Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2

Bruch, Eduardo M.; Zhu, Shaolong; Szymkowicz, Lisa; Blake, Taylor; Kiss, Tara; James, D. Andrew; Rak, Alexey; Narayan, Kartik; Balmer, Matthew T.; Chicz, Roman M.

doi:10.1038/s41598-024-52499-1

Cited by 3 publications

(1 citation statement)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Protein-based vaccines had additional challenges not faced by viral vector or mRNA vaccines, including the need to develop techniques for protein purification and to perform structural characterization of the expressed protein. 19 It is not possible to measure such parameters for mRNA or viral vectors which induce protein expression in vivo . Another challenge for recombinant protein-based approaches is low immunogenicity.…”

Section: Introductionmentioning

confidence: 99%

Clinical development of SpikoGen®, an Advax-CpG55.2 adjuvanted recombinant spike protein vaccine

Petrovsky

2024

Human Vaccines & Immunotherapeutics

View full text Add to dashboard Cite

Section: Introductionmentioning

confidence: 99%

Clinical development of SpikoGen®, an Advax-CpG55.2 adjuvanted recombinant spike protein vaccine

Petrovsky

2024

Human Vaccines & Immunotherapeutics

View full text Add to dashboard Cite

Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN

Herreros,

Mata,

Noddings

et al. 2024

Preprint

View full text Add to dashboard Cite

Single-particle analysis by Cryo-electron microscopy (CryoEM) provides direct access to the conformation of each macromolecule. However, the image's signal-to-noise ratio is low, and some form of classification is usually performed at the image processing level to allow structural modeling. Classical classification methods imply the existence of a discrete number of structural conformations. However, new heterogeneity algorithms introduce a novel reconstruction paradigm, where every state is represented by a lower number of particles, potentially just one, allowing the estimation of conformational landscapes representing the different structural states a biomolecule explores. In this work, we present a novel deep learning-based method called HetSIREN. HetSIREN can fully reconstruct or refine a CryoEM volume in real space based on the structural information summarized in a conformational latent space. The unique characteristics that set HetSIREN apart start with the definition of the approach as a real space-based only method, a fact that allows spatially focused analysis, but also the introduction of a novel network architecture specifically designed to make use of meta-sinusoidal activations, with proven high analytics capacities. Continuing with innovations, HetSIREN can also refine the pose parameters of the images at the same time that it conditions the network with prior information/constraints on the maps, such as Total Variation and L_1 denoising, ultimately yielding cleaner volumes with high-quality structural features. Finally, but very importantly, HetSIREN addresses one of the most confusing issues in heterogeneity analysis, as it is the fact that real structural heterogeneity estimation is entangled with pose estimation (and to a lesser extent with CTF estimation), in this way, HetSIREN introduces a novel encoding architecture able to decouple pose and CTF information from the conformational landscape, resulting in more accurate and interpretable conformational latent spaces. We present results on computer-simulated data, public data from EMPIAR, and data from experimental systems currently being studied in our laboratories. An important finding is the sensitivity of the structure and dynamics of the SARS-CoV-2 Spike protein on the storage temperature.

show abstract

Formulation Development of a COVID-19 Recombinant Spike Protein-Based Vaccine

Xiao,

Mirabel,

Clénet

et al. 2024

Vaccines

View full text Add to dashboard Cite

The purpose of this study was to develop a formulation for a recombinant prefusion spike protein vaccine against SARS-CoV-2. It was found that the spike protein was susceptible to aggregation due to mechanical stress. Therefore, formulation studies were initiated focused on screening pharmaceutical excipients capable of preventing this. The screening of a panel of potential stabilizing conditions found that Tween 20 could inhibit mechanically induced aggregation. A concentration-dependent study indicated that a higher concentration of Tween 20 (0.2% v/v) was required to prevent conformational changes in the trimer. The conformational changes induced by mechanical stress were characterized by size exclusion chromatography (SEC) and hydrogen–deuterium exchange mass spectrometry (HDX-MS), indicating the formation of an extended trimeric conformation that was also unable to bind to antibodies directed to the S2 domain. Long-term stability modeling, using advanced kinetic analysis, indicated that the formulation containing 0.2% (v/v) Tween 20 at a neutral pH was predicted to be stable for at least two years at 2 °C to 8 °C. Additional stabilizer screening conducted by thermal shift assay indicated that sucrose and glycerol were able to significantly increase the spike protein melting temperature (Tm) and improve the overall thermostability of the spike protein in a short-term stability study. Thus, while 0.2% (v/v) Tween 20 was sufficient to prevent aggregation and to maintain spike protein stability under refrigeration, the addition of sucrose further improved vaccine thermostability. Altogether, our study provides a systematic approach to the formulation of protein-based COVID-19 vaccine and highlights the impact of mechanical stress on the conformation of the spike protein and the significance of surfactants and stabilizers in maintaining the structural and functional integrity of the spike protein.

show abstract

Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2

Cited by 3 publications

References 47 publications

Clinical development of SpikoGen®, an Advax-CpG55.2 adjuvanted recombinant spike protein vaccine

Clinical development of SpikoGen®, an Advax-CpG55.2 adjuvanted recombinant spike protein vaccine

Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN

Formulation Development of a COVID-19 Recombinant Spike Protein-Based Vaccine

Contact Info

Product

Resources

About