Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations

• Published in: Briefings in Bioinformatics 2022-01, Vol.23 (1)
• Main Authors: Wu, Leyun, Peng, Cheng, Yang, Yanqing, Shi, Yulong, Zhou, Liping, Xu, Zhijian, Zhu, Weiliang
• Format: Article
• Language: English
• Subjects: Affinity; Amino Acid Substitution; Antibodies; Antibodies, Neutralizing - chemistry; Antibodies, Neutralizing - immunology; Antibodies, Viral - chemistry; Antibodies, Viral - immunology; Binding; Binding energy; Coronaviruses; COVID-19; COVID-19 vaccines; Decomposition; Drug development; Free energy; Humans; Immune Evasion; Molecular dynamics; Molecular Dynamics Simulation; Monoclonal antibodies; Mutants; Mutation; Mutation, Missense; Neutralization; Problem Solving Protocol; Proteins; Residues; SARS-CoV-2 - chemistry; SARS-CoV-2 - genetics; SARS-CoV-2 - immunology; Severe acute respiratory syndrome coronavirus 2; Spike Glycoprotein, Coronavirus - chemistry; Spike Glycoprotein, Coronavirus - genetics; Spike Glycoprotein, Coronavirus - immunology; Spike protein; Vaccines; Viral diseases; Viruses
• ISSN: 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbab383

Abstract Although the current coronavirus disease 2019 (COVID-19) vaccines have been used worldwide to halt spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the emergence of new SARS-CoV-2 variants with E484K mutation shows significant resistance to the neutralization of vaccine sera. To better understand the resistant mechanism, we calculated the binding affinities of 26 antibodies to wild-type (WT) spike protein and to the protein harboring E484K mutation, respectively. The results showed that most antibodies (~85%) have weaker binding affinities to the E484K mutated spike protein than to the WT, indicating the high risk of immune evasion of the mutated virus from most of current antibodies. Binding free energy decomposition revealed that the residue E484 forms attraction with most antibodies, while the K484 has repulsion from most antibodies, which should be the main reason of the weaker binding affinities of E484K mutant to most antibodies. Impressively, a monoclonal antibody (mAb) combination was found to have much stronger binding affinity with E484K mutant than WT, which may work well against the mutated virus. Based on binding free energy decomposition, we predicted that the mutation of four more residues on receptor-binding domain (RBD) of spike protein, viz., F490, V483, G485 and S494, may have high risk of immune evasion, which we should pay close attention on during the development of new mAb therapeutics.