Design of a stabilized RBD enables potently neutralizing SARS-CoV-2 single-component nanoparticle vaccines

Dickey, Thayne H.; Ma, Rui; Orr-Gonzalez, Sachy; Ouahes, Tarik; Patel, Palak; McAleese, Holly; Butler, Brandi; Eudy, Elizabeth; Eaton, Brett; Murphy, Michael; Kwan, Jennifer; Salinas, Nichole D.; Holbrook, Michael R.; Lambert, Lynn; Tolia, Niraj H.

doi:10.1016/j.celrep.2023.112266

Cited by 11 publications

(19 citation statements)

References 52 publications

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“…To increase the stability of the RBDs, we introduced nine amino acid mutations ( Figure 3 A and Figure S1 ), which have been identified using a generalizable computational strategy named SPEEDesign and shown to improve neutralizing antibody titers, production yield, and thermostability of vaccine antigens [ 16 , 49 , 60 ], and which did not overlap with changes between WA-1 and BA.5. SEC profiles of both stabilized RBD proteins can be found in Figure S2 .…”

Section: Resultsmentioning

confidence: 99%

“…This is consistent with the fact that these stabilizing mutations do not overlap with known variant changes. SPEEDesign fixes known neutralizing epitopes in antigens and classifies the remaining amino acids into distinct categories that are allowed to vary to different extents, resulting in enhanced immunogens [ 16 , 49 , 60 ]. It is not entirely clear what degraded the non-stabilized RBD, but we observed no proteolytic digestion, so degradation was likely related to unfolding, with the mutations in RBD improving production yields and thermostability, and likely contributing to the potent and broad response elicited by the BA.5-RBD-Stab-EnDS-NP.…”

Section: Discussionmentioning

confidence: 99%

“…Among the approaches to increase breadth and potency, vaccines based on self-assembling nanoparticles appear to be especially promising [ 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 ]. Such nanoparticle vaccines have multiple advantages.…”

Section: Introductionmentioning

confidence: 99%

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Extraordinary Titer and Broad Anti-SARS-CoV-2 Neutralization Induced by Stabilized RBD Nanoparticles from Strain BA.5

Wang,

Zhang,

et al. 2023

Vaccines

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The receptor-binding domain (RBD) of the SARS-CoV-2 spike is a primary target of neutralizing antibodies and a key component of licensed vaccines. Substantial mutations in RBD, however, enable current variants to escape immunogenicity generated by vaccination with the ancestral (WA1) strain. Here, we produce and assess self-assembling nanoparticles displaying RBDs from WA1 and BA.5 strains by using the SpyTag:SpyCatcher system for coupling. We observed both WA1- and BA.5-RBD nanoparticles to degrade substantially after a few days at 37 °C. Incorporation of nine RBD-stabilizing mutations, however, increased yield ~five-fold and stability such that more than 50% of either the WA1- or BA.5-RBD nanoparticle was retained after one week at 37 °C. Murine immunizations revealed that the stabilized RBD-nanoparticles induced ~100-fold higher autologous neutralization titers than the prefusion-stabilized (S2P) spike at a 2 μg dose. Even at a 25-fold lower dose where S2P-induced neutralization titers were below the detection limit, the stabilized BA.5-RBD nanoparticle induced homologous titers of 12,795 ID50 and heterologous titers against WA1 of 1767 ID50. Assessment against a panel of β-coronavirus variants revealed both the stabilized BA.5-RBD nanoparticle and the stabilized WA1-BA.5-(mosaic)-RBD nanoparticle to elicit much higher neutralization breadth than the stabilized WA1-RBD nanoparticle. The extraordinary titer and high neutralization breadth elicited by stabilized RBD nanoparticles from strain BA.5 make them strong candidates for next-generation COVID-19 vaccines.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Extraordinary Titer and Broad Anti-SARS-CoV-2 Neutralization Induced by Stabilized RBD Nanoparticles from Strain BA.5

