1
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Han AX, de Jong SPJ, Russell CA. Co-evolution of immunity and seasonal influenza viruses. Nat Rev Microbiol 2023; 21:805-817. [PMID: 37532870 DOI: 10.1038/s41579-023-00945-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 08/04/2023]
Abstract
Seasonal influenza viruses cause recurring global epidemics by continually evolving to escape host immunity. The viral constraints and host immune responses that limit and drive the evolution of these viruses are increasingly well understood. However, it remains unclear how most of these advances improve the capacity to reduce the impact of seasonal influenza viruses on human health. In this Review, we synthesize recent progress made in understanding the interplay between the evolution of immunity induced by previous infections or vaccination and the evolution of seasonal influenza viruses driven by the heterogeneous accumulation of antibody-mediated immunity in humans. We discuss the functional constraints that limit the evolution of the viruses, the within-host evolutionary processes that drive the emergence of new virus variants, as well as current and prospective options for influenza virus control, including the viral and immunological barriers that must be overcome to improve the effectiveness of vaccines and antiviral drugs.
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Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Simon P J de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
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2
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Kowalczyk A, Gajda-Walczak A, Ruzycka-Ayoush M, Targonska A, Mosieniak G, Glogowski M, Szumera-Cieckiewicz A, Prochorec-Sobieszek M, Bamburowicz-Klimkowska M, Nowicka AM, Grudzinski IP. Parallel SPR and QCM-D Quantitative Analysis of CD9, CD63, and CD81 Tetraspanins: A Simple and Sensitive Way to Determine the Concentration of Extracellular Vesicles Isolated from Human Lung Cancer Cells. Anal Chem 2023. [PMID: 37307147 DOI: 10.1021/acs.analchem.3c00772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Tetraspanins, including CD9, CD63, and CD81, are transmembrane biomarkers that play a crucial role in regulating cancer cell proliferation, invasion, and metastasis, as well as plasma membrane dynamics and protein trafficking. In this study, we developed simple, fast, and sensitive immunosensors to determine the concentration of extracellular vesicles (EVs) isolated from human lung cancer cells using tetraspanins as biomarkers. We employed surface plasmon resonance (SPR) and quartz crystal microbalance with dissipation (QCM-D) as detectors. The monoclonal antibodies targeting CD9, CD63, and CD81 were oriented vertically in the receptor layer using either a protein A sensor chip (SPR) or a cysteamine layer that modified the gold crystal (QCM-D) without the use of amplifiers. The SPR studies demonstrated that the interaction of EVs with antibodies could be described by the two-state reaction model. Furthermore, the EVs' affinity to monoclonal antibodies against tetraspanins decreased in the following order: CD9, CD63, and CD81, as confirmed by the QCM-D studies. The results indicated that the developed immunosensors were characterized by high stability, a wide analytical range from 6.1 × 104 particles·mL-1 to 6.1 × 107 particles·mL-1, and a low detection limit (0.6-1.8) × 104 particles·mL-1. A very good agreement between the results obtained using the SPR and QCM-D detectors and nanoparticle tracking analysis demonstrated that the developed immunosensors could be successfully applied to clinical samples.
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Affiliation(s)
- Agata Kowalczyk
- Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, University of Warsaw, Pasteura Street 1, PL-02-093 Warsaw, Poland
| | - Aleksandra Gajda-Walczak
- Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, University of Warsaw, Pasteura Street 1, PL-02-093 Warsaw, Poland
| | - Monika Ruzycka-Ayoush
- Department of Toxicology and Food Science, Faculty of Pharmacy, Medical University of Warsaw, Banacha Streer 1, PL-02-097 Warsaw, Poland
| | - Alicja Targonska
- Laboratory of Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura Street 3, PL-02-093 Warsaw, Poland
| | - Grazyna Mosieniak
- Laboratory of Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura Street 3, PL-02-093 Warsaw, Poland
| | - Maciej Glogowski
- Department of Lung Cancer and Chest Tumors, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena Street 5, PL-02-781 Warsaw, Poland
| | - Anna Szumera-Cieckiewicz
- Department of Cancer Pathomorphology, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena Street 5, PL-02-781 Warsaw, Poland
| | - Monika Prochorec-Sobieszek
- Department of Cancer Pathomorphology, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena Street 5, PL-02-781 Warsaw, Poland
| | - Magdalena Bamburowicz-Klimkowska
- Department of Toxicology and Food Science, Faculty of Pharmacy, Medical University of Warsaw, Banacha Streer 1, PL-02-097 Warsaw, Poland
| | - Anna M Nowicka
- Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, University of Warsaw, Pasteura Street 1, PL-02-093 Warsaw, Poland
| | - Ireneusz P Grudzinski
- Department of Toxicology and Food Science, Faculty of Pharmacy, Medical University of Warsaw, Banacha Streer 1, PL-02-097 Warsaw, Poland
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3
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Miao X, Yin Y, Chen Y, Bi W, Yin Y, Chen S, Peng D, Gao L, Qin T, Liu X. Bidirectionally Regulating Viral and Cellular Ferroptosis with Metastable Iron Sulfide Against Influenza Virus. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2206869. [PMID: 37092591 DOI: 10.1002/advs.202206869] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/29/2023] [Indexed: 05/03/2023]
Abstract
Influenza virus with numerous subtypes and frequent variation limits the development of high-efficacy and broad-spectrum antiviral strategy. Here, a novel multi-antiviral metastable iron sulfides (mFeS) against various influenza A/B subtype viruses is developed. This work finds that mFeS induces high levels of lipid peroxidation and •OH free radicals in the conservative viral envelope, which depends on Fe2+ . This phenomenon, termed as a viral ferroptosis, results in the loss of viral infectibility and pathogenicity in vitro and in vivo, respectively. Furthermore, the decoction of mFeS (Dc(mFeS)) inhibits cellular ferroptosis-dependent intracellular viral replication by correcting the virus-induced reprogrammed sulfur metabolism, a conserved cellular metabolism. Notably, personal protective equipment (PPE) that is loaded with mFeS provides good antiviral protection. Aerosol administration of mFeS combined with the decoction (mFeS&Dc) has a potential therapeutic effect against H1N1 lethal infection in mice. Collectively, mFeS represents an antiviral alternative with broad-spectrum activity against intracellular and extracellular influenza virus.
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Affiliation(s)
- Xinyu Miao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
| | - Yinyan Yin
- College of Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
- Guangling College, Yangzhou University, Yangzhou, Jiangsu, 225000, P. R. China
| | - Yulian Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
| | - Wenhui Bi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
| | - Yuncong Yin
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
| | - Sujuan Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
| | - Daxin Peng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
- Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu, 225009, P. R. China
| | - Lizeng Gao
- CAS Engineering Laboratory for Nanozyme, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Tao Qin
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
- Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu, 225009, P. R. China
| | - Xiufan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, P. R. China
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4
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Prevalence and mechanisms of evolutionary contingency in human influenza H3N2 neuraminidase. Nat Commun 2022; 13:6443. [PMID: 36307418 PMCID: PMC9616408 DOI: 10.1038/s41467-022-34060-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/12/2022] [Indexed: 12/25/2022] Open
Abstract
Neuraminidase (NA) of human influenza H3N2 virus has evolved rapidly and been accumulating mutations for more than half-century. However, biophysical constraints that govern the evolutionary trajectories of NA remain largely elusive. Here, we show that among 70 natural mutations that are present in the NA of a recent human H3N2 strain, >10% are deleterious for an ancestral strain. By mapping the permissive mutations using combinatorial mutagenesis and next-generation sequencing, an extensive epistatic network is revealed. Biophysical and structural analyses further demonstrate that certain epistatic interactions can be explained by non-additive stability effect, which in turn modulates membrane trafficking and enzymatic activity of NA. Additionally, our results suggest that other biophysical mechanisms also contribute to epistasis in NA evolution. Overall, these findings not only provide mechanistic insights into the evolution of human influenza NA and elucidate its sequence-structure-function relationship, but also have important implications for the development of next-generation influenza vaccines.
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5
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Ellis D, Lederhofer J, Acton OJ, Tsybovsky Y, Kephart S, Yap C, Gillespie RA, Creanga A, Olshefsky A, Stephens T, Pettie D, Murphy M, Sydeman C, Ahlrichs M, Chan S, Borst AJ, Park YJ, Lee KK, Graham BS, Veesler D, King NP, Kanekiyo M. Structure-based design of stabilized recombinant influenza neuraminidase tetramers. Nat Commun 2022; 13:1825. [PMID: 35383176 PMCID: PMC8983682 DOI: 10.1038/s41467-022-29416-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 03/14/2022] [Indexed: 11/21/2022] Open
Abstract
Influenza virus neuraminidase (NA) is a major antiviral drug target and has recently reemerged as a key target of antibody-mediated protective immunity. Here we show that recombinant NAs across non-bat subtypes adopt various tetrameric conformations, including an "open" state that may help explain poorly understood variations in NA stability across viral strains and subtypes. We use homology-directed protein design to uncover the structural principles underlying these distinct tetrameric conformations and stabilize multiple recombinant NAs in the "closed" state, yielding two near-atomic resolution structures of NA by cryo-EM. In addition to enhancing thermal stability, conformational stabilization improves affinity to protective antibodies elicited by viral infection, including antibodies targeting a quaternary epitope and the broadly conserved catalytic site. Stabilized NAs can also be integrated into viruses without affecting fitness. Our findings provide a deeper understanding of NA structure, stability, and antigenicity, and establish design strategies for reinforcing the conformational integrity of recombinant NA proteins.
