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Mihara E, Watanabe S, Bashiruddin NK, Nakamura N, Matoba K, Sano Y, Maini R, Yin Y, Sakai K, Arimori T, Matsumoto K, Suga H, Takagi J. Lasso-grafting of macrocyclic peptide pharmacophores yields multi-functional proteins. Nat Commun 2021; 12:1543. [PMID: 33750839 PMCID: PMC7943567 DOI: 10.1038/s41467-021-21875-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/17/2021] [Indexed: 12/27/2022] Open
Abstract
Protein engineering has great potential for devising multifunctional recombinant proteins to serve as next-generation protein therapeutics, but it often requires drastic modifications of the parental protein scaffolds e.g., additional domains at the N/C-terminus or replacement of a domain by another. A discovery platform system, called RaPID (Random non-standard Peptides Integrated Discovery) system, has enabled rapid discovery of small de novo macrocyclic peptides that bind a target protein with high binding specificity and affinity. Capitalizing on the optimized binding properties of the RaPID-derived peptides, here we show that RaPID-derived pharmacophore sequences can be readily implanted into surface-exposed loops on recombinant proteins and maintain both the parental peptide binding function(s) and the host protein function. We refer to this protein engineering method as lasso-grafting and demonstrate that it can endow specific binding capacity toward various receptors into a diverse set of scaffolds that includes IgG, serum albumin, and even capsid proteins of adeno-associated virus, enabling us to rapidly formulate and produce bi-, tri-, and even tetra-specific binder molecules.
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Affiliation(s)
- Emiko Mihara
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Satoshi Watanabe
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Nasir K Bashiruddin
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nozomi Nakamura
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kyoko Matoba
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yumi Sano
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Rumit Maini
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yizhen Yin
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Katsuya Sakai
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Takao Arimori
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kunio Matsumoto
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan.
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2
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Zanuy D, Puiggalí-Jou A, Conflitti P, Bocchinfuso G, Palleschi A, Alemán C. Aggregation propensity of therapeutic fibrin-homing pentapeptides: insights from experiments and molecular dynamics simulations. SOFT MATTER 2020; 16:10169-10179. [PMID: 33165494 DOI: 10.1039/d0sm00930j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
CREKA (Cys-Arg-Glu-Lys-Ala) and its engineered analogue CRMeEKA, in which Glu has been replaced by N-methyl-Glu to provide resistance against proteolysis, are emerging pentapeptides that were specifically designed to bind fibrin-fibronectin complexes accumulated in the walls of tumour vessels. However, many of the intrinsic properties of CREKA and CRMeEKA, which are probably responsible for their different behaviour when combined with other materials (such as polymers) for diagnosis and therapeutics, remain unknown yet. The intrinsic tendency of these pentapeptides to form aggregates has been analysed by combining experimental techniques and atomistic Molecular Dynamics (MD) simulations. Dynamic light scattering assays show the formation of nanoaggregates that increase in size with the peptide concentration, even though aggregation occurs sooner for CRMeEKA, independently of the peptide concentration. FTIR and circular dichroism spectroscopy studies suggest that aggregated pentapeptides do not adopt any secondary structure. Atomistic MD trajectories show that CREKA aggregates faster and forms bigger molecular clusters than CRMeEKA. This behaviour has been explained by stability of the conformations adopted by un-associated peptide strands. While CREKA molecules organize by forming intramolecular backbone - side chain hydrogen bonds, CRMeEKA peptides display main chain - main chain hydrogen bonds closing very stable γ- or β-turns. Besides, energetic analyses reveal that CRMeEKA strands are better solvated in water than CREKA ones, independent of whether they are assembled or un-associated.
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Affiliation(s)
- David Zanuy
- Department of Chemical Engineering and Barcelona Research Center in Multiscale Science and Engineering, Universitat Polytècnica de Catalunya, 08019 Barcelona, Spain.
