Studying the Binding of the Γ- AND Δ- Variants of the SARS-CoV-2 Virus to the Angiotensin Converting Enzyme 2 Receptor Using High Performance Computational Simulations

Abstract

The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected billions worldwide and as newer mutant variants are continuing to emerge, the disease is still expanding to several parts of the world. The virus's main route of entry into human cells is through the angiotensin-converting enzyme-2 (ACE2) receptor using the receptor-binding domain (RBD) of the SARS-CoV-2 virus. Several of the variations on RBD occur at the binding interface leading to the possibility of altering its binding affinity towards the angiotensin-converting enzyme 2 (ACE2) receptor. Using high-performance computing simulations, we attempted to relate transmissibility to binding affinity. The procedures for in-silico mutations, setting up of the system, performing molecular dynamics simulations, and results obtained from the simulated data will be presented. This study suggests that the higher transmissibility in delta and omicron variants is tied to the stronger interactions at the binding interface between the spike protein and ACE2.