51
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Chen BL, Wang YJ, Guo H, Zeng GY. Design, synthesis, and biological evaluation of crenatoside analogues as novel influenza neuraminidase inhibitors. Eur J Med Chem 2016; 109:199-205. [PMID: 26774928 DOI: 10.1016/j.ejmech.2015.12.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 12/15/2015] [Accepted: 12/15/2015] [Indexed: 11/25/2022]
Abstract
Natural products, especially derived from TCMH, have been found to exert antiviral effects against influenza virus. Crenatoside, a phenylethanoid glycoside from Pogostemon cablin Benth, which has been shown as a novel effective NA inhibitor previously, is considered as the leading compound for our further SARs studies. This work presented design, synthesis of novel crenatoside analogues from readily available d-Glucose and l-rhamnose in a convergent manner. Furthermore, their biological activities and SARs were also investigated. Especially, compound 2 h showed impressive IC50 = 27.77 μg/mL against NAs, which is 3 folds more potent than the leading compound crenatoside (IC50 = 89.81 μg/mL). These results would promise their therapeutic potential for influenza disease.
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Affiliation(s)
- Bao-Long Chen
- School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Yuelu District, Changsha 410013, PR China
| | | | - Hong Guo
- School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Yuelu District, Changsha 410013, PR China
| | - Guang-Yao Zeng
- School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Yuelu District, Changsha 410013, PR China.
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52
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Henry KA, Arbabi-Ghahroudi M, Scott JK. Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold. Front Microbiol 2015; 6:755. [PMID: 26300850 PMCID: PMC4523942 DOI: 10.3389/fmicb.2015.00755] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 07/10/2015] [Indexed: 12/23/2022] Open
Abstract
For the past 25 years, phage display technology has been an invaluable tool for studies of protein-protein interactions. However, the inherent biological, biochemical, and biophysical properties of filamentous bacteriophage, as well as the ease of its genetic manipulation, also make it an attractive platform outside the traditional phage display canon. This review will focus on the unique properties of the filamentous bacteriophage and highlight its diverse applications in current research. Particular emphases are placed on: (i) the advantages of the phage as a vaccine carrier, including its high immunogenicity, relative antigenic simplicity and ability to activate a range of immune responses, (ii) the phage's potential as a prophylactic and therapeutic agent for infectious and chronic diseases, (iii) the regularity of the virion major coat protein lattice, which enables a variety of bioconjugation and surface chemistry applications, particularly in nanomaterials, and (iv) the phage's large population sizes and fast generation times, which make it an excellent model system for directed protein evolution. Despite their ubiquity in the biosphere, metagenomics work is just beginning to explore the ecology of filamentous and non-filamentous phage, and their role in the evolution of bacterial populations. Thus, the filamentous phage represents a robust, inexpensive, and versatile microorganism whose bioengineering applications continue to expand in new directions, although its limitations in some spheres impose obstacles to its widespread adoption and use.
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Affiliation(s)
- Kevin A. Henry
- Human Health Therapeutics Portfolio, National Research Council Canada, OttawaON, Canada
| | - Mehdi Arbabi-Ghahroudi
- Human Health Therapeutics Portfolio, National Research Council Canada, OttawaON, Canada
- School of Environmental Sciences, University of Guelph, GuelphON, Canada
- Department of Biology, Carleton University, OttawaON, Canada
| | - Jamie K. Scott
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BCCanada
- Faculty of Health Sciences, Simon Fraser University, BurnabyBC, Canada
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53
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Ng S, Lin E, Kitov PI, Tjhung KF, Gerlits OO, Deng L, Kasper B, Sood A, Paschal BM, Zhang P, Ling CC, Klassen JS, Noren CJ, Mahal LK, Woods RJ, Coates L, Derda R. Genetically encoded fragment-based discovery of glycopeptide ligands for carbohydrate-binding proteins. J Am Chem Soc 2015; 137:5248-51. [PMID: 25860443 PMCID: PMC5553193 DOI: 10.1021/ja511237n] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We describe an approach to accelerate the search for competitive inhibitors for carbohydrate-recognition domains (CRDs). Genetically encoded fragment-based discovery (GE-FBD) uses selection of phage-displayed glycopeptides to dock a glycan fragment at the CRD and guide selection of synergistic peptide motifs adjacent to the CRD. Starting from concanavalin A (ConA), a mannose (Man)-binding protein, as a bait, we narrowed a library of 10(8) glycopeptides to 86 leads that share a consensus motif, Man-WYD. Validation of synthetic leads yielded Man-WYDLF that exhibited 40-50-fold enhancement in affinity over methyl α-d-mannopyranoside (MeMan). Lectin array suggested specificity: Man-WYD derivative bound only to 3 out of 17 proteins—ConA, LcH, and PSA—that bind to Man. An X-ray structure of ConA:Man-WYD proved that the trimannoside core and Man-WYD exhibit identical CRD docking, but their extra-CRD binding modes are significantly different. Still, they have comparable affinity and selectivity for various Man-binding proteins. The intriguing observation provides new insight into functional mimicry of carbohydrates by peptide ligands. GE-FBD may provide an alternative to rapidly search for competitive inhibitors for lectins.
