Review Article - Clinical Practice (2020) Volume 17, Issue 6

Novel Coronavirus (COVID-19) outbreak: A review on most targetable proteins (S and N) of SARS-CoV-2

Corresponding Author:
Sana Gul Department of Chemistry, Federal Urdu University of Arts, Sciences and Technology, Pakistan E-mail:


In this review speciï¬ÂÃÂ?c aspect of CoV-host interactions have been discussed. Newly identified COVID-19 virus belongs to β-coronavirus, where genome sequencing of Receptor Binding Domain (RBD) of SARS-CoV-2 shows a close relation with bats viruses. Therefore, similar to MERS and SARS it is also having an animal origin (like bats or civet cats). In contrast to SARS it is highly contagious and rate of transmission is high in person to person. In current situation, there is an urgent need of effective vaccine to cure against life threatens infection. This review focuses to understand the most likely targetable proteins i.e. Spike (S) and Nucleocapsid (N). Due to emergence of Coronavirus outbreak globally, present research based on drug-genes signatures available in the literature. Corona viridae is a family of viruses mainly caused upper respiratory infections from common colds to more severe illnesses such as Severe Acute Respiratory Syndrome (SARS). The S-glycoprotein found on the surface of coronavirus and one of the important enzyme that gain attention due to involvement in viral attachment and entry into host cells. Similarly Nucleocapsid (N) protein is highly immunogenic phosphor protein; it is ï¬ÂÃÂ?lamentous and single-stranded viral RNA. It plays role in genome replication and involve in cell signaling pathways. This review is to be addressed the main challenge i.e. pathogenesis of SARS-CoV-2 by understanding both S protein and N protein.


SARS-CoV-2 ▪ Spike (S) protein ▪ Nucleocapsid (N) protein ▪ Receptor Binding Domain (RBD) ▪ Coronavirus ▪ Severe Acute Respiratory Syndrome (SARS)


Coronaviruses (Latin: corona=crown), named for the crown-like spikes (S glycoprotein) on their surface [1]. It belongs to Coronaviridae family, single strand enveloped viruses and included in the Nidovirales order [2]. It is sub divided into four groups-alpha, beta, gamma, and delta on the basis of genomic structure. Coronavirus not only infect mammals also has broad host range including avian. They may cause mainly upper respiratory tract infection and also cause gastrointestinal, hepatic disease and central nervous system [3]. All corona viruses like SARS-CoV and MERS-CoV have had animal origin generally either bats or rodents and caused diseases to humans [4]. So, genome sequencing of new Coronavirus showed 96.2% sequence identity with Bat CoV RaTG13 [5]. Till December 2019, only six different Coronavirus es were known. Four of these (HCoV-NL63, HCoV-229E, HCoV-OC43 and HKU1) usually caused mild common cold-type symptoms in immunecompetent people and the other two (SARSCoV and MERS-CoV) have caused pandemics in the past two decades. Genome of 2019-nCov was sequenced, it shared 79.5% of the genetic sequence of the SARS-CoV that caused the 2002-2003 pandemic [6] and the International Committee on Taxonomy of Viruses renamed the 2019-nCov as SARS-CoV-2 [7]. Generally Coronaviruses are positive-stranded RNA viruses with a 27-kb to 31-kb genome [8]. Similarly, SARS-CoV and MERS-CoV have positive-sense RNA genomes of 27.9 kb and 30.1 kb, respectively [9]. About two-thirds of the Coronavirus genome (~20,000 bases) encodes the viral replicase that involve in viral RNA synthesis. The replicase gene is comprised of two large open reading frames, designated ORF1a and ORF1b [10], it also encodes 3’ structural proteins includes large glycoprotein Spike (S), Envelope (E), a small glycoprotein Membrane (M) mainly embedded in the membrane and phosphorylated Nucleocapsid (N). These structural proteins have genes that evoke pathogenicity in host cells and involve in viral process and replication [11-14].

A plus-strand (+) RNA virus have genetic diversity and applies to their RNA synthesis machinery. Only one enzyme is conserved i.e. RNA-dependent RNA polymerase (RdRp), whereas in other domains replicative and accessory protein may vary. In most of the targets, both Spike (S) and Nucleocapsid (N) protein gains attention due to fusion of virus on the host and involve in replication, respectively [15]. The S protein comprises into two components, S1 (amino-terminal include amino acids 270 to 510) contains the Receptor Binding Domain (RBD); while S2 (carboxylterminal) contains the fusion peptide and due to conformational changes it allows membrane fusion to host cells, allowing entry of virus [16- 21]. Novel Coronavirus cause severe illness as Angiotensin-Converting Enzyme 2 (ACE2) is found in the lower respiratory tract of humans, resulting into fever, destruction of alveolies and characterized atypical pneumonia [22]. ACE2, is contributing as cell receptor for SARS-CoV-2 during entry of virus into host cells and regulates both the cross-species and human-to-human transmission [23].

