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Long C, Wu F, Lu Q, Xie B, Shen C, Li J, Deng Y, Liang P, Yu Y, Lai R. A Strategy for Efficient Preparation of Genus-Specific Diagnostic Antibodies for Snakebites. Front Immunol 2021; 12:775678. [PMID: 34899734 PMCID: PMC8660121 DOI: 10.3389/fimmu.2021.775678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
As said by former United Nations Secretary-General Kofi Annan, "Snakebite is the most important tropical disease you've never heard of." Listed as a priority neglected tropical disease by the World Health Organization, snakebite envenoming (SBE) kills in excess of 125,000 people per year. However, due to the complexity and overlap of snake venom compositions, few reliable venom diagnostic methods for genus-/species-specific identification, which is crucial for successful SBE therapy, are available. Here, we develop a strategy to select and prepare genus-specific snake venom antibodies, which allows rapid and efficient clinical diagnosis of snakebite. Multi-omics approaches are used to choose candidate antigens from snake venoms and identify genus-specific antigenic epitope peptide fragments (GSAEPs) with ideal immunogenicity, specificity, and spatial accessibility. Double-antibody sandwich ELISA kit was established by matching a polyclonal antibody against a natural antigen and a monoclonal antibody that was prepared by natural protein as antigen and can specifically target the GSAEPs. The kit shows the ability to accurately identify venoms from similar genera of Trimeresurus and Protobothrops with a detection limit of 6.25 ng/ml on the snake venoms and a little cross-reaction, thus proving high feasibility and applicability.
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Affiliation(s)
- Chengbo Long
- Key Laboratory of Animal Models and Human Disease Mechanisms, Key Laboratory of Bioactive Peptides of Yunnan Province, Engineering Laboratory of Bioactive Peptides, The National & Local Joint Engineering Center of Natural bioactive Peptides, Kunming Institute of Zoology-The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Feilong Wu
- Key Laboratory of Animal Models and Human Disease Mechanisms, Key Laboratory of Bioactive Peptides of Yunnan Province, Engineering Laboratory of Bioactive Peptides, The National & Local Joint Engineering Center of Natural bioactive Peptides, Kunming Institute of Zoology-The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Qiumin Lu
- Key Laboratory of Animal Models and Human Disease Mechanisms, Key Laboratory of Bioactive Peptides of Yunnan Province, Engineering Laboratory of Bioactive Peptides, The National & Local Joint Engineering Center of Natural bioactive Peptides, Kunming Institute of Zoology-The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Bing Xie
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Chuanbin Shen
- Department of Laboratory Medicine, Li Ka Shing Knowledge Institute (LKSKI)-Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - Jiayao Li
- Clinical Laboratory, Hospital of Traditional Chinese Medicine of Wuzhou, Wuzhou, China
| | - Yanling Deng
- Clinical Laboratory, Hospital of Traditional Chinese Medicine of Wuzhou, Wuzhou, China
| | - Ping Liang
- Clinical Laboratory, Hospital of Traditional Chinese Medicine of Wuzhou, Wuzhou, China
| | - Yongzhi Yu
- Clinical Laboratory, Hospital of Traditional Chinese Medicine of Wuzhou, Wuzhou, China
| | - Ren Lai
- Key Laboratory of Animal Models and Human Disease Mechanisms, Key Laboratory of Bioactive Peptides of Yunnan Province, Engineering Laboratory of Bioactive Peptides, The National & Local Joint Engineering Center of Natural bioactive Peptides, Kunming Institute of Zoology-The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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2
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Schein CH, Levine CB, McLellan SLF, Negi SS, Braun W, Dreskin SC, Anaya ES, Schmidt J. Synthetic proteins for COVID-19 diagnostics. Peptides 2021; 143:170583. [PMID: 34087220 PMCID: PMC8168367 DOI: 10.1016/j.peptides.2021.170583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022]
Abstract
There is an urgent need for inexpensive, rapid and specific antigen-based assays to test for vaccine efficacy and detect infection with SARS-CoV-2 and its variants. We have identified a small, synthetic protein (JS7), representing a region of maximum variability within the receptor binding domain (RBD), which binds antibodies in sera from nine patients with PCR-verified COVID-19 of varying severity. Antibodies binding to either JS7 or the SARS-CoV-2 recombinant RBD, as well as those that disrupt binding between a fragment of the ACE2 receptor and the RBD, are proportional to disease severity and clinical outcome. Binding to JS7 was inhibited by linear peptides from the RBD interface with ACE2. Variants of JS7, such as E484K or N501Y, can be quickly synthesized in pure form in large quantities by automated methods. JS7 and related synthetic antigens can provide a basis for specific diagnostics for SARS-CoV-2 infections.
