1
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Coppola F, Jafari R, McReynolds KD, Král P. Sulfoglycodendron Antivirals with Scalable Architectures and Activities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.01.606251. [PMID: 39131386 PMCID: PMC11312539 DOI: 10.1101/2024.08.01.606251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Many viruses initiate their cell-entry by binding their multi-protein receptors to human heparan sulfate proteoglycans (HSPG) and other molecular components present on cellular membranes. These viral interactions could be blocked and the whole viruses could be eliminated by suitable HSPG-mimetics providing multivalent binding to viral protein receptors. Here, large sulfoglyco-dendron HSPG-mimetics of different topologies, structures, and sizes were designed to this purpose. Atomistic molecular dynamics simulations were used to examine the ability of these broad-spectrum antivirals to block multi-protein HSPG-receptors in HIV, SARS-CoV-2, HPV, and dengue viruses. To characterize the inhibitory potential of these mimetics, their binding to individual and multiple protein receptors was examined. In particular, vectorial distributions of binding energies between the mimetics and viral protein receptors were introduced and calculated along the simulated trajectories. Space-dependent residual analysis of the mimetic-receptor binding was also performed. This analysis revealed detail nature of binding between these antivirals and viral protein receptors, and provided evidence that large inhibitors with multivalent binding might act like a molecular glue initiating the self-assembly of protein receptors in enveloped viruses.
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Affiliation(s)
- Francesco Coppola
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Roya Jafari
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Katherine D. McReynolds
- Departments of Chemistry, California State University Sacramento, 6000 J Street, Sacramento, CA 95819–6057, USA
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
- Departments of Physics, Pharmaceutical Sciences, and Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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2
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Dutta M, Acharya P. Cryo-electron microscopy in the study of virus entry and infection. Front Mol Biosci 2024; 11:1429180. [PMID: 39114367 PMCID: PMC11303226 DOI: 10.3389/fmolb.2024.1429180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses have been responsible for many epidemics and pandemics that have impacted human life globally. The COVID-19 pandemic highlighted both our vulnerability to viral outbreaks, as well as the mobilization of the scientific community to come together to combat the unprecedented threat to humanity. Cryo-electron microscopy (cryo-EM) played a central role in our understanding of SARS-CoV-2 during the pandemic and continues to inform about this evolving pathogen. Cryo-EM with its two popular imaging modalities, single particle analysis (SPA) and cryo-electron tomography (cryo-ET), has contributed immensely to understanding the structure of viruses and interactions that define their life cycles and pathogenicity. Here, we review how cryo-EM has informed our understanding of three distinct viruses, of which two - HIV-1 and SARS-CoV-2 infect humans, and the third, bacteriophages, infect bacteria. For HIV-1 and SARS-CoV-2 our focus is on the surface glycoproteins that are responsible for mediating host receptor binding, and host and cell membrane fusion, while for bacteriophages, we review their structure, capsid maturation, attachment to the bacterial cell surface and infection initiation mechanism.
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Affiliation(s)
- Moumita Dutta
- Duke Human Vaccine Institute, Durham, NC, United States
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Surgery, Durham, NC, United States
- Department of Biochemistry, Duke University, Durham, NC, United States
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3
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Cottrell CA, Pratap PP, Cirelli KM, Carnathan DG, Enemuo CA, Antanasijevic A, Ozorowski G, Sewall LM, Gao H, Allen JD, Nogal B, Silva M, Bhiman J, Pauthner M, Irvine DJ, Montefiori D, Crispin M, Burton DR, Silvestri G, Crotty S, Ward AB. Priming antibody responses to the fusion peptide in rhesus macaques. NPJ Vaccines 2024; 9:126. [PMID: 38997302 PMCID: PMC11245479 DOI: 10.1038/s41541-024-00918-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/27/2024] [Indexed: 07/14/2024] Open
Abstract
Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies (bnAbs) are major impediments to the development of an effective HIV vaccine. Rational protein vaccine design and non-conventional immunization strategies are potential avenues to overcome these hurdles. Here, we report using implantable osmotic pumps to continuously deliver a series of epitope-targeted immunogens to rhesus macaques over the course of six months to prime and elicit antibody responses against the conserved fusion peptide (FP). GC responses and antibody specificities were tracked longitudinally using lymph node fine-needle aspirates and electron microscopy polyclonal epitope mapping (EMPEM), respectively, to show antibody responses to the FP/N611 glycan hole region were primed, although exhibited limited neutralization breadth. Application of cryoEMPEM delineated key residues for on-target and off-target responses that can drive the next round of structure-based vaccine design.
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Affiliation(s)
- Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Payal P Pratap
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Kimberly M Cirelli
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Diane G Carnathan
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Chiamaka A Enemuo
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Leigh M Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Hongmei Gao
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center Durham, Durham, NC, USA
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Bartek Nogal
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Murillo Silva
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jinal Bhiman
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Matthias Pauthner
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Darrell J Irvine
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David Montefiori
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center Durham, Durham, NC, USA
| | - Max Crispin
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Dennis R Burton
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Guido Silvestri
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Shane Crotty
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
- La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
- Division of Infectious Disease and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA.
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4
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Liang Y, Xiao W, Peng Y, Zhang S, Dong J, Zhao J, Wang Y, Zhang M, Liu Z, Yu B. Development of nanoparticle vaccines utilizing designed Fc-binding homo-oligomers and RBD-Fc of SARS-CoV-2. Antiviral Res 2024; 227:105917. [PMID: 38782067 DOI: 10.1016/j.antiviral.2024.105917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/02/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
The Fc-fused receptor binding domain (RBD-Fc) vaccine for SARS-CoV-2 has garnered significant attention for its capacity to provide effective and specific immune protection. However, its immunogenicity is limited, highlighting the need for improvement in clinical application. Nanoparticle delivery has been shown to be an effective method for enhancing antigen immunogenicity. In this study, we developed bivalent nanoparticle recombinant protein vaccines by assembling the RBD-Fc of SARS-CoV-2 and Fc-binding homo-oligomers o42.1 and i52.3 into octahedral and icosahedral nanoparticles. The formation of RBD-Fc nanoparticles was confirmed through structural characterization and cell binding experiments. Compared to RBD-Fc dimers, the nanoparticle vaccines induced more potent neutralizing antibodies (nAb) and stronger cellular immune responses. Therefore, using bivalent nanoparticle vaccines based on RBD-Fc presents a promising vaccination strategy against SARS-CoV-2 and offers a universal approach for enhancing the immunogenicity of Fc fusion protein vaccines.
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MESH Headings
- Animals
- Female
- Humans
- Mice
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- COVID-19/prevention & control
- COVID-19/immunology
- COVID-19 Vaccines/immunology
- Immunity, Cellular
- Immunogenicity, Vaccine
- Immunoglobulin Fc Fragments/immunology
- Immunoglobulin Fc Fragments/chemistry
- Mice, Inbred BALB C
- Nanovaccines
- Protein Binding
- Protein Multimerization
- Recombinant Fusion Proteins/immunology
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Vaccine Development
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/chemistry
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Affiliation(s)
- Yucai Liang
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, China
| | - Weiling Xiao
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, China
| | - Yuan Peng
- School of Clinical Medicine, Shandong Second Medical University, Weifang, China
| | - Shengshuo Zhang
- School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Jinhua Dong
- School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao, China; International Research Frontiers Initiative, Tokyo Institute of Technology, Yokohama, Japan
| | - Jun Zhao
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Yuhui Wang
- School of Clinical Medicine, Shandong Second Medical University, Weifang, China
| | - Mengtao Zhang
- School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Zhijun Liu
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, China.
| | - Bowen Yu
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, China.
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5
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Gladkov N, Scott EA, Meador K, Lee EJ, Laganowsky AD, Yeates TO, Castells‐Graells R. Design of a symmetry-broken tetrahedral protein cage by a method of internal steric occlusion. Protein Sci 2024; 33:e4973. [PMID: 38533546 PMCID: PMC10966355 DOI: 10.1002/pro.4973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
Methods in protein design have made it possible to create large and complex, self-assembling protein cages with diverse applications. These have largely been based on highly symmetric forms exemplified by the Platonic solids. Prospective applications of protein cages would be expanded by strategies for breaking the designed symmetry, for example, so that only one or a few (instead of many) copies of an exterior domain or motif might be displayed on their surfaces. Here we demonstrate a straightforward design approach for creating symmetry-broken protein cages able to display singular copies of outward-facing domains. We modify the subunit of an otherwise symmetric protein cage through fusion to a small inward-facing domain, only one copy of which can be accommodated in the cage interior. Using biochemical methods and native mass spectrometry, we show that co-expression of the original subunit and the modified subunit, which is further fused to an outward-facing anti-GFP DARPin domain, leads to self-assembly of a protein cage presenting just one copy of the DARPin protein on its exterior. This strategy of designed occlusion provides a facile route for creating new types of protein cages with unique properties.
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Affiliation(s)
- Nika Gladkov
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Elena A. Scott
- Department of ChemistryTexas A&M UniversityCollege StationTexasUSA
| | - Kyle Meador
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Eric J. Lee
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
| | | | - Todd O. Yeates
- Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA
- Molecular Biology InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
- UCLA‐DOE Institute for Genomics and ProteomicsLos AngelesCaliforniaUSA
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6
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Chao CW, Sprouse KR, Miranda MC, Catanzaro NJ, Hubbard ML, Addetia A, Stewart C, Brown JT, Dosey A, Valdez A, Ravichandran R, Hendricks GG, Ahlrichs M, Dobbins C, Hand A, Treichel C, Willoughby I, Walls AC, McGuire AT, Leaf EM, Baric RS, Schäfer A, Veesler D, King NP. Protein nanoparticle vaccines induce potent neutralizing antibody responses against MERS-CoV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584735. [PMID: 38558973 PMCID: PMC10979991 DOI: 10.1101/2024.03.13.584735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic betacoronavirus that causes severe and often lethal respiratory illness in humans. The MERS-CoV spike (S) protein is the viral fusogen and the target of neutralizing antibodies, and has therefore been the focus of vaccine design efforts. Currently there are no licensed vaccines against MERS-CoV and only a few candidates have advanced to Phase I clinical trials. Here we developed MERS-CoV vaccines utilizing a computationally designed protein nanoparticle platform that has generated safe and immunogenic vaccines against various enveloped viruses, including a licensed vaccine for SARS-CoV-2. Two-component protein nanoparticles displaying MERS-CoV S-derived antigens induced robust neutralizing antibody responses and protected mice against challenge with mouse-adapted MERS-CoV. Electron microscopy polyclonal epitope mapping and serum competition assays revealed the specificities of the dominant antibody responses elicited by immunogens displaying the prefusion-stabilized S-2P trimer, receptor binding domain (RBD), or N-terminal domain (NTD). An RBD nanoparticle vaccine elicited antibodies targeting multiple non-overlapping epitopes in the RBD, whereas anti-NTD antibodies elicited by the S-2P- and NTD-based immunogens converged on a single antigenic site. Our findings demonstrate the potential of two-component nanoparticle vaccine candidates for MERS-CoV and suggest that this platform technology could be broadly applicable to betacoronavirus vaccine development.
