(342be) RBD Escape Mutations Span Multiple Antibodies

Neutralizing antibodies for SARS-CoV-2 commonly bind to the receptor binding domain (RBD) on the surface of the trimeric viral fusion Spike (S) protein, to prevent the virus from attaching to its cellular target angiotensin-converting enzyme 2 (ACE2) to gain entry into human cells. Importantly, the S protein is capable of evolving mutations in the RBD to avoid detection by antibodies while still retaining its ability to bind to ACE2. Yet, the RBD remains one of the most highly conserved regions on the S protein and is thus targeted by a number of antibodies originating from a variety of different germlines. A deep molecular understanding of how mutations in the RBD of the S protein permit escape from these antibodies could enable the design of vaccine boosters and monoclonal antibody (Ab) therapies with an increased capacity to protect against SARS-CoV-2. To this end, this presentation will describe the use of molecular dynamics (MD) simulations to investigate key RBD/Ab and RBD/ACE2 interactions underlying the molecular mechanisms of escape of the S protein, incorporated with various point mutations (e.g., D420E, D420K, Y421N, and two currently circulating variants, N501Y and E484K), from multiple Abs with unique germline origins.[1] We observed that RBD mutations at residue 420 resulted in disrupted RBD/Ab hydrogen bonding and increased fluctuations in nearby RBD loops, whereas the Y421N mutation led to reduced aromatic interactions between the Abs and the RBD. These findings are consistent with results from both high throughput experimental assays and pseudo neutralization assays indicating full RBD escape at these positions. However, interesting differences arise between the simulations and experiments in regards to the N501Y and E484K mutations, which we explored in detail. A key conclusion from this work is that many commonalities exist in the observed molecular mechanisms of escape of the S protein from Abs with shared germline origins, despite notable differences in the mature Ab sequences. Such a general understanding of common viral escape pathways could guide the future design of more robust and comprehensive immunotherapeutics against SARS-CoV-2.

[1] I. F. Urdaniz et al., “One-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening,” bioRxiv, p. 2021.03.15.435309, Jan. 2021.