Impact Factor 2019: 1.940 (@Clarivate Analytics)
5-Year Impact Factor: 1.955 (@Clarivate Analytics)
  • Users Online: 667
  • Print this page
  • Email this page

 
Table of Contents
LETTER TO EDITOR
Year : 2020  |  Volume : 13  |  Issue : 6  |  Page : 283-284

Structural biology oriented predicative analysis of immunogenic epitopes on SARS-CoV-2 viral sequence by variable algorithms


Department of Pharmacology and Toxicology, Centre for Laboratory Animal Technology and Research; School of Pharmacy, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Chennai 600119, Tamil Nadu, India; Chinese Association for Laboratory Animal Sciences, Chaoyang District, Beijing 100021, China

Date of Submission27-Mar-2020
Date of Decision25-Apr-2020
Date of Acceptance28-Apr-2020
Date of Web Publication03-Jun-2020

Correspondence Address:
Dhanasekaran Sivaraman
Department of Pharmacology and Toxicology, Centre for Laboratory Animal Technology and Research; School of Pharmacy, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Chennai 600119, Tamil Nadu, India; Chinese Association for Laboratory Animal Sciences, Chaoyang District, Beijing 100021, China

Login to access the Email id

Source of Support: None, Conflict of Interest: None


DOI: 10.4103/1995-7645.283520

Get Permissions


How to cite this article:
Sivaraman D. Structural biology oriented predicative analysis of immunogenic epitopes on SARS-CoV-2 viral sequence by variable algorithms. Asian Pac J Trop Med 2020;13:283-4

How to cite this URL:
Sivaraman D. Structural biology oriented predicative analysis of immunogenic epitopes on SARS-CoV-2 viral sequence by variable algorithms. Asian Pac J Trop Med [serial online] 2020 [cited 2020 Aug 11];13:283-4. Available from: http://www.apjtm.org/text.asp?2020/13/6/283/283520



Epitopes are small segmented antigenic peptides that are able to elicit the immune response by recognizing B and T-cells. In the present scenario, knowledge of immunogenic epitopes specific to severe acute respiratory syndrome coronavirus (SARS-CoV-2) becomes highly essential for understanding the disease pathogenesis, etiology, disease screening and also for the development of suitable viral vaccine candidates.

The immune system of SARS-CoV-2 affected individuals pursue spectacular dynamism in processing the viral antigen. It was evident that the initial phase of infection was generally managed by the adaptive immune mechanisms, hence well balanced human leukocyte antigen populations are highly successful in developing anti-viral immunity. On the other hand, failure of adaptive immune response triggers inflammatory and destructive changes in the vital organs (kidney, intestine and lungs)[1]. Oxidative stress increases the production of inflammatory mediators such as TNFa, IL & IFNy that set up the condition of cytokine storms and further lead to acute respiratory distress[2],[3].

Experts in the field of immunology claim that T-cells respond well to the immunogenic peptides via activated macrophages and B-cells respond by producing specific antibodies, which has potential to neutralize the viral antigen. In this context, vaccination may be expected to boost immunity in the earlier adaptive phase[4].

Earlier publication of the world’s first report on epitope identification grabs the attention of researchers in the field of immunology, and provides insight into their prediction authors have utilized a single algorithm module for distinguishing B-cell specific epitope[5]. Whereas in the event of triggering host immune response, T-cell plays an inevitable role and gains paramount importance in addition to B-cell. Hence, the present investigation aimed at identifying multiple immunogenic epitopes specific for both B and T-cells. This attempt would substantially benefit researchers in understating the residual biology of the antigenic epitopes that serves as a viable target for potential vaccine against novel coronavirus.