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Affiliation(s)
- Catherine H Schein
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States; Institute for Human Infections and immunity (IHII), The University of Texas Medical Branch, Galveston, TX, United States.
| | - Corri B Levine
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
| | - Susan L F McLellan
- Department of Internal medicine - Infectious Diseases, The University of Texas Medical Branch, Galveston, TX, United States
| | - Surendra S Negi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Werner Braun
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States; Institute for Human Infections and immunity (IHII), The University of Texas Medical Branch, Galveston, TX, United States; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Stephen C Dreskin
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, United States
| | - Elizabeth S Anaya
- B-11 Bioenergy and Biome Sciences, Bioscience Division Los Alamos National Laboratory, Los Alamos, NM, 87545, United States
| | - Jurgen Schmidt
- B-11 Bioenergy and Biome Sciences, Bioscience Division Los Alamos National Laboratory, Los Alamos, NM, 87545, United States
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3
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Read CM, Plante K, Rafael G, Rossi SL, Braun W, Weaver SC, Schein CH. Designing multivalent immunogens for alphavirus vaccine optimization. Virology 2021; 561:117-124. [PMID: 33823988 DOI: 10.1016/j.virol.2020.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/15/2020] [Accepted: 11/22/2020] [Indexed: 11/16/2022]
Abstract
There is a pressing need for vaccines against mosquito-borne alphaviruses such as Venezualen and eastern equine encephalitis viruses (VEEV, EEEV). We demonstrate an approach to vaccine development based on physicochemical properties (PCP) of amino acids to design a PCP-consensus sequence of the epitope-rich B domain of the VEEV major antigenic E2 protein. The consensus "spike" domain was incorporated into a live-attenuated VEEV vaccine candidate (ZPC/IRESv1). Mice inoculated with either ZPC/IRESv1 or the same virus containing the consensus E2 protein fragment (VEEVconE2) were protected against lethal challenge with VEEV strains ZPC-738 and 3908, and Mucambo virus (MUCV, related to VEEV), and had comparable neutralizing antibody titers against each virus. Both vaccines induced partial protection against Madariaga virus (MADV), a close relative of EEEV, lowering mortality from 60% to 20%. Thus PCP-consensus sequences can be integrated into a replicating virus that could, with further optimization, provide a broad-spectrum vaccine against encephalitic alphaviruses.
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Affiliation(s)
- C M Read
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Kenneth Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity (IHII), University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Grace Rafael
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Shannan L Rossi
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Department of Pathology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity (IHII), University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Werner Braun
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity (IHII), University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA
| | - Catherine H Schein
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity (IHII), University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555, USA.
