1
|
Kim SM, Heo HR, Kim CS, Shin HH. Genetically engineered bacteriophages as novel nanomaterials: applications beyond antimicrobial agents. Front Bioeng Biotechnol 2024; 12:1319830. [PMID: 38725991 PMCID: PMC11079243 DOI: 10.3389/fbioe.2024.1319830] [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: 10/11/2023] [Accepted: 04/11/2024] [Indexed: 05/12/2024] Open
Abstract
Bacteriophages, also known as phages, are viruses that replicate in bacteria and archaea. Phages were initially discovered as antimicrobial agents, and they have been used as therapeutic agents for bacterial infection in a process known as "phage therapy." Recently, phages have been investigated as functional nanomaterials in a variety of areas, as they can function not only as therapeutic agents but also as biosensors and tissue regenerative materials. Phages are nontoxic to humans, and they possess self-assembled nanostructures and functional properties. Additionally, phages can be easily genetically modified to display specific peptides or to screen for functional peptides via phage display. Here, we demonstrated the application of phage nanomaterials in the context of tissue engineering, sensing, and probing.
Collapse
Affiliation(s)
- Seong-Min Kim
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Hye Ryoung Heo
- Department of Chemical and Biochemical Engineering, Dongguk University, Seoul, Republic of Korea
| | - Chang Sup Kim
- Department of Chemical and Biochemical Engineering, Dongguk University, Seoul, Republic of Korea
| | - Hwa Hui Shin
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| |
Collapse
|
2
|
Li Y, Yang KD, Kong DC, Li XM, Duan HY, Ye JF. Harnessing filamentous phages for enhanced stroke recovery. Front Immunol 2024; 14:1343788. [PMID: 38299142 PMCID: PMC10829096 DOI: 10.3389/fimmu.2023.1343788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 12/27/2023] [Indexed: 02/02/2024] Open
Abstract
Stroke poses a critical global health challenge, leading to substantial morbidity and mortality. Existing treatments often miss vital timeframes and encounter limitations due to adverse effects, prompting the pursuit of innovative approaches to restore compromised brain function. This review explores the potential of filamentous phages in enhancing stroke recovery. Initially antimicrobial-centric, bacteriophage therapy has evolved into a regenerative solution. We explore the diverse role of filamentous phages in post-stroke neurological restoration, emphasizing their ability to integrate peptides into phage coat proteins, thereby facilitating recovery. Experimental evidence supports their efficacy in alleviating post-stroke complications, immune modulation, and tissue regeneration. However, rigorous clinical validation is essential to address challenges like dosing and administration routes. Additionally, genetic modification enhances their potential as injectable biomaterials for complex brain tissue issues. This review emphasizes innovative strategies and the capacity of filamentous phages to contribute to enhanced stroke recovery, as opposed to serving as standalone treatment, particularly in addressing stroke-induced brain tissue damage.
Collapse
Affiliation(s)
- Yang Li
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
- School of Nursing, Jilin University, Changchun, China
| | - Kai-di Yang
- School of Nursing, Jilin University, Changchun, China
| | - De-cai Kong
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Xiao-meng Li
- School of Nursing, Jilin University, Changchun, China
| | - Hao-yu Duan
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jun-feng Ye
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| |
Collapse
|
3
|
Olshefsky A, Benasutti H, Sylvestre M, Butterfield GL, Rocklin GJ, Richardson C, Hicks DR, Lajoie MJ, Song K, Leaf E, Treichel C, Decarreau J, Ke S, Kher G, Carter L, Chamberlain JS, Baker D, King NP, Pun SH. In vivo selection of synthetic nucleocapsids for tissue targeting. Proc Natl Acad Sci U S A 2023; 120:e2306129120. [PMID: 37939083 PMCID: PMC10655225 DOI: 10.1073/pnas.2306129120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/21/2023] [Indexed: 11/10/2023] Open
Abstract
Controlling the biodistribution of protein- and nanoparticle-based therapeutic formulations remains challenging. In vivo library selection is an effective method for identifying constructs that exhibit desired distribution behavior; library variants can be selected based on their ability to localize to the tissue or compartment of interest despite complex physiological challenges. Here, we describe further development of an in vivo library selection platform based on self-assembling protein nanoparticles encapsulating their own mRNA genomes (synthetic nucleocapsids or synNCs). We tested two distinct libraries: a low-diversity library composed of synNC surface mutations (45 variants) and a high-diversity library composed of synNCs displaying miniproteins with binder-like properties (6.2 million variants). While we did not identify any variants from the low-diversity surface library that yielded therapeutically relevant changes in biodistribution, the high-diversity miniprotein display library yielded variants that shifted accumulation toward lungs or muscles in just two rounds of in vivo selection. Our approach should contribute to achieving specific tissue homing patterns and identifying targeting ligands for diseases of interest.
