A Cryptic Site of Vulnerability on the Receptor Binding Domain of the SARS-CoV-2 Spike Glycoprotein

M. Gordon Joyce; Rajeshwer S. Sankhala; Wei-Hung Chen; Misook Choe; Hongjun Bai; Agnes Hajduczki; Lianying Yan; Spencer L. Sterling; Caroline E. Peterson; Ethan C. Green; Clayton Smith; Natalia de Val; Mihret Amare; Paul Scott; Eric D. Laing; Christopher C. Broder; Morgane Rolland; Nelson L. Michael; Kayvon Modjarrad

Although SARS-CoV-2 is a newly identified virus, it shares genetic and morphologic features with others in the Coronaviridae family, particularly those from the Betacoronavirus genus. The genome of the recently isolated SARS-CoV-2 shares 82% nucleotide identity with human SARS-CoV and 89% with bat SARS-like-CoVZXC21 . The spike (S) glycoprotein, in particular, bears significant structural homology with SARS-CoV compared to other coronaviruses such as MERS-CoV. Like SARS-CoV, the surface Spike (S) glycoprotein of SARS-CoV-2 binds the same host receptor, ACE-2, to mediate cell entry (Letko et al., 2020; Yan et al., 2020a) . S-a class I fusion protein-is also a critical determinant of viral host range and tissue tropism and the primary target of the host immune response (Li, 2016) . As such, most coronavirus vaccine candidates are based on S or one of its sub-components. Coronavirus S glycoproteins contain three segments: a large ectodomain, a single-pass transmembrane anchor and a short intracellular tail. The ectodomain consists of a receptor-binding subunit, S1, which contains two subdomains: one at the N-terminus and the other at the C-terminus. The latter comprises the receptor-binding domain (RBD), which serves the vital function of attaching the virus to the host receptor and triggering a conformational change in the protein that results in fusion with the host cell membrane through the S2 subunit. a CC0 license. author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi. org/10.1101 org/10. /2020 amino acids (aa) within each protomer RBD are not modeled, including 40% of the ACE-2 receptor binding site as measured by buried surface area (BSA) (Yan et al., 2020b) . The SARS-CoV RBD-2 compared to liganded (PDB ID: 2AJF) and unliganded (PDB ID: 2GHV) SARS-CoV RBD structures shows high structural similarity, except for residues 473-488 (Figure 1) . A chimeric SARS-CoV-2 RBD structure (PDB ID: 6VW1) with 23 aa differences compared to SARS-CoV-2, in complex with human ACE-2 was recently released in the PDB. Comparisons with previously published structures with the SARS-CoV-2 RBD highlight residues 473-488 as an area with significant structural plasticity. In the RBD structure from this study, we observe electron density for two conformations of the 482-486 loop. One of these conformations is highly similar to the ligand bound form of the RBD, while the second conformation would clash with the ACE2 receptor. Both this structural detail of the unliganded RBD and comparison to previously described RBD structures indicates that this area of the RBD is structurally malleable with implications for antibody or small molecule therapeutics design.