51
|
Silva VL, Ferreira D, Nobrega FL, Martins IM, Kluskens LD, Rodrigues LR. Selection of Novel Peptides Homing the 4T1 CELL Line: Exploring Alternative Targets for Triple Negative Breast Cancer. PLoS One 2016; 11:e0161290. [PMID: 27548261 PMCID: PMC4993384 DOI: 10.1371/journal.pone.0161290] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/27/2016] [Indexed: 11/30/2022] Open
Abstract
The use of bacteriophages to select novel ligands has been widely explored for cancer therapy. Their application is most warranted in cancer subtypes lacking knowledge on how to target the cancer cells in question, such as the triple negative breast cancer, eventually leading to the development of alternative nanomedicines for cancer therapeutics. Therefore, the following study aimed to select and characterize novel peptides for a triple negative breast cancer murine mammary carcinoma cell line– 4T1. Using phage display, 7 and 12 amino acid random peptide libraries were screened against the 4T1 cell line. A total of four rounds, plus a counter-selection round using the 3T3 murine fibroblast cell line, was performed. The enriched selective peptides were characterized and their binding capacity towards 4T1 tissue samples was confirmed by immunofluorescence and flow cytometry analysis. The selected peptides (4T1pep1 –CPTASNTSC and 4T1pep2—EVQSSKFPAHVS) were enriched over few rounds of selection and exhibited specific binding to the 4T1 cell line. Interestingly, affinity to the human MDA-MB-231 cell line was also observed for both peptides, promoting the translational application of these novel ligands between species. Additionally, bioinformatics analysis suggested that both peptides target human Mucin-16. This protein has been implicated in different types of cancer, as it is involved in many important cellular functions. This study strongly supports the need of finding alternative targeting systems for TNBC and the peptides herein selected exhibit promising future application as novel homing peptides for breast cancer therapy.
Collapse
Affiliation(s)
- Vera L. Silva
- CEB—Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - Debora Ferreira
- CEB—Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - Franklin L. Nobrega
- CEB—Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - Ivone M. Martins
- CEB—Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - Leon D. Kluskens
- CEB—Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - Ligia R. Rodrigues
- CEB—Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal
- * E-mail:
| |
Collapse
|
52
|
He B, Kang J, Ru B, Ding H, Zhou P, Huang J. SABinder: A Web Service for Predicting Streptavidin-Binding Peptides. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9175143. [PMID: 27610387 PMCID: PMC5005764 DOI: 10.1155/2016/9175143] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/27/2016] [Indexed: 11/17/2022]
Abstract
Streptavidin is sometimes used as the intended target to screen phage-displayed combinatorial peptide libraries for streptavidin-binding peptides (SBPs). More often in the biopanning system, however, streptavidin is just a commonly used anchoring molecule that can efficiently capture the biotinylated target. In this case, SBPs creeping into the biopanning results are not desired binders but target-unrelated peptides (TUP). Taking them as intended binders may mislead subsequent studies. Therefore, it is important to find if a peptide is likely to be an SBP when streptavidin is either the intended target or just the anchoring molecule. In this paper, we describe an SVM-based ensemble predictor called SABinder. It is the first predictor for SBP. The model was built with the feature of optimized dipeptide composition. It was observed that 89.20% (MCC = 0.78; AUC = 0.93; permutation test, p < 0.001) of peptides were correctly classified. As a web server, SABinder is freely accessible. The tool provides a highly efficient way to exclude potential SBP when they are TUP or to facilitate identification of possibly new SBP when they are the desired binders. In either case, it will be helpful and can benefit related scientific community.
Collapse
Affiliation(s)
- Bifang He
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Juanjuan Kang
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Beibei Ru
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Ding
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Peng Zhou
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jian Huang
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| |
Collapse
|
53
|
Warren JG, Kasun GW, Leonard T, Kirkpatrick BC. A phage display-selected peptide inhibitor of Agrobacterium vitis polygalacturonase. MOLECULAR PLANT PATHOLOGY 2016; 17:480-6. [PMID: 26177065 PMCID: PMC6638516 DOI: 10.1111/mpp.12293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Agrobacterium vitis, the causal agent of crown gall of grapevine, is a threat to viticulture worldwide. A major virulence factor of this pathogen is polygalacturonase, an enzyme that degrades pectin components of the xylem cell wall. A single gene encodes for the polygalacturonase gene. Disruption of the polygalacturonase gene results in a mutant that is less pathogenic and produces significantly fewer root lesions on grapevines. Thus, the identification of peptides or proteins that could inhibit the activity of polygalacturonase could be part of a strategy for the protection of plants against this pathogen. A phage-displayed combinatorial peptide library was used to isolate peptides with a high binding affinity to A. vitis polygalacturonase. These peptides showed sequence similarity to regions of Oryza sativa (EMS66324, Japonica) and Triticum urartu (NP_001054402, wild wheat) polygalacturonase-inhibiting proteins (PGIPs). Furthermore, these panning experiments identified a peptide, SVTIHHLGGGS, which was able to reduce A. vitis polygalacturonase activity by 35% in vitro. Truncation studies showed that the IHHL motif alone is sufficient to inhibit A. vitis polygalacturonase activity.
Collapse
Affiliation(s)
- Jeremy G Warren
- Department of Plant Pathology, University of California, Davis, 95616, CA, USA
| | - George W Kasun
- Department of Plant Pathology, University of California, Davis, 95616, CA, USA
| | - Takara Leonard
- Department of Plant Pathology, University of California, Davis, 95616, CA, USA
| | - Bruce C Kirkpatrick
- Department of Plant Pathology, University of California, Davis, 95616, CA, USA
| |
Collapse
|
54
|
Pakulska MM, Miersch S, Shoichet MS. Designer protein delivery: From natural to engineered affinity-controlled release systems. Science 2016; 351:aac4750. [PMID: 26989257 DOI: 10.1126/science.aac4750] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Exploiting binding affinities between molecules is an established practice in many fields, including biochemical separations, diagnostics, and drug development; however, using these affinities to control biomolecule release is a more recent strategy. Affinity-controlled release takes advantage of the reversible nature of noncovalent interactions between a therapeutic protein and a binding partner to slow the diffusive release of the protein from a vehicle. This process, in contrast to degradation-controlled sustained-release formulations such as poly(lactic-co-glycolic acid) microspheres, is controlled through the strength of the binding interaction, the binding kinetics, and the concentration of binding partners. In the context of affinity-controlled release--and specifically the discovery or design of binding partners--we review advances in in vitro selection and directed evolution of proteins, peptides, and oligonucleotides (aptamers), aided by computational design.
