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Fischer J, Kaufmann JO, Weller MG. Simple Determination of Affinity Constants of Antibodies by Competitive Immunoassays. Methods Protoc 2024; 7:49. [PMID: 38921828 PMCID: PMC11206456 DOI: 10.3390/mps7030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
The affinity constant, also known as the equilibrium constant, binding constant, equilibrium association constant, or the reciprocal value, the equilibrium dissociation constant (Kd), can be considered as one of the most important characteristics for any antibody-antigen pair. Many methods based on different technologies have been proposed and used to determine this value. However, since a very large number of publications and commercial datasheets do not include this information, significant obstacles in performing such measurements seem to exist. In other cases where such data are reported, the results have often proved to be unreliable. This situation may indicate that most of the technologies available today require a high level of expertise and effort that does not seem to be available in many laboratories. In this paper, we present a simple approach based on standard immunoassay technology that is easy and quick to perform. It relies on the effect that the molar IC50 approaches the Kd value in the case of infinitely small concentrations of the reagent concentrations. A two-dimensional dilution of the reagents leads to an asymptotic convergence to Kd. The approach has some similarity to the well-known checkerboard titration used for the optimization of immunoassays. A well-known antibody against the FLAG peptide, clone M2, was used as a model system and the results were compared with other methods. This approach could be used in any case where a competitive assay is available or can be developed. The determination of an affinity constant should belong to the crucial parameters in any quality control of antibody-related products and assays and should be mandatory in papers using immunochemical protocols.
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Affiliation(s)
- Janina Fischer
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Strasse 11, 12489 Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Jan Ole Kaufmann
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Strasse 11, 12489 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Michael G. Weller
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Strasse 11, 12489 Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
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2
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Tscheuschner G, Ponader M, Raab C, Weider PS, Hartfiel R, Kaufmann JO, Völzke JL, Bosc-Bierne G, Prinz C, Schwaar T, Andrle P, Bäßler H, Nguyen K, Zhu Y, Mey ASJS, Mostafa A, Bald I, Weller MG. Efficient Purification of Cowpea Chlorotic Mottle Virus by a Novel Peptide Aptamer. Viruses 2023; 15:v15030697. [PMID: 36992405 PMCID: PMC10051510 DOI: 10.3390/v15030697] [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: 01/26/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/31/2023] Open
Abstract
The cowpea chlorotic mottle virus (CCMV) is a plant virus explored as a nanotechnological platform. The robust self-assembly mechanism of its capsid protein allows for drug encapsulation and targeted delivery. Additionally, the capsid nanoparticle can be used as a programmable platform to display different molecular moieties. In view of future applications, efficient production and purification of plant viruses are key steps. In established protocols, the need for ultracentrifugation is a significant limitation due to cost, difficult scalability, and safety issues. In addition, the purity of the final virus isolate often remains unclear. Here, an advanced protocol for the purification of the CCMV from infected plant tissue was developed, focusing on efficiency, economy, and final purity. The protocol involves precipitation with PEG 8000, followed by affinity extraction using a novel peptide aptamer. The efficiency of the protocol was validated using size exclusion chromatography, MALDI-TOF mass spectrometry, reversed-phase HPLC, and sandwich immunoassay. Furthermore, it was demonstrated that the final eluate of the affinity column is of exceptional purity (98.4%) determined by HPLC and detection at 220 nm. The scale-up of our proposed method seems to be straightforward, which opens the way to the large-scale production of such nanomaterials. This highly improved protocol may facilitate the use and implementation of plant viruses as nanotechnological platforms for in vitro and in vivo applications.
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Affiliation(s)
- Georg Tscheuschner
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Marco Ponader
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Christopher Raab
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Prisca S Weider
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Reni Hartfiel
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Jan Ole Kaufmann
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- Department of Diagnostic and Interventional Radiology, Technical University of Munich, 81675 Munich, Germany
| | - Jule L Völzke
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Gaby Bosc-Bierne
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Carsten Prinz
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | | | - Paul Andrle
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Henriette Bäßler
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Khoa Nguyen
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
| | - Yanchen Zhu
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
| | - Antonia S J S Mey
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
| | - Amr Mostafa
- Institute of Chemistry-Physical Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Ilko Bald
- Institute of Chemistry-Physical Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Michael G Weller
- Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
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4
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Kaufmann JO, Brangsch J, Kader A, Saatz J, Mangarova DB, Zacharias M, Kempf WE, Schwaar T, Ponader M, Adams LC, Möckel J, Botnar RM, Taupitz M, Mägdefessel L, Traub H, Hamm B, Weller MG, Makowski MR. ADAMTS4-specific MR probe to assess aortic aneurysms in vivo using synthetic peptide libraries. Nat Commun 2022; 13:2867. [PMID: 35606349 PMCID: PMC9126943 DOI: 10.1038/s41467-022-30464-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/03/2022] [Indexed: 11/25/2022] Open
Abstract
The incidence of abdominal aortic aneurysms (AAAs) has substantially increased during the last 20 years and their rupture remains the third most common cause of sudden death in the cardiovascular field after myocardial infarction and stroke. The only established clinical parameter to assess AAAs is based on the aneurysm size. Novel biomarkers are needed to improve the assessment of the risk of rupture. ADAMTS4 (A Disintegrin And Metalloproteinase with ThromboSpondin motifs 4) is a strongly upregulated proteoglycan cleaving enzyme in the unstable course of AAAs. In the screening of a one-bead-one-compound library against ADAMTS4, a low-molecular-weight cyclic peptide is discovered with favorable properties for in vivo molecular magnetic resonance imaging applications. After identification and characterization, it's potential is evaluated in an AAA mouse model. The ADAMTS4-specific probe enables the in vivo imaging-based prediction of aneurysm expansion and rupture.
