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Dejager L, Banton S, Marques P, Rinikova G, Lory S, Hickford ES, Martin-Hamka C, Penney M, Grootjans S. BiSim Tool: a binding simulation tool to aid and simplify ligand-binding assay design and development. Bioanalysis 2024; 16:519-533. [PMID: 38629337 PMCID: PMC11299794 DOI: 10.4155/bio-2023-0242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/29/2024] [Indexed: 08/02/2024] Open
Abstract
Ligand-binding assays (LBAs) rely on the reversible, noncovalent binding between the analyte of interest and the assay reagents, and understanding their dynamic equilibrium is key to building robust LBA methods. Although the dynamic interplay of free and bound fractions can be calculated using mathematical models, these are not routinely applied. This approach is costly in terms of both assay development time and reagents, and can result in an under-exploration of the possible parameter combinations. Therefore, we have created a user-friendly simulation tool to facilitate LBA development (the BiSim Tool). We describe the models driving the mathematical simulations and the main features of our software solution by means of case studies, illustrating the tool's value in drug development. To support drug development for all patients worldwide, the BiSim Tool is now available as an open-source code project and as a free web-based tool at https://proteinbindingsimulation.shinyapps.io/BiSim-ProteinBindingSimulation [1].
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Affiliation(s)
- Lien Dejager
- UCB Biopharma, Allée de la Recherche 60, 1070 Brussels, Belgium
| | - Sophia Banton
- UCB Biopharma, Allée de la Recherche 60, 1070 Brussels, Belgium
| | - Patricia Marques
- UCB Biopharma, Allée de la Recherche 60, 1070 Brussels, Belgium
- Employed by UCB at the time the work was undertaken
| | - Gabriela Rinikova
- UCB Biopharma, Allée de la Recherche 60, 1070 Brussels, Belgium
- Employed by UCB at the time the work was undertaken
| | - Sabrina Lory
- UCB Biopharma, Allée de la Recherche 60, 1070 Brussels, Belgium
| | | | | | - Mark Penney
- UCB Biopharma, Bath Road, Slough, SL1 3WE, UK
- Employed by UCB at the time the work was undertaken
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2
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Janezic EM, Doan A, Mai E, Bravo DD, Wang J, Kim HS, Spiess C, Bewley K, ElSohly A, Liang WC, Koerber JT, Richalet P, Vanhove M, Comps-Agrar L. A novel, label-free, pre-equilibrium assay to determine the association and dissociation rate constants of therapeutic antibodies on living cells. Br J Pharmacol 2023. [PMID: 37783572 DOI: 10.1111/bph.16258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/19/2023] [Accepted: 09/23/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND AND PURPOSE Monoclonal antibodies (Ab) represent the fastest growing drug class. Knowledge of the biophysical parameters (kon , koff and KD ) that dictate Ab:receptor interaction is critical during the drug discovery process. However, with the increasing complexity of Ab formats and their targets, it became apparent that existing technologies present limitations and are not always suitable to determine these parameters. Therefore, novel affinity determination methods represent an unmet assay need. EXPERIMENTAL APPROACH We developed a pre-equilibrium kinetic exclusion assay using recent mathematical advances to determine the kon , koff and KD of monoclonal Ab:receptor interactions on living cells. The assay is amenable to all human IgG1 and rabbit Abs. KEY RESULTS Using our novel assay, we demonstrated for several monoclonal Ab:receptor pairs that the calculated kinetic rate constants were comparable with orthogonal methods that were lower throughput or more resource consuming. We ran simulations to predict the critical conditions to improve the performance of the assays. We further showed that this method could successfully be applied to both suspension and adherent cells. Finally, we demonstrated that kon and koff , but not KD , correlate with in vitro potency for a panel of monoclonal Abs. CONCLUSIONS AND IMPLICATIONS Our novel assay has the potential to systematically probe binding kinetics of monoclonal Abs to cells and can be incorporated in a screening cascade to identify new therapeutic candidates. Wide-spread adoption of pre-equilibrium assays using physiologically relevant systems will lead to a more holistic understanding of how Ab binding kinetics influence their potency.
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Affiliation(s)
| | | | - Elaine Mai
- Genentech, Inc, South San Francisco, California, USA
| | | | - Jianyong Wang
- Genentech, Inc, South San Francisco, California, USA
| | - Hok Seon Kim
- Genentech, Inc, South San Francisco, California, USA
| | | | | | - Adel ElSohly
- Genentech, Inc, South San Francisco, California, USA
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Direct bioanalysis or indirect calculation of target engagement and free drug exposure: do we apply double standards? Bioanalysis 2023; 15:5-16. [PMID: 36762451 DOI: 10.4155/bio-2022-0246] [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: 02/11/2023] Open
Abstract
Analysis of "free" drug/target concentrations is important to set up appropriate pharmacokinetic-pharmacodynamic models, to evaluate active-drug exposure and target engagement. Such "free-analyte" determination could be done by direct bioanalysis using an appropriate "free-analyte" assay. Development of "free" assays is often considered challenging from a technological and regulatory perspective. The application of a "total-total" approach, where the "free-analyte" concentration is determined mathematically, is considered a more convenient option. In this perspective, we examine and discuss the challenges of this "total-total" approach, from the affinity data, the importance of applying an appropriate "total" assay, the impact of additional binding partners and the variability of the total drug/target assays and their impact on the quality and variability of the final "free-analyte" dataset.
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4
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Truong PL, Yin Y, Lee D, Ko SH. Advancement in COVID-19 detection using nanomaterial-based biosensors. EXPLORATION (BEIJING, CHINA) 2023; 3:20210232. [PMID: 37323622 PMCID: PMC10191025 DOI: 10.1002/exp.20210232] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/11/2022] [Indexed: 06/17/2023]
Abstract
Coronavirus disease 2019 (COVID-19) pandemic has exemplified how viral growth and transmission are a significant threat to global biosecurity. The early detection and treatment of viral infections is the top priority to prevent fresh waves and control the pandemic. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified through several conventional molecular methodologies that are time-consuming and require high-skill labor, apparatus, and biochemical reagents but have a low detection accuracy. These bottlenecks hamper conventional methods from resolving the COVID-19 emergency. However, interdisciplinary advances in nanomaterials and biotechnology, such as nanomaterials-based biosensors, have opened new avenues for rapid and ultrasensitive detection of pathogens in the field of healthcare. Many updated nanomaterials-based biosensors, namely electrochemical, field-effect transistor, plasmonic, and colorimetric biosensors, employ nucleic acid and antigen-antibody interactions for SARS-CoV-2 detection in a highly efficient, reliable, sensitive, and rapid manner. This systematic review summarizes the mechanisms and characteristics of nanomaterials-based biosensors for SARS-CoV-2 detection. Moreover, continuing challenges and emerging trends in biosensor development are also discussed.
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Affiliation(s)
- Phuoc Loc Truong
- Laser and Thermal Engineering LabDepartment of Mechanical EngineeringGachon UniversitySeongnamKorea
| | - Yiming Yin
- New Materials InstituteDepartment of MechanicalMaterials and Manufacturing EngineeringUniversity of Nottingham Ningbo ChinaNingboChina
- Applied Nano and Thermal Science LabDepartment of Mechanical EngineeringSeoul National UniversityGwanak‐guSeoulKorea
| | - Daeho Lee
- Laser and Thermal Engineering LabDepartment of Mechanical EngineeringGachon UniversitySeongnamKorea
| | - Seung Hwan Ko
- Applied Nano and Thermal Science LabDepartment of Mechanical EngineeringSeoul National UniversityGwanak‐guSeoulKorea
- Institute of Advanced Machinery and Design (SNU‐IAMD)/Institute of Engineering ResearchSeoul National UniversityGwanak‐guSeoulKorea
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5
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Crowley AR, Mehlenbacher MR, Sajadi MM, DeVico AL, Lewis GK, Ackerman ME. Evidence of variable human Fcγ receptor-Fc affinities across differentially-complexed IgG. MAbs 2023; 15:2231128. [PMID: 37405954 PMCID: PMC10324447 DOI: 10.1080/19420862.2023.2231128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/07/2023] Open
Abstract
Antibody-mediated effector functions are widely considered to unfold according to an associative model of IgG-Fcγ receptor (FcγR) interactions. The associative model presupposes that Fc receptors cannot discriminate antigen-bound IgG from free IgG in solution and have equivalent affinities for each. Therefore, the clustering of Fcγ receptors (FcγR) in the cell membrane, cross-activation of intracellular signaling domains, and the formation of the immune synapse are all the result of avid interactions between the Fc region of IgG and FcγRs that collectively overcome the individually weak, transient interactions between binding partners. Antibody allostery, specifically conformational allostery, is a competing model in which antigen-bound antibody molecules undergo a physical rearrangement that causes them to stand out from the background of free IgG by virtue of greater FcγR affinity. Various evidence exists in support of this model of antibody allostery, but it remains controversial. We report observations from multiplexed, label-free kinetic experiments in which the affinity values of FcγR were characterized for covalently immobilized, captured, and antigen-bound IgG. Across the strategies tested, receptors had greater affinity for the antigen-bound mode of IgG presentation. This phenomenon was observed across multiple FcγRs and generalized to multiple antigens, antibody specificities, and subclasses. Furthermore, the thermodynamic signatures of FcγR binding to free or immune-complexed IgG in solution differed when measured by an orthogonal label-free method, but the failure to recapitulate the trend in overall affinity leaves open questions as to what additional factors may be at play.
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Affiliation(s)
- Andrew R. Crowley
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | | | - Mohammad M. Sajadi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
- Baltimore VA Medical Center, VA Maryland Health Care System, Baltimore, USA
| | - Anthony L. DeVico
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - George K. Lewis
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Margaret E. Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
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Campos de Paula HM, Coelho YL, Benhame de Castro AS, Marques IA, Hudson EA, de Paula Rezende J, Dos Santos Pires AC, Mendes da Silva LH. Dynamics and energetics of bovine lactoferrin and phenylmethane dyes interaction followed by surface plasmon resonance. Colloids Surf B Biointerfaces 2022; 219:112794. [PMID: 36162180 DOI: 10.1016/j.colsurfb.2022.112794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/10/2022] [Accepted: 08/21/2022] [Indexed: 10/31/2022]
Abstract
Although toxic and dangerous, Phenylmethane (PhM) dyes have a variety of medicinal functions. To optimize the use of these dyes, it is essential to understand their interaction mechanism with proteins. Through surface plasmon resonance, we investigated the kinetics and thermodynamics of interaction between bovine lactoferrin (BLF) and PhM dyes at pH 7.4, which allowed elucidate the effect of the dyes' functional groups on the binding process. Negative ΔG° revealed that at thermodynamic equilibrium the formed [BLF-PhM]° complex was more stable than the free BLF and PhM molecules. The increase in the number of methyl groups in the PhM structure led to an increase in the rates of association (ka) and dissociation (kd) and the binding constant (Kb). A similar effect was observed when comparing methyl violet B (MVB) and methyl violet 6 B (MV6B), in which the charged MV6B structure promoted an increase in the ka, kd, and Kb values. By contrast, an increase in the number of phenyl groups (2-3 rings) led to a decrease in the Kb values. The [BLF-PhM]° formation was entropically driven, indicating that hydrophobic interactions are critical for stabilizing these complexes These results are beneficial for understanding the molecular dynamics of protein-dye interactions.