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Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, 98195, USA
- Icosavax Inc., Seattle, WA, 98102, USA
| | - Julia Lederhofer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Oliver J Acton
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, 21702, USA
| | - Sally Kephart
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Christina Yap
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Audrey Olshefsky
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, 21702, USA
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Claire Sydeman
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Andrew J Borst
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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6
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Abstract
The neuraminidase (NA) of influenza A and B viruses plays a distinct role in viral replication and has a highly conserved catalytic site. Numerous sialic (neuraminic) acid analogs that competitively bind to the NA active site and potently inhibit enzyme activity have been synthesized and tested. Four NA inhibitors are now licensed in various parts of the world (zanamivir, oseltamivir, peramivir, and laninamivir) to treat influenza A and B infections. NA changes, naturally occurring or acquired under selective pressure, have been shown to reduce drug binding, thereby affecting the effectiveness of NA inhibitors. Drug resistance and other drawbacks have prompted the search for the next-generation NA-targeting therapeutics. One of the promising approaches is the identification of monoclonal antibodies (mAbs) targeting the conserved NA epitopes. Anti-NA mAbs demonstrate Fab-based antiviral activity supplemented with Fc-mediated immune effector functions. Antiviral Fc-conjugates offer another cutting-edge strategy that is based on a multimodal mechanism of action. These novel antiviral agents are composed of a small-molecule NA inhibitor and an Fc-region that simultaneously engages the immune system. The significant advancements made in recent years further support the value of NA as an attractive target for the antiviral development.
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Affiliation(s)
- Larisa Gubareva
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329-4027, USA
| | - Teena Mohan
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329-4027, USA
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7
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Zhang RR, Yang X, Shi CW, Yu LJ, Lian YB, Huang HB, Wang JZ, Jiang YL, Cao X, Zeng Y, Yang GL, Yang WT, Wang CF. Improved pathogenicity of H9N2 subtype of avian influenza virus induced by mutations occurred after serial adaptations in mice. Microb Pathog 2021; 160:105204. [PMID: 34562554 DOI: 10.1016/j.micpath.2021.105204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 02/05/2023]
Abstract
H9N2 subtype, a low pathogenic avian influenza virus, is emerging as a major causative agent circulating poultry workplaces across China and other Asian countries. Increasing case number of interspecies transmissions to mammals reported recently provoked a great concern about its risks inducing global pandemics. In an attempt to understand the underlying mechanism of how the H9N2 virus disrupts the interspecies segregation to transmit to mammals. A mutant H9N2 strain was obtained by passaging the wildtype H9N2 A/chicken/Hong Kong/G9/1997 eight times from lung to lung in BALB/c mice. Our finding revealed that mice manifested severe clinical symptoms including losses of body weight, pathological damages in pulmonary sites and all died within two weeks after infected with the mutated H9N2, whereas all mice survived upon infected with wildtype strain in comparison, which suggested increased pathogenicity of the mutant strain. In addition, mice showed enhanced levels of proinflammatory cytokines in sera, including IL-6, TNF-α and IL-1β compared to those subjected to wildtype viral infections. Sequence analysis showed that five amino acid substitutions occurred at PB2627, HA87, HA234, NP387 and M156, and a deletion mutation happened in the M gene (M157). Of these mutations, PB2 E627K played key roles in modulating lethality in mice. Taken together, the mutant H9N2 strain obtained by serial passaging of its wildtype in mice significantly increased its virulence leading to death of mice, which might be associated the accumulated mutations occurred on its genome.
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Affiliation(s)
- Rong-Rong Zhang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xin Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Chun-Wei Shi
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Ling-Jiao Yu
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yi-Bing Lian
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Hai-Bin Huang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jian-Zhong Wang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yan-Long Jiang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xin Cao
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yan Zeng
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Gui-Lian Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China.
| | - Wen-Tao Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China.
| | - Chun-Feng Wang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China.
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8
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Abstract
The influenza virus neuraminidase (NA) is becoming a focus for novel vaccine designs. However, the epitopes of human anti-NA antibodies have been poorly defined. Using a panel of 10 anti-N2 monoclonal antibodies (MAbs) that bind the H3N2 virus A/Switzerland/9715293/2013, we generated five escape mutant viruses. These viruses contained mutations K199E/T, E258K, A272D, and S331N. We found that mutations at K199 and E258 had the largest impact on MAb binding, NA inhibition and neutralization activity. In addition, a natural isolate from the 2017-2018 season was found to contain the E258K mutation and was resistant to numerous antibodies tested. The mutation S331N, was identified in virus passaged in the presence of antibody; however, it had little impact on MAb activity and greatly decreased viral fitness. This information aids in identifying novel human MAb epitopes on the N2 and helps with the detection of antigenically drifted NAs. IMPORTANCE The influenza virus neuraminidase is an emerging target for universal influenza virus vaccines. However, in contrast to influenza virus hemagglutinin, we know little about antibody epitopes and antigenic sites on the neuraminidase. Characterizing and defining these sites is aiding vaccine development and helping to understand antigenic drift of NA.
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9
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Wilson IA, Stanfield RL. 50 Years of structural immunology. J Biol Chem 2021; 296:100745. [PMID: 33957119 PMCID: PMC8163984 DOI: 10.1016/j.jbc.2021.100745] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Fifty years ago, the first landmark structures of antibodies heralded the dawn of structural immunology. Momentum then started to build toward understanding how antibodies could recognize the vast universe of potential antigens and how antibody-combining sites could be tailored to engage antigens with high specificity and affinity through recombination of germline genes (V, D, J) and somatic mutation. Equivalent groundbreaking structures in the cellular immune system appeared some 15 to 20 years later and illustrated how processed protein antigens in the form of peptides are presented by MHC molecules to T cell receptors. Structures of antigen receptors in the innate immune system then explained their inherent specificity for particular microbial antigens including lipids, carbohydrates, nucleic acids, small molecules, and specific proteins. These two sides of the immune system act immediately (innate) to particular microbial antigens or evolve (adaptive) to attain high specificity and affinity to a much wider range of antigens. We also include examples of other key receptors in the immune system (cytokine receptors) that regulate immunity and inflammation. Furthermore, these antigen receptors use a limited set of protein folds to accomplish their various immunological roles. The other main players are the antigens themselves. We focus on surface glycoproteins in enveloped viruses including SARS-CoV-2 that enable entry and egress into host cells and are targets for the antibody response. This review covers what we have learned over the past half century about the structural basis of the immune response to microbial pathogens and how that information can be utilized to design vaccines and therapeutics.
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MESH Headings
- Adaptive Immunity
- Allergy and Immunology/history
- Animals
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibody Specificity
- Antigen Presentation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- COVID-19/immunology
- COVID-19/virology
- Crystallography/history
- Crystallography/methods
- History, 20th Century
- History, 21st Century
- Humans
- Immunity, Innate
- Protein Folding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Cytokine/chemistry
- Receptors, Cytokine/genetics
- Receptors, Cytokine/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- V(D)J Recombination
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Affiliation(s)
- Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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10
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Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. mBio 2020; 11:mBio.02315-20. [PMID: 33024040 PMCID: PMC7542365 DOI: 10.1128/mbio.02315-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The immune system produces antibodies to protect the human body from harmful invaders. The monoclonal antibody (MAb) is one kind of effective antivirals. In this study, we isolated an antibody (Z2B3) from an H7N9 influenza virus-infected child. It shows cross-reactivity to both group 1 (N1) and group 2 (N9) neuraminidases (NAs) but is sensitive to N1 NA with a K432E substitution. Structural analysis of the NA-antibody fragment antigen-binding (Fab) complex provides a clue for antibody modification, and the modified antibody restored binding and inhibition to recently drifted N1 NA and regained protection against the variant influenza strain. This finding suggests that antibodies to NA may be a useful therapy and can be in principle edited to defeat drifted influenza virus. Here, we investigate a monoclonal antibody, Z2B3, isolated from an H7N9-infected patient, that exhibited cross-reactivity to both N9 (group 2) and a broad range of seasonal and avian N1 (group 1) proteins but lost activity to the N1 with the substitution K432E. This substitution exists in 99.25% of seasonal influenza strains after 2013. The NA-Z2B3 complex structures indicated that Z2B3 binds within the conserved active site of the neuraminidase (NA) protein. A salt bridge between D102 in Z2B3 and K432 in NA plays an important role in binding. Structure-based modification of Z2B3 with D102R in heavy chain reversed the salt bridge and restored the binding and inhibition of N1 with E432. Furthermore, Z2B3-D102R can protect mice from A/Serbia/NS-601/2014 H1N1 virus (NA contains E432) infection while the wild-type Z2B3 antibody shows no protection. This study demonstrates that a broadly reactive and protective antibody to NA can be in principle edited to restore binding and inhibition to recently drifted N1 NA and regain protection against the variant influenza strain.
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11
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Structural Biology of Influenza Hemagglutinin: An Amaranthine Adventure. Viruses 2020; 12:v12091053. [PMID: 32971825 PMCID: PMC7551194 DOI: 10.3390/v12091053] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 12/27/2022] Open
Abstract
Hemagglutinin (HA) glycoprotein is an important focus of influenza research due to its role in antigenic drift and shift, as well as its receptor binding and membrane fusion functions, which are indispensable for viral entry. Over the past four decades, X-ray crystallography has greatly facilitated our understanding of HA receptor binding, membrane fusion, and antigenicity. The recent advances in cryo-EM have further deepened our comprehension of HA biology. Since influenza HA constantly evolves in natural circulating strains, there are always new questions to be answered. The incessant accumulation of knowledge on the structural biology of HA over several decades has also facilitated the design and development of novel therapeutics and vaccines. This review describes the current status of the field of HA structural biology, how we got here, and what the next steps might be.