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3
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Hanyu Y, Kato M. Screening Antibody Libraries with Colony Assay Using scFv-Alkaline Phosphatase Fusion Proteins. Molecules 2020; 25:molecules25122905. [PMID: 32599779 PMCID: PMC7356641 DOI: 10.3390/molecules25122905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 01/17/2023] Open
Abstract
Screening antibody libraries is an important step in establishing recombinant monoclonal antibodies. The colony assay can identify positive clones without almost any false-positives; however, its antibody library is smaller than those used in other recombinant screening methods such as phage display. Thus, to improve the efficiency of colony assays, it is necessary to increase library size per screening. Here, we report developing a colony assay with single-chain variable fragment (scFv) fused to the N-terminus of bacterial alkaline phosphatase (scFv-PhoA). The scFv-PhoA library was constructed in an expression vector specifically designed for this study. Use of this library allowed the successful and direct detection of positive clones exhibiting PhoA activity, without the need for a secondary antibody. Colony assay screening with scFv-PhoA is simple, rapid, offers a higher success rate than previous methods based on scFv libraries, and—most importantly—it enables high-throughput procedures.
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Affiliation(s)
- Yoshiro Hanyu
- Biomaterials Research Group, Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan
- Correspondence: ; Tel.: +81-298-61-5542
| | - Mieko Kato
- Department of Biochemistry, Bio-Peak Co., Ltd., 584-70 Shimonojo, Takasaki 370-0854, Japan;
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4
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Integrating SpyCatcher/SpyTag covalent fusion technology into phage display workflows for rapid antibody discovery. Sci Rep 2019; 9:12815. [PMID: 31492910 PMCID: PMC6731262 DOI: 10.1038/s41598-019-49233-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/20/2019] [Indexed: 12/17/2022] Open
Abstract
An early bottleneck in the rapid isolation of new antibody fragment binders using in vitro library approaches is the inertia encountered in acquiring and preparing soluble antigen fragments. In this report, we describe a simple, yet powerful strategy that exploits the properties of the SpyCatcher/SpyTag (SpyC/SpyT) covalent interaction to improve substantially the speed and efficiency in obtaining functional antibody clones of interest. We demonstrate that SpyC has broad utility as a protein-fusion tag partner in a eukaryotic expression/secretion context, retaining its functionality and permitting the direct, selective capture and immobilization of soluble antigen fusions using solid phase media coated with a synthetic modified SpyT peptide reagent. In addition, we show that the expressed SpyC-antigen format is highly compatible with downstream antibody phage display selection and screening procedures, requiring minimal post-expression handling with no sample modifications. To illustrate the potential of the approach, we have isolated several fully human germline scFvs that selectively recognize therapeutically relevant native cell surface tumor antigens in various in vitro cell-based assay contexts.
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Homology Modeling-Based in Silico Affinity Maturation Improves the Affinity of a Nanobody. Int J Mol Sci 2019; 20:ijms20174187. [PMID: 31461846 PMCID: PMC6747709 DOI: 10.3390/ijms20174187] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 01/08/2023] Open
Abstract
Affinity maturation and rational design have a raised importance in the application of nanobody (VHH), and its unique structure guaranteed these processes quickly done in vitro. An anti-CD47 nanobody, Nb02, was screened via a synthetic phage display library with 278 nM of KD value. In this study, a new strategy based on homology modeling and Rational Mutation Hotspots Design Protocol (RMHDP) was presented for building a fast and efficient platform for nanobody affinity maturation. A three-dimensional analytical structural model of Nb02 was constructed and then docked with the antigen, the CD47 extracellular domain (CD47ext). Mutants with high binding affinity are predicted by the scoring of nanobody-antigen complexes based on molecular dynamics trajectories and simulation. Ultimately, an improved mutant with an 87.4-fold affinity (3.2 nM) and 7.36 °C higher thermal stability was obtained. These findings might contribute to computational affinity maturation of nanobodies via homology modeling using the recent advancements in computational power. The add-in of aromatic residues which formed aromatic-aromatic interaction plays a pivotal role in affinity and thermostability improvement. In a word, the methods used in this study might provide a reference for rapid and efficient in vitro affinity maturation of nanobodies.
