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Xu J, Miao H, Zou L, Tse Sum Bui B, Haupt K, Pan G. Evolution of Molecularly Imprinted Enzyme Inhibitors: From Simple Activity Inhibition to Pathological Cell Regulation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106657] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingjing Xu
- Center for Molecular Recognition and Biosensing School of Life Sciences Shanghai University Shanghai 200444 P. R. China
| | - Haohan Miao
- Institute for Advanced Materials School of Materials Science and Engineering Jiangsu University Zhenjiang Jiangsu 212013 China
| | - Lihua Zou
- Center for Molecular Recognition and Biosensing School of Life Sciences Shanghai University Shanghai 200444 P. R. China
| | - Bernadette Tse Sum Bui
- Université de Technologie de Compiègne CNRS Enzyme and Cell Engineering Laboratory Rue du Docteur Schweitzer 60203 Compiègne Cedex France
| | - Karsten Haupt
- Université de Technologie de Compiègne CNRS Enzyme and Cell Engineering Laboratory Rue du Docteur Schweitzer 60203 Compiègne Cedex France
| | - Guoqing Pan
- Institute for Advanced Materials School of Materials Science and Engineering Jiangsu University Zhenjiang Jiangsu 212013 China
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2
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Xu J, Miao H, Zou L, Tse Sum Bui B, Haupt K, Pan G. Evolution of Molecularly Imprinted Enzyme Inhibitors: From Simple Activity Inhibition to Pathological Cell Regulation. Angew Chem Int Ed Engl 2021; 60:24526-24533. [PMID: 34418248 DOI: 10.1002/anie.202106657] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/11/2021] [Indexed: 02/06/2023]
Abstract
Molecular imprinting represents one of the most promising strategies to design artificial enzyme inhibitors. However, the study of molecularly imprinted enzyme inhibitors (MIEIs) remains at a primary stage. Advanced applications of MIEIs for cell regulation have rarely been explored. Using a solid-phase oriented imprinting strategy so as to leave the active site of the enzymes accessible, we synthesized two MIEIs that exhibit high specificity and potent inhibitory effects (inhibition constant at low nM range) towards trypsin and angiogenin. The trypsin MIEI inhibits trypsin activity, tryptic digestion-induced extracellular matrix lysis and cell membrane destruction, indicating its utility in the treatment of active trypsin-dependent cell injury. The angiogenin MIEI blocks cancer cell proliferation by suppressing the ribonuclease activity of angiogenin and decreasing the angiogenin level inside and outside HeLa cells. Our work demonstrates the versatility of MIEIs for both enzyme inhibition and cell fate manipulation, showing their great potential as therapeutic drugs in biomedicine.
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Affiliation(s)
- Jingjing Xu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Haohan Miao
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Lihua Zou
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Bernadette Tse Sum Bui
- Université de Technologie de Compiègne, CNRS Enzyme and Cell Engineering Laboratory, Rue du Docteur Schweitzer, 60203, Compiègne Cedex, France
| | - Karsten Haupt
- Université de Technologie de Compiègne, CNRS Enzyme and Cell Engineering Laboratory, Rue du Docteur Schweitzer, 60203, Compiègne Cedex, France
| | - Guoqing Pan
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
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3
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Davidson TA, McGoldrick SJ, Kohn DH. Phage Display to Augment Biomaterial Function. Int J Mol Sci 2020; 21:ijms21175994. [PMID: 32825391 PMCID: PMC7504225 DOI: 10.3390/ijms21175994] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Biomaterial design relies on controlling interactions between materials and their biological environments to modulate the functions of proteins, cells, and tissues. Phage display is a powerful tool that can be used to discover peptide sequences with high affinity for a desired target. When incorporated into biomaterial design, peptides identified via phage display can functionalize material surfaces to control the interaction between a biomaterial and its local microenvironment. A targeting peptide has high specificity for a given target, allowing for homing a specific protein, cell, tissue, or other material to a biomaterial. A functional peptide has an affinity for a given protein, cell, or tissue, but also modulates its target's activity upon binding. Biomaterials can be further enhanced using a combination of targeting and/or functional peptides to create dual-functional peptides for bridging two targets or modulating the behavior of a specific protein or cell. This review will examine current and future applications of phage display for the augmentation of biomaterials.
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Affiliation(s)
- Thomas A. Davidson
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (T.A.D.); (S.J.M.)
| | - Samantha J. McGoldrick
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (T.A.D.); (S.J.M.)
| | - David H. Kohn
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (T.A.D.); (S.J.M.)
- Department of Biologic and Material Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence:
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Abstract
Bacteriophages are interesting entities on the border of biology and chemistry. In nature, they are bacteria parasites, while, after genetic manipulation, they gain new properties, e.g., selectively binding proteins. Owing to this, they may be applied as recognition elements in biosensors. Combining bacteriophages with different transducers can then result in the development of innovative sensor designs that may revolutionize bioanalytics and improve the quality of medical services. Therefore, here, we review the use of bacteriophages, or peptides from bacteriophages, as new sensing elements for the recognition of biomarkers and the construction of the highly effective diagnostics tools.
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Marcozzi A, Masini T, Zhu D, Pesce D, Illarionov B, Fischer M, Herrmann A, Hirsch AKH. Phage Display on the Anti-infective Target 1-Deoxy-d-xylulose-5-phosphate Synthase Leads to an Acceptor-Substrate Competitive Peptidic Inhibitor. Chembiochem 2018; 19:58-65. [PMID: 29119720 PMCID: PMC5814854 DOI: 10.1002/cbic.201700402] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Indexed: 01/18/2023]
Abstract
Enzymes of the 2-C-methyl-d-erythritol-4-phosphate pathway for the biosynthesis of isoprenoid precursors are validated drug targets. By performing phage display on 1-deoxy-d-xylulose-5-phosphate synthase (DXS), which catalyzes the first step of this pathway, we discovered several peptide hits and recognized false-positive hits. The enriched peptide binder P12 emerged as a substrate (d-glyceraldehyde-3-phosphate)-competitive inhibitor of Deinococcus radiodurans DXS. The results indicate possible overlap of the cofactor- and acceptor-substrate-binding pockets and provide inspiration for the design of inhibitors of DXS with a unique and novel mechanism of inhibition.
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Affiliation(s)
- Alessio Marcozzi
- Department Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Tiziana Masini
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Di Zhu
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Department of Drug Design and OptimizationCampus Building E8.166123SaarbrückenGermany
| | - Diego Pesce
- Department Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Boris Illarionov
- Hamburg School of Food ScienceInstitute of Food ChemistryGrindelallee 11720146HamburgGermany
| | - Markus Fischer
- Hamburg School of Food ScienceInstitute of Food ChemistryGrindelallee 11720146HamburgGermany
| | - Andreas Herrmann
- Department Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Department of Drug Design and OptimizationCampus Building E8.166123SaarbrückenGermany
- Department of PharmacyMedicinal ChemistrySaarland UniversityCampus Building E8.166123SaarbrückenGermany
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7
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Gordiichuk P, Pesce D, Ocampo OEC, Marcozzi A, Wetzelaer GAH, Paul A, Loznik M, Gloukhikh E, Richter S, Chiechi RC, Herrmann A. Orientation and Incorporation of Photosystem I in Bioelectronics Devices Enabled by Phage Display. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2017; 4:1600393. [PMID: 28546908 PMCID: PMC5441502 DOI: 10.1002/advs.201600393] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/04/2016] [Indexed: 05/23/2023]
Abstract
Interfacing proteins with electrode surfaces is important for the field of bioelectronics. Here, a general concept based on phage display is presented to evolve small peptide binders for immobilizing and orienting large protein complexes on semiconducting substrates. Employing this method, photosystem I is incorporated into solid-state biophotovoltaic cells.