Collapse
Affiliation(s)
- Audrey Olshefsky
- Department of Bioengineering, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Halli Benasutti
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Meilyn Sylvestre
- Department of Bioengineering, University of Washington, Seattle, WA98195
| | - Gabriel L. Butterfield
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Department of Molecular and Cellular Biology, University of Washington, Seattle, WA98195
| | - Gabriel J. Rocklin
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Christian Richardson
- Department of Bioengineering, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Derrick R. Hicks
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Marc J. Lajoie
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Kefan Song
- Department of Bioengineering, University of Washington, Seattle, WA98195
| | - Elizabeth Leaf
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Catherine Treichel
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Justin Decarreau
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Sharon Ke
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Gargi Kher
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Jeffrey S. Chamberlain
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Department of Neurology, University of Washington, Seattle, WA98195
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Suzie H. Pun
- Department of Bioengineering, University of Washington, Seattle, WA98195
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA98195
| |
Collapse
|
4
|
Chang C, Guo W, Yu X, Guo C, Zhou N, Guo X, Huang RL, Li Q, Zhu Y. Engineered M13 phage as a novel therapeutic bionanomaterial for clinical applications: From tissue regeneration to cancer therapy. Mater Today Bio 2023; 20:100612. [PMID: 37063776 PMCID: PMC10102448 DOI: 10.1016/j.mtbio.2023.100612] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
Bacteriophages (phages) are nanostructured viruses with highly selective antibacterial properties that have gained attention beyond eliminating bacteria. Specifically, M13 phages are filamentous phages that have recently been studied in various aspects of nanomedicine due to their biological advantages and more compliant engineering capabilities over other phages. Having nanofiber-like morphology, M13 phages can reach varied target sites and self-assemble into multidimensional scaffolds in a relatively safe and stable way. In addition, genetic modification of the coat proteins enables specific display of peptides and antibodies on the phages, allowing for precise and individualized medicine. M13 phages have also been subjected to novel engineering approaches, including phage-based bionanomaterial engineering and phage-directed nanomaterial combinations that enhance the bionanomaterial properties of M13 phages. In view of these features, researchers have been able to utilize M13 phages for therapeutic applications such as drug delivery, biodetection, tissue regeneration, and targeted cancer therapy. In particular, M13 phages have been utilized as a novel bionanomaterial for precisely mimicking natural tissue environment in order to overcome the shortage in tissue and organ donors. Hence, in this review, we address the recent studies and advances of using M13 phages in the field of nanomedicine as therapeutic agents based upon their characteristics as novel bionanomaterial with biomolecules displayed. This paper also emphasizes the novel engineering approach that enhances M13 phage's bionanomaterial capabilities. Current limitations and future approaches are also discussed to provide insight in further progress for M13 phage-based clinical applications.
Collapse
Affiliation(s)
- Cheng Chang
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Wennan Guo
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Xinbo Yu
- Second Dental Center, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201999, China
| | - Chaoyi Guo
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Nan Zhou
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Xiaokui Guo
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Ru-Lin Huang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Corresponding author.
| | - Qingtian Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Corresponding author.
| | - Yongzhang Zhu
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
- Corresponding author.
| |
Collapse
|
5
|
Aloisio A, Nisticò N, Mimmi S, Maisano D, Vecchio E, Fiume G, Iaccino E, Quinto I. Phage-Displayed Peptides for Targeting Tyrosine Kinase Membrane Receptors in Cancer Therapy. Viruses 2021; 13:649. [PMID: 33918836 PMCID: PMC8070105 DOI: 10.3390/v13040649] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Receptor tyrosine kinases (RTKs) regulate critical physiological processes, such as cell growth, survival, motility, and metabolism. Abnormal activation of RTKs and relative downstream signaling is implicated in cancer pathogenesis. Phage display allows the rapid selection of peptide ligands of membrane receptors. These peptides can target in vitro and in vivo tumor cells and represent a novel therapeutic approach for cancer therapy. Further, they are more convenient compared to antibodies, being less expensive and non-immunogenic. In this review, we describe the state-of-the-art of phage display for development of peptide ligands of tyrosine kinase membrane receptors and discuss their potential applications for tumor-targeted therapy.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Ileana Quinto
- Correspondence: (A.A.); (I.Q.): Tel.: +39-0961-3694057 (I.Q.)
