Development and Application of Computational Methods in Phage Display Technology

Background: Phage display is a powerful and versatile technology for the identification of peptide ligands binding to multiple targets, which has been successfully employed in various fields, such as diagnostics and therapeutics, drug-delivery and material science. The integration of next generation sequencing technology with phage display makes this methodology more productive. With the widespread use of this technique and the fast accumulation of phage display data, databases for these data and computational methods have become an indispensable part in this community. This review aims to summarize and discuss recent progress in the development and application of computational methods in the field of phage display. Methods: We undertook a comprehensive search of bioinformatics resources and computational methods for phage display data via Google Scholar and PubMed. The methods and tools were further divided into different categories according to their uses. Results: We described seven special or relevant databases for phage display data, which provided an evidence-based source for phage display researchers to clean their biopanning results. These databases can identify and report possible target-unrelated peptides (TUPs), thereby excluding false-positive data from peptides obtained from phage display screening experiments. More than 20 computational methods for analyzing biopanning data were also reviewed. These methods were classified into computational methods for reporting TUPs, for predicting epitopes and for analyzing next generation phage display data. Conclusion: The current bioinformatics archives, methods and tools reviewed here have benefitted the biopanning community. To develop better or new computational tools, some promising directions are also discussed.

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Biopanning data bank 2018: hugging next generation phage display

Database ◽

10.1093/database/bay032 ◽

2018 ◽

Vol 2018 ◽

Cited By ~ 8

Author(s):

Bifang He ◽

Lixu Jiang ◽

Yaocong Duan ◽

Guoshi Chai ◽

Yewei Fang ◽

...

Keyword(s):

Phage Display ◽

Chemical Structure ◽

Data Bank ◽

Peptide Ligands ◽

Data Sets ◽

Next Generation ◽

Current Version ◽

Sequencing Technologies ◽

Unselected Population ◽

Generation Sequencing

Abstract The 2018 update of the biopanning data bank (BDB) stores phage display data sequenced by Sanger sequencing and next generation sequencing technologies. In this work, we upgraded the database with more biopanning data sets and several new features, including (i) incorporation of next generation biopanning data and the unselected population where the target is not determined and the round of screening is zero; (ii) addition of sequencing information; (iii) improvement of browsing and searching systems and 3 D chemical structure viewer; (iv) integration of standalone tools for target-unrelated peptides analysis within conventional phage display and next generation phage display (NGPD) data. In the current version of BDB (released on 19 January 2018), the database houses 3291 sets of biopanning data collected from 1540 published articles, including 95 NGPD data sets and 3196 traditional biopanning data sets. The BDB database serves as an important and comprehensive resource for developing peptide ligands. Database URL: The BDB database is available at http://immunet.cn/bdb

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Selection of peptide ligands for the antimucin core antibody C595 using phage display technology: definition of candidate epitopes for a cancer vaccine

Molecular Pathology ◽

10.1136/mp.48.3.m136 ◽

1995 ◽

Vol 48 (3) ◽

pp. M136-M141 ◽

Cited By ~ 5

Author(s):

P Laing ◽

P Tighe ◽

E Kwiatkowski ◽

J Milligan ◽

M Price ◽

...

Keyword(s):

Phage Display ◽

Cancer Vaccine ◽

Peptide Ligands ◽

Phage Display Technology ◽

Display Technology ◽

Definition Of ◽

Selection Of

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Application of Next Generation Phage Display technology to study cross reactivity in closely-related Flavivirus species

Access Microbiology ◽

10.1099/acmi.ac2019.po0526 ◽

2019 ◽

Vol 1 (1A) ◽

Author(s):

Anitha Varghese ◽

Janet Daly ◽

Kevin Gough ◽

Mara Rocchi

Keyword(s):

Phage Display ◽

Cross Reactivity ◽

Next Generation ◽

Phage Display Technology ◽

Display Technology

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Selection of specific peptides recognised by polyclonal antibody from Salmonella enteritidis infected chicken using next generation phage display technology

Access Microbiology ◽

10.1099/acmi.ac2019.po0104 ◽

2019 ◽

Vol 1 (1A) ◽

Author(s):

Ibrahim Naqid ◽

Ben Maddison ◽

Jonathan Owen ◽

Kevin Gough

Keyword(s):

Phage Display ◽

Polyclonal Antibody ◽

Salmonella Enteritidis ◽

Next Generation ◽

Infected Chicken ◽

Phage Display Technology ◽

Display Technology ◽

Selection Of

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Faculty Opinions recommendation of Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.12538961.13766060 ◽

2011 ◽

Author(s):

Martin Maiden

Keyword(s):

Escherichia Coli ◽

Next Generation Sequencing ◽

Enterohemorrhagic Escherichia Coli ◽

Next Generation ◽

Sequencing Technology ◽

Next Generation Sequencing Technology ◽

Generation Sequencing Technology ◽

Genomic Characterization ◽

Generation Sequencing

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Identification of Small Molecule Binding Sites within Proteins Using Phage Display Technology

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207013330779 ◽

2001 ◽

Vol 4 (7) ◽

pp. 553-572 ◽

Cited By ~ 32

Author(s):

D. Rodi ◽

G. Agoston ◽

R. Manon ◽

R. Lapcevich ◽

S. Green ◽

...

