Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2
With an increasing fatality rate, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has emerged as a promising threat to human health worldwide. Recently, the World Health Organization (WHO) has announced the infectious disease caused by SARS-CoV-2, which is known as coronavirus disease-2...
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| Format: | Article |
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MDPI AG
2020-11-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/25/21/5088 |
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| author | Ahmed Rakib Saad Ahmed Sami Md. Ashiqul Islam Shahriar Ahmed Farhana Binta Faiz Bibi Humayra Khanam Kay Kay Shain Marma Maksuda Rahman Mir Muhammad Nasir Uddin Firzan Nainu Talha Bin Emran Jesus Simal-Gandara |
| author_facet | Ahmed Rakib Saad Ahmed Sami Md. Ashiqul Islam Shahriar Ahmed Farhana Binta Faiz Bibi Humayra Khanam Kay Kay Shain Marma Maksuda Rahman Mir Muhammad Nasir Uddin Firzan Nainu Talha Bin Emran Jesus Simal-Gandara |
| author_sort | Ahmed Rakib |
| collection | DOAJ |
| description | With an increasing fatality rate, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has emerged as a promising threat to human health worldwide. Recently, the World Health Organization (WHO) has announced the infectious disease caused by SARS-CoV-2, which is known as coronavirus disease-2019 (COVID-2019), as a global pandemic. Additionally, the positive cases are still following an upward trend worldwide and as a corollary, there is a need for a potential vaccine to impede the progression of the disease. Lately, it has been documented that the nucleocapsid (N) protein of SARS-CoV-2 is responsible for viral replication and interferes with host immune responses. We comparatively analyzed the sequences of N protein of SARS-CoV-2 for the identification of core attributes and analyzed the ancestry through phylogenetic analysis. Subsequently, we predicted the most immunogenic epitope for the T-cell and B-cell. Importantly, our investigation mainly focused on major histocompatibility complex (MHC) class I potential peptides and NTASWFTAL interacted with most human leukocyte antigen (HLA) that are encoded by MHC class I molecules. Further, molecular docking analysis unveiled that NTASWFTAL possessed a greater affinity towards HLA and also available in a greater range of the population. Our study provides a consolidated base for vaccine design and we hope that this computational analysis will pave the way for designing novel vaccine candidates. |
| first_indexed | 2024-03-10T15:08:24Z |
| format | Article |
| id | doaj.art-c81b5e7bbb7a4063b923739ffb30557a |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T15:08:24Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-c81b5e7bbb7a4063b923739ffb30557a2023-11-20T19:32:53ZengMDPI AGMolecules1420-30492020-11-012521508810.3390/molecules25215088Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2Ahmed Rakib0Saad Ahmed Sami1Md. Ashiqul Islam2Shahriar Ahmed3Farhana Binta Faiz4Bibi Humayra Khanam5Kay Kay Shain Marma6Maksuda Rahman7Mir Muhammad Nasir Uddin8Firzan Nainu9Talha Bin Emran10Jesus Simal-Gandara11Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, BangladeshDepartment of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, BangladeshDepartment of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, BangladeshDepartment of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, BangladeshDepartment of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, BangladeshDepartment of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, BangladeshDepartment of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, BangladeshDepartment of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, BangladeshDepartment of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, BangladeshFaculty of Pharmacy, Hasanuddin University, Tamalanrea, Kota Makassar, Sulawesi Selatan 90245, IndonesiaDepartment of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, BangladeshNutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo–Ourense Campus, E32004 Ourense, SpainWith an increasing fatality rate, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has emerged as a promising threat to human health worldwide. Recently, the World Health Organization (WHO) has announced the infectious disease caused by SARS-CoV-2, which is known as coronavirus disease-2019 (COVID-2019), as a global pandemic. Additionally, the positive cases are still following an upward trend worldwide and as a corollary, there is a need for a potential vaccine to impede the progression of the disease. Lately, it has been documented that the nucleocapsid (N) protein of SARS-CoV-2 is responsible for viral replication and interferes with host immune responses. We comparatively analyzed the sequences of N protein of SARS-CoV-2 for the identification of core attributes and analyzed the ancestry through phylogenetic analysis. Subsequently, we predicted the most immunogenic epitope for the T-cell and B-cell. Importantly, our investigation mainly focused on major histocompatibility complex (MHC) class I potential peptides and NTASWFTAL interacted with most human leukocyte antigen (HLA) that are encoded by MHC class I molecules. Further, molecular docking analysis unveiled that NTASWFTAL possessed a greater affinity towards HLA and also available in a greater range of the population. Our study provides a consolidated base for vaccine design and we hope that this computational analysis will pave the way for designing novel vaccine candidates.https://www.mdpi.com/1420-3049/25/21/5088COVID-19SARS-CoV-2vaccinenucleocapsid proteinbioinformaticsimmunoinformatics |
| spellingShingle | Ahmed Rakib Saad Ahmed Sami Md. Ashiqul Islam Shahriar Ahmed Farhana Binta Faiz Bibi Humayra Khanam Kay Kay Shain Marma Maksuda Rahman Mir Muhammad Nasir Uddin Firzan Nainu Talha Bin Emran Jesus Simal-Gandara Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2 Molecules COVID-19 SARS-CoV-2 vaccine nucleocapsid protein bioinformatics immunoinformatics |
| title | Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2 |
| title_full | Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2 |
| title_fullStr | Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2 |
| title_full_unstemmed | Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2 |
| title_short | Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2 |
| title_sort | epitope based immunoinformatics approach on nucleocapsid protein of severe acute respiratory syndrome coronavirus 2 |
| topic | COVID-19 SARS-CoV-2 vaccine nucleocapsid protein bioinformatics immunoinformatics |
| url | https://www.mdpi.com/1420-3049/25/21/5088 |
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