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Affiliation(s)
- Cara W Chao
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Miranda L Hubbard
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack T Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Adian Valdez
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Grace G Hendricks
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Craig Dobbins
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexis Hand
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Isabelle Willoughby
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Andrew T McGuire
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth M Leaf
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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7
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Gee M, Atai K, Coller HA, Yeates TO, Castells-Graells R. Designed fluorescent protein cages as fiducial markers for targeted cell imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582585. [PMID: 38464160 PMCID: PMC10925312 DOI: 10.1101/2024.02.28.582585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Understanding how proteins function within their cellular environments is essential for cellular biology and biomedical research. However, current imaging techniques exhibit limitations, particularly in the study of small complexes and individual proteins within cells. Previously, protein cages have been employed as imaging scaffolds to study purified small proteins using cryo-electron microscopy (cryo-EM). Here we demonstrate an approach to deliver designed protein cages - endowed with fluorescence and targeted binding properties - into cells, thereby serving as fiducial markers for cellular imaging. We used protein cages with anti-GFP DARPin domains to target a mitochondrial protein (MFN1) expressed in mammalian cells, which was genetically fused to GFP. We demonstrate that the protein cages can penetrate cells, are directed to specific subcellular locations, and are detectable with confocal microscopy. This innovation represents a milestone in developing tools for in-depth cellular exploration, especially in conjunction with methods such as cryo-correlative light and electron microscopy (cryo-CLEM).
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Affiliation(s)
- Morgan Gee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | - Kaiser Atai
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Hilary A Coller
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA 90095
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA 90095
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8
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Ellis D, Dosey A, Boyoglu-Barnum S, Park YJ, Gillespie R, Syeda H, Hutchinson GB, Tsybovsky Y, Murphy M, Pettie D, Matheson N, Chan S, Ueda G, Fallas JA, Carter L, Graham BS, Veesler D, Kanekiyo M, King NP. Antigen spacing on protein nanoparticles influences antibody responses to vaccination. Cell Rep 2023; 42:113552. [PMID: 38096058 PMCID: PMC10801709 DOI: 10.1016/j.celrep.2023.113552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/28/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Immunogen design approaches aim to control the specificity and quality of antibody responses elicited by next-generation vaccines. Here, we use computational protein design to generate a nanoparticle vaccine platform based on the receptor-binding domain (RBD) of influenza hemagglutinin (HA) that enables precise control of antigen conformation and spacing. HA RBDs are presented as either monomers or native-like closed trimers that are connected to the underlying nanoparticle by a rigid linker that is modularly extended to precisely control antigen spacing. Nanoparticle immunogens with decreased spacing between trimeric RBDs elicit antibodies with improved hemagglutination inhibition and neutralization potency as well as binding breadth across diverse H1 HAs. Our "trihead" nanoparticle immunogen platform provides insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used in next-generation vaccines against influenza and other viruses.
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Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Rebecca Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Geoffrey B Hutchinson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nick Matheson
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jorge A Fallas
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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9
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Gladkov N, Scott EA, Meador K, Lee EJ, Laganowsky AD, Yeates TO, Castells-Graells R. Design of a symmetry-broken tetrahedral protein cage by a method of internal steric occlusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566319. [PMID: 37986890 PMCID: PMC10659388 DOI: 10.1101/2023.11.08.566319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Methods in protein design have made it possible to create large and complex, self-assembling protein cages with diverse applications. These have largely been based on highly symmetric forms exemplified by the Platonic solids. Prospective applications of protein cages would be expanded by strategies for breaking the designed symmetry, e.g., so that only one or a few (instead of many) copies of an exterior domain or motif might be displayed on their surfaces. Here we demonstrate a straightforward design approach for creating symmetry-broken protein cages able to display singular copies of outward-facing domains. We modify the subunit of an otherwise symmetric protein cage through fusion to a small inward-facing domain, only one copy of which can be accommodated in the cage interior. Using biochemical methods and native mass spectrometry, we show that co-expression of the original subunit and the modified subunit, which is further fused to an outward-facing anti-GFP DARPin domain, leads to self-assembly of a protein cage presenting just one copy of the DARPin protein on its exterior. This strategy of designed occlusion provides a facile route for creating new types of protein cages with unique properties.
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Affiliation(s)
- Nika Gladkov
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States of America
| | - Elena A. Scott
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States of America
| | - Kyle Meador
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States of America
| | - Eric J. Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States of America
| | - Arthur D. Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States of America
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States of America
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, United States of America
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, United States of America
| | - Roger Castells-Graells
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, United States of America
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10
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He W, Ou T, Skamangas N, Bailey CC, Bronkema N, Guo Y, Yin Y, Kobzarenko V, Zhang X, Pan A, Liu X, Xu J, Zhang L, Allwardt AE, Mitra D, Quinlan B, Sanders RW, Choe H, Farzan M. Heavy-chain CDR3-engineered B cells facilitate in vivo evaluation of HIV-1 vaccine candidates. Immunity 2023; 56:2408-2424.e6. [PMID: 37531955 PMCID: PMC11092302 DOI: 10.1016/j.immuni.2023.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/09/2023] [Accepted: 07/05/2023] [Indexed: 08/04/2023]
Abstract
V2-glycan/apex broadly neutralizing antibodies (bnAbs) recognize a closed quaternary epitope of the HIV-1 envelope glycoprotein (Env). This closed structure is necessary to elicit apex antibodies and useful to guide the maturation of other bnAb classes. To compare antigens designed to maintain this conformation, we evaluated apex-specific responses in mice engrafted with a diverse repertoire of B cells expressing the HCDR3 of the apex bnAb VRC26.25. Engineered B cells affinity matured, guiding the improvement of VRC26.25 itself. We found that soluble Env (SOSIP) variants differed significantly in their ability to raise anti-apex responses. A transmembrane SOSIP (SOSIP-TM) delivered as an mRNA-lipid nanoparticle elicited more potent neutralizing responses than multimerized SOSIP proteins. Importantly, SOSIP-TM elicited neutralizing sera from B cells engineered with the predicted VRC26.25-HCDR3 progenitor, which also affinity matured. Our data show that HCDR3-edited B cells facilitate efficient in vivo comparisons of Env antigens and highlight the potential of an HCDR3-focused vaccine approach.
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Affiliation(s)
- Wenhui He
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Tianling Ou
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Nickolas Skamangas
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Charles C Bailey
- The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Naomi Bronkema
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Skaggs Graduate School, Scripps Research, La Jolla, CA 92037, USA
| | - Yan Guo
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Yiming Yin
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Valerie Kobzarenko
- Department of Computer Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Xia Zhang
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Andi Pan
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Skaggs Graduate School, Scripps Research, La Jolla, CA 92037, USA
| | - Xin Liu
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jinge Xu
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Lizhou Zhang
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Ava E Allwardt
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Debasis Mitra
- Department of Computer Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Brian Quinlan
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Hyeryun Choe
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Farzan
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Skaggs Graduate School, Scripps Research, La Jolla, CA 92037, USA.
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11
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Wheatley AK, Kent SJ. Strength in diversity: Widening B cell recruitment for broader vaccine protection. Immunity 2023; 56:2182-2184. [PMID: 37820580 DOI: 10.1016/j.immuni.2023.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
Generating potent neutralizing antibodies is a unifying goal of next-generation vaccines. In this issue of Immunity, Ols et al. show that multivalent nanoparticle vaccines displaying RSV F protein can enable recruitment of more diverse B cell specificities into the vaccine response, resulting in increased potency and breadth of antibody immunity to both RSV and the related human metapneumovirus.
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Affiliation(s)
- Adam K Wheatley
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.
| | - Stephen J Kent
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia.
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12
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Hutchinson GB, Abiona OM, Ziwawo CT, Werner AP, Ellis D, Tsybovsky Y, Leist SR, Palandjian C, West A, Fritch EJ, Wang N, Wrapp D, Boyoglu-Barnum S, Ueda G, Baker D, Kanekiyo M, McLellan JS, Baric RS, King NP, Graham BS, Corbett-Helaire KS. Nanoparticle display of prefusion coronavirus spike elicits S1-focused cross-reactive antibody response against diverse coronavirus subgenera. Nat Commun 2023; 14:6195. [PMID: 37794071 PMCID: PMC10551005 DOI: 10.1038/s41467-023-41661-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 09/06/2023] [Indexed: 10/06/2023] Open
Abstract
Multivalent antigen display is a fast-growing area of interest toward broadly protective vaccines. Current nanoparticle-based vaccine candidates demonstrate the ability to confer antibody-mediated immunity against divergent strains of notably mutable viruses. In coronaviruses, this work is predominantly aimed at targeting conserved epitopes of the receptor binding domain. However, targeting conserved non-RBD epitopes could limit the potential for antigenic escape. To explore new potential targets, we engineered protein nanoparticles displaying coronavirus prefusion-stabilized spike (CoV_S-2P) trimers derived from MERS-CoV, SARS-CoV-1, SARS-CoV-2, hCoV-HKU1, and hCoV-OC43 and assessed their immunogenicity in female mice. Monotypic SARS-1 nanoparticles elicit cross-neutralizing antibodies against MERS-CoV and protect against MERS-CoV challenge. MERS and SARS nanoparticles elicit S1-focused antibodies, revealing a conserved site on the S N-terminal domain. Moreover, mosaic nanoparticles co-displaying distinct CoV_S-2P trimers elicit antibody responses to distant cross-group antigens and protect male and female mice against MERS-CoV challenge. Our findings will inform further efforts toward the development of pan-coronavirus vaccines.
