Effect of Double Mutation (L452R and E484Q) in RBD of Spike Protein on its Interaction with ACE2 Receptor Protein

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) caused coronavirus disease 2019 (COVID-19) pandemic has become a global health issue. Recently, the SARS-CoV-2 strain (B.1.617 double mutant variant) has raised alarms in India and other nations. B.1.617 variant was found to contain two key mutations (L452R and E484Q) in the RBD region of the spike protein. In this work, we have focussed on the effect of the double mutations in spike protein on its binding to the host cell receptor protein, angiotensin-converting enzyme 2 (ACE2). From the molecular dynamics simulation, we observed that the L452R and E484Q double mutant (DM) in spike protein utilizes unique strategies to achieve stable binding to ACE2 compared to the spike protein's wild type (WT). Using MM-GBSA/MM-PBSA algorithms, we found that the binding affinity between spike protein-containing DM and ACE2 is high (GB(TOT) = -47.09 kcal mol(-1), PBTOT= -19.93 kcal mol(-1)) in comparison with spike protein WT and ACE2 (GB(TOT) =-31.79 kcal mol(-1), PBTOT= -6.33 kcal mol(-1)). Stable binding of spike protein to ACE2 is essential for virus entry. They should understand interactions between them while designing drugs and treatment modalities to target or disrupt this interface.