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Felbinger N, Ribeiro-Filho H, Pierce B. Proscan: a structure-based proline design web server. Nucleic Acids Res 2024; 52:W280-W286. [PMID: 38769060 PMCID: PMC11223860 DOI: 10.1093/nar/gkae408] [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: 03/13/2024] [Revised: 04/16/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
The ability to control protein conformations and dynamics through structure-based design has been useful in various scenarios, including engineering of viral antigens for vaccines. One effective design strategy is the substitution of residues to proline amino acids, which due to its unique cyclic side chain can favor and rigidify key backbone conformations. To provide the community with a means to readily identify and explore proline designs for target proteins of interest, we developed the Proscan web server. Proscan provides assessment of backbone angles, energetic and deep learning-based favorability scores, and other parameters for proline substitutions at each position of an input structure, along with interactive visualization of backbone angles and candidate substitution sites on structures. It identifies known favorable proline substitutions for viral antigens, and was benchmarked against datasets of proline substitution stability effects from deep mutational scanning and thermodynamic measurements. This tool can enable researchers to identify and prioritize designs for prospective vaccine antigen targets, or other designs to favor stability of key protein conformations. Proscan is available at: https://proscan.ibbr.umd.edu.
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Affiliation(s)
- Nathaniel Felbinger
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Helder V Ribeiro-Filho
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas 13083-100, Brazil
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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2
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Mpingabo PI, Ylade M, Aogo RA, Crisostomo MV, Thiono DJ, Daag JV, Agrupis KA, Escoto AC, Raimundi-Rodriguez GL, Odio CD, Fernandez MA, White L, de Silva AM, Deen J, Katzelnick LC. Envelope-dimer epitope-like broadly protective antibodies against dengue in children following natural infection and vaccination. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.30.24306574. [PMID: 38746253 PMCID: PMC11092691 DOI: 10.1101/2024.04.30.24306574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Cross-reactive antibodies (Abs) to epitopes that span envelope proteins on the virion surface are hypothesized to protect against dengue. Here, we measured Abs targeting the quaternary envelope dimer epitope (EDE) as well as neutralizing and binding Abs and evaluate their association with dengue virus (DENV) infection, vaccine response, and disease outcome in dengue vaccinated and unvaccinated children (n=252) within a longitudinal cohort in Cebu, Philippines (n=2,996). Abs targeting EDE were prevalent and strongly associated with broad neutralization of DENV1-4 in those with baseline multitypic immunity. Subsequent natural infection and vaccination boosted EDE-like, neutralizing, and binding Abs. EDE-like Abs were associated with reduced dengue risk and mediated the protective effect of binding and neutralizing Abs on symptomatic and severe dengue. Thus, Abs targeting quaternary epitopes help explain broad cross protection in those with multiple prior DENV exposures, making them useful for evaluation and development of future vaccines and therapeutics.
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3
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Hung TI, Hsieh YJ, Lu WL, Wu KP, Chang CEA. What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks. J Mol Biol 2023; 435:168337. [PMID: 37918563 DOI: 10.1016/j.jmb.2023.168337] [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: 09/05/2023] [Revised: 10/13/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023]
Abstract
Identifying residues critical to protein-protein binding and efficient design of stable and specific protein binders are challenging tasks. Extending beyond the direct contacts in a protein-protein binding interface, our study employs computational modeling to reveal the essential network of residue interactions and dihedral angle correlations critical in protein-protein recognition. We hypothesized that mutating residues exhibiting highly correlated dynamic motion within the interaction network could efficiently optimize protein-protein interactions to create tight and selective protein binders. We tested this hypothesis using the ubiquitin (Ub) and MERS coronaviral papain-like protease (PLpro) complex, since Ub is a central player in multiple cellular functions and PLpro is an antiviral drug target. Our designed ubiquitin variant (UbV) hosting three mutated residues displayed a ∼3,500-fold increase in functional inhibition relative to wild-type Ub. Further optimization of two C-terminal residues within the Ub network resulted in a KD of 1.5 nM and IC50 of 9.7 nM for the five-point Ub mutant, eliciting 27,500-fold and 5,500-fold enhancements in affinity and potency, respectively, as well as improved selectivity, without destabilizing the UbV structure. Our study highlights residue correlation and interaction networks in protein-protein interactions, and introduces an effective approach to design high-affinity protein binders for cell biology research and future therapeutics.
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Affiliation(s)
- Ta I Hung
- Department of Chemistry, University of California, Riverside, United States; Department of Bioengineering, University of California, Riverside, United States
| | - Yun-Jung Hsieh
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Wei-Lin Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, United States.