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Affiliation(s)
| | - Yara Luiza Coelho
- Colloidal, Macromolecular and Green Chemistry (QUIVECOM), Chemistry Department, Brazil; Chemistry Institute, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, n° 700, Alfenas, MG 37130000, Brazil
| | | | | | - Eliara Acipreste Hudson
- Applied Molecular Thermodynamic (THERMA), Food Technology Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Jaqueline de Paula Rezende
- Applied Molecular Thermodynamic (THERMA), Food Technology Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil; Food Science Department, Federal University of Lavras, Campus Universitario, Lavras, MG 37200000, Brazil
| | - Ana Clarissa Dos Santos Pires
- Applied Molecular Thermodynamic (THERMA), Food Technology Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil
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Schlör A, Hirschberg S, Amor GB, Meister TL, Arora P, Pöhlmann S, Hoffmann M, Pfaender S, Eddin OK, Kamhieh-Milz J, Hanack K. SARS-CoV-2 neutralizing camelid heavy-chain-only antibodies as powerful tools for diagnostic and therapeutic applications. Front Immunol 2022; 13:930975. [PMID: 36189209 PMCID: PMC9517167 DOI: 10.3389/fimmu.2022.930975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
IntroductionThe ongoing COVID-19 pandemic situation caused by SARS-CoV-2 and variants of concern such as B.1.617.2 (Delta) and recently, B.1.1.529 (Omicron) is posing multiple challenges to humanity. The rapid evolution of the virus requires adaptation of diagnostic and therapeutic applications.ObjectivesIn this study, we describe camelid heavy-chain-only antibodies (hcAb) as useful tools for novel in vitro diagnostic assays and for therapeutic applications due to their neutralizing capacity.MethodsFive antibody candidates were selected out of a naïve camelid library by phage display and expressed as full length IgG2 antibodies. The antibodies were characterized by Western blot, enzyme-linked immunosorbent assays, surface plasmon resonance with regard to their specificity to the recombinant SARS-CoV-2 Spike protein and to SARS-CoV-2 virus-like particles. Neutralization assays were performed with authentic SARS-CoV-2 and pseudotyped viruses (wildtype and Omicron).ResultsAll antibodies efficiently detect recombinant SARS-CoV-2 Spike protein and SARS-CoV-2 virus-like particles in different ELISA setups. The best combination was shown with hcAb B10 as catcher antibody and HRP-conjugated hcAb A7.2 as the detection antibody. Further, four out of five antibodies potently neutralized authentic wildtype SARS-CoV-2 and particles pseudotyped with the SARS-CoV-2 Spike proteins of the wildtype and Omicron variant, sublineage BA.1 at concentrations between 0.1 and 0.35 ng/mL (ND50).ConclusionCollectively, we report novel camelid hcAbs suitable for diagnostics and potential therapy.
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Affiliation(s)
| | - Stefan Hirschberg
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Transfusion Medicine, Berlin, Germany
| | | | - Toni Luise Meister
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Prerna Arora
- Infection Biology Unit, German Primate Center– Leibniz Institute for Primate Research, Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center– Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, University Göttingen, Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center– Leibniz Institute for Primate Research, Göttingen, Germany
| | - Stephanie Pfaender
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | | | - Julian Kamhieh-Milz
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Transfusion Medicine, Berlin, Germany
- Wimedko GmbH, Berlin, Germany
| | - Katja Hanack
- New/era/mabs GmbH, Potsdam, Germany
- Department of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Katja Hanack,
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8
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Gao S, Torrente-Rodríguez RM, Pedrero M, Pingarrón JM, Campuzano S, Rocha-Martin J, Guisán JM. Dextran-coated nanoparticles as immunosensing platforms: Consideration of polyaldehyde density, nanoparticle size and functionality. Talanta 2022; 247:123549. [DOI: 10.1016/j.talanta.2022.123549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/28/2022]
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9
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Nath N, Godat B, Flemming R, Urh M. A homogeneous bioluminescent immunoassay for parallel characterization of binding between a panel of antibodies and a family of Fcγ receptors. Sci Rep 2022; 12:12185. [PMID: 35842448 PMCID: PMC9287719 DOI: 10.1038/s41598-022-15887-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/30/2022] [Indexed: 11/09/2022] Open
Abstract
Fc engineering efforts are increasingly being employed to modulate interaction of antibodies with variety of Fc receptors in an effort to improve the efficacy and safety of the therapeutic antibodies. Among the various Fc receptors, Fc gamma receptors (FcγRs) present on variety of immune cells are especially relevant since they can activate multiple effector functions including antibody dependent cellular cytotoxicity (ADCC) and antibody dependent cellular phagocytosis (ADCP). Depending on the desired mechanism of action (MOA) of the antibody, interactions between Fc domain of the antibody and FcγR (denoted as Fc/FcγR) may need to be enhanced or abolished. Therefore, during the antibody discovery process, biochemical methods are routinely used to measure the affinities of Fc/FcγR interactions. To enable such screening, we developed a plate based, simple to use, homogeneous immunoassays for six FcγRs by leveraging a luminescent protein complementation technology (NanoBiT). An added advantage of the NanoBiT immunoassays is their solution-based format, which minimizes well known surface related artifacts associated with traditional biosensor platforms (e.g., surface plasmon resonance and biolayer interferometry). With NanoBiT FcγRs assays, we demonstrate that assays are specific, report IgG subclass specific affinities and detect modulation in Fc/FcγR interactions in response to the changes in the Fc domain. We subsequently screen a panel of therapeutic antibodies including seven monoclonal antibodies (mAbs) and four polyclonal intravenous immunoglobulin (IVIg) products and highlight the advantages of parallel screening method for developing new antibody therapies.
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Affiliation(s)
- Nidhi Nath
- Promega Corporation, R&D Department, 2800 Woods Hollow Road, Madison, WI, 53711, USA. .,Bio-Techne, R&D Department, 614 McKinley Place NE, Minneapolis, MN, 55413, USA.
| | - Becky Godat
- Promega Corporation, R&D Department, 2800 Woods Hollow Road, Madison, WI, 53711, USA
| | - Rod Flemming
- Promega Corporation, R&D Department, 2800 Woods Hollow Road, Madison, WI, 53711, USA
| | - Marjeta Urh
- Promega Corporation, R&D Department, 2800 Woods Hollow Road, Madison, WI, 53711, USA.
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Kamat V, Boutot C, Rafique A, Granados C, Wang J, Badithe A, Torres M, Chatterjee I, Olsen O, Olson W, Huang T. High affinity human Fc specific monoclonal antibodies for capture kinetic analyses of antibody-antigen interactions. Anal Biochem 2022; 640:114455. [PMID: 34788604 DOI: 10.1016/j.ab.2021.114455] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022]
Abstract
We recently demonstrated that capturing human monoclonal antibodies (hmAbs) using high affinity anti-human Fc (AHC) antibodies allows reliable characterization of antibody-antigen interactions. Here, we characterized six human Fc specific mouse monoclonal antibodies (mAbs) and compared their binding profiles with three previously characterized goat AHC polyclonal antibodies (pAbs), exhibiting properties of a good capture reagent. All six mouse AHC mAbs specifically bound with high affinity to the Fc region of hIgG1, hIgG2, hIgG4 and to 43 different hIgG variants, containing substitutions and/or mutations in the hinge and/or Fc region, that have been reported to exhibit modified antibody effector function and/or pharmacokinetics. Biacore sensor surfaces individually derivatized with mouse AHC mAbs exhibited >2.5-fold higher hIgG binding capacity compared to the three goat AHC pAb surfaces and reproducibly captured hIgG over 300 capture-regeneration cycles. The results of the capture kinetic analyses performed on 31 antibody-antigen interactions using surfaces derivatized with either of the two highest affinity AHC mAbs (REGN7942 or REGN7943) were in concordance with those performed using goat AHC pAb surfaces. Our data demonstrate that AHC mAbs such as REGN7942 and REGN7943 that have properties superior than the three goat AHC pAbs are highly valuable research reagents, especially to perform capture kinetic analyses of antibody-antigen interactions on optical biosensors.
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Affiliation(s)
- Vishal Kamat
- Therapeutic Proteins, Regeneron Pharmaceuticals, USA.
| | | | | | | | - Jing Wang
- Therapeutic Proteins, Regeneron Pharmaceuticals, USA
| | - Ashok Badithe
- Therapeutic Proteins, Regeneron Pharmaceuticals, USA
| | | | | | - Olav Olsen
- Therapeutic Proteins, Regeneron Pharmaceuticals, USA
| | - William Olson
- Therapeutic Proteins, Regeneron Pharmaceuticals, USA
| | - Tammy Huang
- Therapeutic Proteins, Regeneron Pharmaceuticals, USA
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11
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Langer A, Lüdecke A, Bartoschik T, Cehlar O, Duhr S, Baaske P, Streicher W. A New Spectral Shift-Based Method to Characterize Molecular Interactions. Assay Drug Dev Technol 2022; 20:83-94. [PMID: 35171002 PMCID: PMC8968852 DOI: 10.1089/adt.2021.133] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
There are many fluorescence-based applications that can be used to characterize molecular interactions. However, available methods often depend on site-specific labeling techniques or binding-induced changes in conformation or size of the probed target molecule. To overcome these limitations, we applied a ratiometric dual-emission approach that quantifies ligand-induced spectral shifts with sub-nanometer sensitivity. The use of environment-sensitive near-infrared dyes with the method we describe enables affinity measurements and thermodynamic characterization without the explicit need for site-specific labeling or ligand-induced conformational changes. We demonstrate that in-solution spectral shift measurements enable precise characterization of molecular interactions for a variety of biomolecules, including proteins, antibodies, and nucleic acids. Thereby, the described method is not limited to a subset of molecules since even the most challenging samples of research and drug discovery projects like membrane proteins and intrinsically disordered proteins can be analyzed.
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Affiliation(s)
| | | | | | - Ondrej Cehlar
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Stefan Duhr
- NanoTemper Technologies GmbH, Munich, Germany
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12
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Chiodi E, Marn AM, Bakhshpour M, Lortlar Ünlü N, Ünlü MS. The Effects of Three-Dimensional Ligand Immobilization on Kinetic Measurements in Biosensors. Polymers (Basel) 2022; 14:polym14020241. [PMID: 35054650 PMCID: PMC8777619 DOI: 10.3390/polym14020241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 12/22/2022] Open
Abstract
The field of biosensing is in constant evolution, propelled by the need for sensitive, reliable platforms that provide consistent results, especially in the drug development industry, where small molecule characterization is of uttermost relevance. Kinetic characterization of small biochemicals is particularly challenging, and has required sensor developers to find solutions to compensate for the lack of sensitivity of their instruments. In this regard, surface chemistry plays a crucial role. The ligands need to be efficiently immobilized on the sensor surface, and probe distribution, maintenance of their native structure and efficient diffusion of the analyte to the surface need to be optimized. In order to enhance the signal generated by low molecular weight targets, surface plasmon resonance sensors utilize a high density of probes on the surface by employing a thick dextran matrix, resulting in a three-dimensional, multilayer distribution of molecules. Despite increasing the binding signal, this method can generate artifacts, due to the diffusion dependence of surface binding, affecting the accuracy of measured affinity constants. On the other hand, when working with planar surface chemistries, an incredibly high sensitivity is required for low molecular weight analytes, and furthermore the standard method for immobilizing single layers of molecules based on self-assembled monolayers (SAM) of epoxysilane has been demonstrated to promote protein denaturation, thus being far from ideal. Here, we will give a concise overview of the impact of tridimensional immobilization of ligands on label-free biosensors, mostly focusing on the effect of diffusion on binding affinity constants measurements. We will comment on how multilayering of probes is certainly useful in terms of increasing the sensitivity of the sensor, but can cause steric hindrance, mass transport and other diffusion effects. On the other hand, probe monolayers on epoxysilane chemistries do not undergo diffusion effect but rather other artifacts can occur due to probe distortion. Finally, a combination of tridimensional polymeric chemistry and probe monolayer is presented and reviewed, showing advantages and disadvantages over the other two approaches.