Collapse
Affiliation(s)
- Malgosia M Pakulska
- Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shane Miersch
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Molly S Shoichet
- Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
55
|
Discovery of a Biological Mechanism of Active Transport through the Tympanic Membrane to the Middle Ear. Sci Rep 2016; 6:22663. [PMID: 26946957 PMCID: PMC4780071 DOI: 10.1038/srep22663] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/11/2016] [Indexed: 12/12/2022] Open
Abstract
Otitis media (OM) is a common pediatric disease for which systemic antibiotics are often prescribed. While local treatment would avoid the systemic treatment side-effects, the tympanic membrane (TM) represents an impenetrable barrier unless surgically breached. We hypothesized that the TM might harbor innate biological mechanisms that could mediate trans-TM transport. We used two M13-bacteriophage display biopanning strategies to search for mediators of trans-TM transport. First, aliquots of linear phage library displaying 1010th 12mer peptides were applied on the TM of rats with active bacterial OM. The middle ear (ME) contents were then harvested, amplified and the preparation re-applied for additional rounds. Second, the same naïve library was sequentially screened for phage exhibiting TM binding, internalization and then transit. Results revealed a novel set of peptides that transit across the TM to the ME in a time and temperature dependent manner. The peptides with highest transport capacities shared sequence similarities. Historically, the TM was viewed as an impermeable barrier. However, our studies reveal that it is possible to translocate peptide-linked small particles across the TM. This is the first comprehensive biopanning for the isolation of TM transiting peptidic ligands. The identified mechanism offers a new drug delivery platform into the ME.
Collapse
|
56
|
Gross AL, Gillespie JW, Petrenko VA. Promiscuous tumor targeting phage proteins. Protein Eng Des Sel 2016; 29:93-103. [PMID: 26764410 PMCID: PMC4753993 DOI: 10.1093/protein/gzv064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 12/21/2022] Open
Abstract
Cancer cell-specific targeting ligands against numerous cancer cell lines have been selected previously and used as ligands for cell-specific delivery of chemotherapies and various nanomedicines. However, tumor heterogeneity is one recognized problem hampering clinical translation of targeted anti-cancer medicines. Therefore, a novel class of targeting ligands is required that recognize receptors expressed between a variety of cancer phenotypes, identified here as 'promiscuous' ligands. In this work, promiscuous phage fusion proteins were first identified by a novel selection scheme to enrich for pan-cancer cell binding abilities, as indicated by conserved structural motifs identified previously in other cancer types. Additionally, peptide sequences containing a combination of motifs were identified to modulate binding. A panel of phage fusion proteins was studied for their specificity and selectivity for lung and pancreatic cancer cells. Phage displaying the fusion peptides GSLEEVSTL or GEFDELMTM, the two predominate clones with greatest binding ability, were used to modify preformed, doxorubicin-loaded, liposomes. These modified liposomes increased cytotoxicity up to 8.1-fold in several cancer cell lines when compared with unmodified liposomal doxorubicin. Taken together, these data indicate that promiscuous phage proteins, selected against different cancer cell lines, can be used as targeting ligands for treatment of heterogeneous tumor populations.
Collapse
Affiliation(s)
- Amanda L Gross
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
| | - James W Gillespie
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
| | - Valery A Petrenko
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
| |
Collapse
|
57
|
Tjhung KF, Kitov PI, Ng S, Kitova EN, Deng L, Klassen JS, Derda R. Silent Encoding of Chemical Post-Translational Modifications in Phage-Displayed Libraries. J Am Chem Soc 2016; 138:32-5. [PMID: 26683999 DOI: 10.1021/jacs.5b10390] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In vitro selection of chemically modified peptide libraries presented on phage, while a powerful technology, is limited to one chemical post-translational modification (cPTM) per library. We use unique combinations of redundant codons to encode cPTMs with "silent barcodes" to trace multiple modifications within a mixed modified library. As a proof of concept, we produced phage-displayed peptide libraries Ser-[X]4-Gly-Gly-Gly, with Gly and Ser encoded using unique combinations of codons (TCA-[X]4-GGAGGAGGA, AGT-[X]4-GGTGGTGGT, etc., where [X]4 denotes a random NNK library). After separate chemical modification and pooling, mixed-modified libraries can be panned and deep-sequenced to identify the enriched peptide sequence and the accompanying cPTM simultaneously. We panned libraries bearing combinations of modifications (sulfonamide, biotin, mannose) against matched targets (carbonic anhydrase, streptavidin, concanavalin A) to identify desired ligands. Synthesis and validation of sequences identified by deep sequencing revealed that specific cPTMs are significantly enriched in panning against the specific targets. Panning on carbonic anhydrase yielded a potent ligand, sulfonamide-WIVP, with Kd = 6.7 ± 2.1 nM, a 20-fold improvement compared with the control ligand sulfonamide-GGGG. Silent encoding of multiple cPTMs can be readily incorporated into other in vitro display technologies such as bacteriophage T7 or mRNA display.
Collapse
Affiliation(s)
- Katrina F Tjhung
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Pavel I Kitov
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Simon Ng
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Elena N Kitova
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Lu Deng
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - John S Klassen
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Ratmir Derda
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| |
Collapse
|
58
|
Eberhardt M, Lai X, Tomar N, Gupta S, Schmeck B, Steinkasserer A, Schuler G, Vera J. Third-Kind Encounters in Biomedicine: Immunology Meets Mathematics and Informatics to Become Quantitative and Predictive. Methods Mol Biol 2016; 1386:135-179. [PMID: 26677184 DOI: 10.1007/978-1-4939-3283-2_9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The understanding of the immune response is right now at the center of biomedical research. There are growing expectations that immune-based interventions will in the midterm provide new, personalized, and targeted therapeutic options for many severe and highly prevalent diseases, from aggressive cancers to infectious and autoimmune diseases. To this end, immunology should surpass its current descriptive and phenomenological nature, and become quantitative, and thereby predictive.Immunology is an ideal field for deploying the tools, methodologies, and philosophy of systems biology, an approach that combines quantitative experimental data, computational biology, and mathematical modeling. This is because, from an organism-wide perspective, the immunity is a biological system of systems, a paradigmatic instance of a multi-scale system. At the molecular scale, the critical phenotypic responses of immune cells are governed by large biochemical networks, enriched in nested regulatory motifs such as feedback and feedforward loops. This network complexity confers them the ability of highly nonlinear behavior, including remarkable examples of homeostasis, ultra-sensitivity, hysteresis, and bistability. Moving from the cellular level, different immune cell populations communicate with each other by direct physical contact or receiving and secreting signaling molecules such as cytokines. Moreover, the interaction of the immune system with its potential targets (e.g., pathogens or tumor cells) is far from simple, as it involves a number of attack and counterattack mechanisms that ultimately constitute a tightly regulated multi-feedback loop system. From a more practical perspective, this leads to the consequence that today's immunologists are facing an ever-increasing challenge of integrating massive quantities from multi-platforms.In this chapter, we support the idea that the analysis of the immune system demands the use of systems-level approaches to ensure the success in the search for more effective and personalized immune-based therapies.