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Affiliation(s)
- Geoffrey B Hutchinson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Institute for Protein Design, University of Washington School of Medicine, Seattle, WA, USA
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Olubukola M Abiona
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Case Western Reserve University, Cleveland, OH, USA
| | - Cynthia T Ziwawo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anne P Werner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Daniel Ellis
- Institute for Protein Design, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sarah R Leist
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charis Palandjian
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ande West
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ethan J Fritch
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nianshuang Wang
- College of Natural Sciences, University of Texas at Austin, Austin, USA
| | - Daniel Wrapp
- College of Natural Sciences, University of Texas at Austin, Austin, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - George Ueda
- Institute for Protein Design, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, USA
| | - David Baker
- Institute for Protein Design, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jason S McLellan
- College of Natural Sciences, University of Texas at Austin, Austin, USA
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Neil P King
- Institute for Protein Design, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Kizzmekia S Corbett-Helaire
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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13
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Cottrell CA, Pratap PP, Cirelli KM, Carnathan DG, Enemuo CA, Antanasijevic A, Ozorowski G, Sewall LM, Gao H, Greene KM, Allen JD, Ngo JT, Choe Y, Nogal B, Silva M, Bhiman J, Pauthner M, Irvine DJ, Montefiori D, Crispin M, Burton DR, Silvestri G, Crotty S, Ward AB. Focusing antibody responses to the fusion peptide in rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.545779. [PMID: 37425865 PMCID: PMC10327030 DOI: 10.1101/2023.06.26.545779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies (bnAbs) are major impediments to the development of an effective HIV vaccine. Rational protein vaccine design and non-conventional immunization strategies are potential avenues to overcome these hurdles. Here, we report using implantable osmotic pumps to continuously deliver a series of epitope-targeted immunogens to rhesus macaques over the course of six months to elicit immune responses against the conserved fusion peptide. Antibody specificities and GC responses were tracked longitudinally using electron microscopy polyclonal epitope mapping (EMPEM) and lymph node fine-needle aspirates, respectively. Application of cryoEMPEM delineated key residues for on-target and off-target responses that can drive the next round of structure-based vaccine design.
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Affiliation(s)
- Christopher A. Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Payal P. Pratap
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kimberly M. Cirelli
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Diane G. Carnathan
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Chiamaka A Enemuo
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Leigh M. Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hongmei Gao
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Kelli M. Greene
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Julia T. Ngo
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Yury Choe
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Bartek Nogal
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Murillo Silva
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jinal Bhiman
- Centre for HIV and STI, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Darrell J. Irvine
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David Montefiori
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Dennis R. Burton
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA02139, USA
| | - Guido Silvestri
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Shane Crotty
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Division of Infectious Disease and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
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14
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Burn Aschner C, Muthuraman K, Kucharska I, Cui H, Prieto K, Nair MS, Wang M, Huang Y, Christie-Holmes N, Poon B, Lam J, Sultana A, Kozak R, Mubareka S, Rubinstein JL, Rujas E, Treanor B, Ho DD, Jetha A, Julien JP. A multi-specific, multi-affinity antibody platform neutralizes sarbecoviruses and confers protection against SARS-CoV-2 in vivo. Sci Transl Med 2023; 15:eadf4549. [PMID: 37224226 DOI: 10.1126/scitranslmed.adf4549] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 04/26/2023] [Indexed: 05/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has been responsible for a global pandemic. Monoclonal antibodies (mAbs) have been used as antiviral therapeutics; however, these therapeutics have been limited in efficacy by viral sequence variability in emerging variants of concern (VOCs) and in deployment by the need for high doses. In this study, we leveraged the multi-specific, multi-affinity antibody (Multabody, MB) platform, derived from the human apoferritin protomer, to enable the multimerization of antibody fragments. MBs were shown to be highly potent, neutralizing SARS-CoV-2 at lower concentrations than their corresponding mAb counterparts. In mice infected with SARS-CoV-2, a tri-specific MB targeting three regions within the SARS-CoV-2 receptor binding domain was protective at a 30-fold lower dose than a cocktail of the corresponding mAbs. Furthermore, we showed in vitro that mono-specific MBs potently neutralize SARS-CoV-2 VOCs by leveraging augmented avidity, even when corresponding mAbs lose their ability to neutralize potently, and that tri-specific MBs expanded the neutralization breadth beyond SARS-CoV-2 to other sarbecoviruses. Our work demonstrates how avidity and multi-specificity combined can be leveraged to confer protection and resilience against viral diversity that exceeds that of traditional monoclonal antibody therapies.
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Affiliation(s)
- Clare Burn Aschner
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Krithika Muthuraman
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Iga Kucharska
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Hong Cui
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Katherine Prieto
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | | | - Betty Poon
- Combined Containment Level 3 Unit, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jessica Lam
- Combined Containment Level 3 Unit, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Azmiri Sultana
- Combined Containment Level 3 Unit, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert Kozak
- Department of Laboratory Medicine and Molecular Diagnostics, Division of Microbiology, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Samira Mubareka
- Department of Laboratory Medicine and Molecular Diagnostics, Division of Microbiology, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
- Division of Infectious Diseases, Sunnybrook Health Sciences Centre and Department of Medicine, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - John L Rubinstein
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Edurne Rujas
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Pharmacokinetic, Nanotechnology and Gene Therapy Group, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria, Spain
- Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, 01006 Vitoria, Spain
| | - Bebhinn Treanor
- Department of Immunology, University of Toronto, ON M5S 1A8, Canada
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3G5, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Arif Jetha
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Jean-Philippe Julien
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Immunology, University of Toronto, ON M5S 1A8, Canada
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15
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Ellis D, Dosey A, Boyoglu-Barnum S, Park YJ, Gillespie R, Syeda H, Tsybovsky Y, Murphy M, Pettie D, Matheson N, Chan S, Ueda G, Fallas JA, Carter L, Graham BS, Veesler D, Kanekiyo M, King NP. Antigen spacing on protein nanoparticles influences antibody responses to vaccination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541980. [PMID: 37292995 PMCID: PMC10245855 DOI: 10.1101/2023.05.23.541980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Immunogen design approaches aim to control the specificity and quality of antibody responses to enable the creation of next-generation vaccines with improved potency and breadth. However, our understanding of the relationship between immunogen structure and immunogenicity is limited. Here we use computational protein design to generate a self-assembling nanoparticle vaccine platform based on the head domain of influenza hemagglutinin (HA) that enables precise control of antigen conformation, flexibility, and spacing on the nanoparticle exterior. Domain-based HA head antigens were presented either as monomers or in a native-like closed trimeric conformation that prevents exposure of trimer interface epitopes. These antigens were connected to the underlying nanoparticle by a rigid linker that was modularly extended to precisely control antigen spacing. We found that nanoparticle immunogens with decreased spacing between closed trimeric head antigens elicited antibodies with improved hemagglutination inhibition (HAI) and neutralization potency as well as binding breadth across diverse HAs within a subtype. Our "trihead" nanoparticle immunogen platform thus enables new insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used to generate next-generation vaccines against influenza and other viruses.
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Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
- These authors contributed equally: Daniel Ellis and Annie Dosey
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- These authors contributed equally: Daniel Ellis and Annie Dosey
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rebecca Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nick Matheson
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jorge A. Fallas
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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16
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Zhang YN, Paynter J, Antanasijevic A, Allen JD, Eldad M, Lee YZ, Copps J, Newby ML, He L, Chavez D, Frost P, Goodroe A, Dutton J, Lanford R, Chen C, Wilson IA, Crispin M, Ward AB, Zhu J. Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimmers as HIV-1 vaccine candidates. Nat Commun 2023; 14:1985. [PMID: 37031217 PMCID: PMC10082823 DOI: 10.1038/s41467-023-37742-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/29/2023] [Indexed: 04/10/2023] Open
Abstract
Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 native-like Env trimers as vaccine candidates. We characterize the biophysical, structural, and antigenic properties of 1c-SApNPs that present the BG505 UFO trimer with wildtype and modified glycans. For 1c-SApNPs, glycan trimming improves recognition of the CD4 binding site without affecting broadly neutralizing antibodies (bNAbs) to major glycan epitopes. In mice, rabbits, and nonhuman primates, glycan trimming increases the frequency of vaccine responders (FVR) and steers antibody responses away from immunodominant glycan holes and glycan patches. The mechanism of vaccine-induced immunity is examined in mice. Compared with the UFO trimer, the multilayered E2p and I3-01v9 1c-SApNPs show 420 times longer retention in lymph node follicles, 20-32 times greater presentation on follicular dendritic cell dendrites, and up-to-4 times stronger germinal center reactions. These findings can inform future HIV-1 vaccine development.
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Affiliation(s)
- Yi-Nan Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jennifer Paynter
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Joel D Allen
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Mor Eldad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Yi-Zong Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Maddy L Newby
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Deborah Chavez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Pat Frost
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Anna Goodroe
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - John Dutton
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Robert Lanford
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Christopher Chen
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Max Crispin
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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17
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Lacasta A, Kim HC, Kepl E, Gachogo R, Chege N, Ojuok R, Muriuki C, Mwalimu S, Touboul G, Stiber A, Poole EJ, Ndiwa N, Fiala B, King NP, Nene V. Design and immunological evaluation of two-component protein nanoparticle vaccines for East Coast fever. Front Immunol 2023; 13:1015840. [PMID: 36713406 PMCID: PMC9880323 DOI: 10.3389/fimmu.2022.1015840] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/22/2022] [Indexed: 01/14/2023] Open
Abstract
Nanoparticle vaccines usually prime stronger immune responses than soluble antigens. Within this class of subunit vaccines, the recent development of computationally designed self-assembling two-component protein nanoparticle scaffolds provides a powerful and versatile platform for displaying multiple copies of one or more antigens. Here we report the generation of three different nanoparticle immunogens displaying 60 copies of p67C, an 80 amino acid polypeptide from a candidate vaccine antigen of Theileria parva, and their immunogenicity in cattle. p67C is a truncation of p67, the major surface protein of the sporozoite stage of T. parva, an apicomplexan parasite that causes an often-fatal bovine disease called East Coast fever (ECF) in sub-Saharan Africa. Compared to I32-19 and I32-28, we found that I53-50 nanoparticle scaffolds displaying p67C had the best biophysical characteristics. p67C-I53-50 also outperformed the other two nanoparticles in stimulating p67C-specific IgG1 and IgG2 antibodies and CD4+ T-cell responses, as well as sporozoite neutralizing capacity. In experimental cattle vaccine trials, p67C-I53-50 induced significant immunity to ECF, suggesting that the I53-50 scaffold is a promising candidate for developing novel nanoparticle vaccines. To our knowledge this is the first application of computationally designed nanoparticles to the development of livestock vaccines.