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Affiliation(s)
- Elisa Chiodi
- Department of Electrical Engineering, Boston University, Boston, MA 02215, USA; (A.M.M.); (M.B.); (N.L.Ü.)
- Correspondence: (E.C.); (M.S.Ü.)
| | - Allison M. Marn
- Department of Electrical Engineering, Boston University, Boston, MA 02215, USA; (A.M.M.); (M.B.); (N.L.Ü.)
- School of Engineering, Computing, and Construction Management, Roger Williams University, Bristol, RI 02809, USA
| | - Monireh Bakhshpour
- Department of Electrical Engineering, Boston University, Boston, MA 02215, USA; (A.M.M.); (M.B.); (N.L.Ü.)
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Nese Lortlar Ünlü
- Department of Electrical Engineering, Boston University, Boston, MA 02215, USA; (A.M.M.); (M.B.); (N.L.Ü.)
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - M. Selim Ünlü
- Department of Electrical Engineering, Boston University, Boston, MA 02215, USA; (A.M.M.); (M.B.); (N.L.Ü.)
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Correspondence: (E.C.); (M.S.Ü.)
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Bakhshpour M, Chiodi E, Celebi I, Saylan Y, Ünlü NL, Ünlü MS, Denizli A. Sensitive and real-time detection of IgG using interferometric reflecting imaging sensor system. Biosens Bioelectron 2022; 201:113961. [PMID: 35026547 DOI: 10.1016/j.bios.2021.113961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/20/2021] [Accepted: 12/31/2021] [Indexed: 11/16/2022]
Abstract
Considering the limitations of well-known traditional detection techniques, innovative research studies have focused on the development of new sensors to offer label-free, highly sensitive, real-time, low-cost, and rapid detection for biomolecular interactions. In this study, we demonstrate immunoglobulin G (IgG) detection in aqueous solutions by using real-time and label-free kinetic measurements of the Interferometric Reflectance Imaging Sensor (IRIS) system. By performing kinetic characterization experiments, the sensor's performance is comprehensively evaluated and a high correlation coefficient value (>0.94) is obtained in the IgG concentration range of 1-50 μg/mL with a low detection limit (0.25 μg/mL or 1.67 nM). Moreover, the highly sensitive imaging system ensures accurate quantification and reliable validation of recorded binding events, offering new perspectives in terms of direct biomarker detection for clinical applications.
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Affiliation(s)
- Monireh Bakhshpour
- Hacettepe University, Department of Chemistry, Ankara, Turkey; Boston University, Department of Electrical and Computer Engineering, Boston, MA, United States
| | - Elisa Chiodi
- Boston University, Department of Electrical and Computer Engineering, Boston, MA, United States
| | - Iris Celebi
- Boston University, Department of Electrical and Computer Engineering, Boston, MA, United States
| | - Yeşeren Saylan
- Hacettepe University, Department of Chemistry, Ankara, Turkey
| | - Nese Lortlar Ünlü
- Boston University, Department of Biomedical Engineering, Boston, MA, United States
| | - M Selim Ünlü
- Boston University, Department of Electrical and Computer Engineering, Boston, MA, United States; Boston University, Department of Biomedical Engineering, Boston, MA, United States
| | - Adil Denizli
- Hacettepe University, Department of Chemistry, Ankara, Turkey.
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14
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Nath N, Godat B, Flemming R, Urh M. Deciphering the Interaction between Neonatal Fc Receptor and Antibodies Using a Homogeneous Bioluminescent Immunoassay. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:1211-1221. [PMID: 34312257 PMCID: PMC8358922 DOI: 10.4049/jimmunol.2100181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/22/2021] [Indexed: 11/19/2022]
Abstract
Long half-life of therapeutic Abs and Fc fusion proteins is crucial to their efficacy and is, in part, regulated by their interaction with neonatal Fc receptor (FcRn). However, the current methods (e.g., surface plasmon resonance and biolayer interferometry) for measurement of interaction between IgG and FcRn (IgG/FcRn) require either FcRn or IgG to be immobilized on the surface, which is known to introduce experimental artifacts and have led to conflicting data. To study IgG/FcRn interactions in solution, without a need for surface immobilization, we developed a novel (to our knowledge), solution-based homogeneous binding immunoassay based on NanoBiT luminescent protein complementation technology. We optimized the assay (NanoBiT FcRn assay) for human FcRn, mouse FcRn, rat FcRn, and cynomolgus FcRn and used them to determine the binding affinities of a panel of eight Abs. Assays could successfully capture the modulation in IgG/FcRn binding based on changes in Fc fragment of the Abs. We also looked at the individual contribution of Fc and F(ab)2 on the IgG/FcRn interaction and found that Fc is the main driver for the interaction at pH 6. Our work highlights the importance of using orthogonal methods to validate affinity data generated using biosensor platforms. Moreover, the simple add-and-read format of the NanoBiT FcRn assay is amenable for high-throughput screening during early Ab discovery phase.
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Affiliation(s)
- Nidhi Nath
- Research and Development Department, Promega Corp., Madison, WI
| | - Becky Godat
- Research and Development Department, Promega Corp., Madison, WI
| | - Rod Flemming
- Research and Development Department, Promega Corp., Madison, WI
| | - Marjeta Urh
- Research and Development Department, Promega Corp., Madison, WI
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15
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Tiwari PB, Bencheqroun C, Lemus M, Shaw T, Kouassi-Brou M, Alaoui A, Üren A. SPRD: a surface plasmon resonance database of common factors for better experimental planning. BMC Mol Cell Biol 2021; 22:17. [PMID: 33676410 PMCID: PMC7937274 DOI: 10.1186/s12860-021-00354-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022] Open
Abstract
Background Surface plasmon resonance is a label-free biophysical technique that is widely used in investigating biomolecular interactions, including protein-protein, protein-DNA, and protein-small molecule binding. Surface plasmon resonance is a very powerful tool in different stages of small molecule drug development and antibody characterization. Both academic institutions and pharmaceutical industry extensively utilize this method for screening and validation studies involving direct molecular interactions. In most applications of the surface plasmon resonance technology, one of the studied molecules is immobilized on a microchip, while the second molecule is delivered through a microfluidic system over the immobilized molecules. Changes in total mass on the chip surface is recorded in real time as an indicator of the molecular interactions. Main body Quality and accuracy of the surface plasmon resonance data depend on experimental variables, including buffer composition, type of sensor chip, coupling chemistry of molecules on the sensor surface, and surface regeneration conditions. These technical details are generally included in materials and methods sections of published manuscripts and are not easily accessible using the common internet browser search engines or PubMed. Herein, we introduce a surface plasmon resonance database, www.sprdatabase.info that contains technical details extracted from 5140 publications with surface plasmon resonance data. We also provide an analysis of experimental conditions preferred by different laboratories. These experimental variables can be searched within the database and help future users of this technology to design better experiments. Conclusion Amine coupling and CM5 chips were the most common methods used for immobilizing proteins in surface plasmon resonance experiments. However, number of different chips, capture methods and buffer conditions were used by multiple investigators. We predict that the database will significantly help the scientific community using this technology and hope that users will provide feedback to improve and expand the database indefinitely. Publicly available information in the database can save a great amount of time and resources by assisting initial optimization and troubleshooting of surface plasmon resonance experiments.
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Affiliation(s)
| | - Camelia Bencheqroun
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington, DC, 20057, USA
| | - Mario Lemus
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA
| | - Taryn Shaw
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA
| | - Marilyn Kouassi-Brou
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA.,Geisel School of Medicine, Dartmouth College, NH, 03755, Hanover, USA
| | - Adil Alaoui
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington, DC, 20057, USA
| | - Aykut Üren
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA.
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16
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Jankovics H, Kovacs B, Saftics A, Gerecsei T, Tóth É, Szekacs I, Vonderviszt F, Horvath R. Grating-coupled interferometry reveals binding kinetics and affinities of Ni ions to genetically engineered protein layers. Sci Rep 2020; 10:22253. [PMID: 33335217 PMCID: PMC7746762 DOI: 10.1038/s41598-020-79226-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022] Open
Abstract
Reliable measurement of the binding kinetics of low molecular weight analytes to their targets is still a challenging task. Often, the introduction of labels is simply impossible in such measurements, and the application of label-free methods is the only reliable choice. By measuring the binding kinetics of Ni(II) ions to genetically modified flagellin layers, we demonstrate that: (1) Grating-Coupled Interferometry (GCI) is well suited to resolve the binding of ions, even at very low protein immobilization levels; (2) it supplies high quality kinetic data from which the number and strength of available binding sites can be determined, and (3) the rate constants of the binding events can also be obtained with high accuracy. Experiments were performed using a flagellin variant incorporating the C-terminal domain of the nickel-responsive transcription factor NikR. GCI results were compared to affinity data from titration calorimetry. We found that besides the low-affinity binding sites characterized by a micromolar dissociation constant (Kd), tetrameric FliC-NikRC molecules possess high-affinity binding sites with Kd values in the nanomolar range. GCI enabled us to obtain real-time kinetic data for the specific binding of an analyte with molar mass as low as 59 Da, even at signals lower than 1 pg/mm2.
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Affiliation(s)
- Hajnalka Jankovics
- Bio-Nanosystems Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Egyetem u. 10, Veszprém, Hungary
| | - Boglarka Kovacs
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, Budapest, Hungary
| | - Andras Saftics
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, Budapest, Hungary
| | - Tamas Gerecsei
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, Budapest, Hungary
| | - Éva Tóth
- Bio-Nanosystems Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Egyetem u. 10, Veszprém, Hungary
| | - Inna Szekacs
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, Budapest, Hungary
| | - Ferenc Vonderviszt
- Bio-Nanosystems Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Egyetem u. 10, Veszprém, Hungary
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, Budapest, Hungary
| | - Robert Horvath
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, Budapest, Hungary.
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17
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Mamer SB, Page P, Murphy M, Wang J, Gallerne P, Ansari A, Imoukhuede PI. The Convergence of Cell-Based Surface Plasmon Resonance and Biomaterials: The Future of Quantifying Bio-molecular Interactions-A Review. Ann Biomed Eng 2020; 48:2078-2089. [PMID: 31811474 PMCID: PMC8637426 DOI: 10.1007/s10439-019-02429-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/29/2019] [Indexed: 12/20/2022]
Abstract
Cell biology is driven by complex networks of biomolecular interactions. Characterizing the kinetic and thermodynamic properties of these interactions is crucial to understanding their role in different physiological processes. Surface plasmon resonance (SPR)-based approaches have become a key tool in quantifying biomolecular interactions, however conventional approaches require isolating the interacting components from the cellular system. Cell-based SPR approaches have recently emerged, promising to enable precise measurements of biomolecular interactions within their normal biological context. Two major approaches have been developed, offering their own advantages and limitations. These approaches currently lack a systematic exploration of 'best practices' like those existing for traditional SPR experiments. Toward this end, we describe the two major approaches, and identify the experimental parameters that require exploration, and discuss the experimental considerations constraining the optimization of each. In particular, we discuss the requirements of future biomaterial development needed to advance the cell-based SPR technique.
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Affiliation(s)
- Spencer B Mamer
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | - Jiaojiao Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pierrick Gallerne
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Ecole Centrale de Lille, Villeneuve d'Ascq, Hauts-De-France, France
| | - Ali Ansari
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - P I Imoukhuede
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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18
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Toward comparability of anti-drug antibody assays: is the amount of anti-drug antibody–reagent complexes at cut-point (CP-ARC) the missing piece? Bioanalysis 2020; 12:1021-1031. [DOI: 10.4155/bio-2020-0143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Immunogenicity testing is a mandatory and critical activity during the development of therapeutic proteins. Multiple regulatory guidelines provide clear recommendations on appropriate immunogenicity testing strategies and required bioanalytical assay performances. Unfortunately, it is still generally accepted that a comparison of the immunogenicity of different compounds is not possible due to apparent performance differences of the used bioanalytical methods. In this perspective, we propose the ‘cut-point anti-drug antibody–reagents complex’ (CP-ARC) concept for technical comparability of the bioanalytical methods. The feasibility and implementation in routine assay development is discussed as well as the potential improvement of reporting of bioanalytical immunogenicity data to allow comparison across drugs. Scientific sound comparability of the bioanalytical methods is the first step toward comparability of clinical immunogenicity.