| |
Collapse
|
6
|
Indirect Selection against Antibiotic Resistance via Specialized Plasmid-Dependent Bacteriophages. Microorganisms 2021; 9:microorganisms9020280. [PMID: 33572937 PMCID: PMC7911639 DOI: 10.3390/microorganisms9020280] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/15/2021] [Accepted: 01/26/2021] [Indexed: 12/24/2022] Open
Abstract
Antibiotic resistance genes of important Gram-negative bacterial pathogens are residing in mobile genetic elements such as conjugative plasmids. These elements rapidly disperse between cells when antibiotics are present and hence our continuous use of antimicrobials selects for elements that often harbor multiple resistance genes. Plasmid-dependent (or male-specific or, in some cases, pilus-dependent) bacteriophages are bacterial viruses that infect specifically bacteria that carry certain plasmids. The introduction of these specialized phages into a plasmid-abundant bacterial community has many beneficial effects from an anthropocentric viewpoint: the majority of the plasmids are lost while the remaining plasmids acquire mutations that make them untransferable between pathogens. Recently, bacteriophage-based therapies have become a more acceptable choice to treat multi-resistant bacterial infections. Accordingly, there is a possibility to utilize these specialized phages, which are not dependent on any particular pathogenic species or strain but rather on the resistance-providing elements, in order to improve or enlengthen the lifespan of conventional antibiotic approaches. Here, we take a snapshot of the current knowledge of plasmid-dependent bacteriophages.
Collapse
|
7
|
Methods for generating and screening libraries of genetically encoded cyclic peptides in drug discovery. Nat Rev Chem 2020; 4:90-101. [PMID: 37128052 DOI: 10.1038/s41570-019-0159-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2019] [Indexed: 12/14/2022]
Abstract
Drug discovery has traditionally focused on using libraries of small molecules to identify therapeutic drugs, but new modalities, especially libraries of genetically encoded cyclic peptides, are increasingly used for this purpose. Several technologies now exist for the production of libraries of cyclic peptides, including phage display, mRNA display and split-intein circular ligation of peptides and proteins. These different approaches are each compatible with particular methods of screening libraries, such as functional or affinity-based screening, and screening in vitro or in cells. These techniques allow the rapid preparation of libraries of hundreds of millions of molecules without the need for chemical synthesis, and have therefore lowered the entry barrier to generating and screening for inhibitors of a given target. This ease of use combined with the inherent advantages of the cyclic-peptide scaffold has yielded inhibitors of targets that have proved difficult to drug with small molecules. Multiple reports demonstrate that cyclic peptides act as privileged scaffolds in drug discovery, particularly against 'undruggable' targets such as protein-protein interactions. Although substantial challenges remain in the clinical translation of hits from screens of cyclic-peptide libraries, progress continues to be made in this area, with an increasing number of cyclic peptides entering clinical trials. Here, we detail the various platforms for producing and screening libraries of genetically encoded cyclic peptides and discuss and evaluate the advantages and disadvantages of each approach when deployed for drug discovery.
Collapse
|
8
|
Tramontano A. The computational prediction of protein assemblies. Curr Opin Struct Biol 2017; 46:170-175. [PMID: 29102305 DOI: 10.1016/j.sbi.2017.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
Abstract
The function of proteins in the cell is almost always mediated by their interaction with different partners, including other proteins, nucleic acids or small organic molecules. The ability of identifying all of them is an essential step in our quest for understanding life at the molecular level. The inference of the protein complex composition and of its molecular details can also provide relevant clues for the development and the design of drugs. In this short review, I will discuss the computational aspects of the analysis and prediction of protein-protein assemblies and discuss some of the most recent developments as seen in the last Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment.
Collapse
Affiliation(s)
- Anna Tramontano
- Physics Department, Sapienza University of Rome, Piazzale Aldo Moro, 5 I-00185 Roma, Italy; Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro, 5 I-00185 Roma, Italy
| |
Collapse
|
9
|
Genetically Engineered Phage Induced Selective H9c2 Cardiomyocytes Patterning in PDMS Microgrooves. MATERIALS 2017; 10:ma10080973. [PMID: 28825662 PMCID: PMC5578339 DOI: 10.3390/ma10080973] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/01/2017] [Accepted: 08/09/2017] [Indexed: 01/08/2023]
Abstract
A micro-patterned cell adhesive surface was prepared for future design of medical devices. One-dimensional polydimethylsiloxane (PDMS) micro-patterns were prepared by a photolithography process. Afterwards, recombinant filamentous phages that displayed a short binding motif with a cell adhesive peptide (-RGD-) on p8 proteins were immobilized on PDMS microgrooves through simple contact printing to study the cellular response of rat H9c2 cardiomyocyte. While the cell density decreased on PDMS micro-patterns, we observed enhanced cell proliferation and cell to surface interaction on the RGD-phage coated PDMS microgrooves. The RGD-phage coating also supported a better alignment of cell spreading rather than isotropic cell growths as we observed on non-pattered PDMS surface.