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6
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Kato M, Hanyu Y. Single-step colony assay with autoinduction of scFv expression for the screening of antibody libraries. Biotechniques 2019; 66:194-197. [PMID: 30781974 DOI: 10.2144/btn-2018-0195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We present a simple colony assay method for screening antibody libraries based on autoinduction of antibody fragment expression. This protocol eliminates the need for colony size monitoring and a separate induction step for single-chain Fv (scFv) antibody fragment expression. Here, scFvs are expressed in an automatic and timely fashion during the assay, resulting in high yields of positive clones and substantial time savings. The method was used successfully to establish monoclonal scFvs with high affinity and specificity against human IgG.
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Affiliation(s)
- Mieko Kato
- Bio-Peak Co., Ltd, 584-70 Shimonojo, Takasaki 370-0854 Japan
| | - Yoshiro Hanyu
- Structural Physiology Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science & Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566 Japan
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7
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Michel E, Plückthun A, Zerbe O. Peptide binding affinity redistributes preassembled repeat protein fragments. Biol Chem 2018; 400:395-404. [DOI: 10.1515/hsz-2018-0355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/21/2018] [Indexed: 01/21/2023]
Abstract
Abstract
Designed armadillo repeat proteins (dArmRPs) are modular peptide binders composed of N- and C-terminal capping repeats Y and A and a variable number of internal modules M that each specifically recognize two amino acids of the target peptide. Complementary fragments of dArmRPs obtained by splitting the protein between helices H1 and H2 of an internal module show conditional and specific assembly only in the presence of a target peptide (Michel, E., Plückthun, A., and Zerbe, O. (2018). Peptide-guided assembly of repeat protein fragments. Angew. Chem. Int. Ed. 57, 4576–4579). Here, we investigate dArmRP fragments that already spontaneously assemble with high affinity, e.g. those obtained from splits between entire modules or between helices H2 and H3. We find that the interaction of the peptide with the assembled fragments induces distal conformational rearrangements that suggest an induced fit on a global protein level. A population analysis of an equimolar mixture of an N-terminal and three C-terminal fragments with various affinities for the target peptide revealed predominant assembly of the weakest peptide binder. However, adding a target peptide to this mixture altered the population of the protein complexes such that the combination with the highest affinity for the peptide increased and becomes predominant when adding excess of peptide, highlighting the feasibility of peptide-induced enrichment of best binders from inter-modular fragment mixtures.
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Affiliation(s)
- Erich Michel
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zürich , Switzerland
| | - Andreas Plückthun
- Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zürich , Switzerland
| | - Oliver Zerbe
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zürich , Switzerland
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8
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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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9
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Gorman K, McGinnis J, Kay B. Generating FN3-Based Affinity Reagents Through Phage Display. ACTA ACUST UNITED AC 2018; 10:e39. [PMID: 29927113 DOI: 10.1002/cpch.39] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Antibodies are useful tools for detecting individual proteins in complex samples and for learning about their location, amount, binding partners, and function in cells. Unfortunately, generating antibodies is time consuming and laborious, and their affinity and/or specificity is often limited. This protocol offers a fast and inexpensive alternative to generate antibody surrogates through phage display of a library of fibronectin type III (FN3) monobody variants and affinity selection for binders. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Kevin Gorman
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois
| | - Jennifer McGinnis
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois
| | - Brian Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois
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10
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Michel E, Plückthun A, Zerbe O. Peptide‐Guided Assembly of Repeat Protein Fragments. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Erich Michel
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Andreas Plückthun
- Department of Biochemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Oliver Zerbe
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
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11
