Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2

Rakib, Ahmed; Sami, Saad Ahmed; Islam, Md. Ashiqul; Ahmed, Shahriar; Faiz, Farhana Binta; Khanam, Bibi Humayra; Marma, Kay Kay Shain; Rahman, Maksuda; Uddin, Mir Muhammad Nasir; Nainu, Firzan; Emran, Talha Bin; Simal-Gandara, Jesus

doi:10.3390/molecules25215088

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Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2

^1,2,

¹,

¹,

¹,

¹,

¹,

Mir Muhammad Nasir Uddin

¹,

Firzan Nainu

Talha Bin Emran

^4,*

and

Jesus Simal-Gandara

^5,*

Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh

Department of Pharmacy, Mawlana Bhashani Science & Technology University, Santosh, Tangail 1902, Bangladesh

Faculty of Pharmacy, Hasanuddin University, Tamalanrea, Kota Makassar, Sulawesi Selatan 90245, Indonesia

⁴

Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh

⁵

Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo–Ourense Campus, E32004 Ourense, Spain

Authors to whom correspondence should be addressed.

Molecules 2020, 25(21), 5088; https://doi.org/10.3390/molecules25215088

Received: 19 September 2020 / Revised: 26 October 2020 / Accepted: 28 October 2020 / Published: 2 November 2020

(This article belongs to the Special Issue Food and Drug Analysis Ⅱ)

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Abstract

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. View Full-Text

Keywords: COVID-19; SARS-CoV-2; vaccine; nucleocapsid protein; bioinformatics; immunoinformatics; epitope

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MDPI and ACS Style

Rakib, A.; Sami, S.A.; Islam, M.A.; Ahmed, S.; Faiz, F.B.; Khanam, B.H.; Marma, K.K.S.; Rahman, M.; Uddin, M.M.N.; Nainu, F.; Emran, T.B.; Simal-Gandara, J. Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2. Molecules 2020, 25, 5088. https://doi.org/10.3390/molecules25215088

AMA Style

Rakib A, Sami SA, Islam MA, Ahmed S, Faiz FB, Khanam BH, Marma KKS, Rahman M, Uddin MMN, Nainu F, Emran TB, Simal-Gandara J. Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2. Molecules. 2020; 25(21):5088. https://doi.org/10.3390/molecules25215088

Chicago/Turabian Style

Rakib, Ahmed, Saad A. Sami, Md. A. Islam, Shahriar Ahmed, Farhana B. Faiz, Bibi H. Khanam, Kay K.S. Marma, Maksuda Rahman, Mir M.N. Uddin, Firzan Nainu, Talha B. Emran, and Jesus Simal-Gandara. 2020. "Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2" Molecules 25, no. 21: 5088. https://doi.org/10.3390/molecules25215088

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Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2

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