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Affiliation(s)
- Anna Lacasta
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya,*Correspondence: Anna Lacasta, ; Neil P. King,
| | - Hyung Chan Kim
- Department of Biochemistry, University of Washington, Seattle, WA, United States,Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Elizabeth Kepl
- Department of Biochemistry, University of Washington, Seattle, WA, United States,Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Rachael Gachogo
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Naomi Chege
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Rose Ojuok
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Charity Muriuki
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Stephen Mwalimu
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Gilad Touboul
- Department of Biochemistry, University of Washington, Seattle, WA, United States,Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Ariel Stiber
- Summer Undergraduate Research Fellowship Program, Caltech, Pasadena, CA, United States
| | - Elizabeth Jane Poole
- Research Methods Group, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Nicholas Ndiwa
- Research Methods Group, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA, United States,Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA, United States,Institute for Protein Design, University of Washington, Seattle, WA, United States,*Correspondence: Anna Lacasta, ; Neil P. King,
| | - Vishvanath Nene
- Animal and Human Health program, International Livestock Research Institute (ILRI), Nairobi, Kenya
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18
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Brouwer PJM, Antanasijevic A, Ronk AJ, Müller-Kräuter H, Watanabe Y, Claireaux M, Perrett HR, Bijl TPL, Grobben M, Umotoy JC, Schriek AI, Burger JA, Tejjani K, Lloyd NM, Steijaert TH, van Haaren MM, Sliepen K, de Taeye SW, van Gils MJ, Crispin M, Strecker T, Bukreyev A, Ward AB, Sanders RW. Lassa virus glycoprotein nanoparticles elicit neutralizing antibody responses and protection. Cell Host Microbe 2022; 30:1759-1772.e12. [PMID: 36400021 PMCID: PMC9794196 DOI: 10.1016/j.chom.2022.10.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/07/2022] [Accepted: 10/25/2022] [Indexed: 11/18/2022]
Abstract
The Lassa virus is endemic in parts of West Africa, and it causes hemorrhagic fever with high mortality. The development of a recombinant protein vaccine has been hampered by the instability of soluble Lassa virus glycoprotein complex (GPC) trimers, which disassemble into monomeric subunits after expression. Here, we use two-component protein nanoparticles consisting of trimeric and pentameric subunits to stabilize GPC in a trimeric conformation. These GPC nanoparticles present twenty prefusion GPC trimers on the surface of an icosahedral particle. Cryo-EM studies of GPC nanoparticles demonstrated a well-ordered structure and yielded a high-resolution structure of an unliganded GPC. These nanoparticles induced potent humoral immune responses in rabbits and protective immunity against the lethal Lassa virus challenge in guinea pigs. Additionally, we isolated a neutralizing antibody that mapped to the putative receptor-binding site, revealing a previously undefined site of vulnerability. Collectively, these findings offer potential approaches to vaccine and therapeutic design for the Lassa virus.
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Affiliation(s)
- Philip J M Brouwer
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands; Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Adam J Ronk
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA; Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550, USA
| | | | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Mathieu Claireaux
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Hailee R Perrett
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tom P L Bijl
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Marloes Grobben
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Jeffrey C Umotoy
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Angela I Schriek
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Judith A Burger
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Khadija Tejjani
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Nicole M Lloyd
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA; Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Thijs H Steijaert
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Marlies M van Haaren
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Kwinten Sliepen
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Thomas Strecker
- Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA; Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Andrew B Ward
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA.
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19
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Castro KM, Scheck A, Xiao S, Correia BE. Computational design of vaccine immunogens. Curr Opin Biotechnol 2022; 78:102821. [PMID: 36279815 DOI: 10.1016/j.copbio.2022.102821] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
Computational protein engineering has enabled the rational design of customized proteins, which has propelled both sequence-based and structure-based immunogen engineering and delivery. By discerning antigenic determinants of viral pathogens, computational methods have been implemented to successfully engineer representative viral strains able to elicit broadly neutralizing responses or present antigenic sites of viruses for focused immune responses. Combined with improvements in customizable nanoparticle design, immunogens are multivalently displayed to enhance immune responses. These rationally designed immunogens offer unique and powerful approaches to engineer vaccines for pathogens, which have eluded traditional approaches.
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Affiliation(s)
- Karla M Castro
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Andreas Scheck
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Shuhao Xiao
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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20
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Reiss EIMM, van Haaren MM, van Schooten J, Claireaux MAF, Maisonnasse P, Antanasijevic A, Allen JD, Bontjer I, Torres JL, Lee WH, Ozorowski G, Vázquez Bernat N, Kaduk M, Aldon Y, Burger JA, Chawla H, Aartse A, Tolazzi M, Gao H, Mundsperger P, Crispin M, Montefiori DC, Karlsson Hedestam GB, Scarlatti G, Ward AB, Le Grand R, Shattock R, Dereuddre-Bosquet N, Sanders RW, van Gils MJ. Fine-mapping the immunodominant antibody epitopes on consensus sequence-based HIV-1 envelope trimer vaccine candidates. NPJ Vaccines 2022; 7:152. [PMID: 36433972 PMCID: PMC9700725 DOI: 10.1038/s41541-022-00576-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2022] Open
Abstract
The HIV-1 envelope glycoprotein (Env) trimer is the key target for vaccines aimed at inducing neutralizing antibodies (NAbs) against HIV-1. The clinical candidate immunogen ConM SOSIP.v7 is a stabilized native-like HIV-1 Env trimer based on an artificial consensus sequence of all HIV-1 isolates in group M. In preclinical studies ConM SOSIP.v7 trimers induced strong autologous NAb responses in non-human primates (NHPs). To fine-map these responses, we isolated monoclonal antibodies (mAbs) from six cynomolgus macaques that were immunized three times with ConM SOSIP.v7 protein and boosted twice with the closely related ConSOSL.UFO.664 immunogen. A total of 40 ConM and/or ConS-specific mAbs were isolated, of which 18 were retrieved after the three ConM SOSIP.v7 immunizations and 22 after the two immunizations with ConSOSL.UFO.664. 22 mAbs (55%) neutralized the ConM and/or ConS virus. Cross-neutralization of ConS virus by approximately one-third of the mAbs was seen prior to ConSOSL.UFO.664 immunization, albeit with modest potency. Neutralizing antibodies predominantly targeted the V1 and V2 regions of the immunogens, with an apparent extension towards the V3 region. Thus, the V1V2V3 region is immunodominant in the potent NAb response elicited by two consensus sequence native-like HIV-1 Env immunogens. Immunization with these soluble consensus Env proteins also elicited non-neutralizing mAbs targeting the trimer base. These results inform the use and improvement of consensus-based trimer immunogens in combinatorial vaccine strategies.
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Affiliation(s)
- E I M M Reiss
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam, The Netherlands
| | - M M van Haaren
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam, The Netherlands
| | - J van Schooten
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam, The Netherlands
| | - M A F Claireaux
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam, The Netherlands
| | - P Maisonnasse
- Université Paris-Saclay - CEA - INSERM U1184, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, France
| | - A Antanasijevic
- Department of Integrative Structural and Computational Biology, Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - J D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - I Bontjer
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam, The Netherlands
| | - J L Torres
- Department of Integrative Structural and Computational Biology, Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - W-H Lee
- Department of Integrative Structural and Computational Biology, Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - G Ozorowski
- Department of Integrative Structural and Computational Biology, Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - N Vázquez Bernat
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - M Kaduk
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Y Aldon
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam, The Netherlands
| | - J A Burger
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam, The Netherlands
| | - H Chawla
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - A Aartse
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam, The Netherlands
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, the Netherlands
| | - M Tolazzi
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - H Gao
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - P Mundsperger
- Polymun Scientific Immunbiologische Forschung GmbH, Klosterneuburg, Austria
| | - M Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - D C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - G B Karlsson Hedestam
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - G Scarlatti
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - A B Ward
- Department of Integrative Structural and Computational Biology, Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - R Le Grand
- Université Paris-Saclay - CEA - INSERM U1184, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, France
| | - R Shattock
- Division of Mucosal Infection and Immunity, Department of Medicine, Imperial College of Science, Technology and Medicine, London, UK
| | - N Dereuddre-Bosquet
- Université Paris-Saclay - CEA - INSERM U1184, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, France
| | - R W Sanders
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - M J van Gils
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, Amsterdam, The Netherlands.
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21
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Olshefsky A, Richardson C, Pun SH, King NP. Engineering Self-Assembling Protein Nanoparticles for Therapeutic Delivery. Bioconjug Chem 2022; 33:2018-2034. [PMID: 35487503 PMCID: PMC9673152 DOI: 10.1021/acs.bioconjchem.2c00030] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Despite remarkable advances over the past several decades, many therapeutic nanomaterials fail to overcome major in vivo delivery barriers. Controlling immunogenicity, optimizing biodistribution, and engineering environmental responsiveness are key outstanding delivery problems for most nanotherapeutics. However, notable exceptions exist including some lipid and polymeric nanoparticles, some virus-based nanoparticles, and nanoparticle vaccines where immunogenicity is desired. Self-assembling protein nanoparticles offer a powerful blend of modularity and precise designability to the field, and have the potential to solve many of the major barriers to delivery. In this review, we provide a brief overview of key designable features of protein nanoparticles and their implications for therapeutic delivery applications. We anticipate that protein nanoparticles will rapidly grow in their prevalence and impact as clinically relevant delivery platforms.
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Affiliation(s)
- Audrey Olshefsky
- Department
of Bioengineering, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Christian Richardson
- Department
of Bioengineering, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Suzie H. Pun
- Department
of Bioengineering, University of Washington, Seattle, Washington 98195, United States
- Molecular
Engineering and Sciences Institute, University
of Washington, Seattle, Washington 98195, United States
| | - Neil P. King
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
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22
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Think like a Virus: Toward Improving Nanovaccine Development against SARS-CoV-2. Viruses 2022; 14:v14071553. [PMID: 35891532 PMCID: PMC9318803 DOI: 10.3390/v14071553] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022] Open
Abstract
There is no doubt that infectious diseases present global impact on the economy, society, health, mental state, and even political aspects, causing a long-lasting dent, and the situation will surely worsen if and when the viral spread becomes out of control, as seen during the still ongoing coronavirus disease 2019 (COVID-19) pandemic. Despite the considerable achievements made in viral prevention and treatment, there are still significant challenges that can be overcome through careful understanding of the viral mechanism of action to establish common ground for innovating new preventative and treatment strategies. Viruses can be regarded as devil nanomachines, and one innovative approach to face and stop the spread of viral infections is the development of nanoparticles that can act similar to them as drug/vaccine carriers. Moreover, we can use the properties that different viruses have in designing nanoparticles that reassemble the virus conformational structures but that do not present the detrimental threats to human health that native viruses possess. This review discusses the current preventative strategies (i.e., vaccination) used in facing viral infections and the associated limitations, highlighting the importance of innovating new approaches to face viral infectious diseases and discussing the current nanoapplications in vaccine development and the challenges that still face the nanovaccine field.
