1
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Lima GM, Atrazhev A, Sarkar S, Sojitra M, Reddy R, Torres-Obreque K, de Oliveira Rangel-Yagui C, Macauley MS, Monteiro G, Derda R. DNA-Encoded Multivalent Display of Chemically Modified Protein Tetramers on Phage: Synthesis and in Vivo Applications. ACS Chem Biol 2022; 17:3024-3035. [PMID: 34928124 DOI: 10.1021/acschembio.1c00835] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Phage display links the phenotype of displayed polypeptides with the DNA sequence in the phage genome and offers a universal method for the discovery of proteins with novel properties. However, the display of large multisubunit proteins on phages remains a challenge. A majority of protein display systems are based on monovalent phagemid constructs, but methods for the robust display of multiple copies of large proteins are scarce. Here, we describe a DNA-encoded display of a ∼ 200 kDa tetrameric l-asparaginase protein on M13 and fd phages produced by ligation of SpyCatcher-Asparaginase fusion (ScA) and PEGylated-ScA (PEG-ScA) to barcoded phage clones displaying SpyTag peptide. Starting from the SpyTag display on p3 or p8 coat proteins yielded constructs with five copies of ScA displayed on p3 (ScA-p3), ∼100 copies of ScA on p8 protein (ScA-p8) and ∼300 copies of PEG-ScA on p8 protein (PEG-ScA-p8). Display constructs of different valencies and chemical modifications on protein (e.g., PEGylation) can be injected into mice and analyzed by deep sequencing of the DNA barcodes associated with phage clones. In these multiplexed studies, we observed a density and protein-dependent clearance rate in vivo. Our observations link the absence of PEGylation and increase in density of the displayed protein with the increased rate of the endocytosis by cells in vivo. In conclusion, we demonstrate that a multivalent display of l-asparaginase on phages could be used to study the circulation life of this protein in vivo, and such an approach opens the possibility to use DNA sequencing to investigate multiplexed libraries of other multisubunit proteins in vivo.
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Affiliation(s)
- Guilherme M Lima
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, 05508 000, Brazil.,Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Alexey Atrazhev
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Susmita Sarkar
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Mirat Sojitra
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Revathi Reddy
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Karin Torres-Obreque
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, 05508 000, Brazil
| | - Carlota de Oliveira Rangel-Yagui
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, 05508 000, Brazil
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Gisele Monteiro
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, 05508 000, Brazil
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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2
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Preparation of Bacterial Cell-Surface Displayed Semisynthetic Cyclic Peptides. Methods Mol Biol 2021. [PMID: 34596850 DOI: 10.1007/978-1-0716-1689-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Semisynthetic cyclic peptides bearing both non-proteinogenic and genetically encoded amino acids are excellent ligands for peptide-based drug discovery. While semisynthesis expands the chemical space, genetic encoding allows access to a large library via randomization at the nucleic acid level. Selection of novel binders of such macrocyclic ligands requires linking their genotype to phenotype. In this chapter, we report a bacterial cell-surface display system to present cyclic peptides composed of synthetic and genetically encoded fragments. The synthetic fragment along with the split intein partner and an aminooxy moiety is ligated and cyclized with the recombinant backbone containing an unnatural amino acid by protein trans-splicing and intramolecular oxime ligation, respectively. A pH-shift protocol was applied to accelerate on surface cyclization. This method will enable generation of semisynthetic cyclic peptide libraries and their selection by fluorescence-activated cell sorting.
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3
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Palei S, Becher KS, Nienberg C, Jose J, Mootz HD. Bacterial Cell-Surface Display of Semisynthetic Cyclic Peptides. Chembiochem 2018; 20:72-77. [PMID: 30216604 DOI: 10.1002/cbic.201800552] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Indexed: 01/20/2023]
Abstract
Semisynthetic cyclic peptides containing both non-proteinogenic building blocks, as the synthetic part, and a genetically encoded sequence amenable to DNA-based randomization hold great potential to expand the chemical space in the quest for novel bioactive peptides. Key to an efficient selection of novel binders to biomacromolecules is a robust method to link their genotype and phenotype. A novel bacterial cell surface display technology has been developed to present cyclic peptides composed of synthetic and genetically encoded fragments in their backbones. The fragments were combined by protein trans-splicing and intramolecular oxime ligation. To this end, a split intein half and an unnatural amino acid were displayed with the genetically encoded part on the surface of Escherichia coli. Addition of the synthetic fragment equipped with the split intein partner and an aminooxy moiety, as well as the application of a pH-shift protocol, resulted in the onsurface formation of the semisynthetic cyclic peptide. This approach will serve for the generation of cyclic peptide libraries suitable for selection by fluorescence-activated cell sorting, and more generally enables chemical modification of proteins on the bacterial surface.
