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

Liang, Yu; Zhang, Jing; Yuan, Run Yu; Wang, Mei Yu; He, Peng; Su, Ji Guo; Han, Zi Bo; Jin, Yu Qin; Hou, Jun Wei; Zhang, Hao; Zhang, Xue Feng; Shao, Shuai; Hou, Ya Nan; Liu, Zhao Ming; Du, Li Fang; Shen, Fu Jie; Zhou, Wei Min; Tang, Fang; Lei, Ze Hua; Liu, Shuo; Zhen, Wei; Wu, Jin Juan; Zheng, Xiang; Liu, Ning; Chen, Shi; Ma, Zhi Jing; Zheng, Fan; Ren, Si Yu; Hu, Zhong Yu; Wu, Gui Zhen; Huang, Wei Jin; Ke, Chang Wen; Li, Qi Ming

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), 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.