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4
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Goudy OJ, Nallathambi A, Kinjo T, Randolph NZ, Kuhlman B. In silico evolution of autoinhibitory domains for a PD-L1 antagonist using deep learning models. Proc Natl Acad Sci U S A 2023; 120:e2307371120. [PMID: 38032933 PMCID: PMC10710080 DOI: 10.1073/pnas.2307371120] [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: 05/04/2023] [Accepted: 09/24/2023] [Indexed: 12/02/2023] Open
Abstract
There has been considerable progress in the development of computational methods for designing protein-protein interactions, but engineering high-affinity binders without extensive screening and maturation remains challenging. Here, we test a protein design pipeline that uses iterative rounds of deep learning (DL)-based structure prediction (AlphaFold2) and sequence optimization (ProteinMPNN) to design autoinhibitory domains (AiDs) for a PD-L1 antagonist. With the goal of creating an anticancer agent that is inactive until reaching the tumor environment, we sought to create autoinhibited (or masked) forms of the PD-L1 antagonist that can be unmasked by tumor-enriched proteases. Twenty-three de novo designed AiDs, varying in length and topology, were fused to the antagonist with a protease-sensitive linker, and binding to PD-L1 was measured with and without protease treatment. Nine of the fusion proteins demonstrated conditional binding to PD-L1, and the top-performing AiDs were selected for further characterization as single-domain proteins. Without any experimental affinity maturation, four of the AiDs bind to the PD-L1 antagonist with equilibrium dissociation constants (KDs) below 150 nM, with the lowest KD equal to 0.9 nM. Our study demonstrates that DL-based protein modeling can be used to rapidly generate high-affinity protein binders.
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Affiliation(s)
- Odessa J. Goudy
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC27599
| | - Amrita Nallathambi
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC27599
| | - Tomoaki Kinjo
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC27599
| | - Nicholas Z. Randolph
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC27599
- Department of Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, NC27599
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC27599
- Department of Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, NC27599
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC27599
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5
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Ko HL, Lee DK, Kim Y, Jang HJ, Lee YW, Lee HY, Seok SH, Park JW, Limb JK, On DI, Yun JW, Lyoo KS, Song D, Yeom M, Lee H, Seong JK, Lee S. Development of a neutralization monoclonal antibody with a broad neutralizing effect against SARS-CoV-2 variants. Virol J 2023; 20:285. [PMID: 38041113 PMCID: PMC10693169 DOI: 10.1186/s12985-023-02230-9] [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: 08/14/2023] [Accepted: 11/06/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has challenged the effectiveness of current therapeutic regimens. Here, we aimed to develop a potent SARS-CoV-2 antibody with broad neutralizing effect by screening a scFv library with the spike protein receptor-binding domain (RBD) via phage display. METHODS SKAI-DS84 was identified through phage display, and we performed pseudovirus neutralization assays, authentic virus neutralization assays, and in vivo neutralization efficacy evaluations. Furthermore, surface plasmon resonance (SPR) analysis was conducted to assess the physical characteristics of the antibody, including binding kinetics and measure its affinity for variant RBDs. RESULTS The selected clones were converted to human IgG, and among them, SKAI-DS84 was selected for further analyses based on its binding affinity with the variant RBDs. Using pseudoviruses, we confirmed that SKAI-DS84 was strongly neutralizing against wild-type, B.1.617.2, B.1.1.529, and subvariants of SARS-CoV-2. We also tested the neutralizing effect of SKAI-DS84 on authentic viruses, in vivo and observed a reduction in viral replication and improved lung pathology. We performed binding and epitope mapping experiments to understand the mechanisms underlying neutralization and identified quaternary epitopes formed by the interaction between RBDs as the target of SKAI-DS84. CONCLUSIONS We identified, produced, and tested the neutralizing effect of SKAI-DS84 antibody. Our results highlight that SKAI-DS84 could be a potential neutralizing antibody against SARS-CoV-2 and its variants.
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Affiliation(s)
- Hae Li Ko
- Division of Research Program, Scripps Korea Antibody Institute, Chuncheon, 24341, Republic of Korea
- Department of Microbiology, College of Medical Science, Kangwon National University, Chuncheon-si, Gangwon-do, 24341, South Korea
| | - Deuk-Ki Lee
- Division of Research Program, Scripps Korea Antibody Institute, Chuncheon, 24341, Republic of Korea
- Department of Microbiology, College of Medical Science, Kangwon National University, Chuncheon-si, Gangwon-do, 24341, South Korea
| | - Younghyeon Kim
- Division of Research Program, Scripps Korea Antibody Institute, Chuncheon, 24341, Republic of Korea
- Department of Microbiology, College of Medical Science, Kangwon National University, Chuncheon-si, Gangwon-do, 24341, South Korea
| | - Hui Jeong Jang
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, 13620, South Korea
| | - Youn Woo Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, 13620, South Korea
| | - Ho-Young Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, 13620, South Korea
| | - Sang-Hyuk Seok
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon-si, Gangwon-do, 24341, South Korea
| | - Jun Won Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon-si, Gangwon-do, 24341, South Korea
| | - Jin-Kyung Limb
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, 08826, South Korea
| | - Da In On
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, 08826, South Korea
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Program for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea
| | - Jun-Won Yun
- Laboratory of Veterinary Toxicology, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea
| | - Kwang-Soo Lyoo
- College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Daesub Song
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Minjoo Yeom
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hanbyeul Lee
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, 08826, South Korea.
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Program for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea.
- Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX/N-Bio Institute, Seoul National University, Seoul, 08826, South Korea.
| | - Sungjin Lee
- Division of Research Program, Scripps Korea Antibody Institute, Chuncheon, 24341, Republic of Korea.