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Michel E, Plückthun A, Zerbe O. Peptide-Guided Assembly of Repeat Protein Fragments. Angew Chem Int Ed Engl 2018; 57:4576-4579. [DOI: 10.1002/anie.201713377] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Erich Michel
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Andreas Plückthun
- Department of Biochemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Oliver Zerbe
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
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12
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Soler MA, Fortuna S, de Marco A, Laio A. Binding affinity prediction of nanobody-protein complexes by scoring of molecular dynamics trajectories. Phys Chem Chem Phys 2018; 20:3438-3444. [PMID: 29328338 DOI: 10.1039/c7cp08116b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nanobodies offer a viable alternative to antibodies for engineering high affinity binders. Their small size has an additional advantage: it allows exploiting computational protocols for optimizing their biophysical features, such as the binding affinity. The efficient prediction of this quantity is still considered a daunting task especially for modelled complexes. We show how molecular dynamics can successfully assist in the binding affinity prediction of modelled nanobody-protein complexes. The approximate initial configurations obtained by in silico design must undergo large rearrangements before achieving a stable conformation, in which the binding affinity can be meaningfully estimated. The scoring functions developed for the affinity evaluation of crystal structures will provide accurate estimates for modelled binding complexes if the scores are averaged over long finite temperature molecular dynamics simulations.
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13
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Slocik JM, Naik RR. Sequenced defined biomolecules for nanomaterial synthesis, functionalization, and assembly. Curr Opin Biotechnol 2017; 46:7-13. [DOI: 10.1016/j.copbio.2016.11.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 10/20/2022]
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14
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Carter T, Mulholland P, Chester K. Antibody-targeted nanoparticles for cancer treatment. Immunotherapy 2017; 8:941-58. [PMID: 27381686 DOI: 10.2217/imt.16.11] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Nanoparticles (NPs) are diverse and versatile with physical properties that can be employed for use in cancer medicine. Targeting NPs using antibodies and antibody fragments could overcome some of the limitations seen with current targeted therapies. This review will discuss the role of antibody-targeted NPs in the treatment of cancer: as delivery vehicles, targeted theranostic agents and in the evolving field of cancer hyperthermia.
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Affiliation(s)
- Thomas Carter
- UCL Cancer Institute, University College London, London, UK
| | - Paul Mulholland
- UCL Cancer Institute, University College London, London, UK.,University College London Hospitals NHS Foundation Trust, London, UK
| | - Kerry Chester
- UCL Cancer Institute, University College London, London, UK
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15
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Nagamune T. Biomolecular engineering for nanobio/bionanotechnology. NANO CONVERGENCE 2017; 4:9. [PMID: 28491487 PMCID: PMC5401866 DOI: 10.1186/s40580-017-0103-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/29/2017] [Indexed: 05/02/2023]
Abstract
Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.
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Affiliation(s)
- Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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16
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Holmquist EF, B Keiding U, Kold-Christensen R, Salomón T, Jørgensen KA, Kristensen P, Poulsen TB, Johannsen M. ReactELISA: Monitoring a Carbon Nucleophilic Metabolite by ELISA-a Study of Lipid Metabolism. Anal Chem 2017; 89:5066-5071. [PMID: 28376300 DOI: 10.1021/acs.analchem.7b00507] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We here present a conceptually novel reaction-based ELISA principle (ReactELISA) for quantitation of the carbon nucleophilic lipid metabolite acetoacetate. Key to the assay is the utilization of a highly chemoselective Friedländer reaction that captures and simultaneously stabilizes the nucleophilic metabolite directly in the biological matrix. By developing a bifunctional biotinylated capture probe, the Friedländer-acetoacetate adduct can be trapped and purified directly in streptavidin coated wells. Finally, we outline the selection and refinement of a highly selective recombinant antibody for specific adduct quantitation. The setup is very robust and, as we demonstrate via miniaturization for microplate format, amenable for screening of compounds or interventions that alter lipid metabolism in liver cell cultures. The assay-principle should be extendable to quantitation of other nucleophilic or electrophilic and perhaps even more reactive metabolites provided suitable capture probes and antibodies.
