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Stabilization of the SARS-CoV-2 Spike Receptor-Binding Domain Using Deep Mutational Scanning and Structure-Based Design.
Ellis, Daniel; Brunette, Natalie; Crawford, Katharine H D; Walls, Alexandra C; Pham, Minh N; Chen, Chengbo; Herpoldt, Karla-Luise; Fiala, Brooke; Murphy, Michael; Pettie, Deleah; Kraft, John C; Malone, Keara D; Navarro, Mary Jane; Ogohara, Cassandra; Kepl, Elizabeth; Ravichandran, Rashmi; Sydeman, Claire; Ahlrichs, Maggie; Johnson, Max; Blackstone, Alyssa; Carter, Lauren; Starr, Tyler N; Greaney, Allison J; Lee, Kelly K; Veesler, David; Bloom, Jesse D; King, Neil P.
  • Ellis D; Institute for Protein Design, University of Washington, Seattle, WA, United States.
  • Brunette N; Department of Biochemistry, University of Washington, Seattle, WA, United States.
  • Crawford KHD; Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, United States.
  • Walls AC; Institute for Protein Design, University of Washington, Seattle, WA, United States.
  • Pham MN; Department of Biochemistry, University of Washington, Seattle, WA, United States.
  • Chen C; Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.
  • Herpoldt KL; Department of Genome Sciences, University of Washington, Seattle, WA, United States.
  • Fiala B; Medical Scientist Training Program, University of Washington, Seattle, WA, United States.
  • Murphy M; Department of Biochemistry, University of Washington, Seattle, WA, United States.
  • Pettie D; Institute for Protein Design, University of Washington, Seattle, WA, United States.
  • Kraft JC; Department of Biochemistry, University of Washington, Seattle, WA, United States.
  • Malone KD; Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States.
  • Navarro MJ; Biological Physics Structure and Design Program, University of Washington, Seattle, WA, United States.
  • Ogohara C; Institute for Protein Design, University of Washington, Seattle, WA, United States.
  • Kepl E; Department of Biochemistry, University of Washington, Seattle, WA, United States.
  • Ravichandran R; Institute for Protein Design, University of Washington, Seattle, WA, United States.
  • Sydeman C; Department of Biochemistry, University of Washington, Seattle, WA, United States.
  • Ahlrichs M; Institute for Protein Design, University of Washington, Seattle, WA, United States.
  • Johnson M; Department of Biochemistry, University of Washington, Seattle, WA, United States.
  • Blackstone A; Institute for Protein Design, University of Washington, Seattle, WA, United States.
  • Carter L; Department of Biochemistry, University of Washington, Seattle, WA, United States.
  • Starr TN; Institute for Protein Design, University of Washington, Seattle, WA, United States.
  • Greaney AJ; Department of Biochemistry, University of Washington, Seattle, WA, United States.
  • Lee KK; Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.
  • Veesler D; Department of Biochemistry, University of Washington, Seattle, WA, United States.
  • Bloom JD; Institute for Protein Design, University of Washington, Seattle, WA, United States.
  • King NP; Department of Biochemistry, University of Washington, Seattle, WA, United States.
Front Immunol ; 12: 710263, 2021.
Article in English | MEDLINE | ID: covidwho-1315952
Preprint
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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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Immunization Schedule / Spike Glycoprotein, Coronavirus / Protein Domains / Immunogenicity, Vaccine / COVID-19 Vaccines / SARS-CoV-2 / COVID-19 / Mutation Type of study: Prognostic study / Randomized controlled trials Limits: Animals / Female / Humans Language: English Journal: Front Immunol Year: 2021 Document Type: Article Affiliation country: Fimmu.2021.710263

Full text: Available Collection: International databases Database: MEDLINE Main subject: Immunization Schedule / Spike Glycoprotein, Coronavirus / Protein Domains / Immunogenicity, Vaccine / COVID-19 Vaccines / SARS-CoV-2 / COVID-19 / Mutation Type of study: Prognostic study / Randomized controlled trials Limits: Animals / Female / Humans Language: English Journal: Front Immunol Year: 2021 Document Type: Article Affiliation country: Fimmu.2021.710263