1
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Ivanova JR, Benk AS, Schaefer JV, Dreier B, Hermann LO, Plückthun A, Missirlis D, Spatz JP. Designed Ankyrin Repeat Proteins as Actin Labels of Distinct Cytoskeletal Structures in Living Cells. ACS NANO 2024; 18:8919-8933. [PMID: 38489155 DOI: 10.1021/acsnano.3c12265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
The orchestrated assembly of actin and actin-binding proteins into cytoskeletal structures coordinates cell morphology changes during migration, cytokinesis, and adaptation to external stimuli. The accurate and unbiased visualization of the diverse actin assemblies within cells is an ongoing challenge. We describe here the identification and use of designed ankyrin repeat proteins (DARPins) as synthetic actin binders. Actin-binding DARPins were identified through ribosome display and validated biochemically. When introduced or expressed inside living cells, fluorescently labeled DARPins accumulated at actin filaments, validated through phalloidin colocalization on fixed cells. Nevertheless, different DARPins displayed different actin labeling patterns: some DARPins labeled efficiently dynamic structures, such as filopodia, lamellipodia, and blebs, while others accumulated primarily in stress fibers. This differential intracellular distribution correlated with DARPin-actin binding kinetics, as measured by fluorescence recovery after photobleaching experiments. Moreover, the rapid arrest of actin dynamics induced by pharmacological treatment led to the fast relocalization of DARPins. Our data support the hypothesis that the localization of actin probes depends on the inherent dynamic movement of the actin cytoskeleton. Compared to the widely used LifeAct probe, one DARPin exhibited enhanced signal-to-background ratio while retaining a similar ability to label stress fibers. In summary, we propose DARPins as promising actin-binding proteins for labeling or manipulation in living cells.
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Affiliation(s)
- Julia R Ivanova
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
- Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Amelie S Benk
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- CSL Behring AG, 3014 Bern, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Leon O Hermann
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Dimitris Missirlis
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, D-69120 Heidelberg, Germany
| | - Joachim P Spatz
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, D-69120 Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
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2
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Strubel A, Münick P, Hartmann O, Chaikuad A, Dreier B, Schaefer JV, Gebel J, Osterburg C, Tuppi M, Schäfer B, Buck V, Rosenfeldt M, Knapp S, Plückthun A, Diefenbacher ME, Dötsch V. DARPins detect the formation of hetero-tetramers of p63 and p73 in epithelial tissues and in squamous cell carcinoma. Cell Death Dis 2023; 14:674. [PMID: 37828008 PMCID: PMC10570377 DOI: 10.1038/s41419-023-06213-0] [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: 08/30/2023] [Revised: 09/15/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023]
Abstract
The two p53 homologues p63 and p73 regulate transcriptional programs in epithelial tissues and several cell types in these tissues express both proteins. All members of the p53 family form tetramers in their active state through a dedicated oligomerization domain that structurally assembles as a dimer of dimers. The oligomerization domain of p63 and p73 share a high sequence identity, but the p53 oligomerization domain is more divergent and it lacks a functionally important C-terminal helix present in the other two family members. Based on these structural differences, p53 does not hetero-oligomerize with p63 or p73. In contrast, p63 and p73 form hetero-oligomers of all possible stoichiometries, with the hetero-tetramer built from a p63 dimer and a p73 dimer being thermodynamically more stable than the two homo-tetramers. This predicts that in cells expressing both proteins a p632/p732 hetero-tetramer is formed. So far, the tools to investigate the biological function of this hetero-tetramer have been missing. Here we report the generation and characterization of Designed Ankyrin Repeat Proteins (DARPins) that bind with high affinity and selectivity to the p632/p732 hetero-tetramer. Using these DARPins we were able to confirm experimentally the existence of this hetero-tetramer in epithelial mouse and human tissues and show that its level increases in squamous cell carcinoma.
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Affiliation(s)
- Alexander Strubel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Philipp Münick
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Oliver Hartmann
- Department of Biochemistry and Molecular Biology I, University of Würzburg, 97074, Würzburg, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University, 60438, Frankfurt, Germany
- Structural Genomics Consortium, Goethe University, 60438, Frankfurt, Germany
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Jakob Gebel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Christian Osterburg
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Marcel Tuppi
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Birgit Schäfer
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Viktoria Buck
- Department of Pathology, University of Würzburg, 97074, Würzburg, Germany
| | - Mathias Rosenfeldt
- Department of Pathology, University of Würzburg, 97074, Würzburg, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University, 60438, Frankfurt, Germany
- Structural Genomics Consortium, Goethe University, 60438, Frankfurt, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Markus E Diefenbacher
- Department of Biochemistry and Molecular Biology I, University of Würzburg, 97074, Würzburg, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany.
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3
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Ohoka A, Sarkar CA. Facile Display of Homomultivalent Proteins for In Vitro Selections. ACS Synth Biol 2023; 12:634-638. [PMID: 36655840 PMCID: PMC9985468 DOI: 10.1021/acssynbio.2c00563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Low-affinity protein binders are emerging as valuable domains for therapeutic applications because of their higher specificity when presented in multivalent ligands that increase the overall strength and selectivity of receptor binding. De novo discovery of low-affinity binders would be enhanced by the large library sizes attainable with in vitro selection systems, but these platforms generally maximize recovery of high-affinity monovalent binders. Here, we present a facile technology that uses rolling circle amplification to create homomultivalent libraries. We show proof of principle of this approach in ribosome display with off-rate selections of a bivalent ligand against monovalent and bivalent targets, thereby demonstrating high enrichment (up to 166-fold) against a low-affinity target that is bivalent but not monovalent. This approach to homomultivalent library construction can be applied to any binder tolerant of N- and C-terminal fusions and provides a platform for performing in vitro display selections with controlled protein valency and orientation.
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Affiliation(s)
| | - Casim A. Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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4
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Strubel A, Münick P, Chaikuad A, Dreier B, Schaefer J, Gebel J, Osterburg C, Tuppi M, Schäfer B, Knapp S, Plückthun A, Dötsch V. Designed Ankyrin Repeat Proteins as a tool box for analyzing p63. Cell Death Differ 2022; 29:2445-2458. [PMID: 35717504 PMCID: PMC9751120 DOI: 10.1038/s41418-022-01030-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 01/31/2023] Open
Abstract
The function of the p53 transcription factor family is dependent on several folded domains. In addition to a DNA-binding domain, members of this family contain an oligomerization domain. p63 and p73 also contain a C-terminal Sterile α-motif domain. Inhibition of most transcription factors is difficult as most of them lack deep pockets that can be targeted by small organic molecules. Genetic knock-out procedures are powerful in identifying the overall function of a protein, but they do not easily allow one to investigate roles of individual domains. Here we describe the characterization of Designed Ankyrin Repeat Proteins (DARPins) that were selected as tight binders against all folded domains of p63. We determine binding affinities as well as specificities within the p53 protein family and show that DARPins can be used as intracellular inhibitors for the modulation of transcriptional activity. By selectively inhibiting DNA binding of the ΔNp63α isoform that competes with p53 for the same promoter sites, we show that p53 can be reactivated. We further show that inhibiting the DNA binding activity stabilizes p63, thus providing evidence for a transcriptionally regulated negative feedback loop. Furthermore, the ability of DARPins to bind to the DNA-binding domain and the Sterile α-motif domain within the dimeric-only and DNA-binding incompetent conformation of TAp63α suggests a high structural plasticity within this special conformation. In addition, the developed DARPins can also be used to specifically detect p63 in cell culture and in primary tissue and thus constitute a very versatile research tool for studying the function of p63.
