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Identification and Structure of Epitopes on Cashew Allergens Ana o 2 and Ana o 3 Using Phage Display. Molecules 2023; 28:molecules28041880. [PMID: 36838874 PMCID: PMC9964899 DOI: 10.3390/molecules28041880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Cashew (Anacardium occidentale L.) is a commercially important plant. Cashew nuts are a popular food source that belong to the tree nut family. Tree nuts are one of the eight major food allergens identified by the Food and Drug Administration in the USA. Allergies to cashew nuts cause severe and systemic immune reactions. Tree nut allergies are frequently fatal and are becoming more common. AIM We aimed to identify the key allergenic epitopes of cashew nut proteins by correlating the phage display epitope prediction results with bioinformatics analysis. DESIGN We predicted and experimentally confirmed cashew nut allergen antigenic peptides, which we named Ana o 2 (cupin superfamily) and Ana o 3 (prolamin superfamily). The Ana o 2 and Ana o 3 epitopes were predicted using DNAstar and PyMoL (incorporated in the Swiss-model package). The predicted weak and strong epitopes were synthesized as peptides. The related phage library was built. The peptides were also tested using phage display technology. The expressed antigens were tested and confirmed using microtiter plates coated with pooled human sera from patients with cashew nut allergies or healthy controls. RESULTS The Ana o 2 epitopes were represented by four linear peptides, with the epitopes corresponding to amino acids 108-111, 113-119, 181-186, and 218-224. Furthermore, the identified Ana o 3 epitopes corresponding to amino acids 10-24, 13-27, 39-49, 66-70, 101-106, 107-114, and 115-122 were also screened out and chosen as the key allergenic epitopes. DISCUSSION The Ana o 3 epitopes accounted for more than 40% of the total amino acid sequence of the protein; thus, Ana o 3 is potentially more allergenic than Ana o 2. CONCLUSIONS The bioinformatic epitope prediction produced subpar results in this study. Furthermore, the phage display method was extremely effective in identifying the allergenic epitopes of cashew nut proteins. The key allergenic epitopes were chosen, providing important information for the study of cashew nut allergens.
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You T, Ding Y, Chen H, Song G, Huang L, Wang M, Hua X. Development of competitive and noncompetitive immunoassays for clothianidin with high sensitivity and specificity using phage-displayed peptides. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:128011. [PMID: 34896720 DOI: 10.1016/j.jhazmat.2021.128011] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/23/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
Clothianidin is a widely used pesticide that has been banned from outdoor use by the European Union due to its toxicity. To improve the sensitivity and specificity of existing clothianidin immunoassays, we developed competitive and noncompetitive immunoassays for clothianidin based on phage-displayed peptides. Cyclic 8-, 9-, and 10-residue peptide libraries were constructed using an optimized phagemid pComb-pVIII to prevent the loss of theoretical library diversity. Twenty-eight peptidomimetics and two anti-immunocomplex peptides were isolated through a blended panning process and used to develop competitive and noncompetitive phage enzyme-linked immunosorbent assays (P-ELISAs), respectively. After optimization, the half inhibition concentration (IC50) and half saturation concentration (SC50) of competitive and noncompetitive P-ELISAs were 3.83 ± 0.23 and 0.45 ± 0.02 ng/mL, respectively. Competitive P-ELISA showed 2.6-18.2% cross-reactivity with imidaclothiz, nitenpyram and imidacloprid. Importantly, noncompetitive P-ELISA, which has the best specificity and great sensitivity for clothianidin, showed no cross-reactivity with the analogs. The average recoveries of competitive and noncompetitive P-ELISAs were 73.8-104.1% and 76.6-102.2%, respectively, while the relative standard deviations were ≤ 11.0%. In addition, the results of P-ELISAs in the analysis of blind samples were consistent with those of high-performance liquid chromatography.
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Affiliation(s)
- Tianyang You
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Yuan Ding
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - He Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Guangyue Song
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Lianrun Huang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Minghua Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Xiude Hua
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China.
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Jaroszewicz W, Morcinek-Orłowska J, Pierzynowska K, Gaffke L, Węgrzyn G. Phage display and other peptide display technologies. FEMS Microbiol Rev 2021; 46:6407522. [PMID: 34673942 DOI: 10.1093/femsre/fuab052] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Phage display technology, which is based on the presentation of peptide sequences on the surface of bacteriophage virions, was developed over 30 years ago. Improvements in phage display systems have allowed us to employ this method in numerous fields of biotechnology, as diverse as immunological and biomedical applications, the formation of novel materials and many others. The importance of phage display platforms was recognized by awarding the Nobel Prize in 2018 "for the phage display of peptides and antibodies". In contrast to many review articles concerning specific applications of phage display systems published in recent years, we present an overview of this technology, including a comparison of various display systems, their advantages and disadvantages, and examples of applications in various fields of science, medicine, and the broad sense of biotechnology. Other peptide display technologies, which employ bacterial, yeast and mammalian cells, as well as eukaryotic viruses and cell-free systems, are also discussed. These powerful methods are still being developed and improved; thus, novel sophisticated tools based on phage display and other peptide display systems are constantly emerging, and new opportunities to solve various scientific, medical and technological problems can be expected to become available in the near future.
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Affiliation(s)
- Weronika Jaroszewicz
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | | | - Karolina Pierzynowska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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Alsaadi A, Beamud B, Easwaran M, Abdelrahman F, El-Shibiny A, Alghoribi MF, Domingo-Calap P. Learning From Mistakes: The Role of Phages in Pandemics. Front Microbiol 2021; 12:653107. [PMID: 33815346 PMCID: PMC8010138 DOI: 10.3389/fmicb.2021.653107] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
The misuse of antibiotics is leading to the emergence of multidrug-resistant (MDR) bacteria, and in the absence of available treatments, this has become a major global threat. In the middle of the recent severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic, which has challenged the whole world, the emergence of MDR bacteria is increasing due to prophylactic administration of antibiotics to intensive care unit patients to prevent secondary bacterial infections. This is just an example underscoring the need to seek alternative treatments against MDR bacteria. To this end, phage therapy has been proposed as a promising tool. However, further research in the field is mandatory to assure safety protocols and to develop appropriate regulations for its use in clinics. This requires investing more in such non-conventional or alternative therapeutic approaches, to develop new treatment regimens capable of reducing the emergence of MDR and preventing future global public health concerns that could lead to incalculable human and economic losses.
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Affiliation(s)
- Ahlam Alsaadi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Beatriz Beamud
- Institute for Integrative Systems Biology, I2SysBio, Universitat de València-CSIC, Paterna, Spain
- FISABIO-Salud Pública, Generalitat Valenciana, Valencia, Spain
| | - Maheswaran Easwaran
- Department of Biomedical Engineering, Sethu Institute of Technology, Rajapalayam, India
| | - Fatma Abdelrahman
- Center for Microbiology and Phage Therapy, Biomedical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Biomedical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Majed F. Alghoribi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology, I2SysBio, Universitat de València-CSIC, Paterna, Spain
- Department of Genetics, Universitat de València, Paterna, Spain
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Beck-Sickinger AG. [Directed evolution in drug and antibody development : From the Nobel Prize to broad clinical application]. Internist (Berl) 2019; 60:1014-1020. [PMID: 31541280 DOI: 10.1007/s00108-019-00675-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Combinatorial procedures have become established in recent years as alternatives to rational design in drug research, particularly when no structural information is available. This article presents the principle that was originally developed by three scientists and was honored with the Nobel Prize for Chemistry in 2018. Furthermore, the application in the field of monclonal antibodies is discussed.
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Affiliation(s)
- A G Beck-Sickinger
- Fakultät für Lebenswissenschaften, Institut für Biochemie, Universität Leipzig, Brüderstraße 34, 04103, Leipzig, Deutschland.
