Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein Based Novel Epitopes Induce Potent Immune Responses in vivo and Inhibit Viral Replication in vitro

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) initiates infection by attachment of the surface-exposed spike glycoprotein to the host cell receptors. The spike glycoprotein (S) is a promising target for inducing immune responses and providing protection; thus the ongoing efforts for the SARS-CoV-2 vaccine and therapeutic developments are mostly spiraling around S glycoprotein. The matured functional spike glycoprotein is presented on the virion surface as trimers, which contain two subunits, such as S1 (virus attachment) and S2 (virus fusion). The S1 subunit harbors the N-terminal domain (NTD) and the receptor-binding domain (RBD). The RBD is responsible for binding to host-cellular receptor angiotensin-converting enzyme 2 (ACE2). The NTD and RBD of S1, and the S2 of S glycoprotein are the major structural moieties to design and develop spike-based vaccine candidates and therapeutics. Here, we have identified three novel epitopes (20-amino acid peptides) in the regions NTD, RBD, and S2 domains, respectively, by structural and immunoinformatic analysis. We have shown as a proof of principle in the murine model, the potential role of these novel epitopes in-inducing humoral and cellular immune responses. Further analysis has shown that RBD and S2 directed epitopes were able to efficiently inhibit the replication of SARS-CoV-2 wild-type virus in vitro suggesting their role as virus entry inhibitors. Structural analysis revealed that S2-epitope is a part of the heptad repeat 2 (HR2) domain which might have plausible inhibitory effects on virus fusion. Taken together, this study discovered novel epitopes that might have important implications in the development of potential SARS-CoV-2 spike-based vaccine and therapeutics.

Molecular docking and dynamic simulation of conserved B cell epitope of SARS-CoV-2 glycoprotein Indonesian isolates: an immunoinformatic approach

“…The most negative values occurred in the interaction between peptide L9 and HLA-DRB3*02:02, which had an energy value of -890.6 kcal/mol, and L13 peptide, which possessed lower energy (-789.3 kcal/mol) compared to L11 and L12 when binding to HLA-DRB4*01:01 ( Figure 3 ). 35 …”

“…The most negative values occurred in the interaction between peptide L9 and HLA-DRB3*02:02, which had an energy value of -890.6 kcal/mol, and L13 peptide, which possessed lower energy (-789.3 kcal/mol) compared to L11 and L12 when binding to HLA-DRB4*01:01 (Figure 3). 35 The molecular complexes of BCR_B12, HLA-DRB1*01:01_L5, HLA-DRB3*02: 02_L9, and HLA-DRB4*01:01_L13 were analyzed for residual fluctuations in their peptide constituent that interacted through root-mean-square fluctuation (RMSF) level and generated the protein region via the CABS-flex 2.0 server. The results of molecular dynamic simulations exhibited that the BCR_B12 molecular complex contained a fluctuating residue with positions A3, A4, A5, A6, A7, A8, A9, and A10 with RMSF values >0.85 Å to <2.22 Å. Concurrently, the molecular complex of HLA-DRB1*01:01_L5 showed fluctuant residue positions of A9, A10, A11, A12, A13, A14, and A15 with RMSF values >0.52 Å to <1.46 Å.…”

Comparative immunogenicity analysis of intradermal versus intramuscular administration of SARS-CoV-2 RBD epitope peptide-based immunogen In vivo

“…Rest of the IgG responses in both the groups were other IgG isotypes directed (data not shown). Earlier we have shown that in case of IM group, IgG2 responses also makes significant portion in whole IgG [ 17 ]. It might be possible that IgG2 responses would be higher in IM group than the ID, and comparatively more Th2 polarization in case of IM immunization, which could also be reflected by the lower frequency of IFN-γ producing cells in IM group.…”

“…Interestingly, in spleen we observed significantly higher IFN-γ producing CD4+ T response in ID route which might account for the similar IgG1 responses for the two routes despite the fact that the whole IgG response was higher for IM after boost dose. And this observation might be useful for the designing of an effective vaccine candidate against SARS-CoV2 as it might have an impact on the outcome of route of vaccination [ 17 ]. One of the important activities of SARS family of viruses is the formation of receptor-mediated syncytia after the spike protein attaches to hACE2 receptor, thus activating the fusion process [ 36 , 37 ].…”

“…A 20-mer peptide was selected from the receptor binding motif (RBM) region of RBD as peptide immunogen. In our recent study, we have shown that this 20-mer RBD peptide immunogen in combination with Freund's’ adjuvant could induce potent antibody responses in BALB/c mice when immunized intra muscularly [ 17 ]. It was shown that the binding to this region is known to directly interfere with the binding of RBD with hACE2 [ 18 ].…”