Collapse
Affiliation(s)
- Martin Eberhardt
- Laboratory of Systems Tumor Immunology, Department of Dermatology, University Hospital Erlangen and Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Department of Dermatology, University Hospital Erlangen and Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Xin Lai
- Laboratory of Systems Tumor Immunology, Department of Dermatology, University Hospital Erlangen and Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Department of Dermatology, University Hospital Erlangen and Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Namrata Tomar
- Laboratory of Systems Tumor Immunology, Department of Dermatology, University Hospital Erlangen and Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Department of Dermatology, University Hospital Erlangen and Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Bernd Schmeck
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Marburg, Philipps University, Marburg, Germany
- Systems Biology Platform, Institute for Lung Research/iLung, German Center for Lung Research, Universities of Giessen and Marburg Lung Centre, Philipps University Marburg, Marburg, Germany
| | - Alexander Steinkasserer
- Department of Immune Modulation at the Department of Dermatology, University Hospital Erlangen, Erlangen, Germany
| | - Gerold Schuler
- Department of Dermatology, University Hospital Erlangen and Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Julio Vera
- Laboratory of Systems Tumor Immunology, Department of Dermatology, University Hospital Erlangen and Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
- Department of Dermatology, University Hospital Erlangen and Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
| |
Collapse
|
59
|
Gillespie JW, Wei L, Petrenko VA. Selection of Lung Cancer-Specific Landscape Phage for Targeted Drug Delivery. Comb Chem High Throughput Screen 2016; 19:412-22. [PMID: 27095536 PMCID: PMC5066567 DOI: 10.2174/1386207319666160420141024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/01/2016] [Accepted: 03/30/2016] [Indexed: 12/24/2022]
Abstract
Cancer cell-specific diagnostic or therapeutic tools are commonly believed to significantly increase the success rate of cancer diagnosis and targeted therapies. To extend the repertoire of available cancer cell-specific phage fusion proteins and study their efficacy as navigating moieties, we used two landscape phage display libraries f8/8 and f8/9 displaying an 8- or 9-mer random peptide fusion to identify a panel of novel peptide families that are specific to Calu-3 cells. Using a phage capture assay, we showed that two of the selected phage clones, ANGRPSMT and VNGRAEAP (phage and their recombinant proteins are named by the sequence of the fusion peptide), are selective for the Calu-3 cell line in comparison to phenotypically normal lung epithelial cells and distribute into unique subcellular fractions.
Collapse
Affiliation(s)
| | | | - Valery A Petrenko
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA.
| |
Collapse
|
60
|
Wong TM, Ross TM. Use of computational and recombinant technologies for developing novel influenza vaccines. Expert Rev Vaccines 2015; 15:41-51. [PMID: 26595182 DOI: 10.1586/14760584.2016.1113877] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Influenza vaccine design has changed considerably with advancements in bioinformatics and computational biology. Improved surveillance efforts provide up-to-date information about influenza sequence diversity and assist with monitoring the spread of epidemics and vaccine efficacy rates. The advent of next-generation sequencing, epitope scanning and high-throughput analysis all help decipher influenza-associated protein interactions as well as predict immune responsiveness based on host genetic diversity. Computational approaches are utilized in nearly all aspects of vaccine design, from modeling, compatibility predictions, and optimization of antigens in various platforms. This overview discusses how computational techniques strengthen vaccine efforts against highly diverse influenza species.
Collapse
Affiliation(s)
- Terianne M Wong
- a Center for Vaccines and Immunology, Department of Infectious Diseases , University of Georgia , Athens , GA , USA
| | - Ted M Ross
- a Center for Vaccines and Immunology, Department of Infectious Diseases , University of Georgia , Athens , GA , USA
| |
Collapse
|
61
|
Azevedo HS, Pashkuleva I. Biomimetic supramolecular designs for the controlled release of growth factors in bone regeneration. Adv Drug Deliv Rev 2015; 94:63-76. [PMID: 26325686 DOI: 10.1016/j.addr.2015.08.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 08/17/2015] [Accepted: 08/25/2015] [Indexed: 12/13/2022]
Abstract
The extracellular matrix (ECM) of tissues is an assembly of insoluble macromolecules that specifically interact with soluble bioactive molecules and regulate their distribution and availability to cells. Recapitulating this ability has been an important target in controlled growth factor delivery strategies for tissue regeneration and requires the design of multifunctional carriers. This review describes the integration of supramolecular interactions on the design of delivery strategies that encompass self-assembling and engineered affinity components to construct advanced biomimetic carriers for growth factor delivery. Several glycan- and peptide-based self-assemblies reported in the literature are highlighted and commented upon. These examples demonstrate how molecular design and chemistry are successfully employed to create versatile multifunctional molecules which self-assemble/disassemble in a precisely predicted manner, thus controlling compartmentalization, transport and delivery. Finally, we discuss whether recent advances in the design and preparation of supramolecular delivery systems have been sufficient to drive real translation towards a clinical impact.
Collapse
Affiliation(s)
- Helena S Azevedo
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Institute of Bioengineering, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
| | - Iva Pashkuleva
- 3B's Research Group - Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco Guimarães, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
| |
Collapse
|
62
|
He B, Chai G, Duan Y, Yan Z, Qiu L, Zhang H, Liu Z, He Q, Han K, Ru B, Guo FB, Ding H, Lin H, Wang X, Rao N, Zhou P, Huang J. BDB: biopanning data bank. Nucleic Acids Res 2015; 44:D1127-32. [PMID: 26503249 PMCID: PMC4702802 DOI: 10.1093/nar/gkv1100] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/10/2015] [Indexed: 12/19/2022] Open
Abstract
The BDB database (http://immunet.cn/bdb) is an update of the MimoDB database, which was previously described in the 2012 Nucleic Acids Research Database issue. The rebranded name BDB is short for Biopanning Data Bank, which aims to be a portal for biopanning results of the combinatorial peptide library. Last updated in July 2015, BDB contains 2904 sets of biopanning data collected from 1322 peer-reviewed papers. It contains 25,786 peptide sequences, 1704 targets, 492 known templates, 447 peptide libraries and 310 crystal structures of target-template or target-peptide complexes. All data stored in BDB were revisited, and information on peptide affinity, measurement method and procedures was added for 2298 peptides from 411 sets of biopanning data from 246 published papers. In addition, a more professional and user-friendly web interface was implemented, a more detailed help system was designed, and a new on-the-fly data visualization tool and a series of tools for data analysis were integrated. With these new data and tools made available, we expect that the BDB database would become a major resource for scholars using phage display, with improved utility for biopanning and related scientific communities.