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4
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Yang YJ, Mai DJ, Li S, Morris MA, Olsen BD. Tuning Selective Transport of Biomolecules through Site-Mutated Nucleoporin-like Protein (NLP) Hydrogels. Biomacromolecules 2021; 22:289-298. [PMID: 33428378 DOI: 10.1021/acs.biomac.0c01083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Natural selective filtering systems (e.g., the extracellular matrix, nuclear pores, and mucus) separate molecules selectively and efficiently, and the detailed understanding of transport mechanisms exploited in these systems provides important bioinspired design principles for selective filters. In particular, nucleoporins consist of consensus repeat sequences that are readily utilized for engineering repeat proteins. Here, the consensus repeat sequence of Nsp1, a yeast nucleoporin, is polymerized to form a nucleoporin-like protein (NLP) and mutated to understand the effect of sequence on selective transport. The hydrophilic spacers of the NLPs were redesigned considering net charge, charge distribution, and polarity. Mutations were made near to and far from the FSFG interacting domain to explore the role of highly conserved residues as a function of spatial proximity. A nuclear transport receptor-cargo complex, nuclear transport factor 2-green fluorescent protein (NTF2-GFP), was used as a model for changes in transport. For mutations of the charged spacer, some mutations of highly conserved charged residues were possible without knocking out selective transport of the NTF2, but the formation of regions of clustered negative charge has an unfavorable effect on nuclear transporter permeation. Thus, positive net charge and alternating positive and negative charge within the hydrophilic spacer are advantageous for recognition and selective transport. In the polarity panel, mutations that increased the interaction between NTF2-GFP and the gel led to decreased permeation of the NTF2-GFP due to blocking of the interface and inability of the NTF2-GFP to transport into the gel. Therefore, these results provide a strategy for tuning selective permeability of biomolecules using the artificially designed consensus repeat-based hydrogels.
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Affiliation(s)
- Yun Jung Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Biological Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Danielle J Mai
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Shuaili Li
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Melody A Morris
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bradley D Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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5
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Baker WS, Negi S, Braun W, Schein CH. Producing physicochemical property consensus alphavirus protein antigens for broad spectrum vaccine design. Antiviral Res 2020; 182:104905. [PMID: 32800880 DOI: 10.1016/j.antiviral.2020.104905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/19/2020] [Accepted: 08/01/2020] [Indexed: 12/16/2022]
Abstract
There is a pressing need for new vaccines against alphaviruses, which can cause fatal encephalitis (Venezuelan equine encephalitis virus (VEEV) and others) and severe arthralgia (e.g. Chikungunya virus, CHIKV). These positive-strand RNA viruses are diverse and evolve rapidly, meaning that the sequence of any vaccine should cover multiple strains that may be quite different from any previous isolate. Here, consensus proteins were produced to represent the common physicochemical properties (PCPs) of the epitope rich, B domain of the E2 envelope protein. PCP-consensus proteins were based on multiple strains of VEEV (VEEVcon) and CHIKV (CHIKVcon) or the conserved PCPs of 24 different alphaviruses (AllAVcon). The AllAVcon was altered to include binding sites for neutralizing antibodies of both VEEV and CHIKV strains (Mosaikcon). All four designed proteins were produced solubly in E. coli and purified. They formed the β-strand core expected from experimental structures of this region of the wild type E2 proteins as indicated by circular dichroism (CD) spectra. Furthermore, the CHIKVcon protein bound to a structure dependent, CHIKV neutralizing monoclonal antibody. The AllAVcon and Mosaikcon proteins bound to polyclonal antibodies generated during natural infection with either VEEV or CHIKV, indicating they contained epitopes of both serotypes. The Mosaikcon antigen induced antibodies in rabbit sera that recognized both the VEEVcon and CHIKVcon spike proteins. These PCP-consensus antigens are promising starting points for novel, broad-spectrum alphavirus vaccines.