Despite limited information on this new virus, previous findings support that SARS uses Angiotensin-Converting Enzyme 2 (ACE2) to gain entry in to cells [18,24], in similar fashion nCoV uses dipeptidyl peptidase 4 (DPP4 or CD26) as a functional receptor [25]. This finding may be important as the requirement for ACE2 and may be responsible for the pathogenicity of SARS-CoV. Still pathogenesis of nCoV results into pandemic and the reason is still unknown. Once SARS-CoV-2 enters into host cells due to interactions of SARS-S RBD with the cell surface receptor ACE2 [26,27]. These interactions are further followed by endocytosis at low pH, resulting in the cleavage of SARS-S by a host protease called cathepsin L, thus exposing the S2 domain for membrane fusion, the two subunits arrange and fold into a metastable pre-fusion conformation [28-33]. SARS-S also regulates cell stress responses and apoptosis [34].

Thus, it is important to understand the mechanisms of entry of Coronavirus and further followed by fusion to the membrane to eliminate pathogenesis and can prevent Coronavirus infection at earliest [35]. It is critical to understand S protein fusion because viruses exhibit tropism for specific cells in vivo [36]. It is important to evaluate the role of host proteins in relevant primary cell types when experimentally feasible. Evidence suggests that tissue expression of the ACE2 receptor corresponds to the localization of virus during infection in infected individuals [37-40]. Also, the efficiency of infection in humans also correlates with the ability of the ACE2 to support viral replication [37,41-43].

Further studies demonstrated that when the S protein binds to the ACE2 receptor, followed by type 2 Transmembrane Protease TMPRSS2 leading to cleavage of ACE2 and activation of the spike protein [44,45]. Similarly influenza virus use same mechanism to facilitate viral entry into the target cell. It has been suggested that cells in which ACE2 and TMPRSS2 are simultaneously present are most susceptible to entry by SARS-CoV [46]. Early indications are that SARS-CoV-2 virus also requires ACE2 and TMPRSS2 to enter cells [6]. Viral entry triggers the host’s immune response, and the inflammatory cascade is initiated by Antigen- Presenting Cells (APC). The APC performing two functions: (1) presenting the foreign antigen to CD4+-T-helper (Th1) cells, and (2) releasing interleukin-12 to further stimulate the Th1 cell. The Th1 cells stimulate CD8+-T-killer (Tk) cells that will target any cells containing the foreign antigen. In addition, activated Th1 cells stimulate B-cells to produce antigen-specific antibodies [47]. Immuno-compromised patient fails to combat infection via immune response and their lung samples showed alveolar damage resulting into fatality [17].

Another defense mechanism is Autophagy. It is a cellular stress response that functions to recycle proteins and organelles [48,49]. It is studied in Sindbis virus and herpes simplex virus-1 and showed an important defense mechanism against infection with those viruses [50,51]. It might be possible recovered patient may have autophagy defense mechanism.

Next, most targetable protein known as nucleocapsid N protein; works as an antigen and binds with viral RNA genome. It involve in both RNA binding and replication by modulating transcription process. It also contains two noninteracting structural domain, one is N-terminal domain and serve for RNA binding, where second is C-terminal domain exits in dimer form in solution and considered as dimerization domain [52]. Initially ribonucleoprotein core is form by binding of N protein with viral RNA genome, on the onset of infection this ribonucleoprotein core enters into host cell and interacts with host proteins [53-57]. Coronavirus es replicate entirely in the cytoplasm of cells. In newly recognized human Coronavirus , N protein identified as the causative agent of Severe Acute Respiratory Syndrome (SARS) [35] and found most abundantly protein in infected cells. It contains RNA-binding motif and involve in cellular signaling. It is phosphoprotein involve in formation of viral core, packaging and transcription of viral RNA and have high affinity with viral RNA and form ribonucleocapsid structure [58]. In infections of SARS- CoV, N protein has been involved in the induction of Mitogen-Activated Kinases (MAPKs), especially p38MAPK [59,60]. Additionally both, AP-1 signal pathway is activated in response of stress, inflammation or viral infection and weak induction of Akt signaling pathways were also found [22,61- 63]. AP-1 involve in cellular transduction and regulate cellular process, due to stimuli it activates innate or adaptive immunity. Due to deregulation of AP-1 pathway it results into numerous lymphomas.

In Coronavirus infection, viral mRNA parasitize host machinery and affects host transcription and translation processes, due to similar structure of viral mRNAs to eukaryotic hosts, they capture host machinery to translate the viral mRNA [22]. In vrius life cycle, Nucleocapsid protein not only responsible for mRAN generation, M and E protein together intimately participate in genome condensation and packaging [64-66].


In order to understand virus pathogenesis, there are three strategies to employ either to target Receptor-Binding Domain (RBD) of S protein, second to target ACE2 receptor by antibodies to block S protein binding and prevent virus entry, and last to stop viral replication via targeting AP-1 pathway to stop both transcription and translation process of genomic material.