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Affiliation(s)
- Shubhendu Palei
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.,International Graduate School of Chemistry (GSC-MS), University of Münster, 48149, Münster, Germany
| | - Kira S Becher
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany
| | - Christian Nienberg
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, PharmaCampus, 48149, Münster, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, PharmaCampus, 48149, Münster, Germany.,International Graduate School of Chemistry (GSC-MS), University of Münster, 48149, Münster, Germany
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.,International Graduate School of Chemistry (GSC-MS), University of Münster, 48149, Münster, Germany
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4
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Wu CH, Liu IJ, Lu RM, Wu HC. Advancement and applications of peptide phage display technology in biomedical science. J Biomed Sci 2016; 23:8. [PMID: 26786672 PMCID: PMC4717660 DOI: 10.1186/s12929-016-0223-x] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 01/11/2016] [Indexed: 12/25/2022] Open
Abstract
Combinatorial phage library is a powerful research tool for high-throughput screening of protein interactions. Of all available molecular display techniques, phage display has proven to be the most popular approach. Screening phage-displayed random peptide libraries is an effective means of identifying peptides that can bind target molecules and regulate their function. Phage-displayed peptide libraries can be used for (i) B-cell and T-cell epitope mapping, (ii) selection of bioactive peptides bound to receptors or proteins, disease-specific antigen mimics, peptides bound to non-protein targets, cell-specific peptides, or organ-specific peptides, and (iii) development of peptide-mediated drug delivery systems and other applications. Targeting peptides identified using phage display technology may be useful for basic research and translational medicine. In this review article, we summarize the latest technological advancements in the application of phage-displayed peptide libraries to applied biomedical sciences.
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Affiliation(s)
- Chien-Hsun Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - I-Ju Liu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Ruei-Min Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.
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5
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Santoso B, Murray BW. Maleimide-based method for elaboration of cysteine-containing peptide phage libraries. Methods Mol Biol 2015; 1248:267-76. [PMID: 25616339 DOI: 10.1007/978-1-4939-2020-4_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Peptide-based molecules are known to have therapeutic utility, but the generation of phage-focused libraries to optimize peptide properties and functionality is challenging. Genetic approaches are limited to peptide extension on the peptide termini. Current chemical methods are technically challenging and time-consuming. A new chemical method is developed to extend a maleimide-conjugated peptide with a cysteine-containing random peptide phage display library. As a proof of concept, a 15-mer epidermal growth factor receptor (EGFR)-binding peptide was synthesized with a maleimide group at its C-terminus and then conjugated to the cysteine-containing library. After panning and screening, several extended peptides were discovered and tested to have a higher affinity to EGFR. This strategy can have broad utility to optimize pharmacophores of any modalities (peptides, unnatural peptides, drug conjugates) capable of bearing a maleimide group.
