Abstract

The Omicron variant of SARS-CoV-2 (Spike mutant B.1.1.529) carrying more than 30-point mutations in its structure, of which 15 are localized in the receptor-binding domain (RBD), allows to hypothesize a relevant change in interactivity with ACE2. In previous reports we hypothesized that the worse outcome of the COVID-19 disease in diabetes mellitus condition could be related to the non-enzymatic glycation of ACE2 receptor and an in silico evaluation led to the demonstration that the number of interactions is decreased in comparison to the unmodified model, possibly shifting the virus attack through different, multiple alternative entry routes. Given the evidenced features of this variant, we aimed to investigate with a computational approach the characteristics of Omicron SARS-CoV-2 with respect to its binding to human ACE-2 receptor, in a particular population, namely people affected by diabetes mellitus, at risk for unfavorable outcomes of the COVID-19. The computational analysis, considering the case in which all the lysine residues in the system are subjected to non-enzymatic glycation, confirmed that lysine glycation causes a general loss of interactivity between wild-type (WT)-Spike-RBD and ACE2. In the Omicron variant, Lys417 mutates into an asparagine, preventing the possible non-enzymatic glycation of this residue. Therefore, if non-enzymatic glycation seemed to cause a shift in the way in which the virus enters the cell from the ACE2-mediated mechanism to other pathways, in the case of the Omicron variant the ACE2-mediated approach of the virus seems to remain an important event to take into account. Indeed, interaction profile analysis, together with molecular mechanics–generalized Born surface area (MM-GBSA) calculations, suggests that the Omicron-Spike-RBD maintains a higher affinity for ACE2 subsequently to non-enzymatic glycation with respect to WT-Spike-RBD. The finding of the present computational study may suggest a different clinical relevance of the Omicron variant for the diabetes mellitus field, also in the possible direction of a lower severity of the disease.

Highlights

  • The unprecedented occurrence of a set of several genetic mutations in the Omicron variant of the SARS-CoV-2 virus has drawn particular attention within scientists and media

  • The first of these systems represents the wild-type (WT) form of SARS-CoV-2 Spike receptor-binding domain (RBD) complexed with ACE2 receptor (PDB code: 6M0J; method: X-ray diffraction; resolution: 2.45 Å) [20], while the second involves the SARS-CoV-2 Spike-RDB Omicron variant forming a complex with ACE2 (PDB code: 7T9L; method: cryo-electron microscopy (Cryo-EM); resolution: 2.66 Å) [21]

  • As depicted from the results obtained, while for the WT-Spike-RBD/ACE2 situation the reduction in the number of non-polar interactions due to glycation is not linked to an overall change in the number of polar contacts, for the Omicron variant, the small decrease in the number of hydrogen bonds subsequent to the non-enzymatic glycation of lysine amino acids seems to be compensated by an increase in non-polar interactions

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Summary

Introduction

The unprecedented occurrence of a set of several genetic mutations in the Omicron variant of the SARS-CoV-2 virus has drawn particular attention within scientists and media. The Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) has advised WHO that the Omicron variant should be designated as a variant of concern (VOC), due to the epidemiological parameters initially reported in South Africa, and spreading around the world [3]. This is the fifth VOC to be reported since the beginning of the pandemic [4]; following the experience with the previously reported variants associated with new worsening of the pandemic, a great concern has arisen whether a relevant change in transmissibility and binding affinity is to be expected with the new Omicron variant. Preliminary observations from South Africa suggest that the SARS-CoV-2 Omicron variant is linked to a reduced risk of severe disease when compared to the Delta variant [6, 7]

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