Keyword(s):

Phage Display ◽

Small Molecule ◽

Binding Sites ◽

Phage Display Technology ◽

Display Technology

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A Novel Method for Microsatellite Instability Detection by Liquid Biopsy Based on Next- Generation Sequencing

Current Bioinformatics ◽

10.2174/1574893615666200324133451 ◽

2020 ◽

Vol 15 ◽

Author(s):

Zheng Jiang ◽

Hui Liu ◽

Siwen Zhang ◽

Jia Liu ◽

Weitao Wang ◽

...

Keyword(s):

Next Generation Sequencing ◽

Microsatellite Instability ◽

Liquid Biopsy ◽

Tumor Tissue ◽

High Sensitivity ◽

Next Generation ◽

Tissue Samples ◽

Next Generation Sequencing Technology ◽

Medication Selection ◽

Generation Sequencing

Background: Microsatellite instability (MSI) is a prognostic biomarker used to guide medication selection in multiple cancers, such as colorectal cancer. Traditional PCR with capillary electrophoresis and next-generation sequencing using paired tumor tissue and leukocyte samples are the main approaches for MSI detection due to their high sensitivity and specificity. Currently, patient tissue samples are obtained through puncture or surgery, which causes injury and risk of concurrent disease, further illustrating the need for MSI detection by liquid biopsy. Methods: We propose an analytic method using paired plasma/leukocyte samples and MSI detection using next-generation sequencing technology. Based on the theoretical progress of oncogenesis, we hypothesized that the microsatellite site length in plasma equals the combination of the distribution of tumor tissue and leukocytes. Thus, we defined a window-judgement method to identify whether biomarkers were stable. Results: Compared to traditional PCR as the standard, we evaluated three methods in 20 samples (MSI-H:3/MSS:17): peak shifting method using tissue vs. leukocytes, peak shifting method using plasma vs. leukocytes, and our method using plasma vs. leukocytes. Compared to traditional PCR, we observed a sensitivity of 100%, 0%, and 100%, and a specificity of 100.00%, 94.12%, and 88.24%, respectively. Conclusion: Our method has the advantage of possibly detecting MSI in a liquid biopsy and provides a novel direction for future studies to increase the specificity of the method.

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Uniqueness of RNA Coliphage Qβ Display System in Directed Evolutionary Biotechnology

Viruses ◽

10.3390/v13040568 ◽

2021 ◽

Vol 13 (4) ◽

pp. 568

Author(s):

Godwin W. Nchinda ◽

Nadia Al-Atoom ◽

Mamie T. Coats ◽

Jacqueline M. Cameron ◽

Alain Bopda Waffo

Keyword(s):

Life Cycle ◽

Coat Protein ◽

Phage Display ◽

Display System ◽

Phage Display Technology ◽

Library Size ◽

Exterior Surface ◽

Major Coat Protein ◽

Display Technology ◽

Minor Coat Protein

Phage display technology involves the surface genetic engineering of phages to expose desirable proteins or peptides whose gene sequences are packaged within phage genomes, thereby rendering direct linkage between genotype with phenotype feasible. This has resulted in phage display systems becoming invaluable components of directed evolutionary biotechnology. The M13 is a DNA phage display system which dominates this technology and usually involves selected proteins or peptides being displayed through surface engineering of its minor coat proteins. The displayed protein or peptide’s functionality is often highly reduced due to harsh treatment of M13 variants. Recently, we developed a novel phage display system using the coliphage Qβ as a nano-biotechnology platform. The coliphage Qβ is an RNA phage belonging to the family of Leviviridae, a long investigated virus. Qβ phages exist as a quasispecies and possess features making them comparatively more suitable and unique for directed evolutionary biotechnology. As a quasispecies, Qβ benefits from the promiscuity of its RNA dependent RNA polymerase replicase, which lacks proofreading activity, and thereby permits rapid variant generation, mutation, and adaptation. The minor coat protein of Qβ is the readthrough protein, A1. It shares the same initiation codon with the major coat protein and is produced each time the ribosome translates the UGA stop codon of the major coat protein with the of misincorporation of tryptophan. This misincorporation occurs at a low level (1/15). Per convention and definition, A1 is the target for display technology, as this minor coat protein does not play a role in initiating the life cycle of Qβ phage like the pIII of M13. The maturation protein A2 of Qβ initiates the life cycle by binding to the pilus of the F+ host bacteria. The extension of the A1 protein with a foreign peptide probe recognizes and binds to the target freely, while the A2 initiates the infection. This avoids any disturbance of the complex and the necessity for acidic elution and neutralization prior to infection. The combined use of both the A1 and A2 proteins of Qβ in this display system allows for novel bio-panning, in vitro maturation, and evolution. Additionally, methods for large library size construction have been improved with our directed evolutionary phage display system. This novel phage display technology allows 12 copies of a specific desired peptide to be displayed on the exterior surface of Qβ in uniform distribution at the corners of the phage icosahedron. Through the recently optimized subtractive bio-panning strategy, fusion probes containing up to 80 amino acids altogether with linkers, can be displayed for target selection. Thus, combined uniqueness of its genome, structure, and proteins make the Qβ phage a desirable suitable innovation applicable in affinity maturation and directed evolutionary biotechnology. The evolutionary adaptability of the Qβ phage display strategy is still in its infancy. However, it has the potential to evolve functional domains of the desirable proteins, glycoproteins, and lipoproteins, rendering them superior to their natural counterparts.

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