**3.4 SARS CoV2 nsp13 helicase**

SARS-CoV-2 nsp13 is a 66.85 KDa protein, with a chain length of 601 aa. (located replicase polyprotein pp1ab, from 5325 to 5925 aa), also referred to as the Helicase [33]. SARS-CoV Nsp13 is a key enzyme in the disassembly of double stranded oligonucleotides into single strand using hydrolyzed energy of NTPs [34], having a N-terminal zinc-binding domain (ZBD) containing 3 zinc-finger motifs consisting of 2 tandem C-terminal RecA-like helicase domains (RecA1 and RecA2) and bridging stalk and 1B domains (**Figure 6**). The RecA-like domains catalyze the unwinding of the double stranded RNA and the NTP hydrolysis translocation of the complex. The stalk domain acts as a connection between the domain RecAlike/1B and the ZBD, which acts as an interface with other replicative machinery components [35, 36]. Nsp13 is strongly conserved among nidoviruses (percentage

#### **Figure 6.**

*Domain representation of SARS-CoV2 nsp13 and the structural ribbon representation of the SARS-CoV-2 helicase (PDB ID: 6ZSL). The interdomain borders are labeled with residue numbers. The colors of the protein domains are indicated in panel a (ZBD-red, stalk-cyan blue, 1B-green, 1A-orange and 2A-pink). Three zinc atoms are shown as black spheres. The NTPase active site (violet) consists of six residues-Lys288, Ser289, Asp374, Glu375, Gln404 and Arg567.*

*Repurposed Therapeutic Strategies towards COVID-19 Potential Targets Based on Genomics… DOI: http://dx.doi.org/10.5772/intechopen.96728*

similarity of 99.8% with SARS-CoV, the only 1 amino acid substitution I570 V) consists of five domains that fold in a triangular pyramid shape [37]. These domains hold incredibly high conservation of protein sequences along with its essential role in viral replication, thus making it a vital target for a wide variety of therapeutics to target this viral family [38]. Helicase exhibits various enzymatic roles, including not only hydrolysis of NTPs required by the capping process, but also removal of 50–30 directionally RNA duplexes and 50-triphosphatase RNA activity. In addition, the association of Helicase nsp13 with RdRp Nsp12 promotes RNA unwinding activity and is a crucial viral replication enzyme, in all coronaviruses [39].

#### **3.5 Spike glycoprotein (S)**

The newly discovered SARS-CoV2 S-glycoprotein is a glycosylated trimer, each protomer with a chain length of 1260 amino acids (residues 14–1273), with a molecular weight of 141.1 kDa, consisting of two subunits, the surface subunit S1 and the transmembrane unit S2 [40, 41]. The surface subunit S1 is composed of 672 amino acids (residues 14–685) and differentiated into four divisions: N-terminal domain (NTD), a C-terminal domain (CTD, also known as the receptor-binding domain, RBD), and two subdomains (SD1 and SD2). The transmembrane S2 subunit is composed of 588 amino acids (residues 686–1273) and contains an N-terminal hydrophobic fusion peptide (FP), two heptad repeats (HR1 and HR2), a transmembrane anchor (TA), and an intracellular tail (IT), arranged as FP-HR1- HR2-TA-IT (**Figure 7**). A polybasic amino acid bridge (−QTQT-**NSPRRAR**-SVA-), essential for viral targeting studies, links S1 and S2 together (**Figure 1**). The SARS-CoV-2 S glycoprotein shares similar structural, topological and mechanistic features with other class I fusion proteins, including HIV envelope (Env) glycoprotein and influenza virus haemagglutinin (HA), as a standard class I viral fusion protein [42]. However, using crystallography, the actual structure of this protein can be studied. The Protein Data Bank (PDB) model of the glycoprotein shows various regions that are vital for the infection process compose the subunits [43]. Spike glycoprotein of

#### **Figure 7.**

*Crystal structure of SARS-CoV 2 spike protein (S) PDB ID: 6XR8. Different domains of the spike protein that includes; signal sequence (SS), the N-terminal domain (NTD), receptor-binding domain (RBD), subdomain 1 and 2 (SD1&2), protease cleavage sites (S1/S2/S2′), fusion peptide (FP), heptad repeat 1 and 2 (HR1&2), central helix (CH), connector domain (CD), transmembrane anchor (TA), and intracellular tail (IT).*

the Wuhan coronavirus is specified to be modified by homologous recombination which is supposed to be a combination of the SARS-CoV bat and the not identified Beta-CoV bat. The fluorescent study shows SARS-CoV-2 still uses the same ACE2 (angiotensin-converting enzyme 2) receptor and the entrance pathway previously used by SARS-CoV [44]. Both receptor binding expressed on the cell membranes of receptive cells and membrane fusion are responsible for the S protein. However, in the assembly and budding of viral particles, the proteins M and E are involved [9].
