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Immunoinformatics-guided design of an epitope-based vaccine against severe acute respiratory syndrome coronavirus 2 spike glycoprotein.
Comput Biol Med. 2020 09; 124:103967.CB

Abstract

AIMS

With a large number of fatalities, coronavirus disease-2019 (COVID-19) has greatly affected human health worldwide. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes COVID-19. The World Health Organization has declared a global pandemic of this contagious disease. Researchers across the world are collaborating in a quest for remedies to combat this deadly virus. It has recently been demonstrated that the spike glycoprotein (SGP) of SARS-CoV-2 is the mediator by which the virus enters host cells.

MAIN METHODS

Our group comprehensibly analyzed the SGP of SARS-CoV-2 through multiple sequence analysis and a phylogenetic analysis. We predicted the strongest immunogenic epitopes of the SGP for both B cells and T cells.

KEY FINDINGS

We focused on predicting peptides that would bind major histocompatibility complex class I. Two optimal epitopes were identified, WTAGAAAYY and GAAAYYVGY. They interact with the HLA-B*15:01 allele, which was further validated by molecular docking simulation. This study also found that the selected epitopes are able to be recognized in a large percentage of the world's population. Furthermore, we predicted CD4+ T-cell epitopes and B-cell epitopes.

SIGNIFICANCE

Our study provides a strong basis for designing vaccine candidates against SARS-CoV-2. However, laboratory work is required to validate our theoretical results, which would lay the foundation for the appropriate vaccine manufacturing and testing processes.

Authors+Show Affiliations

Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh.Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh.Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh.Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh.Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh.Faculty of Pharmacy, Hasanuddin University, Tamalanrea, Kota Makassar, Sulawesi Selatan, 90245, Indonesia.Drug Discovery, GUSTO A Research Group, Chittagong, 4203, Bangladesh; Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.Department of Microbiology, Stamford University Bangladesh, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh.Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh.Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.Department of Gynaecology and Obstetrics, Banshkhali Upazila Health Complex, Jaldi Union, Chittagong, 4390, Bangladesh.Laboratory of Applied Chemistry & Environment, Faculty of Sciences, University Mohammed the First, BP 524, 60000, Oujda, Morocco; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah Almukkarramah, 21955, Saudi Arabia. Electronic address: taibi.ben.hadda@gmail.com.Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah Almukkarramah, 21955, Saudi Arabia.Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh. Electronic address: talhabmb@bgctub.ac.bd.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32828069

Citation

Rakib, Ahmed, et al. "Immunoinformatics-guided Design of an Epitope-based Vaccine Against Severe Acute Respiratory Syndrome Coronavirus 2 Spike Glycoprotein." Computers in Biology and Medicine, vol. 124, 2020, p. 103967.
Rakib A, Sami SA, Mimi NJ, et al. Immunoinformatics-guided design of an epitope-based vaccine against severe acute respiratory syndrome coronavirus 2 spike glycoprotein. Comput Biol Med. 2020;124:103967.
Rakib, A., Sami, S. A., Mimi, N. J., Chowdhury, M. M., Eva, T. A., Nainu, F., Paul, A., Shahriar, A., Tareq, A. M., Emon, N. U., Chakraborty, S., Shil, S., Mily, S. J., Ben Hadda, T., Almalki, F. A., & Emran, T. B. (2020). Immunoinformatics-guided design of an epitope-based vaccine against severe acute respiratory syndrome coronavirus 2 spike glycoprotein. Computers in Biology and Medicine, 124, 103967. https://doi.org/10.1016/j.compbiomed.2020.103967
Rakib A, et al. Immunoinformatics-guided Design of an Epitope-based Vaccine Against Severe Acute Respiratory Syndrome Coronavirus 2 Spike Glycoprotein. Comput Biol Med. 2020;124:103967. PubMed PMID: 32828069.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Immunoinformatics-guided design of an epitope-based vaccine against severe acute respiratory syndrome coronavirus 2 spike glycoprotein. AU - Rakib,Ahmed, AU - Sami,Saad Ahmed, AU - Mimi,Nusrat Jahan, AU - Chowdhury,Md Mustafiz, AU - Eva,Taslima Akter, AU - Nainu,Firzan, AU - Paul,Arkajyoti, AU - Shahriar,Asif, AU - Tareq,Abu Montakim, AU - Emon,Nazim Uddin, AU - Chakraborty,Sajal, AU - Shil,Sagar, AU - Mily,Sabrina Jahan, AU - Ben Hadda,Taibi, AU - Almalki,Faisal A, AU - Emran,Talha Bin, Y1 - 2020/08/13/ PY - 2020/05/28/received PY - 2020/08/08/revised PY - 2020/08/08/accepted PY - 2020/8/23/pubmed PY - 2020/9/25/medline PY - 2020/8/23/entrez KW - COVID-19 KW - Epitope KW - Immunoinformatics KW - SARS-CoV-2 KW - Spike glycoprotein SP - 103967 EP - 103967 JF - Computers in biology and medicine JO - Comput Biol Med VL - 124 N2 - AIMS: With a large number of fatalities, coronavirus disease-2019 (COVID-19) has greatly affected human health worldwide. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes COVID-19. The World Health Organization has declared a global pandemic of this contagious disease. Researchers across the world are collaborating in a quest for remedies to combat this deadly virus. It has recently been demonstrated that the spike glycoprotein (SGP) of SARS-CoV-2 is the mediator by which the virus enters host cells. MAIN METHODS: Our group comprehensibly analyzed the SGP of SARS-CoV-2 through multiple sequence analysis and a phylogenetic analysis. We predicted the strongest immunogenic epitopes of the SGP for both B cells and T cells. KEY FINDINGS: We focused on predicting peptides that would bind major histocompatibility complex class I. Two optimal epitopes were identified, WTAGAAAYY and GAAAYYVGY. They interact with the HLA-B*15:01 allele, which was further validated by molecular docking simulation. This study also found that the selected epitopes are able to be recognized in a large percentage of the world's population. Furthermore, we predicted CD4+ T-cell epitopes and B-cell epitopes. SIGNIFICANCE: Our study provides a strong basis for designing vaccine candidates against SARS-CoV-2. However, laboratory work is required to validate our theoretical results, which would lay the foundation for the appropriate vaccine manufacturing and testing processes. SN - 1879-0534 UR - https://www.unboundmedicine.com/medline/citation/32828069/Immunoinformatics_guided_design_of_an_epitope_based_vaccine_against_severe_acute_respiratory_syndrome_coronavirus_2_spike_glycoprotein_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0010-4825(20)30300-0 DB - PRIME DP - Unbound Medicine ER -