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Affiliation(s)
- Alexander Strubel
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Philipp Münick
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Apirat Chaikuad
- grid.7839.50000 0004 1936 9721Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt, Germany ,grid.7839.50000 0004 1936 9721Structural Genomics Consortium, Goethe University, 60438 Frankfurt, Germany
| | - Birgit Dreier
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Jonas Schaefer
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Jakob Gebel
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Christian Osterburg
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Marcel Tuppi
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Birgit Schäfer
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Stefan Knapp
- grid.7839.50000 0004 1936 9721Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt, Germany ,grid.7839.50000 0004 1936 9721Structural Genomics Consortium, Goethe University, 60438 Frankfurt, Germany
| | - Andreas Plückthun
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Volker Dötsch
- grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
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5
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Programmable DARPin-based receptors for the detection of thrombotic markers. Nat Chem Biol 2022; 18:1125-1134. [PMID: 35941237 PMCID: PMC9512699 DOI: 10.1038/s41589-022-01095-3] [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] [Received: 06/22/2021] [Accepted: 06/23/2022] [Indexed: 11/08/2022]
Abstract
Cellular therapies remain constrained by the limited availability of sensors for disease markers. Here we present an integrated target-to-receptor pipeline for constructing a customizable advanced modular bispecific extracellular receptor (AMBER) that combines our generalized extracellular molecule sensor (GEMS) system with a high-throughput platform for generating designed ankyrin repeat proteins (DARPins). For proof of concept, we chose human fibrin degradation products (FDPs) as markers with high clinical relevance and screened a DARPin library for FDP binders. We built AMBERs equipped with 19 different DARPins selected from 160 hits, and found 4 of them to be functional as heterodimers with a known single-chain variable fragments binder. Tandem receptors consisting of combinations of the validated DARPins are also functional. We demonstrate applications of these AMBER receptors in vitro and in vivo by constructing designer cell lines that detect pathological concentrations of FDPs and respond with the production of a reporter and a therapeutic anti-thrombotic protein. ![]()
Merging the generalized extracellular molecule sensor (GEMS) system with screening designed ankyrin repeat proteins (DARPins) identifies an advanced modular bispecific extracellular receptor (AMBER) for detection of fibrinogen degradation products.
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6
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Markou GC, Ohoka A, Sarkar CA. Engineering a Minimal Leucine-rich Repeat IgG-binding Module. Appl Biochem Biotechnol 2021; 194:1636-1644. [PMID: 34837634 DOI: 10.1007/s12010-021-03768-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/16/2021] [Indexed: 12/27/2022]
Abstract
Sea lamprey immunization can yield leucine-rich repeat (LRR) protein binders analogous to globular antibodies developed from mammals. A novel minimal LRR was discovered through lamprey immunization with human immunoglobulin G Fc domain (IgG Fc). Initial attempts to solubly express this LRR protein, VLRB.IgGFc, in Escherichia coli proved challenging, so it was analyzed using the cell-free method ribosome display. In ribosome display, VLRB.IgGFc was found to bind specifically to the Fc domain of IgG, with little observed cross-reactivity to IgA or IgM. The minimal repeat protein architecture of VLRB.IgGFc may facilitate modular LRR extensions to incorporate additional or augmented functionality within a continuous, structurally defined scaffold. We exploited this modularity to design a chimera of a well-characterized, soluble LRR repebody and the initially insoluble VLRB.IgGFc to produce soluble Repe-VLRB.IgGFc. The minimal IgG Fc-binding module, Repe-VLRB.IgGFc, and future-engineered variants thereof should be useful additions to the biotechnological toolbox for detecting, purifying, or targeting IgGs. More generally, this two-step approach of minimal LRR binder discovery via sea lamprey immunization followed by modular augmentation of functionality may be of general utility in protein engineering.
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Affiliation(s)
- George C Markou
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ayako Ohoka
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Casim A Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
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7
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Friedrich N, Stiegeler E, Glögl M, Lemmin T, Hansen S, Kadelka C, Wu Y, Ernst P, Maliqi L, Foulkes C, Morin M, Eroglu M, Liechti T, Ivan B, Reinberg T, Schaefer JV, Karakus U, Ursprung S, Mann A, Rusert P, Kouyos RD, Robinson JA, Günthard HF, Plückthun A, Trkola A. Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization. Nat Commun 2021; 12:6705. [PMID: 34795280 PMCID: PMC8602657 DOI: 10.1038/s41467-021-27075-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
The V3 loop of the HIV-1 envelope (Env) protein elicits a vigorous, but largely non-neutralizing antibody response directed to the V3-crown, whereas rare broadly neutralizing antibodies (bnAbs) target the V3-base. Challenging this view, we present V3-crown directed broadly neutralizing Designed Ankyrin Repeat Proteins (bnDs) matching the breadth of V3-base bnAbs. While most bnAbs target prefusion Env, V3-crown bnDs bind open Env conformations triggered by CD4 engagement. BnDs achieve breadth by focusing on highly conserved residues that are accessible in two distinct V3 conformations, one of which resembles CCR5-bound V3. We further show that these V3-crown conformations can, in principle, be attacked by antibodies. Supporting this conclusion, analysis of antibody binding activity in the Swiss 4.5 K HIV-1 cohort (n = 4,281) revealed a co-evolution of V3-crown reactivities and neutralization breadth. Our results indicate a role of V3-crown responses and its conformational preferences in bnAb development to be considered in preventive and therapeutic approaches.
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Affiliation(s)
- Nikolas Friedrich
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Emanuel Stiegeler
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.424277.0Present Address: Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Deutschland
| | - Matthias Glögl
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Thomas Lemmin
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.5801.c0000 0001 2156 2780Department of Computer Science, ETH Zurich, Zurich, Switzerland ,grid.29078.340000 0001 2203 2861Present Address: Euler Institute, Faculty of Biomedicine, Università della Svizzera italiana (USI), Lugano, Switzerland
| | - Simon Hansen
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland ,Present Address: NGM Bio, 333 Oysterpoint Blvd, South San Francisco, CA 94080 USA
| | - Claus Kadelka
- grid.34421.300000 0004 1936 7312Department of Mathematics, Iowa State University, Ames, IA USA
| | - Yufan Wu
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland ,Present Address: Innovent Biologics Inc, 168 Dongping Street, Suzhou Industrial Park, 215123 China
| | - Patrick Ernst
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Present Address: Office Research and Teaching, Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Liridona Maliqi
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Caio Foulkes
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Mylène Morin
- grid.7400.30000 0004 1937 0650Department of Chemistry, University of Zurich (UZH), Zurich, Switzerland ,Present Address: BeiGene Switzerland GmbH, Aeschengraben 27, 4051 Basel, Switzerland
| | - Mustafa Eroglu
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,Present Address: Janssen Vaccines AG, Rehhagstrasse 79, 3018 Bern, Switzerland
| | - Thomas Liechti
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.419681.30000 0001 2164 9667Present Address: ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD USA
| | - Branislav Ivan
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.410567.1Present Address: Laboratory Medicine, Division of Clinical Chemistry, University Hospital Basel, Basel, Switzerland
| | - Thomas Reinberg
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Jonas V. Schaefer
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland ,grid.419481.10000 0001 1515 9979Present Address: Novartis Institutes for BioMedical Research, Chemical Biology & Therapeutics (CBT), Novartis Pharma AG, Virchow 16, 4056 Basel, Switzerland
| | - Umut Karakus
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Stephan Ursprung
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.5335.00000000121885934Present Address: University of Cambridge School of Clinical Medicine, Department of Radiology, Cambridge, CB2 0QQ UK
| | - Axel Mann
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,Present Address: Roche Innovation Center Zurich, Roche Pharmaceutical Research and Early Development (pRED), Wagistrasse 10, 8952 Schlieren, Switzerland
| | - Peter Rusert
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Roger D. Kouyos
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.412004.30000 0004 0478 9977Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - John A. Robinson
- grid.7400.30000 0004 1937 0650Department of Chemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Huldrych F. Günthard
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.412004.30000 0004 0478 9977Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Andreas Plückthun
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland.