Collapse
|
10
|
Zade HM, Keshavarz R, Shekarabi HSZ, Bakhshinejad B. Biased selection of propagation-related TUPs from phage display peptide libraries. Amino Acids 2017; 49:1293-1308. [DOI: 10.1007/s00726-017-2452-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/09/2017] [Indexed: 10/19/2022]
|
11
|
Sakamoto K, Adachi Y, Komoike Y, Kamada Y, Koyama R, Fukuda Y, Kadotani A, Asami T, Sakamoto JI. Novel DOCK2-selective inhibitory peptide that suppresses B-cell line migration. Biochem Biophys Res Commun 2016; 483:183-190. [PMID: 28039053 DOI: 10.1016/j.bbrc.2016.12.170] [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: 12/21/2016] [Accepted: 12/25/2016] [Indexed: 12/13/2022]
Abstract
Dedicator of cytokinesis 2 (DOCK2) is a key molecule for lymphocyte activation and migration. DOCK2 interacts with Ras-related C3 botulinus toxin substrate 1 (Rac1, GTPase) and mediates the GDP-GTP exchange reaction, indicating that inhibitors against protein-protein interaction (PPI) between DOCK2 and Rac1 would be good drug candidates for treating immune-related disorders. Here, we report DOCK2-selective PPI inhibitory peptides discovered using random peptide T7 phage display technology. These peptides inhibited DOCK2 activity at nanomolar concentrations and were delivered to intracellular compartments by combination with cell-penetrating peptide (CPP). Consequently, one peptide, R4-DCpep-2(V2W/K4R/ox)-NH2 (Ac-RRRRCWARYHGYPWCRRRR-NH2), inhibited migration in human B lymphocyte MINO cell line at IC50 = 120 nM. To our knowledge, this is the first report of a DOCK2-selective peptide inhibitor; this study will contribute to the development of novel DOCK2-targeting immunosuppressive drugs.
Collapse
Affiliation(s)
- Kotaro Sakamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
| | - Yusuke Adachi
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yusaku Komoike
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yusuke Kamada
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Ryokichi Koyama
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yasunori Fukuda
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Akito Kadotani
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Taiji Asami
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Jun-Ichi Sakamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| |
Collapse
|
12
|
Recombinant antibodies for specific detection of clostridial [Fe-Fe] hydrogenases. Sci Rep 2016; 6:36034. [PMID: 27786270 PMCID: PMC5081567 DOI: 10.1038/srep36034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/10/2016] [Indexed: 11/21/2022] Open
Abstract
Biological hydrogen production is based on activity of specific enzymes called hydrogenases. Hydrogenases are oxygen sensitive metalloenzymes containing Ni and/or Fe atoms at the active site, catalyzing reversible reduction of protons. Generally, [Fe-Fe] hydrogenases prefer proton reduction to molecular hydrogen, a potential energy carrier molecule that can be produced by bioprocesses in sustainable manner. Thus, monitoring tools have been developed to study the relationship between [Fe-Fe] hydrogenases and biohydrogen production in bioreactors at DNA and RNA levels. In the present study, novel molecular tools are introduced for quantitative monitoring of clostridial [Fe-Fe] hydrogenases at the protein level. Aerobic and anaerobic biopanning (for inactive and active [Fe-Fe] hydrogenase, respectively) of phage displayed single-chain variable fragment (scFv) antibody libraries aided in isolating nine potential scFvs. The enriched antibodies demonstrated high specificity towards Clostridium spp. [Fe-Fe] hydrogenases allowing detection from pure and mixed cultures. Additionally, the antibodies showed different binding characteristics towards hydrogenase catalytic states, providing a possible means for functional detection of clostridial [Fe-Fe] hydrogenases. From hydrogenase-antibody interaction studies we observed that though antibody binding reduced the enzyme catalytic activity, it facilitated to retain hydrogen evolution from oxygen exposed hydrogenases.
Collapse
|
13
|
Wu CY, Wang DH, Wang X, Dixon SM, Meng L, Ahadi S, Enter DH, Chen CY, Kato J, Leon LJ, Ramirez LM, Maeda Y, Reis CF, Ribeiro B, Weems B, Kung HJ, Lam KS. Rapid Discovery of Functional Small Molecule Ligands against Proteomic Targets through Library-Against-Library Screening. ACS COMBINATORIAL SCIENCE 2016; 18:320-9. [PMID: 27053324 PMCID: PMC4908505 DOI: 10.1021/acscombsci.5b00194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Identifying “druggable”
targets and their corresponding
therapeutic agents are two fundamental challenges in drug discovery
research. The one-bead-one-compound (OBOC) combinatorial library method
has been developed to discover peptides or small molecules that bind
to a specific target protein or elicit a specific cellular response.
The phage display cDNA expression proteome library method has been
employed to identify target proteins that interact with specific compounds.
