1
|
Listov D, Goverde CA, Correia BE, Fleishman SJ. Opportunities and challenges in design and optimization of protein function. Nat Rev Mol Cell Biol 2024; 25:639-653. [PMID: 38565617 PMCID: PMC7616297 DOI: 10.1038/s41580-024-00718-y] [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] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calculations, as well as machine learning tools, have dramatically improved protein engineering and design. In this Review, we discuss how these methods have enabled the design of increasingly complex structures and therapeutically relevant activities. Additionally, protein optimization methods have improved the stability and activity of complex eukaryotic proteins. Thanks to their increased reliability, computational design methods have been applied to improve therapeutics and enzymes for green chemistry and have generated vaccine antigens, antivirals and drug-delivery nano-vehicles. Moreover, the high success of design methods reflects an increased understanding of basic rules that govern the relationships among protein sequence, structure and function. However, de novo design is still limited mostly to α-helix bundles, restricting its potential to generate sophisticated enzymes and diverse protein and small-molecule binders. Designing complex protein structures is a challenging but necessary next step if we are to realize our objective of generating new-to-nature activities.
Collapse
Affiliation(s)
- Dina Listov
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Casper A Goverde
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Sarel Jacob Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
2
|
Patel DR, Minns AM, Sim DG, Field CJ, Kerr AE, Heinly TA, Luley EH, Rossi RM, Bator CM, Moustafa IM, Norton EB, Hafenstein SL, Lindner SE, Sutton TC. Intranasal SARS-CoV-2 RBD decorated nanoparticle vaccine enhances viral clearance in the Syrian hamster model. Microbiol Spectr 2024; 12:e0499822. [PMID: 38334387 PMCID: PMC10923206 DOI: 10.1128/spectrum.04998-22] [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: 12/05/2022] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
Multiple vaccines have been developed and licensed for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). While these vaccines reduce disease severity, they do not prevent infection. To prevent infection and limit transmission, vaccines must be developed that induce immunity in the respiratory tract. Therefore, we performed proof-of-principle studies with an intranasal nanoparticle vaccine against SARS-CoV-2. The vaccine candidate consisted of the self-assembling 60-subunit I3-01 protein scaffold covalently decorated with the SARS-CoV-2 receptor-binding domain (RBD) using the SpyCatcher-SpyTag system. We verified the intended antigen display features by reconstructing the I3-01 scaffold to 3.4 A using cryogenicelectron microscopy. Using this RBD-grafted SpyCage scaffold (RBD + SpyCage), we performed two intranasal vaccination studies in the "gold-standard" pre-clinical Syrian hamster model. The initial study focused on assessing the immunogenicity of RBD + SpyCage combined with the LTA1 intranasal adjuvant. These studies showed RBD + SpyCage vaccination induced an antibody response that promoted viral clearance but did not prevent infection. Inclusion of the LTA1 adjuvant enhanced the magnitude of the antibody response but did not enhance protection. Thus, in an expanded study, in the absence of an intranasal adjuvant, we evaluated if covalent bonding of RBD to the scaffold was required to induce an antibody response. Covalent grafting of RBD was required for the vaccine to be immunogenic, and animals vaccinated with RBD + SpyCage more rapidly cleared SARS-CoV-2 from both the upper and lower respiratory tract. These findings demonstrate the intranasal SpyCage vaccine platform can induce protection against SARS-CoV-2 and, with additional modifications to improve immunogenicity, is a versatile platform for the development of intranasal vaccines targeting respiratory pathogens.IMPORTANCEDespite the availability of efficacious COVID vaccines that reduce disease severity, SARS-CoV-2 continues to spread. To limit SARS-CoV-2 transmission, the next generation of vaccines must induce immunity in the mucosa of the upper respiratory tract. Therefore, we performed proof-of-principle, intranasal vaccination studies with a recombinant protein nanoparticle scaffold, SpyCage, decorated with the RBD of the S protein (SpyCage + RBD). We show that SpyCage + RBD was immunogenic and enhanced SARS-CoV-2 clearance from the nose and lungs of Syrian hamsters. Moreover, covalent grafting of the RBD to the scaffold was required to induce an immune response when given via the intranasal route. These proof-of-concept findings indicate that with further enhancements to immunogenicity (e.g., adjuvant incorporation and antigen optimization), the SpyCage scaffold has potential as a versatile, intranasal vaccine platform for respiratory pathogens.