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Peltomaa R, Benito-Peña E, Barderas R, Moreno-Bondi MC. Phage Display in the Quest for New Selective Recognition Elements for Biosensors. ACS OMEGA 2019; 4:11569-11580. [PMID: 31460264 PMCID: PMC6682082 DOI: 10.1021/acsomega.9b01206] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/21/2019] [Indexed: 05/10/2023]
Abstract
Phages are bacterial viruses that have gained a significant role in biotechnology owing to their widely studied biology and many advantageous characteristics. Perhaps the best-known application of phages is phage display that refers to the expression of foreign peptides or proteins outside the phage virion as a fusion with one of the phage coat proteins. In 2018, one half of the Nobel prize in chemistry was awarded jointly to George P. Smith and Sir Gregory P. Winter "for the phage display of peptides and antibodies." The outstanding technology has evolved and developed considerably since its first description in 1985, and today phage display is commonly used in a wide variety of disciplines, including drug discovery, enzyme optimization, biomolecular interaction studies, as well as biosensor development. A cornerstone of all biosensors, regardless of the sensor platform or transduction scheme used, is a sensitive and selective bioreceptor, or a recognition element, that can provide specific binding to the target analyte. Many environmentally or pharmacologically interesting target analytes might not have naturally appropriate binding partners for biosensor development, but phage display can facilitate the production of novel receptors beyond known biomolecular interactions, or against toxic or nonimmunogenic targets, making the technology a valuable tool in the quest of new recognition elements for biosensor development.
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Affiliation(s)
- Riikka Peltomaa
- Chemical
Optosensors & Applied Photochemistry Group (GSOLFA), Department
of Analytical Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Elena Benito-Peña
- Chemical
Optosensors & Applied Photochemistry Group (GSOLFA), Department
of Analytical Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Rodrigo Barderas
- Chronic
Disease Programme (UFIEC), Instituto de
Salud Carlos III, Ctra.
Majadahonda-Pozuelo Km 2.2, 28220 Madrid, Spain
| | - María C. Moreno-Bondi
- Chemical
Optosensors & Applied Photochemistry Group (GSOLFA), Department
of Analytical Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, 28040 Madrid, Spain
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Wilson HD, Li X, Peng H, Rader C. A Sortase A Programmable Phage Display Format for Improved Panning of Fab Antibody Libraries. J Mol Biol 2018; 430:4387-4400. [PMID: 30213726 DOI: 10.1016/j.jmb.2018.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 09/01/2018] [Accepted: 09/05/2018] [Indexed: 11/26/2022]
Abstract
Phage display of combinatorial antibody libraries is a versatile tool in the field of antibody engineering, with diverse applications including monoclonal antibody (mAb) discovery, affinity maturation, and humanization. To improve the selection efficiency of antibody libraries, we developed a new phagemid display system that addresses the complication of bald phage propagation. The phagemid facilitates the biotinylation of fragment of antigen binding (Fab) antibody fragments displayed on phage via Sortase A catalysis and the subsequent enrichment of Fab-displaying phage during selections. In multiple contexts, this selection approach improved the enrichment of target-reactive mAbs by depleting background phage. Panels of cancer cell line-reactive mAbs with high diversity and specificity were isolated from a naïve chimeric rabbit/human Fab library using this approach, highlighting its potential to accelerate antibody engineering efforts and to empower concerted antibody drug and target discovery.
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Affiliation(s)
- Henry D Wilson
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiuling Li
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Haiyong Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.
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8
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Xu P, Andreasen PA, Huang M. Structural Principles in the Development of Cyclic Peptidic Enzyme Inhibitors. Int J Biol Sci 2017; 13:1222-1233. [PMID: 29104489 PMCID: PMC5666521 DOI: 10.7150/ijbs.21597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/28/2017] [Indexed: 01/23/2023] Open
Abstract
This review summarizes our studies in the development of small cyclic peptides for specifically modulating enzyme activity. Serine proteases share highly similar active sites but perform diverse physiological and pathological functions. From a phage-display peptide library, we isolated two mono-cyclic peptides, upain-1 (CSWRGLENHRMC) and mupain-1 (CPAYSRYLDC), which inhibit the activity of human and murine urokinase-type plasminogen activators (huPA and muPA) with Ki values in the micromolar or sub-micromolar range, respectively. The following affinity maturations significantly enhanced the potencies of the two peptides, 10-fold and >250-fold for upain-1 and mupain-1, respectively. The most potent muPA inhibitor has a potency (Ki = 2 nM) and specificity comparable to mono-clonal antibodies. Furthermore, we also found an unusual feature of mupain-1 that its inhibitory potency can be enhanced by increasing the flexibility, which challenges the traditional viewpoint that higher rigidity leading to higher affinity. Moreover, by changing a few key residues, we converted mupain-1 from a uPA inhibitor to inhibitors of other serine proteases, including plasma kallikrein (PK) and coagulation factor XIa (fXIa). PK and fXIa inhibitors showed Ki values in the low nanomolar range and high specificity. Our studies demonstrate the versatility of small cyclic peptides to engineer inhibitory potency against serine proteases and to provide a new strategy for generating peptide inhibitors of serine proteases.
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Affiliation(s)
- Peng Xu
- State Key Laboratory of Structural Chemistry and Danish-Chinese Centre for Proteases and Cancer, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, P.R. China
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Mingdong Huang
- State Key Laboratory of Structural Chemistry and Danish-Chinese Centre for Proteases and Cancer, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, P.R. China.,College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P.R. China
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Guliy OI, Zaitsev BD, Borodina IA, Fomin AS, Staroverov SA, Dykman LA, Shikhabudinov AM. Use of mini-antibodies for detection of bacteriophages by the electroaucoustic analysis method. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s000635091703006x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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10
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Cornelison GL, Pflanz NC, Tipps ME, Mihic SJ. Identification and characterization of heptapeptide modulators of the glycine receptor. Eur J Pharmacol 2016; 780:252-9. [PMID: 27038522 DOI: 10.1016/j.ejphar.2016.03.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/24/2016] [Accepted: 03/29/2016] [Indexed: 02/07/2023]
Abstract
The glycine receptor is a member of the Cys-loop receptor superfamily of ligand-gated ion channels and is implicated as a possible therapeutic target for the treatment of diseases such as alcoholism and inflammatory pain. In humans, four glycine receptor subtypes (α1, α2, α3, and β) co-assemble to form pentameric channel proteins as either α homomers or αβ heteromers. To date, few agents have been identified that can selectively modulate the glycine receptor, especially those possessing subtype specificity. We used a cell-based method of phage display panning, coupled with two-electrode voltage-clamp electrophysiology in Xenopus laevis oocytes, to identify novel heptapeptide modulators of the α1β glycine receptor. This involved a panning procedure in which the phage library initially underwent subtractive panning against Human Embryonic Kidney (HEK) 293 cells expressing alternative glycine receptor subtypes before panning the remaining library over HEK 293 cells expressing the target, the α1β glycine receptor. Peptides were identified that act with selectivity on α1β and α3β, compared to α2β, glycine receptors. In addition, peptide activity at the glycine receptor decreased when zinc was chelated by tricine, similar to previous observations of a decrease in ethanol's enhancing actions at the receptor in the absence of zinc. Comparisons of the amino acid sequences of heptapeptides capable of potentiating glycine receptor function revealed several consensus sequences that may be predictive of a peptide's enhancing ability.