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19
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Smith MH, Fologea D. Kinetic Exclusion Assay of Biomolecules by Aptamer Capture. SENSORS (BASEL, SWITZERLAND) 2020; 20:E3442. [PMID: 32570818 PMCID: PMC7348807 DOI: 10.3390/s20123442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 11/23/2022]
Abstract
DNA aptamers are short nucleotide oligomers selected to bind a target ligand with affinity and specificity rivaling that of antibodies. These remarkable features recommend aptamers as candidates for analytical and therapeutic applications that traditionally use antibodies as biorecognition elements. Numerous traditional and emerging analytical techniques have been proposed and successfully implemented to utilize aptamers for sensing purposes. In this work, we exploited the analytical capabilities offered by the kinetic exclusion assay technology to measure the affinity of fluorescent aptamers for their thrombin target and quantify the concentration of analyte in solution. Standard binding curves constructed by using equilibrated mixtures of aptamers titrated with thrombin were fitted with a 1:1 binding model and provided an effective Kd of the binding in the sub-nanomolar range. However, our experimental results suggest that this simple model does not satisfactorily describe the binding process; therefore, the possibility that the aptamer is composed of a mixture of two or more distinct Kd populations is discussed. The same standard curves, together with a four-parameter logistic equation, were used to determine "unknown" concentrations of thrombin in mock samples. The ability to identify and characterize complex binding stoichiometry, together with the determination of target analyte concentrations in the pM-nM range, supports the adoption of this technology for kinetics, equilibrium, and analytical purposes by employing aptamers as biorecognition elements.
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Affiliation(s)
- Mark H. Smith
- Department of Physics, Boise State University, 1910 University Drive, Boise, ID 83725, USA;
- Biomolecular Sciences Graduate Programs, Boise State University, 1910 University Drive, Boise, ID 83725, USA
| | - Daniel Fologea
- Department of Physics, Boise State University, 1910 University Drive, Boise, ID 83725, USA;
- Biomolecular Sciences Graduate Programs, Boise State University, 1910 University Drive, Boise, ID 83725, USA
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20
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Robin M, Tayakout-Fayolle M, Pitault I, Jallut C, Drazek L. Estimation of Kinetic Parameters Involved in Solid-Phase Immunoassays by Affinity Chromatography. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c00922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maëlenn Robin
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
- bioMérieux SA, Immuno Innovation Department, 376 chemin de l’Orme, 69280 Marcy l’Etoile, France
| | - Mélaz Tayakout-Fayolle
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
| | - Isabelle Pitault
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
| | - Christian Jallut
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
| | - Laurent Drazek
- bioMérieux SA, Biomathematics Departement, 5 rue des Berges, 38024 Grenoble, France
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21
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Daub H, Traxler L, Ismajli F, Groitl B, Itzen A, Rant U. The trimer to monomer transition of Tumor Necrosis Factor-Alpha is a dynamic process that is significantly altered by therapeutic antibodies. Sci Rep 2020; 10:9265. [PMID: 32518229 PMCID: PMC7283243 DOI: 10.1038/s41598-020-66123-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 05/12/2020] [Indexed: 11/09/2022] Open
Abstract
The cytokine tumor necrosis factor-alpha (TNF-α) readily forms homotrimers at sub-nM concentrations to promote inflammation. For the treatment of inflammatory diseases with upregulated levels of TNF-α, a number of therapeutic antibodies are currently used as scavengers to reduce the active TNF-α concentration in patients. Despite their clinical success, the mode-of-action of different antibody formats with regard to a stabilization of the trimeric state is not entirely understood. Here, we use a biosensor with dynamic nanolevers to analyze the monomeric and trimeric states of TNF-α together with the binding kinetics of therapeutic biologics. The intrinsic trimer-to-monomer decay rate k = 1.7 × 10−3 s−1 could be measured directly using a microfluidic system, and antibody binding affinities were analyzed in the pM range. Trimer stabilization effects are quantified for Adalimumab, Infliximab, Etanercept, Certolizumab, Golimumab for bivalent and monovalent binding formats. Clear differences in trimer stabilization are observed, which may provide a deeper insight into the mode-of-action of TNF-α scavengers.
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Affiliation(s)
- Herwin Daub
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany. .,Center for Integrated Protein Science Munich, Technische Universität München, Department Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany.
| | - Lukas Traxler
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany
| | - Fjolla Ismajli
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany
| | - Bastian Groitl
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich, Technische Universität München, Department Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany.,Department of Biochemistry and Signaltransduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246, Hamburg, Germany
| | - Ulrich Rant
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany
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22
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Stack E, McMurray S, McMurray G, Wade J, Clark M, Young G, Marquette K, Jain S, Kelleher K, Chen T, Lin Q, Bloom L, Lin L, Finlay W, Suzuki R, Cunningham O. In vitro affinity optimization of an anti-BDNF monoclonal antibody translates to improved potency in targeting chronic pain states in vivo. MAbs 2020; 12:1755000. [PMID: 32329655 PMCID: PMC7188400 DOI: 10.1080/19420862.2020.1755000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The role of brain-derived neurotrophic factor (BDNF) signaling in chronic pain has been well documented. Given the important central role of BDNF in long term plasticity and memory, we sought to engineer a high affinity, peripherally-restricted monoclonal antibody against BDNF to modulate pain. BDNF shares 100% sequence homology across human and rodents; thus, we selected chickens as an alternative immune host for initial antibody generation. Here, we describe the affinity optimization of complementarity-determining region-grafted, chicken-derived R3bH01, an anti-BDNF antibody specifically blocking the TrkB receptor interaction. Antibody optimization led to the identification of B30, which has a > 300-fold improvement in affinity based on BIAcore, an 800-fold improvement in potency in a cell-based pERK assay and demonstrates exquisite selectivity over related neurotrophins. Affinity improvements measured in vitro translated to in vivo pharmacological activity, with B30 demonstrating a 30-fold improvement in potency over parental R3bH01 in a peripheral nerve injury model. We further demonstrate that peripheral BDNF plays a role in maintaining the plasticity of sensory neurons following nerve damage, with B30 reversing neuron hyperexcitability associated with heat and mechanical stimuli in a dose-dependent fashion. In summary, our data demonstrate that effective sequestration of BDNF via a high affinity neutralizing antibody has potential utility in modulating the pathophysiological mechanisms that drive chronic pain states.
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Affiliation(s)
| | | | | | - Jason Wade
- Biomedicine Design, Pfizer, Dublin, Ireland.,Biomedicine Design, Pfizer, Cambridge, US
| | | | | | | | | | | | - Ting Chen
- Biomedicine Design, Pfizer, Cambridge, US
| | | | | | - Laura Lin
- Biomedicine Design, Pfizer, Cambridge, US
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23
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Brown ME, Bedinger D, Lilov A, Rathanaswami P, Vásquez M, Durand S, Wallace-Moyer I, Zhong L, Nett JH, Burnina I, Caffry I, Lynaugh H, Sinclair M, Sun T, Bukowski J, Xu Y, Abdiche YN. Assessing the binding properties of the anti-PD-1 antibody landscape using label-free biosensors. PLoS One 2020; 15:e0229206. [PMID: 32134960 PMCID: PMC7058304 DOI: 10.1371/journal.pone.0229206] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/31/2020] [Indexed: 12/21/2022] Open
Abstract
Here we describe an industry-wide collaboration aimed at assessing the binding properties of a comprehensive panel of monoclonal antibodies (mAbs) against programmed cell death protein 1 (PD-1), an important checkpoint protein in cancer immunotherapy and validated therapeutic target, with well over thirty unique mAbs either in clinical development or market-approved in the United States, the European Union or China. The binding kinetics of the PD-1/mAb interactions were measured by surface plasmon resonance (SPR) using a Carterra LSA instrument and the results were compared to data collected on a Biacore 8K. The effect of chip type on the SPR-derived binding rate constants and affinities were explored and the results compared with solution affinities from Meso Scale Discovery (MSD) and Kinetic Exclusion Assay (KinExA) experiments. When using flat chip types, the LSA and 8K platforms yielded near-identical kinetic rate and affinity constants that matched solution phase values more closely than those produced on 3D-hydrogels. Of the anti-PD-1 mAbs tested, which included a portion of those known to be in clinical development or approved, the affinities spanned from single digit picomolar to nearly 425 nM, challenging the dynamic range of our methods. The LSA instrument was also used to perform epitope binning and ligand competition studies which revealed over ten unique competitive binding profiles within this group of mAbs.
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Affiliation(s)
- Michael E. Brown
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
- * E-mail: (MEB); (YNA)
| | | | - Asparouh Lilov
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | | | - Maximiliano Vásquez
- Department of Computational Biology, Adimab, Palo Alto, CA, United States of America
| | - Stéphanie Durand
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Ian Wallace-Moyer
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Lihui Zhong
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Juergen H. Nett
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Irina Burnina
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Isabelle Caffry
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Heather Lynaugh
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Melanie Sinclair
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Tingwan Sun
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - John Bukowski
- Department of Antibody Discovery, Adimab, Lebanon, NH, United States of America
| | - Yingda Xu
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
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24
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Kamat V, Rafique A, Huang T, Olsen O, Olson W. The impact of different human IgG capture molecules on the kinetics analysis of antibody-antigen interaction. Anal Biochem 2020; 593:113580. [PMID: 31926892 DOI: 10.1016/j.ab.2020.113580] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/06/2020] [Indexed: 12/12/2022]
Abstract
Surface plasmon resonance (SPR) is a well-established method to characterize biomolecular interactions and is widely used in drug discovery and development. Here, we demonstrate that capture surfaces profoundly impact the binding kinetics parameters that are measured for antibody-antigen interactions. Six unique antibody-antigen interactions were characterized using eight different anti-human IgG capture surfaces. The antigen binding affinities for six different human monoclonal antibodies (hmAbs) captured using three different goat anti-human Fc (AHC) polyclonal antibody (pAb) surfaces were in reasonable agreement (3-7-fold weaker) with those measured by kinetic exclusion assay (KinExA). In contrast, up to 81, 32, 489, 2826, and 219-fold weaker antigen binding affinities were measured using mouse AHC mAb, Protein G, Protein A, Protein A/G, and Protein L surfaces, respectively. Protein A, Protein A/G and Protein G interacted with the Fab of hmAbs, possibly affecting antigen binding to hmAbs captured over these surfaces. Additional studies revealed that mouse AHC mAb binds hmAbs with a weak affinity (5.5-36.3 nM) and t½ values of 1.4-3.3min, compared to the sub-nanomolar affinities of the goat AHC pAbs. These results emphasize the value of measuring binding kinetics of the capture molecule before immobilizing them onto the sensor surface to perform capture kinetics assays on label-free biosensors.
