Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens

Ueda, George; Antanasijevic, Aleksandar; Fallas, Jorge A.; Sheffler, William; Copps, Jeffrey; Ellis, Daniel; Hutchinson, Geoffrey B.; Moyer, Adam; Yasmeen, Anila; Tsybovsky, Yaroslav; Park, Young-Jun; Bick, Matthew J.; Sankaran, Banumathi; Gillespie, Rebecca A.; Brouwer, Philip J.M.; Zwart, Peter H.; Veesler, David; Kanekiyo, Masaru; Graham, Barney S.; Sanders, Rogier W.; Moore, John P.; Klasse, Per Johan; Ward, Andrew B.; King, Neil P.; Baker, David

doi:10.7554/elife.57659

Cited by 142 publications

(158 citation statements)

References 81 publications

(143 reference statements)

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“…Larger nanoparticles are retained longer inside lymph node follicles and presented at the dendrites of follicular dendritic cells [ 20 ]. To mimic natural infection and induce an optimal host immune response, immunogenic domains have been attached to scaffolds, such as capsid proteins of viruses (Qβ, HPV, JCV, HBcAg, cowpea chlorotic mottle virus [ 21 ]); proteins such as ferritin, lumazine synthase, and encapsulin [ 18 , 22 , 23 , 24 , 25 ]; de novo designed protein or DNA cages [ 26 , 27 , 28 , 29 , 30 , 31 ]; or peptide tags with high aggregation propensity.…”

Section: Introductionmentioning

confidence: 99%

A Nanoscaffolded Spike-RBD Vaccine Provides Protection against SARS-CoV-2 with Minimal Anti-Scaffold Response

et al. 2021

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The response of the adaptive immune system is augmented by multimeric presentation of a specific antigen, resembling viral particles. Several vaccines have been designed based on natural or designed protein scaffolds, which exhibited a potent adaptive immune response to antigens; however, antibodies are also generated against the scaffold, which may impair subsequent vaccination. In order to compare polypeptide scaffolds of different size and oligomerization state with respect to their efficiency, including anti-scaffold immunity, we compared several strategies of presentation of the RBD domain of the SARS-CoV-2 spike protein, an antigen aiming to generate neutralizing antibodies. A comparison of several genetic fusions of RBD to different nanoscaffolding domains (foldon, ferritin, lumazine synthase, and β-annulus peptide) delivered as DNA plasmids demonstrated a strongly augmented immune response, with high titers of neutralizing antibodies and a robust T-cell response in mice. Antibody titers and virus neutralization were most potently enhanced by fusion to the small β-annulus peptide scaffold, which itself triggered a minimal response in contrast to larger scaffolds. The β-annulus fused RBD protein increased residence in lymph nodes and triggered the most potent viral neutralization in immunization by a recombinant protein. Results of the study support the use of a nanoscaffolding platform using the β-annulus peptide for vaccine design.

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Section: Introductionmentioning

confidence: 99%

A Nanoscaffolded Spike-RBD Vaccine Provides Protection against SARS-CoV-2 with Minimal Anti-Scaffold Response

et al. 2021

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“…Designing de novo proteins using Rosetta has successfully provided many robust proteins with diverse topologies for various protein engineering purposes, including small molecule binding (Dou et al, 2018;Tinberg et al, 2013), therapeutic developments (Cao et al, 2020;Silva et al, 2019), orthogonal biological signaling system construction (Chen et al, 2019;Langan et al, 2019;Quijano-Rubio et al, 2020), and material formation (Hsia et al, 2020;Pyles, Zhang, De Yoreo, & Baker, 2019;Ueda et al, 2020). A number of de novo proteins designed for the abovementioned applications have significantly different secondary structure features, and were generated using a similar pipeline, which all involved the key step of using the structure modifier in Rosetta, the blueprint builder (Huang et al, 2011;Marcos et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

De Novo Protein Design Using the Blueprint Builder in Rosetta

Lee

2020

CP Protein Science

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While native proteins cover diverse structural spaces and achieve various biological events, not many of them can directly serve human needs. One reason is that the native proteins usually contain idiosyncrasies evolved for their native functions but disfavoring engineering requirements. To overcome this issue, one strategy is to create de novo proteins which are designed to possess improved stability, high environmental tolerance, and enhanced engineering potential. Compared to other protein engineering strategies, in silico design of de novo proteins has significantly expanded the protein structural and sequence spaces, reduced wet lab workload, and incorporated engineered features in a guided and efficient manner. In the Baker laboratory we have been applying a design pipeline that uses the blueprint builder to design different folds of de novo proteins, and have successfully obtained libraries of de novo proteins with improved stability and engineering potential. In this article, we will use the design of de novo β‐barrel proteins as an example to describe the principles and basic procedures of the blueprint builder−based design pipeline. © 2020 Wiley Periodicals LLC. Basic Protocol 1: The construction of blueprints Alternate Protocol: Build blueprints based on existing protein .pdb files Basic Protocol 2: De novo protein design pipeline using the blueprint builder

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“…Our data suggest that antibody engineering strategies that optimize spacing of multiple antibodies through leucine zippers, cysteine bonds, DNA hybridization (Delcassian et al, 2013;Seifert et al, 2014;Sil, Lee, Luo, Holowka, & Baird, 2007) or multimeric scaffolds (Divine et al, 2020;Fallas et al, 2017;X. Huang et al, 2020;Ueda et al, 2020) could lead to stronger FcγR activation and potentially more effective therapies. A macrophage infected with the DNA-CARߛ (green) engulfs a 5 um silica bead coated in a supported lipid bilayer (magenta) and functionalized with 4T origami pegboards.…”

Section: Discussionmentioning

confidence: 93%

Tight nanoscale clustering of Fcγ-receptors using DNA origami promotes phagocytosis

Kern

Dong

Douglas

et al. 2021

Preprint

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Macrophages destroy pathogens and diseased cells through Fcγ receptor (FcγR)-driven phagocytosis of antibody-opsonized targets. Phagocytosis requires activation of multiple FcγRs, but the mechanism controlling the threshold for response is unclear. We developed a DNA origami-based engulfment system that allows precise nanoscale control of the number and spacing of ligands. When the number of ligands remains constant, reducing ligand spacing from 17.5 nm to 7 nm potently enhances engulfment, primarily by increasing efficiency of the engulfment-initiation process. Tighter ligand clustering increases receptor phosphorylation, as well as proximal downstream signals. Increasing the number of signaling domains recruited to a single ligand-receptor complex was not sufficient to recapitulate this effect, indicating that clustering of multiple receptors is required. Our results suggest that macrophages use information about local ligand densities to make critical engulfment decisions, which has implications for the mechanism of antibody-mediated phagocytosis and the design of immunotherapies.

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Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens

Cited by 142 publications

References 81 publications

A Nanoscaffolded Spike-RBD Vaccine Provides Protection against SARS-CoV-2 with Minimal Anti-Scaffold Response

A Nanoscaffolded Spike-RBD Vaccine Provides Protection against SARS-CoV-2 with Minimal Anti-Scaffold Response

De Novo Protein Design Using the Blueprint Builder in Rosetta

Tight nanoscale clustering of Fcγ-receptors using DNA origami promotes phagocytosis

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