Collapse
Affiliation(s)
- Bifang He
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Guoshi Chai
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yaocong Duan
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zhiqiang Yan
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Liuyang Qiu
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Huixiong Zhang
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zechun Liu
- School of Computer Science & Engineering, University of Electronic Science and Technology of China, No.2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu, Sichuan 611731, China
| | - Qiang He
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Ke Han
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Beibei Ru
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Feng-Biao Guo
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Ding
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lin
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Xianlong Wang
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Nini Rao
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Peng Zhou
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jian Huang
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| |
Collapse
|
63
|
Leung NY, Wai CY, Ho MH, Liu R, Lam KS, Wang JJ, Shu SA, Chu KH, Leung PS. Screening and identification of mimotopes of the major shrimp allergen tropomyosin using one-bead-one-compound peptide libraries. Cell Mol Immunol 2015; 14:308-318. [PMID: 26364917 DOI: 10.1038/cmi.2015.83] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/06/2015] [Accepted: 08/06/2015] [Indexed: 12/18/2022] Open
Abstract
The one-bead-one-compound (OBOC) combinatorial peptide library is a powerful tool to identify ligand and receptor interactions. Here, we applied the OBOC library technology to identify mimotopes specific to the immunoglobulin E (IgE) epitopes of the major shellfish allergen tropomyosin. OBOC peptide libraries with 8-12 amino acid residues were screened with serum samples from patients with shellfish allergy for IgE mimotopes of tropomyosin. Twenty-five mimotopes were identified from the screening and their binding reactivity to tropomyosin-specific IgE was confirmed by peptide ELISA. These mimotopes could be divided into seven clusters based on sequence homology, and epitope mapping by EpiSearch of the clustered mimotopes was performed to characterize and confirm the validity of mimotopes. Five out of six of the predicted epitopes were found to overlap with previously identified epitopes of tropomyosin. To further confirm the mimicry potential of mimotopes, BALB/c mice were immunized with mimotopes conjugated to keyhole limpet hemocyanin and assayed for their capacity to induce tropomyosin-specific antibodies. BALB/c mice that received mimotope immunization were found to have an elevated level of tropomyosin-specific immunoglobulin G, but not mice that received an irrelevant mimotope. This study pioneers the successful application of the OBOC libraries using whole sera to screen and identify multiple shrimp allergen mimotopes and validates their mimicry potential using in vitro, in vivo, and in silico methods.Cellular & Molecular Immunology advance online publication, 14 september 2015; doi:10.1038/cmi.2015.83.
Collapse
Affiliation(s)
- Nicki Yh Leung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Christine Yy Wai
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Marco Hk Ho
- Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Jin Jun Wang
- Division of Rheumatology/Allergy, School of Medicine, University of California, Davis, CA 95616, USA
| | - Shang An Shu
- Division of Rheumatology/Allergy, School of Medicine, University of California, Davis, CA 95616, USA
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Patrick Sc Leung
- Division of Rheumatology/Allergy, School of Medicine, University of California, Davis, CA 95616, USA
| |
Collapse
|
64
|
Christiansen A, Kringelum JV, Hansen CS, Bøgh KL, Sullivan E, Patel J, Rigby NM, Eiwegger T, Szépfalusi Z, de Masi F, Nielsen M, Lund O, Dufva M. High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum. Sci Rep 2015; 5:12913. [PMID: 26246327 PMCID: PMC4650709 DOI: 10.1038/srep12913] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022] Open
Abstract
Phage display is a prominent screening technique with a multitude of applications including therapeutic antibody development and mapping of antigen epitopes. In this study, phages were selected based on their interaction with patient serum and exhaustively characterised by high-throughput sequencing. A bioinformatics approach was developed in order to identify peptide motifs of interest based on clustering and contrasting to control samples. Comparison of patient and control samples confirmed a major issue in phage display, namely the selection of unspecific peptides. The potential of the bioinformatic approach was demonstrated by identifying epitopes of a prominent peanut allergen, Ara h 1, in sera from patients with severe peanut allergy. The identified epitopes were confirmed by high-density peptide micro-arrays. The present study demonstrates that high-throughput sequencing can empower phage display by (i) enabling the analysis of complex biological samples, (ii) circumventing the traditional laborious picking and functional testing of individual phage clones and (iii) reducing the number of selection rounds.
Collapse
Affiliation(s)
- Anders Christiansen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jens V Kringelum
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christian S Hansen
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Katrine L Bøgh
- National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Eric Sullivan
- Roche NimbleGen, Madison, Wisconsin, the United States of America
| | - Jigar Patel
- Roche NimbleGen, Madison, Wisconsin, the United States of America
| | - Neil M Rigby
- Institute of Food Research, Norwich, United Kingdom
| | - Thomas Eiwegger
- Department of Paediatrics, Medical University of Vienna, Vienna, Austria
| | - Zsolt Szépfalusi
- Department of Paediatrics, Medical University of Vienna, Vienna, Austria
| | - Federico de Masi
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Morten Nielsen
- 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark [2] Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Ole Lund
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Martin Dufva
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|
65
|
Liu GW, Livesay BR, Kacherovsky NA, Cieslewicz M, Lutz E, Waalkes A, Jensen MC, Salipante SJ, Pun SH. Efficient Identification of Murine M2 Macrophage Peptide Targeting Ligands by Phage Display and Next-Generation Sequencing. Bioconjug Chem 2015; 26:1811-7. [PMID: 26161996 DOI: 10.1021/acs.bioconjchem.5b00344] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide ligands are used to increase the specificity of drug carriers to their target cells and to facilitate intracellular delivery. One method to identify such peptide ligands, phage display, enables high-throughput screening of peptide libraries for ligands binding to therapeutic targets of interest. However, conventional methods for identifying target binders in a library by Sanger sequencing are low-throughput, labor-intensive, and provide a limited perspective (<0.01%) of the complete sequence space. Moreover, the small sample space can be dominated by nonspecific, preferentially amplifying "parasitic sequences" and plastic-binding sequences, which may lead to the identification of false positives or exclude the identification of target-binding sequences. To overcome these challenges, we employed next-generation Illumina sequencing to couple high-throughput screening and high-throughput sequencing, enabling more comprehensive access to the phage display library sequence space. In this work, we define the hallmarks of binding sequences in next-generation sequencing data, and develop a method that identifies several target-binding phage clones for murine, alternatively activated M2 macrophages with a high (100%) success rate: sequences and binding motifs were reproducibly present across biological replicates; binding motifs were identified across multiple unique sequences; and an unselected, amplified library accurately filtered out parasitic sequences. In addition, we validate the Multiple Em for Motif Elicitation tool as an efficient and principled means of discovering binding sequences.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Michael C Jensen
- §Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington 98145, United States
| | | | | |
Collapse
|
66
|
Gupta SK, Jaitly T, Schmitz U, Schuler G, Wolkenhauer O, Vera J. Personalized cancer immunotherapy using Systems Medicine approaches. Brief Bioinform 2015; 17:453-67. [DOI: 10.1093/bib/bbv046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Indexed: 12/27/2022] Open
|
67
|
Roskar I, Molek P, Vodnik M, Stempelj M, Strukelj B, Lunder M. Peptide modulators of alpha-glucosidase. J Diabetes Investig 2015; 6:625-31. [PMID: 26543535 PMCID: PMC4627538 DOI: 10.1111/jdi.12358] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 03/26/2015] [Accepted: 04/27/2015] [Indexed: 01/23/2023] Open
Abstract
AIMS/INTRODUCTION Acute glucose fluctuations during the postprandial period pose great risk for cardiovascular complications and thus represent an important therapeutic approach in type 2 diabetes. In the present study, screening of peptide libraries was used to select peptides with an affinity towards mammalian intestinal alpha-glucosidase as potential leads in antidiabetic agent development. MATERIALS AND METHODS Three phage-displayed peptide libraries were used in independent selections with different elution strategies to isolate target-binding peptides. Selected peptides displayed on phage were tested to compete for an enzyme-binding site with known competitive inhibitors, acarbose and voglibose. The four best performing peptides were synthesized. Their binding to the mammalian alpha-glucosidase and their effect on enzyme activity were evaluated. RESULTS Two linear and two cyclic heptapeptides with high affinity towards intestinal alpha-glucosidase were selected. Phage-displayed as well as synthetic peptides bind into or to the vicinity of the active site on the enzyme. Both cyclic peptides inhibited enzyme activity, whereas both linear peptides increased enzyme activity. CONCLUSIONS Although natural substrates of glycosidase are polysaccharides, in the present study we successfully isolated novel peptide modulators of alpha-glucosidase. Modulatory activity of selected peptides could be further optimized through peptidomimetic design. They represent promising leads for development of efficient alpha-glucosidase inhibitors.