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Affiliation(s)
- Vishal Kamat
- Biomolecular HTS Center, Therapeutic Proteins, Regeneron Pharmaceuticals, Tarrytown, NY, USA.
| | - Ashique Rafique
- Biomolecular HTS Center, Therapeutic Proteins, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Tammy Huang
- Therapeutic Proteins, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Olav Olsen
- Therapeutic Proteins, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - William Olson
- Therapeutic Proteins, Regeneron Pharmaceuticals, Tarrytown, NY, USA
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HiBiT-qIP, HiBiT-based quantitative immunoprecipitation, facilitates the determination of antibody affinity under immunoprecipitation conditions. Sci Rep 2019; 9:6895. [PMID: 31053795 PMCID: PMC6499798 DOI: 10.1038/s41598-019-43319-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/31/2019] [Indexed: 12/23/2022] Open
Abstract
The affinity of an antibody for its antigen serves as a critical parameter for antibody evaluation. The evaluation of antibody-antigen affinity is essential for a successful antibody-based assay, particularly immunoprecipitation (IP), due to its strict dependency on antibody performance. However, the determination of antibody affinity or its quantitative determinant, the dissociation constant (Kd), under IP conditions is difficult. In the current study, we used a NanoLuc-based HiBiT system to establish a HiBiT-based quantitative immunoprecipitation (HiBiT-qIP) assay for determining the Kd of antigen-antibody interactions in solution. The HiBiT-qIP method measures the amount of immunoprecipitated proteins tagged with HiBiT in a simple yet quantitative manner. We used this method to measure the Kd values of epitope tag-antibody interactions. To accomplish this, FLAG, HA, V5, PA and Ty1 epitope tags in their monomeric, dimeric or trimeric form were fused with glutathione S-transferase (GST) and the HiBiT peptide, and these tagged GST proteins were mixed with cognate monoclonal antibodies in IP buffer for the assessment of the apparent Kd values. This HiBiT-qIP assay showed a considerable variation in the Kd values among the examined antibody clones. Additionally, the use of epitope tags in multimeric form revealed a copy number-dependent increase in the apparent affinity.
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Kunc F, Moore CJ, Sully RE, Hall AJ, Gubala V. Polycarboxylated Dextran as a Multivalent Linker: Synthesis and Target Recognition of the Antibody-Nanoparticle Bioconjugates in PBS and Serum. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:4909-4917. [PMID: 30817890 DOI: 10.1021/acs.langmuir.8b03833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanoparticles (NPs) functionalized with antibodies on their surface are used in a wide range of research applications. However, the bioconjugation chemistry between the antibodies and the surface of nanoparticles can be very challenging, often accompanied by several undesired effects such as nanoparticle aggregation, antibody denaturation, or poor target recognition of the surface-bound antibodies. Here, we report on a synthesis of fluorescent silica nanoparticle-antibody (NP-Ab) conjugates, in which polycarboxylated dextran is used as the multivalent linker. First, we present a synthetic methodology to prepare polycarboxylated dextrans with molecular weights of 6, 40, and 70 kDa. Second, we used water-soluble, polycarboxylated dextrans as a multivalent spacers/linkers to immobilize antibodies onto fluorescent silica nanoparticles. The prepared NP-Ab conjugates were tested in a direct binding assay format in both phosphate-buffered saline buffer and whole serum to investigate the role of the spacer/linker in the capacity of the NP-Ab to specifically recognize their target in "clean" and also in complex media. We have compared the dextran conjugates with two standards: (a) NP-Ab with antibodies attached on the surface of nanoparticles through the classical physical adsorption method and (b) NP-Ab where an established poly(amidoamine) (PAMAM) dendrimer was used as the linker. Our results showed that the polycarboxylated 6 kDa dextran facilitates antibody immobilization efficiency of nearly 92%. This was directly translated into the improved molecular recognition of the NP-Ab, which was measured by a direct binding assay. The signal-to-noise ratio in buffered solution for the 6 kDa dextran NP-Ab conjugates was 81, nearly 3 times higher than that of PAMAM G4.5 conjugates and 9 times higher than the physically adsorbed NP-Ab sample. In whole serum, the effect of 6 kDa dextran was more hindered due to the formation of protein corona but the signal-to-noise ratio was at least double that of the physically adsorbed NP-Ab conjugates.
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Affiliation(s)
- Filip Kunc
- National Research Council Canada , 100 Sussex Drive , Ottawa , Ontario K1N 0R6 , Canada
| | - Colin J Moore
- Italian Institute of Technology , 30 Via Morego , Genoa 16163 , Italy
| | - Rachel E Sully
- Medway School of Pharmacy , Universities of Greenwich and Kent , Anson Building, Central Avenue , Chatham ME4 4TB , U.K
| | - Andrew J Hall
- Medway School of Pharmacy , Universities of Greenwich and Kent , Anson Building, Central Avenue , Chatham ME4 4TB , U.K
| | - Vladimir Gubala
- Medway School of Pharmacy , Universities of Greenwich and Kent , Anson Building, Central Avenue , Chatham ME4 4TB , U.K
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The KN-93 Molecule Inhibits Calcium/Calmodulin-Dependent Protein Kinase II (CaMKII) Activity by Binding to Ca 2+/CaM. J Mol Biol 2019; 431:1440-1459. [PMID: 30753871 DOI: 10.1016/j.jmb.2019.02.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/14/2018] [Accepted: 02/04/2019] [Indexed: 12/22/2022]
Abstract
Calcium/calmodulin-dependent protein kinase II (CaMKII) is a multifunctional serine/threonine protein kinase that transmits calcium signals in various cellular processes. CaMKII is activated by calcium-bound calmodulin (Ca2+/CaM) through a direct binding mechanism involving a regulatory C-terminal α-helix in CaMKII. The Ca2+/CaM binding triggers transphosphorylation of critical threonine residues proximal to the CaM-binding site leading to the autoactivated state of CaMKII. The demonstration of its critical roles in pathophysiological processes has elevated CaMKII to a key target in the management of numerous diseases. The molecule KN-93 is the most widely used inhibitor for studying the cellular and in vivo functions of CaMKII. It is widely believed that KN-93 binds directly to CaMKII, thus preventing kinase activation by competing with Ca2+/CaM. Herein, we employed surface plasmon resonance, NMR, and isothermal titration calorimetry to characterize this presumed interaction. Our results revealed that KN-93 binds directly to Ca2+/CaM and not to CaMKII. This binding would disrupt the ability of Ca2+/CaM to interact with CaMKII, effectively inhibiting CaMKII activation. Our findings also indicated that KN-93 can specifically compete with a CaMKIIδ-derived peptide for binding to Ca2+/CaM. As indicated by the surface plasmon resonance and isothermal titration calorimetry data, apparently at least two KN-93 molecules can bind to Ca2+/CaM. Our findings provide new insight into how in vitro and in vivo data obtained with KN-93 should be interpreted. They further suggest that other Ca2+/CaM-dependent, non-CaMKII activities should be considered in KN-93-based mechanism-of-action studies and drug discovery efforts.
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Liddament M, Husten J, Estephan T, Laine D, Mabon D, Pukac L, Lyons J, Clarke AW, Doyle A. Higher Binding Affinity and in vitro Potency of Reslizumab for Interleukin-5 Compared With Mepolizumab. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2019; 11:291-298. [PMID: 30661320 PMCID: PMC6340799 DOI: 10.4168/aair.2019.11.2.291] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 11/21/2022]
Abstract
Reslizumab and mepolizumab are recently approved monoclonal antibodies for the treatment of severe (uncontrolled) eosinophilic asthma. Both are effective in neutralizing the function of interleukin-5 (IL-5). This study is the first to compare the binding affinity and in vitro potency of both antibodies in head-to-head assays. Two assays assessed binding affinity (using the equilibrium dissociation constant [KD]) of each drug for human IL-5. In the Biacore surface plasmon resonance assay, the association constant (kon) values for human IL-5 for reslizumab and mepolizumab were 3.93 × 106 and 1.83 × 105, respectively. The dissociation constant (koff) values were 4.29 × 10−4 and 2.14 × 10−4, respectively. Calculated KD values for human IL-5 for reslizumab and mepolizumab were 109 and 1,170 pM, respectively, representing an approximately 11-fold stronger binding affinity with reslizumab. In the Kinetic Exclusion Assay, the kon values for human IL-5 for reslizumab and mepolizumab were 3.17 × 106 and 1.32 × 105, respectively. The koff values were 1.36 × 10−5 and 1.48 × 10−5, respectively. Measured KD values for human IL-5 for reslizumab and mepolizumab were 4.3 and 112 pM, respectively, representing an approximately 26-fold stronger binding affinity for reslizumab. A human-IL-5-dependent cell proliferation assay was developed to assess in vitro potency, based on a human cell line selected for enhanced surface expression of IL-5 receptor-alpha and consistent proliferation response to IL-5. The concentration at which 50% inhibition occurred (IC50) was determined for both antibodies. Reslizumab and mepolizumab inhibited IL-5-dependent cell proliferation, with IC50 values of approximately 91.1 and 286.5 pM, respectively, representing on average 3.1-fold higher potency with reslizumab. In conclusion, comparative assays show that reslizumab has higher affinity binding for and in vitro potency against human IL-5 compared with mepolizumab. However, these results do not take into consideration the different methods of administration of reslizumab and mepolizumab.
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Affiliation(s)
- Mark Liddament
- R&D, Biologics Lead Antibody Discovery, Teva Pharmaceuticals Australia, Sydney, NSW, Australia.
| | - Jean Husten
- R&D, Biologics, Teva Pharmaceuticals USA, West Chester, PA, USA
| | - Tanya Estephan
- R&D, Biologics Lead Antibody Discovery, Teva Pharmaceuticals Australia, Sydney, NSW, Australia.
| | - David Laine
- R&D, Biologics Lead Antibody Discovery, Teva Pharmaceuticals Australia, Sydney, NSW, Australia
| | - David Mabon
- R&D, Biologics Lead Antibody Discovery, Teva Pharmaceuticals Australia, Sydney, NSW, Australia
| | - Laurie Pukac
- R&D, Biologics, Teva Pharmaceuticals USA, West Chester, PA, USA
| | - Jacquelyn Lyons
- R&D, Biologics, Teva Pharmaceuticals USA, West Chester, PA, USA
| | - Adam W Clarke
- R&D, Biologics Lead Antibody Discovery, Teva Pharmaceuticals Australia, Sydney, NSW, Australia
| | - Anthony Doyle
- R&D, Biologics Lead Antibody Discovery, Teva Pharmaceuticals Australia, Sydney, NSW, Australia
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Prado E, Bonnat L, Bonnet H, Lavergne T, Van der Heyden A, Pratviel G, Dejeu J, Defrancq E. Influence of the SPR Experimental Conditions on the G-Quadruplex DNA Recognition by Porphyrin Derivatives. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:13057-13064. [PMID: 30293430 DOI: 10.1021/acs.langmuir.8b02942] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Surface plasmon resonance (SPR) is a powerful technique to study the interactions of ligands with analytes and therefore a number of biosensor surfaces and injection methods have been developed so far. However, many experimental parameters can affect the interactions and consequently the affinity measurements. In particular, the interactions of positively charged analytes (often used for anionic nucleic acids targets) can be influenced by the sensing surfaces (e.g., negatively charged), leading to significant nonspecific interactions as well as regeneration problems. The aim of the present work is to investigate the effect of different parameters, including ionic strength, SPR biosensor (i.e., nature of the surfaces), and the injection method on the recognition of porphyrin G-quadruplex ligands. We demonstrate that the injection method does not influence the affinity whereas the ionic strength and the nature of the surface impact the recognition properties of the porphyrin for the G-quadruplex DNA. We also found that self-assembled monolayer coating surface presents many advantages in comparison with carboxymethylated dextran surface for SPR studies of G-quadruplex DNA/ligand interactions: (i) the electrostatic interaction with charged analytes is less important, (ii) its structure/composition is less sensitive to the ionic concentration and less prone to unspecific adsorption, (iii) it is easily homemade, and (iv) the cost is approximately 10 times cheaper.