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Affiliation(s)
- Simon Ng
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Edith Lin
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Pavel I. Kitov
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Katrina F. Tjhung
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Oksana O. Gerlits
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6475, United States
| | - Lu Deng
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Brian Kasper
- Biomedical Chemistry Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| | - Amika Sood
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Beth M. Paschal
- New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Ping Zhang
- Alberta Glycomics Centre, Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Chang-Chun Ling
- Alberta Glycomics Centre, Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - John S. Klassen
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | | | - Lara K. Mahal
- Biomedical Chemistry Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6475, United States
| | - Ratmir Derda
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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54
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Tjhung KF, Deiss F, Tran J, Chou Y, Derda R. Intra-domain phage display (ID-PhD) of peptides and protein mini-domains censored from canonical pIII phage display. Front Microbiol 2015; 6:340. [PMID: 25972845 PMCID: PMC4412080 DOI: 10.3389/fmicb.2015.00340] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/06/2015] [Indexed: 12/01/2022] Open
Abstract
In this paper, we describe multivalent display of peptide and protein sequences typically censored from traditional N-terminal display on protein pIII of filamentous bacteriophage M13. Using site-directed mutagenesis of commercially available M13KE phage cloning vector, we introduced sites that permit efficient cloning using restriction enzymes between domains N1 and N2 of the pIII protein. As infectivity of phage is directly linked to the integrity of the connection between N1 and N2 domains, intra-domain phage display (ID-PhD) allows for simple quality control of the display and the natural variations in the displayed sequences. Additionally, direct linkage to phage propagation allows efficient monitoring of sequence cleavage, providing a convenient system for selection and evolution of protease-susceptible or protease-resistant sequences. As an example of the benefits of such an ID-PhD system, we displayed a negatively charged FLAG sequence, which is known to be post-translationally excised from pIII when displayed on the N-terminus, as well as positively charged sequences which suppress production of phage when displayed on the N-terminus. ID-PhD of FLAG exhibited sub-nanomolar apparent Kd suggesting multivalent nature of the display. A TEV-protease recognition sequence (TEVrs) co-expressed in tandem with FLAG, allowed us to demonstrate that 99.9997% of the phage displayed the FLAG-TEVrs tandem and can be recognized and cleaved by TEV-protease. The residual 0.0003% consisted of phage clones that have excised the insert from their genome. ID-PhD is also amenable to display of protein mini-domains, such as the 33-residue minimized Z-domain of protein A. We show that it is thus possible to use ID-PhD for multivalent display and selection of mini-domain proteins (Affibodies, scFv, etc.).