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8
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Rouet R, Mazigi O, Walker GJ, Langley DB, Sobti M, Schofield P, Lenthall H, Jackson J, Ubiparipovic S, Henry JY, Abayasingam A, Burnett D, Kelleher A, Brink R, Bull RA, Turville S, Stewart AG, Goodnow CC, Rawlinson WD, Christ D. Potent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1 antibodies. MAbs 2021; 13:1922134. [PMID: 34024246 PMCID: PMC8158043 DOI: 10.1080/19420862.2021.1922134] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Antibodies against coronavirus spike protein potently protect against infection and disease, but whether such protection can be extended to variant coronaviruses is unclear. This is exemplified by a set of iconic and well-characterized monoclonal antibodies developed after the 2003 SARS outbreak, including mAbs m396, CR3022, CR3014 and 80R, which potently neutralize SARS-CoV-1, but not SARS-CoV-2. Here, we explore antibody engineering strategies to change and broaden their specificity, enabling nanomolar binding and potent neutralization of SARS-CoV-2. Intriguingly, while many of the matured clones maintained specificity of the parental antibody, new specificities were also observed, which was further confirmed by X-ray crystallography and cryo-electron microscopy, indicating that a limited set of VH antibody domains can give rise to variants targeting diverse epitopes, when paired with a diverse VL repertoire. Our findings open up over 15 years of antibody development efforts against SARS-CoV-1 to the SARS-CoV-2 field and outline general principles for the maturation of antibody specificity against emerging viruses.
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Affiliation(s)
- Romain Rouet
- Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia
| | - Ohan Mazigi
- Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia
| | - Gregory J Walker
- Immunology Department, UNSW Sydney, Faculty of Medicine, Sydney, NSW, Australia.,Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, Australia
| | - David B Langley
- Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia
| | - Meghna Sobti
- Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia.,Immunology Department, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Peter Schofield
- Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia
| | - Helen Lenthall
- Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia
| | - Jennifer Jackson
- Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia
| | - Stephanie Ubiparipovic
- Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia
| | - Jake Y Henry
- Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia
| | - Arunasingam Abayasingam
- Immunology Department, UNSW Sydney, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Deborah Burnett
- Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia
| | - Anthony Kelleher
- Immunology Department, UNSW Sydney, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Robert Brink
- Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia
| | - Rowena A Bull
- Immunology Department, UNSW Sydney, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Stuart Turville
- Immunology Department, UNSW Sydney, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Alastair G Stewart
- Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia.,Immunology Department, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Christopher C Goodnow
- Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia
| | - William D Rawlinson
- Immunology Department, UNSW Sydney, Faculty of Medicine, Sydney, NSW, Australia.,Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Daniel Christ
- Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Immunology Department, UNSW Sydney, St Vincent's Clinical School, Sydney, NSW, Australia
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9
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Engineering Af1521 improves ADP-ribose binding and identification of ADP-ribosylated proteins. Nat Commun 2020; 11:5199. [PMID: 33060572 PMCID: PMC7566600 DOI: 10.1038/s41467-020-18981-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 09/23/2020] [Indexed: 11/09/2022] Open
Abstract
Protein ADP-ribosylation is a reversible post-translational modification that regulates important cellular functions. The identification of modified proteins has proven challenging and has mainly been achieved via enrichment methodologies. Random mutagenesis was used here to develop an engineered Af1521 ADP-ribose binding macro domain protein with 1000-fold increased affinity towards ADP-ribose. The crystal structure reveals that two point mutations K35E and Y145R form a salt bridge within the ADP-ribose binding domain. This forces the proximal ribose to rotate within the binding pocket and, as a consequence, improves engineered Af1521 ADPr-binding affinity. Its use in our proteomic ADP-ribosylome workflow increases the ADP-ribosylated protein identification rates and yields greater ADP-ribosylome coverage. Furthermore, generation of an engineered Af1521 Fc fusion protein confirms the improved detection of cellular ADP-ribosylation by immunoblot and immunofluorescence. Thus, this engineered isoform of Af1521 can also serve as a valuable tool for the analysis of cellular ADP-ribosylation under in vivo conditions.
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10
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Gray A, Bradbury ARM, Knappik A, Plückthun A, Borrebaeck CAK, Dübel S. Animal-free alternatives and the antibody iceberg. Nat Biotechnol 2020; 38:1234-1239. [DOI: 10.1038/s41587-020-0687-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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11
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Zimmermann I, Egloff P, Hutter CAJ, Kuhn BT, Bräuer P, Newstead S, Dawson RJP, Geertsma ER, Seeger MA. Generation of synthetic nanobodies against delicate proteins. Nat Protoc 2020; 15:1707-1741. [PMID: 32269381 DOI: 10.1038/s41596-020-0304-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/16/2020] [Indexed: 12/21/2022]
Abstract
Here, we provide a protocol to generate synthetic nanobodies, known as sybodies, against any purified protein or protein complex within a 3-week period. Unlike methods that require animals for antibody generation, sybody selections are carried out entirely in vitro under controlled experimental conditions. This is particularly relevant for the generation of conformation-specific binders against labile membrane proteins or protein complexes and allows selections in the presence of non-covalent ligands. Sybodies are especially suited for cases where binder generation via immune libraries fails due to high sequence conservation, toxicity or insufficient stability of the target protein. The procedure entails a single round of ribosome display using the sybody libraries encoded by mRNA, followed by two rounds of phage display and binder identification by ELISA. The protocol is optimized to avoid undesired reduction in binder diversity and enrichment of non-specific binders to ensure the best possible selection outcome. Using the efficient fragment exchange (FX) cloning method, the sybody sequences are transferred from the phagemid to different expression vectors without the need to amplify them by PCR, which avoids unintentional shuffling of complementary determining regions. Using quantitative PCR (qPCR), the efficiency of each selection round is monitored to provide immediate feedback and guide troubleshooting. Our protocol can be carried out by any trained biochemist or molecular biologist using commercially available reagents and typically gives rise to 10-30 unique sybodies exhibiting binding affinities in the range of 500 pM-500 nM.
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Affiliation(s)
- Iwan Zimmermann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics AG, Zurich, Switzerland
| | - Pascal Egloff
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics AG, Zurich, Switzerland
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Benedikt T Kuhn
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Philipp Bräuer
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Roger J P Dawson
- Linkster Therapeutics AG, Zurich, Switzerland.,Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Eric R Geertsma
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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12
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Stainbrook SC, Tyo KEJ. Model-guided mechanism discovery and parameter selection for directed evolution. Appl Microbiol Biotechnol 2019; 103:9697-9709. [PMID: 31686141 DOI: 10.1007/s00253-019-10179-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/30/2019] [Accepted: 10/09/2019] [Indexed: 10/25/2022]
Abstract
Directed evolution is frequently applied to identify genetic variants with improvements in a single or multiple properties. When used to improve multiple properties simultaneously, a common strategy is to apply alternating rounds of selection criteria to enrich for variants with each desirable trait. In particular, counterselection, or selection against undesired traits rather than for desired ones, has been successfully employed in many studies. Although the sequence and stringency of alternating selective pressures for different traits are known to be highly consequential for the outcome of the screen, the effects of these parameters have not been systematically evaluated. We developed a method for producing a statistical modeling framework to elucidate these effects. The model uses single-cell fluorescence intensity distributions to estimate the proportions of phenotypic populations within a library and then predicts the changes in these proportions depending on specified positive selective or counterselective pressures. We validated the approach using recently described systems for metabolite-responsive bacterial transcription factors and yeast G-protein-coupled receptors. Finally, we applied the model to identify biological sources that exert undesirable selective pressure on libraries during sorting. Notably, these pressures produce substantial artifacts that, if unaddressed, can lead to failure of the screen. This method for model generation can be applied to FACS-based directed evolution experiments to create a quantitative framework that identifies subtle population effects. Such models can guide the choice of experimental design parameters to better enrich for true positive genetic variants and improve the chance of successful directed evolution.
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Affiliation(s)
- Sarah C Stainbrook
- Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Keith E J Tyo
- Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA. .,Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.
