In silico SARS-CoV-2 vaccine development for Omicron strain using reverse vaccinology

By Vladimir Li, Chul Lee, DongAhn Yoo, Seoae Cho, Heebal Kim. 2022

4 citations recorded by the source corpus.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic began in 2019 but it remains as a serious threat today. To reduce and prevent spread of the virus, multiple vaccines have been developed. Despite the efforts in developing vaccines, Omicron strain of the virus has recently been designated as a variant of concern (VOC) by the World Health Organization (WHO). To develop a vaccine candidate against Omicron strain (B.1.1.529, BA.1) of the SARS-CoV-19. We applied reverse vaccinology methods for BA.1 and BA.2 as the vaccine target and a control, respectively. First, we predicted MHC I, MHC II and B cell epitopes based on their viral genome sequences. Second, after estimation of antigenicity, allergenicity and toxicity, a vaccine construct was assembled and tested for physicochemical properties and solubility. Third, AlphaFold2, RaptorX and RoseTTAfold servers were used to predict secondary structures and 3D structures of the vaccine construct. Fourth, molecular docking analysis was performed to test binding of our construct with angiotensin converting enzyme 2 (ACE2). Lastly, we compared mutation profiles on the epitopes between BA.1, BA.2, and wild type to estimate the efficacy of the vaccine. We collected a total of 10 MHC I, 9 MHC II and 5 B cell epitopes for the final vaccine construct for Omicron strain. All epitopes were predicted to be antigenic, non-allergenic and non-toxic. The construct was estimated to have proper stability and solubility. The best modelled tertiary structures were selected for molecular docking analysis with ACE2 receptor. These results suggest the potential efficacy of our newly developed vaccine construct as a novel vaccine candidate against Omicron strain of the coronavirus.

Subfields: General Health Professions, Infectious Diseases, Molecular Biology

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Citations in the corpus

AlphaFold2 and its applications in the fields of biology and medicine (2023, background): “In addition to the application areas mentioned above, AF2 prediction could also be applied to some other ﬁ elds, such as protein evolution, 177 – 180 rare disease treatment studies, 181 effects of mutation on treatment, 182 – 187 vaccine design, 188 – 190 and so on.”