Molecular dynamic and docking study of chemical structure of new corona viruses lineages of Omicron BA.n sub-variants (n=1-5); BA.4 or BA.5 strains exhibit the most concern

Abstract

ABSTRACT The first dominant of Omicron-Covid-19 (BA.1) was produced around thirty mutations in its Spike protein in 2019. Quickly BA. 1 became the dominant variant worldwide. Omicron is dangerous for public health concern due to its high infectivity and antibody evasion. Omicron has three lineages or sub variants, BA.1, BA.2, and BA.3. Among them, BA.1 is the currently prevailing sub variant. Omicron BA.1 has around 65 mutations on non-structure protein (NSP3), NSP4, NSP5, NSP6, NSP12, NSP14, S protein, envelope protein, membrane protein, and nucleus capsid proteins. BA.4 and BA.5 are two newly-designated Omicron lineages. They are Omicron viruses with a new combination of mutations containing critical spike protein as a concern for human. In terms of their mutations, BA.4 and BA.5 share mutations across their genomes with both BA.1 and BA.2, but are most similar to BA.2. L452R that previously seen in Kappa, Delta, Epsilon variants and also F486V, and R493 can be seen in both BA.4 and BA.5 where differ from one another in mutations that are outside of the spike gene Data on BA.4 and BA.5, which were first detected in South Africa in early 2022, remain limited. But, these variants seem to spread more quickly than earlier versions of Omicron, such as BA.2, and may be better at dodging the immune system's defenses. By this work, we simulated the spike protein structures, along with peptide-like inhibitor structure of the 7QO7, 7WE9, 7WPC and 7DF4 structures including small-molecule inhibitors, via molecular dynamic and docking methods. Several genomes of various coronaviruses using BAST and MAFFT software have been evaluated.