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Affiliation(s)
- Garrett L Cornelison
- Department of Neuroscience, Division of Pharmacology and Toxicology, Waggoner Center for Alcohol & Addiction Research, Institutes for Neuroscience and Cell & Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Natasha C Pflanz
- Department of Neuroscience, Division of Pharmacology and Toxicology, Waggoner Center for Alcohol & Addiction Research, Institutes for Neuroscience and Cell & Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Megan E Tipps
- Department of Neuroscience, Division of Pharmacology and Toxicology, Waggoner Center for Alcohol & Addiction Research, Institutes for Neuroscience and Cell & Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - S John Mihic
- Department of Neuroscience, Division of Pharmacology and Toxicology, Waggoner Center for Alcohol & Addiction Research, Institutes for Neuroscience and Cell & Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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Alizadeh AA, Hamzeh-Mivehroud M, Dastmalchi S. Identification of Novel Single Chain Fragment Variable Antibodies Against TNF-α Using Phage Display Technology. Adv Pharm Bull 2015; 5:661-6. [PMID: 26793613 DOI: 10.15171/apb.2015.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 10/31/2015] [Accepted: 11/01/2015] [Indexed: 01/15/2023] Open
Abstract
PURPOSE Tumor necrosis factor alpha (TNF-α) is an inflammatory cytokine, involved in both physiological and pathological pathways. Because of central role of TNF-α in pathogenesis of inflammatory diseases, in the current study, we aimed to identify novel scFv antibodies against TNF-α using phage display technology. METHODS Using libraries composed of phagemid displaying scFv antibodies, four rounds of biopanning against TNF-α were carried out, which led to identification of scFvs capable of binding to TNF-α. The scFv antibody with appropriate binding affinity towards TNF-α, was amplified and used in ELISA experiment. RESULTS Titration of phage achieved from different rounds of biopanning showed an enrichment of specific anti-TNF-α phages during biopanning process. Using ELISA experiment, a binding constant (Kd) of 1.11 ± 0.32 nM was determined for the phage displaying J48 scFv antibody. CONCLUSION The findings in the current work revealed that the identified novel scFv antibody displayed at the N-terminal of minor coat proteins of phagemid binds TNF-α with suitable affinity. However, the soluble form of the antibody is needed to be produced and evaluated in more details regarding its binding properties to TNF-α.
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Affiliation(s)
- Ali Akbar Alizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. ; Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. ; Students Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran. ; School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Hamzeh-Mivehroud
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. ; Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. ; School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. ; School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Sato T, Alles N, Khan M, Nagano K, Takahashi M, Tamura Y, Shimoda A, Ohya K, Akiyoshi K, Aoki K. Nanogel-crosslinked nanoparticles increase the inhibitory effects of W9 synthetic peptide on bone loss in a murine bone resorption model. Int J Nanomedicine 2015; 10:3459-73. [PMID: 25999711 PMCID: PMC4435441 DOI: 10.2147/ijn.s61566] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We investigated the biological activity of W9, a bone resorption inhibitor peptide, using NanoClik nanoparticles as an injectable carrier, where acryloyl group-modified cholesterol-bearing pullulan (CHPOA) nanogels were crosslinked by pentaerythritol tetra (mercaptoethyl) polyoxyethylene. Thirty 5-week-old male C57BL/6J mice were fed a low calcium diet and received once-daily subcutaneous injections of the carrier alone, W9 24 mg/kg/day alone, W9 24 mg/kg/day incorporated in cholesterol bearing pullulan (CHP) nanogels, or W9 (8 and 24 mg/kg/day) incorporated in NanoClik nanoparticles for 4 days (n=5). Mice that received a normal calcium diet with NanoClik nanoparticle injections without W9 were used as a control group. Radiological analyses showed that administration of W9 24 mg/kg/day significantly prevented low calcium-induced reduction of bone mineral density in the long bones and lumbar vertebrae, but only when the NanoClik nanoparticles were used as a carrier. Histomorphometric analyses of the proximal tibiae revealed that W9 24 mg/kg/day incorporated in NanoClik nanoparticles prevented the increase in bone resorption indices induced by a low calcium diet, which was confirmed by measurement of serum bone resorption markers. These data suggest that NanoClik nanoparticles could be a useful carrier for peptide therapeutics, and also demonstrate that daily subcutaneous injections of the W9 peptide with the nanoparticles were able to inhibit bone loss in vivo. An osteoclastogenesis inhibition assay performed in vitro confirmed a slower release profile of W9 from NanoClik nanoparticles compared with conventional CHP nanogels.
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Affiliation(s)
- Toshimi Sato
- Department of Bio-Matrix (Pharmacology), Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Neil Alles
- Department of Bio-Matrix (Pharmacology), Graduate School, Tokyo Medical and Dental University, Tokyo, Japan ; Department of Biochemistry, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Masud Khan
- Department of Bio-Matrix (Pharmacology), Graduate School, Tokyo Medical and Dental University, Tokyo, Japan ; Department of Dental Pharmacology, City Dental College and Hospital, Dhaka, Bangladesh
| | - Kenichi Nagano
- Department of Bio-Matrix (Pharmacology), Graduate School, Tokyo Medical and Dental University, Tokyo, Japan ; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Mariko Takahashi
- Department of Bio-Matrix (Pharmacology), Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yukihiko Tamura
- Department of Bio-Matrix (Pharmacology), Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Asako Shimoda
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura ; ERATO Akiyoshi Bio-Nanotransporter Project, Japan Science and Technology Agency, Katsura Int'tech Center Kyotodaigaku-Katsura, Nishikyo-ku, Kyoto, Japan
| | - Keiichi Ohya
- Department of Bio-Matrix (Pharmacology), Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura ; ERATO Akiyoshi Bio-Nanotransporter Project, Japan Science and Technology Agency, Katsura Int'tech Center Kyotodaigaku-Katsura, Nishikyo-ku, Kyoto, Japan
| | - Kazuhiro Aoki
- Department of Bio-Matrix (Pharmacology), Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
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14
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Lv PC, Zhu HL. EGFR-binding peptide: a patent evaluation of WO2014002836. Expert Opin Ther Pat 2014; 24:1409-11. [PMID: 25407285 DOI: 10.1517/13543776.2014.964686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Peptide ligands have many desirable features enabling them to act as drug molecules and are valuable in the drug discovery processes because of their fewer side effects and great potential to cure diseases. In this patent, three kinds of peptide ligands with 12-50 amino acid residues were identified by phase display technology. Some of them not only could be used as potential therapeutic agents for the treatment of EGFR-overexpressed cancers, but also show promising application in detecting cancer tissue or cancer cells that express the EGFR.
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Affiliation(s)
- Peng-Cheng Lv
- Nanjing University, State Key Laboratory of Pharmaceutical Biotechnology , Nanjing 210093 , People's Republic of China +86 25 8359 2672 ; +86 25 8359 2672 ; ;
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Multiplex single-molecule interaction profiling of DNA-barcoded proteins. Nature 2014; 515:554-7. [PMID: 25252978 DOI: 10.1038/nature13761] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 08/08/2014] [Indexed: 01/26/2023]
Abstract
In contrast with advances in massively parallel DNA sequencing, high-throughput protein analyses are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule protein detection using optical methods is limited by the number of spectrally non-overlapping chromophores. Here we introduce a single-molecular-interaction sequencing (SMI-seq) technology for parallel protein interaction profiling leveraging single-molecule advantages. DNA barcodes are attached to proteins collectively via ribosome display or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide thin film to construct a random single-molecule array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies) and analysed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimetre. Furthermore, protein interactions can be measured on the basis of the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor and antibody-binding profiling, are demonstrated. SMI-seq enables 'library versus library' screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity.
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16
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Bionda N, Cryan AL, Fasan R. Bioinspired strategy for the ribosomal synthesis of thioether-bridged macrocyclic peptides in bacteria. ACS Chem Biol 2014; 9:2008-13. [PMID: 25079213 PMCID: PMC4168796 DOI: 10.1021/cb500311k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Inspired
by the biosynthetic logic of lanthipeptide natural products,
a new methodology was developed to direct the ribosomal synthesis
of macrocyclic peptides constrained by an intramolecular thioether
bond. As a first step, a robust and versatile strategy was implemented
to enable the cyclization of ribosomally derived peptide sequences
via a chemoselective reaction between a genetically encoded cysteine
and a cysteine-reactive unnatural amino acid (O-(2-bromoethyl)-tyrosine).
Combination of this approach with intein-catalyzed protein splicing
furnished an efficient route to achieve the spontaneous, post-translational
formation of structurally diverse macrocyclic peptides in bacterial
cells. The present peptide cyclization strategy was also found to
be amenable to integration with split intein-mediated circular ligation,
resulting in the intracellular synthesis of conformationally constrained
peptides featuring a bicyclic architecture.