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12
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Eichelberger MC, Monto AS. Neuraminidase, the Forgotten Surface Antigen, Emerges as an Influenza Vaccine Target for Broadened Protection. J Infect Dis 2020; 219:S75-S80. [PMID: 30715357 DOI: 10.1093/infdis/jiz017] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
For 50 years it has been known that antibodies to neuraminidase (NA) protect against infection during seasonal and pandemic influenza outbreaks. However, NA is largely ignored in the formulation and standardization of our current influenza vaccines. There are a number of factors that contributed to this antigen being forgotten, including the lack of an easily performed test to measure NA antibody. With the availability of that test, it has been possible to show its independent contribution to protection in various situations. The challenge now is to make it possible to include known amounts of NA in investigational vaccines or to routinely measure NA content in licensed vaccines. Vaccines containing optimal amounts of NA may be particularly useful when there are antigenic changes, either drift or shift, in the hemagglutinin because NA immunity offers broad protection. It is now time to remember the NA as we work toward improved influenza vaccines.
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Affiliation(s)
- Maryna C Eichelberger
- Office of Compliance and Biologics Quality, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Arnold S Monto
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor
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13
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Wan H, Gao J, Yang H, Yang S, Harvey R, Chen YQ, Zheng NY, Chang J, Carney PJ, Li X, Plant E, Jiang L, Couzens L, Wang C, Strohmeier S, Wu WW, Shen RF, Krammer F, Cipollo JF, Wilson PC, Stevens J, Wan XF, Eichelberger MC, Ye Z. The neuraminidase of A(H3N2) influenza viruses circulating since 2016 is antigenically distinct from the A/Hong Kong/4801/2014 vaccine strain. Nat Microbiol 2019; 4:2216-2225. [PMID: 31406333 PMCID: PMC6879794 DOI: 10.1038/s41564-019-0522-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/24/2019] [Indexed: 11/08/2022]
Abstract
A(H3N2) virus predominated recent influenza seasons, which has resulted in the rigorous investigation of haemagglutinin, but whether neuraminidase (NA) has undergone antigenic change and contributed to the predominance of A(H3N2) virus is unknown. Here, we show that the NA of the circulating A(H3N2) viruses has experienced significant antigenic drift since 2016 compared with the A/Hong Kong/4801/2014 vaccine strain. This antigenic drift was mainly caused by amino acid mutations at NA residues 245, 247 (S245N/S247T; introducing an N-linked glycosylation site at residue 245) and 468. As a result, the binding of the NA of A(H3N2) virus by some human monoclonal antibodies, including those that have broad reactivity to the NA of the 1957 A(H2N2) and 1968 A(H3N2) reference pandemic viruses as well as contemporary A(H3N2) strains, was reduced or abolished. This antigenic drift also reduced NA-antibody-based protection against in vivo virus challenge. X-ray crystallography showed that the glycosylation site at residue 245 is within a conserved epitope that overlaps the NA active site, explaining why it impacts antibody binding. Our findings suggest that NA antigenic drift impacts protection against influenza virus infection, thus highlighting the importance of including NA antigenicity for consideration in the optimization of influenza vaccines.
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MESH Headings
- Animals
- Antibodies, Monoclonal
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Catalytic Domain
- Crystallography, X-Ray
- Disease Models, Animal
- Genes, Viral/genetics
- Glycosylation
- Hong Kong
- Humans
- Immunogenicity, Vaccine
- Influenza A Virus, H3N2 Subtype/enzymology
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza Vaccines/immunology
- Influenza, Human/prevention & control
- Mice
- Models, Molecular
- Mutation
- Neuraminidase/chemistry
- Neuraminidase/genetics
- Neuraminidase/immunology
- Orthomyxoviridae Infections/immunology
- Protein Conformation
- Sequence Analysis, Protein
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/immunology
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Affiliation(s)
- Hongquan Wan
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
| | - Jin Gao
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Hua Yang
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shuang Yang
- Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Ruth Harvey
- National Institute for Biological Standards and Control, Potters Bar, UK
| | - Yao-Qing Chen
- Department of Medicine, Section of Rheumatology, The University of Chicago, Chicago, IL, USA
| | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, The University of Chicago, Chicago, IL, USA
| | - Jessie Chang
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul J Carney
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xing Li
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Ewan Plant
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Lianlian Jiang
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Laura Couzens
- Division of Biological Standards and Quantity Control, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Carol Wang
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wells W Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John F Cipollo
- Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, The University of Chicago, Chicago, IL, USA
| | - James Stevens
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, USA
| | - Maryna C Eichelberger
- Division of Biological Standards and Quantity Control, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Zhiping Ye
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
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14
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Gilchuk IM, Bangaru S, Gilchuk P, Irving RP, Kose N, Bombardi RG, Thornburg NJ, Creech CB, Edwards KM, Li S, Turner HL, Yu W, Zhu X, Wilson IA, Ward AB, Crowe JE. Influenza H7N9 Virus Neuraminidase-Specific Human Monoclonal Antibodies Inhibit Viral Egress and Protect from Lethal Influenza Infection in Mice. Cell Host Microbe 2019; 26:715-728.e8. [PMID: 31757769 DOI: 10.1016/j.chom.2019.10.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/20/2019] [Accepted: 10/07/2019] [Indexed: 02/05/2023]
Abstract
H7N9 avian influenza virus causes severe infections and might have the potential to trigger a major pandemic. Molecular determinants of human humoral immune response to N9 neuraminidase (NA) proteins, which exhibit unusual features compared with seasonal influenza virus NA proteins, are ill-defined. We isolated 35 human monoclonal antibodies (mAbs) from two H7N9 survivors and two vaccinees. These mAbs react to NA in a subtype-specific manner and recognize diverse antigenic sites on the surface of N9 NA, including epitopes overlapping with, or distinct from, the enzyme active site. Despite recognizing multiple antigenic sites, the mAbs use a common mechanism of action by blocking egress of nascent virions from infected cells, thereby providing an antiviral prophylactic and therapeutic protection in vivo in mice. Studies of breadth, potency, and diversity of antigenic recognition from four subjects suggest that vaccination with inactivated adjuvanted vaccine induce NA-reactive responses comparable to that of H7N9 natural infection.
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Affiliation(s)
- Iuliia M Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sandhya Bangaru
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Pavlo Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ryan P Irving
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nurgun Kose
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robin G Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Natalie J Thornburg
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - C Buddy Creech
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sheng Li
- Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wenli Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James E Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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15
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Förster A, Schulze-Briese C. A shared vision for macromolecular crystallography over the next five years. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:064302. [PMID: 31832486 PMCID: PMC6892709 DOI: 10.1063/1.5131017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/19/2019] [Indexed: 05/12/2023]
Abstract
Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules, but the method has reached a critical juncture. New diffraction-limited storage rings and upgrades to the existing sources will provide beamlines with higher flux and brilliance, and even the largest detectors can collect at rates of several hundred hertz. Electron cryomicroscopy is successfully competing for structural biologists' most exciting projects. As a result, formerly scarce beam time is becoming increasingly abundant, and beamlines must innovate to attract users and ensure continued funding. Here, we will show how data collection has changed over the preceding five years and how alternative methods have emerged. We then explore how MX at synchrotrons might develop over the next five years. We predict that, despite the continued dominance of rotation crystallography, applications previously considered niche or experimental, such as serial crystallography, pink-beam crystallography, and crystallography at energies above 25 keV and below 5 keV, will rise in prominence as beamlines specialize to offer users the best value. Most of these emerging methods will require new hardware and software. With these advances, MX will more efficiently provide the high-resolution structures needed for drug development. MX will also be able to address a broader range of questions than before and contribute to a deeper understanding of biological processes in the context of integrative structural biology.
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16
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Comparison of the Efficacy of N9 Neuraminidase-Specific Monoclonal Antibodies against Influenza A(H7N9) Virus Infection. J Virol 2018; 92:JVI.01588-17. [PMID: 29167344 DOI: 10.1128/jvi.01588-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/20/2017] [Indexed: 01/07/2023] Open
Abstract
The fifth wave of A(H7N9) virus infection in China from 2016 to 2017 caused great concern due to the large number of individuals infected, the isolation of drug-resistant viruses, and the emergence of highly pathogenic strains. Antibodies against neuraminidase (NA) provide added benefit to hemagglutinin-specific immunity and may be important contributors to the effectiveness of A(H7N9) vaccines. We generated a panel of mouse monoclonal antibodies (MAbs) to identify antigenic domains on NA of the novel A(H7N9) virus and compared their functional properties. The loop formed in the region of residue 250 (250 loop) and the domain formed by the loops containing residues 370, 400, and 430 were identified as major antigenic regions. MAbs 1E8, 2F6, 10F4, and 11B2, which recognize these two antigenic domains, were characterized in depth. These four MAbs differ in their abilities to inhibit cleavage of small and large substrates (methyl-umbelliferyl-acetyl neuraminic acid [MU-NANA] and fetuin, respectively) in NA inhibition assays. 1E8 and 11B2 did not inhibit NA cleavage of either MU-NANA or fetuin, and 2F6 inhibited cleavage of fetuin alone, whereas 10F4 inhibited cleavage of both substrates. All four MAbs reduced the in vitro spread of viruses carrying either the wild-type N9 or N9 with antiviral-resistant mutations but to different degrees. These MAbs have different in vivo levels of effectiveness: 10F4 was the most effective in protecting mice against challenge with A(H7N9) virus, 2F6 was less effective, and 11B2 failed to protect BALB/c mice at the doses tested. Our study confirms that NA-specific antibodies can protect against A(H7N9) infection and suggests that in vitro properties can be used to rank antibodies with therapeutic potential.IMPORTANCE The novel A(H7N9) viruses that emerged in China in 2013 continue to infect humans, with a high fatality rate. The most recent outbreak resulted in a larger number of human cases than previous epidemic waves. Due to the absence of a licensed vaccine and the emergence of drug-resistant viruses, there is a need to develop alternative approaches to prevent or treat A(H7N9) infection. We have made a panel of mouse monoclonal antibodies (MAbs) specific for neuraminidase (NA) of A(H7N9) viruses; some of these MAbs are effective in inhibiting viruses that are resistant to antivirals used to treat A(H7N9) patients. Binding avidity, inhibition of NA activity, and plaque formation correlated with the effectiveness of these MAbs to protect mice against lethal A(H7N9) virus challenge. This study identifies in vitro measures that can be used to predict the in vivo efficacy of NA-specific antibodies, providing a way to select MAbs for further therapeutic development.
