Characterization of the spike glycoprotein and construction of an epitope-based vaccine candidate against Indonesian SARS-CoV-2: In silico study

Irine Normalina, Setyarina Indrasari, Reviany V. Nidom, Muhammad K.J. Kusala, M. Yusuf Alamudi, Kuncoro P. Santoso, Kadek Rachmawati, Chairul A. Nidom

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)

Abstract

Introduction: SARS-CoV-2, a new member of the coronavirus family that originated from Wuhan, China, is the agent of COVID-19 pandemic and has rapidly spread globally. Objective: We characterized the spike (S) glycoprotein gene from the Indonesian SARS-CoV-2 isolates to investigate its genetic composition, predict the B cell epitopes, and construct the molecular phylogenetic among Indonesian SARS-CoV-2 isolates. Methods: We employed Wuhan-Hu-1 isolate available in GenBank, NCBI and fourteen Indonesian SARS-CoV-2 isolates acquired from the database (GISAID EpiCoV). We performed using the MEGA X for genetic and amino acid mutations and construct molecular phylogenetic tree. We used IEDB web server to predict epitopes, evaluated allergenicity by applying AllerTOP v.2.0 web server, and non-toxic antigens applying the ToxinPred web server. Results: Interestingly, we discovered that the Indonesian SARS-CoV-2 isolates genetic composition do not have significant changes compared with the reference sequence based on the S glycoprotein gene. In addition, we proposed NSASFSTFKCYGVSPTKLNDLCFTNV as a candidate for a peptide-based vaccine against COVID-19. Furthermore, we also presented the molecular phylogenetic of Indonesian SARS-CoV-2 isolates and other coronaviruses. Conclusion: In summary, this study supplied data regarding mutations in the S glycoprotein and we proposed a candidate for peptide-based vaccine against COVID-19. However, this research still requires further genetic analysis and we recommend improvement in the molecular epidemiological surveillance on COVID-19 in Indonesia.

Original languageEnglish
Pages (from-to)404-413
Number of pages10
JournalSystematic Reviews in Pharmacy
Volume11
Issue number7
DOIs
Publication statusPublished - Aug 2020

Keywords

  • COVID-19
  • In silico
  • SARS-CoV-2
  • Vaccine design

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