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Sherwood LJ, Hayhurst A. Generating Uniformly Cross-Reactive Ebolavirus spp. Anti-nucleoprotein Nanobodies to Facilitate Forward Capable Detection Strategies. ACS Infect Dis 2022; 8:343-359. [PMID: 34994194 DOI: 10.1021/acsinfecdis.1c00478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It is often challenging for a single monoclonal antibody to cross-react equally with all species of a particular viral genus that are separated by time and geographies to ensure broad long-term global immunodiagnostic use. Here, we set out to isolate nanobodies or single-domain antibodies (sdAbs) with uniform cross-reactivity to the genus Ebolavirus by immunizing a llama with recombinant nucleoprotein (NP) representing the 5 cultivated species to assemble a phage display repertoire for mining. Screening sdAbs for reactivity against the C-terminal domain of NP guided the isolation of clones that could perform as both captor and tracer for polyvalent antigen in sandwich assays. Two promising sdAbs had equivalent reactivities across all 5 species and greatly enhanced the equilibrium concentration at 50% (EC50) for recombinant NP when compared with a differentially cross-reactive nonimmune sdAb isolated previously. Uniform reactivity and enhanced sensitivity were relayed to live virus titrations, resulting in lower limits of detection of 2-5 pfu for the best sdAbs, representing 10-, 20-, and 100-fold improvements for Zaire, Sudan/Reston, and Taï Forest viruses, respectively. Fusions of the sdAbs with ascorbate peroxidase (APEX2) and mNeonGreen generated one-step immunoreagents useful for colorimetric and fluorescent visualization of cellular NP. Both sdAbs were also able to recognize recombinant NPs from the recently discovered Bombali virus, a putative sixth Ebolavirus species unknown at the start of these experiments, validating the forward capabilities of the sdAbs. The simplicity and modularity of these sdAbs should enable advances in antigen-based diagnostic technologies to be retuned toward filoviral detection relatively easily, thereby proactively safeguarding human health.
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Affiliation(s)
- Laura Jo Sherwood
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States
| | - Andrew Hayhurst
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States
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Sherwood LJ, Hayhurst A. Visualizing Filoviral Nucleoproteins Using Nanobodies Fused to the Ascorbate Peroxidase Derivatives APEX2 and dEAPX. Methods Mol Biol 2022; 2446:427-449. [PMID: 35157287 DOI: 10.1007/978-1-0716-2075-5_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fusions of single-domain antibodies (sdAbs, nanobodies) to enzymatic reporters make convenient molecular probes to detect the presence of an antigen of interest. We have previously fused the monomeric hyperactive ascorbate peroxidase derivative APEX2 to anti-Ebolavirus and anti-Marburgvirus sdAbs to generate immunoreagents useful in detecting nucleoprotein (NP) on western blots, ELISA, and within cells following transfection of NP expression plasmids or following virus infection. Here we present the methods used to overexpress and purify these sdAb-APEX2 fusion proteins, and to employ them as probes in various scenarios with colorimetric and fluorometric signal development. We also introduce a dimeric hyperactive ascorbate peroxidase derivative dEAPX that enables bivalent sdAb probes to be produced while avoiding the need to generate more complex tandem sdAbs, leveraging avidity for improved signal strength. The APEX2 and dEAPX reagents appear interchangeable with any existing detection platform and the methods described here should enable a user to study their antigen of interest by simply swapping out the sdAb for their recombinant affinity reagent of choice.
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Affiliation(s)
- Laura Jo Sherwood
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Andrew Hayhurst
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA.
