Collaborative effects of 2019-nCoV-Spike mutants on viral infectivity

Abstract

Background: The emerging mutants of the 2019-nCoV coronavirus are posing unprecedented challenges to the pandemic prevention. A thorough, understanding of the mutational characterization responsible for the pathogenic mechanisms of mutations in 2019-nCoV-Spike is indispensable for developing effective drugs and new vaccines. Methods: We employed computational methods and viral infection assays to examine the interaction pattern and binding affinity between ACE2 and both single- and multi-mutants of the Spike proteins. Results: Using data from the CNCB-NGDC databank and analysis of the 2019-nCoV-Spike/ACE2 interface crystal structure, we identified 31 amino acids that may significantly contribute to viral infectivity. Subsequently, we performed molecular dynamics simulations for 589 single-mutants that emerged from the nonsynonymous substitutions of the aforementioned 31 residues. Ultimately, we discovered 8 single-mutants that exhibited significantly higher binding affinities (<−65.00 kcal/mol) to ACE2 compared with the wild-type Spike protein (−55.07 kcal/mol). The random combination of these 8 single-mutants yielded 184 multi-mutants, of which 60 multi-mutants exhibit markedly enhanced binding affinities (<−65.00 kcal/mol). Moreover, the binding free energy analyses of all 773 mutants (including 589 single- and 184 multi-mutants) revealed that Y449R and S494R had a synergistic effect on the binding affinity with other mutants, which were confirmed by virus infection assays of six randomly selected multi-mutants. More importantly, the findings of virus infection assay further validated a strong association between the binding free energy of Spike/ACE2 complex and the viral infectivity. Conclusions: These findings will greatly contribute to the future surveillance of viruses and rational design of therapeutics.

Keywords

• COVID-19
• Molecular dynamics simulations
• Multi-mutant
• Infection assay
• Spike