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6
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Maloney BE, Carpio KL, Bilyeu AN, Saunders DRD, Park SL, Pohl AE, Ball NC, Raetz JL, Huang CY, Higgs S, Barrett ADT, Roman-Sosa G, Kenney JL, Vanlandingham DL, Huang YJS. Identification of the flavivirus conserved residues in the envelope protein hinge region for the rational design of a candidate West Nile live-attenuated vaccine. NPJ Vaccines 2023; 8:172. [PMID: 37932282 PMCID: PMC10628263 DOI: 10.1038/s41541-023-00765-0] [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: 01/30/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023] Open
Abstract
The flavivirus envelope protein is a class II fusion protein that drives flavivirus-cell membrane fusion. The membrane fusion process is triggered by the conformational change of the E protein from dimer in the virion to trimer, which involves the rearrangement of three domains, EDI, EDII, and EDIII. The movement between EDI and EDII initiates the formation of the E protein trimer. The EDI-EDII hinge region utilizes four motifs to exert the hinge effect at the interdomain region and is crucial for the membrane fusion activity of the E protein. Using West Nile virus (WNV) NY99 strain derived from an infectious clone, we investigated the role of eight flavivirus-conserved hydrophobic residues in the EDI-EDII hinge region in the conformational change of E protein from dimer to trimer and viral entry. Single mutations of the E-A54, E-I130, E-I135, E-I196, and E-Y201 residues affected infectivity. Importantly, the E-A54I and E-Y201P mutations fully attenuated the mouse neuroinvasive phenotype of WNV. The results suggest that multiple flavivirus-conserved hydrophobic residues in the EDI-EDII hinge region play a critical role in the structure-function of the E protein and some contribute to the virulence phenotype of flaviviruses as demonstrated by the attenuation of the mouse neuroinvasive phenotype of WNV. Thus, as a proof of concept, residues in the EDI-EDII hinge region are proposed targets to engineer attenuating mutations for inclusion in the rational design of candidate live-attenuated flavivirus vaccines.
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Affiliation(s)
- Bailey E Maloney
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Kassandra L Carpio
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Ashley N Bilyeu
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Danielle R D Saunders
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
- Department of Biology, Dean of Faculty, United States Air Force Academy, Colorado Springs, CO, 80840, USA
| | - So Lee Park
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Adrienne E Pohl
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Natalia Costa Ball
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Janae L Raetz
- Division of Vector-borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Claire Y Huang
- Division of Vector-borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Stephen Higgs
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Alan D T Barrett
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Gleyder Roman-Sosa
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Institute of Virology, University of Veterinary Medicine Hanover, Foundation, Buentewg 17, 30559, Hanover, Germany
| | - Joanie L Kenney
- Division of Vector-borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Dana L Vanlandingham
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA
| | - Yan-Jang S Huang
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.
- Biosecurity Research Institute, Kansas State University, Manhattan, KS, 66506, USA.
- Department of Microbiology and Immunology and SUNY Center for Vector-Borne Diseases, Institute of Global Health and Translation Science, Upstate Medical University, Syracuse, NY, 13210, USA.
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7
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Kuhn RJ, Barrett ADT, Desilva AM, Harris E, Kramer LD, Montgomery RR, Pierson TC, Sette A, Diamond MS. A Prototype-Pathogen Approach for the Development of Flavivirus Countermeasures. J Infect Dis 2023; 228:S398-S413. [PMID: 37849402 PMCID: PMC10582523 DOI: 10.1093/infdis/jiad193] [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: 02/22/2023] [Accepted: 05/28/2023] [Indexed: 10/19/2023] Open
Abstract
Flaviviruses are a genus within the Flaviviridae family of positive-strand RNA viruses and are transmitted principally through mosquito and tick vectors. These viruses are responsible for hundreds of millions of human infections worldwide per year that result in a range of illnesses from self-limiting febrile syndromes to severe neurotropic and viscerotropic diseases and, in some cases, death. A vaccine against the prototype flavivirus, yellow fever virus, has been deployed for 85 years and is highly effective. While vaccines against some medically important flaviviruses are available, others have proven challenging to develop. The emergence and spread of flaviviruses, including dengue virus and Zika virus, demonstrate their pandemic potential. This review highlights the gaps in knowledge that need to be addressed to allow for the rapid development of vaccines against emerging flaviviruses in the future.
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Affiliation(s)
- Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana, USA
| | - Alan D T Barrett
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas, USA
| | - Aravinda M Desilva
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California, USA
| | - Laura D Kramer
- School of Public Health, State University of New York at Albany, Albany, New York, USA
| | - Ruth R Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Theodore C Pierson
- Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, University of California in San Diego, San Diego, California, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
- Department of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
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8
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Medina-Carrasco D, Pupo D, González-Lodeiro LG, García LE, Martin AM, Huerta V. Activity of domain III-specific antibodies in early convalescence: A case study. Virology 2023; 587:109883. [PMID: 37757730 DOI: 10.1016/j.virol.2023.109883] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/15/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
The Dengue virus complex (DENV), formed by four serotypes, constitutes the most important arbovirus affecting humans. The structural domain III of their envelope protein (DIII) elicits strongly neutralizing serotype-specific antibodies. Contrasting results have been obtained regarding their role in the serum neutralizing activity of infected patients. We used a DENV immune serum from a secondary infection to examine the impact of characterizing the anti-DIII antibody response after affinity purification with recombinant DIII proteins to eliminate potential interferences from the interactions with human plasma proteins and other anti-DENV antibodies. Total anti-DENV IgG repertoire and anti-DIIIE antibodies were compared in functionality. In early convalescence, reactivity of anti-DIII antibodies is serotype specific and exhibits the strongest reactivity with infecting serotypes. Purification of anti-DIII antibodies emphasizes the reactivity profile as compared to total IgG fraction and serum. Serotype-specificity of the virus neutralization activity correlated with the apparent kD of the binding to recombinant DIIIs.
