**2. The structure of the spike protein and its role**

Since the first announcement of the existence of the new virus, many scientific groups around the world began an intensive search for a suitable drug. In their attempts to develop drugs to treat COVID-19, scientists are focusing on a variety of strategies, including identifying / creating agents that attack and neutralize the virus; agents that affect inflammation, prevent the formation of blood clots, etc. [28]. The structure of the Spro, as well as its biological properties and its role in the entry of SARS-CoV-2 into the cell have been the subject of extensive studies and are the key towards development of adequate preventive and curative approaches [29, 30]. The spike glycoprotein is the crucial protein that determines viral host selection and pathology and thus one of the most important targets for diagnosis and therapy. With a total length of 1273 amino acids, the Spro consists of an extracellular N-terminus, a transmembrane domain anchored in the viral membrane (TM), and a short intracellular C-terminal segment. Bound to the protein are specific polysaccharides whose function is to prevent the host immune system from recognizing the viral protein. Once the virus interacts with the host cell, the conformational changes of the Spro lead to the fusion of the virus with the host cell membrane. The protein consists of the signaling protein (1-13) and the S1 (14-685) and S2 (686-1273) subunits. In addition, the S1 domain, which is responsible for receptor binding, is divided into an N-terminal domain (NTD; 14-305) and a receptor-binding domain (RBD; 319-541).

**Figure 2.**

*The structure of the Spro with labeled domains. The model is based on the cryo-EM structure of SARS-CoV-2 spike glycoprotein trimer in prefusion conformation with a single receptor-binding domain (RBD) in "up" conformation (PDB-ID: 6vsb) [31].*

The S2 subunit, whose function is fusion, consists of the fusion peptide (FP) (788- 806 residues), heptapeptide repeat sequence 1 (HR1) (912-984), HR2 (1163-1213), the TM domain (1213-1237), and the cytoplasmic domain (1237-1273). A polybasic insertion (PRRAR) characteristic of joining the S1/S2 and S′ domains of SARS-CoV-2 can be cleaved by furin, and this cleavage is essential for membrane fusion. The model of the Spro with labeled domains shown in **Figure 2** and results from a detailed allatom molecular dynamics simulation (μs trajectory timeframe) of the fully glycosylated full-length Spro in a viral membrane [32].

The Spro is densely coated with polysaccharides. Each monomer of SARS-CoV-2 Spro has 22 N-linked glycans, 18 of which were conserved between SARS-CoV and SARS-CoV-2 Spro [33]. The glycan shielding has several effects on Spro folding, its processing by host cell proteases, immune evasion, and the elicitation of a humoral immune response. Extensive glycan shielding of the Spro, which blocks the surface of the protein, can thereby hide specific epitopes from neutralization by antibodies, masking them and facilitating immune evasion [33]. In addition, it has been observed that both glycosylated and de-glycosylated S ectodomains bind with almost identical affinity to ACE-2 (1.7 nM vs. 1.5 nM); therefore, it has been suggested that glycosylation of the Spro does not alter the binding affinity of the Spro to ACE-2 [18]. However, the glycan shield of the Spro of SARS-CoV-2 is thought to be less dense and less effective compared to glycoproteins of other viruses such as HIV-1, which may be advantageous for the induction of humoral immunity and vaccine development. Therefore, there is great interest in investigating the potential immunogenicity of glycan components as vaccine candidates [34]. Furthermore, the structure bound to ACE2 shows that the *omicron* variant

*Perspective Chapter: Bioinformatics Study of the Evolution of SARS-CoV-2 Spike Protein DOI: http://dx.doi.org/10.5772/intechopen.105915*

**Figure 3.**

*The structure of SARS-CoV-2 (omicron variant) Spro trimer in complex with ACE2 receptor (PDB ID: 7wpa, left) and with Fab antibody (PDB ID: 7wpf, right) [35].*

spike trimer contains an unusual RBD-RBD interaction and other interactions at the ACE2-RBD interface, both of which contribute to the higher affinity of ACE2 for the *omicron* spike trimer, which is six to nine times higher than that of the wild type, WT. The structural analysis of the *omicron* spike trimer also explains why the *omicron* escapes the most therapeutic antibodies and reduces the efficacy of vaccinations. The interaction of *omicron* spike trimer with ACE2 and Fab antibody is shown in **Figure 3** [35].