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23
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Kar U, Khaleeq S, Garg P, Bhat M, Reddy P, Vignesh VS, Upadhyaya A, Das M, Chakshusmathi G, Pandey S, Dutta S, Varadarajan R. Comparative Immunogenicity of Bacterially Expressed Soluble Trimers and Nanoparticle Displayed Influenza Hemagglutinin Stem Immunogens. Front Immunol 2022; 13:890622. [PMID: 35720346 PMCID: PMC9204493 DOI: 10.3389/fimmu.2022.890622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Current influenza vaccines need to be updated annually due to mutations in the globular head of the viral surface protein, hemagglutinin (HA). To address this, vaccine candidates have been designed based on the relatively conserved HA stem domain and have shown protective efficacy in animal models. Oligomerization of the antigens either by fusion to oligomerization motifs or display on self-assembling nanoparticle scaffolds, can induce more potent immune responses compared to the corresponding monomeric antigen due to multivalent engagement of B-cells. Since nanoparticle display can increase manufacturing complexity, and often involves one or more mammalian cell expressed components, it is important to characterize and compare various display and oligomerization scaffolds. Using a structure guided approach, we successfully displayed multiple copies of a previously designed soluble, trimeric influenza stem domain immunogen, pH1HA10, on the ferritin like protein, MsDps2 (12 copies), Ferritin (24 copies) and Encapsulin (180 copies). All proteins were expressed in Escherichia coli. The nanoparticle fusion immunogens were found to be well folded and bound to the influenza stem directed broadly neutralizing antibodies with high affinity. An 8.5 Å Cryo-EM map of Msdps2-pH1HA10 confirmed the successful design of the nanoparticle fusion immunogen. Mice immunization studies with the soluble trimeric stem and nanoparticle fusion constructs revealed that all of them were immunogenic, and protected mice against homologous (A/Belgium/145-MA/2009) and heterologous (A/Puerto Rico/8/1934) challenge with 10MLD50 mouse adapted virus. Although nanoparticle display conferred a small but statistically significant improvement in protection relative to the soluble trimer in a homologous challenge, heterologous protection was similar in both nanoparticle-stem immunized and trimeric stem immunized groups. Such rapidly producible, bacterially expressed antigens and nanoparticle scaffolds are useful modalities to tackle future influenza pandemics.
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Affiliation(s)
- Uddipan Kar
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Sara Khaleeq
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Priyanka Garg
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Madhuraj Bhat
- Mynvax Private Limited, ES12, Entrepreneurship Centre, Society for Innovation and Development (SID), Indian Institute of Science, Bengaluru, India
| | - Poorvi Reddy
- Mynvax Private Limited, ES12, Entrepreneurship Centre, Society for Innovation and Development (SID), Indian Institute of Science, Bengaluru, India
| | | | - Aditya Upadhyaya
- Mynvax Private Limited, ES12, Entrepreneurship Centre, Society for Innovation and Development (SID), Indian Institute of Science, Bengaluru, India
| | - Mili Das
- Mynvax Private Limited, ES12, Entrepreneurship Centre, Society for Innovation and Development (SID), Indian Institute of Science, Bengaluru, India
| | - Ghadiyaram Chakshusmathi
- Mynvax Private Limited, ES12, Entrepreneurship Centre, Society for Innovation and Development (SID), Indian Institute of Science, Bengaluru, India
| | - Suman Pandey
- Mynvax Private Limited, ES12, Entrepreneurship Centre, Society for Innovation and Development (SID), Indian Institute of Science, Bengaluru, India
| | - Somnath Dutta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
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24
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Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
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Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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25
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Antanasijevic A, Bowman CA, Kirchdoerfer RN, Cottrell CA, Ozorowski G, Upadhyay AA, Cirelli KM, Carnathan DG, Enemuo CA, Sewall LM, Nogal B, Zhao F, Groschel B, Schief WR, Sok D, Silvestri G, Crotty S, Bosinger SE, Ward AB. From structure to sequence: Antibody discovery using cryoEM. SCIENCE ADVANCES 2022; 8:eabk2039. [PMID: 35044813 PMCID: PMC8769551 DOI: 10.1126/sciadv.abk2039] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/23/2021] [Indexed: 06/02/2023]
Abstract
One of the rate-limiting steps in analyzing immune responses to vaccines or infections is the isolation and characterization of monoclonal antibodies. Here, we present a hybrid structural and bioinformatic approach to directly assign the heavy and light chains, identify complementarity-determining regions, and discover sequences from cryoEM density maps of serum-derived polyclonal antibodies bound to an antigen. When combined with next-generation sequencing of immune repertoires, we were able to specifically identify clonal family members, synthesize the monoclonal antibodies, and confirm that they interact with the antigen in a manner equivalent to the corresponding polyclonal antibodies. This structure-based approach for identification of monoclonal antibodies from polyclonal sera opens new avenues for analysis of immune responses and iterative vaccine design.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Charles A. Bowman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert N. Kirchdoerfer
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Christopher A. Cottrell
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amit A. Upadhyay
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30329, USA
- Yerkes Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Yerkes Nonhuman Primate Genomics Core, Emory University, Atlanta, GA 30329, USA
| | - Kimberly M. Cirelli
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Diane G. Carnathan
- Yerkes Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Yerkes Nonhuman Primate Genomics Core, Emory University, Atlanta, GA 30329, USA
| | - Chiamaka A. Enemuo
- Yerkes Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Yerkes Nonhuman Primate Genomics Core, Emory University, Atlanta, GA 30329, USA
| | - Leigh M. Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bartek Nogal
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fangzhu Zhao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative–Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bettina Groschel
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R. Schief
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Devin Sok
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative–Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Guido Silvestri
- Yerkes Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Yerkes Nonhuman Primate Genomics Core, Emory University, Atlanta, GA 30329, USA
| | - Shane Crotty
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Steven E. Bosinger
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30329, USA
- Yerkes Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Yerkes Nonhuman Primate Genomics Core, Emory University, Atlanta, GA 30329, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
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26
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Kim NH, Choi H, Shahzad ZM, Ki H, Lee J, Chae H, Kim YH. Supramolecular assembly of protein building blocks: from folding to function. NANO CONVERGENCE 2022; 9:4. [PMID: 35024976 PMCID: PMC8755899 DOI: 10.1186/s40580-021-00294-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.
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Affiliation(s)
- Nam Hyeong Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hojae Choi
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Zafar Muhammad Shahzad
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heesoo Ki
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jaekyoung Lee
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heeyeop Chae
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, 16419, Republic of Korea.
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27
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Tariq H, Batool S, Asif S, Ali M, Abbasi BH. Virus-Like Particles: Revolutionary Platforms for Developing Vaccines Against Emerging Infectious Diseases. Front Microbiol 2022; 12:790121. [PMID: 35046918 PMCID: PMC8761975 DOI: 10.3389/fmicb.2021.790121] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/10/2021] [Indexed: 02/06/2023] Open
Abstract
Virus-like particles (VLPs) are nanostructures that possess diverse applications in therapeutics, immunization, and diagnostics. With the recent advancements in biomedical engineering technologies, commercially available VLP-based vaccines are being extensively used to combat infectious diseases, whereas many more are in different stages of development in clinical studies. Because of their desired characteristics in terms of efficacy, safety, and diversity, VLP-based approaches might become more recurrent in the years to come. However, some production and fabrication challenges must be addressed before VLP-based approaches can be widely used in therapeutics. This review offers insight into the recent VLP-based vaccines development, with an emphasis on their characteristics, expression systems, and potential applicability as ideal candidates to combat emerging virulent pathogens. Finally, the potential of VLP-based vaccine as viable and efficient immunizing agents to induce immunity against virulent infectious agents, including, SARS-CoV-2 and protein nanoparticle-based vaccines has been elaborated. Thus, VLP vaccines may serve as an effective alternative to conventional vaccine strategies in combating emerging infectious diseases.
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Affiliation(s)
- Hasnat Tariq
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sannia Batool
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Saaim Asif
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Mohammad Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
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28
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Mohamed N, Hamad MA, Ghaleb AH, Esmat G, Elsabahy M. Applications of nanoengineered therapeutics and vaccines: special emphasis on COVID-19. IMMUNOMODULATORY EFFECTS OF NANOMATERIALS 2022. [PMCID: PMC9212255 DOI: 10.1016/b978-0-323-90604-3.00003-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nanomedicine provides innovative strategies that had significantly improved drug and gene delivery and allowed control over the engineering of therapeutics, diagnostics, vaccines, and other medical devices, for a diversity of medical applications. This review focuses on the current attempts to develop potent nanoengineered vaccines and therapeutics against coronaviruses, and the recent fabrication strategies and design principles to control acute infections from the escalating SARS-CoV-2 pandemic. Nanomedical approaches provide versatile platforms that can be utilized to enhance the overall potency, safety, and stability of vaccines, thus augmenting the desired immune response. Their modulable conformational features of size, shape, surface charge, antigen display, and composition allow for precise tuning and optimization of the nanoconstructs for the management of a variety of diseases and pathological conditions. The ability to control the release of their encapsulated cargoes and the possibility of surface decoration with various moieties support the construction of multifunctional nanomaterials that ultimately boost and prolong the immune response elicited and/or therapeutic effects, selectively at the diseased tissues and target sites.
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29
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Abstract
Antibody immunodominance refers to the preferential and asymmetric elicitation of antibodies against specific epitopes on a complex protein antigen. Traditional vaccination approaches for rapidly evolving pathogens have had limited success in part because of this phenomenon, as elicited antibodies preferentially target highly variable regions of antigens, and thus do not confer long lasting protection. While antibodies targeting functionally conserved epitopes have the potential to be broadly protective, they often make up a minority of the overall repertoire. Here, we discuss recent protein engineering strategies used to favorably alter patterns of immunodominance, and selectively focus antibody responses toward broadly protective epitopes in the pursuit of next-generation vaccines for rapidly evolving pathogens.