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Affiliation(s)
- Pavlo Gordiichuk
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Diego Pesce
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Olga E. Castañeda Ocampo
- Stratingh Institute for Chemistry and Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Alessio Marcozzi
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Gert‐Jan A. H. Wetzelaer
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Avishek Paul
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Mark Loznik
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Ekaterina Gloukhikh
- The Bio and Molecular Electronics GroupDepartment of Materials Science and EngineeringFaculty of Engineering and University Center for Nano Science and NanotechnologyTel Aviv UniversityTel‐Aviv69978Israel
| | - Shachar Richter
- The Bio and Molecular Electronics GroupDepartment of Materials Science and EngineeringFaculty of Engineering and University Center for Nano Science and NanotechnologyTel Aviv UniversityTel‐Aviv69978Israel
| | - Ryan C. Chiechi
- Stratingh Institute for Chemistry and Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Andreas Herrmann
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
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Microarray Selection of Cooperative Peptides for Modulating Enzyme Activities. MICROARRAYS 2017; 6:microarrays6020008. [PMID: 28445435 PMCID: PMC5487955 DOI: 10.3390/microarrays6020008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/21/2017] [Accepted: 04/24/2017] [Indexed: 11/23/2022]
Abstract
Recently, peptide microarrays have been used to distinguish proteins, antibodies, viruses, and bacteria based on their binding to random sequence peptides. We reported on the use of peptide arrays to identify enzyme modulators that involve screening an array of 10,000 defined and addressable peptides on a microarray. Primary peptides were first selected to inhibit the enzyme at low μM concentrations. Then, new peptides were found to only bind strongly with the enzyme–inhibitor complex, but not the native enzyme. These new peptides served as secondary inhibitors that enhanced the inhibition of the enzyme together with the primary peptides. Without the primary peptides, the secondary effect peptides had little effect on the enzyme activity. Conversely, we also selected peptides that recovered the activities of inhibited enzyme–peptide complex. The selection of cooperative peptide pairs will provide a versatile toolkit for modulating enzyme functions, which may potentially be applied to drug discovery and biocatalysis.
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Warren JG, Kasun GW, Leonard T, Kirkpatrick BC. A phage display-selected peptide inhibitor of Agrobacterium vitis polygalacturonase. MOLECULAR PLANT PATHOLOGY 2016; 17:480-6. [PMID: 26177065 PMCID: PMC6638516 DOI: 10.1111/mpp.12293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Agrobacterium vitis, the causal agent of crown gall of grapevine, is a threat to viticulture worldwide. A major virulence factor of this pathogen is polygalacturonase, an enzyme that degrades pectin components of the xylem cell wall. A single gene encodes for the polygalacturonase gene. Disruption of the polygalacturonase gene results in a mutant that is less pathogenic and produces significantly fewer root lesions on grapevines. Thus, the identification of peptides or proteins that could inhibit the activity of polygalacturonase could be part of a strategy for the protection of plants against this pathogen. A phage-displayed combinatorial peptide library was used to isolate peptides with a high binding affinity to A. vitis polygalacturonase. These peptides showed sequence similarity to regions of Oryza sativa (EMS66324, Japonica) and Triticum urartu (NP_001054402, wild wheat) polygalacturonase-inhibiting proteins (PGIPs). Furthermore, these panning experiments identified a peptide, SVTIHHLGGGS, which was able to reduce A. vitis polygalacturonase activity by 35% in vitro. Truncation studies showed that the IHHL motif alone is sufficient to inhibit A. vitis polygalacturonase activity.
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Affiliation(s)
- Jeremy G Warren
- Department of Plant Pathology, University of California, Davis, 95616, CA, USA
| | - George W Kasun
- Department of Plant Pathology, University of California, Davis, 95616, CA, USA
| | - Takara Leonard
- Department of Plant Pathology, University of California, Davis, 95616, CA, USA
| | - Bruce C Kirkpatrick
- Department of Plant Pathology, University of California, Davis, 95616, CA, USA
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Identification of peptide inhibitors of penicillinase using a phage display library. Anal Biochem 2016; 494:4-9. [DOI: 10.1016/j.ab.2015.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/18/2015] [Accepted: 10/21/2015] [Indexed: 12/20/2022]
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Günay KA, Klok HA. Identification of Soft Matter Binding Peptide Ligands Using Phage Display. Bioconjug Chem 2015; 26:2002-15. [PMID: 26275106 DOI: 10.1021/acs.bioconjchem.5b00377] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phage display is a powerful tool for the selection of highly affine, short peptide ligands. While originally primarily used for the identification of ligands to proteins, the scope of this technique has significantly expanded over the past two decades. Phage display nowadays is also increasingly applied to identify ligands that selectively bind with high affinity to a broad range of other substrates including natural and biological polymers as well as a variety of low-molecular-weight organic molecules. Such peptides are of interest for various reasons. The ability to selectively and with high affinity bind to the substrate of interest allows the conjugation or immobilization of, e.g., nanoparticles or biomolecules, or generally, facilitates interactions at materials interfaces. On the other hand, presentation of peptide ligands that selectively bind to low-molecular-weight organic materials is of interest for the development of sensor surfaces. The aim of this article is to highlight the opportunities provided by phage display for the identification of peptide ligands that bind to synthetic or natural polymer substrates or to small organic molecules. The article will first provide an overview of the different peptide ligands that have been identified by phage display that bind to these "soft matter" targets. The second part of the article will discuss the different characterization techniques that allow the determination of the affinity of the identified ligands to the respective substrates.
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Affiliation(s)
- Kemal Arda Günay
- École Polytechnique Fédérale de Lausanne (EPFL) , Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
| | - Harm-Anton Klok
- École Polytechnique Fédérale de Lausanne (EPFL) , Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
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12
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Leurs U, Lohse B, Ming S, Cole PA, Clausen RP, Kristensen JL, Rand KD. Dissecting the binding mode of low affinity phage display peptide ligands to protein targets by hydrogen/deuterium exchange coupled to mass spectrometry. Anal Chem 2014; 86:11734-41. [PMID: 25325890 PMCID: PMC4255673 DOI: 10.1021/ac503137u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Phage
display (PD) is frequently used to discover peptides capable
of binding to biological protein targets. The structural characterization
of peptide–protein complexes is often challenging due to their
low binding affinities and high structural flexibility. Here, we investigate
the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS)
to characterize interactions of low affinity peptides with their cognate
protein targets. The HDX-MS workflow was optimized to accurately detect
low-affinity peptide–protein interactions by use of ion mobility,
electron transfer dissociation, nonbinding control peptides, and statistical
analysis of replicate data. We show that HDX-MS can identify regions
in the two epigenetic regulator proteins KDM4C and KDM1A that are
perturbed through weak interactions with PD-identified peptides. Two
peptides cause reduced HDX on opposite sides of the active site of
KDM4C, indicating distinct binding modes. In contrast, the perturbation
site of another PD-selected peptide inhibiting the function of KDM1A
maps to a GST-tag. Our results demonstrate that HDX-MS can validate
and map weak peptide–protein interactions and pave the way
for understanding and optimizing the binding of peptide scaffolds
identified through PD and similar ligand discovery approaches.
