Immunoinformatic investigation of three structural protein genes in Indonesian SARS-CoV-2 isolates

Arif N.M. Ansori, Muhammad K.J. Kusala, Irine Normalina, Setyarina Indrasari, Mohammad Y. Alamudi, Reviany V. Nidom, Kuncoro P. Santoso, Kadek Rachmawati, Chairul A. Nidom

Research output: Contribution to journalArticlepeer-review

14 Citations (Scopus)

Abstract

Introduction: SARS-CoV-2 has crossed the species barrier to infect human. It is a rapidly spreading virus that has poses a significant public threat and is a considerable burden on the global economy and human health. Objective: We characterized the nucleocapsid phosphoprotein (N), membrane protein (M), and envelope protein (E) genes of Indonesian isolates to investigate genetic composition, predict B-cell epitopes, and construct a molecular phylogenetic tree. Methods: In the present work, we retrieved the sequences of 16 Indonesian isolates from the GISAID EpiCoV and the Wuhan-Hu-1 isolate (reference sequence) from GenBank, NCBI. We used MEGA X to identify mutations in the three structural protein genes and to construct a molecular phylogenetic tree. The IEDB was employed to reveal the linear B-cell epitopes and other parameters. Allergenicity prediction was evaluated using AllerTOP and ToxinPred was performed to analyze non-toxic antigen prediction. Results: In this study, we report the genetic composition of three structural protein genes in Indonesian SARS-CoV-2 isolates. Furthermore, we identified the peptide RRGPEQTQGNFGDQELIRQGTDYK from nucleocapsid phosphoprotein to generate a peptide-based vaccine contrary to SARS-CoV-2. Conclusion: In summary, we propose a candidate for a peptide-based vaccine contrary to SARS-CoV-2. However, advance trials such as in vitro and in vivo testing are involved for validation.

Original languageEnglish
Pages (from-to)422-434
Number of pages13
JournalSystematic Reviews in Pharmacy
Volume11
Issue number7
DOIs
Publication statusPublished - Aug 2020

Keywords

  • COVID-19
  • SARS-CoV-2
  • Structural protein genes
  • Vaccine design

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