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Affiliation(s)
- Buyung Santoso
- Pfizer Worldwide Research and Development, 10646 Science Center Dr, San Diego, CA, 92121, USA
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6
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Jafari MR, Deng L, Kitov PI, Ng S, Matochko WL, Tjhung KF, Zeberoff A, Elias A, Klassen JS, Derda R. Discovery of light-responsive ligands through screening of a light-responsive genetically encoded library. ACS Chem Biol 2014; 9:443-50. [PMID: 24195775 DOI: 10.1021/cb4006722] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Light-responsive ligands are useful tools in biochemistry and cell biology because the function of these ligands can be spatially and temporally controlled. Conventional design of such ligands relies on previously available data about the structure of both the ligand and the receptor. In this paper, we describe de novo discovery of light-responsive ligands through screening of a genetically encoded light-responsive library. We ligated a photoresponsive azobenzene core to a random CX7C peptide library displayed on the coat protein of M13 phage. A one-pot alkylation/reduction of the cysteines yielded a photoresponsive library of random heptapeptide macrocycles with over 2 × 10(8) members. We characterized the reaction on-phage and optimized the yield of the modifications in phage libraries. Screening of the library against streptavidin yielded three macrocycles that bind to streptavidin in the dark and cease binding upon irradiation with 370 nm light. All ligands restored their binding properties upon thermal relaxation and could be turned ON and OFF for several cycles. We measured dissociation constants, Kd, by electrospray ionization mass spectrometry (ESI-MS) binding assay. For ligand ACGFERERTCG, the Kd of cis and trans isomers differed by 22-fold; an incomplete isomerization (85%), however, resulted in the apparent difference of 4.5-fold between the dark and the irradiated state. We anticipate that the selection strategy described in this report can be used to find light-responsive ligands for many targets that do not have known natural ligands.
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Affiliation(s)
- Mohammad R. Jafari
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Lu Deng
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Pavel I. Kitov
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Simon Ng
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wadim L. Matochko
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Katrina F. Tjhung
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Anthony Zeberoff
- Department
of Chemical and Material Engineering, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Anastasia Elias
- Department
of Chemical and Material Engineering, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S. Klassen
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ratmir Derda
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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7
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A simple and efficient maleimide-based approach for peptide extension with a cysteine-containing peptide phage library. Bioorg Med Chem Lett 2013; 23:5680-3. [DOI: 10.1016/j.bmcl.2013.08.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 11/18/2022]
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8
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Ng S, Jafari MR, Derda R. Bacteriophages and viruses as a support for organic synthesis and combinatorial chemistry. ACS Chem Biol 2012; 7:123-38. [PMID: 21988453 DOI: 10.1021/cb200342h] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Display of polypeptide on the coat proteins of bacteriophages and viruses is a powerful tool for selection and amplification of libraries of great diversity. Chemical diversity of these libraries, however, is limited to libraries made of natural amino acid side chains. Bacteriophages and viruses can be modified chemically; peptide libraries presented on phage thus can be functionalized to yield moieties that cannot be encoded genetically. In this review, we summarize the possibilities for using bacteriophage and viral particles as support for the synthesis of diverse chemically modified peptide libraries. This review critically summarizes the key chemical considerations for on-phage syntheses such as selection of reactions compatible with protein of phage, modification of phage "support" that renders it more suitable for reactions, and characterization of reaction efficiency.
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Affiliation(s)
- Simon Ng
- Department
of Chemistry and Alberta Innovates Centre
for Carbohydrate Science, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Mohammad R. Jafari
- Department
of Chemistry and Alberta Innovates Centre
for Carbohydrate Science, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ratmir Derda
- Department
of Chemistry and Alberta Innovates Centre
for Carbohydrate Science, University of Alberta, Edmonton, AB T6G 2G2, Canada
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9
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Abstract
Molecular imaging allows clinicians to visualize disease-specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology—all essential to progress in molecular imaging probe development. In this review, we discuss target selection, screening techniques, and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents.
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Affiliation(s)
- Fred Reynolds
- From the Robert M. Berne Cardiovascular Research Center and the Department of Biomedical Engineering, University of Virginia, Charlottesville, VA. Reprints not available
| | - Kimberly A. Kelly
- From the Robert M. Berne Cardiovascular Research Center and the Department of Biomedical Engineering, University of Virginia, Charlottesville, VA. Reprints not available
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10
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Peptide phage display as a tool for drug discovery: targeting membrane receptors. Molecules 2011; 16:857-87. [PMID: 21258295 PMCID: PMC6259427 DOI: 10.3390/molecules16010857] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 01/14/2011] [Accepted: 01/19/2011] [Indexed: 12/14/2022] Open
Abstract
Ligands selected from phage-displayed random peptide libraries tend to be directed to biologically relevant sites on the surface of the target protein. Consequently, peptides derived from library screenings often modulate the target protein’s activity in vitro and in vivo and can be used as lead compounds in drug design and as alternatives to antibodies for target validation in both genomics and drug discovery. This review discusses the use of phage display to identify membrane receptor modulators with agonistic or antagonistic activities. Because isolating or producing recombinant membrane proteins for use as target molecules in library screening is often impossible, innovative selection strategies such as panning against whole cells or tissues, recombinant receptor ectodomains, or neutralizing antibodies to endogenous binding partners were devised. Prominent examples from a two-decade history of peptide phage display will be presented, focusing on the design of affinity selection experiments, methods for improving the initial hits, and applications of the identified peptides.