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Affiliation(s)
- Ulrike Leurs
- Department of Pharmacy, University of Copenhagen , Universitetsparken 2, DK-2100 Copenhagen, Denmark
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Thong KL, Tang SS, Tan WS, Devi S. Peptide Mimotopes of Complex Carbohydrates inSalmonella entericaSerovar Typhi Which React with Both Carbohydrate-Specific Monoclonal Antibody and Polyclonal Sera from Typhoid Patients. Microbiol Immunol 2013; 51:1045-52. [DOI: 10.1111/j.1348-0421.2007.tb03997.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kwai-Lin Thong
- Institute of Biological Sciences, Faculty of Science; University of Malaya; Kuala Lumpur Malaysia
| | - Swee-Seong Tang
- Institute of Biological Sciences, Faculty of Science; University of Malaya; Kuala Lumpur Malaysia
| | - Wen-Siang Tan
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences; University Putra Malaysia; Kuala Lumpur Malaysia
| | - Shamala Devi
- Department of Microbiology, Faculty of Medicine; University of Malaya; Kuala Lumpur Malaysia
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Nirantar SR, Yeo KS, Chee S, Lane DP, Ghadessy FJ. A generic scaffold for conversion of peptide ligands into homogenous biosensors. Biosens Bioelectron 2013; 47:421-8. [DOI: 10.1016/j.bios.2013.03.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/21/2013] [Accepted: 03/21/2013] [Indexed: 11/17/2022]
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Hamilton PT, Jansen MS, Ganesan S, Benson RE, Hyde-DeRuyscher R, Beyer WF, Gile JC, Nair SA, Hodges JA, Grøn H. Improved bone morphogenetic protein-2 retention in an injectable collagen matrix using bifunctional peptides. PLoS One 2013; 8:e70715. [PMID: 23950987 PMCID: PMC3738572 DOI: 10.1371/journal.pone.0070715] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 06/28/2013] [Indexed: 11/19/2022] Open
Abstract
To promote healing of many orthopedic injuries, tissue engineering approaches are being developed that combine growth factors such as Bone Morphogenetic Proteins (BMP) with biomaterial carriers. Although these technologies have shown great promise, they still face limitations. We describe a generalized approach to create target-specific modular peptides that bind growth factors to implantable biomaterials. These bifunctional peptide coatings provide a novel way to modulate biology on the surface of an implant. Using phage display techniques, we have identified peptides that bind with high affinity to BMP-2. The peptides that bind to BMP-2 fall into two different sequence clusters. The first cluster of peptide sequences contains the motif W-X-X-F-X-X-L (where X can be any amino acid) and the second cluster contains the motif F-P-L-K-G. We have synthesized bifunctional peptide linkers that contain BMP-2 and collagen-binding domains. Using a rat ectopic bone formation model, we have injected rhBMP-2 into a collagen matrix with or without a bifunctional BMP-2: collagen peptide (BC-1). The presence of BC-1 significantly increased osteogenic cellular activity, the area of bone formed, and bone maturity at the site of injection. Our results suggest that bifunctional peptides that can simultaneously bind to a growth factor and an implantable biomaterial can be used to control the delivery and release of growth factors at the site of implantation.
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Affiliation(s)
- Paul T. Hamilton
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Michelle S. Jansen
- Affinergy, LLC, Research Triangle Park, North Carolina, United States of America
| | - Sathya Ganesan
- Affinergy, LLC, Research Triangle Park, North Carolina, United States of America
| | - R. Edward Benson
- Platform Technology and Science, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | - Robin Hyde-DeRuyscher
- Manufacturing Sciences, Biogen Idec, Research Triangle Park, North Carolina, United States of America
| | - Wayne F. Beyer
- QNS Group, LLC, Durham, North Carolina, United States of America
| | - Joseph C. Gile
- Gile Surgical Support, Bangor, Maine, United States of America
| | - Shrikumar A. Nair
- Affinergy, LLC, Research Triangle Park, North Carolina, United States of America
| | - Jonathan A. Hodges
- Affinergy, LLC, Research Triangle Park, North Carolina, United States of America
- * E-mail:
| | - Hanne Grøn
- Haemophilia Biochemistry, Novo Nordisk, Måløv, Denmark
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16
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Wada A. Development of Next-Generation Peptide Binders Using In vitro Display Technologies and Their Potential Applications. Front Immunol 2013; 4:224. [PMID: 23914189 PMCID: PMC3730117 DOI: 10.3389/fimmu.2013.00224] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/29/2013] [Indexed: 12/02/2022] Open
Abstract
During the last decade, a variety of monoclonal antibodies have been developed and used as molecular targeting drugs in medical therapies. Although antibody drugs tend to have intense pharmacological activities and negligible side effects, several issues in their development and prescription remain to be resolved. Synthetic peptides with affinities and specificities for a desired target have received significant attention as alternatives to antibodies. In vitro display technologies are powerful methods for the selection of such peptides from combinatorial peptide libraries. Various types of peptide binders are being selected with such technologies for use in a wide range of fields from bioscience to medicine. This mini review article focuses on the current state of in vitro display selection of synthetic peptide binders and compares the selected peptides with natural peptides/proteins to provide a better understanding of the target affinities and inhibitory activities derived from their amino acid sequences and structural frameworks. The potential of synthetic peptide binders as alternatives to antibody drugs in therapeutic applications is also reviewed.
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Jenkins RJ, Dotson GD. Dual targeting antibacterial peptide inhibitor of early lipid A biosynthesis. ACS Chem Biol 2012; 7:1170-7. [PMID: 22530734 DOI: 10.1021/cb300094a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
UDP-3-O-(R-3-hydroxyacyl)GlcN N-acyltransferase (LpxD) has been shown to be essential to survival of lipid A producing Gram-negative bacteria. In this study, LpxD-binding peptides 12 amino acids in length were identified from a phage-bound random peptide library screen. Three peptides displayed antibacterial activity when expressed intracellularly, one of which (RJPXD33) represented 15% of the total hits. RJPXD33 binds to E. coli LpxD with a K(d) of 6 μM and is competitive with R-3-hydroxymyristoyl-ACP binding. RJPXD33 can be C-terminally fused in vivo with thioredoxin or N-terminally modified in vitro with β-alanyl-fluorescein and maintain LpxD binding. The latter was used to develop an LpxD fluorescent binding assay used to evaluate unlabeled ligands and is amenable to small molecule library screening. Furthermore, RJPXD33 also binds to and inhibits E. coli UDP-N-acetylglucosamine acyltransferase (LpxA) with a K(d) of 20 μM, unearthing the possibility for the development of small molecule, dual-binding LpxA/LpxD inhibitors as novel antimicrobials.
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Affiliation(s)
- Ronald J. Jenkins
- Department of Medicinal Chemistry,
College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Garry D. Dotson
- Department of Medicinal Chemistry,
College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
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18
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Chen T, Hoffmann K, Ostman S, Sandberg AS, Olsson O. Identification of gliadin-binding peptides by phage display. BMC Biotechnol 2011; 11:16. [PMID: 21329494 PMCID: PMC3051897 DOI: 10.1186/1472-6750-11-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 02/17/2011] [Indexed: 12/30/2022] Open
Abstract
Background Coeliac disease (CD) is a common and complex disorder of the small intestine caused by intolerance to wheat gluten and related edible cereals like barley and rye. Peptides originating from incomplete gliadin digestion activate the lamina propria infiltrating T cells to release proinflammatory cytokines, which in turn cause profound tissue remodelling of the small intestinal wall. There is no cure for CD except refraining from consuming gluten-containing products. Results Phage from a random oligomer display library were enriched by repeated pannings against immobilised gliadin proteins. Phage from the final panning round were plated, individual plaques picked, incubated with host bacteria, amplified to a population size of 1011 to 1012 and purified. DNA was isolated from 1000 purified phage populations and the region covering the 36 bp oligonucleotide insert from which the displayed peptides were translated, was sequenced. Altogether more than 150 different peptide-encoding sequences were identified, many of which were repeatedly isolated under various experimental conditions. Amplified phage populations, each expressing a single peptide, were tested first in pools and then one by one for their ability to inhibit binding of human anti-gliadin antibodies in ELISA assays. These experiments showed that several of the different peptide-expressing phage tested inhibited the interaction between gliadin and anti-gliadin antibodies. Finally, four different peptide-encoding sequences were selected for further analysis, and the corresponding 12-mer peptides were synthesised in vitro. By ELISA assays it was demonstrated that several of the peptides inhibited the interaction between gliadin molecules and serum anti-gliadin antibodies. Moreover, ELISA competition experiments as well as dot-blot and western blot revealed that the different peptides interacted with different molecular sites of gliadin. Conclusions We believe that several of the isolated and characterised gliadin-binding peptides described here could provide valuable tools for researchers in the field of CD by facilitating studies on localisation and uptake of various gliadin peptides in the small intestine. In future work, the potential of these peptides to detoxify gluten will be investigated.