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17
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Wu NC, Wilson IA. A Perspective on the Structural and Functional Constraints for Immune Evasion: Insights from Influenza Virus. J Mol Biol 2017. [PMID: 28648617 DOI: 10.1016/j.jmb.2017.06.015] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Influenza virus evolves rapidly to constantly escape from natural immunity. Most humoral immune responses to influenza virus target the hemagglutinin (HA) glycoprotein, which is the major antigen on the surface of the virus. The HA is composed of a globular head domain for receptor binding and a stem domain for membrane fusion. The major antigenic sites of HA are located in the globular head subdomain, which is highly tolerant of amino acid substitutions and continual addition of glycosylation sites. Nonetheless, the evolution of the receptor-binding site and the stem region on HA is severely constrained by their functional roles in engaging the host receptor and in mediating membrane fusion, respectively. Here, we review how broadly neutralizing antibodies (bnAbs) exploit these evolutionary constraints to protect against diverse influenza strains. We also discuss the emerging role of other epitopes that are conserved only in subsets of viruses. This rapidly increasing knowledge of the evolutionary biology, immunology, structural biology, and virology of influenza virus is invaluable for development and design of more universal influenza vaccines and novel therapeutics.
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Affiliation(s)
- Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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18
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Du T, Yang L, Luo H, Zhou P, Mei H, Xuan J, Xing Q, Ning B, Mendrick DL, Shi L. HLADR: a database system for enhancing the discovery of biomarkers for predicting human leukocyte antigen-mediated idiosyncratic adverse drug reactions. Biomark Med 2015; 9:1079-93. [DOI: 10.2217/bmm.15.98] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim: To establish a database for the associations between idiosyncratic drug reactions (IDRs) and human leukocyte antigens (HLAs) and to systematically assess the characteristics of the drug–HLA associations. Materials & methods: Electronic databases were searched to extensively identify drug–HLA association studies from 1966 to present. Results: A drug-HLA-IDR database, HLADR, was created. The drug–HLA relationship network clearly reflected an ethnicity dependency of the associations. The positive predictive values and the negative predictive values demonstrated that other potential factors may also regulate the occurrence of HLA-specific IDRs. Conclusions: Constructing studies with samples from homogeneous ethnic groups and identifying cofactors that affect negative predictive values and positive predictive values will become necessary to enhance the predictability of HLA biomarkers for future research on IDRs.
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Affiliation(s)
- Tingting Du
- Center for Pharmacogenomics & State Key Laboratory of Genetic Engineering, School of Life Sciences & School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Lun Yang
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Heng Luo
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
- University of Arkansas at Little Rock/University of Arkansas for Medical Sciences Joint Bioinformatics Graduate Program, 2801 South University Avenue, Little Rock, AR 72204, USA
| | - Peng Zhou
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Hu Mei
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Jiekun Xuan
- Center for Pharmacogenomics & State Key Laboratory of Genetic Engineering, School of Life Sciences & School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Qinghe Xing
- Institutes of Biomedical Science, Fudan University, 138 Shanghai Medical School Road, Shanghai 200032, China
| | - Baitang Ning
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Donna L Mendrick
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Leming Shi
- Center for Pharmacogenomics & State Key Laboratory of Genetic Engineering, School of Life Sciences & School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
- University of Arkansas at Little Rock/University of Arkansas for Medical Sciences Joint Bioinformatics Graduate Program, 2801 South University Avenue, Little Rock, AR 72204, USA
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19
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Santra S, Tomaras GD, Warrier R, Nicely NI, Liao HX, Pollara J, Liu P, Alam SM, Zhang R, Cocklin SL, Shen X, Duffy R, Xia SM, Schutte RJ, Pemble IV CW, Dennison SM, Li H, Chao A, Vidnovic K, Evans A, Klein K, Kumar A, Robinson J, Landucci G, Forthal DN, Montefiori DC, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Robb ML, Michael NL, Kim JH, Soderberg KA, Giorgi EE, Blair L, Korber BT, Moog C, Shattock RJ, Letvin NL, Schmitz JE, Moody MA, Gao F, Ferrari G, Shaw GM, Haynes BF. Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques. PLoS Pathog 2015; 11:e1005042. [PMID: 26237403 PMCID: PMC4523205 DOI: 10.1371/journal.ppat.1005042] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 06/23/2015] [Indexed: 11/19/2022] Open
Abstract
HIV-1 mucosal transmission begins with virus or virus-infected cells moving through mucus across mucosal epithelium to infect CD4+ T cells. Although broadly neutralizing antibodies (bnAbs) are the type of HIV-1 antibodies that are most likely protective, they are not induced with current vaccine candidates. In contrast, antibodies that do not neutralize primary HIV-1 strains in the TZM-bl infection assay are readily induced by current vaccine candidates and have also been implicated as secondary correlates of decreased HIV-1 risk in the RV144 vaccine efficacy trial. Here, we have studied the capacity of anti-Env monoclonal antibodies (mAbs) against either the immunodominant region of gp41 (7B2 IgG1), the first constant region of gp120 (A32 IgG1), or the third variable loop (V3) of gp120 (CH22 IgG1) to modulate in vivo rectal mucosal transmission of a high-dose simian-human immunodeficiency virus (SHIV-BaL) in rhesus macaques. 7B2 IgG1 or A32 IgG1, each containing mutations to enhance Fc function, was administered passively to rhesus macaques but afforded no protection against productive clinical infection while the positive control antibody CH22 IgG1 prevented infection in 4 of 6 animals. Enumeration of transmitted/founder (T/F) viruses revealed that passive infusion of each of the three antibodies significantly reduced the number of T/F genomes. Thus, some antibodies that bind HIV-1 Env but fail to neutralize virus in traditional neutralization assays may limit the number of T/F viruses involved in transmission without leading to enhancement of viral infection. For one of these mAbs, gp41 mAb 7B2, we provide the first co-crystal structure in complex with a common cyclical loop motif demonstrated to be critical for infection by other retroviruses.
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Affiliation(s)
- Sampa Santra
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (SS); (GDT); (BFH)
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (SS); (GDT); (BFH)
| | - Ranjit Warrier
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nathan I. Nicely
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Justin Pollara
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Pinghuang Liu
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Ruijun Zhang
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Sarah L. Cocklin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Ryan Duffy
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Robert J. Schutte
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Charles W. Pemble IV
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - S. Moses Dennison
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Hui Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrew Chao
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kora Vidnovic
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Abbey Evans
- Department of Medicine, St Mary’s Campus, Imperial College London, London, United Kingdom
| | - Katja Klein
- Department of Medicine, St Mary’s Campus, Imperial College London, London, United Kingdom
| | - Amit Kumar
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - James Robinson
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Gary Landucci
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, Irvine, California, United States of America
| | - Donald N. Forthal
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, Irvine, California, United States of America
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | | | - Sorachai Nitayaphan
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | | | | | - Merlin L. Robb
- US Military Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Nelson L. Michael
- US Military Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Jerome H. Kim
- US Military Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Kelly A. Soderberg
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Elena E. Giorgi
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Lily Blair
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Bette T. Korber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Christiane Moog
- U1109, INSERM University of Strasbourg, Strasbourg, Alsace, France
| | - Robin J. Shattock
- Department of Medicine, St Mary’s Campus, Imperial College London, London, United Kingdom
| | - Norman L. Letvin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joern E. Schmitz
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - M. A. Moody
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Feng Gao
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - George M. Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (SS); (GDT); (BFH)
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20
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Hoffmann T, Krackhardt AM, Antes I. Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition. PLoS Comput Biol 2015; 11:e1004244. [PMID: 26185983 PMCID: PMC4505886 DOI: 10.1371/journal.pcbi.1004244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/17/2015] [Indexed: 02/01/2023] Open
Abstract
T-cell receptors (TCR) play an important role in the adaptive immune system as they recognize pathogen- or cancer-based epitopes and thus initiate the cell-mediated immune response. Therefore there exists a growing interest in the optimization of TCRs for medical purposes like adoptive T-cell therapy. However, the molecular mechanisms behind T-cell signaling are still predominantly unknown. For small sets of TCRs it was observed that the angle between their Vα- and Vβ-domains, which bind the epitope, can vary and might be important for epitope recognition. Here we present a comprehensive, quantitative study of the variation in the Vα/Vβ interdomain-angle and its influence on epitope recognition, performing a systematic bioinformatics analysis based on a representative set of experimental TCR structures. For this purpose we developed a new, cuboid-based superpositioning method, which allows a unique, quantitative analysis of the Vα/Vβ-angles. Angle-based clustering led to six significantly different clusters. Analysis of these clusters revealed the unexpected result that the angle is predominantly influenced by the TCR-clonotype, whereas the bound epitope has only a minor influence. Furthermore we could identify a previously unknown center of rotation (CoR), which is shared by all TCRs. All TCR geometries can be obtained by rotation around this center, rendering it a new, common TCR feature with the potential of improving the accuracy of TCR structure prediction considerably. The importance of Vα/Vβ rotation for signaling was confirmed as we observed larger variances in the Vα/Vβ-angles in unbound TCRs compared to epitope-bound TCRs. Our results strongly support a two-step mechanism for TCR-epitope: First, preformation of a flexible TCR geometry in the unbound state and second, locking of the Vα/Vβ-angle in a TCR-type specific geometry upon epitope-MHC association, the latter being driven by rotation around the unique center of rotation. The recognition of antigenic peptides by cytotoxic T-cells is one of the crucial steps during the adaptive immune response. Thus a detailed understanding of this process is not only important for elucidating the mechanism behind T-cell signaling, but also for various emerging new medical applications like T-cell based immunotherapies and designed bio-therapeutics. However, despite the fast growing interest in this field, the mechanistic basis of the immune response is still largely unknown. Previous qualitative studies suggested that the T-cell receptor (TCR) Vα/Vβ-interdomain angle plays a crucial role in epitope recognition as it predetermines the relative position of its antigen-recognizing CDR1-3 loops and thus TCR specificity. In the manuscript we present a systematic bioinformatic analysis of the structural characteristics of bound and unbound TCR molecules focusing on the Vα/Vβ-angle. Our results demonstrate the importance of this angle for signaling, as several distinct Vα/Vβ-angle based structural clusters could be observed and larger angle flexibilities exist for unbound TCRs than for bound TCRs, providing quantitative proof for a two-step locking mechanism upon epitope recognition. In this context, we could identify a unique rotational point, which allows a quantitative, yet intuitive description of all observed angle variations and the structural changes upon epitope binding.
