Specific epitopes form extensive hydrogen-bonding networks to ensure efficient antibody binding of SARS-CoV-2:...

Neutralizing antibody targeting to the SARS-CoV-2 could provide powerful therapies. A neutralizing antibody CC12.1 which was found in SARS-CoV-2 patient samples provides potential protection from disease. The aim of molecular dynamics simulations is to identify key epitopes that are crucial to the antibody binding of SARS-CoV-2 spike glycoprotein receptor binding domain (RBD) to promote the development of superior antibodies. Binding modes of the antibody were investigated and compared with RBD bound receptor ACE2. Key epitopes were revealed and a distal motif of RBD (residue numbers 473-488) was demonstrated by analyzing dynamic trajectories. Compared to the receptor ACE2, conformation of RBD could be better stabilized through additional interaction of antibody with the distal motif of RBD, which was further found driven by electrostatic complementarity. By further analysis of the extensive hydrogen-bonding networks, residues D405, K417, Y421, Y453, L455, R457, Y473, A475, N487, G502, Y505 of RBD, which mainly interacted with CDR H3/L3 and two conserved motifs SNY, SGGS, were identified as key epitopes. Higher binding free energy calculated after point mutations on key residues confirms the crucial role for the specific binding. Subsequently, mutations of V_H V98E and V_L G68D in CC12.1, which could significantly enhance the binding affinity of the antibody, were also proposed. The results indicate the key epitopes for antibody binding and give explanations for failure of neutralization antibody caused by specific residues mutations on structural basis. Simulations of two point mutations on antibody provide feasible information for advanced antibody design.