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13
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Abstract
Ribosome display has proven to be a powerful in vitro selection and evolution method for generating high-affinity binders from libraries of folded proteins. It works entirely in vitro, and this has two important consequences. First, since no transformation of any cells is required, libraries with much greater diversity can be handled than with most other techniques. Second, since a library does not have to be cloned and transformed, it is very convenient to introduce random errors in the library by PCR-based methods and select improved binders. Thus, a true directed evolution, an iteration between randomization and selection over several generations, can be conveniently carried out, e.g., for affinity maturation, either on a given clone or on the whole library. Ribosome display has been successfully applied to antibody single-chain Fv fragments (scFv), which can be selected not only for specificity but also for stability and catalytic activity. High-affinity binders with new target specificity can be obtained from highly diverse libraries in only a few selection rounds. In this protocol, the selection from the library and the process of affinity maturation and off-rate selection are explained in detail.
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14
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Li R, Kang G, Hu M, Huang H. Ribosome Display: A Potent Display Technology used for Selecting and Evolving Specific Binders with Desired Properties. Mol Biotechnol 2018; 61:60-71. [DOI: 10.1007/s12033-018-0133-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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15
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Advances in the Application of Designed Ankyrin Repeat Proteins (DARPins) as Research Tools and Protein Therapeutics. Methods Mol Biol 2018; 1798:307-327. [PMID: 29868969 DOI: 10.1007/978-1-4939-7893-9_23] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nonimmunoglobulin scaffolds have been developed to overcome the limitations of monoclonal antibodies with regard to stability and size. Of these scaffolds, the class of designed ankyrin repeat proteins (DARPins) has advanced the most in biochemical and biomedical applications. This review focuses on the recent progress in DARPin technology, highlighting the scaffold's potential and possibilities.
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16
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17
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Ahmad S, Pecqueur L, Dreier B, Hamdane D, Aumont-Nicaise M, Plückthun A, Knossow M, Gigant B. Destabilizing an interacting motif strengthens the association of a designed ankyrin repeat protein with tubulin. Sci Rep 2016; 6:28922. [PMID: 27380724 PMCID: PMC4933879 DOI: 10.1038/srep28922] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/13/2016] [Indexed: 01/10/2023] Open
Abstract
Affinity maturation by random mutagenesis and selection is an established technique to make binding molecules more suitable for applications in biomedical research, diagnostics and therapy. Here we identified an unexpected novel mechanism of affinity increase upon in vitro evolution of a tubulin-specific designed ankyrin repeat protein (DARPin). Structural analysis indicated that in the progenitor DARPin the C-terminal capping repeat (C-cap) undergoes a 25° rotation to avoid a clash with tubulin upon binding. Additionally, the C-cap appears to be involved in electrostatic repulsion with tubulin. Biochemical and structural characterizations demonstrated that the evolved mutants achieved a gain in affinity through destabilization of the C-cap, which relieves the need of a DARPin conformational change upon tubulin binding and removes unfavorable interactions in the complex. Therefore, this specific case of an order-to-disorder transition led to a 100-fold tighter complex with a subnanomolar equilibrium dissociation constant, remarkably associated with a 30% decrease of the binding surface.
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Affiliation(s)
- Shoeb Ahmad
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Ludovic Pecqueur
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Magali Aumont-Nicaise
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Marcel Knossow
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Benoît Gigant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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18
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Multivalent display of minimal Clostridium difficile glycan epitopes mimics antigenic properties of larger glycans. Nat Commun 2016; 7:11224. [PMID: 27091615 PMCID: PMC4838876 DOI: 10.1038/ncomms11224] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 02/26/2016] [Indexed: 12/31/2022] Open
Abstract
Synthetic cell-surface glycans are promising vaccine candidates against Clostridium difficile. The complexity of large, highly antigenic and immunogenic glycans is a synthetic challenge. Less complex antigens providing similar immune responses are desirable for vaccine development. Based on molecular-level glycan–antibody interaction analyses, we here demonstrate that the C. difficile surface polysaccharide-I (PS-I) can be resembled by multivalent display of minimal disaccharide epitopes on a synthetic scaffold that does not participate in binding. We show that antibody avidity as a measure of antigenicity increases by about five orders of magnitude when disaccharides are compared with constructs containing five disaccharides. The synthetic, pentavalent vaccine candidate containing a peptide T-cell epitope elicits weak but highly specific antibody responses to larger PS-I glycans in mice. This study highlights the potential of multivalently displaying small oligosaccharides to achieve antigenicity characteristic of larger glycans. The approach may result in more cost-efficient carbohydrate vaccines with reduced synthetic effort. Immunologically-active glycans are promising vaccine candidates but can be difficult to synthesize. Here, the authors show that pentavalent display of a minimal disaccharde epitope on a chemical scaffold can mimic a native C. difficile glycan antigen, representing a simple approach to synthetic vaccine production.
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19
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Generation of Fluorogen-Activating Designed Ankyrin Repeat Proteins (FADAs) as Versatile Sensor Tools. J Mol Biol 2016; 428:1272-1289. [PMID: 26812208 DOI: 10.1016/j.jmb.2016.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/12/2016] [Accepted: 01/15/2016] [Indexed: 11/21/2022]
Abstract
Fluorescent probes constitute a valuable toolbox to address a variety of biological questions and they have become irreplaceable for imaging methods. Commonly, such probes consist of fluorescent proteins or small organic fluorophores coupled to biological molecules of interest. Recently, a novel class of fluorescence-based probes, fluorogen-activating proteins (FAPs), has been reported. These binding proteins are based on antibody single-chain variable fragments and activate fluorogenic dyes, which only become fluorescent upon activation and do not fluoresce when free in solution. Here we present a novel class of fluorogen activators, termed FADAs, based on the very robust designed ankyrin repeat protein scaffold, which also readily folds in the reducing environment of the cytoplasm. The FADA generated in this study was obtained by combined selections with ribosome display and yeast surface display. It enhances the fluorescence of malachite green (MG) dyes by a factor of more than 11,000 and thus activates MG to a similar extent as FAPs based on single-chain variable fragments. As shown by structure determination and in vitro measurements, this FADA was evolved to form a homodimer for the activation of MG dyes. Exploiting the favorable properties of the designed ankyrin repeat protein scaffold, we created a FADA biosensor suitable for imaging of proteins on the cell surface, as well as in the cytosol. Moreover, based on the requirement of dimerization for strong fluorogen activation, a prototype FADA biosensor for in situ detection of a target protein and protein-protein interactions was developed. Therefore, FADAs are versatile fluorescent probes that are easily produced and suitable for diverse applications and thus extend the FAP technology.
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20
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Huang R, Gorman KT, Vinci CR, Dobrovetsky E, Gräslund S, Kay BK. Streamlining the Pipeline for Generation of Recombinant Affinity Reagents by Integrating the Affinity Maturation Step. Int J Mol Sci 2015; 16:23587-603. [PMID: 26437402 PMCID: PMC4632715 DOI: 10.3390/ijms161023587] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 09/18/2015] [Accepted: 09/23/2015] [Indexed: 12/26/2022] Open
Abstract
Often when generating recombinant affinity reagents to a target, one singles out an individual binder, constructs a secondary library of variants, and affinity selects a tighter or more specific binder. To enhance the throughput of this general approach, we have developed a more integrated strategy where the "affinity maturation" step is part of the phage-display pipeline, rather than a follow-on process. In our new schema, we perform two rounds of affinity selection, followed by error-prone PCR on the pools of recovered clones, generation of secondary libraries, and three additional rounds of affinity selection, under conditions of off-rate competition. We demonstrate the utility of this approach by generating low nanomolar fibronectin type III (FN3) monobodies to five human proteins: ubiquitin-conjugating enzyme E2 R1 (CDC34), COP9 signalosome complex subunit 5 (COPS5), mitogen-activated protein kinase kinase 5 (MAP2K5), Splicing factor 3A subunit 1 (SF3A1) and ubiquitin carboxyl-terminal hydrolase 11 (USP11). The affinities of the resulting monobodies are typically in the single-digit nanomolar range. We demonstrate the utility of two binders by pulling down the targets from a spiked lysate of HeLa cells. This integrated approach should be applicable to directed evolution of any phage-displayed affinity reagent scaffold.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
| | - Kevin T Gorman
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
| | - Chris R Vinci
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
| | - Elena Dobrovetsky
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, ON M5G1L7, Canada.