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MESH Headings
- Binding Sites
- Computer Simulation
- Epitope Mapping/methods
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/ultrastructure
- Models, Chemical
- Models, Immunological
- Models, Molecular
- Protein Binding
- Protein Conformation
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/ultrastructure
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Affiliation(s)
- Thomas Hoffmann
- Department of Biosciences and Center for Integrated Protein Science Munich,Technische Universität München, Freising-Weihenstephan, Germany
| | - Angela M. Krackhardt
- Medizinische Klinik III, Innere Medizin mit Schwerpunkt Hämatologie und Onkologie, Technische Universität München, Munich, Germany
- Clinical Cooperation Group, Antigen specific T cell therapy, Helmholtz Zentrum München (GmbH), German Center for Environmental Health, Munich, Germany
- German Cancer Consortium (DKTK), Munich, Germany
| | - Iris Antes
- Department of Biosciences and Center for Integrated Protein Science Munich,Technische Universität München, Freising-Weihenstephan, Germany
- * E-mail:
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21
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Westgeest KB, Bestebroer TM, Spronken MIJ, Gao J, Couzens L, Osterhaus ADME, Eichelberger M, Fouchier RAM, de Graaf M. Optimization of an enzyme-linked lectin assay suitable for rapid antigenic characterization of the neuraminidase of human influenza A(H3N2) viruses. J Virol Methods 2015; 217:55-63. [PMID: 25712563 DOI: 10.1016/j.jviromet.2015.02.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 02/06/2015] [Accepted: 02/16/2015] [Indexed: 10/24/2022]
Abstract
Antibodies to neuraminidase (NA), the second most abundant surface protein of the influenza virus, contribute to protection against influenza virus infection. Although traditional and miniaturized thiobarbituric acid (TBA) neuraminidase inhibition (NI) assays have been successfully used to characterize the antigenic properties of NA, these methods are cumbersome and not easily amendable to rapid screening. An additional difficulty of the NI assay is the interference by hemagglutinin (HA)-specific antibodies. To prevent interference of HA-specific antibodies, most NI assays are performed with recombinant viruses containing a mismatched HA. However, generation of these viruses is time consuming and unsuitable for large-scale surveillance. The feasibility of using the recently developed enzyme-linked lectin assay (ELLA) to evaluate the antigenic relatedness of NA of wild type A(H3N2) viruses was assessed. Rather than using recombinant viruses, wild type A(H3N2) viruses were used as antigen with ferret sera elicited against recombinant viruses with a mismatched HA. In this study, details of the critical steps that are needed to modify and optimize the NI ELLA in a format that is reproducible, highly sensitive, and useful for influenza virus surveillance to monitor antigenic drift of NA are provided.
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Affiliation(s)
- Kim B Westgeest
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Jin Gao
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Laura Couzens
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | | | - Maryna Eichelberger
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
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22
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Wan H, Yang H, Shore DA, Garten RJ, Couzens L, Gao J, Jiang L, Carney PJ, Villanueva J, Stevens J, Eichelberger MC. Structural characterization of a protective epitope spanning A(H1N1)pdm09 influenza virus neuraminidase monomers. Nat Commun 2015; 6:6114. [PMID: 25668439 PMCID: PMC4347215 DOI: 10.1038/ncomms7114] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 12/18/2014] [Indexed: 11/28/2022] Open
Abstract
A(H1N1)pdm09 influenza A viruses predominated in the 2013–2014 USA influenza season, and although most of these viruses remain sensitive to Food and Drug Administration-approved neuraminidase (NA) inhibitors, alternative therapies are needed. Here we show that monoclonal antibody CD6, selected for binding to the NA of the prototypic A(H1N1)pdm09 virus, A/California/07/2009, protects mice against lethal virus challenge. The crystal structure of NA in complex with CD6 Fab reveals a unique epitope, where the heavy-chain complementarity determining regions (HCDRs) 1 and 2 bind one NA monomer, the light-chain CDR2 binds the neighbouring monomer, whereas HCDR3 interacts with both monomers. This 30-amino-acid epitope spans the lateral face of an NA dimer and is conserved among circulating A(H1N1)pdm09 viruses. These results suggest that the large, lateral CD6 epitope may be an effective target of antibodies selected for development as therapeutic agents against circulating H1N1 influenza viruses. Neuraminidase inhibitors offer a line of defence against flu infections, but resistance can occur even in the absence of prior exposure. Here Wan et al. describe the mode of action of CD6, a monoclonal antibody that protects against a common influenza strain, as a new therapeutic intervention model.
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Affiliation(s)
- Hongquan Wan
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, USA
| | - Hua Yang
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30333, USA
| | - David A Shore
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30333, USA
| | - Rebecca J Garten
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30333, USA
| | - Laura Couzens
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, USA
| | - Jin Gao
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, USA
| | - Lianlian Jiang
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, USA
| | - Paul J Carney
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30333, USA
| | - Julie Villanueva
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30333, USA
| | - James Stevens
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30333, USA
| | - Maryna C Eichelberger
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, USA
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23
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Abstract
Peptide antibodies recognize epitopes with amino acid residues adjacent in sequence ("linear" epitopes). Such antibodies can be made to virtually any sequence and have been immensely important in all areas of molecular biology and diagnostics due to their versatility and to the rapid growth in protein sequence information. Today, peptide antibodies can be routinely and rapidly made to large numbers of peptides, including peptides with posttranslationally modified residues, and are used for immunoblotting, immunocytochemistry, immunohistochemistry, and immunoassays. In the future, peptide antibodies will continue to be immensely important for molecular biology, TCR- and MHC-like peptide antibodies may be produced routinely, peptide antibodies with predetermined conformational specificities may be designed, and peptide-based vaccines may become part of vaccination programs.
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Affiliation(s)
- Gunnar Houen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark.
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24
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Large scale characterization of the LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: a molecular dynamics simulation study. PLoS Comput Biol 2014; 10:e1003748. [PMID: 25101830 PMCID: PMC4125040 DOI: 10.1371/journal.pcbi.1003748] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/28/2014] [Indexed: 12/29/2022] Open
Abstract
The interplay between T cell receptors (TCRs) and peptides bound by major histocompatibility complexes (MHCs) is one of the most important interactions in the adaptive immune system. Several previous studies have computationally investigated their structural dynamics. On the basis of these simulations several structural and dynamical properties have been proposed as effectors of the immunogenicity. Here we present the results of a large scale Molecular Dynamics simulation study consisting of 100 ns simulations of 172 different complexes. These complexes consisted of all possible point mutations of the Epstein Barr Virus peptide FLRGRAYGL bound by HLA-B*08:01 and presented to the LC13 TCR. We compare the results of these 172 structural simulations with experimental immunogenicity data. We found that simulations with more immunogenic peptides and those with less immunogenic peptides are in fact highly similar and on average only minor differences in the hydrogen binding footprints, interface distances, and the relative orientation between the TCR chains are present. Thus our large scale data analysis shows that many previously suggested dynamical and structural properties of the TCR/peptide/MHC interface are unlikely to be conserved causal factors for peptide immunogenicity.
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25
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Single-domain antibodies targeting neuraminidase protect against an H5N1 influenza virus challenge. J Virol 2014; 88:8278-96. [PMID: 24829341 DOI: 10.1128/jvi.03178-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Influenza virus neuraminidase (NA) is an interesting target of small-molecule antiviral drugs. We isolated a set of H5N1 NA-specific single-domain antibodies (N1-VHHm) and evaluated their in vitro and in vivo antiviral potential. Two of them inhibited the NA activity and in vitro replication of clade 1 and 2 H5N1 viruses. We then generated bivalent derivatives of N1-VHHm by two methods. First, we made N1-VHHb by genetically joining two N1-VHHm moieties with a flexible linker. Second, bivalent N1-VHH-Fc proteins were obtained by genetic fusion of the N1-VHHm moiety with the crystallizable region of mouse IgG2a (Fc). The in vitro antiviral potency against H5N1 of both bivalent N1-VHHb formats was 30- to 240-fold higher than that of their monovalent counterparts, with 50% inhibitory concentrations in the low nanomolar range. Moreover, single-dose prophylactic treatment with bivalent N1-VHHb or N1-VHH-Fc protected BALB/c mice against a lethal challenge with H5N1 virus, including an oseltamivir-resistant H5N1 variant. Surprisingly, an N1-VHH-Fc fusion without in vitro NA-inhibitory or antiviral activity also protected mice against an H5N1 challenge. Virus escape selection experiments indicated that one amino acid residue close to the catalytic site is required for N1-VHHm binding. We conclude that single-domain antibodies directed against influenza virus NA protect against H5N1 virus infection, and when engineered with a conventional Fc domain, they can do so in the absence of detectable NA-inhibitory activity. IMPORTANCE Highly pathogenic H5N1 viruses are a zoonotic threat. Outbreaks of avian influenza caused by these viruses occur in many parts of the world and are associated with tremendous economic loss, and these viruses can cause very severe disease in humans. In such cases, small-molecule inhibitors of the viral NA are among the few treatment options for patients. However, treatment with such drugs often results in the emergence of resistant viruses. Here we show that single-domain antibody fragments that are specific for NA can bind and inhibit H5N1 viruses in vitro and can protect laboratory mice against a challenge with an H5N1 virus, including an oseltamivir-resistant virus. In addition, plant-produced VHH fused to a conventional Fc domain can protect in vivo even in the absence of NA-inhibitory activity. Thus, NA of influenza virus can be effectively targeted by single-domain antibody fragments, which are amenable to further engineering.
