Insight into Vaccine Development for Alphacoronaviruses Based on Structural and Immunological Analyses of Spike Proteins

Abstract

Coronaviruses that infect humans belong to the Alpha-coronavirus (including HCoV-229E) and Beta-coronavirus (including SARS-CoV and SARS-CoV-2) genera. In particular, SARS-CoV-2 is currently a major threat to public health worldwide. The spike (S) homotrimers bind to their receptors via the receptor-binding domain (RBD), which is a major target to block viral entry. In this study, we selected Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) as models. Their RBDs exist two different conformational states (lying or standing) in the prefusion S-trimer structure. Then, the differences in the immune responses to RBDs from these coronaviruses were analyzed structurally and immunologically. Our results showed that more RBD-specific antibodies (antibody titers: 1.28×105; 2.75×105) were induced by the S-trimer with the RBD in the “standing” state (SARS-CoV and SARS-CoV-2) than the S-trimer with the RBD in the “lying” state (HCoV-229E, antibody titers: <500), and more S-trimer-specific antibodies were induced by the RBD in the SARS-CoV and SARS-CoV-2 (antibody titers: 6.72×105; 5×105) than HCoV-229E (antibody titers:1.125×103). Besides, we found that the ability of the HCoV-229E RBD to induce neutralizing antibodies was lower than S-trimer, and the intact and stable S1 subunit was essential for producing efficient neutralizing antibodies against HCoV-229E. Importantly, our results reveal different vaccine strategies for coronaviruses, and S-trimer is better than RBD as a target for vaccine development in Alpha-coronavirus. Our findings will provide important implications for future development of coronavirus vaccines. Importance Outbreak of coronaviruses, especially SARS-CoV-2, poses a serious threat to global public health. Development of vaccines to prevent the coronaviruses that can infect humans has always been a top priority. Coronavirus spike (S) protein is considered as a major target for vaccine development. Currently, structural studies have shown that Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) RBDs are in “lying” and “standing” states in the prefusion S-trimer structure. Here, we evaluated the ability of S-trimer and RBD to induce neutralizing antibodies among these coronaviruses. Our results showed that the S-trimer and RBD are both candidates for subunit vaccines in Beta-coronavirus (SARS-CoV and SARS-CoV-2) with a RBD “standing” state. However, for Alpha-coronavirus (HCoV-229E) with a RBD “lying” state, the S-trimer may be more suitable for subunit vaccines than the RBD. Our results will provide novel ideas for the development of vaccines targeting S protein in the future.

Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes

“…The S1 subunit of Spike in Alphacoronaviruses has been shown to play important functional roles in host cellular interactions ( Li and Goff 2015 ) and immune evasion ( Shi et al. 2022 , 2021 ). Yang et al.…”

“…Protein binding functionality is often contained within the CTD of the S1 subunit, which usually occurs within the RBD ( Li and Goff 2015 ). Shi et al (2021) examined the Spike structure of CoVs and remarked on the ‘lying’ vs. ‘standing’ (‘up’ vs. ‘down’, respectively) orientation of the RBD, where the Alphacoronaviruses studied had a ‘lying’ or ‘down’ RBD orientation. The group showed that an intact NTD from the Spike of HCoV-229E, an Alphacoronavirus , was essential for producing effective neutralizing antibodies (NAbs), compared to the Spike’s with a ‘standing’ or ‘up’ RBD that could generate effective NAbs from the RBD alone.…”

The clinical and virological features of two children's coinfections with human adenovirus type 7 and human coronavirus-229E virus

“…Meanwhile, HCoV-229E has a low prevalence in this area. As a result, most of population has no immunity to these two viruses ( 24 ). Thirdly, adenoviruses are non-enveloped viruses that are unusually resistant to physical and chemical agents, which gives them prolonged survival capacity in various environments ( 25 ).…”

Application of the Nicoya OpenSPR to Studies of Biomolecular Binding: A Review of the Literature from 2016 to 2022

“…SPR is a powerful tool for real-time, label-free measurement of binding affinity and kinetics, and the vast majority of papers citing the use of the OpenSPR fit neatly underneath this umbrella [ 3 , 5 , 7 , 9 , 15 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 ,…”

“…Researchers have used this technique to assess the binding affinity and kinetics of potential new therapeutics and affinity reagents, to study aggregation, to perform competition studies or inhibition assays, and other applications. OpenSPR has been leveraged to study diverse biochemical questions, including critical problems in human health such as Alzheimer’s disease (AD) [ 43 , 44 , 45 , 46 ], non-small cell lung cancer (NSCLC) [ 47 , 48 , 49 , 50 , 51 ], and COVID-19 [ 34 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 ]. This paper provides the first comprehensive review of the literature reporting the use of the OpenSPR.…”