Structure and computation-guided design of a mutation-integrated trimeric RBD candidate vaccine with broad neutralization against SARS-CoV-2
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Abstract
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.
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SciScore for 10.1101/2021.06.18.448958: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources After incubating the plate at 37 ℃ for 1 h and washing 3 times with PBST, the HRP-conjugated secondary antibody (goat anti-mouse IgG) at 1:10000 dilution was added into the wells of the plate. anti-mouse IgGsuggested: (LSBio (LifeSpan Cat# LS-C149336-10000, RRID:AB_11143677)Experimental Models: Cell Lines Sentences Resources Then, the generated plasmids were transfected into the HEK293T cells for transient expression. HEK293Tsuggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)The Huh-7 cells were digested and suspended in the culture medium with viable cell density of 2×105 per mL, which were then added … SciScore for 10.1101/2021.06.18.448958: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources After incubating the plate at 37 ℃ for 1 h and washing 3 times with PBST, the HRP-conjugated secondary antibody (goat anti-mouse IgG) at 1:10000 dilution was added into the wells of the plate. anti-mouse IgGsuggested: (LSBio (LifeSpan Cat# LS-C149336-10000, RRID:AB_11143677)Experimental Models: Cell Lines Sentences Resources Then, the generated plasmids were transfected into the HEK293T cells for transient expression. HEK293Tsuggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)The Huh-7 cells were digested and suspended in the culture medium with viable cell density of 2×105 per mL, which were then added into the well with 100 μL per well. Huh-7suggested: NoneAfter incubation at 37 ℃ for 2 h, the serum-and-virus mixed solution was added into the well of the plate containing Vero-E6 cells with density of 2×10 5 per mL, which was then cultured at 37 ℃ for 5 to 7 days. Vero-E6suggested: NoneExperimental Models: Organisms/Strains Sentences Resources In order to compare the immunogenicity of the mutI tri-RBD with the homo-tri-RBD, another two groups of BALB/c mice (6 mice in each group) were also immunized with the homo-tri-RBD plus aluminum adjuvant by two-shot of high dose (2.0 μg/dose) or three-shot of middle dose (0.5μg/dose). BALB/csuggested: RRID:IMSR_ORNL:BALB/cRl)Software and Algorithms Sentences Resources The trimeric structure generated by Modeller was solvated using TIP3P water molecules in a cubic box, with the protein atoms being at least 1.6 nm away from the box edges. Modellersuggested: (MODELLER, RRID:SCR_008395)Based on the MD simulation trajectories, the changes in the root mean square deviation (RMSD) of the Cα atoms of the system as a function of time were calculated by using the built-in tool of “gmx rms” in Gromacs to evaluate the stability of the trimeric RBD proteins, and the motion movies were generated by using Chimera software to display the intrinsic conformational movements of the trimeric RBD proteins. Chimerasuggested: (Chimera, RRID:SCR_002959)The MS raw data files were processed using BioPharma Finder software (version 3.2). BioPharma Findersuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04869592 Recruiting A Clinical Trial to Evaluate the Recombinant SARS-CoV-2 Vacc… Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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