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Sherwood LJ, Hayhurst A. Toolkit for Quickly Generating and Characterizing Molecular Probes Specific for SARS-CoV-2 Nucleocapsid as a Primer for Future Coronavirus Pandemic Preparedness. ACS Synth Biol 2021; 10:379-390. [PMID: 33534552 PMCID: PMC7875338 DOI: 10.1021/acssynbio.0c00566] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Indexed: 12/31/2022]
Abstract
Generating and characterizing immunoreagents to enable studies of novel emerging viruses is an area where ensembles of synthetic genes, recombinant antibody pipelines, and modular antibody-reporter fusion proteins can respond rapidly. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread through the global population causing widespread morbidity, mortality, and socioeconomic chaos. Using SARS-CoV-2 as our model and starting with a gBlocks encoded nucleocapsid (N) gene, we purified recombinant protein from E. coli, to serve as bait for selecting semisynthetic nanobodies from our Nomad single-pot library. Clones were isolated in days and first fused to Gaussia luciferase to determine EC50 in the tens of nM range, and second fused to the ascorbate peroxidase derivative APEX2 for sensitive detection of SARS-CoV-2 infected cells. To generate inherently fluorescent immunoreagents, we introduce novel periplasmic sdAb fusions made with mNeonGreen and mScarlet-I, which were produced at milligram amounts. The fluorescent fusion proteins enabled concise visualization of SARS-CoV-2 N in the cytoplasm but not in the nucleus 24 h post infection, akin to the distribution of SARS-CoV N, thereby validating these useful imaging tools. SdAb reactivity appeared specific to SARS-CoV-2 with very much weaker binding to SARS-CoV, and no noticeable cross-reactivity to a panel of overexpressed human codon optimized N proteins from other CoV. High periplasmic expression levels and in silico immortalization of the nanobody constructs guarantees a cost-effective and reliable source of SARS-CoV-2 immunoreagents. Our proof-of-principle study should be applicable to known and newly emerging CoV to broaden the tools available for their analysis and help safeguard human health in a more proactive than reactive manner.
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Affiliation(s)
- Laura Jo Sherwood
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Andrew Hayhurst
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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de Marco A. Recombinant expression of nanobodies and nanobody-derived immunoreagents. Protein Expr Purif 2020; 172:105645. [PMID: 32289357 PMCID: PMC7151424 DOI: 10.1016/j.pep.2020.105645] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022]
Abstract
Antibody fragments for which the sequence is available are suitable for straightforward engineering and expression in both eukaryotic and prokaryotic systems. When produced as fusions with convenient tags, they become reagents which pair their selective binding capacity to an orthogonal function. Several kinds of immunoreagents composed by nanobodies and either large proteins or short sequences have been designed for providing inexpensive ready-to-use biological tools. The possibility to choose among alternative expression strategies is critical because the fusion moieties might require specific conditions for correct folding or post-translational modifications. In the case of nanobody production, the trend is towards simpler but reliable (bacterial) methods that can substitute for more cumbersome processes requiring the use of eukaryotic systems. The use of these will not disappear, but will be restricted to those cases in which the final immunoconstructs must have features that cannot be obtained in prokaryotic cells. At the same time, bacterial expression has evolved from the conventional procedure which considered exclusively the nanobody and nanobody-fusion accumulation in the periplasm. Several reports show the advantage of cytoplasmic expression, surface-display and secretion for at least some applications. Finally, there is an increasing interest to use as a model the short nanobody sequence for the development of in silico methodologies aimed at optimizing the yields, stability and affinity of recombinant antibodies. There is an increasing request for immunoreagents based on nanobodies. The multiplicity of their applications requires constructs with different structural complexity. Alternative expression methods are necessary to achieve such structural requirements. In silico optimization of nanobody biophysical characteristics becomes more and more reliable.
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Affiliation(s)
- Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, S-5000, Nova Gorica, Slovenia.
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Sherwood LJ, Taylor AB, Hart PJ, Hayhurst A. Paratope Duality and Gullying are Among the Atypical Recognition Mechanisms Used by a Trio of Nanobodies to Differentiate Ebolavirus Nucleoproteins. J Mol Biol 2019; 431:4848-4867. [PMID: 31626803 PMCID: PMC6990103 DOI: 10.1016/j.jmb.2019.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/28/2019] [Accepted: 10/07/2019] [Indexed: 02/08/2023]
Abstract
We had previously shown that three anti–Marburg virus nanobodies (VHH or single-domain antibody [sdAb]) targeted a cryptotope within an alpha-helical assembly at the nucleoprotein (NP) C-terminus that was conserved through half a century of viral evolution. Here, we wished to determine whether an anti–Ebola virus sdAb, that was cross-reactive within the Ebolavirus genus, recognized a similar structural feature upstream of the ebolavirus NP C-terminus. In addition, we sought to determine whether the specificities of a less cross-reactive anti–Zaire ebolavirus sdAb and a totally specific anti–Sudan ebolavirus sdAb were the result of exclusion from this region. Binding and X-ray crystallographic studies revealed that the primary determinant of cross-reactivity did indeed appear to be a preference for the helical feature. Specificity, in the case of the Zaire ebolavirus–specific sdAb, arose from the footprint shifting away from the helices to engage more variable residues. While both sdAbs used CDRs, they also had atypical side-on approaches, with framework 2 helping to accommodate parts of the epitope in sizeable paratope gullies. The Sudan ebolavirus–specific sdAb was more remarkable and appeared to bind two C-terminal domains simultaneously via nonoverlapping epitopes—“paratope duality.” One mode involved paratope gullying, whereas the other involved only CDRs, with CDR3 restructuring to wedge in between opposing walls of an interdomain crevice. The varied routes used by sdAbs to engage antigens discovered here deepen our appreciation of the small scaffold’s architectural versatility and also reveal lucrative opportunities within the ebolavirus NP C-termini that might be leveraged for diagnostics and novel therapeutic targeting.
