The SARS-CoV-2 B.1.618 variant slightly alters the spike RBD-ACE2 binding affinity and is an antibody escaping variant: a computational structural perspective

Abstract

Continuing reports of new SARS-CoV-2 variants have caused worldwide concern and created a challenging situation for clinicians. The recently reported variant B.1.618, which possesses the E484K mutation specific to the receptor-binding domain (RBD), as well as two deletions of Tyr145 and His146 at the N-terminal binding domain (NTD) of the spike protein, must be studied in depth to devise new therapeutic options. Structural variants reported in the RBD and NTD may play essential roles in the increased pathogenicity of this SARS-CoV-2 new variant. We explored the binding differences and structural-dynamic features of the B.1.618 variant using structural and biomolecular simulation approaches. Our results revealed that the E484K mutation in the RBD slightly altered the binding affinity through affecting the hydrogen bonding network. We also observed that the flexibility of three important loops in the RBD required for binding was increased, which may improve the conformational optimization and consequently binding of the new variant. Furthermore, we found that deletions of Tyr145 and His146 at the NTD reduced the binding affinity of the monoclonal antibody (mAb) 4A8, and that the hydrogen bonding network was significantly affected consequently. This data show that the new B.1.618 variant is an antibody-escaping variant with slightly altered ACE2-RBD affinity. Moreover, we provide insights into the binding and structural-dynamics changes resulting from novel mutations in the RBD and NTD. Our results suggest the need for further in vitro and in vivo studies that will facilitate the development of possible therapies for new variants such as B.1.618.

Fig. 1. The comparative structural evaluation of wild-type and mutant domains. (A) The complete structure of the spike trimeric protein with domain organization, (B) the superimposed structures of wild-type and B.1.618 RBDs, (C) the superimposed structures of wild-type and truncated (B.1.618) NTDs, and (D) the structure of mAb along with the distribution of three complementarity-determining regions (CDRs), which are compulsory for interaction with the NTD.

Fig. 2. The interaction pattern of the wild-type and B.1.618 variant (E484K) mutant docking complexes. (A) A stick representation of the wild-type-RBD and ACE2. Marine blue represents ACE2 while yellow represents the wild-type spike-RBD. (B) The binding interface of B.1.618 and ACE2 shown as sticks. The cyan colour represents ACE2 while the orange colour represents mutated RBD.

Fig. 3. The interaction patterns of the wild-type and B.1.618 variant (Y145–H146 deleted) NTD docking complexes. (A) A stick representation of the wild-type-NTD and mAb. (B) The binding interface of Y145–H146 deleted and mAb (as sticks).

Fig. 4. The RMSD(s) and R_g(s) of all the complexes in different colours. (a) and (b) The RMSDs of the wild-type-RBD–ACE2 and wild-type-NTD are shown in black while the RMSDs of B.1.618-RBD–ACE2 and B.1.618-NTD are shown in red and blue, respectively. (c) and (d) The R_g(s) of wild-type-RBD–ACE2 and wild-type-NTD are shown in black while the R_g(s) of B.1.618-RBD–ACE2 and B.1.618-NTD are shown in red and blue, respectively.

Fig. 5. Root mean square fluctuations to estimate the residual flexibility. (A) The RMSF for the wild-type and mutant complexes. (B) The RMSF for the wild-type and mutant RBD. (C) The RMSF for ACE2. (D–F) The RMSF values of the three important loops in the RBD required for binding.

Fig. 6. Root mean square fluctuations to estimate the residual flexibility. (A) The RMSF for the wild-type and mutant complexes. (B) The RMSF for the wild-type and mutant NTD. (C) The RMSF for the mAb.

Fig. 7. H-bonding analysis of the 500 ns trajectory of wild-type-RBD–ACE2. (A) The interacting hotspots, (B) the hydrogen bond percentages, and (C–E) the key interactions observed to be sustained during the simulation.

Fig. 8. H-bonding analysis of the 500 ns trajectory of B.1.618-RBD–ACE2. (A) The interacting hotspots. (B) The hydrogen bond percentages. (C–E) The key interactions observed to be sustained during the simulation.

Fig. 9. H-bonding analysis of the 500 ns trajectory of the wild-type-NTD. (A) The interacting hotspots. (B) The hydrogen bond percentages. (C), (D) and (E) The key interactions observed to be sustained during the simulation.

Fig. 10. H-bonding analysis of the 500 ns trajectory of the B.1.618-NTD. (A) The interacting hotspots. (B) The hydrogen bond percentages. (C–E) The key interactions observed to be sustained during the simulation.

Fig. 11. Hydrogen bonding analysis of all the complexes. (A) The H-bonds for the wild-type-RBD–ACE2 and B.1.618-RBD–ACE2 complexes and (B) the H-bonds for the wild-type-NTD and B.1.618-NTD complexes.