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Affiliation(s)
- Tingsu Chen
- Department of Plant and Environmental Sciences, University of Gothenburg, SE-40530, Gothenburg, Sweden
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19
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Chen K, Chen X. Design and development of molecular imaging probes. Curr Top Med Chem 2011; 10:1227-36. [PMID: 20388106 DOI: 10.2174/156802610791384225] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 02/27/2010] [Indexed: 01/17/2023]
Abstract
Molecular imaging, the visualization, characterization and measurement of biological processes at the cellular, subcellular level, or even molecular level in living subjects, has rapidly gained importance in the dawning era of personalized medicine. Molecular imaging takes advantage of the traditional diagnostic imaging techniques and introduces molecular imaging probes to determine the expression of indicative molecular markers at different stages of diseases and disorders. As a key component of molecular imaging, molecular imaging probe must be able to specifically reach the target of interest in vivo while retaining long enough to be detected. A desirable molecular imaging probe with clinical translation potential is expected to have unique characteristics. Therefore, design and development of molecular imaging probe is frequently a challenging endeavor for medicinal chemists. This review summarizes the general principles of molecular imaging probe design and some fundamental strategies of molecular imaging probe development with a number of illustrative examples.
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Affiliation(s)
- Kai Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
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20
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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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21
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Shu Q, Chi Y, Zheng L, Dong Y, Zhang L, Chen G. Electrochemiluminescence for probing interactions between a mimic enzyme and biological molecules. Electrochem commun 2009. [DOI: 10.1016/j.elecom.2008.11.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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22
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Hamzeh-Mivehroud M, Mahmoudpour A, Rezazadeh H, Dastmalchi S. Non-specific translocation of peptide-displaying bacteriophage particles across the gastrointestinal barrier. Eur J Pharm Biopharm 2008; 70:577-81. [DOI: 10.1016/j.ejpb.2008.06.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 06/09/2008] [Accepted: 06/09/2008] [Indexed: 10/21/2022]
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23
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Han X, Lu C. Biological activity and identification of a peptide inhibitor of LuxS from Streptococcus suis serotype 2. FEMS Microbiol Lett 2008; 294:16-23. [PMID: 19493004 DOI: 10.1111/j.1574-6968.2009.01534.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The virulence of bacterial communities may be regulated by mechanisms involving the synthesis of the quorum-sensing signal autoinducer 2 (AI-2), which allows both intra- and interspecies communication. AI-2 is produced in bacteria that express the gene luxS. In the present study, expressed and purified LuxS from Streptococcus suis serotype 2 (SS2) was used to catalyze the substrate S-ribosylhomocysteine in a reaction that leads to the production of AI-2. The biological activity of the in vitro synthesized AI-2 was demonstrated in a Vibrio harveyi strain BB170 bioassay; real-time PCR results showed that biosynthesis of AI-2 can increase the virulence of SS2. Phage-encoded peptides that specifically interact with the LuxS enzyme were selected following three rounds of phage display. One such peptide inhibitor (TNRHNPHHLHHV) of LuxS was shown to partially inhibit the activity of the enzyme. Furthermore, 14 peptides containing the consensus sequence HSIR showed high affinity with LuxS. The selected and characterized specific inhibitor as well as the high-affinity ligands may facilitate the identification of new vaccination targets, opening up new approaches to the development of therapeutic drugs.
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Affiliation(s)
- Xiangan Han
- Key Laboratory of Animal Disease Diagnostics and Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
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24
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Kay BK, Castagnoli L. Mapping protein-protein interactions with phage-displayed combinatorial peptide libraries. ACTA ACUST UNITED AC 2008; Chapter 17:Unit 17.4. [PMID: 18228422 DOI: 10.1002/0471143030.cb1704s17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This unit describes the process and analysis of affinity selecting bacteriophage M13 from libraries displaying combinatorial peptides fused to either a minor or major capsid protein. Direct affinity selection uses target protein bound to a microtiter plate followed by purification of selected phage by ELISA. Alternatively, there is a bead-based affinity selection method. These methods allow one to readily isolate peptide ligands that bind to a protein target of interest and use the consensus sequence to search proteomic databases for putative interacting proteins.
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Affiliation(s)
- Brian K Kay
- Argonne National Laboratory, Argonne, Illinois, USA
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25
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Abstract
AbstractAntibiotic resistance is increasing at a rate that far exceeds the pace of new development of drugs. Antimicrobial peptides, both synthetic and from natural sources, have raised interest as pathogens become resistant against conventional antibiotics. Indeed, one of the major strengths of this class of molecules is their ability to kill multidrug-resistant bacteria. Antimicrobial peptides are relatively small (6 to 100 aminoacids), amphipathic molecules of variable length, sequence and structure with activity against a wide range of microorganisms including bacteria, protozoa, yeast, fungi, viruses and even tumor cells. They usually act through relatively non-specific mechanisms resulting in membranolytic activity but they can also stimulate the innate immune response. Several peptides have already entered pre-clinical and clinical trials for the treatment of catheter site infections, cystic fibrosis, acne, wound healing and patients undergoing stem cell transplantation. We review the advantages of these molecules in clinical applications, their disadvantages including their low in vivo stability, high costs of production and the strategies for their discovery and optimization.
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26
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Molina-López J, Sanschagrin F, Levesque RC. A peptide inhibitor of MurA UDP-N-acetylglucosamine enolpyruvyl transferase: the first committed step in peptidoglycan biosynthesis. Peptides 2006; 27:3115-21. [PMID: 17030076 DOI: 10.1016/j.peptides.2006.08.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 08/22/2006] [Accepted: 08/23/2006] [Indexed: 10/24/2022]
Abstract
The MurA enzyme from Pseudomonas aeruginosa was purified to homogeneity and found to be biologically active as a UDP-N-acetylglucosamine (UNAG) enolpyruvyl transferase in a coupled enzyme assay where ATPase activity was measured by the release of inorganic phosphate. A microtiter plate assay coupled to competitive biopanning using the UDP-N-acetylglucosamine was used to screen 10(9) C-7-C and 12-mers peptides from phage display libraries. From 60 phage-encoded peptides identified after the fourth round of biopanning, deduced amino acid sequences were aligned and two peptides were synthesized and tested for inhibition of the MurA-catalyzed reaction. The PEP 1354 peptide inhibited the ATPase activity of MurA with an IC(50) value of 200muM and was found to be a competitive inhibitor of UNAG. The pre-incubation of MurA with inhibitor indicated a time-independent inhibition. This time-dependent inhibition is the first report of peptide inhibitors of MurA, which represent the scaffold for the synthesis of inhibitory peptidomimetic molecules.