Collapse
Affiliation(s)
- Devanshi R. Patel
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Allen M. Minns
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Center for Malaria Research, University Park, Pennsylvania, USA
| | - Derek G. Sim
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Cassandra J. Field
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Abigail E. Kerr
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Talia A. Heinly
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Erin H. Luley
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Randall M. Rossi
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Carol M. Bator
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ibrahim M. Moustafa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Elizabeth B. Norton
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, USA
| | - Susan L. Hafenstein
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Medicine, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Scott E. Lindner
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Center for Malaria Research, University Park, Pennsylvania, USA
| | - Troy C. Sutton
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| |
Collapse
|
3
|
Hsieh CL, Leist SR, Miller EH, Zhou L, Powers JM, Tse AL, Wang A, West A, Zweigart MR, Schisler JC, Jangra RK, Chandran K, Baric RS, McLellan JS. Prefusion-stabilized SARS-CoV-2 S2-only antigen provides protection against SARS-CoV-2 challenge. Nat Commun 2024; 15:1553. [PMID: 38378768 PMCID: PMC10879192 DOI: 10.1038/s41467-024-45404-x] [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: 08/25/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Ever-evolving SARS-CoV-2 variants of concern (VOCs) have diminished the effectiveness of therapeutic antibodies and vaccines. Developing a coronavirus vaccine that offers a greater breadth of protection against current and future VOCs would eliminate the need to reformulate COVID-19 vaccines. Here, we rationally engineer the sequence-conserved S2 subunit of the SARS-CoV-2 spike protein and characterize the resulting S2-only antigens. Structural studies demonstrate that the introduction of interprotomer disulfide bonds can lock S2 in prefusion trimers, although the apex samples a continuum of conformations between open and closed states. Immunization with prefusion-stabilized S2 constructs elicits broadly neutralizing responses against several sarbecoviruses and protects female BALB/c mice from mouse-adapted SARS-CoV-2 lethal challenge and partially protects female BALB/c mice from mouse-adapted SARS-CoV lethal challenge. These engineering and immunogenicity results should inform the development of next-generation pan-coronavirus therapeutics and vaccines.
Collapse
Affiliation(s)
- Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Emily Happy Miller
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Medicine-Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - John M Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexandra L Tse
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Albert Wang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Mark R Zweigart
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jonathan C Schisler
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rohit K Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, 71103, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
4
|
Muñoz-Alía MÁ, Nace RA, Balakrishnan B, Zhang L, Packiriswamy N, Singh G, Warang P, Mena I, Narjari R, Vandergaast R, Peng KW, García-Sastre A, Schotsaert M, Russell SJ. Surface-modified measles vaccines encoding oligomeric, prefusion-stabilized SARS-CoV-2 spike glycoproteins boost neutralizing antibody responses to Omicron and historical variants, independent of measles seropositivity. mBio 2024; 15:e0292823. [PMID: 38193729 PMCID: PMC10865805 DOI: 10.1128/mbio.02928-23] [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: 11/02/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024] Open
Abstract
Serum titers of SARS-CoV-2-neutralizing antibodies (nAbs) correlate well with protection from symptomatic COVID-19 but decay rapidly in the months following vaccination or infection. In contrast, measles-protective nAb titers are lifelong after measles vaccination, possibly due to persistence of the live-attenuated virus in lymphoid tissues. We, therefore, sought to generate a live recombinant measles vaccine capable of driving high SARS-CoV-2 nAb responses. Since previous clinical testing of a live measles vaccine encoding a SARS-CoV-2 spike glycoprotein resulted in suboptimal anti-spike antibody titers, our new vectors were designed to encode prefusion-stabilized SARS-CoV-2 spike glycoproteins, trimerized via an inserted peptide domain, and displayed on a dodecahedral miniferritin scaffold. Additionally, to circumvent the blunting of vaccine efficacy by preformed anti-measles antibodies, we extensively modified the measles surface glycoproteins. Comprehensive in vivo mouse testing demonstrated the potent induction of high titer nAbs in measles-immune mice and confirmed the significant contributions to overall potency afforded by prefusion stabilization, trimerization, and miniferritin display of the SARS-CoV-2 spike glycoprotein. In animals primed and boosted with a measles virus (MeV) vaccine encoding the ancestral SARS-CoV-2 spike, high-titer nAb responses against ancestral virus strains were only weakly cross-reactive with the Omicron variant. However, in primed animals that were boosted with a MeV vaccine encoding the Omicron BA.1 spike, antibody titers to both ancestral and Omicron strains were robustly elevated, and the passive transfer of serum from these animals protected K18-ACE2 mice from infection and morbidity after exposure to BA.1 and WA1/2020 strains. Our results demonstrate that by engineering the antigen, we can develop potent measles-based vaccine candidates against SARS-CoV-2.IMPORTANCEAlthough the live-attenuated measles virus (MeV) is one of the safest and most efficacious human vaccines, a measles-vectored COVID-19 vaccine candidate expressing the SARS-CoV-2 spike failed to elicit neutralizing antibody (nAb) responses in a phase-1 clinical trial, especially in measles-immune individuals. Here, we constructed a comprehensive panel of MeV-based COVID-19 vaccine candidates using a MeV with extensive modifications on the envelope glycoproteins (MeV-MR). We show that artificial trimerization of the spike is critical for the induction of nAbs and that their magnitude can be significantly augmented when the spike protein is synchronously fused to a dodecahedral scaffold. Furthermore, preexisting measles immunity did not abolish heterologous immunity elicited by our vector. Our results highlight the importance of antigen optimization in the development of spike-based COVID-19 vaccines and therapies.
