Structure and computation-guided design of a mutation-integrated trimeric RBD candidate vaccine with broad neutralization against SARS-CoV-2

The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 is an attractive target for COVID-19 vaccine developments, which naturally exists in a trimeric form. Here, guided by structural and computational analyses, we present a mutation-integrated trimeric form of RBD (mutI tri-RBD) as a broadly protective vaccine candidate, in which three RBDs were individually grafted from three different circulating SARS-CoV-2 strains including the prototype, Beta (B.1.351) and Kappa (B.1.617). The three RBDs were then connected end-to-end and co-assembled to possibly mimic the native trimeric arrangements in the natural S protein trimer. The recombinant expression of the mutI tri-RBD, as well as the homo-tri-RBD where the three RBDs were all truncated from the prototype strain, by mammalian cell exhibited correct folding, strong bio-activities, and high stability. The immunization of both the mutI tri-RBD and homo-tri-RBD plus aluminum adjuvant induced high levels of specific IgG and neutralizing antibodies against the SARS-CoV-2 prototype strain in mice. Notably, regarding to the “immune-escape” Beta (B.1.351) variant, mutI tri-RBD elicited significantly higher neutralizing antibody titers than homo-tri-RBD. Furthermore, due to harboring the immune-resistant mutations as well as the evolutionarily convergent hotspots, the designed mutI tri-RBD also induced strong broadly neutralizing activities against various SARS-CoV-2 variants, especially the variants partially resistant to homo-tri-RBD. Homo-tri-RBD has been approved by the China National Medical Products Administration to enter clinical trial (No. [NCT04869592][1]), and the superior broad neutralization performances against SARS-CoV-2 support the mutI tri-RBD as a more promising vaccine candidate for further clinical developments. ### Competing Interest Statement Q. M. Li, Y. Liang, J. Zhang, J. G. Su, Y. Q. Jin, J. W. Hou, L. F. Du, Z. B. Han, X. F. Zhang, S. Shao, H. Zhang, F. Tang, Z. M. Liu, Y. N. Hou, S. Chen, Z. H. Lei, Z. J. Ma, F. Zheng, N. Liu are listed as inventors of the pending patients for the homo-tri-RBD and mutI tri-RBD vaccines. All the other authors declared no competing interests. [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT04869592&atom=%2Fbiorxiv%2Fearly%2F2021%2F06%2F18%2F2021.06.18.448958.atom