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Affiliation(s)
- José Molina-López
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico.
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27
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Kenan DJ, Walsh EB, Meyers SR, O'Toole GA, Carruthers EG, Lee WK, Zauscher S, Prata CAH, Grinstaff MW. Peptide-PEG Amphiphiles as Cytophobic Coatings for Mammalian and Bacterial Cells. ACTA ACUST UNITED AC 2006; 13:695-700. [PMID: 16873017 DOI: 10.1016/j.chembiol.2006.06.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 06/07/2006] [Accepted: 06/20/2006] [Indexed: 11/18/2022]
Abstract
Amphiphilic macromolecules containing a polystyrene-adherent peptide domain and a cell-repellent poly(ethylene glycol) domain were designed, synthesized, and evaluated as a cytophobic surface coating. Such cytophobic, or cell-repellent, coatings are of interest for varied medical and biotechnological applications. The composition of the polystyrene binding peptide domain was identified using an M13 phage display library. ELISA and atomic force spectroscopy were used to evaluate the binding affinity of the amphiphile peptide domain to polystyrene. When coated onto polystyrene, the amphiphile reduced cell adhesion of two distinct mammalian cell lines and pathogenic Staphylococcus aureus strains.
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Affiliation(s)
- Daniel J Kenan
- Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, USA.
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28
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Paradis-Bleau C, Beaumont M, Boudreault L, Lloyd A, Sanschagrin F, Bugg TDH, Levesque RC. Selection of peptide inhibitors against the Pseudomonas aeruginosa MurD cell wall enzyme. Peptides 2006; 27:1693-700. [PMID: 16517013 DOI: 10.1016/j.peptides.2006.01.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Revised: 01/20/2006] [Accepted: 01/23/2006] [Indexed: 11/24/2022]
Abstract
The purified Pseudomonas aeruginosa cell wall biosynthesis MurD amide ligase enzyme was used to screen C-7-C and 12 mers peptides from phage display libraries using competitive biopanning approaches with the specific substrates D-glutamate and ATP. From the 60 phage-encoded peptides identified, DNA was sequenced, deduced amino acid sequences aligned and two peptides were synthesized from consensus sequences identified. The UDP-N-acetylmuramyl-L-alanine MurD substrate was synthesized, purified and used to develop a spectrophotometric assay. One peptide synthesized was found to specifically inhibit ATPase activity of MurD. The IC50 value was estimated at 4 microM for the C-7-C MurDp1 peptide. The loop conformation of MurDp1 was shown to be important for the inhibition of the UDP-N-acetylmuramyl-L-alanine:D-glutamate MurD ligase. The linear 12 mers MurD2 peptide has an IC50 value of 15 mM. A conserved amino acid motif was found between MurDp2 and the bacterial glyceraldehyde 3-phosphate dehydrogenase indicating that MurDp2 binds at a protein-protein interacting site. The approach proposed and results obtained suggest that efficient peptide inhibitors as well as protein-protein interaction domains can be identified by phage display.
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Affiliation(s)
- Catherine Paradis-Bleau
- CREFSIP, Département de Biologie Médicale, Faculté de Médecine, Université Laval, Sainte-Foy, Québec, Canada G1K 7P4.
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29
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Björklund M, Aitio O, Stefanidakis M, Suojanen J, Salo T, Sorsa T, Koivunen E. Stabilization of the activated alphaMbeta2 integrin by a small molecule inhibits leukocyte migration and recruitment. Biochemistry 2006; 45:2862-71. [PMID: 16503641 DOI: 10.1021/bi052238b] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Integrins are potential targets for the development of antiinflammatory agents. Here we develop a novel high-throughput assay by allowing a chemical library to compete with phage display peptide binding and identify a novel small-molecule ligand to the leukocyte-specific alpha(M)beta(2) integrin. The identified thioxothiazolidine-containing compound, IMB-10, had an unexpected activity in that it stabilized binding of alpha(M)beta(2) to its endogenous ligands proMMP-9 and fibrinogen. Single amino acid substitutions in the activity-regulating C-terminal helix and the underlying region in the ligand-binding I domain of the integrin suppressed the effect of IMB-10. A computational model indicated that IMB-10 occupies a distinct cavity present only in the activated form of the integrin I domain. IMB-10 inhibited alpha(M)beta(2)-dependent migration in vitro and inflammation-induced neutrophil emigration in vivo. Stabilization of integrin-mediated adhesion by a small molecule is a novel means to inhibit cell migration and may have a utility in treatment of inflammatory diseases involving leukocyte recruitment.
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Affiliation(s)
- Mikael Björklund
- Department of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
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30
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Wassaf D, Kuang G, Kopacz K, Wu QL, Nguyen Q, Toews M, Cosic J, Jacques J, Wiltshire S, Lambert J, Pazmany CC, Hogan S, Ladner RC, Nixon AE, Sexton DJ. High-throughput affinity ranking of antibodies using surface plasmon resonance microarrays. Anal Biochem 2006; 351:241-53. [PMID: 16510109 DOI: 10.1016/j.ab.2006.01.043] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Revised: 01/17/2006] [Accepted: 01/26/2006] [Indexed: 11/25/2022]
Abstract
A method was developed to rapidly identify high-affinity human antibodies from phage display library selection outputs. It combines high-throughput Fab fragment expression and purification with surface plasmon resonance (SPR) microarrays to determine kinetic constants (kon and koff) for 96 different Fab fragments in a single experiment. Fabs against human tissue kallikrein 1 (hK1, KLK1 gene product) were discovered by phage display, expressed in Escherichia coli in batches of 96, and purified using protein A PhyTip columns. Kinetic constants were obtained for 191 unique anti-hK1 Fabs using the Flexchip SPR microarray device. The highest affinity Fabs discovered had dissociation constants of less than 1 nM. The described SPR method was also used to categorize Fabs according to their ability to recognize an apparent active site epitope. The ability to rapidly determine the affinities of hundreds of antibodies significantly accelerates the discovery of high-affinity antibody leads.
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31
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Gasanov U, Koina C, Beagley KW, Aitken RJ, Hansbro PM. Identification of the insulin-like growth factor II receptor as a novel receptor for binding and invasion by Listeria monocytogenes. Infect Immun 2006; 74:566-77. [PMID: 16369013 PMCID: PMC1346592 DOI: 10.1128/iai.74.1.566-577.2006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The gram-positive bacterium Listeria monocytogenes causes a life-threatening disease known as listeriosis. The mechanism by which L. monocytogenes invades mammalian cells is not fully understood, but the processes involved may provide targets to prevent and treat listeriosis. Here, for the first time, we have identified the insulin-like growth factor II receptor (IGFIIR; also known as the cation-independent mannose 6-phosphate receptor (CI)M6PR or CD222) as a novel receptor for binding and invasion of Listeria species. Random peptide phage display was employed to select a peptide sequence by panning with immobilized L. monocytogenes cells; this peptide sequence corresponds to a sequence within the mannose 6-phosphate binding site of the IGFIIR. All Listeria spp. specifically bound the labeled peptide but not a control peptide, which was demonstrated using fluorescence spectrophotometry and fluorescence-activated cell sorting. Further evidence for binding of the receptor by L. monocytogenes and L. innocua was provided by affinity purification of the bovine IGFIIR from fetal calf serum by use of magnetic beads coated with cell preparations of Listeria spp. as affinity matrices. Adherence to and invasion of mammalian cells by L. monocytogenes was significantly inhibited by both the synthetic peptide and mannose 6-phosphate but not by appropriate controls. These observations indicate a role for the IGFIIR in the adherence and invasion of L. monocytogenes of mammalian cells, perhaps in combination with known mechanisms. Ligation of IGFIIR by L. monocytogenes may be a novel mechanism that contributes to the regulation of infectivity, possibly in combination with other mechanisms.