Collapse
Affiliation(s)
- Miguel Á. Muñoz-Alía
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Vyriad Inc, Rochester, Minnesota, USA
| | - Rebecca A. Nace
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Lianwen Zhang
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Prajakta Warang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | - Kah-Whye Peng
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Vyriad Inc, Rochester, Minnesota, USA
- Imanis Life Sciences, Rochester, Minnesota, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen J. Russell
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Vyriad Inc, Rochester, Minnesota, USA
- Imanis Life Sciences, Rochester, Minnesota, USA
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
5
|
Nagar N, Naidu G, Mishra A, Poluri KM. Protein-Based Nanocarriers and Nanotherapeutics for Infection and Inflammation. J Pharmacol Exp Ther 2024; 388:91-109. [PMID: 37699711 DOI: 10.1124/jpet.123.001673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/04/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
Infectious and inflammatory diseases are one of the leading causes of death globally. The status quo has become more prominent with the onset of the coronavirus disease 2019 (COVID-19) pandemic. To combat these potential crises, proteins have been proven as highly efficacious drugs, drug targets, and biomarkers. On the other hand, advancements in nanotechnology have aided efficient and sustained drug delivery due to their nano-dimension-acquired advantages. Combining both strategies together, the protein nanoplatforms are equipped with the advantageous intrinsic properties of proteins as well as nanoformulations, eloquently changing the field of nanomedicine. Proteins can act as carriers, therapeutics, diagnostics, and theranostics in their nanoform as fusion proteins or as composites with other organic/inorganic materials. Protein-based nanoplatforms have been extensively explored to target the major infectious and inflammatory diseases of clinical concern. The current review comprehensively deliberated proteins as nanocarriers for drugs and nanotherapeutics for inflammatory and infectious agents, with special emphasis on cancer and viral diseases. A plethora of proteins from diverse organisms have aided in the synthesis of protein-based nanoformulations. The current study specifically presented the proteins of human and pathogenic origin to dwell upon the field of protein nanotechnology, emphasizing their pharmacological advantages. Further, the successful clinical translation and current bottlenecks of the protein-based nanoformulations associated with the infection-inflammation paradigm have also been discussed comprehensively. SIGNIFICANCE STATEMENT: This review discusses the plethora of promising protein-based nanocarriers and nanotherapeutics explored for infectious and inflammatory ailments, with particular emphasis on protein nanoparticles of human and pathogenic origin with reference to the advantages, ADME (absorption, distribution, metabolism, and excretion parameters), and current bottlenecks in development of protein-based nanotherapeutic interventions.
Collapse
Affiliation(s)
- Nupur Nagar
- Department of Biosciences and Bioengineering (N.N., G.N., K.M.P.) and Centre for Nanotechnology (K.M.P.), Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; and Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India (A.M.)
| | - Goutami Naidu
- Department of Biosciences and Bioengineering (N.N., G.N., K.M.P.) and Centre for Nanotechnology (K.M.P.), Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; and Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India (A.M.)
| | - Amit Mishra
- Department of Biosciences and Bioengineering (N.N., G.N., K.M.P.) and Centre for Nanotechnology (K.M.P.), Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; and Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India (A.M.)