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30
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The development of natural and designed protein nanocages for encapsulation and delivery of active compounds. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.107004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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31
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Escolano A, Gristick HB, Gautam R, DeLaitsch AT, Abernathy ME, Yang Z, Wang H, Hoffmann MAG, Nishimura Y, Wang Z, Koranda N, Kakutani LM, Gao H, Gnanapragasam PNP, Raina H, Gazumyan A, Cipolla M, Oliveira TY, Ramos V, Irvine DJ, Silva M, West AP, Keeffe JR, Barnes CO, Seaman MS, Nussenzweig MC, Martin MA, Bjorkman PJ. Sequential immunization of macaques elicits heterologous neutralizing antibodies targeting the V3-glycan patch of HIV-1 Env. Sci Transl Med 2021; 13:eabk1533. [PMID: 34818054 DOI: 10.1126/scitranslmed.abk1533] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Amelia Escolano
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rajeev Gautam
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew T DeLaitsch
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Morgan E Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Haoqing Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Magnus A G Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Nicholas Koranda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leesa M Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Henna Raina
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ana Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Darrell J Irvine
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Murillo Silva
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Malcolm A Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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32
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Williams WB, Wiehe K, Saunders KO, Haynes BF. Strategies for induction of HIV-1 envelope-reactive broadly neutralizing antibodies. J Int AIDS Soc 2021; 24 Suppl 7:e25831. [PMID: 34806332 PMCID: PMC8606870 DOI: 10.1002/jia2.25831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/23/2021] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION A primary focus of HIV-1 vaccine development is the activation of B cell receptors for naïve or precursor broadly neutralizing antibodies (bnAbs), followed by expansion and maturation of bnAb B cell lineage intermediates leading to highly affinity-matured bnAbs. HIV-1 envelope (Env) encodes epitopes for bnAbs of different specificities. Design of immunogens to induce bnAb precursors of different specificities and mature them into bnAb status is a goal for HIV-1 vaccine development. We review vaccine strategies for bnAb lineages development and highlight the immunological barriers that these strategies must overcome to generate bnAbs. METHODS We provide perspectives based on published research articles and reviews. DISCUSSION The recent Antibody Mediated Protection (AMP) trial that tested the protective efficacy of one HIV-1 Env bnAb specificity demonstrated that relatively high levels of long-lasting serum titers of multiple specificities of bnAbs will be required for protection from HIV-1 transmission. Current vaccine efforts for induction of bnAb lineages are focused on immunogens designed to expand naïve HIV-1 bnAb precursor B cells following the recent success of vaccine-induction of bnAb precursor B cells in macaques and humans. BnAb precursor B cells serve as templates for priming-immunogen design. However, design of boosting immunogens for bnAb maturation requires knowledge of the optimal immunogen design and immunological environment for bnAb B cell lineage affinity maturation. BnAb lineages acquire rare genetic changes as mutations during B cell maturation. Moreover, the immunological environment that supports bnAb development during HIV-1 infection is perturbed with an altered B cell repertoire and dysfunctional immunoregulatory controls, suggesting that in normal settings, bnAb development will be disfavoured. Thus, strategies for vaccine induction of bnAbs must circumvent immunological barriers for bnAb development that normally constrain bnAb B cell affinity maturation. CONCLUSIONS A fully protective HIV-1 vaccine needs to induce durable high titers of bnAbs that can be generated by a sequential set of Env immunogens for expansion and maturation of bnAb B cell lineages in a permitted immunological environment. Moreover, multiple specificities of bnAbs will be required to be sufficiently broad to prevent the escape of HIV-1 strains during transmission.
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Affiliation(s)
- Wilton B. Williams
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of SurgeryDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Kevin Wiehe
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Kevin O. Saunders
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of SurgeryDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of ImmunologyDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Barton F. Haynes
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of ImmunologyDuke University School of MedicineDurhamNorth CarolinaUSA
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33
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Hallinan JP, Doyle LA, Shen BW, Gewe MM, Takushi B, Kennedy MA, Friend D, Roberts JM, Bradley P, Stoddard BL. Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces. Commun Biol 2021; 4:1240. [PMID: 34716407 PMCID: PMC8556268 DOI: 10.1038/s42003-021-02766-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 10/07/2021] [Indexed: 01/16/2023] Open
Abstract
Circular tandem repeat proteins (‘cTRPs’) are de novo designed protein scaffolds (in this and prior studies, based on antiparallel two-helix bundles) that contain repeated protein sequences and structural motifs and form closed circular structures. They can display significant stability and solubility, a wide range of sizes, and are useful as protein display particles for biotechnology applications. However, cTRPs also demonstrate inefficient self-assembly from smaller subunits. In this study, we describe a new generation of cTRPs, with longer repeats and increased interaction surfaces, which enhanced the self-assembly of two significantly different sizes of homotrimeric constructs. Finally, we demonstrated functionalization of these constructs with (1) a hexameric array of peptide-binding SH2 domains, and (2) a trimeric array of anti-SARS CoV-2 VHH domains. The latter proved capable of sub-nanomolar binding affinities towards the viral receptor binding domain and potent viral neutralization function. Jazmine Hallinan et al. report the development of a new generation of circular tandem repeat proteins with enhanced self-assembly. Functionalisation of these constructs with SARS CoV-2 VHH domains resulted in sub-nanomolar binding affinity to the viral receptor binding domain.
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Affiliation(s)
- Jazmine P Hallinan
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Lindsey A Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Betty W Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Mesfin M Gewe
- Lumen Bioscience Inc., 1441 North 34th Street, Seattle, WA, 98103, USA
| | - Brittany Takushi
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Madison A Kennedy
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Della Friend
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - James M Roberts
- Lumen Bioscience Inc., 1441 North 34th Street, Seattle, WA, 98103, USA
| | - Philip Bradley
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA. .,Division of Public Health Sciences and Program in Computational Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, 98009, USA.
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA.
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34
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Antanasijevic A, Sewall LM, Cottrell CA, Carnathan DG, Jimenez LE, Ngo JT, Silverman JB, Groschel B, Georgeson E, Bhiman J, Bastidas R, LaBranche C, Allen JD, Copps J, Perrett HR, Rantalainen K, Cannac F, Yang YR, de la Peña AT, Rocha RF, Berndsen ZT, Baker D, King NP, Sanders RW, Moore JP, Crotty S, Crispin M, Montefiori DC, Burton DR, Schief WR, Silvestri G, Ward AB. Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM. Nat Commun 2021; 12:4817. [PMID: 34376662 PMCID: PMC8355326 DOI: 10.1038/s41467-021-25087-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/23/2021] [Indexed: 11/08/2022] Open
Abstract
Engineered ectodomain trimer immunogens based on BG505 envelope glycoprotein are widely utilized as components of HIV vaccine development platforms. In this study, we used rhesus macaques to evaluate the immunogenicity of several stabilized BG505 SOSIP constructs both as free trimers and presented on a nanoparticle. We applied a cryoEM-based method for high-resolution mapping of polyclonal antibody responses elicited in immunized animals (cryoEMPEM). Mutational analysis coupled with neutralization assays were used to probe the neutralization potential at each epitope. We demonstrate that cryoEMPEM data can be used for rapid, high-resolution analysis of polyclonal antibody responses without the need for monoclonal antibody isolation. This approach allowed to resolve structurally distinct classes of antibodies that bind overlapping sites. In addition to comprehensive mapping of commonly targeted neutralizing and non-neutralizing epitopes in BG505 SOSIP immunogens, our analysis revealed that epitopes comprising engineered stabilizing mutations and of partially occupied glycosylation sites can be immunogenic.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Leigh M Sewall
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher A Cottrell
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Diane G Carnathan
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Luis E Jimenez
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Julia T Ngo
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Jennifer B Silverman
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Bettina Groschel
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Erik Georgeson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jinal Bhiman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Raiza Bastidas
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Jeffrey Copps
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Hailee R Perrett
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kimmo Rantalainen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Fabien Cannac
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yuhe R Yang
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alba Torrents de la Peña
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rebeca Froes Rocha
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Zachary T Berndsen
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - David Baker
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Neil P King
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rogier W Sanders
- Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - John P Moore
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Shane Crotty
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | | | - Dennis R Burton
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - William R Schief
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Andrew B Ward
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
- International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
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35
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van Schooten J, van Haaren MM, Li H, McCoy LE, Havenar-Daughton C, Cottrell CA, Burger JA, van der Woude P, Helgers LC, Tomris I, Labranche CC, Montefiori DC, Ward AB, Burton DR, Moore JP, Sanders RW, Crotty S, Shaw GM, van Gils MJ. Antibody responses induced by SHIV infection are more focused than those induced by soluble native HIV-1 envelope trimers in non-human primates. PLoS Pathog 2021; 17:e1009736. [PMID: 34432859 PMCID: PMC8423243 DOI: 10.1371/journal.ppat.1009736] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/07/2021] [Accepted: 06/21/2021] [Indexed: 12/22/2022] Open
Abstract
The development of an effective human immunodeficiency virus (HIV-1) vaccine is a high global health priority. Soluble native-like HIV-1 envelope glycoprotein trimers (Env), including those based on the SOSIP design, have shown promise as vaccine candidates by inducing neutralizing antibody responses against the autologous virus in animal models. However, to overcome HIV-1's extreme diversity a vaccine needs to induce broadly neutralizing antibodies (bNAbs). Such bNAbs can protect non-human primates (NHPs) and humans from infection. The prototypic BG505 SOSIP.664 immunogen is based on the BG505 env sequence isolated from an HIV-1-infected infant from Kenya who developed a bNAb response. Studying bNAb development during natural HIV-1 infection can inform vaccine design, however, it is unclear to what extent vaccine-induced antibody responses to Env are comparable to those induced by natural infection. Here, we compared Env antibody responses in BG505 SOSIP-immunized NHPs with those in BG505 SHIV-infected NHPs, by analyzing monoclonal antibodies (mAbs). We observed three major differences between BG505 SOSIP immunization and BG505 SHIV infection. First, SHIV infection resulted in more clonal expansion and less antibody diversity compared to SOSIP immunization, likely because of higher and/or prolonged antigenic stimulation and increased antigen diversity during infection. Second, while we retrieved comparatively fewer neutralizing mAbs (NAbs) from SOSIP-immunized animals, these NAbs targeted more diverse epitopes compared to NAbs from SHIV-infected animals. However, none of the NAbs, either elicited by vaccination or infection, showed any breadth. Finally, SOSIP immunization elicited antibodies against the base of the trimer, while infection did not, consistent with the base being placed onto the virus membrane in the latter setting. Together these data provide new insights into the antibody response against BG505 Env during infection and immunization and limitations that need to be overcome to induce better responses after vaccination.
