Computational studies on the interaction of SARS-CoV-2 Omicron SGp RBD with human receptor ACE2, limonin and glycyrrhizic acid

Abstract

On November 24, 2021, the SARS-CoV-2 Omicron variant (B.1.1.529) was first identified in South Africa. The World Health Organization (WHO) declared the Omicron as a variant of concern (VoC) because of the unexpected and large numbers of mutations occurred in the genome, higher viral transmission and immune evasions. The present study was performed to explore the interactions of SARS-CoV-2 spike glycoprotein receptor-binding domain (SGp RBD) of the three variants (Omicron, Delta, and WT) with the receptor hACE2. The structural changes occurred in Omicron due to the mutations at key positions improved the ability to mediate SARS-CoV-2 viral infection compared to other VoCs. The phytochemicals limonin and glycyrrhizic acid were docked with the SGp RBD of the variants WT, Delta and Omicron. The computed dock score revealed that limonin and glycyrrhizic acid binds effectively at the SGp RBD of all three variants, and showed almost similar binding affinity at the binding interface of ACE2. Therefore, despite the multiple mutations occurred in Omicron and its viral transmission is comparatively high, the computed binding affinity of the phytochemicals limonin and glycyrrhizic acid supported that the traditional medicines can be useful in formulating adjuvant therapies to fight against the SARS-CoV-2 Omicron.

Graphical abstract