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Affiliation(s)
- Danya Medina-Carrasco
- Department of Systems Biology, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
| | - Dianne Pupo
- Department of Systems Biology, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
| | - Luis G González-Lodeiro
- Department of Systems Biology, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
| | - Lisandra E García
- Department of Systems Biology, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
| | - Alejandro M Martin
- Department of Systems Biology, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba
| | - Vivian Huerta
- Department of Systems Biology, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba.
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9
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Meganck RM, Zhu D, Dong S, Snoderly-Foster LJ, Dalben YR, Thiono D, White LJ, DeSilva AM, Baric RS, Tse LV. Evolution of a functionally intact but antigenically distinct DENV fusion loop. eLife 2023; 12:RP87555. [PMID: 37725085 PMCID: PMC10508882 DOI: 10.7554/elife.87555] [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] [Indexed: 09/21/2023] Open
Abstract
A hallmark of dengue virus (DENV) pathogenesis is the potential for antibody-dependent enhancement, which is associated with deadly DENV secondary infection, complicates the identification of correlates of protection, and negatively impacts the safety and efficacy of DENV vaccines. Antibody-dependent enhancement is linked to antibodies targeting the fusion loop (FL) motif of the envelope protein, which is completely conserved in mosquito-borne flaviviruses and required for viral entry and fusion. In the current study, we utilized saturation mutagenesis and directed evolution to engineer a functional variant with a mutated FL (D2-FL), which is not neutralized by FL-targeting monoclonal antibodies. The FL mutations were combined with our previously evolved prM cleavage site to create a mature version of D2-FL (D2-FLM), which evades both prM- and FL-Abs but retains sensitivity to other type-specific and quaternary cross-reactive (CR) Abs. CR serum from heterotypic (DENV4)-infected non-human primates (NHP) showed lower neutralization titers against D2-FL and D2-FLM than isogenic wildtype DENV2 while similar neutralization titers were observed in serum from homotypic (DENV2)-infected NHP. We propose D2-FL and D2-FLM as valuable tools to delineate CR Ab subtypes in serum as well as an exciting platform for safer live-attenuated DENV vaccines suitable for naïve individuals and children.
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Affiliation(s)
- Rita M Meganck
- Department of Molecular Microbiology and Immunology, Saint Louis UniversitySaint LouisUnited States
| | - Deanna Zhu
- Department of Epidemiology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Stephanie Dong
- Department of Epidemiology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Lisa J Snoderly-Foster
- Department of Molecular Microbiology and Immunology, Saint Louis UniversitySaint LouisUnited States
| | - Yago R Dalben
- Department of Molecular Microbiology and Immunology, Saint Louis UniversitySaint LouisUnited States
| | - Devina Thiono
- Department of Microbiology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Laura J White
- Department of Microbiology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Arivianda M DeSilva
- Department of Microbiology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Longping V Tse
- Department of Molecular Microbiology and Immunology, Saint Louis UniversitySaint LouisUnited States
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10
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Praetorius F, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker D. Design of stimulus-responsive two-state hinge proteins. Science 2023; 381:754-760. [PMID: 37590357 PMCID: PMC10697137 DOI: 10.1126/science.adg7731] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/11/2023] [Indexed: 08/19/2023]
Abstract
In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here we describe the design of "hinge" proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled.
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Affiliation(s)
- Florian Praetorius
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Philip J. Y. Leung
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Maxx H. Tessmer
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Adam Broerman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Cullen Demakis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, Washington, USA
| | - Acacia F. Dishman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical Scientist Training Program, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Arvind Pillai
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Abbas Idris
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - David Juergens
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Paul M. Levine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ryanne K. Ballard
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Stacey R. Gerben
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Brian F. Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jeff Nivala
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA,USA
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11
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Meganck RM, Zhu D, Dong S, Snoderly-Foster LJ, Dalben YR, Thiono D, White LJ, DeSilva AM, Baric RS, Tse LV. Evolution of a Functionally Intact but Antigenically Distinct DENV Fusion Loop. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533803. [PMID: 37034784 PMCID: PMC10081285 DOI: 10.1101/2023.03.22.533803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A hallmark of Dengue virus (DENV) pathogenesis is the potential for antibody-dependent enhancement, which is associated with deadly DENV secondary infection, complicates the identification of correlates of protection, and negatively impacts the safety and efficacy of DENV vaccines. ADE is linked to antibodies targeting the fusion loop (FL) motif of the envelope protein, which is completely conserved in mosquito-borne flaviviruses and required for viral entry and fusion. In the current study, we utilized saturation mutagenesis and directed evolution to engineer a functional variant with a mutated FL (D2-FL) which is not neutralized by FL-targeting monoclonal antibodies. The FL mutations were combined with our previously evolved prM cleavage site to create a mature version of D2-FL (D2-FLM), which evades both prM- and FL-Abs but retains sensitivity to other type-specific and quaternary cross-reactive (CR) Abs. CR serum from heterotypic (DENV4) infected non-human primates (NHP) showed lower neutralization titers against D2-FL and D2-FLM than isogenic wildtype DENV2 while similar neutralization titers were observed in serum from homotypic (DENV2) infected NHP. We propose D2-FL and D2-FLM as valuable tools to delineate CR Ab subtypes in serum as well as an exciting platform for safer live attenuated DENV vaccines suitable for naïve individuals and children.