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Affiliation(s)
- E Prado
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - L Bonnat
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - H Bonnet
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - T Lavergne
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | | | - G Pratviel
- CNRS, Laboratoire de Chimie de Coordination , 205 route de Narbonne, BP44099 , F-31077 Toulouse Cedex 4, France
- Université de Toulouse, UPS, INPT , Toulouse , France
| | - J Dejeu
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - E Defrancq
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
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Carbodiimide-mediated immobilization of acidic biomolecules on reversed-charge zwitterionic sensor chip surfaces. Anal Bioanal Chem 2018; 410:4109-4122. [PMID: 29707751 DOI: 10.1007/s00216-018-1048-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/15/2018] [Accepted: 03/27/2018] [Indexed: 02/05/2023]
Abstract
The carbodiimide-mediated amine coupling of protein ligands to sensor chips coated with anionic polycarboxylate hydrogels, such as carboxymethyl dextran, is the predominant covalent immobilization procedure utilized in optical biosensors, namely surface plasmon resonance (SPR) biosensors. Usually, electrostatic interactions at a slightly acidic pH and low ionic strength are employed to efficiently accumulate neutral and basic ligands on the chip surface, which are then covalently coupled by surface-bound active N-hydroxysuccinimide (NHS) esters. Unfortunately, this approach is not suitable for acidic proteins or other ligands with low isoelectric points (IEPs), such as nucleic acids, because the charge density of the polycarboxylates is greatly reduced at acidic pH or because electrostatic attraction cannot be achieved. To overcome these drawbacks, we have established a charge-reversal approach that allows the preconcentration of acidic proteins above their IEPs. A precisely controlled amount of tertiary amines is applied to reverse the previous anionic surface charge while maintaining carbodiimide compatibility with future protein immobilization. The mechanism of this reversed-charge immobilization approach was demonstrated employing protein A as a model protein and using attenuated total reflectance Fourier transform infrared spectroscopy, dynamic contact angle measurements, colorimetric quantification, and SPR analysis to characterize surface derivatization. Furthermore, even though it had previously proven impossible to preconcentrate DNA electrostatically and to covalently couple it to polyanionic chip surfaces, we demonstrated that our approach allowed DNA to be preconcentrated and immobilized in good yields. Graphical abstract Principle of the covalent immobilization of acidic ligands on reversed-charge zwitterionic sensor chip surfaces.
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31
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Discovery of High-Affinity PDGF-VEGFR Interactions: Redefining RTK Dynamics. Sci Rep 2017; 7:16439. [PMID: 29180757 PMCID: PMC5704011 DOI: 10.1038/s41598-017-16610-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/14/2017] [Indexed: 01/15/2023] Open
Abstract
Nearly all studies of angiogenesis have focused on uni-family ligand-receptor binding, e.g., VEGFs bind to VEGF receptors, PDGFs bind to PDGF receptors, etc. The discovery of VEGF-PDGFRs binding challenges this paradigm and calls for investigation of other ligand-receptor binding possibilities. We utilized surface plasmon resonance to identify and measure PDGF-to-VEGFR binding rates, establishing cut-offs for binding and non-binding interactions. We quantified the kinetics of the recent VEGF-A:PDGFRβ interaction for the first time with KD = 340 pM. We discovered new PDGF:VEGFR2 interactions with PDGF-AA:R2 KD = 530 nM, PDGF-AB:R2 KD = 110 pM, PDGF-BB:R2 KD = 40 nM, and PDGF-CC:R2 KD = 70 pM. We computationally predict that cross-family PDGF binding could contribute up to 96% of VEGFR2 ligation in healthy conditions and in cancer. Together the identification, quantification, and simulation of these novel cross-family interactions posits new mechanisms for understanding anti-angiogenic drug resistance and presents an expanded role of growth factor signaling with significance in health and disease.
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32
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de Paula HMC, Coelho YL, Agudelo AJP, Rezende JDP, Ferreira GMD, Ferreira GMD, Pires ACDS, da Silva LHM. Kinetics and thermodynamics of bovine serum albumin interactions with Congo red dye. Colloids Surf B Biointerfaces 2017; 159:737-742. [DOI: 10.1016/j.colsurfb.2017.08.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/17/2017] [Accepted: 08/19/2017] [Indexed: 10/19/2022]
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Lu D, Pang G, Xie J. A new phosphothreonine lyase electrochemical immunosensor for detecting Salmonella based on horseradish peroxidase/GNPs-thionine/chitosan. Biomed Microdevices 2017; 19:12. [PMID: 28194610 DOI: 10.1007/s10544-017-0149-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In the current study, a novel double-layer gold nanoparticles- electrochemical immunosensor electrode (DGN-EIE) immobilized with Salmonella plasmid virulence C (SpvC) antibody was developed. To increase the fixed quantity of antibodies and electrochemical signal, an electrochemical biosensing signal amplification system was utilized with gold nanoparticles-thionine-chitosan absorbing horseradish peroxidase (HRP). In addition, the SpvC monoclonal antibodies (derived from Balb/c mice) were prepared and screened with a high affinity to SpvC. To evaluate the quality of DGN-EIE, the amperometric I-t curve method was applied to determine Salmonella in PBS. The results showed that the response current had a good linear correlation with the bacterial quantity ranged from 1.0 × 101-5.0 × 104 cfu/mL. The lowest detection limit was found at 5 cfu/mL. Furthermore, the proposed immunosensor has been demonstrated with high sensitivity, good selectivity and reproducibility. Apparently, DGN-EIE may be a very useful tool for monitoring the bacteria.
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Affiliation(s)
- Dingqiang Lu
- Biotechnology & Food Science College, Tianjin University of Commerce, Tianjin, 300314, China
| | - Guangchang Pang
- Biotechnology & Food Science College, Tianjin University of Commerce, Tianjin, 300314, China. .,Tianjin Key Laboratory of Food Biotechnology, Tianjin, 300314, China.
| | - Junbo Xie
- Biotechnology & Food Science College, Tianjin University of Commerce, Tianjin, 300314, China. .,Tianjin Key Laboratory of Food Biotechnology, Tianjin, 300314, China.
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Zong H, Han L, Ding K, Wang J, Sun T, Zhang X, Cagliero C, Jiang H, Xie Y, Xu J, Zhang B, Zhu J. Producing defucosylated antibodies with enhanced in vitro antibody-dependent cellular cytotoxicity via FUT8 knockout CHO-S cells. Eng Life Sci 2017; 17:801-808. [PMID: 32624826 DOI: 10.1002/elsc.201600255] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/15/2017] [Accepted: 02/21/2017] [Indexed: 12/21/2022] Open
Abstract
To engineer a host cell line that produces defucosylated mAbs with superior antibody-dependent cellular cytotoxicity, we disrupted α-1, 6 fucosyltransferase (FUT8) gene in CHO-S (CHO is Chinese hamster ovary) cells by clustered regularly interspaced short palindromic repeats-CRISPR associated nuclease 9. The gene knockout cell line was evaluated for growth, stability, and product quality. The growth profile of FUT8 gene knockout CHO-S (FUT8 -/-) cells was comparable with wild type CHO-S cells. FUT8 catalyzes the transfer of a fucose residue from GDP-fucose to N-glycans residue. Defucosylated IgG1 antibodies produced by FUT8 -/- cells showed increased binding affinities to human FcγRIIIa and higher activities in mediating antibody-dependent cellular cytotoxicity, comparing with conventional fucosylated IgG1. Our results demonstrated the potential of using the clustered regularly interspaced short palindromic repeats-CRISPR associated nuclease 9 technology in cell line engineering for biopharmaceutical industrial applications.
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Affiliation(s)
- Huifang Zong
- Engineering Research Center of Cell & Therapeutic Antibody Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University Shanghai People's Republic of China
| | - Lei Han
- Engineering Research Center of Cell & Therapeutic Antibody Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University Shanghai People's Republic of China
| | - Kai Ding
- Engineering Research Center of Cell & Therapeutic Antibody Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University Shanghai People's Republic of China
| | - Jiaxian Wang
- Engineering Research Center of Cell & Therapeutic Antibody Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University Shanghai People's Republic of China
| | - Tao Sun
- Engineering Research Center of Cell & Therapeutic Antibody Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University Shanghai People's Republic of China
| | - Xinyu Zhang
- Engineering Research Center of Cell & Therapeutic Antibody Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University Shanghai People's Republic of China
| | | | | | | | - Jianrong Xu
- School of Medicine Shanghai Jiao Tong University Shanghai People's Republic of China
| | - Baohong Zhang
- Engineering Research Center of Cell & Therapeutic Antibody Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University Shanghai People's Republic of China
| | - Jianwei Zhu
- Engineering Research Center of Cell & Therapeutic Antibody Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University Shanghai People's Republic of China
- Jecho Laboratories Frederick MD USA
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Kamat V, Rafique A. Exploring sensitivity & throughput of a parallel flow SPRi biosensor for characterization of antibody-antigen interaction. Anal Biochem 2017; 525:8-22. [PMID: 28223164 DOI: 10.1016/j.ab.2017.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/06/2017] [Accepted: 02/14/2017] [Indexed: 12/12/2022]
Abstract
Rapid growth in the field of biotherapeutics has led to an increased demand for high-throughput, label-free biosensors exhibiting high sensitivity. To support the current needs, Sierra Sensors introduced a surface plasmon resonance imaging (SPRi) based biosensor, Molecular Affinity Screening System (MASS-1). We assessed the potential utility of MASS-1 to support Regeneron's therapeutic antibody discovery. A large panel of antibody-antigen interactions was characterized using MASS-1 and the kinetic data were compared with the Biacore 4000 biosensor. Less than 10% deviation in the binding rate constants measured across eight flow channels of MASS-1 was observed. The single injection cycle kinetic assay allowed rapid measurement of binding rate constants for antibody-antigen interactions. MASS-1 sensitivity was independent of protein immobilization level and kinetic analysis performed using ultra-low density mAb surfaces allowed characterization of picomolar affinity interactions without mass transport limitation. High-throughput characterization of a panel of 189 monoclonal antibodies to 13 different antigens with molecular weights ranging from 14kD to 105kD revealed that binding kinetic parameters measured on MASS-1 were comparable to those measured on Biacore 4000. Our data demonstrate that MASS-1 measures reliable binding kinetic parameters and has an appropriate combination of throughput and sensitivity to support discovery and development of therapeutic antibodies.
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Affiliation(s)
- Vishal Kamat
- Biomolecular HTS Center, Therapeutic Proteins, Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
| | - Ashique Rafique
- Biomolecular HTS Center, Therapeutic Proteins, Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
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36
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Scherag FD, Niestroj-Pahl R, Krusekopf S, Lücke K, Brandstetter T, Rühe J. Highly Selective Capture Surfaces on Medical Wires for Fishing Tumor Cells in Whole Blood. Anal Chem 2017; 89:1846-1854. [PMID: 28208267 DOI: 10.1021/acs.analchem.6b04219] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The detection of circulating tumor cells (CTCs) in the blood of cancer patients is a challenging task. CTCs are, especially at the early stages of cancer development, extremely rare cells hidden in a vast background of regular blood cells. We describe a new strategy for the isolation of CTCs from whole blood. The key component is a medical wire coated with a multilayer assembly that allows highly specific capture of EpCAM (epithelial cell adhesion molecule) positive CTCs from blood. The assembly is generated in a layer-by-layer fashion through photochemically induced C,H insertion reactions and consists of a protective layer, which shields the contacting solution from the metal, a protein resistant layer, which prevents nonspecific interactions with proteins and a layer containing the EpCAM antibodies. In vitro experiments show that these surfaces can capture tumor cells from whole blood with enrichment factors (specifically vs nonspecifically bound cells) of up to about 3000 compared to the number of leucocytes in the blood. The purity of the isolated cells is greater than 90%. After "fishing" them from the blood, the cells, still bound to the wire, can be genetically analyzed. This demonstrates that this strategy might prove useful for next generation sequencing.
