate Immune System: A Review

“…However, the amyloidogenic properties of the Spike protein of Omicron variants BA.1 and BA.2 are enhanced by mutations affecting the RBD domain. This results in a stabilization of the Spike protein in the "up" conformation (and hence greater affinity for its ACE2 receptor), enhanced thermal stability, and, potentially, more pronounced amyloid interactions, notably with heparin or fibrinogen, which may impact coagulation [ 136 ].…”

“…Then, one may wonder to what extent the S1/Aβ42 complex contributes to the inflammatory mechanisms and what are the consequences. This is even more important as the Spike protein in Omicron variants appears to have enhanced amyloid properties [ 136 ].…”