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Affiliation(s)
- Wendy S Baker
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Surendra Negi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA; Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Werner Braun
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA; Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Catherine H Schein
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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6
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Nesbit JB, Schein CH, Braun BA, Gipson SAY, Cheng H, Hurlburt BK, Maleki SJ. Epitopes with similar physicochemical properties contribute to cross reactivity between peanut and tree nuts. Mol Immunol 2020; 122:223-231. [PMID: 32442779 DOI: 10.1016/j.molimm.2020.03.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/11/2020] [Accepted: 03/26/2020] [Indexed: 12/28/2022]
Abstract
Many individuals with peanut (PN) allergy have severe reactions to tree nuts (TN) such as walnuts or cashews. Although allergenic proteins in TN and PN have overall low identity, they share discrete sequences similar in physicochemical properties (PCP) to known IgE epitopes. Here, PCP-consensus peptides (cp, 13 aa and 31 aa) were identified from an alignment of epitope rich regions of walnut vicilin, Jug r 2, leader sequence (J2LS) and cross-reactive epitopes in the 2S albumins of peanut and synthesized. A peptide similarity search in the Structural Database of Allergenic Proteins (SDAP) revealed a network of peptides similar (low property distance, PD) to the 13 aa cp (13cp) in many different plant allergens. Peptides similar to the 13cp in PN and TN allergens bound IgE from sera of patients allergic to PN and TN in peptide microarray analysis. The 13cp was used to produce a rabbit consensus peptide antibody (cpAB) that detected proteins containing repeats similar to the 13cp in western blots of various nut extracts, in which reactive proteins were identified by mass spectrometry. The cpAB bound more specifically to allergens and nut extracts containing multiple repeats similar to the 13 cp, such as almond (Pru du 6), peanut (Ara h 2) and walnut (Jug r 2). IgE binding to various nut extracts is inhibited by recombinant J2LS sequence and synthetic 31cp. Thus, several repeated sequences similar to the 13cp are bound by IgE. Multiple similar repeats in several allergens could account for reaction severity and clinically relevant cross-reactivity to PN and TN. These findings may help improve detection, diagnostic, and therapeutic tools.
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Affiliation(s)
- Jacqueline B Nesbit
- Dept of Agriculture-Agricultural Research Service-Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA, United States
| | - Catherine H Schein
- Department of Biochemistry and Molecular Biology, Institute for Human Infection and Immunity, University of Texas Medical Branch at Galveston (UTMB), TX, United States.
| | - Benjamin A Braun
- Department of Computer Science, Stanford University, United States
| | - Stephen A Y Gipson
- Dept of Agriculture-Agricultural Research Service-Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA, United States
| | - Hsiaopo Cheng
- Dept of Agriculture-Agricultural Research Service-Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA, United States
| | - Barry K Hurlburt
- Dept of Agriculture-Agricultural Research Service-Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA, United States
| | - Soheila J Maleki
- Dept of Agriculture-Agricultural Research Service-Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA, United States.
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7
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Wang R, Zheng X, Sun J, Feng K, Gao N, Fan D, Chen H, Jin X, An J. Vaccination With a Single Consensus Envelope Protein Ectodomain Sequence Administered in a Heterologous Regimen Induces Tetravalent Immune Responses and Protection Against Dengue Viruses in Mice. Front Microbiol 2019; 10:1113. [PMID: 31134046 PMCID: PMC6524413 DOI: 10.3389/fmicb.2019.01113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 05/01/2019] [Indexed: 12/24/2022] Open
Abstract
The development of a safe and effective tetravalent dengue vaccine that elicits protection against all dengue virus (DENV) serotypes is urgently needed. The consensus sequence of the ectodomain of envelope (E) protein of DENV (cE80) has been examined as an immunogen previously. In the current study, a cE80 DNA (D) vaccine was constructed and evaluated in conjunction with the cE80 protein (P) vaccine to examine whether both vaccines used together can further improve the immune responses. The cE80 DNA vaccine was administrated using either a homologous (DNA alone, DDD) or heterologous (DNA prime-protein boost: DDP or DPP) regimen, and evaluated for immunogenicity and protective efficacy in mice. Among the three DNA-based immunization regimens tested, DDP immunization is the optimal immunization regimen that elicited the greatest systemic immune response and conferred protection against all four DENV serotypes. This work provides innovative ideas for the development of consensus E-based dengue vaccines and the testing of optimal immunization regimens.