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Affiliation(s)
- Katrina F Tjhung
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta Edmonton, AB, Canada
| | - Frédérique Deiss
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta Edmonton, AB, Canada
| | - Jessica Tran
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta Edmonton, AB, Canada
| | - Ying Chou
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta Edmonton, AB, Canada
| | - Ratmir Derda
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta Edmonton, AB, Canada
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55
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Saito F, Noda H, Bode JW. Critical evaluation and rate constants of chemoselective ligation reactions for stoichiometric conjugations in water. ACS Chem Biol 2015; 10:1026-33. [PMID: 25572124 DOI: 10.1021/cb5006728] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Chemoselective ligation reactions have contributed immensely to the development of organic synthesis and chemical biology. However, the ligation of stoichiometric amounts of large molecules for applications such as protein-protein conjugates is still challenging. Conjugation reactions need to be fast enough to proceed under dilute conditions and chemoselective in the presence of unprotected functional groups; the starting materials and products must be stable under the reaction conditions. To compare known ligation reactions for their suitability under these conditions, we determined the second-order rate constants of ligation reactions using peptide substrates with unprotected functional groups. The reaction conditions, the chemoselectivity of the reactions, and the stability of the starting materials and products were carefully evaluated. In some cases, the stability could be improved by modifying the substrate structure. These data obtained under the ligation conditions provide a useful guide to choose an appropriate ligation reaction for synthesis of large molecules by covalent ligation reactions of unprotected substrates in water.
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Affiliation(s)
- Fumito Saito
- Laboratorium
für Organische Chemie, Department of Chemistry and Applied
Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | - Hidetoshi Noda
- Laboratorium
für Organische Chemie, Department of Chemistry and Applied
Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | - Jeffrey W. Bode
- Laboratorium
für Organische Chemie, Department of Chemistry and Applied
Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
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56
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Heinis C, Winter G. Encoded libraries of chemically modified peptides. Curr Opin Chem Biol 2015; 26:89-98. [PMID: 25768886 DOI: 10.1016/j.cbpa.2015.02.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 02/09/2015] [Accepted: 02/09/2015] [Indexed: 12/22/2022]
Abstract
The use of powerful technologies for generating and screening DNA-encoded protein libraries has helped drive the development of proteins as pharmaceutical ligands. However the development of peptides as pharmaceutical ligands has been more limited. Although encoded peptide libraries are typically several orders of magnitude larger than classical chemical libraries, can be more readily screened, and can give rise to higher affinity ligands, their use as pharmaceutical ligands is limited by their intrinsic properties. Two of the intrinsic limitations include the rotational flexibility of the peptide backbone and the limited number (20) of natural amino acids. However these limitations can be overcome by use of chemical modification. For example, the libraries can be modified to introduce topological constraints such as cyclization linkers, or to introduce new chemical entities such as small molecule ligands, fluorophores and photo-switchable compounds. This article reviews the chemistry involved, the properties of the peptide ligands, and the new opportunities offered by chemical modification of DNA-encoded peptide libraries.
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Affiliation(s)
- Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - Greg Winter
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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57
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Affiliation(s)
- Omar Boutureira
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili , C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
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58
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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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59
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Ng S, Tjhung KF, Paschal BM, Noren CJ, Derda R. Chemical posttranslational modification of phage-displayed peptides. Methods Mol Biol 2015; 1248:155-72. [PMID: 25616332 DOI: 10.1007/978-1-4939-2020-4_11] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phage-displayed peptide library has fueled the discovery of novel ligands for diverse targets. A new type of phage libraries that displays not only linear and disulfide-constrained cyclic peptides but moieties that cannot be encoded genetically or incorporated easily by bacterial genetic machinery has emerged recently. Chemical posttranslational modification of phage library is one of the simplest approaches to encode nonnatural moieties. It confers the library with new functionality and makes it possible to select and evolve molecules with properties not found in the peptides, for instance, glycopeptides recognized by carbohydrate-binding protein and peptides with photoswitching capability. To this end, we describe the newly emerging techniques to chemically modify the phage library and quantify the efficiency of the reaction with a biotin-capture assay. Finally, we provide the methods to construct N-terminal Ser peptide library that allows site-selective modification of phage.
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Affiliation(s)
- Simon Ng
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta, 11227 Saskatchewan Dr., Edmonton, AB, Canada, T6G 2G2
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60
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Bernard JML, Francis MB. Chemical strategies for the covalent modification of filamentous phage. Front Microbiol 2014; 5:734. [PMID: 25566240 PMCID: PMC4274979 DOI: 10.3389/fmicb.2014.00734] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/04/2014] [Indexed: 01/16/2023] Open
Abstract
Historically filamentous bacteriophage have been known to be the workhorse of phage display due to their ability to link genotype to phenotype. More recently, the filamentous phage scaffold has proven to be powerful outside the realm of phage display technology in fields such as molecular imaging, cancer research and materials, and vaccine development. The ability of the virion to serve as a platform for a variety of applications heavily relies on the functionalization of the phage coat proteins with a wide variety of functionalities. Genetic modification of the coat proteins has been the most widely used strategy for functionalizing the virion; however, complementary chemical modification strategies can help to diversify the range of materials that can be developed. This review emphasizes the recent advances that have been made in the chemical modification of filamentous phage as well as some of the challenges that are involved in functionalizing the virion.