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26
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Lu X, Liu F, Zeng H, Sheu T, Achenbach JE, Veguilla V, Gubareva LV, Garten R, Smith C, Yang H, Stevens J, Xu X, Katz JM, Tumpey TM. Evaluation of the antigenic relatedness and cross-protective immunity of the neuraminidase between human influenza A (H1N1) virus and highly pathogenic avian influenza A (H5N1) virus. Virology 2014; 454-455:169-75. [PMID: 24725943 DOI: 10.1016/j.virol.2014.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 01/29/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
Abstract
To determine the genetic and antigenic relatedness as well as the cross-protective immunity of human H1N1 and avian H5N1 influenza virus neuraminidase (NA), we immunized rabbits with either a baculovirus-expressed recombinant NA from A/Beijing/262/95 (BJ/262) H1N1 or A/Hong Kong/483/97 (HK/483) H5N1 virus. Cross-reactive antibody responses were evaluated by multiple serological assays and cross-protection against H5N1 virus challenge was evaluated in mice. In a neuraminidase inhibition (NI) test, the antisera exhibited substantial inhibition of NA activity of the homologous virus, but failed to inhibit the NA activity of heterologous virus. However, these antisera exhibited low levels of cross-reactivity measured by plaque size reduction, replication inhibition, single radial hemolysis, and ELISA assays. Passive immunization with HK/483 NA-specific antisera significantly reduced virus replication and disease, and afforded almost complete protection against lethal homologous virus challenge in mice. However, passive immunization with BJ/262 (H1N1) NA-specific antisera was ineffective at providing cross-protection against lethal H5N1 virus challenge and only slightly reduced weight loss. Substantial amino acid variation among the NA antigenic sites was observed between BJ/262 and HK/483 virus, which was consistent with the lack of cross-reactive NI activity by the antibody and limited cross-protective immunity in mice. These results show a strong correlation between the lack of cross-protective immunity and low structural similarities of NA from a human seasonal H1N1 virus and an avian H5N1 influenza virus.
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Affiliation(s)
- Xiuhua Lu
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Feng Liu
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Hui Zeng
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Tiffany Sheu
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Jenna E Achenbach
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Vic Veguilla
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Larisa V Gubareva
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Rebecca Garten
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Catherine Smith
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Hua Yang
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - James Stevens
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Xiyan Xu
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Jacqueline M Katz
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Terrence M Tumpey
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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27
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Addis PW, Hall CJ, Bruton S, Veverka V, Wilkinson IC, Muskett FW, Renshaw PS, Prosser CE, Carrington B, Lawson ADG, Griffin R, Taylor RJ, Waters LC, Henry AJ, Carr MD. Conformational heterogeneity in antibody-protein antigen recognition: implications for high affinity protein complex formation. J Biol Chem 2014; 289:7200-7210. [PMID: 24436329 DOI: 10.1074/jbc.m113.492215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Specific, high affinity protein-protein interactions lie at the heart of many essential biological processes, including the recognition of an apparently limitless range of foreign proteins by natural antibodies, which has been exploited to develop therapeutic antibodies. To mediate biological processes, high affinity protein complexes need to form on appropriate, relatively rapid timescales, which presents a challenge for the productive engagement of complexes with large and complex contact surfaces (∼600-1800 Å(2)). We have obtained comprehensive backbone NMR assignments for two distinct, high affinity antibody fragments (single chain variable and antigen-binding (Fab) fragments), which recognize the structurally diverse cytokines interleukin-1β (IL-1β, β-sheet) and interleukin-6 (IL-6, α-helical). NMR studies have revealed that the hearts of the antigen binding sites in both free anti-IL-1β Fab and anti-IL-6 single chain variable exist in multiple conformations, which interconvert on a timescale comparable with the rates of antibody-antigen complex formation. In addition, we have identified a conserved antigen binding-induced change in the orientation of the two variable domains. The observed conformational heterogeneity and slow dynamics at protein antigen binding sites appears to be a conserved feature of many high affinity protein-protein interfaces structurally characterized by NMR, suggesting an essential role in protein complex formation. We propose that this behavior may reflect a soft capture, protein-protein docking mechanism, facilitating formation of high affinity protein complexes on a timescale consistent with biological processes.
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Affiliation(s)
- Philip W Addis
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Catherine J Hall
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Shaun Bruton
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Vaclav Veverka
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Ian C Wilkinson
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Frederick W Muskett
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Philip S Renshaw
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Christine E Prosser
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom; Research and Development, UCB, Slough SL1 3WE, United Kingdom
| | | | | | - Robert Griffin
- Research and Development, UCB, Slough SL1 3WE, United Kingdom
| | | | - Lorna C Waters
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom.
| | | | - Mark D Carr
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom.
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28
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An eight-segment swine influenza virus harboring H1 and H3 hemagglutinins is attenuated and protective against H1N1 and H3N2 subtypes in pigs. J Virol 2013; 87:10114-25. [PMID: 23843633 DOI: 10.1128/jvi.01348-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Swine influenza virus (SIV) infections continue to cause production losses in the agricultural industry in addition to being a human public health concern. The primary method of controlling SIV is through vaccination. The killed SIV vaccines currently in use must be closely matched to the challenge virus, and their protective efficacy is limited. Live attenuated influenza vaccines (LAIV) provide strong, long-lived cell-mediated and humoral immunity against different influenza virus subtypes with no need for antigen matching. Here we report the generation of a new potential LAIV, an eight-segment SIV harboring two different SIV hemagglutinins (HAs), H1 and H3, in the genetic background of H1N1 SIV. This mutant SIV was generated by fusing the H3 HA ectodomain from A/Swine/Texas/4199-2/98 (H3N2) to the cytoplasmic tail, transmembrane domain, and stalk region of neuraminidase (NA) from A/Swine/Saskatchewan/18789/02 (H1N1) SIV. While this H1-H3 chimeric SIV, when propagated in vitro in the presence of exogenous neuraminidase, showed kinetics and growth properties similar to those of the parental wild-type virus, in vivo it was highly attenuated in pigs, demonstrating a great potential for serving as a dual LAIV. Furthermore, vaccination with the H1-H3 virus elicited robust immune responses, which conferred complete protection against infections with both H1 and H3 SIV subtypes in pigs.
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29
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Dunbar J, Fuchs A, Shi J, Deane CM. ABangle: characterising the VH-VL orientation in antibodies. Protein Eng Des Sel 2013; 26:611-20. [DOI: 10.1093/protein/gzt020] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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30
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Doyle TM, Jaentschke B, Van Domselaar G, Hashem AM, Farnsworth A, Forbes NE, Li C, Wang J, He R, Brown EG, Li X. The universal epitope of influenza A viral neuraminidase fundamentally contributes to enzyme activity and viral replication. J Biol Chem 2013; 288:18283-9. [PMID: 23645684 DOI: 10.1074/jbc.m113.468884] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The only universally conserved sequence among all influenza A viral neuraminidases is located between amino acids 222 and 230. However, the potential roles of these amino acids remain largely unknown. Through an array of experimental approaches including mutagenesis, reverse genetics, and growth kinetics, we found that this sequence could markedly affect viral replication. Additional experiments revealed that enzymes with mutations in this region demonstrated substantially decreased catalytic activity, substrate binding, and thermostability. Consistent with viral replication analyses and enzymatic studies, protein modeling suggests that these amino acids could either directly bind to the substrate or contribute to the formation of the active site in the enzyme. Collectively, these findings reveal the essential role of this unique region in enzyme function and viral growth, which provides the basis for evaluating the validity of this sequence as a potential target for antiviral intervention and vaccine development.
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Affiliation(s)
- Tracey M Doyle
- Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario K1A 0K9, Canada
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31
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Rudraraju R, Jones BG, Sealy R, Surman SL, Hurwitz JL. Respiratory syncytial virus: current progress in vaccine development. Viruses 2013; 5:577-94. [PMID: 23385470 PMCID: PMC3640515 DOI: 10.3390/v5020577] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/01/2013] [Accepted: 02/04/2013] [Indexed: 12/18/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the etiological agent for a serious lower respiratory tract disease responsible for close to 200,000 annual deaths worldwide. The first infection is generally most severe, while re-infections usually associate with a milder disease. This observation and the finding that re-infection risks are inversely associated with neutralizing antibody titers suggest that immune responses generated toward a first RSV exposure can significantly reduce morbidity and mortality throughout life. For more than half a century, researchers have endeavored to design a vaccine for RSV that can mimic or improve upon natural protective immunity without adverse events. The virus is herein described together with the hurdles that must be overcome to develop a vaccine and some current vaccine development approaches.