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Affiliation(s)
- Nina Bionda
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Abby L. Cryan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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17
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Henry BL, Desai UR. Discovery methodology for the development of direct factor VIIa inhibitors. Expert Opin Drug Discov 2014; 9:859-72. [PMID: 24882057 DOI: 10.1517/17460441.2014.923398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Heparin and warfarin have historically been the only antithrombotics available. Recently, however, newer anticoagulants have been developed. Factor VIIa (fVIIa) inhibitors represent one of the new and potentially exciting classes of anticoagulants currently under development. Indeed, several methodologies have been used to develop fVIIa inhibitors. AREAS COVERED The authors highlight some of the methologies applied for the discovery of fVIIa inhibitors including phage display, isolation of endogenous peptides from hematophagous animals and the use of the 1,5-benzothiazepine molecular scaffolds and screens of large chemical libraries previously used to identify other serine protease inhibitors. Although these screens were intended to identify thrombin and factor Xa inhibitors, the compounds often had concomitant fVIIa activity. The authors also discuss the utilization of medical chemistry techniques for the discovery of these compounds. EXPERT OPINION FVIIa inhibitors represent a viable option for the development of new anticoagulants. There are theoretical advantages that fVIIa inhibitors may possess over existing anticoagulants and highly specific inhibitors that possess oral bioavailability and low bleeding risk may succeed.
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Affiliation(s)
- Brian L Henry
- University of Pittsburgh Medical Center, Heart and Vascular Institute Pittsburgh, Department of Cardiology , Scaife Hall, Suite B-571.3, 200 Lothrop Street, Pittsburgh, PA 15213 , USA +1 412 647 3429 ; +1 412 647 0481 ;
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18
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The hidden potential of small synthetic molecules and peptides as affinity ligands for bioseparations. ACTA ACUST UNITED AC 2013. [DOI: 10.4155/pbp.13.54] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Baral TN, MacKenzie R, Arbabi Ghahroudi M. Single-domain antibodies and their utility. ACTA ACUST UNITED AC 2013; 103:2.17.1-2.17.57. [PMID: 24510545 DOI: 10.1002/0471142735.im0217s103] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Engineered monoclonal antibody fragments have gained market attention due to their versatility and tailor-made potential and are now considered to be an important part of future immunobiotherapeutics. Single-domain antibodies (sdAbs), also known as nanobodies, are derived from VHHs [variable domains (V) of heavy-chain-only antibodies (HCAb)] of camelid heavy-chain antibodies. These nature-made sdAbs are well suited for various applications due to their favorable characteristics such as small size, ease of genetic manipulation, high affinity and solubility, overall stability, resistance to harsh conditions (e.g., low pH, high temperature), and low immunogenicity. Most importantly, sdAbs have the feature of penetrating into cavities and recognizing hidden epitopes normally inaccessible to conventional antibodies, mainly due to their protruding CDR3/H3 loops. In this unit, we will present and discuss comprehensive and step-by-step protocols routinely practiced in our laboratory for isolating sdAbs from immunized llamas (or other members of the Camelidae family) against target antigens using phage-display technology. Expression, purification, and characterization of the isolated sdAbs will then be described, followed by presentation of several examples of applications of sdAbs previously characterized in our laboratory and elsewhere.
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Affiliation(s)
- Toya Nath Baral
- Human Health Therapeutics, Life Sciences Division, National Research Council Canada, Ottawa, Ontario, Canada
| | - Roger MacKenzie
- Human Health Therapeutics, Life Sciences Division, National Research Council Canada, Ottawa, Ontario, Canada.,University of Guelph, Guelph, Ontario, Canada
| | - Mehdi Arbabi Ghahroudi
- Human Health Therapeutics, Life Sciences Division, National Research Council Canada, Ottawa, Ontario, Canada.,University of Guelph, Guelph, Ontario, Canada.,Department of Biology, Carleton University, Ottawa, Ontario, Canada
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20
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Ryu JS, Cho AY, Seo SW, Min H. Engineering bioactive peptide-based therapeutic molecules. Methods Mol Biol 2013; 1088:35-50. [PMID: 24146395 DOI: 10.1007/978-1-62703-673-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Peptides are increasingly emerging as human therapeutic drugs. By screening very large phage display libraries, novel bioactive peptides that bind to the target of interest with desired biological properties can be identified. Peptides that are obtained in this fashion become the basis for therapeutic molecule development. However, naked peptides are usually not sufficient to be therapeutic molecules by themselves. They need to be chemically modified or conjugated to other molecules to obtain desired physicochemical and in vivo properties. In this chapter, we describe a general methodology of identifying bioactive peptides by biopanning of peptide phage libraries. As an example of therapeutic peptide modifications, we also describe a method for fusing the peptides to the Fc portion of antibody molecule to increase in vivo stability and activity.
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Affiliation(s)
- Jong Sang Ryu
- Bio Lab, Emerging Technology Center, SAIT, Samsung Electronics, Giheung-Gu, Yongin-Si, Gyeonggi-Do, Republic of Korea
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21
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Knez K, Noppe W, Geukens N, Janssen KPF, Spasic D, Heyligen J, Vriens K, Thevissen K, Cammue BPA, Petrenko V, Ulens C, Deckmyn H, Lammertyn J. Affinity Comparison of p3 and p8 Peptide Displaying Bacteriophages Using Surface Plasmon Resonance. Anal Chem 2013; 85:10075-82. [DOI: 10.1021/ac402192k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Karel Knez
- BIOSYST-MeBioS, KU Leuven, Willem De Croylaan 42, P.O. Box 2428, B-3001 Leuven, Belgium
| | - Wim Noppe
- IRF
Life Siences, KU Leuven Kulak, E. Sabbelaan 53, B-8500 Kortrijk, Belgium
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, O&N II, Herestraat 49, P.O. Box 824, B-3000 Leuven, Belgium
| | - Kris P. F. Janssen
- BIOSYST-MeBioS, KU Leuven, Willem De Croylaan 42, P.O. Box 2428, B-3001 Leuven, Belgium
| | - Dragana Spasic
- BIOSYST-MeBioS, KU Leuven, Willem De Croylaan 42, P.O. Box 2428, B-3001 Leuven, Belgium
| | - Jeroen Heyligen
- BIOSYST-MeBioS, KU Leuven, Willem De Croylaan 42, P.O. Box 2428, B-3001 Leuven, Belgium
| | - Kim Vriens
- Centre
for Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, P.O. 2460, B-3001 Heverlee, Belgium
| | - Karin Thevissen
- Centre
for Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, P.O. 2460, B-3001 Heverlee, Belgium
| | - Bruno P. A. Cammue
- Centre
for Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, P.O. 2460, B-3001 Heverlee, Belgium
| | - Valery Petrenko
- Auburn University, College of Veterinary Medicine,
Department of Pathobiology, 269 Greene Hall, Auburn, Alabama 36849-5519, United States
| | - Chris Ulens
- Laboratory for Structural Neurobiology, KU Leuven, O&N I, Herestraat 49, P.O. Box 601, B-3000 Leuven, Belgium
| | - Hans Deckmyn
- IRF
Life Siences, KU Leuven Kulak, E. Sabbelaan 53, B-8500 Kortrijk, Belgium
- PharmAbs, The KU Leuven Antibody Center, O&N II, Herestraat 49, P.O. Box 824, B-3000 Leuven, Belgium
| | - Jeroen Lammertyn
- BIOSYST-MeBioS, KU Leuven, Willem De Croylaan 42, P.O. Box 2428, B-3001 Leuven, Belgium
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22
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Hamzeh-Mivehroud M, Alizadeh AA, Morris MB, Church WB, Dastmalchi S. Phage display as a technology delivering on the promise of peptide drug discovery. Drug Discov Today 2013; 18:1144-57. [PMID: 24051398 DOI: 10.1016/j.drudis.2013.09.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 08/29/2013] [Accepted: 09/09/2013] [Indexed: 01/24/2023]
Abstract
Phage display represents an important approach in the development pipeline for producing peptides and peptidomimetics therapeutics. Using randomly generated DNA sequences and molecular biology techniques, large diverse peptide libraries can be displayed on the phage surface. The phage library can be incubated with a target of interest and the phage which bind can be isolated and sequenced to reveal the displayed peptides' primary structure. In this review, we focus on the 'mechanics' of the phage display process, whilst highlighting many diverse and subtle ways it has been used to further the drug-development process, including the potential for the phage particle itself to be used as a drug carrier targeted to a particular pathogen or cell type in the body.