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Affiliation(s)
- Uta Gasanov
- Discipline of Immunology & Microbiology, Faculty of Health, The University of Newcastle, Royal Newcastle Hospital, Newcastle, New South Wales 2300, Australia
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32
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Tanaka F. Development of protein, peptide, and small molecule catalysts using catalysis-based selection strategies. CHEM REC 2006; 5:276-85. [PMID: 16211623 DOI: 10.1002/tcr.20051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We have developed peptide catalysts and antibody catalysts that catalyze aldol, retro-aldol, and Michael reactions via an enamine mechanism using reaction-based selections with 1,3-diketone derivatives. Nucleophilic amino groups of the catalysts were covalently trapped during the selections. We have also developed fluorogenic substrates that are useful for real-time monitoring of the progress of bond-forming reactions, such as aldol reactions, by an increase in fluorescence. These fluorogenic substrates have been used to monitor peptide-catalyzed, antibody-catalyzed, enzyme-catalyzed, and small molecule-catalyzed reactions. Catalysis-based screening using fluorogenic substrates will accelerate rapid identification of superior catalysts and reaction conditions.
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Affiliation(s)
- Fujie Tanaka
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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33
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Johnston CA, Willard FS, Jezyk MR, Fredericks Z, Bodor ET, Jones MB, Blaesius R, Watts VJ, Harden TK, Sondek J, Ramer JK, Siderovski DP. Structure of Galpha(i1) bound to a GDP-selective peptide provides insight into guanine nucleotide exchange. Structure 2005; 13:1069-80. [PMID: 16004878 PMCID: PMC1405235 DOI: 10.1016/j.str.2005.04.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2005] [Accepted: 04/14/2005] [Indexed: 01/30/2023]
Abstract
Heterotrimeric G proteins are molecular switches that regulate numerous signaling pathways involved in cellular physiology. This characteristic is achieved by the adoption of two principal states: an inactive, GDP bound state and an active, GTP bound state. Under basal conditions, G proteins exist in the inactive, GDP bound state; thus, nucleotide exchange is crucial to the onset of signaling. Despite our understanding of G protein signaling pathways, the mechanism of nucleotide exchange remains elusive. We employed phage display technology to identify nucleotide state-dependent Galpha binding peptides. Herein, we report a GDP-selective Galpha binding peptide, KB-752, that enhances spontaneous nucleotide exchange of Galpha(i) subunits. Structural determination of the Galpha(i1)/peptide complex reveals unique changes in the Galpha switch regions predicted to enhance nucleotide exchange by creating a GDP dissociation route. Our results cast light onto a potential mechanism by which Galpha subunits adopt a conformation suitable for nucleotide exchange.
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Affiliation(s)
- Christopher A Johnston
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Abstract
New ligands for a variety of biological targets can be selected from biological or synthetic combinatorial peptide libraries. The use of different libraries to select novel peptides with potential therapeutic applications is reviewed. The possible combination of molecular diversity provided by combinatorial libraries and a rational approach derived from computational modeling is also considered. Advantages and disadvantages of different approaches are compared. Possible strategies to bypass loss of peptide bioactivity in the transition from ligand selection to in vivo use are discussed.
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Affiliation(s)
- Chiara Falciani
- Department of Molecular Biology, University of Siena, I-53100 Siena, Italy
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Bratkovic T, Lunder M, Popovic T, Kreft S, Turk B, Strukelj B, Urleb U. Affinity selection to papain yields potent peptide inhibitors of cathepsins L, B, H, and K. Biochem Biophys Res Commun 2005; 332:897-903. [PMID: 15913550 DOI: 10.1016/j.bbrc.2005.05.028] [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] [Received: 05/04/2005] [Accepted: 05/09/2005] [Indexed: 11/24/2022]
Abstract
Endogenous cysteine proteases were given much attention lately, as their role in a variety of pathophysiological disorders became evident. Amongst them cathepsins, which are thought to be implicated in mediation of osteoporosis, cancer progression, atherosclerosis, and many other conditions, are of considerable interest as drug targets. In the presented work, papain was chosen as a model cysteine protease and panning protocol was optimized for selection of papain-binding phage-displayed peptides from a commercially available combinatorial peptide library. Different selection strategies were applied in order to select high-affinity binders. Ultimately, five cyclic peptides (CNWAAGYNCGGGS-NH2, CWSMMGFQCGGGS-NH2, CWEWGGWHCGGSS-OH, CNWTLGGYKCGGGS-NH2 (all cyclized through formation of intramolecular disulphide bond), and GNWTLGGYKGG (cyclized head-to-tail)) were synthesized and tested for inhibitory activity towards papain and human cathepsins L, B, H, and K. The peptides possess inhibitory constants in the low micromolar to mid-nanomolar range and exhibit certain selectivity for different lysosomal cysteine proteases included in this study.
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Affiliation(s)
- Tomaz Bratkovic
- Faculty of Pharmacy, Department of Pharmaceutical Biology, University of Ljubljana, Askerceva 7, SI-1000 Ljubljana, Slovenia.
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Sticht J, Humbert M, Findlow S, Bodem J, Müller B, Dietrich U, Werner J, Kräusslich HG. A peptide inhibitor of HIV-1 assembly in vitro. Nat Struct Mol Biol 2005; 12:671-7. [PMID: 16041387 DOI: 10.1038/nsmb964] [Citation(s) in RCA: 183] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2005] [Accepted: 06/20/2005] [Indexed: 01/05/2023]
Abstract
Formation of infectious HIV-1 involves assembly of Gag polyproteins into immature particles and subsequent assembly of mature capsids after proteolytic disassembly of the Gag shell. We report a 12-mer peptide, capsid assembly inhibitor (CAI), that binds the capsid (CA) domain of Gag and inhibits assembly of immature- and mature-like capsid particles in vitro. CAI was identified by phage display screening among a group of peptides with similar sequences that bind to a single reactive site in CA. Its binding site was mapped to CA residues 169-191, with an additional contribution from the last helix of CA. This result was confirmed by a separate X-ray structure analysis showing that CAI inserts into a conserved hydrophobic groove and alters the CA dimer interface. The CAI binding site is a new target for antiviral development, and CAI is the first known inhibitor directed against assembly of immature HIV-1.
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Affiliation(s)
- Jana Sticht
- Department of Virology, Universitätsklinikum Heidelberg, 69120 Heidelberg, Germany
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37
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Lunder M, Bratkovic T, Kreft S, Strukelj B. Peptide inhibitor of pancreatic lipase selected by phage display using different elution strategies. J Lipid Res 2005; 46:1512-6. [PMID: 15863836 DOI: 10.1194/jlr.m500048-jlr200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Interference with fat hydrolysis results in the reduced use of ingested lipids. Inhibition of pancreatic lipase reduces the efficiency of fat absorption in the small intestine and thereby initiates modest long-term reduction in body weight. In an attempt to select peptides with affinity for the surface of pancreatic lipase and potential inhibitory activity, a random, cyclic heptapeptide phage-displayed library was used. Five independent selections, differing in elution step, were performed. In three selection protocols, a sequential elution strategy was applied in anticipation of improving the selection of high-affinity clones. Four heptapeptides with the highest affinity, seemingly for pancreatic lipase, were selected, synthesized, and characterized for their capacity to inhibit enzyme function. Although no clear consensus among the sequenced peptides was found, one of the selected peptides inhibited pancreatic lipase with an apparent inhibition constant of 16 muM.