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Affiliation(s)
- Jenna M L Bernard
- Department of Chemistry, University of California at Berkeley Berkeley, CA, USA ; Materials Sciences Division - Lawrence Berkeley National Laboratories Berkeley, CA, USA
| | - Matthew B Francis
- Department of Chemistry, University of California at Berkeley Berkeley, CA, USA ; Materials Sciences Division - Lawrence Berkeley National Laboratories Berkeley, CA, USA
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61
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Chung WJ, Lee DY, Yoo SY. Chemical modulation of M13 bacteriophage and its functional opportunities for nanomedicine. Int J Nanomedicine 2014; 9:5825-36. [PMID: 25540583 PMCID: PMC4270384 DOI: 10.2147/ijn.s73883] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
M13 bacteriophage (phage) has emerged as an attractive bionanomaterial owing to its genetically tunable surface chemistry and its potential to self-assemble into hierarchical structures. Furthermore, because of its unique nanoscopic structure, phage has been proposed as a model system in soft condensed physics and as a biomimetic building block for structured functional materials. Genetic engineering of phage provides great opportunities to develop novel nanomaterials with functional surface peptide motifs; however, this biological approach is generally limited to peptides containing the 20 natural amino acids. To extend the scope of phage applications, strategies involving chemical modification have been employed to incorporate a wider range of functional groups, including synthetic chemical compounds. In this review, we introduce the design of chemoselective phage functionalization and discuss how such a strategy is combined with genetic engineering for a variety of medical applications, as reported in recent literature.
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Affiliation(s)
- Woo-Jae Chung
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Doe-Young Lee
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - So Young Yoo
- BIO-IT Foundry Technology Institute, Pusan National University, Busan, Republic of Korea ; Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
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62
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Kitov PI, Vinals DF, Ng S, Tjhung KF, Derda R. Rapid, Hydrolytically Stable Modification of Aldehyde-Terminated Proteins and Phage Libraries. J Am Chem Soc 2014; 136:8149-52. [DOI: 10.1021/ja5023909] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pavel I. Kitov
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Daniel F. Vinals
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Simon Ng
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Katrina F. Tjhung
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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63
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Horiya S, Bailey JK, Temme JS, Guillen Schlippe YV, Krauss IJ. Directed evolution of multivalent glycopeptides tightly recognized by HIV antibody 2G12. J Am Chem Soc 2014; 136:5407-15. [PMID: 24645849 PMCID: PMC4004241 DOI: 10.1021/ja500678v] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Herein,
we report a method for in vitro selection of multivalent
glycopeptides, combining mRNA display with incorporation of unnatural
amino acids and “click” chemistry. We have demonstrated
the use of this method to design potential glycopeptide vaccines against
HIV. From libraries of ∼1013 glycopeptides containing
multiple Man9 glycan(s), we selected variants that bind
to HIV broadly neutralizing antibody 2G12 with picomolar to low nanomolar
affinity. This is comparable to the strength of the natural 2G12–gp120
interaction, and is the strongest affinity achieved to date with constructs
containing 3–5 glycans. These glycopeptides are therefore of
great interest in HIV vaccine design.