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Affiliation(s)
- Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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23
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Korkmaz N. Recombinant bacteriophages as gold binding bio-templates. Colloids Surf B Biointerfaces 2013; 112:219-28. [PMID: 23994747 DOI: 10.1016/j.colsurfb.2013.07.063] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 07/03/2013] [Accepted: 07/30/2013] [Indexed: 12/31/2022]
Abstract
Bacteriophages are nano-sized virion particles infecting bacteria. In this study, it is shown that metal binding properties of filamentous fd-bacteriophages can be enhanced by genetic engineering. Quartz crystal microbalance (QCM) analyses, UV-vis absorption spectra measurements and scanning electron microscopy (SEM) imaging revealed that expression of MMM short amino acid sequence on major coat protein p8 facilitates recombinant MMM-phage binding to Au surfaces and nanoparticles (NPs) via gold-sulfur (AuS) interaction. Electroless deposition of Au particles on phage assemblies was investigated upon chemical reduction reaction with NaBH4 at different HAuCl4 precursor concentrations. Energy dispersive X-ray spectroscopy (EDX) measurements confirmed the presence of Au on both AuNP decorated and chemically metallized phage structures. Further studies on patterning and controlled immobilization of recombinant bacteriophages on specific surfaces may contribute to bio-templated nanowire development field and biosensor application studies.
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Affiliation(s)
- Nuriye Korkmaz
- Convergence Bioscience Group, Nanomedicine Team, Korea Institute of Science and Technology, Europe Forschungsgesellschaft mbH, Campus E 71, D-66123 Saarbrücken, Germany.
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24
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Korkmaz N, Kim YJ, Nam CH. Bacteriophages as Templates for Manufacturing Supramolecular Structures. Macromol Biosci 2012; 13:376-87. [DOI: 10.1002/mabi.201200290] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 09/18/2012] [Indexed: 01/31/2023]
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25
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Menegatti S, Hussain M, Naik AD, Carbonell RG, Rao BM. mRNA display selection and solid-phase synthesis of Fc-binding cyclic peptide affinity ligands. Biotechnol Bioeng 2012; 110:857-70. [DOI: 10.1002/bit.24760] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/09/2012] [Accepted: 10/12/2012] [Indexed: 12/25/2022]
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26
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Practical tips for construction of custom Peptide libraries and affinity selection by using commercially available phage display cloning systems. J Nucleic Acids 2012; 2012:295719. [PMID: 22991651 PMCID: PMC3444042 DOI: 10.1155/2012/295719] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/25/2012] [Accepted: 08/01/2012] [Indexed: 02/01/2023] Open
Abstract
Phage display technology is undoubtedly a powerful tool for affinity selection of target-specific peptide. Commercially available premade phage libraries allow us to take screening in the easiest way. On the other hand, construction of a custom phage library seems to be inaccessible, because several practical tips are absent in instructions. This paper focuses on what should be born in mind for beginners using commercially available cloning kits (Ph.D. with type 3 vector and T7Select systems for M13 and T7 phage, respectively). In the M13 system, Pro or a basic amino acid (especially, Arg) should be avoided at the N-terminus of peptide fused to gp3. In both systems, peptides containing odd number(s) of Cys should be designed with caution. Also, DNA sequencing of a constructed library before biopanning is highly recommended for finding unexpected bias.
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27
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Abstract
Peptibodies or peptide-Fc fusions are an attractive alternative therapeutic format to monoclonal antibodies. They consist of biologically active peptides grafted onto an Fc domain. This approach retains certain desirable features of antibodies, notably an increased apparent affinity through the avidity conferred by the dimerization of two Fcs and a long plasma residency time. Peptibodies can be made in E. coli using recombinant technology. The manufacturing process involves fermentation and downstream processing, including refolding and multiple column chromatographic steps, that result in overall yields and quality suitable for commercial development. Romiplostim, marketed under the brand name Nplate®, is the first peptibody to be approved by the United States Food and Drug Administration and the European Medicines Agency and is indicated for the treatment of immune thrombocytopenic purpura. AMG 386, a peptibody antagonist to angiopoietins 1 and 2, is being evaluated in Phase 3 clinical testing in combination with chemotherapy in women with ovarian cancer. AMG 819, a peptibody targeting nerve growth factor for pain has also progressed to clinical trials. These peptibodies illustrate the versatility of the modality.
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28
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Aoki K, Alles N, Soysa N, Ohya K. Peptide-based delivery to bone. Adv Drug Deliv Rev 2012; 64:1220-38. [PMID: 22709649 DOI: 10.1016/j.addr.2012.05.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 05/29/2012] [Accepted: 05/29/2012] [Indexed: 01/26/2023]
Abstract
Peptides are attractive as novel therapeutic reagents, since they are flexible in adopting and mimicking the local structural features of proteins. Versatile capabilities to perform organic synthetic manipulations are another unique feature of peptides compared to protein-based medicines, such as antibodies. On the other hand, a disadvantage of using a peptide for a therapeutic purpose is its low stability and/or high level of aggregation. During the past two decades, numerous peptides were developed for the treatment of bone diseases, and some peptides have already been used for local applications to repair bone defects in the clinic. However, very few peptides have the ability to form bone themselves. We herein summarize the effects of the therapeutic peptides on bone loss and/or local bone defects, including the results from basic studies. We also herein describe some possible methods for overcoming the obstacles associated with using therapeutic peptide candidates.
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Affiliation(s)
- Kazuhiro Aoki
- Dept. of Hard Tissue Engineering (Pharmacology), Graduate School, Tokyo Medical & Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.
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29
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Hamzeh-Mivehroud M, Mahmoudpour A, Dastmalchi S. Identification of new peptide ligands for epidermal growth factor receptor using phage display and computationally modeling their mode of binding. Chem Biol Drug Des 2012; 79:246-59. [PMID: 22136656 DOI: 10.1111/j.1747-0285.2011.01282.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Peptide phage display, a powerful method for ligand identification, was used to identify new peptide ligands for epidermal growth factor receptor. A-431 cells expressing epidermal growth factor receptor were used as the matrix in a cell-based subtractive biopanning approach using a 7-mer peptide displaying phage library. Two novel peptide ligands were identified and tested for their affinities and functional effects on epidermal growth factor receptor. The identified peptides were able to inhibit the epidermal growth factor-induced phosphorylation of epidermal growth factor receptor in a concentration-dependent manner. The results of affinity binding experiments showed that the natural ligand, that is epidermal growth factor, was able to inhibit competitively the binding of peptide-bearing phage to epidermal growth factor receptor expressing A-431 cells. Molecular modeling studies were used to calculate the free energies for the binding of peptides to the receptor-binding site as well as proposing the interaction modes for this binding. The calculated values for the binding energies were found to be similar to our experimental data and those of previously reported studies.
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30
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Kaplan G, Gershoni JM. A general insert label for peptide display on chimeric filamentous bacteriophages. Anal Biochem 2011; 420:68-72. [PMID: 21945353 PMCID: PMC7094602 DOI: 10.1016/j.ab.2011.08.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 08/29/2011] [Accepted: 08/30/2011] [Indexed: 12/12/2022]
Abstract
The foreign insert intended to be displayed via recombinant phage proteins can have a negative effect on protein expression and phage assembly. A typical example is the case of display of peptides longer than 6 amino acid residues on the major coat protein, protein VIII of the filamentous bacteriophages M13 and fd. A solution to this problem has been the use of “two-gene systems” generating chimeric phages that concomitantly express wild-type protein VIII along with recombinant protein VIII. Although the two-gene systems are much more permissive in regard to insert length and composition, some cases can still adversely affect phage assembly. Although these phages genotypically contain the desired DNA of the insert, they appear to be phenotypically wild type. To avoid false-negative results when using chimeric phages in binding studies, it is necessary to confirm that the observed lack of phage recognition is not due to faulty assembly and display of the intended insert. Here we describe a strategy for generating antibodies that specifically recognize recombinant protein VIII regardless of the nature of its foreign insert. These antibodies can be used as a general monitor of the display of recombinant protein VIII into phage particles.