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Affiliation(s)
- Rajeev Rudraraju
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; E-Mails: (R.R.); (B.J.); (R.S.); (S.S.)
| | - Bart G. Jones
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; E-Mails: (R.R.); (B.J.); (R.S.); (S.S.)
| | - Robert Sealy
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; E-Mails: (R.R.); (B.J.); (R.S.); (S.S.)
| | - Sherri L. Surman
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; E-Mails: (R.R.); (B.J.); (R.S.); (S.S.)
| | - Julia L. Hurwitz
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; E-Mails: (R.R.); (B.J.); (R.S.); (S.S.)
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN 38163, USA
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Tong H, Zhang L, Kaspar A, Rames MJ, Huang L, Woodnutt G, Ren G. Peptide-conjugation induced conformational changes in human IgG1 observed by optimized negative-staining and individual-particle electron tomography. Sci Rep 2013; 3:1089. [PMID: 23346347 PMCID: PMC3549606 DOI: 10.1038/srep01089] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 12/11/2012] [Indexed: 12/20/2022] Open
Abstract
Peptides show much promise as potent and selective drug candidates. Fusing peptides to a scaffold monoclonal antibody produces a conjugated antibody which has the advantages of peptide activity yet also has the pharmacokinetics determined by the scaffold antibody. However, the conjugated antibody often has poor binding affinity to antigens that may be related to unknown structural changes. The study of the conformational change is difficult by conventional techniques because structural fluctuation under equilibrium results in multiple structures co-existing. Here, we employed our two recently developed electron microscopy (EM) techniques: optimized negative-staining (OpNS) EM and individual-particle electron tomography (IPET). Two-dimensional (2D) image analyses and three-dimensional (3D) maps have shown that the domains of antibodies present an elongated peptide-conjugated conformational change, suggesting that our EM techniques may be novel tools to monitor the structural conformation changes in heterogeneous and dynamic macromolecules, such as drug delivery vehicles after pharmacological synthesis and development.
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Affiliation(s)
- Huimin Tong
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049, China
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Sela-Culang I, Alon S, Ofran Y. A systematic comparison of free and bound antibodies reveals binding-related conformational changes. THE JOURNAL OF IMMUNOLOGY 2012; 189:4890-9. [PMID: 23066154 DOI: 10.4049/jimmunol.1201493] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
To study structural changes that occur in Abs upon Ag binding, we systematically compared free and bound structures of all 141 crystal structures of the 49 Abs that were solved in these two forms. We found that many structural changes occur far from the Ag binding site. Some of them may constitute a mechanism for the recently suggested allosteric effects in Abs. Within the binding site itself, CDR-H3 is the only element that shows significant binding-related conformational changes; however, this occurs in only one third of the Abs. Beyond the binding site, Ag binding is associated with changes in the relative orientation of the H and L chains in both the variable and constant domains. An even larger change occurs in the elbow angle between the variable and the constant domains, and it is significantly larger for binding of big Ags than for binding of small ones. The most consistent and substantial conformational changes occur in a loop in the H chain constant domain. This loop is implicated in the interaction between the H and L chains, is often intrinsically disordered, and is involved in complement binding. Hence, we suggest that it may have a role in Ab function. These findings provide structural insight into the recently proposed allosteric effects in Abs.
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Westgeest KB, de Graaf M, Fourment M, Bestebroer TM, van Beek R, Spronken MIJ, de Jong JC, Rimmelzwaan GF, Russell CA, Osterhaus ADME, Smith GJD, Smith DJ, Fouchier RAM. Genetic evolution of the neuraminidase of influenza A (H3N2) viruses from 1968 to 2009 and its correspondence to haemagglutinin evolution. J Gen Virol 2012; 93:1996-2007. [PMID: 22718569 DOI: 10.1099/vir.0.043059-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Each year, influenza viruses cause epidemics by evading pre-existing humoral immunity through mutations in the major glycoproteins: the haemagglutinin (HA) and the neuraminidase (NA). In 2004, the antigenic evolution of HA of human influenza A (H3N2) viruses was mapped (Smith et al., Science 305, 371-376, 2004) from its introduction in humans in 1968 until 2003. The current study focused on the genetic evolution of NA and compared it with HA using the dataset of Smith and colleagues, updated to the epidemic of the 2009/2010 season. Phylogenetic trees and genetic maps were constructed to visualize the genetic evolution of NA and HA. The results revealed multiple reassortment events over the years. Overall rates of evolutionary change were lower for NA than for HA1 at the nucleotide level. Selection pressures were estimated, revealing an abundance of negatively selected sites and sparse positively selected sites. The differences found between the evolution of NA and HA1 warrant further analysis of the evolution of NA at the phenotypic level, as has been done previously for HA.
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Affiliation(s)
- Kim B Westgeest
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Miranda de Graaf
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.,Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Mathieu Fourment
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Theo M Bestebroer
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Ruud van Beek
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Monique I J Spronken
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Jan C de Jong
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Guus F Rimmelzwaan
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Colin A Russell
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | | | - Gavin J D Smith
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Derek J Smith
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.,Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Department of Virology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
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Stray SJ, Pittman LB. Subtype- and antigenic site-specific differences in biophysical influences on evolution of influenza virus hemagglutinin. Virol J 2012; 9:91. [PMID: 22569196 PMCID: PMC3499391 DOI: 10.1186/1743-422x-9-91] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 04/10/2012] [Indexed: 11/14/2022] Open
Abstract
Background Influenza virus undergoes rapid evolution by both antigenic shift and antigenic drift. Antibodies, particularly those binding near the receptor-binding site of hemagglutinin (HA) or the neuraminidase (NA) active site, are thought to be the primary defense against influenza infection, and mutations in antibody binding sites can reduce or eliminate antibody binding. The binding of antibodies to their cognate antigens is governed by such biophysical properties of the interacting surfaces as shape, non-polar and polar surface area, and charge. Methods To understand forces shaping evolution of influenza virus, we have examined HA sequences of human influenza A and B viruses, assigning each amino acid values reflecting total accessible surface area, non-polar and polar surface area, and net charge due to the side chain. Changes in each of these values between neighboring sequences were calculated for each residue and mapped onto the crystal structures. Results Areas of HA showing the highest frequency of pairwise changes agreed well with previously identified antigenic sites in H3 and H1 HAs, and allowed us to propose more detailed antigenic maps and novel antigenic sites for H1 and influenza B HA. Changes in biophysical properties differed between HAs of different subtypes, and between different antigenic sites of the same HA. For H1, statistically significant differences in several biophysical quantities compared to residues lying outside antigenic sites were seen for some antigenic sites but not others. Influenza B antigenic sites all show statistically significant differences in biophysical quantities for all antigenic sites, whereas no statistically significant differences in biophysical quantities were seen for any antigenic site is seen for H3. In many cases, residues previously shown to be under positive selection at the genetic level also undergo rapid change in biophysical properties. Conclusions The biophysical consequences of amino acid changes introduced by antigenic drift vary from subtype to subtype, and between different antigenic sites. This suggests that the significance of antibody binding in selecting new variants may also be variable for different antigenic sites and influenza subtypes.
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Affiliation(s)
- Stephen J Stray
- Department of Microbiology, University of Mississippi Medical Center, 2500 N State St, Jackson, MS 39216, USA.
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36
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Johansson BE, Cox MMJ. Influenza viral neuraminidase: the forgotten antigen. Expert Rev Vaccines 2012; 10:1683-95. [PMID: 22085172 DOI: 10.1586/erv.11.130] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Influenza is the most common cause of vaccine-preventable morbidity and mortality despite the availability of the conventional trivalent inactivated vaccine and the live-attenuated influenza vaccine. These vaccines induce an immunity dominated by the response to hemagglutinin (HA) and are most effective when there is sufficient antigenic relatedness between the vaccine strain and the HA of the circulating wild-type virus. Vaccine strategies against influenza may benefit from inclusion of other viral antigens in addition to HA. Epidemiologic evidence and studies in animals and humans indicate that anti-neuraminidase (NA) immunity will provide protection against severe illness or death in the event of a significant antigenic change in the HA component of the vaccine. However, there is little NA immunity induced by trivalent inactivated vaccine and live-attenuated influenza vaccine. The quantity of NA in influenza vaccines is not standardized and varies significantly among manufacturers, production lots and tested strains. The activity and stability of the NA enzyme is influenced by concentration of divalent cations. If immunity against NA is desirable, a better understanding of how the enzymatic properties affect the immunogenicity is needed.
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Affiliation(s)
- Bert E Johansson
- Department of Pediatrics, Texas Tech University Health Sciences Center, Paul H Foster School of Medicine and El Paso Children?s Hospital, 4825 Alameda Avenue El Paso, TX 79905, USA.
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37
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Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint. Structure 2012; 20:259-69. [DOI: 10.1016/j.str.2011.11.016] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 11/22/2011] [Accepted: 11/22/2011] [Indexed: 11/18/2022]
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38
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Mancini N, Solforosi L, Clementi N, De Marco D, Clementi M, Burioni R. A potential role for monoclonal antibodies in prophylactic and therapeutic treatment of influenza. Antiviral Res 2011; 92:15-26. [DOI: 10.1016/j.antiviral.2011.07.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/19/2011] [Accepted: 07/12/2011] [Indexed: 10/17/2022]
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Mapping of protein-protein interaction sites in the plant-type [2Fe-2S] ferredoxin. PLoS One 2011; 6:e21947. [PMID: 21760931 PMCID: PMC3132287 DOI: 10.1371/journal.pone.0021947] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 06/13/2011] [Indexed: 11/19/2022] Open
Abstract
Knowing the manner of protein-protein interactions is vital for understanding biological events. The plant-type [2Fe-2S] ferredoxin (Fd), a well-known small iron-sulfur protein with low redox potential, partitions electrons to a variety of Fd-dependent enzymes via specific protein-protein interactions. Here we have refined the crystal structure of a recombinant plant-type Fd I from the blue green alga Aphanothece sacrum (AsFd-I) at 1.46 Å resolution on the basis of the synchrotron radiation data. Incorporating the revised amino-acid sequence, our analysis corrects the 3D structure previously reported; we identified the short α-helix (67-71) near the active center, which is conserved in other plant-type [2Fe-2S] Fds. Although the 3D structures of the four molecules in the asymmetric unit are similar to each other, detailed comparison of the four structures revealed the segments whose conformations are variable. Structural comparison between the Fds from different sources showed that the distribution of the variable segments in AsFd-I is highly conserved in other Fds, suggesting the presence of intrinsically flexible regions in the plant-type [2Fe-2S] Fd. A few structures of the complexes with Fd-dependent enzymes clearly demonstrate that the protein-protein interactions are achieved through these variable regions in Fd. The results described here will provide a guide for interpreting the biochemical and mutational studies that aim at the manner of interactions with Fd-dependent enzymes.
