Several coronaviruses can infect humans, and the disease can range from the mild condition like the common cold caused by HCoV-229E, HCoV-NL63, HCoVHKU1, and HCoV-OC43 to severe disease or even death (MERS-CoV, SARS-CoV and COVID-19) (Huang et al., 2020a); Dandekar and Perlman, 2005). The SARS-CoV-2 disease pathogenesis may be due to direct viral infection, cytokine dysregulation, or coagulopathy (Cevik et al., 2020). In SARS, antibody to S protein is protective, but CD8+ T-cell mediated damage is responsible for acute respiratory distress syndrome, multi-organ failure, and cardiac injury (Zheng et al., 2020). ACE2 and dipeptidyl peptidase 4 are two COVID-19 receptors and transducers involved in normal physiological processes such as maintaining glucose homeostasis, renal and cardiovascular physiology, and regulating inflammation. Hence, any disturbance in these receptors leads to many physiological disturbances in many organs (Valencia et al., 2020).
According to the complete genome sequence analysis, the evolutionary relationship rate of SARS-CoV 2 with bat SARS coronavirus (SARSr-CoV RaTG13) was 96.00%. This indicates that SARS-CoV-2 may have originated in bats. These Coronaviruses have a diameter of 80 to 120 nm. The virion surface is made up of three proteins: spike (S), membrane (M), and tiny membrane protein (E), which gives the virus a crownlike appearance under electron microscopy. The ORF1ab polyprotein, which is found at the viral genome’s five prime ends, encodes for 15 or 16 non-structural proteins. It accounts for two-thirds of the viral proteome. Other than structural and non-structural proteins some accessory proteins were discovered, including ORF7b, ORF3a, orf7a, ORF8, ORF10, and ORF6 (Chan et al., 2020a; Zhang et al., 2020). The non-structural gene ORF1ab, which includes ORF1a and ORF1b, is the most significant gene component of SARS-CoV-2. Papain-like protease (PLpro) and 3C-like protease cleave the replicase ORF1ab (3CLpro). In addition, many non-structural proteins (NSP1-NSP16) are cleaved from ORF1ab.
Analysis and construction of BORF1ab cell epitope with TLR3 are carried out with a bioinformatic approach (molecular docking). First, the ORF1ab polyprotein was docked with toll-like receptor-3 (TLR3) using the Cluspro.2 webserver for ligand-receptor binding interaction analysis, which yielded ten distinct docking models. Model 0 was chosen for this study since it has the most cluster members (159) and the lowest energy (-603.4 kcal/mol). The PDMsum webserver’s analysis of molecular docking results revealed a significant interaction. It showed that the interface area of the construct ORF1ab construct was 872(Å2), while TLR3 had a 749 (Å2). Moreover, the interaction revealed seven salt bridges 127 non-bonded contacts. Because hydrogen bonds are critical for vaccine formation and stability, the design includes 15 hydrogen bonds between chain-9 (vaccine) and chain A (receptor).
Before 2019, six coronavirus strains had been identified as potentially pathogenic to humans. However, the seventh strain of SARS-CoV-2 was discovered in Wuhan, China, in December 2019. About 214.27 million confirmed cases of COVID-19, with 4.27 million deaths, have been reported by WHO since January 2020 (WHO, 2021). Therefore, searching for a definitive solution to manage the infection of COVID-19 is an urgent need. Vaccination is an effective way to prevent the spread of Covid-19, but vaccine development is expensive. This burden can be reduced by employing viroinformatic techniques and looking for ways to produce subunit vaccines using viruses’ whole genomes and proteomes.
The current research is based on the three Surabaya B.1.465 isolates generated at RCVTD- ITD of the University of Airlangga Surabaya from the nasopharyngeal swabs of Covid-19 patients. Several studies on the characterization of SARS-CoV-2 and its protein have recently been published mentions SARS CoV-2 has various resistance due to a high mutational rate in its genome; because that, the viral protein of SARS-CoV-2 is the primary focus of our research.
The phylogenetic analysis explains the evolutionary history and relationships among organisms. The phylogenetic relationship of Surabaya isolates was carried out using Mega 11 software by the Neighbor-Joining method. The evolutionary distances were computed using the Maximum Composite Likelihood method. According to phylogenetic results, it is proved that Surabaya isolates RSDS-RCVTD-UNAIR42-A is very close to Pakistan isolate JRCGRKHI13/2020 and Bangladesh isolate BCSIR-DU16/2020. The other two Surabaya isolates, RSDSRCVTD-UNAIR-54-A and RSDS-RCVTD-UNAIR-49A/2021, are close to the Egyptian isolate MASRI11/2020 and Pakistans isolate RCGR-KHI25/2020. The same SARS-CoV-2 lineage B.1.465 circulated India, North America, France, Hongkong, Africa, Spain, Italy, Finland, Germany, UK (GISAD, 2021).
SARS-CoV-2 has various resistance due to a high mutation rate in its genome. Therefore, the protein that covers the virus is the target of this research. This study focused on three structural SARS-CoV-2 protein fusion forms to find the best immunogenic protein to trigger humoral and cellular immune responses.
According to this study, the SARS-CoV-2 virus is constantly mutating. These mutations are the most significant barrier to developing an effective vaccine to combat the COVID-19 infection. Moreover, using a bioinformatics approach, the predicted, antigenic, nonallergic, non-toxic B-cell epitopes (KNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTK HSSGV, DRDAAMQRK, and GSYKDWSYSGQSTQL) conserved in ORF1ab polyproteins: elicited strong humoral and cellular immune responses. These findings suggested that incorporating ORF1ab polyprotein B-cell epitopes into developing subunit vaccines against SARS-CoV-2 might result in significant immunological responses. Furthermore, for the sake of humanity, these findings should be tested in the laboratory and in the field to assess actual immunogenic responses.
Author: Fedik Abdul Rantam
Journal: Shehzad A., Tacharina M.R.,Kuncorojakti S., Ahmad H.I., A’la R., Wijaya A.Y., Tyasningsih W. and Rantam, F.A. 2021. Molecular Characterization and prediction of B-Cell Epitopes for the development of SARS-CoV2 vaccine through bioinformatics approach. J.Pharm & Pharm Res. 10 (3), 429-444, 2022.