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Affiliation(s)
- Jelle van Schooten
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marlies M. van Haaren
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Hui Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Laura E. McCoy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Colin Havenar-Daughton
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Christopher A. Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Judith A. Burger
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Patricia van der Woude
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Leanne C. Helgers
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ilhan Tomris
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Celia C. Labranche
- Laboratory for AIDS Vaccine Research and Development, Duke University Medical Center, Durham, North Carolina, United States of America
| | - David C. Montefiori
- Laboratory for AIDS Vaccine Research and Development, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative—Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, California, United States of America
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative—Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, California, United States of America
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - John P. Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - George M. Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
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Turner HL, Andrabi R, Cottrell CA, Richey ST, Song G, Callaghan S, Anzanello F, Moyer TJ, Abraham W, Melo M, Silva M, Scaringi N, Rakasz EG, Sattentau QJ, Irvine DJ, Burton DR, Ward AB. Disassembly of HIV envelope glycoprotein trimer immunogens is driven by antibodies elicited via immunization. SCIENCE ADVANCES 2021; 7:eabh2791. [PMID: 34321200 PMCID: PMC8318364 DOI: 10.1126/sciadv.abh2791] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Rationally designed protein subunit vaccines are being developed for a variety of viruses including influenza, RSV, SARS-CoV-2, and HIV. These vaccines are based on stabilized versions of the primary targets of neutralizing antibodies on the viral surface, namely, viral fusion glycoproteins. While these immunogens display the epitopes of potent neutralizing antibodies, they also present epitopes recognized by non-neutralizing or weakly neutralizing ("off-target") antibodies. Using our recently developed electron microscopy polyclonal epitope mapping approach, we have uncovered a phenomenon wherein off-target antibodies elicited by HIV trimer subunit vaccines cause the otherwise highly stabilized trimeric proteins to degrade into cognate protomers. Further, we show that these protomers expose an expanded suite of off-target epitopes, normally occluded inside the prefusion conformation of trimer, that subsequently elicit further off-target antibody responses. Our study provides critical insights for further improvement of HIV subunit trimer vaccines for future rounds of the iterative vaccine design process.
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Affiliation(s)
- Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Raiees Andrabi
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative-Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ge Song
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative-Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sean Callaghan
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative-Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fabio Anzanello
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative-Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tyson J Moyer
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wuhbet Abraham
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mariane Melo
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Murillo Silva
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nicole Scaringi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eva G Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Quentin J Sattentau
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Dennis R Burton
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative-Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative-Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
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Kumar S, Lin X, Ngo T, Shapero B, Sou C, Allen JD, Copps J, Zhang L, Ozorowski G, He L, Crispin M, Ward AB, Wilson IA, Zhu J. Neutralizing Antibodies Induced by First-Generation gp41-Stabilized HIV-1 Envelope Trimers and Nanoparticles. mBio 2021; 12:e0042921. [PMID: 34156262 PMCID: PMC8262854 DOI: 10.1128/mbio.00429-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/25/2021] [Indexed: 12/24/2022] Open
Abstract
The immunogenicity of gp41-stabilized HIV-1 BG505 envelope (Env) trimers and nanoparticles (NPs) was recently assessed in mice and rabbits. Here, we combined Env-specific B-cell sorting and repertoire sequencing to identify neutralizing antibodies (NAbs) from immunized animals. A panel of mouse NAbs was isolated from mice immunized with a 60-meric I3-01 NP presenting 20 stabilized trimers. Three mouse NAbs potently neutralized BG505.T332N by recognizing a glycan epitope centered in the C3/V4 region on BG505 Env, as revealed by electron microscopy (EM), X-ray crystallography, and epitope mapping. A set of rabbit NAbs was isolated from rabbits immunized with a soluble trimer and a 24-meric ferritin NP presenting 8 trimers. Neutralization assays against BG505.T332N variants confirmed that potent rabbit NAbs targeted previously described glycan holes on BG505 Env and accounted for a significant portion of the autologous NAb response in both the trimer and ferritin NP groups. Last, we examined NAb responses that were induced by non-BG505 Env immunogens. We determined a 3.4-Å-resolution crystal structure for the clade C transmitted/founder (T/F) Du172.17 Env with a redesigned heptad repeat 1 (HR1) bend in gp41. This clade C Env, in a soluble trimer form and in a multivalent form with 8 trimers attached to ferritin NP, and the gp41-stabilized clade A Q482-d12 Env trimer elicited distinct NAb responses in rabbits, with notable differences in neutralization breadth. Although eliciting a broad NAb response remains a major challenge, our study provides valuable information on an HIV-1 vaccine design strategy that combines gp41 stabilization and NP display. IMPORTANCE Self-assembling protein nanoparticles (NPs) presenting BG505 envelope (Env) trimers can elicit tier 2 HIV-1-neutralizing antibody (NAb) responses more effectively than soluble trimers. In the present study, monoclonal NAbs were isolated from previously immunized mice and rabbits for structural and functional analyses, which revealed that potent mouse NAbs recognize the C3/V4 region and small NP-elicited rabbit NAbs primarily target known glycan holes on BG505 Env. This study validates the gp41 stabilization strategy for HIV-1 Env vaccine design and highlights the challenge in eliciting a broad NAb response.
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Affiliation(s)
- Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Timothy Ngo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Benjamin Shapero
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Lei Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
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38
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Karch CP, Matyas GR. The current and future role of nanovaccines in HIV-1 vaccine development. Expert Rev Vaccines 2021; 20:935-944. [PMID: 34184607 DOI: 10.1080/14760584.2021.1945448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: An efficacious vaccine for HIV-1 has been sought for over 30 years to eliminate the virus from the human population. Many challenges have occurred in the attempt to produce a successful immunogen, mainly caused by the basic biology of the virus. Immunogens have been developed focusing on inducing one or more of the following types of immune responses; neutralizing antibodies, non-neutralizing antibodies, and T-cell mediated responses. One way to better present and develop an immunogen for HIV-1 is through the use of nanotechnology and nanoparticles.Areas covered: This article gives a basic overview of the HIV-1 vaccine field, as well as nanotechnology, specifically nanovaccines. It then covers the application of nanovaccines made from biological macromolecules to HIV-1 vaccine development for neutralizing antibodies, non-neutralizing antibodies, and T-cell-mediated responses.Expert opinion: Nanovaccines are an area that is ripe for further exploration in HIV-1 vaccine field. Not only are nanovaccines capable of carrying and presenting antigens in native-like conformations, but they have also repeatedly been shown to increase immunogenicity over recombinant antigens alone. Only through further research can the true role of nanovaccines in the development of an efficacious HIV-1 vaccine be established.
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Affiliation(s)
- Christopher P Karch
- Laboratory of Adjuvant and Antigen Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Laboratory of Adjuvant and Antigen Research, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Gary R Matyas
- Laboratory of Adjuvant and Antigen Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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39
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Corrigan AR, Duan H, Cheng C, Gonelli CA, Ou L, Xu K, DeMouth ME, Geng H, Narpala S, O'Connell S, Zhang B, Zhou T, Basappa M, Boyington JC, Chen SJ, O'Dell S, Pegu A, Stephens T, Tsybovsky Y, van Schooten J, Todd JP, Wang S, Doria-Rose NA, Foulds KE, Koup RA, McDermott AB, van Gils MJ, Kwong PD, Mascola JR. Fusion peptide priming reduces immune responses to HIV-1 envelope trimer base. Cell Rep 2021; 35:108937. [PMID: 33826898 PMCID: PMC8070658 DOI: 10.1016/j.celrep.2021.108937] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/02/2021] [Accepted: 03/10/2021] [Indexed: 11/16/2022] Open
Abstract
Soluble "SOSIP"-stabilized envelope (Env) trimers are promising HIV-vaccine immunogens. However, they induce high-titer responses against the glycan-free trimer base, which is occluded on native virions. To delineate the effect on base responses of priming with immunogens targeting the fusion peptide (FP) site of vulnerability, here, we quantify the prevalence of trimer-base antibody responses in 49 non-human primates immunized with various SOSIP-stabilized Env trimers and FP-carrier conjugates. Trimer-base responses account for ∼90% of the overall trimer response in animals immunized with trimer only, ∼70% in animals immunized with a cocktail of SOSIP trimer and FP conjugate, and ∼30% in animals primed with FP conjugates before trimer immunization. Notably, neutralization breadth in FP-conjugate-primed animals correlates inversely with trimer-base responses. Our data provide methods to quantify the prevalence of trimer-base responses and reveal that FP-conjugate priming, either alone or as part of a cocktail, can reduce the trimer-base response and improve the neutralization outcome.
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Affiliation(s)
- Angela R Corrigan
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hongying Duan
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher A Gonelli
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ou
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Xu
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megan E DeMouth
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hui Geng
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandeep Narpala
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah O'Connell
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Manjula Basappa
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey C Boyington
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven J Chen
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21710, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21710, USA
| | - Jelle van Schooten
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, the Netherlands
| | - John P Todd
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard A Koup
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, the Netherlands
| | - Peter D Kwong
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - John R Mascola
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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40
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Khmelinskaia A, Wargacki A, King NP. Structure-based design of novel polyhedral protein nanomaterials. Curr Opin Microbiol 2021; 61:51-57. [PMID: 33784513 DOI: 10.1016/j.mib.2021.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023]
Abstract
Organizing matter at the atomic scale is a central goal of nanotechnology. Bottom-up approaches, in which molecular building blocks are programmed to assemble via supramolecular interactions, are a proven and versatile route to new and useful nanomaterials. Although a wide variety of molecules have been used as building blocks, proteins have several intrinsic features that present unique opportunities for designing nanomaterials with sophisticated functions. There has been tremendous recent progress in designing proteins to fold and assemble to highly ordered structures. Here we review the leading approaches to the design of closed polyhedral protein assemblies, highlight the importance of considering the assembly process itself, and discuss various applications and future directions for the field. We emphasize throughout the exciting opportunities presented by recent advances as well as challenges that remain.
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Affiliation(s)
- Alena Khmelinskaia
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Adam Wargacki
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Neil P King
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA.