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Affiliation(s)
- Rita M. Meganck
- Department of Molecular Microbiology and Immunology, Saint Louis University
| | - Deanna Zhu
- Department of Epidemiology, University of North Carolina at Chapel Hill
| | - Stephanie Dong
- Department of Epidemiology, University of North Carolina at Chapel Hill
| | | | - Yago R. Dalben
- Department of Molecular Microbiology and Immunology, Saint Louis University
| | - Devina Thiono
- Department of Microbiology, University of North Carolina at Chapel Hill
| | - Laura J. White
- Department of Microbiology, University of North Carolina at Chapel Hill
| | | | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill
| | - Longping V. Tse
- Department of Molecular Microbiology and Immunology, Saint Louis University
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12
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Odio CD, Lowman KE, Law M, Aogo RA, Hunsberger S, Wood BJ, Kassin M, Levy E, Callier V, Firdous S, Hasund CM, Voirin C, Kattappuram R, Yek C, Manning J, Durbin A, Whitehead SS, Katzelnick LC. Phase 1 trial to model primary, secondary, and tertiary dengue using a monovalent vaccine. BMC Infect Dis 2023; 23:345. [PMID: 37221466 DOI: 10.1186/s12879-023-08299-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND The four co-circulating and immunologically interactive dengue virus serotypes (DENV1-4) pose a unique challenge to vaccine design because sub-protective immunity can increase the risk of severe dengue disease. Existing dengue vaccines have lower efficacy in DENV seronegative individuals but higher efficacy in DENV exposed individuals. There is an urgent need to identify immunological measures that are strongly associated with protection against viral replication and disease following sequential exposure to distinct serotypes. METHODS/DESIGN This is a phase 1 trial wherein healthy adults with neutralizing antibodies to zero (seronegative), one non-DENV3 (heterotypic), or more than one (polytypic) DENV serotype will be vaccinated with the live attenuated DENV3 monovalent vaccine rDEN3Δ30/31-7164. We will examine how pre-vaccine host immunity influences the safety and immunogenicity of DENV3 vaccination in a non-endemic population. We hypothesize that the vaccine will be safe and well tolerated, and all groups will have a significant increase in the DENV1-4 neutralizing antibody geometric mean titer between days 0 and 28. Compared to the seronegative group, the polytypic group will have lower mean peak vaccine viremia, due to protection conferred by prior DENV exposure, while the heterotypic group will have higher mean peak viremia, due to mild enhancement. Secondary and exploratory endpoints include characterizing serological, innate, and adaptive cell responses; evaluating proviral or antiviral contributions of DENV-infected cells; and immunologically profiling the transcriptome, surface proteins, and B and T cell receptor sequences and affinities of single cells in both peripheral blood and draining lymph nodes sampled via serial image-guided fine needle aspiration. DISCUSSION This trial will compare the immune responses after primary, secondary, and tertiary DENV exposure in naturally infected humans living in non-endemic areas. By evaluating dengue vaccines in a new population and modeling the induction of cross-serotypic immunity, this work may inform vaccine evaluation and broaden potential target populations. TRIAL REGISTRATION NCT05691530 registered on January 20, 2023.
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Affiliation(s)
- Camila D Odio
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Kelsey E Lowman
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Melissa Law
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rosemary A Aogo
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sally Hunsberger
- Division of Clinical Research, Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brad J Wood
- Interventional Radiology and Center for Interventional Oncology, NIH Clinical Center and National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Kassin
- Interventional Radiology and Center for Interventional Oncology, NIH Clinical Center and National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elliot Levy
- Interventional Radiology and Center for Interventional Oncology, NIH Clinical Center and National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Viviane Callier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Saba Firdous
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chloe M Hasund
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Charlie Voirin
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Robbie Kattappuram
- Department of Pharmacy, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Christina Yek
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Phnom Penh, Cambodia
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jessica Manning
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Phnom Penh, Cambodia
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anna Durbin
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Stephen S Whitehead
- Arbovirus Vaccine Research Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Leah C Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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13
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Goudy OJ, Nallathambi A, Kinjo T, Randolph N, Kuhlman B. In silico evolution of protein binders with deep learning models for structure prediction and sequence design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539278. [PMID: 37205527 PMCID: PMC10187191 DOI: 10.1101/2023.05.03.539278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
There has been considerable progress in the development of computational methods for designing protein-protein interactions, but engineering high-affinity binders without extensive screening and maturation remains challenging. Here, we test a protein design pipeline that uses iterative rounds of deep learning (DL)-based structure prediction (AlphaFold2) and sequence optimization (ProteinMPNN) to design autoinhibitory domains (AiDs) for a PD-L1 antagonist. Inspired by recent advances in therapeutic design, we sought to create autoinhibited (or masked) forms of the antagonist that can be conditionally activated by proteases. Twenty-three de novo designed AiDs, varying in length and topology, were fused to the antagonist with a protease sensitive linker, and binding to PD-L1 was tested with and without protease treatment. Nine of the fusion proteins demonstrated conditional binding to PD-L1 and the top performing AiDs were selected for further characterization as single domain proteins. Without any experimental affinity maturation, four of the AiDs bind to the PD-L1 antagonist with equilibrium dissociation constants (KDs) below 150 nM, with the lowest KD equal to 0.9 nM. Our study demonstrates that DL-based protein modeling can be used to rapidly generate high affinity protein binders.