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, ON M5G1L7, Canada.
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
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21
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Plückthun A. Designed ankyrin repeat proteins (DARPins): binding proteins for research, diagnostics, and therapy. Annu Rev Pharmacol Toxicol 2015; 55:489-511. [PMID: 25562645 DOI: 10.1146/annurev-pharmtox-010611-134654] [Citation(s) in RCA: 406] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Designed ankyrin repeat proteins (DARPins) can recognize targets with specificities and affinities that equal or surpass those of antibodies, but because of their robustness and extreme stability, they allow a multitude of more advanced formats and applications. This review highlights recent advances in DARPin design, illustrates their properties, and gives some examples of their use. In research, they have been established as intracellular, real-time sensors of protein conformations and as crystallization chaperones. For future therapies, DARPins have been developed by advanced, structure-based protein engineering to selectively induce apoptosis in tumors by uncoupling surface receptors from their signaling cascades. They have also been used successfully for retargeting viruses. In ongoing clinical trials, DARPins have shown good safety and efficacy in macular degeneration diseases. These developments all ultimately exploit the high stability, solubility, and aggregation resistance of these molecules, permitting a wide range of conjugates and fusions to be produced and purified.
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Affiliation(s)
- Andreas Plückthun
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland;
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22
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Dodevski I, Markou GC, Sarkar CA. Conceptual and methodological advances in cell-free directed evolution. Curr Opin Struct Biol 2015; 33:1-7. [PMID: 26093059 DOI: 10.1016/j.sbi.2015.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/14/2015] [Accepted: 04/30/2015] [Indexed: 12/13/2022]
Abstract
Although cell-free directed evolution methods have been used to engineer proteins for nearly two decades, selections on more complex phenotypes have largely remained in the domain of cell-based engineering approaches. Here, we review recent conceptual advances that now enable in vitro display of multimeric proteins, integral membrane proteins, and proteins with an expanded amino acid repertoire. Additionally, we discuss methodological improvements that have enhanced the accessibility, efficiency, and robustness of cell-free approaches. Coupling these advances with the in vitro advantages of creating exceptionally large libraries and precisely controlling all experimental conditions, cell-free directed evolution is poised to contribute significantly to our understanding and engineering of more complex protein phenotypes.
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Affiliation(s)
- Igor Dodevski
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - George C Markou
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Casim A Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
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23
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He ZY, He QH, Xu Y, Li YP, Liu X, Chen B, Lei D, Sun CH. Ochratoxin A Mimotope from Second-Generation Peptide Library and Its Application in Immunoassay. Anal Chem 2013; 85:10304-11. [DOI: 10.1021/ac402127t] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Zhen-yun He
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Qing-hua He
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Yang Xu
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Yan-ping Li
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Xing Liu
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Bo Chen
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Da Lei
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Cheng-hao Sun
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
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24
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Fennell BJ, McDonnell B, Tam ASP, Chang L, Steven J, Broadbent ID, Gao H, Kieras E, Alley J, Luxenberg D, Edmonds J, Fitz LJ, Miao W, Whitters MJ, Medley QG, Guo YJ, Darmanin-Sheehan A, Autin B, Shúilleabháin DN, Cummins E, King A, Krebs MRH, Grace C, Hickling TP, Boisvert A, Zhong X, McKenna M, Francis C, Olland S, Bloom L, Paulsen J, Somers W, Jensen A, Lin L, Finlay WJJ, Cunningham O. CDR-restricted engineering of native human scFvs creates highly stable and soluble bifunctional antibodies for subcutaneous delivery. MAbs 2013; 5:882-95. [PMID: 23995618 PMCID: PMC3896602 DOI: 10.4161/mabs.26201] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
While myriad molecular formats for bispecific antibodies have been examined to date, the simplest structures are often based on the scFv. Issues with stability and manufacturability in scFv-based bispecific molecules, however, have been a significant hindrance to their development, particularly for high-concentration, stable formulations that allow subcutaneous delivery. Our aim was to generate a tetravalent bispecific molecule targeting two inflammatory mediators for synergistic immune modulation. We focused on an scFv-Fc-scFv format, with a flexible (A4T)3 linker coupling an additional scFv to the C-terminus of an scFv-Fc. While one of the lead scFvs isolated directly from a naïve library was well-behaved and sufficiently potent, the parental anti-CXCL13 scFv 3B4 required optimization for affinity, stability, and cynomolgus ortholog cross-reactivity. To achieve this, we eschewed framework-based stabilizing mutations in favor of complementarity-determining region (CDR) mutagenesis and re-selection for simultaneous improvements in both affinity and thermal stability. Phage-displayed 3B4 CDR-mutant libraries were used in an aggressive "hammer-hug" selection strategy that incorporated thermal challenge, functional, and biophysical screening. This approach identified leads with improved stability and>18-fold, and 4,100-fold higher affinity for both human and cynomolgus CXCL13, respectively. Improvements were exclusively mediated through only 4 mutations in VL-CDR3. Lead scFvs were reformatted into scFv-Fc-scFvs and their biophysical properties ranked. Our final candidate could be formulated in a standard biopharmaceutical platform buffer at 100 mg/ml with<2% high molecular weight species present after 7 weeks at 4 °C and viscosity<15 cP. This workflow has facilitated the identification of a truly manufacturable scFv-based bispecific therapeutic suitable for subcutaneous administration.
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Affiliation(s)
- Brian J Fennell
- Pfizer; Global Biotherapeutics Technologies; Dublin, Ireland
| | - Barry McDonnell
- Pfizer; Global Biotherapeutics Technologies; Dublin, Ireland
| | - Amy Sze Pui Tam
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | - Lijun Chang
- Pfizer; Global Biotherapeutics Technologies, Foresterhill; Aberdeen, UK
| | - John Steven
- Pfizer; Global Biotherapeutics Technologies, Foresterhill; Aberdeen, UK
| | - Ian D Broadbent
- Pfizer; Global Biotherapeutics Technologies, Foresterhill; Aberdeen, UK
| | - Huilan Gao
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | | | | | | | | | | | | | | | | | - Yongjing J Guo
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | | | - Bénédicte Autin
- Pfizer; Global Biotherapeutics Technologies; Dublin, Ireland
| | | | - Emma Cummins
- Pfizer; Global Biotherapeutics Technologies; Dublin, Ireland
| | - Amy King
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | - Mark R H Krebs
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | | | | | - Angela Boisvert
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | - Xiaotian Zhong
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | - Matthew McKenna
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | | | - Stephane Olland
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | - Laird Bloom
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | - Janet Paulsen
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | - Will Somers
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | - Allan Jensen
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | - Laura Lin
- Pfizer; Global Biotherapeutics Technologies; Cambridge, MA USA
| | | | - Orla Cunningham
- Pfizer; Global Biotherapeutics Technologies; Dublin, Ireland
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25
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Conformation-dependent recognition of HIV gp120 by designed ankyrin repeat proteins provides access to novel HIV entry inhibitors. J Virol 2013; 87:5868-81. [PMID: 23487463 DOI: 10.1128/jvi.00152-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we applied the designed ankyrin repeat protein (DARPin) technology to develop novel gp120-directed binding molecules with HIV entry-inhibiting capacity. DARPins are interesting molecules for HIV envelope inhibitor design, as their high-affinity binding differs from that of antibodies. DARPins in general prefer epitopes with a defined folded structure. We probed whether this capacity favors the selection of novel gp120-reactive molecules with specificities in epitope recognition and inhibitory activity that differ from those found among neutralizing antibodies. The preference of DARPins for defined structures was notable in our selections, since of the four gp120 modifications probed as selection targets, gp120 arrested by CD4 ligation proved the most successful. Of note, all the gp120-specific DARPin clones with HIV-neutralizing activity isolated recognized their target domains in a conformation-dependent manner. This was particularly pronounced for the V3 loop-specific DARPin 5m3_D12. In stark contrast to V3-specific antibodies, 5m3_D12 preferentially recognized the V3 loop in a specific conformation, as probed by structurally arrested V3 mimetic peptides, but bound linear V3 peptides only very weakly. Most notably, this conformation-dependent V3 recognition allowed 5m3_D12 to bypass the V1V2 shielding of several tier 2 HIV isolates and to neutralize these viruses. These data provide a proof of concept that the DARPin technology holds promise for the development of HIV entry inhibitors with a unique mechanism of action.