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Sultana I, Gao J, Markoff L, Eichelberger MC. Influenza neuraminidase-inhibiting antibodies are induced in the presence of zanamivir. Vaccine 2011; 29:2601-6. [DOI: 10.1016/j.vaccine.2011.01.047] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 12/31/2010] [Accepted: 01/18/2011] [Indexed: 10/18/2022]
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Abhinandan KR, Martin ACR. Analysis and prediction of VH/VL packing in antibodies. Protein Eng Des Sel 2010; 23:689-97. [PMID: 20591902 DOI: 10.1093/protein/gzq043] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The packing of V(H) and V(L) domains in antibodies can vary, influencing the topography of the antigen-combining site. However, until recently, this has largely been ignored in modelling antibody structure. We present an analysis of the degree of variability observed in known structures together with a machine-learning approach to predict the packing angle. A neural network was trained on sets of interface residues and a genetic algorithm designed to perform 'feature selection' to define which sets of interface residues could be used most successfully to perform the prediction. While this training procedure was very computationally intensive, prediction is performed in a matter of seconds. Thus, not only do we provide a rapid method for predicting the packing angle, but also we define a set of residues that may be important in antibody humanization in order to obtain the correct binding site topography.
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Affiliation(s)
- K R Abhinandan
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK
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43
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Kondo A, Takamatsu H, Katoh S, Sada E. Adsorption equilibrium in immunoaffnity chromatography with antibodies to synthetic peptides. Biotechnol Bioeng 2010; 35:146-51. [PMID: 18592504 DOI: 10.1002/bit.260350206] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The effects of charged residues in peptide antigens on the binding characteristics of polyclonal antipeptide antibodies were studied using immunoadsorbents prepared by coupling the antibodies to CNBr-activated Sepharose 4B. Among the antipeptide antibodies, an antibody to the peptide without charged residues showed the most stable interaction with the peptide to the changes in pH. Conversely, the binding affinity of antibodies to the pep-tides with histidine residues having a unique pKa value of 6.0 decreased steeply with pH at around 6.0. The binding affinity of an antibody to the peptide with many charged residues decreased steeply with an increase in the ionic strength (adjusted by NaCl). Since circular dichroism (CD) spectrum measurements indicate that these peptides show disordered structures in the pH range of adsorption measurement, the dependence of peptide-antibody interaction on environmental conditions is attributed to the characteristics of side chains of the peptides. These results indicate that the dependence of the binding affinity of antipeptide antibodies on pH and the ionic strength is dominantly affected by the number and the pKa values of charged residues in the peptides.
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Affiliation(s)
- A Kondo
- Chemical Engineering Department, Kyoto University, Kyoto 606, Japan
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Malik A, Firoz A, Jha V, Sunderasan E, Ahmad S. Modeling the three-dimensional structures of an unbound single-chain variable fragment (scFv) and its hypothetical complex with a Corynespora cassiicola toxin, cassiicolin. J Mol Model 2010; 16:1883-93. [DOI: 10.1007/s00894-010-0680-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 01/26/2010] [Indexed: 02/02/2023]
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Comparison of the results obtained by ELISA and surface plasmon resonance for the determination of antibody affinity. J Immunol Methods 2009; 352:13-22. [PMID: 19854197 DOI: 10.1016/j.jim.2009.10.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 09/22/2009] [Accepted: 10/08/2009] [Indexed: 11/22/2022]
Abstract
The aim of this study was to compare the affinity values obtained for a monoclonal antibody/antigen complex using two different techniques, surface plasmon resonance (SPR) and an enzyme linked immunosorbent assay (ELISA) approach recently described by Bobrovnik S.A. and by Stevens F.J. These two techniques can be used in particular to determine the equilibrium dissociation constant, K(D), of the complex in solution or on a surface. Bobrovnik's method gives two K(D) values that differ by a factor of 100, demonstrating that two populations of complexes are present in solution. In an initial step, one protein binds relatively weakly to the other (high K(D)) and this is followed by a conformational change in the most flexible portion of the antigen, which increases the affinity (low K(D)). Only the higher of the two K(D) values can be detected when complex formation in solution is investigated using SPR, because the interaction measured concerns the fibronectin/antibody complexes of lowest affinity. In contrast, when measuring association at the sensor surface, SPR gives an average result between the two K(D) values because complexes corresponding to both affinities can form in this situation. The constants that characterise the kinetics of the fibronectin-antibody interaction obtained by SPR and ELISA are therefore different, because the methods do not allow the same phenomena to be observed. However they are consistent and complementary.
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Affiliation(s)
- Peter M. Colman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia 3050;
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47
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Crystal structure of the engineered neutralizing antibody M18 complexed to domain 4 of the anthrax protective antigen. J Mol Biol 2009; 387:680-93. [PMID: 19361425 DOI: 10.1016/j.jmb.2009.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 02/03/2009] [Accepted: 02/03/2009] [Indexed: 11/24/2022]
Abstract
The virulence of Bacillus anthracis is critically dependent on the cytotoxic components of the anthrax toxin, lethal factor (LF) and edema factor (EF). LF and EF gain entry into host cells through interactions with the protective antigen (PA), which binds to host cellular receptors such as CMG2. Antibodies that neutralize PA have been shown to confer protection in animal models and are undergoing intense clinical development. A murine monoclonal antibody, 14B7, has been reported to interact with domain 4 of PA (PAD4) and block its binding to CMG2. More recently, the 14B7 antibody was used as the platform for the selection of very high affinity, single-chain antibodies that have tremendous potential as a combination anthrax prophylactic and treatment. Here, we report the high-resolution X-ray structures of three high-affinity, single-chain antibodies in the 14B7 family; 14B7 and two high-affinity variants 1H and M18. In addition, we present the first neutralizing antibody-PA structure, M18 in complex with PAD4 at 3.8 A resolution. These structures provide insights into the mechanism of neutralization, and the effect of various mutations on antibody affinity, and enable a comparison between the binding of the M18 antibody and CMG2 with PAD4.
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Sugrue RJ, Tan BH, Yeo DSY, Sutejo R. Antiviral Drugs for the Control of Pandemic Influenza Virus. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2008. [DOI: 10.47102/annals-acadmedsg.v37n6p518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the advent of an influenza virus pandemic it is likely that the administration of antiviral drugs will be an important first line of defence against the virus. The drugs currently in use are effective against seasonal influenza virus infection, and some cases have been used in the treatment of patients infected with the avian H5N1 influenza virus. However, it is becoming clear that the emergence of drug-resistant viruses will potentially be a major problem in the future efforts to control influenza virus infection. In addition, during a new pandemic, sufficient quantities of these agents will need to be distributed to many different parts of the world, possibly at short notice. In this review we provide an overview of some of the drugs that are currently available for the treatment and prevention of influenza virus infection. In addition, basic research on influenza virus is providing a much better understanding of the biology of the virus, which is offering the possibility of new anti-influenza virus drugs. We therefore also review some new antiviral strategies that are being reported in the scientific literature, which may form the basis of the next generation of antiviral strategies during a future influenza virus pandemic.
Key words: Antiviral, Amantadine, Pandemic influenza virus, Oseltamivir, siRNA
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Nakajima S, Nakajima K, Nobusawa E, Zhao J, Tanaka S, Fukuzawa K. Comparison of epitope structures of H3HAs through protein modeling of influenza A virus hemagglutinin: mechanism for selection of antigenic variants in the presence of a monoclonal antibody. Microbiol Immunol 2008; 51:1179-87. [PMID: 18094536 DOI: 10.1111/j.1348-0421.2007.tb04013.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Starting with nine plaques of influenza A/Kamata/14/91(H3N2) virus, we selected mutants in the presence of monoclonal antibody 203 (mAb203). In total, amino acid substitutions were found at nine positions (77, 80, 131, 135, 141, 142, 143, 144 and 146), which localized in the antigenic site A of the hemagglutinin (HA). The escape mutants differed in the extent to which they had lost binding to mAb203. HA protein with substitutions of some amino acid residues created by site-directed mutagenesis in the escape mutants retained the ability to bind to mAb203. Changes in the amino acid character affecting charge or hydrophobicity accounted for the binding capacity to the antibody of the HA with most of the substitutions in the escape mutants and binding-positive mutants. However, the effect of some amino acid substitutions remained unexplained. A three-dimensional model of the 1991 HA was constructed and used to analyze substituted amino acids in these mutants for the accessible surface hydrophobic and hydrophilic characters. One amino acid substitution in an escape mutant and another amino acid substitution in a binding-positive mutant seemed to be explained by the changes noted on this model.
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Affiliation(s)
- Setsuko Nakajima
- Department of Virology, Medical School, Nagoya City University, Mizuho-ku, Aichi, Japan.
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50
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