Frontiers in Immunology (Jun 2021)
Stabilization of the SARS-CoV-2 Spike Receptor-Binding Domain Using Deep Mutational Scanning and Structure-Based Design
- Daniel Ellis,
- Daniel Ellis,
- Daniel Ellis,
- Natalie Brunette,
- Natalie Brunette,
- Katharine H. D. Crawford,
- Katharine H. D. Crawford,
- Katharine H. D. Crawford,
- Alexandra C. Walls,
- Minh N. Pham,
- Minh N. Pham,
- Chengbo Chen,
- Chengbo Chen,
- Karla-Luise Herpoldt,
- Karla-Luise Herpoldt,
- Brooke Fiala,
- Brooke Fiala,
- Michael Murphy,
- Michael Murphy,
- Deleah Pettie,
- Deleah Pettie,
- John C. Kraft,
- John C. Kraft,
- Keara D. Malone,
- Mary Jane Navarro,
- Cassandra Ogohara,
- Cassandra Ogohara,
- Elizabeth Kepl,
- Elizabeth Kepl,
- Rashmi Ravichandran,
- Rashmi Ravichandran,
- Claire Sydeman,
- Claire Sydeman,
- Maggie Ahlrichs,
- Maggie Ahlrichs,
- Max Johnson,
- Max Johnson,
- Alyssa Blackstone,
- Alyssa Blackstone,
- Lauren Carter,
- Lauren Carter,
- Tyler N. Starr,
- Allison J. Greaney,
- Allison J. Greaney,
- Allison J. Greaney,
- Kelly K. Lee,
- Kelly K. Lee,
- David Veesler,
- Jesse D. Bloom,
- Jesse D. Bloom,
- Jesse D. Bloom,
- Neil P. King,
- Neil P. King
Affiliations
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Daniel Ellis
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, United States
- Natalie Brunette
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Natalie Brunette
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Katharine H. D. Crawford
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Katharine H. D. Crawford
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
- Katharine H. D. Crawford
- Medical Scientist Training Program, University of Washington, Seattle, WA, United States
- Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Minh N. Pham
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Minh N. Pham
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Chengbo Chen
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States
- Chengbo Chen
- Biological Physics Structure and Design Program, University of Washington, Seattle, WA, United States
- Karla-Luise Herpoldt
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Karla-Luise Herpoldt
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Brooke Fiala
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Deleah Pettie
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- John C. Kraft
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- John C. Kraft
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Keara D. Malone
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Cassandra Ogohara
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Cassandra Ogohara
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Elizabeth Kepl
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Elizabeth Kepl
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Rashmi Ravichandran
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Claire Sydeman
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Max Johnson
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Alyssa Blackstone
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Alyssa Blackstone
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Tyler N. Starr
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Allison J. Greaney
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Allison J. Greaney
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
- Allison J. Greaney
- Medical Scientist Training Program, University of Washington, Seattle, WA, United States
- Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States
- Kelly K. Lee
- Biological Physics Structure and Design Program, University of Washington, Seattle, WA, United States
- David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- Jesse D. Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Jesse D. Bloom
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
- Jesse D. Bloom
- Howard Hughes Medical Institute, Seattle, WA, United States
- Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- DOI
- https://doi.org/10.3389/fimmu.2021.710263
- Journal volume & issue
-
Vol. 12
Abstract
The unprecedented global demand for SARS-CoV-2 vaccines has demonstrated the need for highly effective vaccine candidates that are thermostable and amenable to large-scale manufacturing. Nanoparticle immunogens presenting the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein (S) in repetitive arrays are being advanced as second-generation vaccine candidates, as they feature robust manufacturing characteristics and have shown promising immunogenicity in preclinical models. Here, we used previously reported deep mutational scanning (DMS) data to guide the design of stabilized variants of the RBD. The selected mutations fill a cavity in the RBD that has been identified as a linoleic acid binding pocket. Screening of several designs led to the selection of two lead candidates that expressed at higher yields than the wild-type RBD. These stabilized RBDs possess enhanced thermal stability and resistance to aggregation, particularly when incorporated into an icosahedral nanoparticle immunogen that maintained its integrity and antigenicity for 28 days at 35-40°C, while corresponding immunogens displaying the wild-type RBD experienced aggregation and loss of antigenicity. The stabilized immunogens preserved the potent immunogenicity of the original nanoparticle immunogen, which is currently being evaluated in a Phase I/II clinical trial. Our findings may improve the scalability and stability of RBD-based coronavirus vaccines in any format and more generally highlight the utility of comprehensive DMS data in guiding vaccine design.
Keywords
- SARS-CoV-2
- vaccine
- nanoparticle
- antigen stabilization
- receptor-binding domain
- computational protein design