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering (N.N., G.N., K.M.P.) and Centre for Nanotechnology (K.M.P.), Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; and Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India (A.M.)
| |
Collapse
|
6
|
Guarra F, Colombo G. Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens. J Chem Theory Comput 2023; 19:5315-5333. [PMID: 37527403 PMCID: PMC10448727 DOI: 10.1021/acs.jctc.3c00513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Indexed: 08/03/2023]
Abstract
The design of new biomolecules able to harness immune mechanisms for the treatment of diseases is a prime challenge for computational and simulative approaches. For instance, in recent years, antibodies have emerged as an important class of therapeutics against a spectrum of pathologies. In cancer, immune-inspired approaches are witnessing a surge thanks to a better understanding of tumor-associated antigens and the mechanisms of their engagement or evasion from the human immune system. Here, we provide a summary of the main state-of-the-art computational approaches that are used to design antibodies and antigens, and in parallel, we review key methodologies for epitope identification for both B- and T-cell mediated responses. A special focus is devoted to the description of structure- and physics-based models, privileged over purely sequence-based approaches. We discuss the implications of novel methods in engineering biomolecules with tailored immunological properties for possible therapeutic uses. Finally, we highlight the extraordinary challenges and opportunities presented by the possible integration of structure- and physics-based methods with emerging Artificial Intelligence technologies for the prediction and design of novel antigens, epitopes, and antibodies.
Collapse
Affiliation(s)
- Federica Guarra
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| |
Collapse
|
7
|
Ptak CP, Hsieh CL, Garnett JA, Rappuoli R, Lin YP. Editorial: Intersection of biophysical and structural approaches in vaccine design. Front Mol Biosci 2023; 10:1142656. [PMID: 36865381 PMCID: PMC9972083 DOI: 10.3389/fmolb.2023.1142656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 02/16/2023] Open
Affiliation(s)
- Christopher P. Ptak
- NMR Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, United States,*Correspondence: Christopher P. Ptak,
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States,Sanofi S.A., Cambridge, MA, United States
| | - James A. Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
| | - Rino Rappuoli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy,Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy,GSK, Siena, Italy
| | - Yi-Pin Lin
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, United States,Department of Biomedical Sciences, SUNY Albany, Albany, NY, United States
| |
Collapse
|
8
|
Muñoz-Alía MÁ, Nace RA, Balakrishnan B, Zhang L, Packiriswamy N, Singh G, Warang P, Mena I, Narjari R, Vandergaast R, García-Sastre A, Schotsaert M, Russell SJ. Surface-modified measles vaccines encoding oligomeric, fusion-stabilized SARS-CoV-2 spike glycoproteins bypass measles seropositivity, boosting neutralizing antibody responses to omicron and historical variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.16.520799. [PMID: 36561187 PMCID: PMC9774211 DOI: 10.1101/2022.12.16.520799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Serum titers of SARS-CoV-2 neutralizing antibodies (nAb) correlate well with protection from symptomatic COVID-19, but decay rapidly in the months following vaccination or infection. In contrast, measles-protective nAb titers are life-long after measles vaccination, possibly due to persistence of the live-attenuated virus in lymphoid tissues. We therefore sought to generate a live recombinant measles vaccine capable of driving high SARS-CoV-2 nAb responses. Since previous clinical testing of a live measles vaccine encoding a SARS-CoV-2 spike glycoprotein resulted in suboptimal anti-spike antibody titers, our new vectors were designed to encode prefusion-stabilized SARS-CoV-2 spike glycoproteins, trimerized via an inserted peptide domain and displayed on a dodecahedral miniferritin scaffold. Additionally, to circumvent the blunting of vaccine efficacy by preformed anti-measles antibodies, we extensively modified the measles surface glycoproteins. Comprehensive in vivo mouse testing demonstrated potent induction of high titer nAb in measles-immune mice and confirmed the significant incremental contributions to overall potency afforded by prefusion stabilization, trimerization, and miniferritin-display of the SARS-CoV-2 spike glycoprotein, and vaccine resurfacing. In animals primed and boosted with a MeV vaccine encoding the ancestral SARS-CoV-2 spike, high titer nAb responses against ancestral virus strains were only weakly cross-reactive with the omicron variant. However, in primed animals that were boosted with a MeV vaccine encoding the omicron BA.1 spike, antibody titers to both ancestral and omicron strains were robustly elevated and the passive transfer of serum from these animals protected K18-ACE2 mice from infection and morbidity after exposure to BA.1 and WA1/2020 strains. Our results demonstrate that antigen engineering can enable the development of potent measles-based SARS-CoV-2 vaccine candidates.
