Comprehensive deep mutational scanning reveals the pH induced stability and binding differences between SARS-CoV-2 spike RBD and human ACE2

Abstract

The SARS-CoV-2 spike (S) glycoprotein with its mobile receptor-binding domain (RBD), binds to the human ACE2 receptor and thus facilitates virus entry through low-pH-endosomal pathways. The high degree of SARS-CoV-2 mutability has raised concern among scientists and medical professionals because it created doubt about the effectiveness of drugs and vaccinations designed specifically for COVID-19. In this study, we used computational saturation mutagenesis approach, including structure-based free energy calculations to analyse the effects of the missense mutations on the SARS-CoV-2 S-RBD stability and the S-RBD binding affinity with ACE2 at three different pH (pH 4.5, pH 6.5, and pH 7.4). A total of 3705 mutations in the S-RBD protein were analyzed, and we discovered that most of these mutations destabilize the RBD protein. Specifically, residues G404, G431, G447, A475, and G526 were important for RBD protein stability. In addition, RBD residues Y449, Y489, Y495, Q498, and N487 were critical for the RBD-ACE2 interaction. Next, we found that the distribution of the mean stability changes and mean binding energy changes of RBD due to mutations at both serological and endosomal pH correlated well, indicating the similar effects of mutations. Overall, this computational analysis is useful for understanding the effects of missense mutations in SARS-CoV-2 pathogenesis at different pH.

Communicated by Ramaswamy H. Sarma

Keywords:

• SARS-CoV-2 S-RBD
• missense mutations
• saturation mutagenesis
• stability
• RBD-ACE2 binding affinity

Acknowledgements

The authors extend their appreciation to the Deputyship for Research & Innovation, Ministry of Education in Saudi Arabia for funding this research work through the project number RUP3-7.

Authors’ contributions

Conceptualization, S.H., D.M.M., and V.K.; methodology, S.H., D.M.M., M.F.A., F.B., and V.K.; software, A.M.M, and H.F.; formal analysis, F.B., A.M.M, H.F., and N.A.J; data curation, S.H., D.M.M., and V.K.; writing—original draft preparation, S.H., D.M.M., F.B., and N.A.J.; writing—review and editing, all authors; supervision, A.M.M., N.A.J., and V.K. All authors contributed to the article and have approved the submitted version.

Disclosure statement

The authors declare that there is no conflict of interest.

Consent for publication

All authors consent for the publication of this study.

Data availability statement

The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.

Correction Statement

This article has been corrected with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

Deputyship for Research & Innovation, Ministry of Education in Saudi Arabia through the Project Number RUP3-7.