Here, we combined these two high-throughput approaches, efficiently
interrogated approximately 1013 possible molecular interactions,
and identified 91 small molecule compound beads that interacted strongly
with the phage library. Of 19 compounds resynthesized, 4 were cytotoxic
against cancer cells; one of these compounds was found to interact
with EIF5B and inhibit protein translation. As more binding pairs
are confirmed and evaluated, the “library-against-library”
screening approach and the resulting small molecule–protein
domain interaction database may serve as a valuable tool for basic
research and drug development.
Collapse
Affiliation(s)
- Chun-Yi Wu
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- Pharmacology
and Toxicology Graduate Group, University of California, Davis, Davis, California 95616, United States
| | - Don-Hong Wang
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- Genetic
Graduate Group, University of California, Davis, California 95616, United States
| | - Xiaobing Wang
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Seth M. Dixon
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Liping Meng
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Sara Ahadi
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Daniel H. Enter
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- Center
for Biophotonics Science and Technology, University of California, Davis, Sacramento, California 95817, United States
| | - Chao-Yu Chen
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- Pharmacology
and Toxicology Graduate Group, University of California, Davis, Davis, California 95616, United States
| | - Jason Kato
- Pharmacology
and Toxicology Graduate Group, University of California, Davis, Davis, California 95616, United States
| | - Leonardo J. Leon
- Pharmacology
and Toxicology Graduate Group, University of California, Davis, Davis, California 95616, United States
| | - Laura M. Ramirez
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- Center
for Biophotonics Science and Technology, University of California, Davis, Sacramento, California 95817, United States
| | - Yoshiko Maeda
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Carolina F. Reis
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Brianna Ribeiro
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Brittany Weems
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Hsing-Jien Kung
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- National Health Research Institutes, Miaoli
County 35053, Taiwan
| | - Kit S. Lam
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| |
Collapse
|
14
|
Hwang HJ, Ryu MY, Lee GB, Park JP. Selection of High Affinity Peptides for Prediction of Colorectal Adenoma-to-Carcinoma Progression. ChemistrySelect 2016. [DOI: 10.1002/slct.201600173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hye Jin Hwang
- Department of Pharmaceutical Engineering; Daegu Haany University; 290 Yugok-dong Gyeongsan 38610 Republic of Korea
| | - Myung Yi Ryu
- Department of Pharmaceutical Engineering; Daegu Haany University; 290 Yugok-dong Gyeongsan 38610 Republic of Korea
| | - Gyu Bum Lee
- Department of Pharmaceutical Engineering; Daegu Haany University; 290 Yugok-dong Gyeongsan 38610 Republic of Korea
| | - Jong Pil Park
- Department of Pharmaceutical Engineering; Daegu Haany University; 290 Yugok-dong Gyeongsan 38610 Republic of Korea
| |
Collapse
|
15
|
Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016; 11:738-56. [PMID: 26864455 PMCID: PMC7162211 DOI: 10.1002/cmdc.201500495] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/08/2016] [Indexed: 12/14/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
Collapse
Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
| |
Collapse
|
16
|
Domingo-Calap P, Georgel P, Bahram S. Back to the future: bacteriophages as promising therapeutic tools. HLA 2016; 87:133-40. [PMID: 26891965 DOI: 10.1111/tan.12742] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 01/18/2016] [Indexed: 01/21/2023]
Abstract
Bacteriophages (phages), natural predators of bacteria, are becoming increasingly attractive in medical and pharmaceutical applications. After their discovery almost a century ago, they have been particularly instrumental in the comprehension of basic molecular biology and genetics processes. The more recent emergence of multi-drug-resistant bacteria requires novel therapeutic strategies, and phages are being (re)considered as promising potential antibacterial tools. Furthermore, phages are also used for other purposes, e.g. vaccine production, gene/drug carriers, bacterial detection and typing. These new alternative approaches using phages are of major interest and have allowed unexpected developments, from the decipherment of fundamental biological processes to potential clinical applications.
Collapse
Affiliation(s)
- P Domingo-Calap
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Fédération Hospitalo-Universitaire OMICARE, Centre de Recherche d'Immunologie et d'Hématologie, Strasbourg, France
| | - P Georgel
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Fédération Hospitalo-Universitaire OMICARE, Centre de Recherche d'Immunologie et d'Hématologie, Strasbourg, France
| | - S Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Fédération Hospitalo-Universitaire OMICARE, Centre de Recherche d'Immunologie et d'Hématologie, Strasbourg, France
| |
Collapse
|
17
|
Wu CH, Liu IJ, Lu RM, Wu HC. Advancement and applications of peptide phage display technology in biomedical science. J Biomed Sci 2016; 23:8. [PMID: 26786672 PMCID: PMC4717660 DOI: 10.1186/s12929-016-0223-x] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 01/11/2016] [Indexed: 12/25/2022] Open
Abstract
Combinatorial phage library is a powerful research tool for high-throughput screening of protein interactions. Of all available molecular display techniques, phage display has proven to be the most popular approach. Screening phage-displayed random peptide libraries is an effective means of identifying peptides that can bind target molecules and regulate their function. Phage-displayed peptide libraries can be used for (i) B-cell and T-cell epitope mapping, (ii) selection of bioactive peptides bound to receptors or proteins, disease-specific antigen mimics, peptides bound to non-protein targets, cell-specific peptides, or organ-specific peptides, and (iii) development of peptide-mediated drug delivery systems and other applications. Targeting peptides identified using phage display technology may be useful for basic research and translational medicine. In this review article, we summarize the latest technological advancements in the application of phage-displayed peptide libraries to applied biomedical sciences.