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Affiliation(s)
- Gilad Kaplan
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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31
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Noppe W, Galaev IY, Mattiasson B, Deckmyn H. Apparent heterogeneity in the pIII-peptide fusion protein in single-phage clones isolated from peptide libraries. Protein Eng Des Sel 2011; 24:721-6. [PMID: 21705774 DOI: 10.1093/protein/gzr033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ligand homogeneity is an important issue in affinity chromatography. Using phages expressing peptides on the pIII protein, a heterogeneity in the binding of monoclonal phages was observed during affinity chromatography on supermacroporous cryogels. Fractions with different apparent binding affinities could be separated by stepwise elution. When these different fractions were re-applied, the respective differences in affinity were retained. However, when phage fractions with different apparent affinities were first amplified, an offspring was generated with again variable affinities. As the sequence of the peptide insert was the same, the heterogeneity must be ascribed to differences in avidity and although no direct evidence could be generated, we hypothesize that this is possibly due to phages displaying different numbers of the same peptide as a consequence of either proteolytic or packaging events during the amplification step in Escherichia coli.
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Affiliation(s)
- Wim Noppe
- IRF Life Sciences, Katholieke Universiteit Leuven Campus Kortrijk, Kortrijk, Belgium.
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32
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Castel G, Chtéoui M, Heyd B, Tordo N. Phage display of combinatorial peptide libraries: application to antiviral research. Molecules 2011; 16:3499-518. [PMID: 21522083 PMCID: PMC6263255 DOI: 10.3390/molecules16053499] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Revised: 04/21/2011] [Accepted: 04/22/2011] [Indexed: 12/14/2022] Open
Abstract
Given the growing number of diseases caused by emerging or endemic viruses, original strategies are urgently required: (1) for the identification of new drugs active against new viruses and (2) to deal with viral mutants in which resistance to existing antiviral molecules has been selected. In this context, antiviral peptides constitute a promising area for disease prevention and treatment. The identification and development of these inhibitory peptides require the high-throughput screening of combinatorial libraries. Phage-display is a powerful technique for selecting unique molecules with selective affinity for a specific target from highly diverse combinatorial libraries. In the last 15 years, the use of this technique for antiviral purposes and for the isolation of candidate inhibitory peptides in drug discovery has been explored. We present here a review of the use of phage display in antiviral research and drug discovery, with a discussion of optimized strategies combining the strong screening potential of this technique with complementary rational approaches for identification of the best target. By combining such approaches, it should be possible to maximize the selection of molecules with strong antiviral potential.
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Affiliation(s)
| | | | | | - Noël Tordo
- Unité Postulante des Stratégies Antivirales, CNRS URA-3015, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
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33
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Post-translational modification of genetically encoded polypeptide libraries. Curr Opin Chem Biol 2011; 15:355-61. [PMID: 21489857 DOI: 10.1016/j.cbpa.2011.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/17/2011] [Accepted: 03/17/2011] [Indexed: 10/18/2022]
Abstract
The genetic encoding of polypeptides with biological display systems enables the facile generation and screening of very large combinatorial libraries of molecules. By post-translationally modifying the encoded polypeptides, chemically and structurally more diverse molecules beyond linear amino acid polymers can be generated. The first post-translational modification applied to encoded polypeptides, the oxidation of cysteine residues to form disulfide bridges, is a natural one and was used to cyclise short peptides soon after the invention of phage display. Recently a range of non-natural chemical strategies for the post-translational modification of encoded polypeptide repertoires were applied to generate optical biosensors, semisynthetic polypeptides, peptide-drug conjugates, redox-insensitive monocyclic peptides or multicyclic peptides, and these strategies are reviewed in this article.
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Coxon A, Bready J, Min H, Kaufman S, Leal J, Yu D, Lee TA, Sun JR, Estrada J, Bolon B, McCabe J, Wang L, Rex K, Caenepeel S, Hughes P, Cordover D, Kim H, Han SJ, Michaels ML, Hsu E, Shimamoto G, Cattley R, Hurh E, Nguyen L, Wang SX, Ndifor A, Hayward IJ, Falcón BL, McDonald DM, Li L, Boone T, Kendall R, Radinsky R, Oliner JD. Context-dependent role of angiopoietin-1 inhibition in the suppression of angiogenesis and tumor growth: implications for AMG 386, an angiopoietin-1/2-neutralizing peptibody. Mol Cancer Ther 2011; 9:2641-51. [PMID: 20937592 DOI: 10.1158/1535-7163.mct-10-0213] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
AMG 386 is an investigational first-in-class peptide-Fc fusion protein (peptibody) that inhibits angiogenesis by preventing the interaction of angiopoietin-1 (Ang1) and Ang2 with their receptor, Tie2. Although the therapeutic value of blocking Ang2 has been shown in several models of tumorigenesis and angiogenesis, the potential benefit of Ang1 antagonism is less clear. To investigate the consequences of Ang1 neutralization, we have developed potent and selective peptibodies that inhibit the interaction between Ang1 and its receptor, Tie2. Although selective Ang1 antagonism has no independent effect in models of angiogenesis-associated diseases (cancer and diabetic retinopathy), it induces ovarian atrophy in normal juvenile rats and inhibits ovarian follicular angiogenesis in a hormone-induced ovulation model. Surprisingly, the activity of Ang1 inhibitors seems to be unmasked in some disease models when combined with Ang2 inhibitors, even in the context of concurrent vascular endothelial growth factor inhibition. Dual inhibition of Ang1 and Ang2 using AMG 386 or a combination of Ang1- and Ang2-selective peptibodies cooperatively suppresses tumor xenograft growth and ovarian follicular angiogenesis; however, Ang1 inhibition fails to augment the suppressive effect of Ang2 inhibition on tumor endothelial cell proliferation, corneal angiogenesis, and oxygen-induced retinal angiogenesis. In no case was Ang1 inhibition shown to (a) confer superior activity to Ang2 inhibition or dual Ang1/2 inhibition or (b) antagonize the efficacy of Ang2 inhibition. These results imply that Ang1 plays a context-dependent role in promoting postnatal angiogenesis and that dual Ang1/2 inhibition is superior to selective Ang2 inhibition for suppression of angiogenesis in some postnatal settings.
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Affiliation(s)
- Angela Coxon
- Department of Oncology Research, Amgen, Inc., Thousand Oaks, California 91320, USA
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35
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Yabe T, Hosoda-Yabe R, Kanamaru Y, Kiso M. A peptide found by phage display discriminates a specific structure of a trisaccharide in heparin. J Biol Chem 2011; 286:12397-406. [PMID: 21335559 DOI: 10.1074/jbc.m110.172155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A number of recent studies have shown that heparan sulfate can control several important biological events on the cell surface through changes in sulfation pattern. The in vivo modification of sugar chains with sulfates, however, is complicated, and the discrimination of different sulfation patterns is difficult. Heparin, which is primarily produced by mast cells, is closely approximated by the structural analog heparan sulfate. Screening of heparin-associating peptides using phage display and antithrombin-bound affinity chromatography identified a peptide, heparin-associating peptide Y (HappY), that acts as a target of immobilized heparin. The peptide consists of 12 amino acid residues with characteristic three arginines and exclusively binds to heparin and heparan sulfate but does not associate with other glycosaminoglycans. HappY recognizes three consecutive monosaccharide residues in heparin through its three arginine residues. HappY should be a useful probe to detect heparin and heparan sulfate in studies of glycobiology.
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Affiliation(s)
- Tomio Yabe
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan.