Sequences of SARS-CoV-2 that causes COVID-19 were retrieved from the National Center for Biotechnology Information (Ref Seq: NC_045512.2). The corresponding protein structure was generated using a docking server platform simulated by Autodock 4. Epitope identification screening was performed by Phyre version 2, Ez Mol viewer and also by immune epitope database analysis/BepiPred- 2.0. Three dimensional structures of SARS-CoV-2 viral amino acid highlighting the potential antigenic epitopes specific for T and B-cells are illustrated in [Figure 1].
Figure 1: 3D structure of SARS-CoV-2 viral amino acid highlighting potential antigenic epitopes specific for T and B-cells

Click here to view


Five potential antigenic peptide sequences specific for B-cells were identified using variable algorithm based immune prediction analysis. The first peptide sequence (EDEEEGD) located at position 122 was suggested by Parker hydrophilicity prediction; the second sequence RKQDDK at position 323 by Emini surface accessibility; the third immunogenic sequence (KHCLHVV) at position 235 by using Kolaskar and Tongaonkar Antigenicity prediction; the fourth sequence (GSNQNGE) at position 959 by Karplus and Schulz Flexibility and the fifth sequence (PGDSSSG) at position 1431 by Chou and Fasman-Turn beta-turn predictions as shown in [Table 1].
Table 1: Summarising B-cell antigenic epitopes by variable algorithms

Click here to view


Our results further summarize that nearly 26 different peptides with T-cell immunogenic potential (MHC-HLA-DRB1, 3, 4, 5 specific) have been identified in the viral genome, of which the sequence 25 (SNFRVQPTESIQHRF) ranked first with the highest immunogenic score of 99.54, followed by the sequence 5 (AGIFGADPIHSLRVC), ranked second with 99.29 and the sequence 17 (AALALLLLDRLNQLE) ranked third with 98.03 in the scale of immunogenicity [supplementary Table 1] [Additional file 1].

The pandemic triggered by SARS-CoV-2 is already on the list of the greatest threats that human beings have ever encountered in modern history. Further emerging infection rates urge the need of potential vaccines that necessarily strengthen the immune system through humoral and adaptive backup.

In conclusion, the present analysis explores promising immunogenic epitopes of SARS-CoV-2 virus that could serve as an ideal target for potential vaccines.

Conflict of interest statement

The author declares no competing interests.

Acknowledgement

The author thanks the Indian Council of Medical Research (ICMR), Government of India, New Delhi.

Author’s contribution

Dr. D. Sivaraman involved in study design, in-silico investigation, data collection and compilation of the article.



 
  References Top

1.
Shi Y, Wang Y, Shao C, Huang J, Gan J, Huang X, et al. COVID-19 infection: The perspectives on immune responses. Cell Death Differ 2020. doi: https://doi.org/10.1038/s41418-020-0530-3.  Back to cited text no. 1
    
2.
Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 2020; 395: 497-506.  Back to cited text no. 2
    
3.
Xu Z, Shi L, Wang Y, Zhang J, Huang L, Zhang C, et al. Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet Respir Med 2020; doi: https://doi.org/10.1016/S2213- 2600(20)30076-X.  Back to cited text no. 3
    
4.
Eakachai P, Chutitorn K, Tanapat P. Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic. Asian Pac J Allergy Immunol 2020. doi: 10.12932/AP-200220-0772.  Back to cited text no. 4
    
5.
Joob B, Wiwanitkit V. Epitope finding in 2019 novel coronavirus (2019- nCoV): The first world report. Asian Pac J Trop Med 2020; 13(3). doi:10.4103/1995-7645.277515.  Back to cited text no. 5
    


    Figures

  [Figure 1]
 
 
    Tables

  [Table 1]



 

Top
 
  Search
 
    Similar in PUBMED
   Search Pubmed for
   Search in Google Scholar for
    Access Statistics
    Email Alert *
    Add to My List *
* Registration required (free)  

 
  In this article
References
Article Figures
Article Tables

 Article Access Statistics
    Viewed169    
    Printed6    
    Emailed0    
    PDF Downloaded59    
    Comments [Add]    

Recommend this journal