An in silico Method to developing an epitope-based peptide vaccination against SARS-CoV-2's Envelope Protein (E)
This thesis is submitted in partial fulfillment of the requirements for the degree of Bachelor of Pharmacy, 2022.
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Brac University
2023
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10361-177542023-01-18T21:01:38Z An in silico Method to developing an epitope-based peptide vaccination against SARS-CoV-2's Envelope Protein (E) Intesar, Mohammad Nafees Siam, Mohammad Kawsar Sharif Department of Pharmacy, Brac University SARS-CoV-2 Envelope Protein (E) Peptide vaccination COVID-19 (Disease) This thesis is submitted in partial fulfillment of the requirements for the degree of Bachelor of Pharmacy, 2022. Cataloged from PDF version of thesis. Includes bibliographical references (pages 43-46). The new coronavirus (SARS-CoV-2) pandemic, which has killed millions of people throughout the world, has afflicted millions of people. SARS-CoV-2 therapies were severely limited due to the virus's quick pathogenicity. As a result, immunizations were desperately needed because there were no effective medical therapies. Immunoinformatic approaches were employed in this work to develop a multi-epitope vaccine that has the potential to activate the body’s immune system against SARS-CoV-2. The viral structural protein was screened for the first group of epitopes. VaxiJen v2.0, AllerTOP v2.0, and ToxinPred were used to identify probable antigenic, non-toxic, and non-allergenic T-cell and B-cell epitopes, and a projected model was developed. IFNepitope, IL4pred, and IL10pred were used to test cytokine inducing epitopes. One MHC I binding cytotoxic T lymphocyte (CTL) (9-mer) and one MHC II binding helper T lymphocyte (HTL) (9-mer) were tested for T-cell, as both have significant binding affinity and are antigenic, with scores of 0.7476 and 0.5993, respectively. Interferon-gamma, interleukin-4, and interleukin-10 were all induced by the HTL epitope. The chosen B-cell epitope was non-toxic and non-allergenic, with a length of 15 and an antigen score of 0.4992. Epitopes were connected together using appropriate linkers, and biochemical analysis in PROTPARAM revealed the vaccine's instability index (44.39) and GRAVY (-0.023). Through homology modeling, the Phyre2 server projected a PDB model of the final vaccination, which had 100 percent confidence and 47 percent coverage. The z-score (-4.75) was used to determine the overall quality of the model using ProSA online. Patchdock achieved a molecular docking score of 16070 in a 2366.10 square angstrom region by combining complementing form concepts. The C-IMMSIM server was used to examine the proposed vaccine's immunogenic profile. Immune responses, whether tertiary, secondary, or primary, all played a part in vaccination immunity. Mohammad Nafees Intesar B. Pharmacy 2023-01-18T05:34:38Z 2023-01-18T05:34:38Z 2022 2022-06 Thesis ID 13346017 http://hdl.handle.net/10361/17754 en Brac University theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. 46 pages application/pdf Brac University |
| institution |
Brac University |
| collection |
Institutional Repository |
| language |
English |
| topic |
SARS-CoV-2 Envelope Protein (E) Peptide vaccination COVID-19 (Disease) |
| spellingShingle |
SARS-CoV-2 Envelope Protein (E) Peptide vaccination COVID-19 (Disease) Intesar, Mohammad Nafees An in silico Method to developing an epitope-based peptide vaccination against SARS-CoV-2's Envelope Protein (E) |
| description |
This thesis is submitted in partial fulfillment of the requirements for the degree of Bachelor of Pharmacy, 2022. |
| author2 |
Siam, Mohammad Kawsar Sharif |
| author_facet |
Siam, Mohammad Kawsar Sharif Intesar, Mohammad Nafees |
| format |
Thesis |
| author |
Intesar, Mohammad Nafees |
| author_sort |
Intesar, Mohammad Nafees |
| title |
An in silico Method to developing an epitope-based peptide vaccination against SARS-CoV-2's Envelope Protein (E) |
| title_short |
An in silico Method to developing an epitope-based peptide vaccination against SARS-CoV-2's Envelope Protein (E) |
| title_full |
An in silico Method to developing an epitope-based peptide vaccination against SARS-CoV-2's Envelope Protein (E) |
| title_fullStr |
An in silico Method to developing an epitope-based peptide vaccination against SARS-CoV-2's Envelope Protein (E) |
| title_full_unstemmed |
An in silico Method to developing an epitope-based peptide vaccination against SARS-CoV-2's Envelope Protein (E) |
| title_sort |
in silico method to developing an epitope-based peptide vaccination against sars-cov-2's envelope protein (e) |
| publisher |
Brac University |
| publishDate |
2023 |
| url |
http://hdl.handle.net/10361/17754 |
| work_keys_str_mv |
AT intesarmohammadnafees aninsilicomethodtodevelopinganepitopebasedpeptidevaccinationagainstsarscov2senvelopeproteine AT intesarmohammadnafees insilicomethodtodevelopinganepitopebasedpeptidevaccinationagainstsarscov2senvelopeproteine |
| _version_ |
1814308976175611904 |