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Ebersbach H, Geisse S. Antigen generation and display in therapeutic antibody drug discovery -- a neglected but critical player. Biotechnol J 2012; 7:1433-43. [PMID: 23139179 DOI: 10.1002/biot.201200066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/26/2012] [Accepted: 09/25/2012] [Indexed: 01/17/2023]
Abstract
Disease intervention by targeting a critical pathway molecule through a blocking antibody or interference by therapeutic proteins is currently en vogue. Generation of blocking antibodies or therapeutic proteins inevitably requires the production of recombinant proteins or cell-based immunogens. Thus, one could call the antigen molecule the neglected player in antibody drug discovery. The variety of methods available for making recombinant proteins or recombinant cell lines that present the target on the cell surface is extensive. These need to be addressed in conjunction with biochemical and biophysical quality criteria and the experimental application intended. Fundamentally, successful production and isolation of monoclonal antibodies requires optimized antigen preparation and presentation to the immune host. This review summarizes the most important aspects of antigen generation and display, enabling logical decision making to give rise to potent high-affinity antibodies.
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Affiliation(s)
- Hilmar Ebersbach
- NBC/NT, Novartis Institutes for BioMedical Research, Basel, Switzerland.
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Pecqueur L, Duellberg C, Dreier B, Jiang Q, Wang C, Plückthun A, Surrey T, Gigant B, Knossow M. A designed ankyrin repeat protein selected to bind to tubulin caps the microtubule plus end. Proc Natl Acad Sci U S A 2012; 109:12011-6. [PMID: 22778434 PMCID: PMC3409770 DOI: 10.1073/pnas.1204129109] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Microtubules are cytoskeleton filaments consisting of αβ-tubulin heterodimers. They switch between phases of growth and shrinkage. The underlying mechanism of this property, called dynamic instability, is not fully understood. Here, we identified a designed ankyrin repeat protein (DARPin) that interferes with microtubule assembly in a unique manner. The X-ray structure of its complex with GTP-tubulin shows that it binds to the β-tubulin surface exposed at microtubule (+) ends. The details of the structure provide insight into the role of GTP in microtubule polymerization and the conformational state of tubulin at the very microtubule end. They show in particular that GTP facilitates the tubulin structural switch that accompanies microtubule assembly but does not trigger it in unpolymerized tubulin. Total internal reflection fluorescence microscopy revealed that the DARPin specifically blocks growth at the microtubule (+) end by a selective end-capping mechanism, ultimately favoring microtubule disassembly from that end. DARPins promise to become designable tools for the dissection of microtubule dynamic properties selective for either of their two different ends.
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Affiliation(s)
- Ludovic Pecqueur
- Laboratoire d’Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France
| | - Christian Duellberg
- Microtubule Cytoskeleton Laboratory, London Research Institute, Cancer Research United Kingdom, London WC2A 4LY, United Kingdom
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland; and
| | - Qiyang Jiang
- Institute of Protein Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chunguang Wang
- Institute of Protein Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland; and
| | - Thomas Surrey
- Microtubule Cytoskeleton Laboratory, London Research Institute, Cancer Research United Kingdom, London WC2A 4LY, United Kingdom
| | - Benoît Gigant
- Laboratoire d’Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France
| | - Marcel Knossow
- Laboratoire d’Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France
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Miersch S, Sidhu SS. Synthetic antibodies: concepts, potential and practical considerations. Methods 2012; 57:486-98. [PMID: 22750306 DOI: 10.1016/j.ymeth.2012.06.012] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 06/18/2012] [Accepted: 06/21/2012] [Indexed: 01/08/2023] Open
Abstract
The last 100 years of enquiry into the fundamental basis of humoral immunity has resulted in the identification of antibodies as key molecular sentinels responsible for the in vivo surveillance, neutralization and clearance of foreign substances. Intense efforts aimed at understanding and exploiting their exquisite molecular specificity have positioned antibodies as a cornerstone supporting basic research, diagnostics and therapeutic applications [1]. More recently, efforts have aimed to circumvent the limitations of developing antibodies in animals by developing wholly in vitro techniques for designing antibodies of tailored specificity. This has been realized with the advent of synthetic antibody libraries that possess diversity outside the scope of natural immune repertoires and are thus capable of yielding specificities not otherwise attainable. This review examines the convergence of technologies that have contributed to the development of combinatorial phage-displayed antibody libraries. It further explores the practical concepts that underlie phage display, antibody diversity and the methods used in the generation of and selection from phage-displayed synthetic antibody libraries, highlighting specific applications in which design approaches gave rise to specificities that could not easily be obtained with libraries based upon natural immune repertories.
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Affiliation(s)
- S Miersch
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
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Conroy PJ, O'Kennedy RJ, Hearty S. Cardiac troponin I: a case study in rational antibody design for human diagnostics. Protein Eng Des Sel 2012; 25:295-305. [PMID: 22509048 DOI: 10.1093/protein/gzs018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In vitro diagnostic (IVD) platforms provide rapid and accurate determination of disease status. The clinical performance of antibody-based diagnostic platforms is paramount as the information provided often informs the medical intervention taken and, ultimately, the patient's outcome. Breaking down such an immuno-IVD device into its component elements, the biorecognition entity is key to the analytical specificity of the test. Furthermore, tailored optimisation of the antibody is often necessary to impart the desired biophysical properties for the specific application. This tailoring is now widely facilitated by advances in combinatorial approaches to antibody generation, molecular evolution strategies and the availability of truly high-throughput (HT), refined surface plasmon resonance-based screening tools. In this paper, we demonstrate a rational, knowledge-driven approach to the generation of epitope-specific antibodies for the early detection of cardiovascular disease, discuss the merits of the approaches taken and offer a perspective on HT strategies to mining large antibody libraries. These results highlight the expedience of such methodologies for the development of truly superior cardiovascular disease biorecognition elements.
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Affiliation(s)
- P J Conroy
- Biomedical Diagnostics Institute, National Centre for Sensor Research and School of Biotechnology, Dublin City University, Dublin 9, Ireland
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30
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Sepp A, Griffiths A. Cell-free selection of domain antibodies by in vitro compartmentalization. Methods Mol Biol 2012; 911:183-198. [PMID: 22886253 DOI: 10.1007/978-1-61779-968-6_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Efficient identification of antibodies, or any fragments thereof, displaying desired specificity and affinity is critical for the development of novel immunotherapeutics. Here we describe the adaptation of in vitro compartmentalization for the cell-free selection of Vκ and VH domain antibodies (dAbs™) from large combinatorial libraries. The dAbs™ are in vitro expressed in fusion to the N-terminus of single-chain variant of phage P22 Arc repressor DNA-binding domain that links the compartmentally expressed protein molecules to their encoding PCR fragment-based genes via cognate operator sites present on the DNA. Libraries of up to 10(10) in size can be rapidly assembled and selected for improved affinity in equilibrium and off-rate conditions.
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Affiliation(s)
- Armin Sepp
- Innovation Biopharm Discovery Unit, Biopharm R&D, GlaxoSmithKline Plc, Cambridge, UK.
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31
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Abstract
In the last few decades, several new methods have been established to isolate full antibodies and fragments thereof, some even using alternative scaffolds from in vivo and in vitro sources. These methods encompass robust techniques including immunization and hybridoma technology or phage display and also more laborious and novel approaches including ribosome display or B-cell immortalization. All methodologies are dependent upon proper antigen presentation for isolation, screening, and further characterization of the selected binding molecules. Here, antigens are classes of molecules including soluble or membrane proteins, part or domains thereof (extracellular domains of GPCRs), peptides, carbohydrates, and small-molecular-weight moieties. Presentation of the antigen in a functional state or perhaps even mimicking the intended application is crucial for successful isolation of useful binding molecules. Moreover, it is also necessary to consider the expression host and any posttranslational modifications of target proteins. The increasing demand to target more complex antigens, for instance, receptors and ion channels, is leading to the development of alternative procedures to present these proteins appropriately, for example by the use of virus-like particles and DNA immunization. This chapter describes in general approaches for the preparation of different forms of immunogens including synthetic peptides, proteins, cell-based antigens for immunization and in vitro display systems and in detail the preparation of a soluble protein as antigen.