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Affiliation(s)
- Emil F Holmquist
- Department of Forensic Medicine, Aarhus University , Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark.,Department of Chemistry, Aarhus University , Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Ulrik B Keiding
- Department of Forensic Medicine, Aarhus University , Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark.,Department of Chemistry, Aarhus University , Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Rasmus Kold-Christensen
- Department of Forensic Medicine, Aarhus University , Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark.,Department of Chemistry, Aarhus University , Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Trine Salomón
- Department of Forensic Medicine, Aarhus University , Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Karl Anker Jørgensen
- Department of Chemistry, Aarhus University , Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Peter Kristensen
- Department of Engineering, Aarhus University , Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Thomas B Poulsen
- Department of Chemistry, Aarhus University , Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Mogens Johannsen
- Department of Forensic Medicine, Aarhus University , Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
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17
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Pérez-Gamarra S, Hattara L, Batra G, Saviranta P, Lamminmäki U. Array-in-well binding assay for multiparameter screening of phage displayed antibodies. Methods 2016; 116:43-50. [PMID: 27956240 DOI: 10.1016/j.ymeth.2016.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/03/2016] [Accepted: 12/05/2016] [Indexed: 12/27/2022] Open
Abstract
Phage display is a well-established and powerful tool for the development of recombinant antibodies. In a standard phage display selection process using a high quality antibody phage library, a large number of unique antibody clones can be generated in short time. However, the pace of the antibody discovery project eventually depends on the methodologies used in the next screening phase to identify the clones with the most promising binding characteristics e.g., in terms of specificity, affinity and epitope. Here, we report an array-in-well binding assay, a miniaturized and multiplexed immunoassay that integrates the epitope mapping to the evaluation of the binding activity of phage displayed antibody fragments in a single well. The array-in-well assay design used here incorporates a set of partially overlapping 15-mer peptides covering the complete primary sequence of the target antigen, the intact antigen itself and appropriate controls printed as an array with 10×10 layout at the bottom of a well of a 96-well microtiter plate. The streptavidin-coated surface of the well facilitates the immobilization of the biotinylated analytes as well-confined spots. Phage displayed antibody fragments bound to the analyte spots are traced using anti-phage antibody labelled with horseradish peroxidase for tyramide signal amplification based highly sensitive detection. In this study, we generated scFv antibodies against HIV-1 p24 protein using a synthetic antibody phage library, evaluated the binders with array-in-well binding assay and further classified them into epitopic families based on their capacity to recognize linear epitopes. The array-in-well assay enables the integration of epitope mapping to the screening assay for early classification of antibodies with simplicity and speed of a standard ELISA procedure to advance the antibody development projects.
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Affiliation(s)
- Susan Pérez-Gamarra
- Department of Biochemistry/Biotechnology, University of Turku, Tykistökatu 6A, FI-20520 Turku, Finland
| | - Liisa Hattara
- Medical Biotechnology Centre, VTT Technical Research Centre of Finland, Espoo FI-02044 VTT, Finland
| | - Gaurav Batra
- Centre for Biodesign and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 122001, India
| | - Petri Saviranta
- Medical Biotechnology Centre, VTT Technical Research Centre of Finland, Espoo FI-02044 VTT, Finland
| | - Urpo Lamminmäki
- Department of Biochemistry/Biotechnology, University of Turku, Tykistökatu 6A, FI-20520 Turku, Finland.
