Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study

Abstract

At present, novel Coronavirus (2019-nCoV, the causative agent of COVID-19) has caused worldwide social and economic disruption. The disturbing statistics of this infection promoted us to develop an effective vaccine candidate against the COVID-19. In this study, bioinformatics approaches were employed to design and introduce a novel multi-epitope vaccine against 2019-nCoV that can potentially trigger both CD 4þ and CD 8þ T-cell immune responses and investigated its biological activities by computational tools. Three known antigenic proteins (Nucleocapsid, ORF3a, and Membrane protein, hereafter called NOM) from the virus were selected and analyzed for prediction of the potential immunogenic B and T-cell epitopes and then validated using bioinformatics tools. Based on in silico analysis, we have constructed a multi-epitope vaccine candidate (NOM) with five rich-epitopes domain including highly scored T and B-cell epitopes. After predicting and evaluating of the third structure of the protein candidate, the best 3 D predicted model was applied for docking studies with Toll-like receptor 4 (TLR4) and HLA-A Ã 11:01. In the next step, molecular dynamics (MD) simulation was used to evaluate the stability of the designed fusion protein with TLR4 and HLA-A Ã 11:01 receptors. MD studies demonstrated that the NOM-TLR4 and NOM-HLA-A Ã 11:01 docked models were stable during simulation time. In silico evaluation showed that the designed chimeric protein could simultaneously elicit humoral and cell-mediated immune responses.

A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2

“…Finally, MD simulation was performed for 100 ns long and snapshots were saved at every 100 ps into MD trajectory for further analysis. Root-mean-square deviation (RMSD), rootmean-square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and total number of Hbond count were calculated from the MD simulations similar to other studies (Elfiky & Azzam, 2020;Enayatkhani et al, 2020;Muralidharan et al, 2020;Pant et al, 2020).…”

COVID-19 Pandemic: an Overview of epidemiology, pathogenesis, Diagnostics and Potential Vaccines and Therapeutics

“…Medicago company has announced the development of a plant-based vaccine for the SARS-CoV-2 release in March 2020. Besides, further attempts for vaccine development from Moderna utilizing mRNA platform, Inovios DNA vaccine and College of Medicine and University of Queensland's utilizing subunit recombinant expression of potential vaccines [56][57][58][59][60][61][62][63].…”

SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: anin silicoperspective

“…(Doublie & Ellenberger, 1998;Elfiky, 2020a;Elfiky & Ismail, 2018). Several studies are suggesting the effectiveness of different anti-viral drugs and compounds against the coronavirus proteins (Aanouz et al, 2020;Boopathi et al, 2020;Elfiky & Azzam, 2020;Elmezayen et al, 2020;Enayatkhani et al, 2020;Gupta et al, 2020;Khan et al, 2020aKhan et al, , 2020bMuralidharan et al, 2020;Pant et al, 2020;Sarma et al, 2020).…”