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Affiliation(s)
- Ran Wang
- Department of Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xiaoyan Zheng
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, The Second Clinical Medical College of Capital Medical University, Beijing, China
| | - Jin Sun
- Viral Disease and Vaccine Translational Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Kaihao Feng
- Department of Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Na Gao
- Department of Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Dongying Fan
- Department of Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Hui Chen
- Department of Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xia Jin
- Viral Disease and Vaccine Translational Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Jing An
- Department of Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Center of Epilepsy, Beijing Institute for Brain Disorders, Beijing, China
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Abstract
This review explores the presence and functions of polyglutamine (polyQ) in viral proteins. In mammals, mutations in polyQ segments (and CAG repeats at the nucleotide level) have been linked to neural disorders and ataxias. PolyQ regions in normal human proteins have documented functional roles, in transcription factors and, more recently, in regulating autophagy. Despite the high frequency of polyQ repeats in eukaryotic genomes, little attention has been given to the presence or possible role of polyQ sequences in virus genomes. A survey described here revealed that polyQ repeats occur rarely in RNA viruses, suggesting that they have detrimental effects on virus replication at the nucleotide or protein level. However, there have been sporadic reports of polyQ segments in potyviruses and in reptilian nidoviruses (among the largest RNA viruses known). Conserved polyQ segments are found in the regulatory control proteins of many DNA viruses. Variable length polyQ tracts are found in proteins that contribute to transmissibility (cowpox A-type inclusion protein (ATI)) and control of latency (herpes viruses). New longer-read sequencing methods, using original biological samples, should reveal more details on the presence and functional role of polyQ in viruses, as well as the nucleotide regions that encode them. Given the known toxic effects of polyQ repeats, the role of these segments in neurovirulent and tumorigenic viruses should be further explored.
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9
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Schein CH, Rowold D, Choi KH. Allosteric inhibitors of Coxsackie virus A24 RNA polymerase. Bioorg Med Chem 2016; 24:570-7. [PMID: 26762834 PMCID: PMC4743507 DOI: 10.1016/j.bmc.2015.12.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/04/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Coxsackie virus A24 (CVA24), a causative agent of acute hemorrhagic conjunctivitis, is a prototype of enterovirus (EV) species C. The RNA polymerase (3D(pol)) of CVA24 can uridylylate the viral peptide linked to the genome (VPg) from distantly related EV and is thus, a good model for studying this reaction. Once UMP is bound, VPgpU primes RNA elongation. Structural and mutation data have identified a conserved binding surface for VPg on the RNA polymerase (3D(pol)), located about 20Å from the active site. Here, computational docking of over 60,000 small compounds was used to select those with the lowest (best) specific binding energies (BE) for this allosteric site. Compounds with varying structures and low BE were assayed for their effect on formation of VPgU by CVA24-3D(pol). Two compounds with the lowest specific BE for the site inhibited both uridylylation and formation of VPgpolyU at 10-20μM. These small molecules can be used to probe the role of this allosteric site in polymerase function, and may be the basis for novel antiviral compounds.
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Affiliation(s)
- Catherine H Schein
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Box 7, Alachua, FL 32616, United States; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, United States.
