scholarly journals Coronavirus epitope prediction from highly conserved region of spike protein

2020 ◽  
Vol 9 (2) ◽  
pp. 169
Author(s):  
Valentina Yurina
Keyword(s):  
Epitope Prediction ◽  
Spike Protein ◽  
Conserved Region

scholarly journals Impact of glycan cloud on the B-cell epitope prediction of SARS-CoV-2 Spike protein

npj Vaccines ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
René Wintjens ◽  
Amanda Makha Bifani ◽  
Pablo Bifani
Keyword(s):  
B Cell ◽  
Cell Epitope ◽  
Epitope Prediction ◽  
Spike Protein ◽  
B Cell Epitope

scholarly journals Oral and Intranasal Immunization with Recombinant Food-Grade Lactococcus Lactis Expressing High Conserved Region of SARS-CoV-2 Spike Protein Triggers Immunity Responses in Mice

2021 ◽  
Author(s):  
Valentina Yurina ◽  
Oktavia Rahayu Adianingsih ◽  
Nashi Widodo
Keyword(s):  
Viral Infections ◽  
Spike Protein ◽  
Nasal Administration ◽  
Oral Vaccination ◽  
Gene Encoding ◽  
Effective Prevention ◽  
Less Invasive ◽  
Humoral Immune ◽  
Long Time ◽  
Conserved Region

Abstract Background: The COVID-19 pandemic began at the end of 2019 in Wuhan, China, and has spread throughout the world until mid-2021. Thus far, no specific therapy has been found for the coronavirus family. Vaccination still becomes the most effective prevention of pathogenic infections, including viral infections. However, little data show that this vaccination can protect against SARS-CoV-2 virus for a long time. Thus, revaccination needs to be regularly carried out to prevent the occurrence of COVID-19. Vaccination by injection is invasive, and it becomes one of the reasons people refuse to get revaccinated. Therefore, we developed a less invasive vaccine based on oral or nasal administration. The gene encoding the high conserved region (HCR) spike protein was inserted into pNZ8149 and expressed in L. lactis NZ3900. Results: The results of nasal and oral administration in experimental animals showed that L. lactis carrying the HCR gene could induce a humoral immune response, as indicated by an increasing IgG and IgA against SARS-CoV-2 (IgG/IgA-SARS-CoV-2) levels and the lymph cell population after nasal and oral vaccination in mice (p<0.05). Conclusion: This study shows promising results that can be developed into a less invasive alternative to nasal and oral vaccination.

scholarly journals The answer lies in the energy: how simple atomistic molecular dynamics simulations may hold the key to epitope prediction on the fully glycosylated SARS-CoV-2 spike protein

2020 ◽  
Author(s):  
Stefano Serapian ◽  
Filippo Marchetti ◽  
Alice Triveri ◽  
Giulia Morra ◽  
Massimiliano Meli ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Information ◽  
Epitope Prediction ◽  
Spike Protein ◽  
Cell Infection ◽  
Monosaccharide Residue ◽  
Decomposition Approach ◽  
S Protein ◽  
Dynamics Simulations

AbstractBetacoronavirus SARS-CoV-2 is posing a major threat to human health and its diffusion around the world is having dire socioeconomical consequences. Thanks to the scientific community’s unprecedented efforts, the atomic structure of several viral proteins has been promptly resolved. As the crucial mediator of host cell infection, the heavily glycosylated trimeric viral Spike protein (S) has been attracting the most attention and is at the center of efforts to develop antivirals, vaccines, and diagnostic solutions.Herein, we use an energy-decomposition approach to identify antigenic domains and antibody binding sites on the fully glycosylated S protein. Crucially, all that is required by our method are unbiased atomistic molecular dynamics simulations; no prior knowledge of binding properties or ad hoc combinations of parameters/measures extracted from simulations is needed. Our method simply exploits the analysis of energy interactions between all intra-protomer aminoacid and monosaccharide residue pairs, and cross-compares them with structural information (i.e., residueresidue proximity), identifying potential immunogenic regions as those groups of spatially contiguous residues with poor energetic coupling to the rest of the protein.Our results are validated by several experimentally confirmed structures of the S protein in complex with anti- or nanobodies. We identify poorly coupled sub-domains: on the one hand this indicates their role in hosting (several) epitopes, and on the other hand indicates their involvement in large functional conformational transitions. Finally, we detect two distinct behaviors of the glycan shield: glycans with stronger energetic coupling are structurally relevant and protect underlying peptidic epitopes; those with weaker coupling could themselves be poised for antibody recognition. Predicted Immunoreactive regions can be used to develop optimized antigens (recombinant subdomains, synthetic (glyco)peptidomimetics) for therapeutic applications.

scholarly journals Designing multi-epitope based peptide vaccine targeting spike protein SARS-CoV-2 B1.1.529 (Omicron) variant using computational approaches.