Wang,

Zhang,

et al. 2023

Vaccines

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“…The ectodomain comprises Spike's receptor‐binding domain (RBD), which directly engages the ACE2 receptor to mediate viral entry [ 7 ]. Moreover, RBD is the primary target of the multiple potent neutralizing antibodies that terminate the physical interaction between RBD and ACE2, and mediate immune response and virus neutralization [ 8 , 9 , 10 ]. Therefore, Spike's RBD (including its mutant forms) became a popular research and bio‐industrial target to study SARS‐CoV‐2.…”

mentioning

confidence: 99%

“…Therefore, Spike's RBD (including its mutant forms) became a popular research and bio‐industrial target to study SARS‐CoV‐2. The RBD was used to establish biosensors to detect viral infection and seroconversion [ 11 , 12 ] for research, preventive or diagnostic purposes, and to develop vaccines and therapies against viral infection and the COVID‐19 disease [ 10 , 13 , 14 ].…”

mentioning

confidence: 99%

Expression and purification of the receptor‐binding domain of SARS‐CoV‐2 spike protein in mammalian cells for immunological assays

Ábrahám,

Bajusz,

Marton

et al. 2024

FEBS Open Bio

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The receptor‐binding domain (RBD) of the spike glycoprotein of SARS‐CoV‐2 virus mediates the interaction with the host cell and is required for virus internalization. It is, therefore, the primary target of neutralizing antibodies. RBD soon became the major target for COVID‐19 research and the development of diagnostic tools and new‐generation vaccines. Here, we provide a detailed protocol for high‐yield expression and one‐step affinity purification of recombinant RBD from transiently transfected Expi293F cells. Expi293F mammalian cells can be grown to extremely high densities in a specially formulated serum‐free medium in suspension cultures, which makes them an excellent tool for secreted protein production. The highly purified RBD is glycosylated, structurally intact, and forms homomeric complexes. With this quick and easy method, we are able to produce large quantities of RBD (80 mg/L culture) that we have successfully used in immunological assays to examine antibody titers and seroconversion after mRNA‐based vaccination of mice.

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Structure‐based design of a Plasmodium vivax Duffy‐binding protein immunogen focuses the antibody response to functional epitopes

Dickey,

McAleese,

Salinas

et al. 2024

Protein Science

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The Duffy‐binding protein (DBP) is a promising antigen for a malaria vaccine that would protect against clinical symptoms caused by Plasmodium vivax infection. Region II of DBP (DBP‐II) contains the receptor‐binding domain that engages host red blood cells, but DBP‐II vaccines elicit many non‐neutralizing antibodies that bind distal to the receptor‐binding surface. Here, we engineered a truncated DBP‐II immunogen that focuses the immune response to the receptor‐binding surface. This immunogen contains the receptor‐binding subdomain S1S2 and lacks the immunodominant subdomain S3. Structure‐based computational design of S1S2 identified combinatorial amino acid changes that stabilized the isolated S1S2 without perturbing neutralizing epitopes. This immunogen elicited DBP‐II‐specific antibodies in immunized mice that were significantly enriched for blocking activity compared to the native DBP‐II antigen. This generalizable design process successfully stabilized an integral core fragment of a protein and focused the immune response to desired epitopes to create a promising new antigen for malaria vaccine development.

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Design of a stabilized RBD enables potently neutralizing SARS-CoV-2 single-component nanoparticle vaccines

Cited by 11 publications

References 52 publications

Extraordinary Titer and Broad Anti-SARS-CoV-2 Neutralization Induced by Stabilized RBD Nanoparticles from Strain BA.5

Extraordinary Titer and Broad Anti-SARS-CoV-2 Neutralization Induced by Stabilized RBD Nanoparticles from Strain BA.5

Expression and purification of the receptor‐binding domain of SARS‐CoV‐2 spike protein in mammalian cells for immunological assays

Structure‐based design of a Plasmodium vivax Duffy‐binding protein immunogen focuses the antibody response to functional epitopes

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