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Affiliation(s)
- Satoru Horiya
- Department of Chemistry, Brandeis University , Waltham, Massachusetts 02454-9110, United States
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64
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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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65
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Tokunaga Y, Azetsu Y, Fukunaga K, Hatanaka T, Ito Y, Taki M. Pharmacophore generation from a drug-like core molecule surrounded by a library peptide via the 10BASEd-T on bacteriophage T7. Molecules 2014; 19:2481-96. [PMID: 24566316 PMCID: PMC6271298 DOI: 10.3390/molecules19022481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/10/2014] [Accepted: 02/12/2014] [Indexed: 11/16/2022] Open
Abstract
We have achieved site-specific conjugation of several haloacetamide derivatives into designated cysteines on bacteriophage T7-displayed peptides, which are fused to T7 capsid protein gp10. This easiest gp10 based-thioetherification (10BASEd-T) undergoes almost quantitatively like a click reaction without side reaction or loss of phage infectivity. The post-translational modification yield, as well as the site-specificity, is quantitatively analyzed by a fluorescent densitometric analysis after gel electrophoresis. The detailed structure of the modified peptide on phage is identified with tandem mass spectrometry. Construction of such a peptide-fused phage library possessing non-natural core structures will be useful for future drug discovery. For this aim, we propose a novel concept of pharmacophore generation from a drug-like molecule (i.e., salicylic acid) conjugated with surrounding randomized peptides. By using the hybrid library, streptavidin-specific binders are isolated through four rounds of biopanning.
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Affiliation(s)
- Yuuki Tokunaga
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Yuuki Azetsu
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Keisuke Fukunaga
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Takaaki Hatanaka
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, Kagoshima 890-0065, Japan.
| | - Yuji Ito
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, Kagoshima 890-0065, Japan.
| | - Masumi Taki
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
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Chen S, Touati J, Heinis C. Tracking chemical reactions on the surface of filamentous phage using mass spectrometry. Chem Commun (Camb) 2014; 50:5267-9. [DOI: 10.1039/c3cc47496h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ulrich S, Boturyn D, Marra A, Renaudet O, Dumy P. Oxime Ligation: A Chemoselective Click-Type Reaction for Accessing Multifunctional Biomolecular Constructs. Chemistry 2013; 20:34-41. [DOI: 10.1002/chem.201302426] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Arai K, Tsutsumi H, Mihara H. A monosaccharide-modified peptide phage library for screening of ligands to carbohydrate-binding proteins. Bioorg Med Chem Lett 2013; 23:4940-3. [DOI: 10.1016/j.bmcl.2013.06.059] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/17/2013] [Accepted: 06/21/2013] [Indexed: 11/28/2022]
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Carrico ZM, Farkas ME, Zhou Y, Hsiao SC, Marks JD, Chokhawala H, Clark DS, Francis MB. N-Terminal labeling of filamentous phage to create cancer marker imaging agents. ACS NANO 2012; 6:6675-80. [PMID: 22830952 PMCID: PMC3435507 DOI: 10.1021/nn301134z] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We report a convenient new technique for the labeling of filamentous phage capsid proteins. Previous reports have shown that phage coat protein residues can be modified, but the lack of chemically distinct amino acids in the coat protein sequences makes it difficult to attach high levels of synthetic molecules without altering the binding capabilities of the phage. To modify the phage with polymer chains, imaging groups, and other molecules, we have developed chemistry to convert the N-terminal amines of the ~4200 coat proteins into ketone groups. These sites can then serve as chemospecific handles for the attachment of alkoxyamine groups through oxime formation. Specifically, we demonstrate the attachment of fluorophores and up to 3000 molecules of 2 kDa poly(ethylene glycol) (PEG2k) to each of the phage capsids without significantly affecting the binding of phage-displayed antibody fragments to EGFR and HER2 (two important epidermal growth factor receptors). We also demonstrate the utility of the modified phage for the characterization of breast cancer cells using multicolor fluorescence microscopy. Due to the widespread use of filamentous phage as display platforms for peptide and protein evolution, we envision that the ability to attach large numbers of synthetic functional groups to their coat proteins will be of significant value to the biological and materials communities.
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Affiliation(s)
| | | | - Yu Zhou
- Department of Anesthesia and Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
| | - Sonny C. Hsiao
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - James D. Marks
- Department of Anesthesia and Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
| | - Harshal Chokhawala
- Department of Chemical Engineering, University of California, Berkeley, CA 94720
| | - Douglas S. Clark
- Department of Chemical Engineering, University of California, Berkeley, CA 94720
| | - Matthew B. Francis
- Department of Chemistry, University of California, Berkeley, CA 94720
- Corresponding author:
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