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Affiliation(s)
- Odessa J Goudy
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Amrita Nallathambi
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Tomoaki Kinjo
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Nicholas Randolph
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
- Department of Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
- Department of Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
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14
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Zhang JA, Wang JJ, Zhang WT, Zhang L, Zheng BY, Liu GB, Liang J, Lu YB, Wu XJ, Yao SY, Chen GY, Xie YQ, Wu JY, Shi JH, Pi J, Li SP, Xu JF. Elevated Interleukin-37 Associated with Dengue Viral Load in Patients with Dengue Fever. Curr Microbiol 2023; 80:171. [PMID: 37024713 PMCID: PMC10079153 DOI: 10.1007/s00284-023-03239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/22/2023] [Indexed: 04/08/2023]
Abstract
Dengue remains a public health issue worldwide. Similar to chronic infectious diseases, stimulation of cytokine production is not enough to drive immune effector cells for effective virus clearance. One possible mechanism is the virus induces a large number of negative stimulatory cytokines inhibiting immune response. Interleukin 37 (IL-37) plays a crucial regulatory role in infection and immunity, inhibits innate and adaptive immunity as an anti-inflammatory cytokine by inhibiting proinflammatory mediators and pathways. To date, there are few studies reporting correlations between dengue fever (DF) and IL-37. In this study we found that the serum IL-37b and IL-37b-producing monocytes in patients were significantly increased in DF patients. A majority of the IL-37b produced by DF patients was produced by monocytes, not lymphocytes. Increased levels of IL-6, IL-10, and IFN-α were also found in DF patients. However, we failed to detect IL-1β, IL-17A and TNF-α in plasma, because of off-target. In our study, there was no relation between IL-6, IL-10, and IFN-α expressions and IL-37b in serum (P > 0.05). The IL-37b-producing monocytes were negatively correlated with the level of IFN-α in serum and platelet count, and positively correlated with lymphocytes percentage (P < 0.05, respectively). Additionally, serum DENV nonstructural protein 1 levels were positively correlated with monocytes percentages (P < 0.05). Our data represents findings for IL-37b expression and its potential mechanisms in DF patients' immune response.
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Affiliation(s)
- Jun-Ai Zhang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Jia-Jun Wang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Wen-Ting Zhang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Li Zhang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Bi-Ying Zheng
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Gan-Bin Liu
- Department of Respiration, Dongguan 6th Hospital, Dongguan, China
| | - Jing Liang
- Department of Respiration, Dongguan 6th Hospital, Dongguan, China
| | - Yuan-Bin Lu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Xian-Jin Wu
- Department of Clinical Laboratory, Huizhou Central People's Hospital, Huizhou, China
| | - Shu-Ying Yao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Guo-Ying Chen
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Yun-Qi Xie
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Jun-Yi Wu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Jia-Hua Shi
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Jiang Pi
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Si-Ping Li
- Dongguan Eighth People's Hospital, Dongguan, China.
| | - Jun-Fa Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China.
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan, China.
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15
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Young E, Yount B, Pantoja P, Henein S, Meganck RM, McBride J, Munt JE, Baric TJ, Zhu D, Scobey T, Dong S, Tse LV, Martinez MI, Burgos AG, Graham RL, White L, DeSilva A, Sariol CA, Baric RS. A live dengue virus vaccine carrying a chimeric envelope glycoprotein elicits dual DENV2-DENV4 serotype-specific immunity. Nat Commun 2023; 14:1371. [PMID: 36914616 PMCID: PMC10009830 DOI: 10.1038/s41467-023-36702-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: 06/10/2022] [Accepted: 02/10/2023] [Indexed: 03/16/2023] Open
Abstract
The four dengue virus serotypes co-circulate globally and cause significant human disease. Dengue vaccine development is challenging because some virus-specific antibodies are protective, while others are implicated in enhanced viral replication and more severe disease. Current dengue tetravalent vaccines contain four live attenuated serotypes formulated to theoretically induce balanced protective immunity. Among the number of vaccine candidates in clinical trials, only Dengvaxia is licensed for use in DENV seropositive individuals. To simplify live-virus vaccine design, we identify co-evolutionary constraints inherent in flavivirus virion assembly and design chimeric viruses to replace domain II (EDII) of the DENV2 envelope (E) glycoprotein with EDII from DENV4. The chimeric DENV2/4EDII virus replicates efficiently in vitro and in vivo. In male macaques, a single inoculation of DENV2/4EDII induces type-specific neutralizing antibodies to both DENV2 and DENV4, thereby providing a strategy to simplify DENV vaccine design by utilizing a single bivalent E glycoprotein immunogen for two DENV serotypes.
