Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity

Abstract

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak in December 2019 has caused a global pandemic. The rapid mutation rate in the virus has created alarming situations worldwide and is being attributed to the false negativity in RT-PCR tests. It has also increased the chances of reinfection and immune escape. Recently various lineages namely, B.1.1.7 (Alpha), B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.617.3 have caused rapid infection around the globe. To understand the biophysical perspective, we have performed molecular dynamic simulations of four different spikes (receptor binding domain)-hACE2 complexes, namely wildtype (WT), Alpha variant (N501Y spike mutant), Kappa (L452R, E484Q) and Delta (L452R, T478K), and compared their dynamics, binding energy and molecular interactions. Our results show that mutation has caused significant increase in the binding energy between the spike and hACE2 in Alpha and Kappa variants. In the case of Kappa and Delta variants, the mutations at L452R, T478K and E484Q increased the stability and intra-chain interactions in the spike protein, which may change the interaction ability of neutralizing antibodies to these spike variants. Further, we found that the Alpha variant had increased hydrogen interaction with Lys353 of hACE2 and more binding affinity in comparison to WT. The current study provides the biophysical basis for understanding the molecular mechanism and rationale behind the increase in the transmissivity and infectivity of the mutants compared to wild-type SARS-CoV-2.

Keywords: B.1.1.7; B.1.617.2; COVID-19; E484Q; N501Y mutation; T478K and L452R mutation; spike protein.

Figure 1

The structure of the receptor binding domain (RBD) of SARS-CoV-2 spike protein complexed with human angiotensin converting enzyme 2 (hACE2) receptor. (A) The sphere shape residues in hot pink colour show N501Y mutation in the spike protein of SARS-CoV-2. (B) At L452R, T478K and E484Q mutations in the spike protein (RBD) of B.1.617 lineage.

Figure 2

MD simulation analysis of the three simulated complexes. (A) RMSD plot showing similar deviation of all the simulated structures. (B) RMSF plot reveals that Residues 350-400 of the spike receptor binding domain (RBD) are more flexible, while the mutated residues have lesser fluctuation and are also comparable in all three structures. (C) The number of hydrogen bond count indicates that WT and Kappa variant have similar and higher number hydrogen bonds compared to Delta and Alpha variants. (D) MM/GBSA binding free energy of the 20 structure complexes extracted from each trajectory at equal span, suggesting that Kappa and Alpha spike variants have higher affinity for hACE2 in comparison to Delta and WT.

Figure 3

Comparing the interaction of the mutated residues and wild-type residues in the three structures extracted at 50 ns span from the simulated trajectories: spike protein (turquois color), and hACE2 (orange color). (A) Kappa spike variant and its interactions; Gln484 of the spike protein making intra-chain hydrogen bonding with Ser349 and Asn450 in the 100th and 150th ns frame. (B) Alpha spike variant interactions. The hydrogen bond interaction of Tyr501 of mutant spike protein with Lys353 of hACE2 in the 100th and 150th ns frame. (C) The interaction of wild type residues at 50th, 100th and 150th ns of the simulation shows that Glu484 of spike protein had only one hydrogen bond interaction with Ser349 or Tyr351 of spike itself. Similarly, Asn501 of spike was making hydrogen bond interactions with its residues only. (D) In the Delta spike variant, at 100th ns frame, an addition of a hydrogen bond of Lys478 with Ser476 was observed.