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11
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Pande J, Szewczyk MM, Grover AK. Phage display: concept, innovations, applications and future. Biotechnol Adv 2010; 28:849-58. [PMID: 20659548 DOI: 10.1016/j.biotechadv.2010.07.004] [Citation(s) in RCA: 330] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Revised: 06/27/2010] [Accepted: 07/08/2010] [Indexed: 12/17/2022]
Abstract
Phage display is the technology that allows expression of exogenous (poly)peptides on the surface of phage particles. The concept is simple in principle: a library of phage particles expressing a wide diversity of peptides is used to select those that bind the desired target. The filamentous phage M13 is the most commonly used vector to create random peptide display libraries. Several methods including recombinant techniques have been developed to increase the diversity of the library. On the other extreme, libraries with various biases can be created for specific purposes. For instance, when the sequence of the peptide that binds the target is known, its affinity and selectivity can be increased by screening libraries created with limited mutagenesis of the peptide. Phage libraries are screened for binding to synthetic or native targets. The initial screening of library by basic biopanning has been extended to column chromatography including negative screening and competition between selected phage clones to identify high affinity ligands with greater target specificity. The rapid isolation of specific ligands by phage display is advantageous in many applications including selection of inhibitors for the active and allosteric sites of the enzymes, receptor agonists and antagonists, and G-protein binding modulatory peptides. Phage display has been used in epitope mapping and analysis of protein-protein interactions. The specific ligands isolated from phage libraries can be used in therapeutic target validation, drug design and vaccine development. Phage display can also be used in conjunction with other methods. The past innovations and those to come promise a bright future for this field.
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Affiliation(s)
- Jyoti Pande
- Department of Medicine, HSC 4N41 McMaster Univ, Hamilton, ON, Canada
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12
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In vitro identification of targeting ligands of human M cells by phage display. Int J Pharm 2010; 394:35-42. [DOI: 10.1016/j.ijpharm.2010.04.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2010] [Revised: 04/13/2010] [Accepted: 04/17/2010] [Indexed: 01/02/2023]
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13
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Bratkovic T. Progress in phage display: evolution of the technique and its application. Cell Mol Life Sci 2010; 67:749-67. [PMID: 20196239 PMCID: PMC11115567 DOI: 10.1007/s00018-009-0192-2] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 10/18/2009] [Accepted: 10/23/2009] [Indexed: 10/20/2022]
Abstract
Phage display, the presentation of (poly)peptides as fusions to capsid proteins on the surface of bacterial viruses, celebrates its 25th birthday in 2010. The technique, coupled with in vitro selection, enables rapid identification and optimization of proteins based on their structural or functional properties. In the last two decades, it has advanced tremendously and has become widely accepted by the scientific community. This by no means exhaustive review aims to inform the reader of the key modifications in phage display. Novel display formats, innovative library designs and screening strategies are discussed. I will also briefly review some recent uses of the technology to illustrate its incredible versatility.
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Affiliation(s)
- Tomaz Bratkovic
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Askerceva 7, 1000 Ljubljana, Slovenia.
