Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening

Abstract

Background. Coronaviruses (CoVs) are enveloped positive-strand RNA viruses which have club-like spikes at the surface with a unique replication process. Coronaviruses are categorized as major pathogenic viruses causing a variety of diseases in birds and mammals including humans (lethal respiratory dysfunctions). Nowadays, a new strain of coronaviruses is identified and named as SARS-CoV-2. Multiple cases of SARS-CoV-2 attacks are being reported all over the world. SARS-CoV-2 showed high death rate; however, no specific treatment is available against SARS-CoV-2. Methods. In the current study, immunoinformatics approaches were employed to predict the antigenic epitopes against SARS-CoV-2 for the development of the coronavirus vaccine. Cytotoxic T-lymphocyte and B-cell epitopes were predicted for SARS-CoV-2 coronavirus protein. Multiple sequence alignment of three genomes (SARS-CoV, MERS-CoV, and SARS-CoV-2) was used to conserved binding domain analysis. Results. The docking complexes of 4 CTL epitopes with antigenic sites were analyzed followed by binding affinity and binding interaction analyses of top-ranked predicted peptides with MHC-I HLA molecule. The molecular docking (Food and Drug Regulatory Authority library) was performed, and four compounds exhibiting least binding energy were identified. The designed epitopes lead to the molecular docking against MHC-I, and interactional analyses of the selected docked complexes were investigated. In conclusion, four CTL epitopes (GTDLEGNFY, TVNVLAWLY, GSVGFNIDY, and QTFSVLACY) and four FDA-scrutinized compounds exhibited potential targets as peptide vaccines and potential biomolecules against deadly SARS-CoV-2, respectively. A multiepitope vaccine was also designed from different epitopes of coronavirus proteins joined by linkers and led by an adjuvant. Conclusion. Our investigations predicted epitopes and the reported molecules that may have the potential to inhibit the SARS-CoV-2 virus. These findings can be a step towards the development of a peptide-based vaccine or natural compound drug target against SARS-CoV-2.

Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for Indonesia and the World Population

“…There have been several reports employing immunoinformatics to identify T-cell epitopes and formulate a vaccine for SARS-CoV-2 infection. PubMed search using keywords 'peptide-based vaccine', 'SARS-CoV-2', and 'immunoinformatics' conducted on 14 October 2021 resulted in 15 research articles [94][95][96][97][98][99][100][101][102][103][104][105][106][107][108]. In this study, we made a prediction based on the HLA alleles that are present with at least 5% frequency in the Indonesian population.…”

Immune Response to SARS-CoV-2 Vaccines

“…The molecular docking revealed strong binding affinities for TLR3 and TLR8. These vaccines could protect against a wide range of diseases, particularly emerging variations of concern (VOC) [ 141 ].…”

SARS-CoV-2 subunit vaccine adjuvants and their signaling pathways

“…For instance, B-defensin adjuvanted multi-epitope (28 epitopes including 3 from replicase, 3 from NSp1, 2 from envelope, 5 from membrane, 6 from nucleocapsid, and 9 from spikes proteins) subunit vaccines have been constructed. The molecular docking demonstrated excellent affinities against TLR3 and TLR8 [ 87 ]. Such types of vaccines might have broad spectrum action including against the emerging variants of concern (VOC).…”