NSRRC Activity Report 2023

048 NSRRC ACTIVITY REPORT 2023 T he causative agent of the COVID-19 pandemic is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), classified as a betacoronavirus. It was confirmed that human angiotensin-converting enzyme 2 (ACE2) serves as the receptor for the SARS-CoV-2 virus, utilizing the spike protein on the virus surface to infect human cells in a similar manner to SARS-CoV. The interaction between the spike protein and the ACE2 receptor enables the virus to enter cells. The spike protein is located on the surface of the virus and is composed of two subunits, S1 and S2 ( Fig. 1 ). The S1 subunit contains the receptor-binding domain (RBD) that binds to ACE2, facilitating the interaction and triggering a conformational change in the spike protein. The conformational change allows the S2 subunit to utilize its fusion core, comprised of regions of heptad repeat 1 (HR1) and heptad repeat 2 (HR2), to insert into the host cell membrane. 1 According to the World Health Organization (WHO) data, as of December 2023, SARS-CoV-2 has infected over 770 million people, resulting in nearly 7 million deaths worldwide. Despite the significant challenges posed by the COVID-19 pandemic, there have been numerous global efforts to develop strategies for treatment, vaccines, and controlling the spread of the virus. Role of the Spike Protein in the Entry of SARS-CoV-2 into Cells and in Vaccine Design Through the analysis of the complex structures of the receptor-binding domain of the spike protein with monoclonal antibodies and the fusion core of the spike protein, the utilization of this structural information to design potential vaccines or drugs is elucidated. Fig. 1 : Schematic illustration for SARS-CoV-2 spike protein, which can be split into two subunits, S1 and S2, at this site between 685 and 686. S1 subunit contains signal peptide (SP), N-terminal domain (NTD), and receptor-binding domain (RBD) with receptor-binding motif (RBM); S2 subunit contains fusion peptide (FP), heptad repeat 1 (HR1), heptad repeat 2 (HR2), transmembrane domain (TM), and cytoplasmic peptide (CP). [Reproduced from Ref. 1] Two research teams, led by Che Ma (Academia Sinica) and Chun-Hua Hsu (National Taiwan University), collected X-ray diffraction data at TPS 05A and TLS 15A1 , and TPS 05A , respectively. They separately solved the structures of the RBD– antibody complex and the fusion core. Using the structural information, relevant biochemical experiments were conducted. The following content briefly introduces their experimental results. Researchers from Ma’s group isolated eight neutralizing monoclonal antibodies, including EY-6A, FP-12A, IV-6D, IV-4B, IV-10C, IS-9A, IS-11B and IY-2A, from Taiwan patient samples. They all coincidentally bind to a buried region in the spike protein’s RBD, thereby the antigenic determinant (epitope) was categorized as “Class 4 antibodies.” Class 4 antibodies can only detect and bind to the buried site when the RBD is in an upward conformation and are therefore referred to as “cryptic antibodies.” Furthermore, because this is a hidden region, not prone to mutations, it can be considered a hotspot for broadly effective antibody targeting. The research team further analyzed the binding strengths of these eight antibodies with different variants of SARS-CoV-2. In neutralization experiments, these antibodies could broadly and effectively inhibit Omicron BA.5 and other variant strains such as Beta and Delta. In particular, the antibody IY-2A induces structural changes in the RBD and generates new neutralizing binding sites, making it the latest breakthrough discovery in current COVID-19 research ( Fig. 2 ). 2 In Ma’s study, the research team described a series of antibodies identified as Class 4 antibodies, as they exhibit complete or partial competition with similar antibodies in RBD binding. Structural analysis of their binding footprints and comparison with examples in the literature allowed the identification of antigenic regions comprising multiple overlapping epitopes. One of these epitopes is newly characterized by our antibody IY-2A. These antibodies prefer binding to highly conserved epitopes and demonstrate broad effectiveness against SARS-CoV-2 variants.