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Affiliation(s)
- Laura Jo Sherwood
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Alexander Bryan Taylor
- X-ray Crystallography Core Laboratory, Institutional Research Cores and Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Peter John Hart
- X-ray Crystallography Core Laboratory, Institutional Research Cores and Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA; Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
| | - Andrew Hayhurst
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA. http://
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Itoh K, Reis AH, Hayhurst A, Sokol SY. Isolation of nanobodies against Xenopus embryonic antigens using immune and non-immune phage display libraries. PLoS One 2019; 14:e0216083. [PMID: 31048885 PMCID: PMC6497274 DOI: 10.1371/journal.pone.0216083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/12/2019] [Indexed: 12/17/2022] Open
Abstract
The use of Xenopus laevis as a model for vertebrate developmental biology is limited by a lack of antibodies specific for embryonic antigens. This study evaluated the use of immune and non-immune phage display libraries for the isolation of single domain antibodies, or nanobodies, with specificities for Xenopus embryonic antigens. The immune nanobody library was derived from peripheral blood lymphocyte RNA obtained from a llama immunized with Xenopus gastrula homogenates. Screening this library by immunostaining of embryonic tissues with pooled periplasmic material and sib-selection led to the isolation of several monoclonal phages reactive with the cytoplasm and nuclei of gastrula cells. One antigen recognized by a group of nanobodies was identified using a reverse proteomics approach as nucleoplasmin, an abundant histone chaperone. As an alternative strategy, a semi-synthetic non-immune llama nanobody phage display library was panned on highly purified Xenopus proteins. This proof-of-principle approach isolated monoclonal nanobodies that specifically bind Nuclear distribution element-like 1 (Ndel1) in multiple immunoassays. Our results suggest that immune and non-immune phage display screens on crude and purified embryonic antigens can efficiently identify nanobodies useful to the Xenopus developmental biology community.
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Affiliation(s)
- Keiji Itoh
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Alice H Reis
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Sergei Y Sokol
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
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Periplasmic Nanobody-APEX2 Fusions Enable Facile Visualization of Ebola, Marburg, and Mĕnglà virus Nucleoproteins, Alluding to Similar Antigenic Landscapes among Marburgvirus and Dianlovirus. Viruses 2019; 11:v11040364. [PMID: 31010013 PMCID: PMC6521291 DOI: 10.3390/v11040364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 11/26/2022] Open
Abstract
We explore evolved soybean ascorbate peroxidase (APEX2) as a reporter when fused to the C-termini of llama nanobodies (single-domain antibodies, sdAb; variable domains of heavy chain-only antibodies, VHH) targeted to the E. coli periplasm. Periplasmic expression preserves authentic antibody N-termini, intra-domain disulphide bond(s), and capitalizes on efficient haem loading through the porous E. coli outer membrane. Using monomeric and dimeric anti-nucleoprotein (NP) sdAb cross-reactive within the Marburgvirus genus and cross-reactive within the Ebolavirus genus, we show that periplasmic sdAb–APEX2 fusion proteins are easily purified at multi-mg amounts. The fusions were used in Western blotting, ELISA, and microscopy to visualize NPs using colorimetric and fluorescent imaging. Dimeric sdAb–APEX2 fusions were superior at binding NPs from viruses that were evolutionarily distant to that originally used to select the sdAb. Partial conservation of the anti-Marburgvirus sdAb epitope enabled the recognition of a novel NP encoded by the recently discovered Mĕnglà virus genome. Antibody–antigen interactions were rationalized using monovalent nanoluciferase titrations and contact mapping analysis of existing crystal structures, while molecular modelling was used to reveal the potential landscape of the Mĕnglà NP C-terminal domain. The sdAb–APEX2 fusions also enabled live Marburgvirus and Ebolavirus detection 24 h post-infection of Vero E6 cells within a BSL-4 laboratory setting. The simple and inexpensive mining of large amounts of periplasmic sdAb–APEX2 fusion proteins should help advance studies of past, contemporary, and perhaps Filovirus species yet to be discovered.
