A1 Refereed original research article in a scientific journal
Proteomic Approach for Comparative Analysis of the Spike Protein of SARS-CoV-2 Omicron (B.1.1.529) Variant and Other Pango Lineages
Authors: Jain Mukul, Patil Nil, Gor Darshil, Sharma Mohit Kumar, Goel Neha, Kaushik Prashant
Publisher: MDPI
Publishing place: Basel
Publication year: 2022
Journal: Proteomes
Journal name in source: PROTEOMES
Journal acronym: PROTEOMES
Article number: 34
Volume: 10
Issue: 4
Number of pages: 14
DOI: https://doi.org/10.3390/proteomes10040034
Web address : https://doi.org/10.3390/proteomes10040034
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/178101317
Additional information: Correction to this article: https://www.mdpi.com/2227-7382/12/3/19 ; DOI: 10.3390/proteomes12030019
The novel SARS-CoV-2 variant, Omicron (B.1.1.529), is being testified, and the WHO has characterized Omicron as a variant of concern due to its higher transmissibility and very contagious behavior, immunization breakthrough cases. Here, the comparative proteomic study has been conducted on spike-protein, hACE2 of five lineages (alpha, beta, delta, gamma and Omicron. The docking was performed on spike protein- hACE-2 protein using HADDOCK, and PRODIGY was used to analyze the binding energy affinity using a reduced Haddock score. Followed by superimposition in different variant-based protein structures and calculated the esteem root mean square deviation (RMSD). This study reveals that Omicron was seen generating a monophyletic clade. Further, as alpha variant is the principal advanced strain after Wuhan SARS-CoV-2, and that is the reason it was showing the least likeness rate with the Omicron and connoting Omicron has developed of late with the extreme number of mutations. alpha variant has shown the highest binding affinity with hACE2, followed by beta strain, and followed with gamma. Omicron showed a penultimate binding relationship, while the delta variant was seen as having the least binding affinity. This proteomic basis in silico analysis of variable spike proteins of variants will impart light on the development of vaccines and the identification of mutations occurring in the upcoming variants.
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