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Affiliation(s)
- M Lunder
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Ljubljana, Slovenia.
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38
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Paradis-Bleau C, Sanschagrin F, Levesque RC. Peptide inhibitors of the essential cell division protein FtsA. Protein Eng Des Sel 2005; 18:85-91. [PMID: 15790573 DOI: 10.1093/protein/gzi008] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The revolutionary era of antibiotics has been overwhelmed by the evolutionary capacity of microorganisms such as Pseudomonas aeruginosa to develop resistance to all classes of antibiotics. In the perspective of identifying new antimicrobials using novel strategies, we targeted the essential and highly conserved FtsA protein from the bacterial cell division machinery of P.aeruginosa. In a series of experiments we cloned, overproduced and purified the FtsA and FtsZ proteins. Expression of FtsA into Escherichia coli cells led to its accumulation in inclusion bodies. We developed a protocol permitting the purification and refolding of enzymatically active FtsA hydrolysing ATP. The purified enzyme was used to screen for peptide inhibitors of ATPase activity using phage display. Selective biopanning assays were done and phages were eluted using ATP, a non-hydrolysable ATP analogue and the protein FtsZ known to interact with FtsA in the divisome during the process of bacterial cell division. We identified two consensus peptide sequences interacting with FtsA and a competitive ELISA was used to identify peptides having high affinity for the target protein. Five of the six peptides synthesized showed specific inhibition of ATPase activity of FtsA with IC50 values between 0.7 and 35 mM. Discovery of peptides inhibiting the essential cell division machinery in bacteria is the first step for the future development of antimicrobial agents via peptidomimetism.
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Brown ED, Wright GD. New Targets and Screening Approaches in Antimicrobial Drug Discovery. Chem Rev 2005; 105:759-74. [PMID: 15700964 DOI: 10.1021/cr030116o] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eric D Brown
- Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada L8N 3Z5
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40
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He XG, Gerona-Navarro G, Jaffrey SR. Ligand discovery using small molecule microarrays. J Pharmacol Exp Ther 2004; 313:1-7. [PMID: 15537823 DOI: 10.1124/jpet.104.076943] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Small molecule microarrays have recently been used to identify ligands for several proteins, and several themes regarding screening strategies and limitations have emerged. In this review, some of the technical issues related to the manufacture and screening of small molecule microarrays, as well as prospects for small molecule microarrays in several areas of drug discovery and chemistry, are discussed.
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Affiliation(s)
- Xuezhong G He
- Department of Pharmacology, Weill Medical College, Cornell University, 1300 York Avenue, Box 70, New York, NY 10021, USA
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41
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Olszewski A, Sato K, Aron ZD, Cohen F, Harris A, McDougall BR, Robinson WE, Overman LE, Weiss GA. Guanidine alkaloid analogs as inhibitors of HIV-1 Nef interactions with p53, actin, and p56lck. Proc Natl Acad Sci U S A 2004; 101:14079-84. [PMID: 15371598 PMCID: PMC521092 DOI: 10.1073/pnas.0406040101] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With current anti-HIV treatments targeting only 4 of the 15 HIV proteins, many potential viral vulnerabilities remain unexploited. We report small-molecule inhibitors of the HIV-1 protein Nef. In addition to expanding the anti-HIV arsenal, small-molecule inhibitors against untargeted HIV proteins could be used to dissect key events in the HIV lifecycle. Numerous incompletely characterized interactions between Nef and cellular ligands, for example, present a challenge to understanding molecular events during HIV progression to AIDS. Assays with phage-displayed Nef from HIV(NL4-3) were used to identify a series of guanidine alkaloid-based inhibitors of Nef interactions with p53, actin, and p56(lck). The guanidines, synthetic analogs of batzellidine and crambescidin natural products, inhibit the Nef-ligand interactions with IC(50) values in the low micromolar range. In addition, sensitive in vivo assays for Nef inhibition are reported. Although compounds that are effective in vitro proved to be too cytotoxic for cellular assays, the reported Nef inhibitors provide proof-of-concept for disrupting a new HIV target and offer useful leads for drug development.
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Affiliation(s)
- Allison Olszewski
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
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42
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Abstract
Bacterial genomics has provided a plethora of potential targets for antibacterial drug discovery, however, success in the hunt for new antibiotics will hinge on selecting targets with the highest potential. A recent paper by Liu and coworkers describes a new approach to target selection that uncovers strategies used by bacteriophage to disable bacteria. The method uses key phage proteins to identify and validate vulnerable targets and exploits them further in the identification of new antibacterial leads.
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Affiliation(s)
- Eric D Brown
- Department of Biochemistry, McMaster University, 1200 Main Street West, Hamilton, Ontario, L8N 3Z5, Canada.
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Szardenings M. Phage display of random peptide libraries: applications, limits, and potential. J Recept Signal Transduct Res 2004; 23:307-49. [PMID: 14753295 DOI: 10.1081/rrs-120026973] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The identification of ligands from large biological libraries by phage display has now been used for almost 15 years. Most of the successful reports on high-affinity ligand identification originated from work with different antibody libraries. In contrast, the progress of applying phage display to random peptide libraries was relatively slow. However, in the last few years several improvements have led to an increasing number of published peptide ligands identified by phage display from such libraries and which exhibited good biological activity and high affinity. This review summarizes the current state and the technical progress of the application of random peptide libraries using filamentous phage for ligand identification.
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Affiliation(s)
- Michael Szardenings
- Institute of Biochemistry and Biotechnology, Technical University of Braunschweig, Braunschweig, Germany.
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44
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Han Z, Simpson JT, Fivash MJ, Fisher R, Mori T. Identification and characterization of peptides that bind to cyanovirin-N, a potent human immunodeficiency virus-inactivating protein. Peptides 2004; 25:551-61. [PMID: 15165709 DOI: 10.1016/j.peptides.2004.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2003] [Accepted: 02/25/2004] [Indexed: 11/23/2022]
Abstract
Cyanovirin-N (CV-N) exerts a potent human immunodeficiency virus (HIV)-inactivating activity against diverse strains of HIV by binding to the viral surface envelope glycoprotein gp120 and blocking its essential interactions with cellular receptors. Based on previous thermodynamic analyses, it has been speculated that discrete protein-protein interactions might play an important ancillary role in the CV-N/gp120 binding event, in addition to the interactions of CV-N with specific oligosaccharides present on gp120. Here, we report the identification and characterization of CV-N-binding peptides, which were isolated by screening of M13 phage-displayed peptide libraries. After performing three rounds of biopanning of the libraries against biotinylated CV-N, a CV-N-binding motif, X3CX6(W/F)(Y/F)CX2(Y/F), was evident. A vector was designed to express CV-N-binding peptides as a fusion with thioredoxin (Trx) containing a penta-His affinity tag. The CV-N-binding peptides fused with His-tagged Trx inhibited binding of the corresponding peptide-bearing phages to CV-N, confirming that the peptides possessed CV-N-binding activity. Optical biosensor binding studies showed that the one of the CV-N-binding peptide, TN10-1, bound to CV-N with a KD value of 1.9 microM. The results of alanine scanning mutagenesis of the peptide showed that aromatic residues at positions 11, 12, and 16, as well as the conformational structure of the peptide secured by a disulfide bond, were important for the binding interactions. A series of competitive binding assays confirmed that gp120 inhibited CV-N binding of the corresponding peptide-bearing phages, and suggested that TN10-1 peptides were mimicking the protein component of gp120 rather than mimicking specific oligosaccharides present on gp120.