Collapse
Affiliation(s)
- Chien-Hsun Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - I-Ju Liu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Ruei-Min Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.
| |
Collapse
|
18
|
Sagona AP, Grigonyte AM, MacDonald PR, Jaramillo A. Genetically modified bacteriophages. Integr Biol (Camb) 2016; 8:465-74. [DOI: 10.1039/c5ib00267b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Applications of genetically modified bacteriophages.
Collapse
Affiliation(s)
- Antonia P. Sagona
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences
- University of Warwick
- Coventry
- UK
| | - Aurelija M. Grigonyte
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences
- University of Warwick
- Coventry
- UK
- Synthetic Biology Centre for Doctoral Training
| | - Paul R. MacDonald
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences
- University of Warwick
- Coventry
- UK
- MOAC DTC
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences
- University of Warwick
- Coventry
- UK
- iSSB
| |
Collapse
|
19
|
Liu Q, Zhang C, Yu L, Shi Y, Zhang L, Peng J, Ji X, Hou M. Study of a humanized inhibitory anti-platelet glycoprotein VI phage antibody from a phage antibody library. ACTA ACUST UNITED AC 2015; 21:60-7. [PMID: 26330203 DOI: 10.1179/1607845415y.0000000047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Objective The aims of the study were to study the effect of anti-platelet glycoprotein (GP) VI auto-antibodies on platelet aggregation and use phage surface display technology to produce anti-platelet GPVI phage antibody fragment, which may be developed to inhibit platelet aggregation in the treatment of cardiovascular disease. Methods Plasma samples from patients with immune thrombocytopenia (ITP) were screened by monoclonal antibody immobilization of the platelet antigen assay and the platelet aggregation test for anti-platelet GPVI auto-antibody with an inhibitory effect. The humanized anti-platelet GPVI phage antibody was produced by phage surface display technology. The function of the phage antibody fragment against platelet aggregation was examined by the platelet aggregation test. Results Of 726 ITP patients, 2 (0.27%) patients' plasma significantly inhibited platelet aggregation induced by collagen-1. After five rounds of selection, enrichment, and purification, a soluble phage antibody fragment was produced, which can inhibit platelet aggregation induced by collagen-1. The results demonstrate that only a few of the screened anti-platelet GPVI auto-antibodies showed an inhibitory effect on platelet aggregation. Discussion A completely humanized anti-GPVI soluble phage antibody can be produced by phage surface display technology. The antibody was able to specifically block collagen-induced platelet aggregation without influencing the aggregation responses to other agonists. Conclusions Results of the present study suggest that very few anti-platelet GPVI auto-antibodies inhibit the aggregation function of platelet. The humanized anti-platelet GPVI produced by phage surface display technology is promising to be used to inhibit platelet aggregation in the treatment of cardiovascular disease.
Collapse
|
20
|
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.
Collapse
Affiliation(s)
- Simon Ng
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta, 11227 Saskatchewan Dr., Edmonton, AB, Canada, T6G 2G2
| | | | | | | | | |
Collapse
|
21
|
Çelik E, Ollis AA, Lasanajak Y, Fisher AC, Gür G, Smith DF, DeLisa MP. Glycoarrays with engineered phages displaying structurally diverse oligosaccharides enable high-throughput detection of glycan-protein interactions. Biotechnol J 2014; 10:199-209. [PMID: 25263089 DOI: 10.1002/biot.201400354] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/21/2014] [Accepted: 09/24/2014] [Indexed: 02/02/2023]
Abstract
Glycan microarrays have become a powerful platform to investigate the interactions of carbohydrates with a variety of biomolecules. However, the number and diversity of glycans available for use in such arrays represent a key bottleneck in glycan array fabrication. To address this challenge, we describe a novel glycan array platform based on surface patterning of engineered glycophages that display unique carbohydrate epitopes. Specifically, we show that glycophages are compatible with surface immobilization procedures and that phage-displayed oligosaccharides retain the ability to be recognized by different glycan-binding proteins (e.g. antibodies and lectins) after immobilization. A key advantage of glycophage arrays is that large quantities of glycophages can be produced biosynthetically from recombinant bacteria and isolated directly from bacterial supernatants without laborious purification steps. Taken together, the glycophage array technology described here should help to expand the diversity of glycan libraries and provide a complement to the existing toolkit for high-throughput analysis of glycan-protein interactions.
