Investigation of the binding and dynamic features of A.30 variant revealed higher binding of RBD for hACE2 and escapes the neutralizing antibody: A molecular simulation approach

Abstract

With the emergence of Delta and Omicron variants, many other important variants of SARS-CoV-2, which cause Coronavirus disease-2019, including A.30, are reported to increase the concern created by the global pandemic. The A.30 variant, reported in Tanzania and other countries, harbors spike gene mutations that help this strain to bind more robustly and to escape neutralizing antibodies. The present study uses molecular modelling and simulation-based approaches to investigate the key features of this strain that result in greater infectivity. The protein-protein docking results for the spike protein demonstrated that additional interactions, particularly two salt-bridges formed by the mutated residue Lys484, increase binding affinity, while the loss of key residues at the N terminal domain (NTD) result in a change to binding conformation with monoclonal antibodies, thus escaping their neutralizing effects. Moreover, we deeply studied the atomic features of these binding complexes through molecular simulation, which revealed differential dynamics when compared to wild type. Analysis of the binding free energy using MM/GBSA revealed that the total binding free energy (TBE) for the wild type receptor-binding domain (RBD) complex was -58.25 kcal/mol in contrast to the A.30 RBD complex, which reported -65.59 kcal/mol. The higher TBE for the A.30 RBD complex signifies a more robust interaction between A.30 variant RBD with ACE2 than the wild type, allowing the variant to bind and spread more promptly. The BFE for the wild type NTD complex was calculated to be -65.76 kcal/mol, while the A.30 NTD complex was estimated to be -49.35 kcal/mol. This shows the impact of the reported substitutions and deletions in the NTD of A.30 variant, which consequently reduce the binding of mAb, allowing it to evade the immune response of the host. The reported results will aid the development of cross-protective drugs against SARS-CoV-2 and its variants.

Keywords: A.30 variant; Dissociation constant; Free energy; Protein-protein docking; Simulation.

Fig. 1

(A) Mutational landscape of A.30 variant RBD and NTD. (B) Superimposed structure of the wild type RBD and A.30 RBD with R346K, T478K and E484K mutations. (C) Demonstrates the superimposed structures of the wild type NTD and A.30 NTD.

Fig. 2

Interaction profiling of wild type and A.30 RBD-ACE2 complexes. (A) Shows the binding mode of wild type-RBD with ACE2. (B) Shows the binding mode of A.30-RBD with ACE2.

Fig. 3

The comparative binding analysis of wild type and A.30 NTD to the mAb. (A) Shows the binding mode of wild type NTD with mAb while (B) demonstrates the binding of A.30 NTD with mAb.

Fig. 4

Structural and dynamic stability analysis of wild type/A.30 RBD-ACE2 predicted by RMSD analysis. (A) shows the RMSD of wild type/A.30 complexes, (B) Rg plot for wild type/A.30 RBD variants, (C) hydrogen bonds analysis of the wild type and variant.

Fig. 5

(A) Residue flexibility of wild type and A.30 variants calculated as RMSF. (B–D) represent the flexibility index for the three important loops from residues 484–505.

Fig. 6

Structural and dynamic stability analysis of wild type/A.30 NTD variant complexes with mAb, predicted by RMSD analysis. (A) shows the RMSD of wild type/A.30 NTD complexes, (B) Rg plot for wild type/A.30 NTD variants, (C) hydrogen bonds analysis of the wild type and A.30 variant NTD.

Fig. 7

Residual flexibility of wild type and A.30 NTDs in complex with mAb, calculated as RMSF.