| | - Diane Rowold
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Box 7, Alachua, FL 32616, United States
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, United States; Sealy Center for Structural Biology and Molecular Biophysics, UTMB, United States
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10
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Schein CH, Ye M, Paul AV, Oberste MS, Chapman N, van der Heden van Noort GJ, Filippov DV, Choi KH. Sequence specificity for uridylylation of the viral peptide linked to the genome (VPg) of enteroviruses. Virology 2015; 484:80-85. [PMID: 26074065 PMCID: PMC4567471 DOI: 10.1016/j.virol.2015.05.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/17/2015] [Accepted: 05/22/2015] [Indexed: 12/16/2022]
Abstract
Enteroviruses (EV) uridylylate a peptide, VPg, as the first step in their replication. VPgpUpU, found free in infected cells, serves as the primer for RNA elongation. The abilities of four polymerases (3D(pol)), from EV-species A-C, to uridylylate VPgs that varied by up to 60% of their residues were compared. Each 3D(pol) was able to uridylylate all five VPgs using polyA RNA as template, while showing specificity for its own genome encoded peptide. All 3D(pol) uridylylated a consensus VPg representing the physical chemical properties of 31 different VPgs. Thus the residues required for uridylylation and the enzymatic mechanism must be similar in diverse EV. As VPg-binding sites differ in co-crystal structures, the reaction is probably done by a second 3D(pol) molecule. The conservation of polymerase residues whose mutation reduces uridylylation but not RNA elongation is compared.
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Affiliation(s)
- Catherine H Schein
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd., Alachua, FL 32616, United States.
| | - Mengyi Ye
- Dept. Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Aniko V Paul
- Dept. Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11790, United States
| | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, MS G-17, Atlanta, GA 30333, United States
| | - Nora Chapman
- Dept. Pathology and Microbiology, University of Nebraska Medical Center, NE 68198, United States
| | | | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Kyung H Choi
- Dept. Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, United States
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van der Heden van Noort GJ, Schein CH, Overkleeft HS, van der Marel GA, Filippov DV. A general synthetic method toward uridylylated picornavirus VPg proteins. J Pept Sci 2013; 19:333-6. [PMID: 23606631 DOI: 10.1002/psc.2508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/27/2013] [Accepted: 02/27/2013] [Indexed: 01/29/2023]
Abstract
Small proteins called viral protein genome-linked (VPg), attached to the 5'-end of the viral RNA genome are found as common structure in the large family of picornaviruses. The replication of these viruses is primed by this VPg protein linked to a single uridylyl residue. We report a general procedure to obtain such nucleoproteins employing a pre-uridylylated tyrosine building block in an on-line solid phase-based approach.
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Bowen DM, Lewis JA, Lu W, Schein CH. Simplifying complex sequence information: a PCP-consensus protein binds antibodies against all four Dengue serotypes. Vaccine 2012; 30:6081-7. [PMID: 22863657 DOI: 10.1016/j.vaccine.2012.07.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 07/13/2012] [Accepted: 07/18/2012] [Indexed: 12/15/2022]
Abstract
Designing proteins that reflect the natural variability of a pathogen is essential for developing novel vaccines and drugs. Flaviviruses, including Dengue (DENV) and West Nile (WNV), evolve rapidly and can "escape" neutralizing monoclonal antibodies by mutation. Designing antigens that represent many distinct strains is important for DENV, where infection with a strain from one of the four serotypes may lead to severe hemorrhagic disease on subsequent infection with a strain from another serotype. Here, a DENV physicochemical property (PCP)-consensus sequence was derived from 671 unique sequences from the Flavitrack database. PCP-consensus proteins for domain 3 of the envelope protein (EdomIII) were expressed from synthetic genes in Escherichia coli. The ability of the purified consensus proteins to bind polyclonal antibodies generated in response to infection with strains from each of the four DENV serotypes was determined. The initial consensus protein bound antibodies from DENV-1-3 in ELISA and Western blot assays. This sequence was altered in 3 steps to incorporate regions of maximum variability, identified as significant changes in the PCPs, characteristic of DENV-4 strains. The final protein was recognized by antibodies against all four serotypes. Two amino acids essential for efficient binding to all DENV antibodies are part of a discontinuous epitope previously defined for a neutralizing monoclonal antibody. The PCP-consensus method can significantly reduce the number of experiments required to define a multivalent antigen, which is particularly important when dealing with pathogens that must be tested at higher biosafety levels.
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Affiliation(s)
- David M Bowen
- Computational Biology, Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0857, United States
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