2021 ◽  
Author(s):  
Meet Parmar ◽  
Ritik Thumar ◽  
Jigar Sheth ◽  
Dhaval Patel
Keyword(s):  
Transmission Rate ◽  
Peptide Vaccine ◽  
Epitope Prediction ◽  
Spike Protein ◽  
Vaccine Production ◽  
Cell Mediated Immune Response ◽  
New Variant ◽  
A Cell ◽  
Prediction Server ◽  
Multiple Variants

Since the SARS-CoV-2 outbreak in 2019, millions of people have been infected with the virus, and due to its high human-to-human transmission rate, there is a need for a vaccine to protect people. Although some vaccines are in use, due to the high mutation rate in the SARS-CoV-2 multiple variants, the current vaccines may not be sufficient to immunize people against new variant threats. One of the emerging variants of concern is B1.1.529 (Omicron), which carries ~30 mutations in the Spike protein of SARS-CoV-2 is predicted to evade antibodies recognition even from vaccinated people. We used a structure-based approach along with an epitope prediction server to develop a Multi-Epitope based Subunit Vaccine (MESV) involving SARS-CoV-2 B1.1.529 variant spike glycoprotein. The predicted epitope with better antigenicity and non-toxicity were used for designing and predicting vaccine construct features and structure models. The MESV construct In-silico cloning in pET28a expression vector predicted the construct to be highly translational. The proposed MESV vaccine construct was also subjected to immune simulation prediction and was found to be highly antigenic and elicit a cell-mediated immune response. The proposed MESV in the present study has the potential to be evaluated further for vaccine production against the newly identified B1.1.529 (Omicron) variant of concern.

scholarly journals SARS-CoV-2 Omicron variant escapes neutralization by vaccinated and convalescent sera and therapeutic monoclonal antibodies

2021 ◽  
Author(s):  
Nariko Ikemura ◽  
Atsushi Hoshino ◽  
Yusuke Higuchi ◽  
Shunta Taminishi ◽  
Tohru Inaba ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Viral Escape ◽  
Spike Protein ◽  
The Novel ◽  
Neutralization Titer ◽  
Neutralization Activity ◽  
Therapeutic Drugs ◽  
Conserved Region ◽  
Therapeutic Monoclonal Antibodies

The novel SARS-CoV-2 variant, Omicron (B.1.1.529) contains about 30 mutations in the spike protein and the numerous mutations raise the concern of escape from vaccine, convalescent sera and therapeutic drugs. Here we analyze the alteration of their neutralizing titer with Omicron pseudovirus. Sera of 3 months after double BNT162b2 vaccination exhibite ~27-fold lower neutralization titers against Omicron than D614G mutation. Neutralization titer is also reduced in convalescent sera from Alpha and Delta patients. However, some Delta patients have relatively preserved neutralization activity up to the level of 3-month double BNT162b2 vaccination. Omicron escapes from the cocktail of imdevimab and casirivimab, whereas sotrovimab that targets the conserved region to prevent viral escape is effective to Omicron similarly to the original SARS-CoV-2. The ACE2 decoy is another modality that neutralize the virus independently of mutational escape and Omicron is also sensitive to the engineered ACE2.

scholarly journals Prediction of SARS-CoV2 spike protein epitopes reveals HLA-associated susceptibility

2020 ◽  
Author(s):  
Romero-López JP ◽  
Carnalla-Cortés M ◽  
Pacheco-Olvera DL ◽  
Ocampo M ◽  
Oliva-Ramírez J ◽  
...  
Keyword(s):  
Cumulative Incidence ◽  
Epitope Prediction ◽  
Hla Class I ◽  
Statistical Correlation ◽  
Spike Protein ◽  
Class I ◽  
T Cell Epitopes ◽  
Hla Alleles ◽  
Modeling Analysis ◽  
Antigen Presenting

Abstract SARS-CoV2 infection is causing a pandemic disease that is reflected in important public health problems worldwide. HLA-based epitope prediction and association with susceptibility provides an important base for treatment design. Hence the aim of this study is to predict the best antigen-presenting HLA-class I and II alleles in top affected populations and determine probable susceptibility associations. A bioinformatic prediction of T cell epitopes and their restricted HLA class I and II alleles was performed to predict immunogenic epitopes and HLA alleles from the spike protein of the SARS-CoV-2 virus, together with molecular modeling analysis and a correlation with the cumulative incidence of COVID-19 infection in 14 countries. Here, we describe a set of ten highly immunogenic epitopes, together with different HLA alleles that can efficiently present these epitopes to T cells. Most of these epitopes are located within the S1 subunit of the spike protein, suggesting that this area is highly immunogenic. A statistical correlation was found between the frequency of HLA-A*02:03 and HLA-A*31:01 and a low cumulative incidence in the selected countries.

Thermodynamics of the interaction between the spike protein of severe acute respiratory syndrome- coronavirus-2 and the receptor of human angiotensin converting enzyme 2. Effects of possible ligands

2020 ◽  
Author(s):  
Cristina Garcia-Iriepa ◽  
Cecilia Hognon ◽  
Antonio Francés-Monerris ◽  
Isabel Iriepa ◽  
Tom Miclot ◽  
...  
Keyword(s):  
Angiotensin Converting Enzyme ◽  
Molecular Mechanisms ◽  
Molecular Design ◽  
Binding Free Energy ◽  
Transmembrane Protein ◽  
Spike Protein ◽  
Converting Enzyme ◽  
Angiotensin Converting Enzyme 2 ◽  
Rational Molecular Design ◽  
Rational Evaluation

<div><p>Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 180,000 deaths all over the world, still lacking a medical treatment despite the concerns of the whole scientific community. Human Angiotensin-Converting Enzyme 2 (ACE2) was recently recognized as the transmembrane protein serving as SARS-CoV-2 entry point into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the complex and of the effects of possible ligands. Moreover, binding free energy between ACE2 and the active Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein is evaluated quantitatively, assessing the molecular mechanisms at the basis of the recognition and the ligand-induced decreased affinity. These results boost the knowledge on the molecular grounds of the SARS-CoV-2 infection and allow to suggest rationales useful for the subsequent rational molecular design to treat severe COVID-19 cases.</p></div>

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