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Affiliation(s)
- Jan O Kaufmann
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489, Berlin, Germany
- Federal Institute for Materials Research and Testing (BAM), Division 1.5 Protein Analysis, Richard-Willstätter-Str. 11, 12489, Berlin, Germany
| | - Julia Brangsch
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
- Institute of Animal Welfare, Animal Behavior and Laboratory Animal Science, Freie Universität Berlin, Königsweg 67, Building 21, 14163, Berlin, Germany
| | - Avan Kader
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 1-3, 14195, Berlin, Germany
- Department of Radiology, Klinikum rechts der Isar, Technische Universität München (TUM), Ismaninger Straße 22, 81675, Munich, Germany
| | - Jessica Saatz
- Federal Institute for Materials Research and Testing (BAM), Division 1.1 Inorganic Trace Analysis, Richard-Willstätter-Str. 11, 12489, Berlin, Germany
| | - Dilyana B Mangarova
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
- Institute of Veterinary Pathology, Freie Universität Berlin, Robert-von-Ostertag-Str. 15, Building 12, 14163, Berlin, Germany
| | - Martin Zacharias
- Center of Functional Protein Assemblies, Technische Universität München (TUM), Ernst-Otto-Fischer-Str. 9, 85748, Garching, Germany
| | - Wolfgang E Kempf
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technische Universität München (TUM), 81675, Munich, Germany
| | - Timm Schwaar
- Federal Institute for Materials Research and Testing (BAM), Division 1.0 SAFIA Technologies, Richard-Willstätter-Str. 11, 12489, Berlin, Germany
| | - Marco Ponader
- Federal Institute for Materials Research and Testing (BAM), Division 1.5 Protein Analysis, Richard-Willstätter-Str. 11, 12489, Berlin, Germany
| | - Lisa C Adams
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Jana Möckel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Rene M Botnar
- King's College London, School of Biomedical Engineering and Imaging Sciences, London, UK
- Wellcome Trust / EPSRC Centre for Medical Engineering, King's College London, London, UK
- BHF Centre of Excellence, King's College London, London, UK
- Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute in Intelligent Healthcare Engineering, Santiago de Chile, Campus San Joaquín - Avda.Vicuña Mackenna, 4860, Macul, Santiago, Chile
- St Thomas' Hospital Westminster Bridge Road, London, SE1 7EH, UK
- Denmark Hill Campus, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Matthias Taupitz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Lars Mägdefessel
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technische Universität München (TUM), 81675, Munich, Germany
| | - Heike Traub
- Federal Institute for Materials Research and Testing (BAM), Division 1.1 Inorganic Trace Analysis, Richard-Willstätter-Str. 11, 12489, Berlin, Germany
| | - Bernd Hamm
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Michael G Weller
- Federal Institute for Materials Research and Testing (BAM), Division 1.5 Protein Analysis, Richard-Willstätter-Str. 11, 12489, Berlin, Germany
| | - Marcus R Makowski
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany.
- Department of Radiology, Klinikum rechts der Isar, Technische Universität München (TUM), Ismaninger Straße 22, 81675, Munich, Germany.
- King's College London, School of Biomedical Engineering and Imaging Sciences, London, UK.
- St Thomas' Hospital Westminster Bridge Road, London, SE1 7EH, UK.
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5
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Kim H, Jang JH, Jung IY, Cho JH. A Novel Peptide as a Specific and Selective Probe for Klebsiella pneumoniae Detection. BIOSENSORS 2022; 12:bios12030153. [PMID: 35323423 PMCID: PMC8946155 DOI: 10.3390/bios12030153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 11/25/2022]
Abstract
Klebsiella pneumoniae is infamous for generating hospital-acquired infections, many of which are difficult to treat due to the bacterium’s multidrug resistance. A sensitive and robust detection method of K. pneumoniae can help prevent a disease outbreak. Herein, we used K. pneumoniae cells as bait to screen a commercially available phage-displayed random peptide library for peptides that could be used to detect K. pneumoniae. The biopanning-derived peptide TSATKFMMNLSP, named KP peptide, displayed a high selectivity for the K. pneumoniae with low cross-reactivity to related Gram-negative bacteria. The specific interaction between KP peptide and K. pneumoniae lipopolysaccharide resulted in the peptide’s selectivity against K. pneumoniae. Quantitative analysis of this interaction by enzyme-linked immunosorbent assay revealed that the KP peptide possessed higher specificity and sensitivity toward K. pneumoniae than commercially available anti-Klebsiella spp. antibodies and could detect K. pneumoniae at a detection limit of 104 CFU/mL. These results suggest that KP peptide can be a promising alternative to antibodies in developing a biosensor system for K. pneumoniae detection.