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36
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Pande J, Szewczyk MM, Grover AK. Phage display: concept, innovations, applications and future. Biotechnol Adv 2010; 28:849-58. [PMID: 20659548 DOI: 10.1016/j.biotechadv.2010.07.004] [Citation(s) in RCA: 336] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Revised: 06/27/2010] [Accepted: 07/08/2010] [Indexed: 12/17/2022]
Abstract
Phage display is the technology that allows expression of exogenous (poly)peptides on the surface of phage particles. The concept is simple in principle: a library of phage particles expressing a wide diversity of peptides is used to select those that bind the desired target. The filamentous phage M13 is the most commonly used vector to create random peptide display libraries. Several methods including recombinant techniques have been developed to increase the diversity of the library. On the other extreme, libraries with various biases can be created for specific purposes. For instance, when the sequence of the peptide that binds the target is known, its affinity and selectivity can be increased by screening libraries created with limited mutagenesis of the peptide. Phage libraries are screened for binding to synthetic or native targets. The initial screening of library by basic biopanning has been extended to column chromatography including negative screening and competition between selected phage clones to identify high affinity ligands with greater target specificity. The rapid isolation of specific ligands by phage display is advantageous in many applications including selection of inhibitors for the active and allosteric sites of the enzymes, receptor agonists and antagonists, and G-protein binding modulatory peptides. Phage display has been used in epitope mapping and analysis of protein-protein interactions. The specific ligands isolated from phage libraries can be used in therapeutic target validation, drug design and vaccine development. Phage display can also be used in conjunction with other methods. The past innovations and those to come promise a bright future for this field.
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Affiliation(s)
- Jyoti Pande
- Department of Medicine, HSC 4N41 McMaster Univ, Hamilton, ON, Canada
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37
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Abbineni G, Safiejko-Mroczka B, Mao C. Development of an optimized protocol for studying the interaction of filamentous bacteriophage with mammalian cells by fluorescence microscopy. Microsc Res Tech 2010; 73:548-54. [PMID: 19937750 DOI: 10.1002/jemt.20793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Filamentous bacteriophage has been proposed as a vehicle that can carry and deliver therapeutics into mammalian cells for disease treatment, thus a protocol for imaging phage-cell interaction is essential. Because high signal intensity is necessary to study the mechanism of interaction between filamentous bacteriophage and mammalian cells, it is important to optimize the procedure for fluorescence labeling of phage in order to understand such interaction. Here, we describe a procedure that gives intense fluorescence labeling and can show interactions between fd-tet bacteriophage selected from phage libraries and mammalian cells (SKBR-3 and MCF-10A). The indirect labeling of phage with dye-conjugated antibody and cytoskeleton associated proteins was significantly enhanced in the presence of a cross-linking reagent called dithiobissuccinimidylpropionate (DSP) as shown by qualitative and quantitative fluorescence microscopy. The use of DSP resulted in high signal intensity in fluorescence imaging of phage-cell complex. The DSP cross-linker is believed to preserve soluble unbound proteins for fluorescence imaging. The interaction between the phage and mammalian cells was further confirmed by scanning electron microscopy.
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Affiliation(s)
- Gopal Abbineni
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma 73019, USA
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38
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Ma Z, Wu X, Cao M, Pan W, Zhu F, Chen J, Qi Z. Selection of trkB-binding peptides from a phage-displayed random peptide library. ACTA ACUST UNITED AC 2010; 46:77-86. [PMID: 20213364 DOI: 10.1007/bf03182687] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2001] [Revised: 02/25/2002] [Indexed: 10/19/2022]
Abstract
Brain-derived neurotrophic factor (BDNF) shows potential in the treatment of neurodegenerative diseases, but the therapeutic application of BDNF has been greatly limited because it is too large in molecular size to permeate blood-brain barrier. To develop low-molecular-weight BDNF-like peptides, we selected a phage-displayed random peptide library using trkB expressed on NIH 3T3 cells as target in the study. With the strategy of peptide library incubation with NIH 3T3 cells and competitive elution with 1 microg/mL of BDNF in the last round of selection, the specific phages able to bind to the natural conformation of trkB and antagonize BDNF binding to trkB were enriched effectively. Five trkB-binding peptides were obtained, in which a core sequence of CRA/TXphiXXphiXXC (X represents the random amino acids, phi represents T, L or I) was identified. The BDNF-like activity of these five peptides displayed on phages was not observed, though all of them antagonized the activity of BDNF in a dose-dependent manner. Similar results were obtained with the synthetic peptide of C1 clone, indicating that the 5 phage-derived peptides were trkB antagonists. These low-molecular-weight antagonists of trkB may be of potential application in the treatment of neuroblastoma and chronic pain. Meanwhile, the obtained core sequence also could be used as the base to construct the secondary phage-displayed peptide library for further development of small peptides mimicking BDNF activity.
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Affiliation(s)
- Zhongcai Ma
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China
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39
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Castel G, Tordo N. [New strategies for the development of antiviral molecules]. REVUE FRANCOPHONE DES LABORATOIRES : RFL 2009; 2009:91-100. [PMID: 32288807 PMCID: PMC7140268 DOI: 10.1016/s1773-035x(09)70313-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 09/30/2009] [Indexed: 11/29/2022]
Abstract
Antiviral research is a recent discipline and the number of molecules available to fight against viral infections remains still insufficient. However, both diseases caused by emerging endemic viruses and the existence of resistance from some viruses against antiviral make necessary a constant search for new antiviral drugs. Parallel to the development of traditional molecules such as nucleoside analogues, whose effectiveness is well demonstrated, pharmaceutical industry is now turning to new solutions such as antiviral peptides, which constitute a new exploration field in therapy. The recent progress in disciplines such as genomics, proteomics and structural biology have improved our fundamental understanding of the viral world. These advances can be used to efficiently create new drugs more selective and more effective. Identification and development of these molecules require the use of newer techniques such as high-throughput screening of combinatorial compound libraries and the use of new bioinformatics tools. This review aims to present some recent methods for the development of antiviral molecules.
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Affiliation(s)
- Guillaume Castel
- Unité postulante des stratégies antivirales – CNRS URA-3015, Institut Pasteur, 25, rue du Docteur-Roux, 75724 Paris cedex 15
| | - Noël Tordo
- Unité postulante des stratégies antivirales – CNRS URA-3015, Institut Pasteur, 25, rue du Docteur-Roux, 75724 Paris cedex 15
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40
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Pieraccini S, Saladino G, Cappelletti G, Cartelli D, Francescato P, Speranza G, Manitto P, Sironi M. In silico design of tubulin-targeted antimitotic peptides. Nat Chem 2009; 1:642-8. [DOI: 10.1038/nchem.401] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 09/08/2009] [Indexed: 11/09/2022]
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41
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Eldridge B, Cooley RN, Odegrip R, McGregor DP, FitzGerald KJ, Ullman CG. An in vitro selection strategy for conferring protease resistance to ligand binding peptides. Protein Eng Des Sel 2009; 22:691-8. [DOI: 10.1093/protein/gzp052] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Devemy E, Blaschuk OW. Identification of a novel dual E- and N-cadherin antagonist. Peptides 2009; 30:1539-47. [PMID: 19465078 DOI: 10.1016/j.peptides.2009.05.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 05/12/2009] [Accepted: 05/13/2009] [Indexed: 01/31/2023]
Abstract
E- and N-cadherin are related calcium-dependent cell adhesion molecules that exert an influence over multiple biological and disease processes. Antagonists of these cadherins can therefore be envisaged as therapeutically useful drugs. We have used phage display technology to discover such antagonists. A peptide phage library was screened against a chimeric protein composed of the human E-cadherin ectodomain fused to the Fc fragment of human immunoglobulin G1 (E-cad/Fc). All of the phage clones that were isolated also bound a chimeric protein composed of the human N-cadherin ectodomain fused to the Fc fragment of human immunoglobulin G1 (N-cad/Fc). A peptide displayed by several of the isolated phage clones was synthesized (H-SWELYYPLRANL-NH2) and found to bind both E- and N-cad/Fc chimeric proteins with affinities (K(D)) of 9.4 microM and 323 nM, respectively, as judged by surface plasmon resonance spectroscopy. This peptide was also capable of blocking the aggregation of E- and N-cad/Fc chimeric protein-coated beads, as well as the aggregation of MCF-7 and MDA-MB435 human breast cancer cells (these cells express E- and N-cadherin, respectively). Finally, we showed that the peptide disrupted MCF-7 and MDA-MB435 cell monolayers. The peptide, H-SWELYYPLRANL-NH(2) thus proved to be a biologically active, dual E- and N-cadherin antagonist. Such an antagonist has application in a wide variety of biological contexts.