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18
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Hashimoto Y, Yagi K, Kondoh M. Current progress in a second-generation claudin binder, anti-claudin antibody, for clinical applications. Drug Discov Today 2016; 21:1711-1718. [DOI: 10.1016/j.drudis.2016.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 05/29/2016] [Accepted: 07/05/2016] [Indexed: 12/22/2022]
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19
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Phipps ML, Lillo AM, Shou Y, Schmidt EN, Paavola CD, Naranjo L, Bemdich S, Swanson BI, Bradbury ARM, Martinez JS. Beyond Helper Phage: Using "Helper Cells" to Select Peptide Affinity Ligands. PLoS One 2016; 11:e0160940. [PMID: 27626637 PMCID: PMC5023105 DOI: 10.1371/journal.pone.0160940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 07/27/2016] [Indexed: 12/16/2022] Open
Abstract
Peptides are important affinity ligands for microscopy, biosensing, and targeted delivery. However, because they can have low affinity for their targets, their selection from large naïve libraries can be challenging. When selecting peptidic ligands from display libraries, it is important to: 1) ensure efficient display; 2) maximize the ability to select high affinity ligands; and 3) minimize the effect of the display context on binding. The “helper cell” packaging system has been described as a tool to produce filamentous phage particles based on phagemid constructs with varying display levels, while remaining free of helper phage contamination. Here we report on the first use of this system for peptide display, including the systematic characterization and optimization of helper cells, their inefficient use in antibody display and their use in creating and selecting from a set of phage display peptide libraries. Our libraries were analyzed with unprecedented precision by standard or deep sequencing, and shown to be superior in quality than commercial gold standards. Using our helper cell libraries, we have obtained ligands recognizing Yersinia pestis surface antigen F1V and L-glutamine-binding periplasmic protein QBP. In the latter case, unlike any of the peptide library selections described so far, we used a combination of phage and yeast display to select intriguing peptide ligands. Based on the success of our selections we believe that peptide libraries obtained with helper cells are not only suitable, but preferable to traditional phage display libraries for selection of peptidic ligands.
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Affiliation(s)
- M. Lisa Phipps
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Antoinetta M. Lillo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Yulin Shou
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Emily N. Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Chad D. Paavola
- Space Biosciences Division, National Aeronautics and Space Administration Ames Research Center, Moffett Field, CA 94035, United States of America
| | - Leslie Naranjo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Sara Bemdich
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Basil I. Swanson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Andrew R. M. Bradbury
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Jennifer S. Martinez
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
- Institute for Materials Science, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
- * E-mail:
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Chiu ML, Gilliland GL. Engineering antibody therapeutics. Curr Opin Struct Biol 2016; 38:163-73. [PMID: 27525816 DOI: 10.1016/j.sbi.2016.07.012] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 02/07/2023]
Abstract
The successful introduction of antibody-based protein therapeutics into the arsenal of treatments for patients has within a few decades fostered intense innovation in the production and engineering of antibodies. Reviewed here are the methods currently used to produce antibodies along with how our knowledge of the structural and functional characterization of immunoglobulins has resulted in the engineering of antibodies to produce protein therapeutics with unique properties, both biological and biophysical, that are leading to novel therapeutic approaches. Antibody engineering includes the introduction of the antibody combining site (variable regions) into a host of architectures including bi and multi-specific formats that further impact the therapeutic properties leading to further advantages and successes in patient treatment.
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Affiliation(s)
- Mark L Chiu
- Janssen Research & Development LLC, 1400 McKean Road, Spring House, PA 19477, USA.
| | - Gary L Gilliland
- Janssen Research & Development LLC, 1400 McKean Road, Spring House, PA 19477, USA.
