Structural basis for SARS-CoV-2 neutralizing antibodies with novel binding epitopes

Abstract

The ongoing Coronavirus Disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) threatens global public health and economy unprecedentedly, requiring accelerating development of prophylactic and therapeutic interventions. Molecular understanding of neutralizing antibodies (NAbs) would greatly help advance the development of monoclonal antibody (mAb) therapy, as well as the design of next generation recombinant vaccines. Here, we applied H2L2 transgenic mice encoding the human immunoglobulin variable regions, together with a state-of-the-art antibody discovery platform to immunize and isolate NAbs. From a large panel of isolated antibodies, 25 antibodies showed potent neutralizing activities at sub-nanomolar levels by engaging the spike receptor-binding domain (RBD). Importantly, one human NAb, termed PR1077, from the H2L2 platform and 2 humanized NAb, including PR953 and PR961, were further characterized and subjected for subsequent structural analysis. High-resolution X-ray crystallography structures unveiled novel epitopes on the receptor-binding motif (RBM) for PR1077 and PR953, which directly compete with human angiotensin-converting enzyme 2 (hACE2) for binding, and a novel non-blocking epitope on the neighboring site near RBM for PR961. Moreover, we further tested the antiviral efficiency of PR1077 in the Ad5-hACE2 transduction mouse model of COVID-19. A single injection provided potent protection against SARS-CoV-2 infection in either prophylactic or treatment groups. Taken together, these results shed light on the development of mAb-related therapeutic interventions for COVID-19.

Epitope Profiling Reveals the Critical Antigenic Determinants in SARS-CoV-2 RBD-Based Antigen

“…However, there is a gap in knowledge on the broad cross-protective epitopes shared between SARS-CoV-2 and SARS-CoV. Currently, findings on SARS-CoV-2 B cell epitopes mainly include the determination of antigen-antibody structural complex, bioinformatics prediction and Pepscan (26)(27)(28)(29). Undoubtedly, determination the complex structure is the most accurate method for epitope identification, but it is not readily applicable to many antigens and antibodies, for its laborious efforts with a low success rate.…”

Potential Immunogenic Activity of Computationally Designed mRNA- and Peptide-Based Prophylactic Vaccines against MERS, SARS-CoV, and SARS-CoV-2: A Reverse Vaccinology Approach

“…This B-cell response is triggered by the identification of epitope sequences by the antigen. Moreover, the identification of highly immunogenic B-cell epitopes is a prerequisite in peptide-based vaccine designs [ 32 , 33 , 34 ]. The total number of B-cell epitopes was predicted for each CoV species.…”

Combined Subcutaneous-Intranasal Immunization With Epitope-Based Antigens Elicits Binding and Neutralizing Antibody Responses in Serum and Mucosae Against PRRSV-2 and SARS-CoV-2

“…Another reason was the documented participation of the GP5 ectodomain in virus attachment and internalization into porcine macrophages, aided by N-glycans localized in epitope B, as it interacts with heparan sulfate proteoglycans ( 106 ), sialoadhesin ( 107 , 108 ), and the non-muscle myosin heavy chain 9 (MYH9) ( 109 , 110 ). In the case of SARS-CoV-2, RBD binds to angiotensin-converting enzyme 2 (ACE2) to enter cell cytoplasm, representing a key target for nAbs ( 111 , 112 ). Different RBD-specific cross-reactive monoclonal antibodies that neutralize SARS-CoV and SARS-CoV-2 have been isolated from convalescent sera, which implies that RBD could be used in pan-sarbecovirus vaccines ( 113 , 114 ).…”