Exploring the rise in hACE2 binding affinity of SARS-CoV-2 Omicron variant

In a latest research posted to the bioRxiv* preprint server, researchers evaluated the interactions of the extreme acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron and wild-type (wt) variants with human angiotensin-converting enzyme 2 (hACE2) receptor.

Study: Improved binding affinity of the OmicronResearch: Improved binding affinity of the Omicron’s spike protein with hACE2 receptor is the important thing issue behind its elevated virulence. Picture Credit score: Match Ztudio/Shutterstock


Significance of the Omicron variant

A novel SARS-CoV-2 variant referred to as Omicron recognized in South Africa in November 2021 was later labeled as a variant of concern (VOC) as a consequence of a lot of mutations in its spike (S) protein receptor-binding area (RBD) in comparison with different SARS-CoV-2 variants just like the wt, Alpha, and Delta. There’s a large surge within the COVID-19 instances after the emergence of the Omicron variant, which poses a significant risk to public well being. Because of the adjustments in Omicron’s genomic sequence, it’s extra transmissible than the opposite SARS-CoV-2 variants, which highlights the significance of extra in-depth research on its mutation sample and pathogenesis to develop efficient remedy methods.

Concerning the research

Within the current research, the authors decided the interactions between the RBD of each SARS-CoV-2 wt and Omicron variants with the hACE2 receptor utilizing molecular dynamics (MD) research and binding free vitality calculations based mostly on molecular mechanics-generalized born floor space strategy (MM-GBSA).

The receptor-binding motif (RBM) adjustments in the entire SARS-CoV-2 variants had been decided by a comparative evaluation. The info concerning the RBM sequences of the SARS-CoV-2 variants had been collected from the NCBI database utilizing the BlastP program. The redundant sequences had been eliminated, and the remaining sequences had been aligned via the EBI-MUSCLE program.  

The RBD mannequin construction of Omicron for the computational modeling was obtained by integrating 15 RBD substitutions (G496S, S371L, S373P, S375F, Y505H, N440K, G446S, S477N, T478K, E484A, 326 Q493R, G339D, Q498R, N501Y, and K417N) into the unique resolved crystal construction utilizing PyMOL software program, which was then vitality minimized for the MD research and binding free vitality calculations.

The protein-protein interplay of the SARS-CoV-2 Omicron and wt variants RBD with hACE2 receptor had been explored and in contrast utilizing MD simulation research. Throughout MD simulations of the RBD-hACE2 complexes by the AMBER 18.0 package deal, f14SB drive discipline parameters had been utilized to the proteins. These complexes had been solvated with water molecules and neutralized with counterions in an orthorhombic simulation field and low-temperature simulations had been carried out.  

The non-covalent intermolecular interactions had been analyzed utilizing UCSF Chimera and VMD software program. Subsequently, the binding free energies of Omicron and wt S RBD with the hACE2 receptor had been computed utilizing MM-GBSA calculations.

Outcomes

The outcomes indicated that the RBM sequence of the SARS-CoV-2 variants together with Omicron has numerous amino acids substitutions in 22 totally different positions within the comparative sequence evaluation.

A complete of 10 mutations had been recognized in Omicron RBM: E484A, G446S, G496S, T478K, N440K, Q493R, S477N, Q498R, Y505H, and N501Y. Among the many 10 mutations, six at positions G496S, G446S, Y505H, Q493R, Q498R, and E484A had been distinctive for Omicron and the remaining 4 mutations had been additionally current in different SARS-CoV-2 variants.

Throughout the MD simulations, the RBD:hACE2 complexes of Omicron and wt variants confirmed some instability within the loop areas. Nonetheless, the computed root imply sq. fluctuation (RMSF) indicated that the conformational flexibility of the Omicron variant RBD:hACE2 advanced was not altered when in comparison with the wt RBD:hACE2 advanced.  

The binding free vitality of Omicron S protein with the hACE2 receptor was lower than -8.6 kcal/mol in comparison with wt S protein affinity with the hACE2 receptor. Between the R493 and R498 residues of Omicron RBD, sturdy electrostatic interactions and hydrogen bonding had been noticed with D30/E35 and D38 residues of the hACE2 receptor RBD, respectively.  

Aside from that, numerous different mutated amino acids in Omicron RBD together with S496 and H505 had hydrogen bonding with the hACE2 receptor.,.  The pi-stacking interplay between the RBD and hACE2 tyrosine residues (RBD-Tyr501: hACE2-Tyr41) was recognized within the Omicron RBD:hACE2 advanced.

Conclusion

The research supplied detailed details about the molecular degree binding interplay sample of the SARS-CoV-2 Omicron and wt variant with the hACE2 receptor.

The variations between the binding free vitality of the SARS-CoV-2 Omicron and the wt variant indicated that the S protein of Omicron has the next binding affinity for the hACE2 receptor leading to the next an infection fee.

Equally, mutated residues of Omicron RBD had sturdy interactions with the amino acid sequences of the hACE2 receptor. The pi-stacking interplay noticed within the Omicron RBD:hACE2 advanced was one of many key interactions stabilizing the advanced formation.

This detailed details about the SARS-CoV-2 Omicron and wt variants’ RBD:hACE2 advanced construction, residue sensible contributions to binding free vitality, and the binding mode assist perceive the transmissibility of Omicron and develop and optimize antiviral therapies in opposition to COVID-19.

*Vital discover

bioRxiv publishes preliminary scientific studies that aren’t peer-reviewed and, subsequently, shouldn’t be considered conclusive, information scientific apply/health-related conduct, or handled as established data.

Journal reference:

Rajender Kumar, Murugan Natarajan Arul, Vaibhav Srivastava. (2021). Improved binding affinity of the Omicron’s spike protein with the hACE2 receptor is the important thing issue behind its elevated virulence. bioRxivdoi: https://doi.org/10.1101/2021.12.28.474338 https://www.biorxiv.org/content material/10.1101/2021.12.28.474338v1

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