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Affiliation(s)
- Frank D Scherag
- Department of Microsystems Engineering, University of Freiburg , Georges-Köhler-Allee 103, D-79110 Freiburg, Germany
| | | | | | - Klaus Lücke
- GILUPI GmbH , Hermannswerder 20a, 14473 Potsdam, Germany
| | - Thomas Brandstetter
- Department of Microsystems Engineering, University of Freiburg , Georges-Köhler-Allee 103, D-79110 Freiburg, Germany
| | - Jürgen Rühe
- Department of Microsystems Engineering, University of Freiburg , Georges-Köhler-Allee 103, D-79110 Freiburg, Germany
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Abstract
Monoclonal antibodies (MAbs) have become a substantial part of many pharmaceutical company portfolios. However, the development process of MAbs for clinical use is quite different than for small-molecule drugs. MAb development programs require careful interdisciplinary evaluations to ensure the pharmacology of both the MAb and the target antigen are well-understood. Selection of appropriate preclinical species must be carefully considered and the potential development of anti-drug antibodies (ADA) during these early studies can limit the value and complicate the performance and possible duration of preclinical studies. In human studies, many of the typical pharmacology studies such as renal or hepatic impairment evaluations may not be needed but the pharmacokinetics and pharmacodynamics of these agents is complex, often necessitating more comprehensive evaluation of clinical data and more complex bioanalytical assays than might be used for small molecules. This paper outlines concerns and strategies for development of MAbs from the early in vitro assessments needed through preclinical and clinical development. This review focuses on how to develop, submit, and comply with regulatory requirements for MAb therapeutics.
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38
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Chan YN, Boesch AW, Osei-Owusu NY, Emileh A, Crowley AR, Cocklin SL, Finstad SL, Linde CH, Howell RA, Zentner I, Cocklin S, Miles AR, Eckman JW, Alter G, Schmitz JE, Ackerman ME. IgG Binding Characteristics of Rhesus Macaque FcγR. THE JOURNAL OF IMMUNOLOGY 2016; 197:2936-47. [PMID: 27559046 DOI: 10.4049/jimmunol.1502252] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 07/26/2016] [Indexed: 11/19/2022]
Abstract
Indian rhesus macaques (Macaca mulatta) are routinely used in preclinical studies to evaluate therapeutic Abs and candidate vaccines. The efficacy of these interventions in many cases is known to rely heavily on the ability of Abs to interact with a set of Ab FcγR expressed on innate immune cells. Yet, despite their presumed functional importance, M. mulatta Ab receptors are largely uncharacterized, posing a fundamental limit to ensuring accurate interpretation and translation of results from studies in this model. In this article, we describe the binding characteristics of the most prevalent allotypic variants of M. mulatta FcγR for binding to both human and M. mulatta IgG of varying subclasses. The resulting determination of the affinity, specificity, and glycan sensitivity of these receptors promises to be useful in designing and evaluating studies of candidate vaccines and therapeutic Abs in this key animal model and exposes significant evolutionary divergence between humans and macaques.
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Affiliation(s)
- Ying N Chan
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755
| | - Austin W Boesch
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755
| | - Nana Y Osei-Owusu
- Molecular and Cellular Biology Program, Dartmouth College, Hanover, NH 03755
| | - Ali Emileh
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755
| | - Andrew R Crowley
- Molecular and Cellular Biology Program, Dartmouth College, Hanover, NH 03755
| | - Sarah L Cocklin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115
| | - Samantha L Finstad
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115
| | - Caitlyn H Linde
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115
| | - Rebecca A Howell
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115
| | - Isaac Zentner
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Simon Cocklin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Adam R Miles
- Wasatch Microfluidics, Salt Lake City, UT 84103; and
| | | | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | - Joern E Schmitz
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755; Molecular and Cellular Biology Program, Dartmouth College, Hanover, NH 03755;
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Fleming JK, Glass TR, Lackie SJ, Wojciak JM. A novel approach for measuring sphingosine-1-phosphate and lysophosphatidic acid binding to carrier proteins using monoclonal antibodies and the Kinetic Exclusion Assay. J Lipid Res 2016; 57:1737-47. [PMID: 27444045 DOI: 10.1194/jlr.d068866] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Indexed: 01/01/2023] Open
Abstract
Sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA) are bioactive signaling lysophospholipids that activate specific G protein-coupled receptors on the cell surface triggering numerous biological events. In circulation, S1P and LPA associate with specific carrier proteins or chaperones; serum albumin binds both S1P and LPA while HDL shuttles S1P via interactions with apoM. We used a series of kinetic exclusion assays in which monoclonal anti-S1P and anti-LPA antibodies competed with carrier protein for the lysophospholipid to measure the equilibrium dissociation constants (Kd) for these carrier proteins binding S1P and the major LPA species. Fatty acid-free (FAF)-BSA binds these lysophospholipids with the following Kd values: LPA(16:0), 68 nM; LPA(18:1), 130 nM; LPA(18:2), 350 nM; LPA(20:4), 2.2 μM; and S1P, 41 μM. FAF human serum albumin binds each lysophospholipid with comparable affinities. By measuring the apoM concentration and expanding the model to include endogenous ligand, we were able to resolve the Kd values for S1P binding apoM in the context of human HDL and LDL particles (21 nM and 2.4 nM, respectively). The novel competitive assay and analysis described herein enables measurement of Kd values of completely unmodified lysophospholipids binding unmodified carrier proteins in solution, and thus provide insights into S1P and LPA storage in the circulation system and may be useful in understanding chaperone-dependent receptor activation and signaling.
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40
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Lathwal S, Sikes HD. A Method for Designing Instrument-Free Quantitative Immunoassays. Anal Chem 2016; 88:3194-202. [DOI: 10.1021/acs.analchem.5b04538] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Shefali Lathwal
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hadley D. Sikes
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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41
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Abdiche YN, Harriman R, Deng X, Yeung YA, Miles A, Morishige W, Boustany L, Zhu L, Izquierdo SM, Harriman W. Assessing kinetic and epitopic diversity across orthogonal monoclonal antibody generation platforms. MAbs 2015; 8:264-77. [PMID: 26652308 PMCID: PMC4966639 DOI: 10.1080/19420862.2015.1118596] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The ability of monoclonal antibodies (mAbs) to target specific antigens with high precision has led to an increasing demand to generate them for therapeutic use in many disease areas. Historically, the discovery of therapeutic mAbs has relied upon the immunization of mammals and various in vitro display technologies. While the routine immunization of rodents yields clones that are stable in serum and have been selected against vast arrays of endogenous, non-target self-antigens, it is often difficult to obtain species cross-reactive mAbs owing to the generally high sequence similarity shared across human antigens and their mammalian orthologs. In vitro display technologies bypass this limitation, but lack an in vivo screening mechanism, and thus may potentially generate mAbs with undesirable binding specificity and stability issues. Chicken immunization is emerging as an attractive mAb discovery method because it combines the benefits of both in vivo and in vitro display methods. Since chickens are phylogenetically separated from mammals, their proteins share less sequence homology with those of humans, so human proteins are often immunogenic and can readily elicit rodent cross-reactive clones, which are necessary for in vivo proof of mechanism studies. Here, we compare the binding characteristics of mAbs isolated from chicken immunization, mouse immunization, and phage display of human antibody libraries. Our results show that chicken-derived mAbs not only recapitulate the kinetic diversity of mAbs sourced from other methods, but appear to offer an expanded repertoire of epitopes. Further, chicken-derived mAbs can bind their native serum antigen with very high affinity, highlighting their therapeutic potential.
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Affiliation(s)
| | | | - Xiaodi Deng
- a Protein Engineering, Rinat-Pfizer Inc. , South San Francisco , CA , USA
| | - Yik Andy Yeung
- a Protein Engineering, Rinat-Pfizer Inc. , South San Francisco , CA , USA
| | - Adam Miles
- c Wasatch Microfluidics , Salt Lake City , UT , USA
| | - Winse Morishige
- a Protein Engineering, Rinat-Pfizer Inc. , South San Francisco , CA , USA
| | - Leila Boustany
- a Protein Engineering, Rinat-Pfizer Inc. , South San Francisco , CA , USA
| | - Lei Zhu
- b Crystal Bioscience , CA , USA
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42
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Abdiche YN, Yeung YA, Chaparro-Riggers J, Barman I, Strop P, Chin SM, Pham A, Bolton G, McDonough D, Lindquist K, Pons J, Rajpal A. The neonatal Fc receptor (FcRn) binds independently to both sites of the IgG homodimer with identical affinity. MAbs 2015; 7:331-43. [PMID: 25658443 PMCID: PMC4622529 DOI: 10.1080/19420862.2015.1008353] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The neonatal Fc receptor (FcRn) is expressed by cells of epithelial, endothelial and myeloid lineages and performs multiple roles in adaptive immunity. Characterizing the FcRn/IgG interaction is fundamental to designing therapeutic antibodies because IgGs with moderately increased binding affinities for FcRn exhibit superior serum half-lives and efficacy. It has been hypothesized that 2 FcRn molecules bind an IgG homodimer with disparate affinities, yet their affinity constants are inconsistent across the literature. Using surface plasmon resonance biosensor assays that eliminated confounding experimental artifacts, we present data supporting an alternate hypothesis: 2 FcRn molecules saturate an IgG homodimer with identical affinities at independent sites, consistent with the symmetrical arrangement of the FcRn/Fc complex observed in the crystal structure published by Burmeister et al. in 1994. We find that human FcRn binds human IgG1 with an equilibrium dissociation constant (KD) of 760 ± 60 nM (N = 14) at 25°C and pH 5.8, and shows less than 25% variation across the other human subtypes. Human IgG1 binds cynomolgus monkey FcRn with a 2-fold higher affinity than human FcRn, and binds both mouse and rat FcRn with a 10-fold higher affinity than human FcRn. FcRn/IgG interactions from multiple species show less than a 2-fold weaker affinity at 37°C than at 25°C and appear independent of an IgG's variable region. Our in vivo data in mouse and rat models demonstrate that both affinity and avidity influence an IgG's serum half-life, which should be considered when choosing animals, especially transgenic systems, as surrogates.
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Key Words
- CFCA, calibration-free concentration analysis
- FcRn
- FcRn, neonatal Fc receptor
- IgG
- RU, response units
- Rmax, maximum binding response
- SPR
- SPR, surface plasmon resonance
- WT, wild-type
- anti-Id, anti-idiotypic
- cyFcRn, cynomolgus monkey FcRn
- cyIgG, cynomolgus monkey IgG
- hErbB2, human ErbB2
- hFcRn, human FcRn
- hIgG, human IgG
- label-free biosensor
- mAb, monoclonal antibody
- mFcRn, mouse FcRn
- neonatal Fc receptor
- pI, isoelectric point
- rFcRn, rat FcRn
- rIgG, rat IgG
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43
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Yamniuk AP, Newitt JA, Doyle ML, Arisaka F, Giannetti AM, Hensley P, Myszka DG, Schwarz FP, Thomson JA, Eisenstein E. Development of a Model Protein Interaction Pair as a Benchmarking Tool for the Quantitative Analysis of 2-Site Protein-Protein Interactions. J Biomol Tech 2015; 26:125-41. [PMID: 26543437 DOI: 10.7171/jbt.15-2604-001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A significant challenge in the molecular interaction field is to accurately determine the stoichiometry and stepwise binding affinity constants for macromolecules having >1 binding site. The mission of the Molecular Interactions Research Group (MIRG) of the Association of Biomolecular Resource Facilities (ABRF) is to show how biophysical technologies are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core technologies [such as biosensor, microcalorimetry, or analytic ultracentrifugation (AUC)]. In the present work, the MIRG has developed a robust model protein interaction pair consisting of a bivalent variant of the Bacillus amyloliquefaciens extracellular RNase barnase and a variant of its natural monovalent intracellular inhibitor protein barstar. It is demonstrated that this system can serve as a benchmarking tool for the quantitative analysis of 2-site protein-protein interactions. The protein interaction pair enables determination of precise binding constants for the barstar protein binding to 2 distinct sites on the bivalent barnase binding partner (termed binase), where the 2 binding sites were engineered to possess affinities that differed by 2 orders of magnitude. Multiple MIRG laboratories characterized the interaction using isothermal titration calorimetry (ITC), AUC, and surface plasmon resonance (SPR) methods to evaluate the feasibility of the system as a benchmarking model. Although general agreement was seen for the binding constants measured using solution-based ITC and AUC approaches, weaker affinity was seen for surface-based method SPR, with protein immobilization likely affecting affinity. An analysis of the results from multiple MIRG laboratories suggests that the bivalent barnase-barstar system is a suitable model for benchmarking new approaches for the quantitative characterization of complex biomolecular interactions.