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41
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Gidley F, Parmeggiani F. Repeat proteins: designing new shapes and functions for solenoid folds. Curr Opin Struct Biol 2021; 68:208-214. [PMID: 33721772 DOI: 10.1016/j.sbi.2021.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 10/21/2022]
Abstract
The modular nature of repeat proteins has inspired the design of regular and completely novel sequences and structures. Research in the past years has provided a broad set of design approaches and new repeat proteins that have found applications in molecular recognition, taking advantage of the natural ability of some of these families to bind proteins, peptides and nucleic acids. Here, we provide an overview on the recent trends in design of repeat proteins, particularly solenoid folds, and their applications. By exploiting the intrinsic modularity of repeats, new architectures have been designed that combine different types of repeat, are easily scalable by changing the number of repeats and can be quickly generated by using existing modular building blocks.
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Affiliation(s)
- Frances Gidley
- School of Chemistry, School of Biochemistry, Bristol Biodesign Institute, University of Bristol, United Kingdom
| | - Fabio Parmeggiani
- School of Chemistry, School of Biochemistry, Bristol Biodesign Institute, University of Bristol, United Kingdom.
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42
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Brouwer PJM, Brinkkemper M, Maisonnasse P, Dereuddre-Bosquet N, Grobben M, Claireaux M, de Gast M, Marlin R, Chesnais V, Diry S, Allen JD, Watanabe Y, Giezen JM, Kerster G, Turner HL, van der Straten K, van der Linden CA, Aldon Y, Naninck T, Bontjer I, Burger JA, Poniman M, Mykytyn AZ, Okba NMA, Schermer EE, van Breemen MJ, Ravichandran R, Caniels TG, van Schooten J, Kahlaoui N, Contreras V, Lemaître J, Chapon C, Fang RHT, Villaudy J, Sliepen K, van der Velden YU, Haagmans BL, de Bree GJ, Ginoux E, Ward AB, Crispin M, King NP, van der Werf S, van Gils MJ, Le Grand R, Sanders RW. Two-component spike nanoparticle vaccine protects macaques from SARS-CoV-2 infection. Cell 2021; 184:1188-1200.e19. [PMID: 33577765 PMCID: PMC7834972 DOI: 10.1016/j.cell.2021.01.035] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/23/2020] [Accepted: 01/21/2021] [Indexed: 02/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is continuing to disrupt personal lives, global healthcare systems, and economies. Hence, there is an urgent need for a vaccine that prevents viral infection, transmission, and disease. Here, we present a two-component protein-based nanoparticle vaccine that displays multiple copies of the SARS-CoV-2 spike protein. Immunization studies show that this vaccine induces potent neutralizing antibody responses in mice, rabbits, and cynomolgus macaques. The vaccine-induced immunity protects macaques against a high-dose challenge, resulting in strongly reduced viral infection and replication in the upper and lower airways. These nanoparticles are a promising vaccine candidate to curtail the SARS-CoV-2 pandemic.
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Affiliation(s)
- Philip J M Brouwer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Mitch Brinkkemper
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Pauline Maisonnasse
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Nathalie Dereuddre-Bosquet
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Marloes Grobben
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Mathieu Claireaux
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Marlon de Gast
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Romain Marlin
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | | | | | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Julia M Giezen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Gius Kerster
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karlijn van der Straten
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Cynthia A van der Linden
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Yoann Aldon
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Thibaut Naninck
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Ilja Bontjer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Meliawati Poniman
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Anna Z Mykytyn
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Nisreen M A Okba
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Edith E Schermer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Marielle J van Breemen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tom G Caniels
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Jelle van Schooten
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Nidhal Kahlaoui
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Vanessa Contreras
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Julien Lemaître
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Catherine Chapon
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | - Raphaël Ho Tsong Fang
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France
| | | | - Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Yme U van der Velden
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Godelieve J de Bree
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105 AZ Amsterdam, the Netherlands
| | - Eric Ginoux
- Life and Soft, 92350 Le Plessis-Robinson, France
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université de Paris, Paris, France; National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, Fontenay-aux-Roses, France.
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands.
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43
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Turner HL, Andrabi R, Cottrell CA, Richey ST, Song G, Callaghan S, Anzanello F, Moyer TJ, Abraham W, Melo M, Silva M, Scaringi N, Rakasz EG, Sattentau Q, Irvine DJ, Burton DR, Ward AB. Disassembly of HIV envelope glycoprotein trimer immunogens is driven by antibodies elicited via immunization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33619491 PMCID: PMC7899455 DOI: 10.1101/2021.02.16.431310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Rationally designed protein subunit vaccines are being developed for a variety of viruses including influenza, RSV, SARS-CoV-2 and HIV. These vaccines are based on stabilized versions of the primary targets of neutralizing antibodies on the viral surface, namely viral fusion glycoproteins. While these immunogens display the epitopes of potent neutralizing antibodies, they also present epitopes recognized by non or weakly neutralizing (“off-target”) antibodies. Using our recently developed electron microscopy epitope mapping approach, we have uncovered a phenomenon wherein off-target antibodies elicited by HIV trimer subunit vaccines cause the otherwise highly stabilized trimeric proteins to degrade into cognate protomers. Further, we show that these protomers expose an expanded suite of off-target epitopes, normally occluded inside the prefusion conformation of trimer, that subsequently elicit further off-target antibody responses. Our study provides critical insights for further improvement of HIV subunit trimer vaccines for future rounds of the iterative vaccine design process. HIV Env trimers elicit antibodies that lead to their own destruction
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Affiliation(s)
- Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Raiees Andrabi
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative - Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ge Song
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative - Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sean Callaghan
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative - Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fabio Anzanello
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative - Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tyson J Moyer
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wuhbet Abraham
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mariane Melo
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Murillo Silva
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nicole Scaringi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eva G Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Quentin Sattentau
- The Sir William Dunn School of Pathology, The University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Dennis R Burton
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative - Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative - Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
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44
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Brouwer PJM, Antanasijevic A, de Gast M, Allen JD, Bijl TPL, Yasmeen A, Ravichandran R, Burger JA, Ozorowski G, Torres JL, LaBranche C, Montefiori DC, Ringe RP, van Gils MJ, Moore JP, Klasse PJ, Crispin M, King NP, Ward AB, Sanders RW. Immunofocusing and enhancing autologous Tier-2 HIV-1 neutralization by displaying Env trimers on two-component protein nanoparticles. NPJ Vaccines 2021; 6:24. [PMID: 33563983 PMCID: PMC7873233 DOI: 10.1038/s41541-021-00285-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/07/2021] [Indexed: 01/09/2023] Open
Abstract
The HIV-1 envelope glycoprotein trimer is poorly immunogenic because it is covered by a dense glycan shield. As a result, recombinant Env glycoproteins generally elicit inadequate antibody levels that neutralize clinically relevant, neutralization-resistant (Tier-2) HIV-1 strains. Multivalent antigen presentation on nanoparticles is an established strategy to increase vaccine-driven immune responses. However, due to nanoparticle instability in vivo, the display of non-native Env structures, and the inaccessibility of many neutralizing antibody (NAb) epitopes, the effects of nanoparticle display are generally modest for Env trimers. Here, we generate two-component self-assembling protein nanoparticles presenting twenty SOSIP trimers of the clade C Tier-2 genotype 16055. We show in a rabbit immunization study that these nanoparticles induce 60-fold higher autologous Tier-2 NAb titers than the corresponding SOSIP trimers. Epitope mapping studies reveal that the presentation of 16055 SOSIP trimers on these nanoparticle focuses antibody responses to an immunodominant apical epitope. Thus, these nanoparticles are a promising platform to improve the immunogenicity of Env trimers with apex-proximate NAb epitopes.
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Affiliation(s)
- Philip J M Brouwer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marlon de Gast
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Tom P L Bijl
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | | | - Rajesh P Ringe
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
- Institute of Microbial Technology, Chandigarh, India
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.
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45
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Martin JT, Cottrell CA, Antanasijevic A, Carnathan DG, Cossette BJ, Enemuo CA, Gebru EH, Choe Y, Viviano F, Fischinger S, Tokatlian T, Cirelli KM, Ueda G, Copps J, Schiffner T, Menis S, Alter G, Schief WR, Crotty S, King NP, Baker D, Silvestri G, Ward AB, Irvine DJ. Targeting HIV Env immunogens to B cell follicles in nonhuman primates through immune complex or protein nanoparticle formulations. NPJ Vaccines 2020; 5:72. [PMID: 32802411 PMCID: PMC7406516 DOI: 10.1038/s41541-020-00223-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/11/2020] [Indexed: 01/26/2023] Open
Abstract
Following immunization, high-affinity antibody responses develop within germinal centers (GCs), specialized sites within follicles of the lymph node (LN) where B cells proliferate and undergo somatic hypermutation. Antigen availability within GCs is important, as B cells must acquire and present antigen to follicular helper T cells to drive this process. However, recombinant protein immunogens such as soluble human immunodeficiency virus (HIV) envelope (Env) trimers do not efficiently accumulate in follicles following traditional immunization. Here, we demonstrate two strategies to concentrate HIV Env immunogens in follicles, via the formation of immune complexes (ICs) or by employing self-assembling protein nanoparticles for multivalent display of Env antigens. Using rhesus macaques, we show that within a few days following immunization, free trimers were present in a diffuse pattern in draining LNs, while trimer ICs and Env nanoparticles accumulated in B cell follicles. Whole LN imaging strikingly revealed that ICs and trimer nanoparticles concentrated in as many as 500 follicles in a single LN within two days after immunization. Imaging of LNs collected seven days postimmunization showed that Env nanoparticles persisted on follicular dendritic cells in the light zone of nascent GCs. These findings suggest that the form of antigen administered in vaccination can dramatically impact localization in lymphoid tissues and provides a new rationale for the enhanced immune responses observed following immunization with ICs or nanoparticles.
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Affiliation(s)
- Jacob T. Martin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Christopher A. Cottrell
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Aleksandar Antanasijevic
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Diane G. Carnathan
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322 USA
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Benjamin J. Cossette
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Chiamaka A. Enemuo
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322 USA
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Etse H. Gebru
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322 USA
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Yury Choe
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322 USA
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Federico Viviano
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322 USA
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Stephanie Fischinger
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139 USA
- University of Duisburg-Essen, 47057 Essen, Germany
| | - Talar Tokatlian
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Kimberly M. Cirelli
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037 USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195 USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Torben Schiffner
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Sergey Menis
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139 USA
| | - William R. Schief
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139 USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Shane Crotty
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037 USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037 USA
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195 USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195 USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195 USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815 USA
| | - Guido Silvestri
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322 USA
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Andrew B. Ward
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Darrell J. Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139 USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815 USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
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