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8
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Shriver-Lake LC, Liu JL, Zabetakis D, Sugiharto VA, Lee CR, Defang GN, Wu SJL, Anderson GP, Goldman ER. Selection and Characterization of Anti-Dengue NS1 Single Domain Antibodies. Sci Rep 2018; 8:18086. [PMID: 30591706 PMCID: PMC6308234 DOI: 10.1038/s41598-018-35923-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023] Open
Abstract
Reliable detection and diagnosis of dengue virus (DENV) is important for both patient care and epidemiological control. Starting with a llama immunized with a mixture of recombinant nonstructural protein 1 (NS1) antigen from the four DENV serotypes, a phage display immune library of single domain antibodies was constructed and binders selected which exhibited specificity and affinity for DENV NS1. Each of these single domain antibodies was evaluated for its binding affinity to NS1 from the four serotypes, and incorporated into a sandwich format for NS1 detection. An optimal pair was chosen that provided the best combination of sensitivity for all four DENV NS1 antigens spiked into 50% human serum while showing no cross reactivity to NS1 from Zika virus, yellow fever virus, tick-borne encephalitis virus, and minimal binding to NS1 from Japanese encephalitis virus and West Nile virus. These rugged and robust recombinant binding molecules offer attractive alternatives to conventional antibodies for implementation into immunoassays destined for resource limited locals.
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Affiliation(s)
- Lisa C Shriver-Lake
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Jinny L Liu
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Dan Zabetakis
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Victor A Sugiharto
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Cheng-Rei Lee
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Gabriel N Defang
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Shuenn-Jue L Wu
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - George P Anderson
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Ellen R Goldman
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA.
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9
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Liu JL, Shriver-Lake LC, Zabetakis D, Goldman ER, Anderson GP. Selection of Single-Domain Antibodies towards Western Equine Encephalitis Virus. Antibodies (Basel) 2018; 7:E44. [PMID: 31544894 PMCID: PMC6698954 DOI: 10.3390/antib7040044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/12/2018] [Accepted: 12/12/2018] [Indexed: 12/21/2022] Open
Abstract
In this work, we describe the selection and characterization of single-domain antibodies (sdAb) towards the E2/E3E2 envelope protein of the Western equine encephalitis virus (WEEV). Our purpose was to identify novel recognition elements which could be used for the detection, diagnosis, and perhaps treatment of western equine encephalitis (WEE). To achieve this goal, we prepared an immune phage display library derived from the peripheral blood lymphocytes of a llama that had been immunized with an equine vaccine that includes killed WEEV (West Nile Innovator + VEWT). This library was panned against recombinant envelope (E2/E3E2) protein from WEEV, and seven representative sdAb from the five identified sequence families were characterized. The specificity, affinity, and melting point of each sdAb was determined, and their ability to detect the recombinant protein in a MagPlex sandwich immunoassay was confirmed. Thus, these new binders represent novel recognition elements for the E2/E3E2 proteins of WEEV that are available to the research community for further investigation into their applicability for use in the diagnosis or treatment of WEE.
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Affiliation(s)
- Jinny L Liu
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Lisa C Shriver-Lake
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Dan Zabetakis
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Ellen R Goldman
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - George P Anderson
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
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Anderson GP, Shriver-Lake LC, Walper SA, Ashford L, Zabetakis D, Liu JL, Breger JC, Brozozog Lee PA, Goldman ER. Genetic Fusion of an Anti-BclA Single-Domain Antibody with Beta Galactosidase. Antibodies (Basel) 2018; 7:antib7040036. [PMID: 31544886 PMCID: PMC6698959 DOI: 10.3390/antib7040036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 02/06/2023] Open
Abstract
The Bacillus collagen-like protein of anthracis (BclA), found in Bacillus anthracis spores, is an attractive target for immunoassays. Previously, using phage display we had selected llama-derived single-domain antibodies that bound to B. anthracis spore proteins including BclA. Single-domain antibodies (sdAbs), the recombinantly expressed heavy domains from the unique heavy-chain-only antibodies found in camelids, provide stable and well-expressed binding elements with excellent affinity. In addition, sdAbs offer the important advantage that they can be tailored for specific applications through protein engineering. A fusion of a BclA targeting sdAb with the enzyme Beta galactosidase (β-gal) would enable highly sensitive immunoassays with no need for a secondary reagent. First, we evaluated five anti-BclA sdAbs, including four that had been previously identified but not characterized. Each was tested to determine its binding affinity, melting temperature, producibility, and ability to function as both capture and reporter in sandwich assays for BclA. The sdAb with the best combination of properties was constructed as a fusion with β-gal and shown to enable sensitive detection. This fusion has the potential to be incorporated into highly sensitive assays for the detection of anthrax spores.