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Affiliation(s)
- Zhaozhong Han
- Molecular Targets Development Program, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, MD 21702-1201, USA
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45
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Troitskaya LA, Kodadek T. Peptides as modulators of enzymes and regulatory proteins. Methods 2004; 32:406-15. [PMID: 15003603 DOI: 10.1016/j.ymeth.2003.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2003] [Indexed: 11/18/2022] Open
Abstract
There is currently great interest in the development of methods to modulate the function of diverse classes of target proteins with chemicals (agonists or antagonists). These would be valuable reagents for biomedical research and some might serve as potential drug leads. Traditionally, most chemicals that modulate protein function have been enzyme inhibitors isolated in functional screens specific for the enzyme of interest. However, recent efforts from many laboratories have suggested that relatively simple binding assays may provide a more convenient and general route to chemical modulators. We review here this work with a particular emphasis on peptide modulators.
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Affiliation(s)
- Larisa A Troitskaya
- Department of Internal Medicine and Molecular Biology, Center for Biomedical Inventions, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8573, USA
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Benson RE, Gottlin EB, Christensen DJ, Hamilton PT. Intracellular expression of Peptide fusions for demonstration of protein essentiality in bacteria. Antimicrob Agents Chemother 2003; 47:2875-81. [PMID: 12936988 PMCID: PMC182649 DOI: 10.1128/aac.47.9.2875-2881.2003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe a "protein knockout" technique that can be used to identify essential proteins in bacteria. This technique uses phage display to select peptides that bind specifically to purified target proteins. The peptides are expressed intracellularly and cause inhibition of growth when the protein is essential. In this study, peptides that each specifically bind to one of seven essential proteins were identified by phage display and then expressed as fusions to glutathione S-transferase in Escherichia coli. Expression of peptide fusions directed against E. coli DnaN, LpxA, RpoD, ProRS, SecA, GyrA, and Era each dramatically inhibited cell growth. Under the same conditions, a fusion with a randomized peptide sequence did not inhibit cell growth. In growth-inhibited cells, inhibition could be relieved by concurrent overexpression of the relevant target protein but not by coexpression of an irrelevant protein, indicating that growth inhibition was due to a specific interaction of the expressed peptide with its target. The protein knockout technique can be used to assess the essentiality of genes of unknown function emerging from the sequencing of microbial genomes. This technique can also be used to validate proteins as drug targets, and their corresponding peptides as screening tools, for discovery of new antimicrobial agents.
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Carroll PM, Dougherty B, Ross-Macdonald P, Browman K, FitzGerald K. Model systems in drug discovery: chemical genetics meets genomics. Pharmacol Ther 2003; 99:183-220. [PMID: 12888112 DOI: 10.1016/s0163-7258(03)00059-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Animal model systems are an intricate part of the discovery and development of new medicines. The sequencing of not only the human genome but also those of the various pathogenic bacteria, the nematode Caenorhabditis elegans, the fruitfly Drosophila, and the mouse has enabled the discovery of new drug targets to push forward at an unprecedented pace. The knowledge and tools in these "model" systems are allowing researchers to carry out experiments more efficiently and are uncovering previously hidden biological connections. While the history of bacteria, yeast, and mice in drug discovery are long, their roles are ever evolving. In contrast, the history of Drosophila and C. elegans at pharmaceutical companies is short. We will briefly review the historic role of each model organism in drug discovery and then update the readers as to the abilities and liabilities of each model within the context of drug development.
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Affiliation(s)
- Pamela M Carroll
- Department of Applied Genomics, Bristol-Myers Squibb, Pennington NJ 08534, USA
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48
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Gottlin EB, Benson RE, Conary S, Antonio B, Duke K, Payne ES, Ashraf SS, Christensen DJ. High-throughput screen for inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase by surrogate ligand competition. JOURNAL OF BIOMOLECULAR SCREENING 2003; 8:332-9. [PMID: 12857387 DOI: 10.1177/1087057103008003011] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
1-Deoxy-D-xylulose 5-phosphate reductoisomerase (Dxr) is a key enzyme in a biosynthetic pathway for isoprenoids that is unique to eubacteria and plants. Dxr catalyzes the rearrangement and NADPH-dependent reduction of 1-deoxy-D-xylulose 5-phosphate to 2-C-methyl-D-erythritol 4-phosphate. The authors have purified Escherichia coli Dxr and devised a high-throughput screen (HTS) for compounds that bind to this enzyme at a functional site. Evidence is presented that the surrogate ligand directly binds or allosterically affects both the D-1-deoxyxylulose 5-phosphate (DXP) and NADPH binding sites. Compounds that bind at either or both sites that compete for binding with the surrogate ligand register as hits. The time-resolved fluorescence-based assay represents an improvement over the Dxr enzyme assay that relies on relatively insensitive measurements of NADPH oxidation. Screening 32,000 compounds from a diverse historical library, the authors obtained 89 potent inhibitors in the surrogate ligand competition assay. The results presented here suggest that peptide surrogate ligands may be useful in formatting HTS for proteins with difficult biochemical assays or targets of unknown function.
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49
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Ashraf SS, Anderson E, Duke K, Hamilton PT, Fredericks Z. Identification and characterization of peptide probes directed against PKCalpha conformations. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2003; 61:263-73. [PMID: 12662360 DOI: 10.1034/j.1399-3011.2003.00056.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phage display is a powerful technology that allows identification of high affinity peptides that bind specifically to a given molecular target. Using a highly complex peptide display library, we have identified separate classes of peptides that bind to protein kinase C alpha (PKCalpha) only under activation conditions. Furthermore, peptide binding was specific to PKCalpha and not to any of the other closely related PKC isoforms. The conformational and isoform specificity of the peptide binding was demonstrated using surface plasmon resonance as well as time-resolved fluorescence assays. Kinase assays showed that these peptides were not direct substrates for PKC nor did they inhibit phosphorylation of PKC substrates. These peptides are most likely directed against protein-protein interaction sites on PKC. The data presented here offers another example of application of phage display technology to identify conformation-dependent peptide probes against therapeutically important drug targets. These peptides are ideally suited to be used as surrogate ligands to identify compounds that bind specifically to PKCalpha, as well as conformational probes to detect activated forms of PKCalpha.
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Affiliation(s)
- S S Ashraf
- Karo Bio USA Inc., 4222 Emperor Blvd, Ste 560, Durham, NC 27703, USA.
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50
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Lapan KA, Chapple JP, Galcheva-Gargova Z, Yang M, Tao J. Peptide ligands in antibacterial drug discovery: use as inhibitors in target validation and target-based screening. Expert Opin Ther Targets 2002; 6:507-16. [PMID: 12223065 DOI: 10.1517/14728222.6.4.507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
There is an urgent need to develop novel classes of antibiotics to counter the inexorable rise of resistant bacterial pathogens. Modern antibacterial drug discovery is focused on the identification and validation of novel protein targets that may have a suitable therapeutic index. In combination with assays for function, the advent of microbial genomics has been invaluable in identifying novel antibacterial drug targets. The major challenge in this field is the implementation of methods that validate protein targets leading to the discovery of new chemical entities. Ligand-directed drug discovery has the distinct advantage of having a concurrent analysis of both the importance of a target in the disease process and its amenability to functional modulation by small molecules. VITA is a process that enables a target-based paradigm by using peptide ligands for direct in vitro and in vivo validation of antibacterial targets and the implementation of high-throughput assays to identify novel inhibitory molecules. This process can establish sufficient levels of confidence indicating that the target is relevant to the disease process and inhibition of the target will lead to effective disease treatment.
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Affiliation(s)
- Kirsty A Lapan
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, MA 02421, USA
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