Collapse
Affiliation(s)
- Irena Roskar
- Entrapharm d.o.o., University of Ljubljana Ljubljana, Slovenia
| | - Peter Molek
- Chair of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana Ljubljana, Slovenia
| | - Miha Vodnik
- Chair of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana Ljubljana, Slovenia
| | - Mateja Stempelj
- Entrapharm d.o.o., University of Ljubljana Ljubljana, Slovenia
| | - Borut Strukelj
- Chair of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana Ljubljana, Slovenia
| | - Mojca Lunder
- Chair of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana Ljubljana, Slovenia
| |
Collapse
|
68
|
Tjhung KF, Deiss F, Tran J, Chou Y, Derda R. Intra-domain phage display (ID-PhD) of peptides and protein mini-domains censored from canonical pIII phage display. Front Microbiol 2015; 6:340. [PMID: 25972845 PMCID: PMC4412080 DOI: 10.3389/fmicb.2015.00340] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/06/2015] [Indexed: 12/01/2022] Open
Abstract
In this paper, we describe multivalent display of peptide and protein sequences typically censored from traditional N-terminal display on protein pIII of filamentous bacteriophage M13. Using site-directed mutagenesis of commercially available M13KE phage cloning vector, we introduced sites that permit efficient cloning using restriction enzymes between domains N1 and N2 of the pIII protein. As infectivity of phage is directly linked to the integrity of the connection between N1 and N2 domains, intra-domain phage display (ID-PhD) allows for simple quality control of the display and the natural variations in the displayed sequences. Additionally, direct linkage to phage propagation allows efficient monitoring of sequence cleavage, providing a convenient system for selection and evolution of protease-susceptible or protease-resistant sequences. As an example of the benefits of such an ID-PhD system, we displayed a negatively charged FLAG sequence, which is known to be post-translationally excised from pIII when displayed on the N-terminus, as well as positively charged sequences which suppress production of phage when displayed on the N-terminus. ID-PhD of FLAG exhibited sub-nanomolar apparent Kd suggesting multivalent nature of the display. A TEV-protease recognition sequence (TEVrs) co-expressed in tandem with FLAG, allowed us to demonstrate that 99.9997% of the phage displayed the FLAG-TEVrs tandem and can be recognized and cleaved by TEV-protease. The residual 0.0003% consisted of phage clones that have excised the insert from their genome. ID-PhD is also amenable to display of protein mini-domains, such as the 33-residue minimized Z-domain of protein A. We show that it is thus possible to use ID-PhD for multivalent display and selection of mini-domain proteins (Affibodies, scFv, etc.).
Collapse
Affiliation(s)
- Katrina F Tjhung
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta Edmonton, AB, Canada
| | - Frédérique Deiss
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta Edmonton, AB, Canada
| | - Jessica Tran
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta Edmonton, AB, Canada
| | - Ying Chou
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta Edmonton, AB, Canada
| | - Ratmir Derda
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta Edmonton, AB, Canada
| |
Collapse
|
69
|
Solid-binding peptides: smart tools for nanobiotechnology. Trends Biotechnol 2015; 33:259-68. [PMID: 25796487 DOI: 10.1016/j.tibtech.2015.02.005] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/15/2015] [Accepted: 02/23/2015] [Indexed: 12/12/2022]
Abstract
Over the past decade, solid-binding peptides (SBPs) have been used increasingly as molecular building blocks in nanobiotechnology. These peptides show selectivity and bind with high affinity to the surfaces of a diverse range of solid materials including metals, metal oxides, metal compounds, magnetic materials, semiconductors, carbon materials, polymers, and minerals. They can direct the assembly and functionalisation of materials, and have the ability to mediate the synthesis and construction of nanoparticles and complex nanostructures. As the availability of newly synthesised nanomaterials expands rapidly, so too do the potential applications for SBPs.
Collapse
|
70
|
Khemthongcharoen N, Ruangpracha A, Sarapukdee P, Rattanavarin S, Jolivot R, Jarujareet U, Plaimas K, Bhattarakosol P, Patumraj S, Piyawattanametha W. Novel p16 binding peptide development for p16-overexpressing cancer cell detection using phage display. J Pept Sci 2015; 21:265-73. [PMID: 25754556 DOI: 10.1002/psc.2726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 11/24/2014] [Accepted: 11/24/2014] [Indexed: 12/31/2022]
Abstract
Protein p(16INK4a) (p16) is a well-known biomarker for diagnosis of human papillomavirus (HPV) related cancers. In this work, we identify novel p16 binding peptides by using phage display selection method. A random heptamer phage display library was screened on purified recombinant p16 protein-coated plates to elute only the bound phages from p16 surfaces. Binding affinity of the bound phages was compared with each other by enzyme-linked immunosorbent assay (ELISA), fluorescence imaging technique, and bioinformatic computations. Binding specificity and binding selectivity of the best candidate phage-displayed p16 binding peptide were evaluated by peptide blocking experiment in competition with p16 monoclonal antibody and fluorescence imaging technique, respectively. Five candidate phage-displayed peptides were isolated from the phage display selection method. All candidate p16 binding phages show better binding affinity than wild-type phage in ELISA test, but only three of them can discriminate p16-overexpressing cancer cell, CaSki, from normal uterine fibroblast cell, HUF, with relative fluorescence intensities from 2.6 to 4.2-fold greater than those of wild-type phage. Bioinformatic results indicate that peptide 'Ser-His-Ser-Leu-Leu-Ser-Ser' binds to p16 molecule with the best binding score and does not interfere with the common protein functions of p16. Peptide blocking experiment shows that the phage-displayed peptide 'Ser-His-Ser-Leu-Leu-Ser-Ser' can conceal p16 from monoclonal antibody interaction. This phage clone also selectively interacts with the p16 positive cell lines, and thus, it can be applied for p16-overexpressing cell detection.