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Affiliation(s)
- Hilmar Ebersbach
- NIBR Biologics Center, Novartis Institutes for BioMedical Research, Basel, Switzerland.
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32
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Abstract
Ribosome display has proven to be a powerful in vitro selection and evolution method for generating high-affinity binders from libraries of folded proteins. It has been successfully applied to single-chain Fv fragments of antibodies and alternative scaffolds, such as Designed Ankyrin Repeat Proteins (DARPins). High-affinity binders with new target specificity can be obtained from highly diverse DARPin libraries in only a few selection rounds. In this protocol, the selection from the library and the process of affinity maturation and off-rate selection are explained in detail.
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Affiliation(s)
- Birgit Dreier
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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33
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Abstract
Ribosome display is an in vitro evolution technology for proteins. It is based on in vitro translation, but prevents the newly synthesized protein and the mRNA encoding it from leaving the ribosome. It thereby couples phenotype and genotype. Since no cells need to be transformed, very large libraries can be used directly in selections, and the in vitro amplification provides a very convenient integration of random mutagenesis that can be incorporated into the procedure. This review highlights concepts, mechanisms, and different variations of ribosome display and compares it to related methods. Applications of ribosome display are summarized, e.g., the directed evolution of proteins for higher binding affinity, for higher stability or other improved biophysical parameters and enzymatic properties. Ribosome display has developed into a robust technology used in academia and industry alike, and it has made the cell-free Darwinian evolution of proteins over multiple generations a reality.
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Affiliation(s)
- Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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35
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Lewis L, Lloyd C. Optimisation of antibody affinity by ribosome display using error-prone or site-directed mutagenesis. Methods Mol Biol 2012; 805:139-161. [PMID: 22094805 DOI: 10.1007/978-1-61779-379-0_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Affinity optimisation of antibodies can be achieved with great success by using directed evolution approaches, that is, the creation of and selection from diverse libraries. Here, we describe in detail methods to optimise antibody affinity for an antigen through directed evolution using ribosome display. Diversification of antibody single chain variable (scFv) domains is carried out by error-prone PCR and oligonucleotide-directed mutagenesis to generate random and targeted libraries respectively. Subsequent libraries are converted to ribosome display format and taken through cycles of transcription, translation, and selection. Since the starting point and the recovered product are linear DNA, this can easily be manipulated further to allow accumulation of beneficial mutations through iterative cycles of selection.
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Affiliation(s)
- Leeanne Lewis
- Department of Antibody Discovery and Protein Engineering, MedImmune Limited, Cambridge, UK
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36
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Harms BD, Kearns JD, Su SV, Kohli N, Nielsen UB, Schoeberl B. Optimizing properties of antireceptor antibodies using kinetic computational models and experiments. Methods Enzymol 2012; 502:67-87. [PMID: 22208982 DOI: 10.1016/b978-0-12-416039-2.00004-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Monoclonal antibodies are valuable as anticancer therapeutics because of their ability to selectively bind tumor-associated target proteins like receptor tyrosine kinases. Kinetic computational models that capture protein-protein interactions using mass action kinetics are a valuable tool for understanding the binding properties of monoclonal antibodies to their targets. Insights from the models can be used to explore different formats, to set antibody design specifications such as affinity and valence, and to predict potency. Antibody binding to target is driven by both intrinsic monovalent affinity and bivalent avidity. In this chapter, we describe a combined experimental and computational method of assessing the relative importance of these effects on observed drug potency. The method, which we call virtual flow cytometry (VFC), merges experimental measurements of monovalent antibody binding kinetics and affinity curves of antibody-antigen binding into a kinetic computational model of antibody-antigen interaction. The VFC method introduces a parameter χ, the avidity factor, which characterizes the ability of an antibody to cross-link its target through bivalent binding. This simple parameterization of antibody cross-linking allows the model to successfully describe and predict antibody binding curves across a wide variety of experimental conditions, including variations in target expression level and incubation time of antibody with target. We further demonstrate how computational models of antibody binding to cells can be used to predict target inhibition potency. Importantly, we demonstrate computationally that antibodies with high ability to cross-link antigen have significant potency advantages. We also present data suggesting that the parameter χ is a physical, epitope-dependent property of an antibody, and as a result propose that determination of antibody cross-linking and avidity should be incorporated into the screening of antibody panels for therapeutic development. Overall, our results suggest that antibody cross-linking, in addition to monovalent binding affinity, is a key design parameter of antibody performance.
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Affiliation(s)
- Brian D Harms
- Merrimack Pharmaceuticals, Cambridge, Massachusetts, USA
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37
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Boersma YL, Plückthun A. DARPins and other repeat protein scaffolds: advances in engineering and applications. Curr Opin Biotechnol 2011; 22:849-57. [DOI: 10.1016/j.copbio.2011.06.004] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/27/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
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38
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Ullman CG, Frigotto L, Cooley RN. In vitro methods for peptide display and their applications. Brief Funct Genomics 2011; 10:125-34. [PMID: 21628313 DOI: 10.1093/bfgp/elr010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The presentation of recombinant peptide libraries linked to their coding sequence can be referred to as 'peptide display'. Phage display is the most widely practiced peptide display technology but more recent alternatives such as CIS display, ribosome display and mRNA display offer advantages over phage for speed, library size and the display of unnatural amino acids. These have provided researchers with tools to address some of the failings of peptides such as their low affinity, low stability and inability to cross biological membranes. In this review, we assess some of the recent advances in peptide display and its application.
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Affiliation(s)
- Christopher G Ullman
- Isogenica Ltd., The Mansion, Chesterford Research Park, Little Chesterford, Essex, UK.
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39
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Dyson MR, Zheng Y, Zhang C, Colwill K, Pershad K, Kay BK, Pawson T, McCafferty J. Mapping protein interactions by combining antibody affinity maturation and mass spectrometry. Anal Biochem 2011; 417:25-35. [PMID: 21704603 PMCID: PMC3171153 DOI: 10.1016/j.ab.2011.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/27/2011] [Accepted: 05/03/2011] [Indexed: 12/24/2022]
Abstract
Mapping protein interactions by immunoprecipitation is limited by the availability of antibodies recognizing available native epitopes within protein complexes with sufficient affinity. Here we demonstrate a scalable approach for generation of such antibodies using phage display and affinity maturation. We combined antibody variable heavy (V(H)) genes from target-specific clones (recognizing Src homology 2 (SH2) domains of LYN, VAV1, NCK1, ZAP70, PTPN11, CRK, LCK, and SHC1) with a repertoire of 10(8) to 10(9) new variable light (V(L)) genes. Improved binders were isolated by stringent selections from these new "chain-shuffled" libraries. We also developed a predictive 96-well immunocapture screen and found that only 12% of antibodies had sufficient affinity/epitope availability to capture endogenous target from lysates. Using antibodies of different affinities to the same epitope, we show that affinity improvement was a key determinant for success and identified a clear affinity threshold value (60 nM for SHC1) that must be breached for success in immunoprecipitation. By combining affinity capture using matured antibodies to SHC1 with mass spectrometry, we identified seven known binding partners and two known SHC1 phosphorylation sites in epidermal growth factor (EGF)-stimulated human breast cancer epithelial cells. These results demonstrate that antibodies capable of immunoprecipitation can be generated by chain shuffling, providing a scalable approach to mapping protein-protein interaction networks.