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Affiliation(s)
- George P Anderson
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Lisa C Shriver-Lake
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Scott A Walper
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Lauryn Ashford
- The Washington Center for Internships and Academic Seminars, 1333 16th Street N.W., Washington, DC 20036, USA.
| | - Dan Zabetakis
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Jinny L Liu
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | - Joyce C Breger
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
| | | | - Ellen R Goldman
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC 20375, USA.
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Garza JA, Taylor AB, Sherwood LJ, Hart PJ, Hayhurst A. Unveiling a Drift Resistant Cryptotope within Marburgvirus Nucleoprotein Recognized by Llama Single-Domain Antibodies. Front Immunol 2017; 8:1234. [PMID: 29038656 PMCID: PMC5630700 DOI: 10.3389/fimmu.2017.01234] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/19/2017] [Indexed: 12/29/2022] Open
Abstract
Marburg virus (MARV) is a highly lethal hemorrhagic fever virus that is increasingly re-emerging in Africa, has been imported to both Europe and the US, and is also a Tier 1 bioterror threat. As a negative sense RNA virus, MARV has error prone replication which can yield progeny capable of evading countermeasures. To evaluate this vulnerability, we sought to determine the epitopes of 4 llama single-domain antibodies (sdAbs or VHH) specific for nucleoprotein (NP), each capable of forming MARV monoclonal affinity reagent sandwich assays. Here, we show that all sdAb bound the C-terminal region of NP, which was produced recombinantly to derive X-ray crystal structures of the three best performing antibody-antigen complexes. The common epitope is a trio of alpha helices that form a novel asymmetric basin-like depression that accommodates each sdAb paratope via substantial complementarity-determining region (CDR) restructuring. Shared core contacts were complemented by unique accessory contacts on the sides and overlooks of the basin yielding very different approach routes for each sdAb to bind the antigen. The C-terminal region of MARV NP was unable to be crystallized alone and required engagement with sdAb to form crystals suggesting the antibodies acted as crystallization chaperones. While gross structural homology is apparent between the two most conserved helices of MARV and Ebolavirus, the positions and morphologies of the resulting basins were markedly different. Naturally occurring amino acid variations occurring in bat and human Marburgvirus strains all mapped to surfaces distant from the predicted sdAb contacts suggesting a vital role for the NP interface in virus replication. As an essential internal structural component potentially interfacing with a partner protein it is likely the C-terminal epitope remains hidden or “cryptic” until virion disruption occurs. Conservation of this epitope over 50 years of Marburgvirus evolution should make these sdAb useful foundations for diagnostics and therapeutics resistant to drift.
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Affiliation(s)
- John Anthony Garza
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Alexander Bryan Taylor
- X-Ray Crystallography Core Laboratory, Department of Biochemistry and Structural Biology, Institutional Research Cores, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Laura Jo Sherwood
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Peter John Hart
- X-Ray Crystallography Core Laboratory, Department of Biochemistry and Structural Biology, Institutional Research Cores, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX, United States
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
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Darling TL, Sherwood LJ, Hayhurst A. Intracellular Crosslinking of Filoviral Nucleoproteins with Xintrabodies Restricts Viral Packaging. Front Immunol 2017; 8:1197. [PMID: 29021793 PMCID: PMC5623874 DOI: 10.3389/fimmu.2017.01197] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/11/2017] [Indexed: 12/24/2022] Open
Abstract