Collapse
Affiliation(s)
- Numfon Khemthongcharoen
- NECTEC, National Science and Technology Development Agency (NSTDA), Pathumthani, 12120, Thailand; Advanced Imaging Research Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | | | | | | | | | | | | | | | | | | |
Collapse
|
71
|
Peptide based diagnostics: Are random-sequence peptides more useful than tiling proteome sequences? J Immunol Methods 2015; 417:10-21. [DOI: 10.1016/j.jim.2014.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/08/2014] [Accepted: 12/05/2014] [Indexed: 11/19/2022]
|
72
|
Conformational B-cell epitope prediction method based on antigen preprocessing and mimotopes analysis. BIOMED RESEARCH INTERNATIONAL 2015; 2015:257030. [PMID: 25705652 PMCID: PMC4326220 DOI: 10.1155/2015/257030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 11/08/2014] [Accepted: 11/11/2014] [Indexed: 02/02/2023]
Abstract
Identification of epitopes which invokes strong humoral responses is an essential issue in the field of immunology. Various computational methods that have been developed based on the antigen structures and the mimotopes these years narrow the search for experimental validation. These methods can be divided into two categories: antigen structure-based methods and mimotope-based methods. Though new methods of the two kinds have been proposed in these years, they cannot maintain a high degree of satisfaction in various circumstances. In this paper, we proposed a new conformational B-cell epitope prediction method based on antigen preprocessing and mimotopes analysis. The method classifies the antigen surface residues into “epitopes” and “nonepitopes” by six epitope propensity scales, removing the “nonepitopes” and using the preprocessed antigen for epitope prediction based on mimotope sequences. The proposed method gives out the mean F score of 0.42 on the testing dataset. When compared with other publicly available servers by using the testing dataset, the new method yields better performance. The results demonstrate the proposed method is competent for the conformational B-cell epitope prediction.
Collapse
|
73
|
Gabryelczyk B, Szilvay GR, Linder MB. The structural basis for function in diamond-like carbon binding peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8798-8802. [PMID: 25007096 DOI: 10.1021/la502396p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The molecular structural basis for the function of specific peptides that bind to diamond-like carbon (DLC) surfaces was investigated. For this, a competition assay that provided a robust way of comparing relative affinities of peptide variants was set up. Point mutations of specific residues resulted in significant effects, but it was shown that the chemical composition of the peptide was not sufficient to explain peptide affinity. More significantly, rearrangements in the sequence indicated that the binding is a complex recognition event that is dependent on the overall structure of the peptide. The work demonstrates the unique properties of peptides for creating functionality at interfaces via noncovalent binding for potential applications in, for example, nanomaterials, biomedical materials, and sensors.
Collapse
Affiliation(s)
- Bartosz Gabryelczyk
- VTT Technical Research Centre of Finland , P.O. Box 1000, 02044 VTT, Finland
| | | | | |
Collapse
|
74
|
Peptide Vaccine: Progress and Challenges. Vaccines (Basel) 2014; 2:515-36. [PMID: 26344743 PMCID: PMC4494216 DOI: 10.3390/vaccines2030515] [Citation(s) in RCA: 443] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/10/2014] [Accepted: 06/13/2014] [Indexed: 12/17/2022] Open
Abstract
Conventional vaccine strategies have been highly efficacious for several decades in reducing mortality and morbidity due to infectious diseases. The bane of conventional vaccines, such as those that include whole organisms or large proteins, appear to be the inclusion of unnecessary antigenic load that, not only contributes little to the protective immune response, but complicates the situation by inducing allergenic and/or reactogenic responses. Peptide vaccines are an attractive alternative strategy that relies on usage of short peptide fragments to engineer the induction of highly targeted immune responses, consequently avoiding allergenic and/or reactogenic sequences. Conversely, peptide vaccines used in isolation are often weakly immunogenic and require particulate carriers for delivery and adjuvanting. In this article, we discuss the specific advantages and considerations in targeted induction of immune responses by peptide vaccines and progresses in the development of such vaccines against various diseases. Additionally, we also discuss the development of particulate carrier strategies and the inherent challenges with regard to safety when combining such technologies with peptide vaccines.
Collapse
|
75
|
Nguyen KTH, Adamkiewicz MA, Hebert LE, Zygiel EM, Boyle HR, Martone CM, Meléndez-Ríos CB, Noren KA, Noren CJ, Hall MF. Identification and characterization of mutant clones with enhanced propagation rates from phage-displayed peptide libraries. Anal Biochem 2014; 462:35-43. [PMID: 24952360 DOI: 10.1016/j.ab.2014.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 06/04/2014] [Accepted: 06/08/2014] [Indexed: 01/25/2023]
Abstract
A target-unrelated peptide (TUP) can arise in phage display selection experiments as a result of a propagation advantage exhibited by the phage clone displaying the peptide. We previously characterized HAIYPRH, from the M13-based Ph.D.-7 phage display library, as a propagation-related TUP resulting from a G→A mutation in the Shine-Dalgarno sequence of gene II. This mutant was shown to propagate in Escherichia coli at a dramatically faster rate than phage bearing the wild-type Shine-Dalgarno sequence. We now report 27 additional fast-propagating clones displaying 24 different peptides and carrying 14 unique mutations. Most of these mutations are found either in or upstream of the gene II Shine-Dalgarno sequence, but still within the mRNA transcript of gene II. All 27 clones propagate at significantly higher rates than normal library phage, most within experimental error of wild-type M13 propagation, suggesting that mutations arise to compensate for the reduced virulence caused by the insertion of a lacZα cassette proximal to the replication origin of the phage used to construct the library. We also describe an efficient and convenient assay to diagnose propagation-related TUPS among peptide sequences selected by phage display.