Collapse
Affiliation(s)
- Miguel Á. Muñoz-Alía
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
- Vyriad Inc, Rochester, MN, USA
| | - Rebecca A. Nace
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Lianwen Zhang
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Prajakta Warang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen J. Russell
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
- Vyriad Inc, Rochester, MN, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Imanis Life Sciences, Rochester, MN, USA
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
9
|
Patel DR, Minns AM, Sim DG, Field CJ, Kerr AE, Heinly T, Luley EH, Rossi RM, Bator C, Moustafa IM, Hafenstein SL, Lindner SE, Sutton TC. Intranasal SARS-CoV-2 RBD decorated nanoparticle vaccine enhances viral clearance in the Syrian hamster model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.27.514054. [PMID: 36324809 PMCID: PMC9628200 DOI: 10.1101/2022.10.27.514054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Multiple vaccines have been developed and licensed for SARS-CoV-2. While these vaccines reduce disease severity, they do not prevent infection, and SARS-CoV-2 continues to spread and evolve. To prevent infection and limit transmission, vaccines must be developed that induce immunity in the respiratory tract. Therefore, we performed proof-of-principle vaccination studies with an intranasal nanoparticle vaccine against SARS-CoV-2. The vaccine candidate consisted of the self-assembling 60-subunit I3-01 protein scaffold covalently decorated with the SARS-CoV-2 receptor binding domain (RBD) using the SpyCatcher-SpyTag system. We verified the intended antigen display features by reconstructing the I3-01 scaffold to 3.4A using cryo-EM, and then demonstrated that the scaffold was highly saturated when grafted with RBD. Using this RBD-grafted SpyCage scaffold (RBD+SpyCage), we performed two unadjuvanted intranasal vaccination studies in the "gold-standard" preclinical Syrian hamster model. Hamsters received two vaccinations 28 days apart, and were then challenged 28 days post-boost with SARS-CoV-2. The initial study focused on assessing the immunogenicity of RBD+SpyCage, which indicated that vaccination of hamsters induced a non-neutralizing antibody response that enhanced viral clearance but did not prevent infection. In an expanded study, we demonstrated that covalent bonding of RBD to the scaffold was required to induce an antibody response. Consistent with the initial study, animals vaccinated with RBD+SpyCage more rapidly cleared SARS-CoV-2 from both the upper and lower respiratory tract. These findings demonstrate the intranasal SpyCage vaccine platform can induce protection against SARS-CoV-2 and, with additional modifications to improve immunogenicity, is a versatile platform for the development of intranasal vaccines targeting respiratory pathogens.
Collapse
Affiliation(s)
- D R Patel
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University
- The Huck Institutes of Life Sciences, Pennsylvania State University
| | - A M Minns
- Department of Biochemistry and Molecular Biology, Pennsylvania State University
- The Huck Institutes of Life Sciences, Pennsylvania State University
- The Huck Center for Malaria Research
| | - D G Sim
- Department of Biology, Pennsylvania State University
- The Huck Institutes of Life Sciences, Pennsylvania State University
| | - C J Field
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University
- Department of Biochemistry and Molecular Biology, Pennsylvania State University
| | - A E Kerr
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University
- The Huck Institutes of Life Sciences, Pennsylvania State University
| | - T Heinly
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University
- The Huck Institutes of Life Sciences, Pennsylvania State University
| | - E H Luley
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University
- Animal Diagnostic Laboratory, Pennsylvania State University
| | - R M Rossi
- The Huck Institutes of Life Sciences, Pennsylvania State University
| | - C Bator
- The Huck Institutes of Life Sciences, Pennsylvania State University
| | - I M Moustafa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University
| | - S L Hafenstein
- Department of Biochemistry and Molecular Biology, Pennsylvania State University
- The Huck Institutes of Life Sciences, Pennsylvania State University
- Department of Medicine, Pennsylvania State University
| | - S E Lindner
- Department of Biochemistry and Molecular Biology, Pennsylvania State University
- The Huck Institutes of Life Sciences, Pennsylvania State University
- The Huck Center for Malaria Research
| | - T C Sutton
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University
- The Huck Institutes of Life Sciences, Pennsylvania State University
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|