Viruses assemble large macromolecular repeat structures that become part of the infectious particles or virions. Ribonucleocapsids (RNCs) of negative strand RNA viruses are a prime example where repetition of nucleoprotein (NP) along the genome creates a core polymeric helical scaffold that accommodates other nucleocapsid proteins including viral polymerase. The RNCs are transported through the cytosol for packaging into virions through association with viral matrix proteins at cell membranes. We hypothesized that RNC would be ideal targets for crosslinkers engineered to promote aberrant protein–protein interactions, thereby blocking their orderly transport and packaging. Previously, we had generated single-domain antibodies (sdAbs) against Filoviruses that have all targeted highly conserved C-terminal regions of NP known to be repetitively exposed along the length of the RNCs of Marburgvirus (MARV) and Ebolavirus (EBOV). Our crosslinker design consisted of dimeric sdAb expressed intracellularly, which we call Xintrabodies (X- for crosslinking). Electron microscopy of purified NP polymers incubated with purified sdAb constructs showed NP aggregation occurred in a genus-specific manner with dimeric and not monomeric sdAb. A virus-like particle (VLP) assay was used for initial evaluation where we found that dimeric sdAb inhibited NP incorporation into VP40-based VLPs whereas monomeric sdAb did not. Inhibition of NP packaging was genus specific. Confocal microscopy revealed dimeric sdAb was diffuse when expressed alone but focused on pools of NP when the two were coexpressed, while monomeric sdAb showed ambivalent partition. Infection of stable Vero cell lines expressing dimeric sdAb specific for either MARV or EBOV NP resulted in smaller plaques and reduced progeny of cognate virus relative to wild-type Vero cells. Though the impact was marginal at later time-points, the collective data suggest that viral replication can be reduced by crosslinking intracellular NP using relatively small amounts of dimeric sdAb to restrict NP packaging. The stoichiometry and ease of application of the approach would likely benefit from transitioning away from intracellular expression of crosslinking sdAb to exogenous delivery of antibody. By retuning sdAb specificity, the approach of crosslinking highly conserved regions of assembly critical proteins may well be applicable to inhibiting replication processes of a broad spectrum of viruses.
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Affiliation(s)
- Tamarand Lee Darling
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States.,Department of Microbiology, Immunology and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Laura Jo Sherwood
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
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Shriver-Lake LC, Zabetakis D, Goldman ER, Anderson GP. Evaluation of anti-botulinum neurotoxin single domain antibodies with additional optimization for improved production and stability. Toxicon 2017; 135:51-58. [DOI: 10.1016/j.toxicon.2017.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 01/27/2023]
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14
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Anderson GP, Teichler DD, Zabetakis D, Shriver-Lake LC, Liu JL, Lonsdale SG, Goodchild SA, Goldman ER. Importance of Hypervariable Region 2 for Stability and Affinity of a Shark Single-Domain Antibody Specific for Ebola Virus Nucleoprotein. PLoS One 2016; 11:e0160534. [PMID: 27494523 PMCID: PMC4975481 DOI: 10.1371/journal.pone.0160534] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/20/2016] [Indexed: 12/18/2022] Open
Abstract
Single-domain antibodies derived from the unique New Antigen Receptor found in sharks have numerous potential applications, ranging from diagnostic reagents to therapeutics. Shark-derived single-domain antibodies possess the same characteristic ability to refold after heat denaturation found in single-domain antibodies derived from camelid heavy-chain-only antibodies. Recently, two shark derived single-domain antibodies specific for the nucleoprotein of Ebola virus were described. Our evaluation confirmed their high affinity for the nucleoprotein, but found their melting temperatures to be low relative to most single-domain antibodies. Our first approach towards improving their stability was grafting antigen-binding regions (complementarity determining regions) of one of these single-domain antibodies onto a high melting temperature shark single-domain antibody. This resulted in two variants: one that displayed excellent affinity with a low melting temperature, while the other had poor affinity but a higher melting temperature. These new proteins, however, differed in only 3 amino acids within the complementarity determining region 2 sequence. In shark single-domain antibodies, the complementarity determining region 2 is often referred to as hypervariable region 2, as this segment of the antibody domain is truncated compared to the sequence in camelid single-domain antibodies and conventional heavy chain variable domains. To elucidate which of the three amino acids or combinations thereof were responsible for the affinity and stability we made the 6 double and single point mutants that covered the intermediates between these two clones. We found a single amino acid change that achieved a 10°C higher melting temperature while maintaining sub nM affinity. This research gives insights into the impact of the shark sdAb hypervariable 2 region on both stability and affinity.