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Affiliation(s)
- Emmanuelle Devemy
- Division of Urology, Department of Surgery, McGill University, Urology Research Laboratories, Royal Victoria Hospital, Room H6.15, 687 Pine Avenue West, Montreal, Quebec, Canada H3A 1A1.
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Matsuhisa K, Kondoh M, Takahashi A, Yagi K. Tight junction modulator and drug delivery. Expert Opin Drug Deliv 2009; 6:509-15. [PMID: 19413458 DOI: 10.1517/17425240902902315] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Recent progress in pharmaceutical technology based on genomic and proteomic research has provided many drug candidates, including not only chemicals but peptides, antibodies and nucleic acids. These candidates do not show pharmaceutical activity without their absorption into systemic flow and movement from the systemic flow into the target tissue. Epithelial and endothelial cell sheets play a pivotal role in the barrier between internal and external body and tissues. Tight junctions (TJs) between adjacent epithelial cells limit the movement of molecules through the intercellular space in epithelial and endothelial cell sheets. Thus, a promising strategy for drug delivery is the modulation of TJ components to allow molecules to pass through the TJ-based cellular barriers. In this review, we discuss recent progress in the development of TJ modulators and the possibility of absorption enhancers and drug-delivery systems based on TJ components.
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Affiliation(s)
- Koji Matsuhisa
- Department of Bio Functional Molecular Chemistry, Osaka University, Graduate School of Pharmaceutical Sciences, Suita, Osaka 565-0871, Japan.
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44
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Molecular Evolution of Cystine-Stabilized Miniproteins as Stable Proteinaceous Binders. Structure 2009; 17:620-31. [DOI: 10.1016/j.str.2009.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Revised: 01/16/2009] [Accepted: 01/16/2009] [Indexed: 11/17/2022]
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45
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Arbabi-Ghahroudi M, Tanha J, MacKenzie R. Isolation of monoclonal antibody fragments from phage display libraries. Methods Mol Biol 2009; 502:341-64. [PMID: 19082566 DOI: 10.1007/978-1-60327-565-1_20] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Techniques developed over the past 20 years for the display of foreign peptides and proteins on the surfaces of filamentous bacteriophages have been a major driving force in the rapid development of recombinant antibody technology in recent years. With phage display of antibodies as one of its key components, recombinant antibody technology has led to the development of an increasing number of therapeutic monoclonal antibodies. Antibody gene libraries are fused to a gene encoding a phage coat protein. Recombinant phage expressing the resulting antibody libraries in fusion with the coat protein are propagated in Escherichia coli. Phage displaying monoclonal antibodies with specificities for target antigens are isolated from the libraries by a process called panning. The genes encoding the desired antibodies selected from the libraries are packaged within the phage particles, linking genotype and phenotype. Here, we describe the application of this technology to the construction of a phage-displayed single-domain antibody (sdAb) library based on the heavy chain antibody repertoire of a llama, the panning of the library against a peptide antigen and the expression, purification, and characterization of sdAbs isolated by panning.
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Affiliation(s)
- Mehdi Arbabi-Ghahroudi
- Institute for Biological Sciences, National Research Council, The Antibody Engineering Group, Ottawa, Ontario, Canada
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46
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Yao N, Xiao W, Wang X, Marik J, Park SH, Takada Y, Lam KS. Discovery of targeting ligands for breast cancer cells using the one-bead one-compound combinatorial method. J Med Chem 2009; 52:126-33. [PMID: 19055415 DOI: 10.1021/jm801062d] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Four "one-bead one-compound" (OBOC) combinatorial libraries were designed, synthesized, and screened against MDA-MB-231 breast cancer cells. A novel cyclic peptide 1 (LXY1) with high binding specificity to alpha3 integrin was identified. Molecular interactions between alpha3 integrin and 1 were characterized by using a series of K562 cells transfected with various mutant alpha3 integrins. Using analytic flow cytometry, the binding affinity (K(d)) of 1 to alpha3 integrin on MDA-MB-231 breast cancer cells was determined to be approximately 0.4 microM. Based on the established structure-activity relationship (SAR) study, two highly focused cyclic peptide libraries were further designed, synthesized, and screened against MDA-MB-231 breast cancer cells under stringent conditions. A novel cyclic peptide 2 (LXY3) with a high binding affinity (IC(50) = 57 nM) was identified. Moreover, the targeting efficiency and specificity of 2 to the breast adenocarcinoma tumors in mouse xenografts were further confirmed by in vivo and ex vivo near-infrared fluorescence optical imaging.
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Affiliation(s)
- Nianhuan Yao
- Department of Internal Medicine, Division of Hematology and Oncology, UC Davis Cancer Center, University of California, Davis, Sacramento, California 95817, USA
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47
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Arbabi-Ghahroudi M, MacKenzie R, Tanha J. Selection of non-aggregating VH binders from synthetic VH phage-display libraries. Methods Mol Biol 2009; 525:187-216, xiii. [PMID: 19252860 DOI: 10.1007/978-1-59745-554-1_10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The particular interest in VH antibody fragments stems from the fact that they can rival their "naturally occurring" single-domain antibody (sdAb) counterparts (camelid VHHs and shark VNARs) with regard to such desirable characteristics as stability, solubility, expression, and ability to penetrate cryptic epitopes and outperform them in terms of less immunogenicity, a much valued property in human immunotherapy applications. However, human VHs are typically prone to aggregation. Various approaches for developing non-aggregating human VHs with binding specificities have relied on a combination of recombinant DNA technology and phage-display technology. VH gene libraries are constructed synthetically by randomizing the CDRs of a single VH scaffold fused to a gene encoding a phage coat protein. Recombinant phage expressing the resulting VH libraries in fusion with the pIII protein is propagated in Escherichia coli. Monoclonal phage displaying VHs with specificities for target antigens are isolated from the libraries by a process called panning. The exertion of stability pressure in addition to binding pressure during panning ensures that the isolated VH binders are also non-aggregating. The genes encoding the desired VHs selected from the libraries are packaged within the phage particles, linking genotype and phenotype, hence making possible the identification of the selected VHs through identifying its physically linked genotype. Here, we describe the application of recombinant DNA and phage-display technologies for the construction of a phage-displayed human VH library, the panning of the library against a protein, and the expression, purification, and characterization of non-aggregating VHs isolated by panning.
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Affiliation(s)
- Mehdi Arbabi-Ghahroudi
- National Research Council of Canada, Institute for Biological Sciences, Ottawa, Ontario, Canada
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48
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Petrenko V. Evolution of phage display: from bioactive peptides to bioselective nanomaterials. Expert Opin Drug Deliv 2008; 5:825-36. [PMID: 18712993 DOI: 10.1517/17425247.5.8.825] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND New phage-derived biorecognition nanomaterials have emerged recently as a result of the in-depth study of the genetics and structure of filamentous phage and the evolution of phage display technology. OBJECTIVE This review focuses on the progress made in the development of these new nanomaterials and discusses the prospects of using phage as a bioselectable molecular recognition interface in medical and technical devices. METHODS The author used data obtained both in his research group and sourced using Science Citation Index (Web of Science) search resources. RESULTS/CONCLUSION The merging of phage display technologies with nanotechnology over the past few years has proved promising and has already shown its vitality and productivity by contributing vigorously to different areas of medicine and technology, such as medical diagnostics and monitoring, molecular imaging, targeted drug and gene delivery, vaccine development, as well as bone and tissue repair.
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Affiliation(s)
- Va Petrenko
- Auburn University, Department of Pathobiology, AL 36849, USA.
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49
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Construction and characterization of a 9-mer phage display pVIII-library with regulated peptide density. Appl Microbiol Biotechnol 2008; 80:925-36. [DOI: 10.1007/s00253-008-1630-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 07/23/2008] [Accepted: 07/23/2008] [Indexed: 10/21/2022]
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50
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Bratkovič T, Lunder M, Urleb U, Štrukelj B. Peptide inhibitors of MurD and MurE, essential enzymes of bacterial cell wall biosynthesis. J Basic Microbiol 2008; 48:202-6. [DOI: 10.1002/jobm.200700133] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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