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Affiliation(s)
- Ellen Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Boyd Yount
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Petraleigh Pantoja
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
| | - Sandra Henein
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Rita M Meganck
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, MO, USA
| | - Jennifer McBride
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Jennifer E Munt
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Thomas J Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Deanna Zhu
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Trevor Scobey
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Stephanie Dong
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Longping V Tse
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, MO, USA
| | - Melween I Martinez
- Caribbean Primate Research Center, School of Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
| | - Armando G Burgos
- Caribbean Primate Research Center, School of Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
| | - Rachel L Graham
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Laura White
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Aravinda DeSilva
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Carlos A Sariol
- Unit of Comparative Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
- Caribbean Primate Research Center, School of Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
- Department of Internal Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
- Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
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16
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Thi Hue Kien D, Edenborough K, da Silva Goncalves D, Thuy Vi T, Casagrande E, Thi Le Duyen H, Thi Long V, Thi Dui L, Thi Tuyet Nhu V, Thi Giang N, Thi Xuan Trang H, Lee E, Donovan-Banfield I, Thi Thuy Van H, Minh Nguyet N, Thanh Phong N, Van Vinh Chau N, Wills B, Yacoub S, Flores H, Simmons C. Genome evolution of dengue virus serotype 1 under selection by Wolbachia pipientis in Aedes aegypti mosquitoes. Virus Evol 2023; 9:vead016. [PMID: 37744653 PMCID: PMC10517695 DOI: 10.1093/ve/vead016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/26/2023] [Accepted: 03/03/2023] [Indexed: 09/26/2023] Open
Abstract
The introgression of antiviral strains of Wolbachia into Aedes aegypti mosquito populations is a public health intervention for the control of dengue. Plausibly, dengue virus (DENV) could evolve to bypass the antiviral effects of Wolbachia and undermine this approach. Here, we established a serial-passage system to investigate the evolution of DENV in Ae. aegypti mosquitoes infected with the wMel strain of Wolbachia. Using this system, we report on virus genetic outcomes after twenty passages of serotype 1 of DENV (DENV-1). An amino acid substitution, E203K, in the DENV-1 envelope protein was more frequently detected in the consensus sequence of virus populations passaged in wMel-infected Ae. aegypti than wild-type counterparts. Positive selection at residue 203 was reproducible; it occurred in passaged virus populations from independent DENV-1-infected patients and also in a second, independent experimental system. In wild-type mosquitoes and human cells, the 203K variant was rapidly replaced by the progenitor sequence. These findings provide proof of concept that wMel-associated selection of virus populations can occur in experimental conditions. Field-based studies are needed to explore whether wMel imparts selective pressure on DENV evolution in locations where wMel is established.
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Affiliation(s)
| | - Kathryn Edenborough
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Daniela da Silva Goncalves
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
| | - Tran Thuy Vi
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Etiene Casagrande
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Huynh Thi Le Duyen
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Vo Thi Long
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Le Thi Dui
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Vu Thi Tuyet Nhu
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Giang
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Huynh Thi Xuan Trang
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Elvina Lee
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
| | - I’ah Donovan-Banfield
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
| | - Huynh Thi Thuy Van
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | | | - Nguyen Thanh Phong
- Hospital for Tropical Diseases, 190 Ben Ham Tu, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Vinh Chau
- Hospital for Tropical Diseases, 190 Ben Ham Tu, District 5, Ho Chi Minh City, Vietnam
| | - Bridget Wills
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie Yacoub
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
| | - Heather Flores
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Cameron Simmons
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, VIC 3800, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Oxford University Clinical Research Unit, Hospital for Tropical Disease, Ho Chi Minh City, Vietnam
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17
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Goudy OJ, Peng A, Tripathy A, Kuhlman B. Design of a protease-activated PD-L1 inhibitor. Protein Sci 2023; 32:e4578. [PMID: 36705186 PMCID: PMC9926466 DOI: 10.1002/pro.4578] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/18/2023] [Accepted: 01/25/2023] [Indexed: 01/28/2023]
Abstract
Immune checkpoint inhibitors that bind to the cell surface receptor PD-L1 are effective anti-cancer agents but suffer from immune-related adverse events as PD-L1 is expressed on both healthy and cancer cells. To mitigate toxicity, researchers are testing prodrugs that have low affinity for checkpoint targets until activated with proteases enriched in the tumor microenvironment. Here, we engineer a prodrug form of a PD-L1 inhibitor. The inhibitor is a soluble PD-1 mimetic that was previously engineered to have high affinity for PD-L1. In the basal state, the binding surface of the PD-1 mimetic is masked by fusing it to a soluble variant of its natural ligand, PD-L1. Proteolytic cleavage of the linker that connects the mask to the inhibitor activates the molecule. To optimize the mask so that it effectively blocks binding to PD-L1 but releases upon cleavage, we tested a set of mutants with varied affinity for the inhibitor. The top-performing mask reduces the affinity of the prodrug for PD-L1 120-fold, and binding is nearly fully recovered upon cleavage. In a cell-based assay measuring inhibition of the PD-1:PD-L1 interaction on the surface of cells, the IC50s of the masked inhibitors were up to 40-fold higher than their protease-treated counterparts. The changes in activity we observe upon protease treatment are comparable to systems currently tested in the clinic and provide evidence that natural binding partners are an excellent starting point for creating a prodrug.