Collapse
Affiliation(s)
- Kieu T H Nguyen
- Department of Chemistry, Stonehill College, 320 Washington Street, Easton, MA 02357, USA
| | - Marta A Adamkiewicz
- Department of Chemistry, Stonehill College, 320 Washington Street, Easton, MA 02357, USA
| | - Lauren E Hebert
- Department of Chemistry, Stonehill College, 320 Washington Street, Easton, MA 02357, USA
| | - Emily M Zygiel
- Department of Chemistry, Stonehill College, 320 Washington Street, Easton, MA 02357, USA
| | - Holly R Boyle
- Department of Chemistry, Stonehill College, 320 Washington Street, Easton, MA 02357, USA
| | - Christina M Martone
- Department of Chemistry, Stonehill College, 320 Washington Street, Easton, MA 02357, USA
| | - Carola B Meléndez-Ríos
- Department of Chemistry, Stonehill College, 320 Washington Street, Easton, MA 02357, USA
| | - Karen A Noren
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | | | | |
Collapse
|
76
|
Nirantar SR, Li X, Siau JW, Ghadessy FJ. Rapid screening of protein–protein interaction inhibitors using the protease exclusion assay. Biosens Bioelectron 2014; 56:250-7. [DOI: 10.1016/j.bios.2013.12.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/13/2013] [Accepted: 12/26/2013] [Indexed: 10/25/2022]
|
77
|
Ru B, 't Hoen PAC, Nie F, Lin H, Guo FB, Huang J. PhD7Faster: predicting clones propagating faster from the Ph.D.-7 phage display peptide library. J Bioinform Comput Biol 2014; 12:1450005. [PMID: 24467763 DOI: 10.1142/s021972001450005x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phage display can rapidly discover peptides binding to any given target; thus, it has been widely used in basic and applied research. Each round of panning consists of two basic processes: Selection and amplification. However, recent studies have showed that the amplification step would decrease the diversity of phage display libraries due to different propagation capacity of phage clones. This may induce phages with growth advantage rather than specific affinity to appear in the final experimental results. The peptides displayed by such phages are termed as propagation-related target-unrelated peptides (PrTUPs). They would mislead further analysis and research if not removed. In this paper, we describe PhD7Faster, an ensemble predictor based on support vector machine (SVM) for predicting clones with growth advantage from the Ph.D.-7 phage display peptide library. By using reduced dipeptide composition (ReDPC) as features, an accuracy (Acc) of 79.67% and a Matthews correlation coefficient (MCC) of 0.595 were achieved in 5-fold cross-validation. In addition, the SVM-based model was demonstrated to perform better than several representative machine learning algorithms. We anticipate that PhD7Faster can assist biologists to exclude potential PrTUPs and accelerate the finding of specific binders from the popular Ph.D.-7 library. The web server of PhD7Faster can be freely accessed at http://immunet.cn/sarotup/cgi-bin/PhD7Faster.pl.
Collapse
Affiliation(s)
- Beibei Ru
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China
| | | | | | | | | | | |
Collapse
|
78
|
Abstract
Identification and characterization of B-cell epitopes in target antigens is one of the key steps in epitope-driven vaccine design, immunodiagnostic tests, and antibody production. For localizing epitopes by experimental methods is time consuming and cost expensive, researchers have been developing in silico or computational models for the prediction of B-cell epitopes, enabling immunologists and clinicians to identify the most promising epitopes for characterization in the laboratory. A sufficient number of available B-cell epitopes are indispensable for establishing the prediction models. To our knowledge, some popular databases associated with the B-cell epitopes are proposed and widely used in the immunoinformatics. In this chapter, we present an overview of the important databases and introduce how to compile datasets for the development of B-cell epitope prediction tools.
Collapse
Affiliation(s)
- Juan Liu
- School of Computer, Wuhan University, No. 37, Luoyu Road, Wuchang, Wuhan, 430072, China,
| | | |
Collapse
|
79
|
Abstract
Mimotopes are peptides mimicking epitopes on the corresponding antigen. They can be obtained via panning the phage-displayed random peptide library against the corresponding monoclonal antibody or specific sera. Besides mimotopes however, the experimental results also include all kinds of unwanted sequences called "target-unrelated peptides," which often interfere with the subsequent experimental and computational analyses. Nevertheless, the prediction of B-cell epitopes based on the experimental result of phage display has shown to be a promising and reliable strategy with acceptable precision. In this chapter, we summarize mimotope-based prediction of B-cell epitopes under three conditions and focus on protocols and tips for retrieving, cleaning, and decoding the data from phage display technology.
Collapse
Affiliation(s)
- Jian Huang
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Room 341, Yifu Building, Shahe Campus, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, China,
| | | | | |
Collapse
|
80
|
Phage display informatics. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:698395. [PMID: 24454540 PMCID: PMC3880736 DOI: 10.1155/2013/698395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 08/22/2013] [Indexed: 11/17/2022]
|
81
|
Matochko WL, Cory Li S, Tang SKY, Derda R. Prospective identification of parasitic sequences in phage display screens. Nucleic Acids Res 2013; 42:1784-98. [PMID: 24217917 PMCID: PMC3919620 DOI: 10.1093/nar/gkt1104] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Phage display empowered the development of proteins with new function and ligands for clinically relevant targets. In this report, we use next-generation sequencing to analyze phage-displayed libraries and uncover a strong bias induced by amplification preferences of phage in bacteria. This bias favors fast-growing sequences that collectively constitute <0.01% of the available diversity. Specifically, a library of 109 random 7-mer peptides (Ph.D.-7) includes a few thousand sequences that grow quickly (the ‘parasites’), which are the sequences that are typically identified in phage display screens published to date. A similar collapse was observed in other libraries. Using Illumina and Ion Torrent sequencing and multiple biological replicates of amplification of Ph.D.-7 library, we identified a focused population of 770 ‘parasites’. In all, 197 sequences from this population have been identified in literature reports that used Ph.D.-7 library. Many of these enriched sequences have confirmed function (e.g. target binding capacity). The bias in the literature, thus, can be viewed as a selection with two different selection pressures: (i) target-binding selection, and (ii) amplification-induced selection. Enrichment of parasitic sequences could be minimized if amplification bias is removed. Here, we demonstrate that emulsion amplification in libraries of ∼106 diverse clones prevents the biased selection of parasitic clones.
Collapse
Affiliation(s)
- Wadim L Matochko
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada, Department of Bioengineering, MIT, Cambridge, MA 02139, USA and Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA
| | | | | | | |
Collapse
|
82
|
Kubrycht J, Sigler K, Souček P, Hudeček J. Structures composing protein domains. Biochimie 2013; 95:1511-24. [DOI: 10.1016/j.biochi.2013.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 04/02/2013] [Indexed: 12/21/2022]
|
83
|
Sun P, Ju H, Liu Z, Ning Q, Zhang J, Zhao X, Huang Y, Ma Z, Li Y. Bioinformatics resources and tools for conformational B-cell epitope prediction. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:943636. [PMID: 23970944 PMCID: PMC3736542 DOI: 10.1155/2013/943636] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/22/2013] [Accepted: 06/01/2013] [Indexed: 11/22/2022]
Abstract
Identification of epitopes which invoke strong humoral responses is an essential issue in the field of immunology. Localizing epitopes by experimental methods is expensive in terms of time, cost, and effort; therefore, computational methods feature for its low cost and high speed was employed to predict B-cell epitopes. In this paper, we review the recent advance of bioinformatics resources and tools in conformational B-cell epitope prediction, including databases, algorithms, web servers, and their applications in solving problems in related areas. To stimulate the development of better tools, some promising directions are also extensively discussed.