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Affiliation(s)
- George P. Anderson
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States of America
| | - Daniel D. Teichler
- Science and Engineering Apprenticeship Program, Naval Research Laboratory, Washington, DC, United States of America
| | - Dan Zabetakis
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States of America
| | - Lisa C. Shriver-Lake
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States of America
| | - Jinny L. Liu
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States of America
| | - Stephen G. Lonsdale
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Sarah A. Goodchild
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Ellen R. Goldman
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States of America
- * E-mail:
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15
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Liu JL, Walper SA, Turner KB, Lee AB, Medintz IL, Susumu K, Oh E, Zabetakis D, Goldman ER, Anderson GP. Conjugation of biotin-coated luminescent quantum dots with single domain antibody-rhizavidin fusions. ACTA ACUST UNITED AC 2016; 10:56-65. [PMID: 28352525 PMCID: PMC5040863 DOI: 10.1016/j.btre.2016.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 12/28/2022]
Abstract
Single domain antibody—rhizavidin fusion bioconjugated biotin coated quantum dots. Provided facile and effective method to orient antibodies on QD surface. Accomplished improved production of His-tagged rhizavidin (RZh) in E. coli. Demonstrated utility of RZh as a replacement for tetrameric biotin binders.
Straightforward and effective methods are required for the bioconjugation of proteins to surfaces and particles. Previously we demonstrated that the fusion of a single domain antibody with the biotin binding molecule rhizavidin provided a facile method to coat biotin-modified surfaces with a highly active and oriented antibody. Here, we constructed similar single domain antibody—rhizavidin fusions as well as unfused rhizavidin with a His-tag. The unfused rhizavidin produced efficiently and its utility for assay development was demonstrated in surface plasmon resonance experiments. The single domain antibody-rhizavidin fusions were utilized to coat quantum dots that had been prepared with surface biotins. Preparation of antibody coated quantum dots by this means was found to be both easy and effective. The prepared single domain antibody-quantum dot reagent was characterized by surface plasmon resonance and applied to toxin detection in a fluoroimmunoassay sensing format.
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Affiliation(s)
- Jinny L Liu
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - Scott A Walper
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - Kendrick B Turner
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | | | - Igor L Medintz
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - Kimihiro Susumu
- Sotera Defense Solutions, Inc., 7230 Lee Deforest Drive, Columbia, MD 21046, USA
| | - Eunkeu Oh
- Sotera Defense Solutions, Inc., 7230 Lee Deforest Drive, Columbia, MD 21046, USA
| | - Dan Zabetakis
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - Ellen R Goldman
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
| | - George P Anderson
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington DC 20375, USA
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16
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Turner KB, Alves NJ, Medintz IL, Walper SA. Improving the targeting of therapeutics with single-domain antibodies. Expert Opin Drug Deliv 2016; 13:561-70. [DOI: 10.1517/17425247.2016.1133583] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Rossotti MA, Pirez M, Gonzalez-Techera A, Cui Y, Bever CS, Lee KSS, Morisseau C, Leizagoyen C, Gee S, Hammock BD, González-Sapienza G. Method for Sorting and Pairwise Selection of Nanobodies for the Development of Highly Sensitive Sandwich Immunoassays. Anal Chem 2015; 87:11907-14. [PMID: 26544909 PMCID: PMC4666776 DOI: 10.1021/acs.analchem.5b03561] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Single domain heavychain binders (nanobodies) obtained from camelid antibody libraries hold a great promise for immunoassay development. However, there is no simple method to select the most valuable nanobodies from the crowd of positive clones obtained after the initial screening. In this paper, we describe a novel nanobody-based platform that allows comparison of the reactivity of hundreds of clones with the labeled antigen, and identifies the best nanobody pairs for two-site immunoassay development. The output clones are biotinylated in vivo in 96-well culture blocks and then used to saturate the biotin binding capacity of avidin coated wells. This standardizes the amount of captured antibody allowing their sorting by ranking their reactivity with the labeled antigen. Using human soluble epoxide hydrolase (sEH) as a model antigen, we were able to classify 96 clones in four families and confirm this classification by sequencing. This provided a criterion to select a restricted panel of five capturing antibodies and to test each of them against the rest of the 96 clones. The method constitutes a powerful tool for epitope binning, and in our case allowed development of a sandwich ELISA for sEH with a detection limit of 63 pg/mL and four log dynamic range, which performed with excellent recovery in different tissue extracts. This strategy provides a systematic way to test nanobody pairwise combinations and would have a broad utility for the development of highly sensitive sandwich immunoassays.