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Affiliation(s)
- Odessa J. Goudy
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Alice Peng
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Ashutosh Tripathy
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Brian Kuhlman
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
- Lineberger Comprehensive Cancer CenterUniversity of North CarolinaChapel HillNorth CarolinaUSA
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18
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Thieker DF, Maguire JB, Kudlacek ST, Leaver‐Fay A, Lyskov S, Kuhlman B. Stabilizing proteins, simplified: A Rosetta-based webtool for predicting favorable mutations. Protein Sci 2022; 31:e4428. [PMID: 36173174 PMCID: PMC9490798 DOI: 10.1002/pro.4428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/06/2022] [Accepted: 08/21/2022] [Indexed: 11/07/2022]
Abstract
Many proteins have low thermodynamic stability, which can lead to low expression yields and limit functionality in research, industrial and clinical settings. This article introduces two, web-based tools that use the high-resolution structure of a protein along with the Rosetta molecular modeling program to predict stabilizing mutations. The protocols were recently applied to three genetically and structurally distinct proteins and successfully predicted mutations that improved thermal stability and/or protein yield. In all three cases, combining the stabilizing mutations raised the protein unfolding temperatures by more than 20°C. The first protocol evaluates point mutations and can generate a site saturation mutagenesis heatmap. The second identifies mutation clusters around user-defined positions. Both applications only require a protein structure and are particularly valuable when a deep multiple sequence alignment is not available. These tools were created to simplify protein engineering and enable research that would otherwise be infeasible due to poor expression and stability of the native molecule.
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Affiliation(s)
- David F. Thieker
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Jack B. Maguire
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Stephan T. Kudlacek
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Andrew Leaver‐Fay
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Sergey Lyskov
- Department of Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Brian Kuhlman
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
- Lineburger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
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19
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Phan TTN, Hvasta MG, Kudlacek ST, Thiono DJ, Tripathy A, Nicely NI, de Silva AM, Kuhlman B. A conserved set of mutations for stabilizing soluble envelope protein dimers from dengue and Zika viruses to advance the development of subunit vaccines. J Biol Chem 2022; 298:102079. [PMID: 35643320 PMCID: PMC9249817 DOI: 10.1016/j.jbc.2022.102079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022] Open
Abstract
Dengue viruses (DENV serotypes 1-4) and Zika virus (ZIKV) are related flaviviruses that continue to be a public health concern, infecting hundreds of millions of people annually. The traditional live-attenuated virus vaccine approach has been challenging for the four DENV serotypes because of the need to achieve balanced replication of four independent vaccine components. Subunit vaccines represent an alternative approach that may circumvent problems inherent with live-attenuated DENV vaccines. In mature virus particles, the envelope (E) protein forms a homodimer that covers the surface of the virus and is the major target of neutralizing antibodies. Many neutralizing antibodies bind to quaternary epitopes that span across both E proteins in the homodimer. For soluble E (sE) protein to be a viable subunit vaccine, the antigens should be easy to produce and retain quaternary epitopes recognized by neutralizing antibodies. However, WT sE proteins are primarily monomeric at conditions relevant for vaccination and exhibit low expression yields. Previously, we identified amino acid mutations that stabilize the sE homodimer from DENV2 and dramatically raise expression yields. Here, we tested whether these same mutations raise the stability of sE from other DENV serotypes and ZIKV. We show that the mutations raise thermostability for sE from all the viruses, increase production yields from 4-fold to 250-fold, stabilize the homodimer, and promote binding to dimer-specific neutralizing antibodies. Our findings suggest that these sE variants could be valuable resources in the efforts to develop effective subunit vaccines for DENV serotypes 1 to 4 and ZIKV.
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Affiliation(s)
- Thanh T N Phan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew G Hvasta
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephan T Kudlacek
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Devina J Thiono
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nathan I Nicely
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Aravinda M de Silva
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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20
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Georgiev GI, Malonis RJ, Wirchnianski AS, Wessel AW, Jung HS, Cahill SM, Nyakatura EK, Vergnolle O, Dowd KA, Cowburn D, Pierson TC, Diamond MS, Lai JR. Resurfaced ZIKV EDIII nanoparticle immunogens elicit neutralizing and protective responses in vivo. Cell Chem Biol 2022; 29:811-823.e7. [PMID: 35231399 DOI: 10.1016/j.chembiol.2022.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/10/2021] [Accepted: 02/09/2022] [Indexed: 11/25/2022]
Abstract
Zika virus (ZIKV) is a flavivirus that can cause severe disease, but there are no approved treatments or vaccines. A complication for flavivirus vaccine development is the potential of immunogens to enhance infection via antibody-dependent enhancement (ADE), a process mediated by poorly neutralizing and cross-reactive antibodies. Thus, there is a great need to develop immunogens that minimize the potential to elicit enhancing antibodies. Here we utilized structure-based protein engineering to develop "resurfaced" (rs) ZIKV immunogens based on E glycoprotein domain III (ZDIIIs), in which epitopes bound by variably neutralizing antibodies were masked by combinatorial mutagenesis. We identified one resurfaced ZDIII immunogen (rsZDIII-2.39) that elicited a protective but immune-focused response. Compared to wild type ZDIII, immunization with resurfaced rsZDIII-2.39 protein nanoparticles produced fewer numbers of ZIKV EDIII antigen-reactive B cells and elicited serum that had a lower magnitude of induced ADE against dengue virus serotype 1 (DENV1) Our findings enhance our understanding of the structural and functional determinants of antibody protection against ZIKV.
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Affiliation(s)
- George I Georgiev
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ryan J Malonis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ariel S Wirchnianski
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Alex W Wessel
- Department of Medicine, School of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Helen S Jung
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Sean M Cahill
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Elisabeth K Nyakatura
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Olivia Vergnolle
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kimberly A Dowd
- Viral Pathogenesis Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Theodore C Pierson
- Viral Pathogenesis Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael S Diamond
- Department of Medicine, School of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Pathology & Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jonathan R Lai
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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