B-cell epitope of SARS-CoV-2 and COVID-19 vaccine candidate



J Pharm Pharmacogn Res 9(6): 766-779, 2021.

Original article

Viroinformatics investigation of B-cell epitope conserved region in SARS-CoV-2 lineage B.1.1.7 isolates originated from Indonesia to develop vaccine candidate against COVID-19

[Investigación viroinformática de la región conservada del epítopo de células B en el linaje SARS-CoV-2 B.1.1.7 aislamientos originados en Indonesia para desarrollar una vacuna candidata contra COVID-19]

Arif N. M. Ansori1,2#, Reviany V. Nidom1,3*#, Muhammad K. J. Kusala1,2, Setyarina Indrasari1,3, Irine Normalina1,4, Astria N. Nidom1,3, Balqis Afifah1,3, Kartika B. Sari1,5, Nor L. Ramadhaniyah1,5, Mohammad Y. Alamudi1,3, Umi Cahyaningsih6, Kuncoro P. Santoso1,2, Heri Kuswanto5, Chairul A. Nidom1,2,3*

1Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia.

2Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia.

3Riset AIRC Indonesia, Surabaya, Indonesia.

4Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.

5Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia.

6Faculty of Veterinary Medicine, IPB University, Bogor, Indonesia.

#Both authors contributed equally.

*E-mail: reviany@pnfinstitute.org, nidomca@pnfinstitute.org, nidomca@fkh.unair.ac.id

Abstract

Context: SARS-CoV-2, a member of family Coronaviridae and the causative agent of COVID-19, is a virus which is transmitted to human and other mammals.

Aims: To analyze the B-cell epitope conserved region and viroinformatics-based study of the SARS-CoV-2 lineage from Indonesian B.1.1.7 isolates to invent a vaccine nominee for overcoming COVID-19.

Methods: The sequences of seven Indonesian B.1.1.7 isolates, Wuhan-Hu-1 isolate, and WIV04 isolate were extracted from the GISAID EpiCoV and GenBank, NCBI. MEGA X was employed to understand the transformations of amino acid in the S protein and to develop a molecular phylogenetic tree. The IEDB was implemented to reveal the linear B-cell epitopes. In addition, PEP-FOLD3 web server was utilized to perform peptide modeling, while docking was performed using PatchDock, FireDock, and the PyMOL software. Moreover, in silico cloning was developed by using SnapGene v.3.2.1 software.

Results: In this study, the changes of amino acid in all seven Indonesian B.1.1.7 isolates were uncovered. Furthermore, various peptides based on the B-cell epitope prediction, allergenicity prediction, toxicity prediction from S protein to generate a vaccine contrary to SARS-CoV-2 were identified. Furthermore, the development of in silico cloning using pET plasmid was successfully achieved.

Conclusions: This study exhibits the transformations of amino acid in Indonesian B.1.1.7 isolates, and proposes four peptides (“LTPGDSSSGWTAG”, “VRQIAPGQTGKIAD”, “ILPDPSKPSKRS”, and “KNHTSPDVDLG”) from S protein as the candidate for a peptide-based vaccine. However, further advance trials such as in vitro and in vivo testing are involved for validation.

Keywords: COVID-19; SARS-CoV-2; vaccine design; viroinformatics.

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Resumen

Contexto: SARS-CoV-2, un miembro de la familia Coronaviridae y el agente causante de COVID-19, es un virus que se transmite a humanos y otros mamíferos.

Objetivos: Analizar la región conservada del epítopo de células B y el estudio basado en viroinformática del linaje SARS-CoV-2 de los aislados B.1.1.7 de Indonesia para inventar una vacuna candidata para superar COVID-19.

Métodos: Las secuencias de siete aislamientos B.1.1.7 indonesios, el aislado Wuhan-Hu-1 y el aislado WIV04 se extrajeron de GISAID EpiCoV y GenBank, NCBI. Se empleó MEGA X para comprender las transformaciones de aminoácidos en la proteína S y para desarrollar un árbol filogenético molecular. El IEDB se implementó para revelar los epítopos de células B lineales. Además, se utilizó el servidor web PEP-FOLD3 para realizar el modelado de péptidos, mientras que el acoplamiento se realizó mediante PatchDock, FireDock y el software PyMOL. Además, la clonación in silico se desarrolló utilizando el software SnapGene v.3.2.1.

Resultados: En este estudio, se descubrieron los cambios de aminoácidos en los siete aislamientos de B.1.1.7 de Indonesia. Además, se identificaron varios péptidos basados en la predicción del epítopo de células B, la predicción de la alergenicidad, la predicción de la toxicidad de la proteína S para generar una vacuna contraria al SARS-CoV-2. Además, se logró con éxito el desarrollo de la clonación in silico utilizando el plásmido pET.

Conclusiones: Este estudio exhibe las transformaciones de aminoácidos en aislados B.1.1.7 de Indonesiay propone cuatro péptidos (“LTPGDSSSGWTAG”, “VRQIAPGQTGKIAD”, “ILPDPSKPSKRS” y “KNHTSPDVDLG”) de la proteína S como candidato para una vacuna basada en péptidos. Sin embargo, para la validación se requieren más ensayos in vitro e in vivo.

Palabras Clave: COVID-19; SARS-CoV-2; vaccine design; viroinformatics.

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Citation Format: Ansori ANM, Nidom RV, Kusala MKJ, Indrasari S, Normalina I, Nidom AN, Afifah B, Sari KB, Ramadhaniyah NL, Alamudi MY, Cahyaningsih U, Santoso KP, Kuswanto H, Nidom CA (2021) Viroinformatics investigation of B-cell epitope conserved region in SARS-CoV-2 lineage B.1.1.7 isolates originated from Indonesia to develop vaccine candidate against COVID-19. J Pharm Pharmacogn Res 9(6): 766–779.

© 2021 Journal of Pharmacy & Pharmacognosy Research (JPPRes)