Collapse
Affiliation(s)
- Eda Çelik
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA; Department of Chemical Engineering, Hacettepe University, Beytepe, Ankara, Turkey; Bioengineering Division, Institute of Science, Hacettepe University, Beytepe, Ankara, Turkey
| | | | | | | | | | | | | |
Collapse
|
22
|
Bakhshinejad B, Sadeghizadeh M. Bacteriophages and their applications in the diagnosis and treatment of hepatitis B virus infection. World J Gastroenterol 2014; 20:11671-11683. [PMID: 25206272 PMCID: PMC4155358 DOI: 10.3748/wjg.v20.i33.11671] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/11/2014] [Accepted: 04/16/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) infection is a major global health challenge leading to serious disorders such as cirrhosis and hepatocellular carcinoma. Currently, there exist various diagnostic and therapeutic approaches for HBV infection. However, prevalence and hazardous effects of chronic viral infection heighten the need to develop novel methodologies for the detection and treatment of this infection. Bacteriophages, viruses that specifically infect bacterial cells, with a long-established tradition in molecular biology and biotechnology have recently been introduced as novel tools for the prevention, diagnosis and treatment of HBV infection. Bacteriophages, due to tremendous genetic flexibility, represent potential to undergo a huge variety of surface modifications. This property has been the rationale behind introduction of phage display concept. This powerful approach, together with combinatorial chemistry, has shaped the concept of phage display libraries with diverse applications for the detection and therapy of HBV infection. This review aims to offer an insightful overview of the potential of bacteriophages in the development of helpful prophylactic (vaccine design), diagnostic and therapeutic strategies for HBV infection thereby providing new perspectives to the growing field of bacteriophage researches directing towards HBV infection.
Collapse
|
23
|
Marvin DA, Symmons MF, Straus SK. Structure and assembly of filamentous bacteriophages. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:80-122. [PMID: 24582831 DOI: 10.1016/j.pbiomolbio.2014.02.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/09/2014] [Indexed: 12/24/2022]
Abstract
Filamentous bacteriophages are interesting paradigms in structural molecular biology, in part because of the unusual mechanism of filamentous phage assembly. During assembly, several thousand copies of an intracellular DNA-binding protein bind to each copy of the replicating phage DNA, and are then displaced by membrane-spanning phage coat proteins as the nascent phage is extruded through the bacterial plasma membrane. This complicated process takes place without killing the host bacterium. The bacteriophage is a semi-flexible worm-like nucleoprotein filament. The virion comprises a tube of several thousand identical major coat protein subunits around a core of single-stranded circular DNA. Each protein subunit is a polymer of about 50 amino-acid residues, largely arranged in an α-helix. The subunits assemble into a helical sheath, with each subunit oriented at a small angle to the virion axis and interdigitated with neighbouring subunits. A few copies of "minor" phage proteins necessary for infection and/or extrusion of the virion are located at each end of the completed virion. Here we review both the structure of the virion and aspects of its function, such as the way the virion enters the host, multiplies, and exits to prey on further hosts. In particular we focus on our understanding of the way the components of the virion come together during assembly at the membrane. We try to follow a basic rule of empirical science, that one should chose the simplest theoretical explanation for experiments, but be prepared to modify or even abandon this explanation as new experiments add more detail.
Collapse
Affiliation(s)
- D A Marvin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - M F Symmons
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - S K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
| |
Collapse
|
24
|
Sánchez-Martín D, Sanz L, Ruoslahti E, Alvarez-Vallina L. In vivo selection of tumor-specific antibodies. Oncotarget 2013; 4:1547. [PMID: 24077798 PMCID: PMC3858540 DOI: 10.18632/oncotarget.1407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 09/18/2013] [Indexed: 01/08/2023] Open
Affiliation(s)
- David Sánchez-Martín
- Molecular Immunology Unit, Hospital Universitario Puerta de Hierro Majadahonda, 28222 Majadahonda, Madrid, Spain
| | | | | | | |
Collapse
|
25
|
Celik E, Fisher AC, Guarino C, Mansell TJ, DeLisa MP. A filamentous phage display system for N-linked glycoproteins. Protein Sci 2011; 19:2006-13. [PMID: 20669235 DOI: 10.1002/pro.472] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We have developed a filamentous phage display system for the detection of asparagine-linked glycoproteins in Escherichia coli that carry a plasmid encoding the protein glycosylation locus (pgl) from Campylobacter jejuni. In our assay, fusion of target glycoproteins to the minor phage coat protein g3p results in the display of glycans on phage. The glyco-epitope displayed on phage is the product of biosynthetic enzymes encoded by the C. jejuni pgl pathway and minimally requires three essential factors: a pathway for oligosaccharide biosynthesis, a functional oligosaccharyltransferase, and an acceptor protein with a D/E-X(1)-N-X(2)-S/T motif. Glycosylated phages could be recovered by lectin chromatography with enrichment factors as high as 2 × 10(5) per round of panning and these enriched phages retained their infectivity after panning. Using this assay, we show that desired glyco-phenotypes can be reliably selected by panning phage-displayed glycoprotein libraries on lectins that are specific for the glycan. For instance, we used our phage selection to identify permissible residues in the -2 position of the bacterial consensus acceptor site sequence. Taken together, our results demonstrate that a genotype-phenotype link can be established between the phage-associated glyco-epitope and the phagemid-encoded genes for any of the three essential components of the glycosylation process. Thus, we anticipate that our phage display system can be used to isolate interesting variants in any step of the glycosylation process, thereby making it an invaluable tool for genetic analysis of protein glycosylation and for glycoengineering in E. coli cells.
