A possible solution
One such alternative is the peptide vaccine. Due to the availability of enormous data regarding the virus across different databases, computer-assisted peptide vaccine design is a feasible way of creating vaccines at a much quicker rate. So far, there are various ‘alignment’ methods to design such peptide vaccines but, here, the discussion focuses on an ‘alignment-free’ and ‘in silico’ technique (Biswas et al, 2021), that involves much less computation and is simpler and easier to execute. With the help of a well-defined mathematical foundation, this approach considers the surface glycoprotein of the virus and predicts specific regions on the protein as therapeutic drug targets. In the first step of the method, a value called the ‘w parameter’ identifies certain regions on the protein surface that have so far mutated the least and are not sequestered by neighbouring amino acids. After this, a precise computational model named ‘2D Polygon representation’ considers these regions and selects the ones covering a larger area on the surface. In the end, it is also ensured that these selected peptides produce enough immunogenic response and form epitopes through T cells and B cells and do not cause any autoimmune disease in the host body. The study carried out by Biswas et al applies this entire protocol to predict such vaccine targets for SARS-CoV-2 with the help of its surface-situated spike glycoprotein.
As shown in the 2021 study (Biswas et al, 2021), there are four peptide regions in the spike protein that can be used to design suitable vaccines – SANLAATKMSECVLG, VEAEVQIDRLITGRL, SNLKPFERDIST and PKKSTNLVKNKCVNF. They are fully surface exposed, least prone to mutation, have high epitope formation capability and have a negligible chance of generating autoimmunity. Most importantly, these target regions have not yet been affected by mutations occurring in the currently existing variants of concern or interest of SARS-CoV-2, which means that these drug targets may work efficiently against the current and future variants of the virus.
The road ahead
The study continues to explain how this computer-assisted approach extends its use against other viruses like Zika and Hendra and how, in the long run, it can effectively design peptide vaccine candidates for any other virus in general (Biswas et al, 2021). As in the case of SARS-CoV-2, the onus is now on the wet lab experts to utilize these four peptide candidates and develop novel vaccines, keeping in mind the necessary steps for production as discussed by the World Health Organization (WHO 1999).
This work has been performed under the supervision of Professor Subhash C Basak, University of Minnesota Duluth, US, and Dr Ashesh Nandy, Center for Interdisciplinary Research and Education, Kolkata, India.
References Nandy A, Dey S, Roy P, Basak SC (2018) Epidemics and Peptide Vaccine response – A brief review. Current Topics in Medicinal Chemistry, 18:2202- 2208. www.doi.org/10.2174/1568026618666181112144745
 Biswas S, Manna S, Nandy A, Basak SC (2021) New Computational Approach for Peptide Vaccine Design Against SARS-CoV-2. International Journal of Peptide Research and Therapeutics. doi.org/10.1007/s10989-021-10251-7
 World Health Organization (1999) Guidelines for the production and quality control of synthetic peptide vaccines [online], www.who.int/publications/m/item/synthetic-peptide-vaccines-annex-1-trs-no-889 [Accessed 30/10/2021]