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Affiliation(s)
- Hyun Kim
- Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Korea; (H.K.); (J.H.J.)
| | - Ju Hye Jang
- Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Korea; (H.K.); (J.H.J.)
| | - In Young Jung
- Division of Applied Life Science (BK21Four), Gyeongsang National University, Jinju 52828, Korea;
| | - Ju Hyun Cho
- Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Korea; (H.K.); (J.H.J.)
- Division of Applied Life Science (BK21Four), Gyeongsang National University, Jinju 52828, Korea;
- Division of Life Science, Gyeongsang National University, Jinju 52828, Korea
- Correspondence: ; Tel.: +82-55-772-1347; Fax: +82-55-772-1349
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6
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Jendryczko K, Rzeszotko J, Krzyscik MA, Szymczyk J, Otlewski J, Szlachcic A. Peptibody Based on FGFR1-Binding Peptides From the FGF4 Sequence as a Cancer-Targeting Agent. Front Pharmacol 2021; 12:748936. [PMID: 34867353 PMCID: PMC8636100 DOI: 10.3389/fphar.2021.748936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/28/2021] [Indexed: 12/04/2022] Open
Abstract
Targeted therapies are a promising alternative to conventional chemotherapy, with an increasing number of therapeutics targeting specific molecular aberrancies in cancer cells. One of the emerging targets for directed cancer treatments is fibroblast growth factor receptors (FGFRs), which are known to be involved in the pathogenesis and progression of multiple cancer types, specially in lung, bladder, and breast cancers. Here, we are demonstrating the development of the FGFR1-targeting agent based on the interactome screening approach, based on the isolation of binding regions from ligands interacting with the receptor. The parallel analysis by FGFR1 pull-down of chymotryptic peptides coupled with MS analysis, and PepSpot analysis yielded equivalent peptide sequences from FGF4, one of the FGFR1 ligands. Three sequences served as a basis for peptibody (Fc-fusion) generation, to overcome clinical limitations of peptidic agents, and two of them showed favorable FGFR1-binding in vitro and FGFR1-dependent internalization into cells. To validate if developed FGFR1-targeting peptibodies can be used for drug delivery, similar to the well-established concept of antibody-drug conjugates (ADCs), peptibodyF4_1 was successfully conjugated with monomethylauristatin E (MMAE), and has shown significant and specific toxicity toward FGFR1-expressing lung cancer cell lines, with nanomolar EC50 values. Essentially, the development of new effective FGFR1 binders that comprise the naturally occurring FGFR-recognition peptides and Fc region ensuring high plasma stability, and long bloodstream circulation is an interesting strategy expanding targeted anticancer agents' portfolio. Furthermore, identifying peptides effectively binding the receptor from sequences of its ligands is not limited to FGFRs and is an approach versatile enough to be a basis for a new peptide/peptibodies development strategy.
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Affiliation(s)
| | | | | | | | | | - Anna Szlachcic
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
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7
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Siriwardena T, Gan BH, Köhler T, van Delden C, Javor S, Reymond JL. Stereorandomization as a Method to Probe Peptide Bioactivity. ACS CENTRAL SCIENCE 2021; 7:126-134. [PMID: 33532575 PMCID: PMC7845017 DOI: 10.1021/acscentsci.0c01135] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 06/01/2023]
Abstract
Solid-phase peptide synthesis (SPPS) is usually performed with optically pure building blocks to prepare peptides as single enantiomers. Herein we report that SPPS using racemic amino acids provides stereorandomized (sr) peptides, containing up to billions of different stereoisomers, as well-defined single HPLC peaks, single mass products with high yield, which can be used to investigate peptide bioactivity. To exemplify our method, we show that stereorandomization abolishes the membrane-disruptive effect of α-helical amphiphilic antimicrobial peptides but preserves their antibiofilm effect, implying different mechanisms involving folded versus disordered conformations. For antimicrobial peptide dendrimers by contrast, stereorandomization preserves antibacterial, membrane-disruptive, and antibiofilm effects but reduces hemolysis and cytotoxicity, thereby increasing their therapeutic index. Finally, we identify partially stereorandomized analogues of the last resort cyclic peptide antibiotic polymyxin B with preserved antibacterial activity but lacking membrane-disruptive and lipopolysaccharide-neutralizing activity, pointing to the existence of additional targets.
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Affiliation(s)
- Thissa
N. Siriwardena
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Bee-Ha Gan
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Thilo Köhler
- Department
of Microbiology and Molecular Medicine, University of Geneva, Service
of Infectious Diseases, University Hospital
of Geneva, 1211 Geneva, Switzerland
| | - Christian van Delden
- Department
of Microbiology and Molecular Medicine, University of Geneva, Service
of Infectious Diseases, University Hospital
of Geneva, 1211 Geneva, Switzerland
| | - Sacha Javor
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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