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Affiliation(s)
- Martín A. Rossotti
- Cátedra de Inmunología, DEPBIO, Facultad de Química, Instituto de Higiene, UDELAR, Montevideo, Uruguay
| | - Macarena Pirez
- Cátedra de Inmunología, DEPBIO, Facultad de Química, Instituto de Higiene, UDELAR, Montevideo, Uruguay
| | - Andres Gonzalez-Techera
- Cátedra de Inmunología, DEPBIO, Facultad de Química, Instituto de Higiene, UDELAR, Montevideo, Uruguay
| | - Yongliang Cui
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California, Davis, California, USA
| | - Candace S. Bever
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California, Davis, California, USA
| | - Kin S. S. Lee
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California, Davis, California, USA
| | - Christophe Morisseau
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California, Davis, California, USA
| | | | - Shirley Gee
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California, Davis, California, USA
| | - Bruce D. Hammock
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California, Davis, California, USA
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Kavanagh O, Elliott CT, Campbell K. Progress in the development of immunoanalytical methods incorporating recombinant antibodies to small molecular weight biotoxins. Anal Bioanal Chem 2015; 407:2749-70. [PMID: 25716465 DOI: 10.1007/s00216-015-8502-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 01/08/2023]
Abstract
Rapid immunoanalytical screening of food and environmental samples for small molecular weight (hapten) biotoxin contaminations requires the production of antibody reagents that possess the requisite sensitivity and specificity. To date animal-derived polyclonal (pAb) and monoclonal (mAb) antibodies have provided the binding element of the majority of these assays but recombinant antibodies (rAb) isolated from in vitro combinatorial phage display libraries are an exciting alternative due to (1) circumventing the need for experimental animals, (2) speed of production in commonly used in vitro expression systems and (3) subsequent molecular enhancement of binder performance. Short chain variable fragments (scFv) have been the most commonly employed rAb reagents for hapten biotoxin detection over the last two decades but antibody binding fragments (Fab) and single domain antibodies (sdAb) are increasing in popularity due to increased expression efficiency of functional binders and superior resistance to solvents. rAb-based immunochromatographic assays and surface plasmon resonance (SPR) biosensors have been reported to detect sub-regulatory levels of fungal (mycotoxins), marine (phycotoxins) and aquatic biotoxins in a wide range of food and environmental matrices, however this technology has yet to surpass the performances of the equivalent mAb- and pAb-based formats. As such the full potential of rAb technology in hapten biotoxin detection has yet to be achieved, but in time the inherent advantages of engineered rAb are set to provide the next generation of ultra-high performing binder reagents for the rapid and specific detection of hapten biotoxins.
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Affiliation(s)
- Owen Kavanagh
- Institute for Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK,
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Sherwood LJ, Hayhurst A. Ebolavirus nucleoprotein C-termini potently attract single domain antibodies enabling monoclonal affinity reagent sandwich assay (MARSA) formulation. PLoS One 2013; 8:e61232. [PMID: 23577211 PMCID: PMC3618483 DOI: 10.1371/journal.pone.0061232] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 03/06/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Antigen detection assays can play an important part in environmental surveillance and diagnostics for emerging threats. We are interested in accelerating assay formulation; targeting the agents themselves to bypass requirements for a priori genome information or surrogates. Previously, using in vitro affinity reagent selection on Marburg virus we rapidly established monoclonal affinity reagent sandwich assay (MARSA) where one recombinant antibody clone was both captor and tracer for polyvalent nucleoprotein (NP). Hypothesizing that the closely related Ebolavirus genus may share the same Achilles' heel, we redirected the scheme to see whether similar assays could be delivered and began to explore their mechanism. METHODS AND FINDINGS In parallel we selected panels of llama single domain antibodies (sdAb) from a semi-synthetic library against Zaire, Sudan, Ivory Coast, and Reston Ebola viruses. Each could perform as both captor and tracer in the same antigen sandwich capture assay thereby forming MARSAs. All sdAb were specific for NP and those tested required the C-terminal domain for recognition. Several clones were cross-reactive, indicating epitope conservation across the Ebolavirus genus. Analysis of two immune shark sdAb revealed they also targeted the C-terminal domain, and could be similarly employed, yet were less sensitive than a comparable llama sdAb despite stemming from immune selections. CONCLUSIONS The C-terminal domain of Ebolavirus NP is a strong attractant for antibodies and enables sensitive sandwich immunoassays to be rapidly generated using a single antibody clone. The polyvalent nature of nucleocapsid borne NP and display of the C-terminal region likely serves as a bountiful affinity sink during selections, and a highly avid target for subsequent immunoassay capture. Combined with the high degree of amino acid conservation through 37 years and across wide geographies, this domain makes an ideal handle for monoclonal affinity reagent driven antigen sandwich assays for the Ebolavirus genus.
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Affiliation(s)
- Laura J. Sherwood
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
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