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Affiliation(s)
- Michael R. Dyson
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Yong Zheng
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Cunjie Zhang
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Karen Colwill
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Kritika Pershad
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Brian K. Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Tony Pawson
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - John McCafferty
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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Khurana S, Verma N, Yewdell JW, Hilbert AK, Castellino F, Lattanzi M, Del Giudice G, Rappuoli R, Golding H. MF59 adjuvant enhances diversity and affinity of antibody-mediated immune response to pandemic influenza vaccines. Sci Transl Med 2011; 3:85ra48. [PMID: 21632986 DOI: 10.1126/scitranslmed.3002336] [Citation(s) in RCA: 264] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Oil-in-water adjuvants have been shown to improve immune responses against pandemic influenza vaccines as well as reduce the effective vaccine dose, increasing the number of doses available to meet global vaccine demand. Here, we use genome fragment phage display libraries and surface plasmon resonance to elucidate the effects of MF59 on the quantity, diversity, specificity, and affinity maturation of human antibody responses to the swine-origin H1N1 vaccine in different age groups. In adults and children, MF59 selectively enhanced antibody responses to the hemagglutinin 1 (HA1) globular head relative to the more conserved HA2 domain in terms of increased antibody titers as well as a more diverse antibody epitope repertoire. Antibody affinity, as inferred by greatly diminished (≥10-fold) off-rate constants, was significantly increased in toddlers and children who received the MF59-adjuvanted vaccine. Moreover, MF59 also improved antibody affinity maturation after each sequential vaccination against avian H5N1 in adults. For both pandemic influenza vaccines, there was a close correlation between serum antibody affinity and virus-neutralizing capacity. Thus, MF59 quantitatively and qualitatively enhances functional antibody responses to HA-based vaccines by improving both epitope breadth and binding affinity, demonstrating the added value of such adjuvants for influenza vaccines.
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Affiliation(s)
- Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA
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41
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Stefan N, Martin-Killias P, Wyss-Stoeckle S, Honegger A, Zangemeister-Wittke U, Plückthun A. DARPins recognizing the tumor-associated antigen EpCAM selected by phage and ribosome display and engineered for multivalency. J Mol Biol 2011; 413:826-43. [PMID: 21963989 DOI: 10.1016/j.jmb.2011.09.016] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 09/08/2011] [Indexed: 01/28/2023]
Abstract
Designed Ankyrin Repeat Proteins (DARPins) represent a novel class of binding molecules. Their favorable biophysical properties such as high affinity, stability and expression yields make them ideal candidates for tumor targeting. Here, we describe the selection of DARPins specific for the tumor-associated antigen epithelial cell adhesion molecule (EpCAM), an approved therapeutic target on solid tumors. We selected DARPins from combinatorial libraries by both phage display and ribosome display and compared their binding on tumor cells. By further rounds of random mutagenesis and ribosome display selection, binders with picomolar affinity were obtained that were entirely monomeric and could be expressed at high yields in the cytoplasm of Escherichia coli. One of the binders, denoted Ec1, bound to EpCAM with picomolar affinity (K(d)=68 pM), and another selected DARPin (Ac2) recognized a different epitope on EpCAM. Through the use of a variety of bivalent and tetravalent arrangements with these DARPins, the off-rate on cells was further improved by up to 47-fold. All EpCAM-specific DARPins were efficiently internalized by receptor-mediated endocytosis, which is essential for intracellular delivery of anticancer agents to tumor cells. Thus, using EpCAM as a target, we provide evidence that DARPins can be conveniently selected and rationally engineered to high-affinity binders of various formats for tumor targeting.
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Affiliation(s)
- Nikolas Stefan
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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42
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Liew FF, Hasegawa T, Fukuda M, Nakata E, Morii T. Construction of dopamine sensors by using fluorescent ribonucleopeptide complexes. Bioorg Med Chem 2011; 19:4473-81. [PMID: 21742507 DOI: 10.1016/j.bmc.2011.06.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 11/18/2022]
Abstract
A facile strategy of stepwise molding of a ribonucleopeptide (RNP) complex affords fluorescent RNP sensors with selective dopamine recognition. In vitro selection of a RNA-derived RNP library, a complex of the Rev peptide and its binding site Rev Responsive Element (RRE) RNA appended with random nucleotides in variable lengths, afforded RNP receptors specific for dopamine. The modular structure of the RNP receptor enables conversion of dopamine-binding RNP receptors to fluorescent dopamine sensors. Application of conditional selection schemes, such as the variation of salt concentrations and application of a counter-selection step by using a competitor ligand norepinephrine resulted in isolation of RNP receptors with defined dopamine-binding characteristics. Increasing the salt condition at the in vitro selection stage afforded RNP receptors with higher dopamine affinity, while addition of norepinephrine in the in vitro selection milieu at the counter-selection step reinforced the selectivity of RNP receptors to dopamine against norepinephrine. Thermodynamic analyses and circular dichroismic studies of the dopamine-RNP complexes suggest that the dopamine-binding RNP with higher selectivity against norepinephrine forms a pre-organized binding pocket and that the dopamine-binding RNP with higher affinity binds dopamine through the induced-fit mechanism. These results indicate that the selection condition controls the ligand-binding mechanism of RNP receptors.
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Affiliation(s)
- Fong Fong Liew
- Institute of Advanced Energy, Kyoto University, Kyoto 611-0011, Japan
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43
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Dreier B, Plückthun A. Ribosome display: a technology for selecting and evolving proteins from large libraries. Methods Mol Biol 2011; 687:283-306. [PMID: 20967617 DOI: 10.1007/978-1-60761-944-4_21] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The selection and concomitant affinity maturation of proteins to bind to user-defined target molecules have become a key technology in biochemical research, diagnostics, and therapy. One of the most potent selection technologies for such applications is ribosome display. It works entirely in vitro, and this has two important consequences. First, since no transformation of any cells is required, libraries with much greater diversity can be handled than with most other techniques. Second, since a library does not have to be cloned and transformed, it is very convenient to introduce random errors in the library by PCR-based methods and select improved binders. Thus, a true directed evolution, an iteration between randomization and selection over several generations, can be conveniently carried out, e.g., for affinity maturation. Ribosome display has been used successfully for the selection of antibody fragments and other binding proteins, such as Designed Ankyrin Repeat Proteins (DARPins).
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Affiliation(s)
- Birgit Dreier
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
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44
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Dreier B, Mikheeva G, Belousova N, Parizek P, Boczek E, Jelesarov I, Forrer P, Plückthun A, Krasnykh V. Her2-specific multivalent adapters confer designed tropism to adenovirus for gene targeting. J Mol Biol 2010; 405:410-26. [PMID: 21056576 DOI: 10.1016/j.jmb.2010.10.040] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 10/20/2010] [Accepted: 10/22/2010] [Indexed: 11/18/2022]
Abstract
Adenoviruses (Ads) hold great promise as gene vectors for diagnostic or therapeutic applications. The native tropism of Ads must be modified to achieve disease site-specific gene delivery by Ad vectors and this should be done in a programmable way and with technology that can realistically be scaled up. To this end, we applied the technologies of designed ankyrin repeat proteins (DARPins) and ribosome display to develop a DARPin that binds the knob domain of the Ad fiber protein with low nanomolar affinity (K(D) 1.35 nM) and fused this protein with a DARPin specific for Her2, an established cell-surface biomarker of human cancers. The stability of the complex formed by this bispecific targeting adapter and the Ad virion resulted in insufficient gene transfer and was subsequently improved by increasing the valency of adapter-virus binding. In particular, we designed adapters that chelated the knob in a bivalent or trivalent fashion and showed that the efficacy of gene transfer by the adapter-Ad complex increased with the functional affinity of these molecules. This enabled efficient transduction at low stoichiometric adapter-to-fiber ratios. We confirmed the Her2 specificity of this transduction and its dependence on the Her2-binding DARPin component of the adapters. Even the adapter molecules with four fused DARPins could be produced and purified from Escherichia coli at very high levels. In principle, DARPins can be generated against any target and this adapter approach provides a versatile strategy for developing a broad range of disease-specific gene vectors.
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Affiliation(s)
- Birgit Dreier
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland
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