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Nagumo Y, Fujiwara K, Horisawa K, Yanagawa H, Doi N. PURE mRNA display for in vitro selection of single-chain antibodies. J Biochem 2015; 159:519-26. [PMID: 26711234 DOI: 10.1093/jb/mvv131] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/09/2015] [Indexed: 11/13/2022] Open
Abstract
mRNA display is a method to form a covalent linkage between a cell-free synthesized protein (phenotype) and its encoding mRNA (genotype) through puromycin for in vitro selection of proteins. Although a wheat germ cell-free translation system has been previously used in our mRNA display system, a protein synthesis using recombinant elements (PURE) system is a more attractive approach because it contains no endogenous nucleases and proteases and is optimized for folding of antibodies with disulphide bonds. However, when we used the PURE system for mRNA display of single-chain Fv (scFv) antibodies, the formation efficiency of the mRNA-protein conjugates was quite low. To establish an efficient platform for the PURE mRNA display of scFv, we performed affinity selection of a library of scFv antibodies with a C-terminal random sequence and obtained C-terminal sequences that increased the formation of mRNA-protein conjugates. We also identified unexpected common substitution mutations around the start codon of scFv antibodies, which were inferred to destabilize the mRNA secondary structure. This destabilization causes an increase in protein expression and the efficiency of the formation of mRNA-protein conjugates. We believe these improvements should make the PURE mRNA display more efficient for selecting antibodies for diagnostic and therapeutic applications.
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Affiliation(s)
- Yu Nagumo
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama 223-8522, Japan
| | - Kenichi Horisawa
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama 223-8522, Japan
| | - Hiroshi Yanagawa
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama 223-8522, Japan
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Methodology for preservation of yeast-bound single chain fragment variable antibody affinity reagents. J Immunol Methods 2015; 427:134-7. [PMID: 26571425 DOI: 10.1016/j.jim.2015.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 11/22/2022]
Abstract
Readily accessible affinity reagents are critical to the validation of biomarkers and to the development of new diagnostic tests. As alternatives to monoclonal antibodies, yeast-bound single chain fragment variable antibody (yeast-scFv) can be rapidly selected from yeast display libraries. An important characteristic for any diagnostic reagent is its stability or ability to store it. A lyophilization procedure that has extended the shelf life of yeast-scFv by a factor of ≥10-fold relative to previous reports is reported. Real time stability for three yeast-scFv clones to three distinct Entamoeba histolytica potential diagnostic antigen targets for one year at room temperature as well as at 37°C and 45°C. Retention of full binding activity and specificity of the yeast-scFv clones for their cognate antigens is shown by flow cytometry. Lyophilization can easily be carried out in batches and in single-use vials.
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Current advances in the development of high-throughput purification strategies for the generation of therapeutic antibodies. ACTA ACUST UNITED AC 2015. [DOI: 10.4155/pbp.15.23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Villamil Giraldo AM, Mary C, Sivanesan D, Baron C. VirB6 and VirB10 from the Brucella type IV secretion system interact via the N-terminal periplasmic domain of VirB6. FEBS Lett 2015; 589:1883-9. [PMID: 26071378 DOI: 10.1016/j.febslet.2015.05.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 05/27/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022]
Abstract
Type IV secretion systems are multi-protein complexes that transfer macromolecules across the cell envelope of bacteria. Identifying the sites of interaction between the twelve proteins (VirB1-VirB11 and VirD4) that form these complexes is key to understanding their assembly and function. We have here used phage display, bacterial two-hybrid and fluorescence-based interaction assays to identify an N-terminal domain of the inner membrane protein VirB6 as a site of interaction with the envelope-spanning VirB10 protein. Our results are consistent with the notion that VirB6 acts in concert with VirB10 as well as with VirB8 during secretion system assembly and function.
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Affiliation(s)
- Ana Maria Villamil Giraldo
- Université de Montréal, Pavillon Roger-Gaudry, Department of Biochemistry and Molecular Medicine, C.P. 6128, Succ. Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Charline Mary
- Université de Montréal, Pavillon Roger-Gaudry, Department of Biochemistry and Molecular Medicine, C.P. 6128, Succ. Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Durgajini Sivanesan
- Université de Montréal, Pavillon Roger-Gaudry, Department of Biochemistry and Molecular Medicine, C.P. 6128, Succ. Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Christian Baron
- Université de Montréal, Pavillon Roger-Gaudry, Department of Biochemistry and Molecular Medicine, C.P. 6128, Succ. Centre-Ville, Montréal, QC H3C 3J7, Canada.
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