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14
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Heinis C, Rutherford T, Freund S, Winter G. Phage-encoded combinatorial chemical libraries based on bicyclic peptides. Nat Chem Biol 2009; 5:502-7. [PMID: 19483697 DOI: 10.1038/nchembio.184] [Citation(s) in RCA: 533] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 04/29/2009] [Indexed: 02/07/2023]
Abstract
Here we describe a phage strategy for the selection of ligands based on bicyclic or linear peptides attached covalently to an organic core. We designed peptide repertoires with three reactive cysteine residues, each spaced apart by several random amino acid residues, and we fused the repertoires to the phage gene-3-protein. Conjugation with tris-(bromomethyl)benzene via the reactive cysteines generated repertoires of peptide conjugates with two peptide loops anchored to a mesitylene core. Iterative affinity selections yielded several enzyme inhibitors; after further mutagenesis and selection, we were able to chemically synthesize a lead inhibitor (PK15; Ki =1.5 nM) specific to human plasma kallikrein that efficiently interrupted the intrinsic coagulation pathway in human plasma tested ex vivo. This approach offers a powerful means of generating and selecting bicyclic macrocycles (or if cleaved, linear derivatives thereof) as ligands poised at the interface of small-molecule drugs and biologics.
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Affiliation(s)
- Christian Heinis
- Laboratory of Molecular Biology, Medical Research Council, Cambridge, UK
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15
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Boldt GE, Dickerson TJ, Janda KD. Emerging chemical and biological approaches for the preparation of discovery libraries. Drug Discov Today 2006; 11:143-8. [PMID: 16533712 DOI: 10.1016/s1359-6446(05)03697-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The term of combinatorial chemistry has come to embrace all types of small-molecule library strategies. In both academic and industrial settings, the development of many combinatorial techniques has been driven by a desire to generate diverse libraries of molecules. Recently, chemical approaches have been reported that range from alternative library design concepts to new synthetic procedures that allow for selective product formation in extremely short reaction times. Concurrently, biological techniques have made great strides by adapting naturally occurring strategies for library preparation and screening. With proper understanding of library design, combinatorial endeavors and molecular libraries will continue to impact on the development of the next generation of tools for modern medicine.
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Affiliation(s)
- Grant E Boldt
- Department of Chemistry, The Skaggs Institute for Chemical Biology, Worm Institute for Research and Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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16
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Affiliation(s)
- John W Kehoe
- Biosciences Division, Argonne National Laboratory, Building 202, Argonne, Illinois 60439, USA
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17
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Yin J, Liu F, Schinke M, Daly C, Walsh CT. Phagemid encoded small molecules for high throughput screening of chemical libraries. J Am Chem Soc 2004; 126:13570-1. [PMID: 15493886 DOI: 10.1021/ja045127t] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new strategy for monovalently displaying small molecules on phage surfaces was developed and applied to high throughput screening for molecules with high binding affinity to the target protein. Peptidyl carrier protein (PCP) excised from nonribosomal peptide synthetase was monovalently displayed on the surface of M13 phage as pIII fusion proteins. Small molecules of diverse structures were conjugated to coenzyme A (CoA) and then covalently attached to the phage displayed PCP by Sfp phosphopantetheinyl transferase. Because Sfp is broadly promiscuous for the transfer of small molecule linked phosphopantetheinyl moieties to apo PCP domains, this approach will enable displaying libraries of small molecules on phage surfaces. Unique 20-base-pair (bp) DNA sequences were also incorporated into the phagemid DNA so that each compound displayed on the phage surface was encoded by a DNA bar code encapsulated inside the phage coat protein. Single round selection of phage displayed small molecules achieved more than 2000-fold enrichment of small molecules with nM binding affinity to the target protein. The selection process is further accelerated by the use of DNA decoding arrays for identifying the selected small molecules.
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Affiliation(s)
- Jun Yin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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18
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Brown DM, Pellecchia M, Ruoslahti E. Drug Identification through in vivo Screening of Chemical Libraries. Chembiochem 2004; 5:871-5. [PMID: 15174173 DOI: 10.1002/cbic.200300824] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Darren M Brown
- Cancer Research Center, The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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19
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Biology. Drug Discov Today 2004. [DOI: 10.1016/s1359-6446(04)02922-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Abstract
Technology has been developed to display small molecules on phage particles. This innovation enables the generation of libraries of phage-tagged compounds with novel properties that are well suited for in vivo assays.
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Affiliation(s)
- Frederic Fellouse
- Department of Protein Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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