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Affiliation(s)
- Aaron P Yamniuk
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - John A Newitt
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - Michael L Doyle
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - Fumio Arisaka
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - Anthony M Giannetti
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - Preston Hensley
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - David G Myszka
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - Fred P Schwarz
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - James A Thomson
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
| | - Edward Eisenstein
- 1 Bristol-Myers Squibb, Princeton, New Jersey 08540, USA; 2 Tokyo Institute of Technology, Yokohama 226-8503, Japan; 3 Google[x], Google Life Sciences, Mountain View, California 94043, USA; 4 SystaMedic, Incorporated, Groton, Connecticut 06340, USA; 5 Biosensor Tools LLC, Salt Lake City, Utah 84103, USA; 6 National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 7 Polaris Pharmaceuticals, Incorporated, San Diego, California 92121, USA; and 8 Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland 20850, USA
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44
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Yu Y, Mitchell S, Lynaugh H, Brown M, Nobrega RP, Zhi X, Sun T, Caffry I, Cao Y, Yang R, Burnina I, Xu Y, Estep P. Understanding ForteBio's Sensors for High-Throughput Kinetic and Epitope Screening for Purified Antibodies and Yeast Culture Supernatant. ACTA ACUST UNITED AC 2015; 21:88-95. [PMID: 26442912 PMCID: PMC4708621 DOI: 10.1177/1087057115609564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/09/2015] [Indexed: 01/26/2023]
Abstract
Real-time and label-free antibody screening systems are becoming more popular because of the increasing output of purified antibodies and antibody supernatant from many antibody discovery platforms. However, the properties of the biosensor can greatly affect the kinetic and epitope binning results generated by these label-free screening systems. ForteBio human-specific ProA, anti-human IgG quantitation (AHQ), anti-human Fc capture (AHC) sensors, and custom biotinylated-anti-human Fc capture (b-AHFc) sensors were evaluated in terms of loading ability, regeneration, kinetic characterization, and epitope binning with both purified IgG and IgG supernatant. AHC sensors proved unreliable for kinetic or binning assays at times, whereas AHQ sensors showed poor loading and regeneration abilities. ProA sensors worked well with both purified IgG and IgG supernatant. However, the interaction between ProA sensors and the Fab region of the IgG with VH3 germline limited the application of ProA sensors, especially in the epitope binning experiment. In an attempt to generate a biosensor type that would be compatible with a variety of germlines and sample types, we found that the custom b-AHFc sensors appeared to be robust working with both purified IgG and IgG supernatant, with little evidence of sensor-related artifacts.
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Affiliation(s)
- Yao Yu
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | - Scott Mitchell
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | | | | | | | - Xiaoyong Zhi
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | - Tingwan Sun
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | | | - Yuan Cao
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | - Rong Yang
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | | | - Yingda Xu
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
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45
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Lux G, Langer A, Pschenitza M, Karsunke X, Strasser R, Niessner R, Knopp D, Rant U. Detection of the Carcinogenic Water Pollutant Benzo[a]pyrene with an Electro-Switchable Biosurface. Anal Chem 2015; 87:4538-45. [DOI: 10.1021/acs.analchem.5b00648] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Gregor Lux
- Technische Universität
München, 85748 Garching, Germany
| | - Andreas Langer
- Technische Universität
München, 85748 Garching, Germany
- Dynamic Biosensors
GmbH, Lochhamer Strasse 15, 82152 Martinsried/Planegg, Germany
| | - Michael Pschenitza
- Institute
of Hydrochemistry and Chair of Analytical Chemistry, Technische Universität München, Marchioninistrasse 17, 81377 München, Germany
| | - Xaver Karsunke
- Institute
of Hydrochemistry and Chair of Analytical Chemistry, Technische Universität München, Marchioninistrasse 17, 81377 München, Germany
| | - Ralf Strasser
- Dynamic Biosensors
GmbH, Lochhamer Strasse 15, 82152 Martinsried/Planegg, Germany
| | - Reinhard Niessner
- Institute
of Hydrochemistry and Chair of Analytical Chemistry, Technische Universität München, Marchioninistrasse 17, 81377 München, Germany
| | - Dietmar Knopp
- Institute
of Hydrochemistry and Chair of Analytical Chemistry, Technische Universität München, Marchioninistrasse 17, 81377 München, Germany
| | - Ulrich Rant
- Dynamic Biosensors
GmbH, Lochhamer Strasse 15, 82152 Martinsried/Planegg, Germany
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46
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Abstract
Protein-protein interactions regulate many important cellular processes, including carbohydrate and lipid metabolism, cell cycle and cell death regulation, protein and nucleic acid metabolism, signal transduction, and cellular architecture. A complete understanding of cellular function depends on full characterization of the complex network of cellular protein-protein interactions, including measurements of their kinetic and binding properties. Surface plasmon resonance (SPR) is one of the commonly used technologies for detailed and quantitative studies of protein-protein interactions and determination of their equilibrium and kinetic parameters. SPR provides excellent instrumentation for a label-free, real-time investigation of protein-protein interactions. This chapter details the experimental design and proper use of the instrumentation for a kinetic experiment. It will provide readers with basic theory, assay setup, and the proper way of reporting this type of results with practical tips useful for SPR-based studies. A generic protocol for immobilizing ligands using amino coupling chemistry, also useful if an antibody affinity capture approach is used, performing kinetic studies, and collecting and analyzing data is described.
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Affiliation(s)
- Zaneta Nikolovska-Coleska
- Department of Pathology, University of Michigan Medical School, 4510E MSRB I, 1150 West Medical Center Drive, Ann Arbor, MI, 48109, USA,
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47
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Moore CJ, Montón H, O'Kennedy R, Williams DE, Nogués C, Crean (née Lynam) C, Gubala V. Controlling colloidal stability of silica nanoparticles during bioconjugation reactions with proteins and improving their longer-term stability, handling and storage. J Mater Chem B 2015; 3:2043-2055. [DOI: 10.1039/c4tb01915f] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Robust protocols for antibody-nanoparticle (Ab-NP) conjugation, and improved method for long-term stability and storage of Ab-NPs using cryoprotectants.
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Affiliation(s)
- C. J. Moore
- Medway School of Pharmacy
- Universities of Kent and Greenwich
- Chatham
- UK
| | - H. Montón
- Departament de Biologia Ceŀlular
- Fisiologia i Immunologia
- Universitat Autònoma de Barcelona
- Bellaterra
- Spain
| | - R. O'Kennedy
- National Centre for Sensor Research
- Biomedical Diagnostics Institute
- Dublin City University
- Dublin 9
- Ireland
| | - D. E. Williams
- National Centre for Sensor Research
- Biomedical Diagnostics Institute
- Dublin City University
- Dublin 9
- Ireland
| | - C. Nogués
- Departament de Biologia Ceŀlular
- Fisiologia i Immunologia
- Universitat Autònoma de Barcelona
- Bellaterra
- Spain
| | | | - V. Gubala
- Medway School of Pharmacy
- Universities of Kent and Greenwich
- Chatham
- UK
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48
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Wu Y, Ma H, Gu D, He J. A quartz crystal microbalance as a tool for biomolecular interaction studies. RSC Adv 2015. [DOI: 10.1039/c5ra05549k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A quartz crystal microbalance was successfully applied to quantitatively analyze biomolecular interactions using a poly(ethylene glycol) matrix and equations for impedance analysis of frequency changes at multiple overtones.
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Affiliation(s)
- Yuanzi Wu
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215125
- P. R. China
| | - Hongwei Ma
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215125
- P. R. China
| | - Dayong Gu
- Institute of Disease Control and Prevention
- Shenzhen International Travel Health Care Center
- Shenzhen Entry-exit Inspection and Quarantine Bureau
- Shenzhen
- P. R. China
| | - Jian'an He
- Institute of Disease Control and Prevention
- Shenzhen International Travel Health Care Center
- Shenzhen Entry-exit Inspection and Quarantine Bureau
- Shenzhen
- P. R. China
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49
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Affinity of FVIII-specific antibodies reveals major differences between neutralizing and nonneutralizing antibodies in humans. Blood 2014; 125:1180-8. [PMID: 25515962 DOI: 10.1182/blood-2014-09-598268] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recently, we reported that distinct immunoglobulin (Ig) isotypes and IgG subclasses of factor VIII (FVIII)-specific antibodies are found in different cohorts of patients with hemophilia A and in healthy individuals. Prompted by these findings, we further investigated the distinguishing properties among the different populations of FVIII-specific antibodies. We hypothesized that the affinity of antibodies would discriminate between the neutralizing and nonneutralizing antibodies found in different study cohorts. To test this idea, we established a competition-based enzyme-linked immunosorbent assay technology to assess the apparent affinities for each isotype and IgG subclass of FVIII-specific antibodies without the need for antibody purification. We present a unique data set of apparent affinities of FVIII-specific antibodies found in healthy individuals, patients with congenital hemophilia A with and without FVIII inhibitors, and patients with acquired hemophilia A. Our data indicate that FVIII-specific antibodies found in patients with FVIII inhibitors have an up to 100-fold higher apparent affinity than that of antibodies found in patients without inhibitors and in healthy individuals. High-affinity FVIII-specific antibodies could be retrospectively detected in longitudinal samples of an individual patient with FVIII inhibitors 543 days before the first positive Bethesda assay. This finding suggests that these antibodies might serve as potential biomarkers for evolving FVIII inhibitor responses.
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50
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Li F, Yang X, Li X, Li R, Zhao J, Wu H. Determination and Prediction of the Binding Interaction between Organophosphate Flame Retardants and p53. Chem Res Toxicol 2014; 27:1918-25. [DOI: 10.1021/tx5002157] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Fei Li
- Key
Laboratory of Coastal Zone Environmental Processes and Ecological
Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Shandong Provincial Key Laboratory
of Coastal Zone Environmental Processes, YICCAS, Yantai Shandong 264003, People’s Republic of China
| | - Xianhai Yang
- Key
Laboratory of Industrial Ecology and Environmental Engineering (MOE),
School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Xuehua Li
- Key
Laboratory of Industrial Ecology and Environmental Engineering (MOE),
School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Renmin Li
- Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong People’s Republic of China
| | - Jianmin Zhao
- Key
Laboratory of Coastal Zone Environmental Processes and Ecological
Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Shandong Provincial Key Laboratory
of Coastal Zone Environmental Processes, YICCAS, Yantai Shandong 264003, People’s Republic of China
| | - Huifeng Wu
- Key
Laboratory of Coastal Zone Environmental Processes and Ecological
Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Shandong Provincial Key Laboratory
of Coastal Zone Environmental Processes, YICCAS, Yantai Shandong 264003, People’s Republic of China
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