Collapse
Affiliation(s)
- Eda Celik
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA
| | | | | | | | | |
Collapse
|
26
|
Peptide phage display as a tool for drug discovery: targeting membrane receptors. Molecules 2011; 16:857-87. [PMID: 21258295 PMCID: PMC6259427 DOI: 10.3390/molecules16010857] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 01/14/2011] [Accepted: 01/19/2011] [Indexed: 12/14/2022] Open
Abstract
Ligands selected from phage-displayed random peptide libraries tend to be directed to biologically relevant sites on the surface of the target protein. Consequently, peptides derived from library screenings often modulate the target protein’s activity in vitro and in vivo and can be used as lead compounds in drug design and as alternatives to antibodies for target validation in both genomics and drug discovery. This review discusses the use of phage display to identify membrane receptor modulators with agonistic or antagonistic activities. Because isolating or producing recombinant membrane proteins for use as target molecules in library screening is often impossible, innovative selection strategies such as panning against whole cells or tissues, recombinant receptor ectodomains, or neutralizing antibodies to endogenous binding partners were devised. Prominent examples from a two-decade history of peptide phage display will be presented, focusing on the design of affinity selection experiments, methods for improving the initial hits, and applications of the identified peptides.
Collapse
|
27
|
González E, Robles Y, Govezensky T, Bobes RJ, Gevorkian G, Manoutcharian K. Isolation of neurocysticercosis-related antigens from a genomic phage display library of Taenia solium. ACTA ACUST UNITED AC 2010; 15:1268-73. [PMID: 20974903 DOI: 10.1177/1087057110385229] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this study, the authors have generated a tapeworm Taenia solium genomic DNA expression library where foreign peptides/proteins were fused to N-termini of M13 cpVIII and expressed at a high copy number on the phage surface, and they showed that this library may be used in bioselection against antipathogen immune sera, allowing the identification of disease-related antigens recognizing antibodies present in clinical samples. They isolated 2 phage clones expressing T. solium-derived antigens specifically reacting with antibodies present in plasma and cerebrospinal fluid samples of neuroimaging-confirmed neurocysticercosis patients. The described antigen discovery strategy may be used for the direct identification of antigens useful for host-pathogen interaction studies as well as for the development of molecular vaccines and diagnostics.
Collapse
Affiliation(s)
- Erik González
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México DF, México
| | | | | | | | | | | |
Collapse
|
28
|
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: 329] [Impact Index Per Article: 23.5] [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.
Collapse
Affiliation(s)
- Jyoti Pande
- Department of Medicine, HSC 4N41 McMaster Univ, Hamilton, ON, Canada
| | | | | |
Collapse
|
29
|
Bratkovic T. Progress in phage display: evolution of the technique and its application. Cell Mol Life Sci 2010; 67:749-67. [PMID: 20196239 PMCID: PMC11115567 DOI: 10.1007/s00018-009-0192-2] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 10/18/2009] [Accepted: 10/23/2009] [Indexed: 10/20/2022]
Abstract
Phage display, the presentation of (poly)peptides as fusions to capsid proteins on the surface of bacterial viruses, celebrates its 25th birthday in 2010. The technique, coupled with in vitro selection, enables rapid identification and optimization of proteins based on their structural or functional properties. In the last two decades, it has advanced tremendously and has become widely accepted by the scientific community. This by no means exhaustive review aims to inform the reader of the key modifications in phage display. Novel display formats, innovative library designs and screening strategies are discussed. I will also briefly review some recent uses of the technology to illustrate its incredible versatility.
Collapse
Affiliation(s)
- Tomaz Bratkovic
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Askerceva 7, 1000 Ljubljana, Slovenia.
| |
Collapse
|