Collapse
Affiliation(s)
- Pingping Sun
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun 130024, China
| | - Haixu Ju
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
| | - Zhenbang Liu
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
| | - Qiao Ning
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
| | - Jian Zhang
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
| | - Xiaowei Zhao
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
| | - Yanxin Huang
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun 130024, China
| | - Zhiqiang Ma
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
| | - Yuxin Li
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun 130024, China
| |
Collapse
|
84
|
Castelli M, Cappelletti F, Diotti RA, Sautto G, Criscuolo E, Dal Peraro M, Clementi N. Peptide-based vaccinology: experimental and computational approaches to target hypervariable viruses through the fine characterization of protective epitopes recognized by monoclonal antibodies and the identification of T-cell-activating peptides. Clin Dev Immunol 2013; 2013:521231. [PMID: 23878584 PMCID: PMC3710646 DOI: 10.1155/2013/521231] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/06/2013] [Indexed: 12/20/2022]
Abstract
Defining immunogenic domains of viral proteins capable of eliciting a protective immune response is crucial in the development of novel epitope-based prophylactic strategies. This is particularly important for the selective targeting of conserved regions shared among hypervariable viruses. Studying postinfection and postimmunization sera, as well as cloning and characterization of monoclonal antibodies (mAbs), still represents the best approach to identify protective epitopes. In particular, a protective mAb directed against conserved regions can play a key role in immunogen design and in human therapy as well. Experimental approaches aiming to characterize protective mAb epitopes or to identify T-cell-activating peptides are often burdened by technical limitations and can require long time to be correctly addressed. Thus, in the last decade many epitope predictive algorithms have been developed. These algorithms are continually evolving, and their use to address the empirical research is widely increasing. Here, we review several strategies based on experimental techniques alone or addressed by in silico analysis that are frequently used to predict immunogens to be included in novel epitope-based vaccine approaches. We will list the main strategies aiming to design a new vaccine preparation conferring the protection of a neutralizing mAb combined with an effective cell-mediated response.
Collapse
Affiliation(s)
- Matteo Castelli
- Microbiology and Virology Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Francesca Cappelletti
- Microbiology and Virology Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Roberta Antonia Diotti
- Microbiology and Virology Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Giuseppe Sautto
- Microbiology and Virology Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Elena Criscuolo
- Microbiology and Virology Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, Institute of Bioingeneering, School of Life Sciences, Ecole Polytechnique Fédérale, 1015 Lausanne, Switzerland
| | - Nicola Clementi
- Microbiology and Virology Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy
| |
Collapse
|
85
|
Epitope mapping of metuximab on CD147 using phage display and molecular docking. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:983829. [PMID: 23861727 PMCID: PMC3686076 DOI: 10.1155/2013/983829] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/07/2013] [Indexed: 01/13/2023]
Abstract
Metuximab is the generic name of Licartin, a new drug for radioimmunotherapy of hepatocellular carcinoma. Although it is known to be a mouse monoclonal antibody against CD147, the complete epitope mediating the binding of metuximab to CD147 remains unknown. We panned the Ph.D.-12 phage display peptide library against metuximab and got six mimotopes. The following bioinformatics analysis based on mimotopes suggested that metuximab recognizes a conformational epitope composed of more than 20 residues. The residues of its epitope may include T28, V30, K36, L38, K57, F74, D77, S78, D79, D80, Q81, G83, S86, N98, Q100, L101, H102, G103, P104, V131, P132, and K191. The homology modeling of metuximab and the docking of CD147 to metuximab were also performed. Based on the top one docking model, the epitope was predicted to contain 28 residues: AGTVFTTV (23–30), I37, D45, E84, V88, EPMGTANIQLH (92–102), VPP (131–133), Q164, and K191. Almost half of the residues predicted on the basis of mimotope analysis also appear in the docking result, indicating that both results are reliable. As the predicted epitopes of metuximab largely overlap with interfaces of CD147-CD147 interactions, a structural mechanism of metuximab is proposed as blocking the formation of CD147 dimer.
Collapse
|
86
|
Potential of peptides as inhibitors and mimotopes: selection of carbohydrate-mimetic peptides from phage display libraries. J Nucleic Acids 2012; 2012:740982. [PMID: 23094142 PMCID: PMC3474289 DOI: 10.1155/2012/740982] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/31/2012] [Accepted: 08/02/2012] [Indexed: 11/28/2022] Open
Abstract
Glycoconjugates play various roles in biological processes. In particular, oligosaccharides on the surface of animal cells are involved in virus infection and cell-cell communication. Inhibitors of carbohydrate-protein interactions are potential antiviral drugs. Several anti-influenza drugs such as oseltamivir and zanamivir are derivatives of sialic acid, which inhibits neuraminidase. However, it is very difficult to prepare a diverse range of sugar derivatives by chemical synthesis or by the isolation of natural products. In addition, the pathogenic capsular polysaccharides of bacteria are carbohydrate antigens, for which a safe and efficacious method of vaccination is required. Phage-display technology has been improved to enable the identification of peptides that bind to carbohydrate-binding proteins, such as lectins and antibodies, from a large repertoire of peptide sequences. These peptides are known as “carbohydrate-mimetic peptides (CMPs)” because they mimic carbohydrate structures. Compared to carbohydrate derivatives, it is easy to prepare mono- and multivalent peptides and then to modify them to create various derivatives. Such mimetic peptides are available as peptide inhibitors of carbohydrate-protein interactions and peptide mimotopes that are conjugated with adjuvant for vaccination.
Collapse
|
87
|
Kubrycht J, Sigler K, Souček P. Virtual interactomics of proteins from biochemical standpoint. Mol Biol Int 2012; 2012:976385. [PMID: 22928109 PMCID: PMC3423939 DOI: 10.1155/2012/976385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/18/2012] [Accepted: 05/18/2012] [Indexed: 12/24/2022] Open
Abstract
Virtual interactomics represents a rapidly developing scientific area on the boundary line of bioinformatics and interactomics. Protein-related virtual interactomics then comprises instrumental tools for prediction, simulation, and networking of the majority of interactions important for structural and individual reproduction, differentiation, recognition, signaling, regulation, and metabolic pathways of cells and organisms. Here, we describe the main areas of virtual protein interactomics, that is, structurally based comparative analysis and prediction of functionally important interacting sites, mimotope-assisted and combined epitope prediction, molecular (protein) docking studies, and investigation of protein interaction networks. Detailed information about some interesting methodological approaches and online accessible programs or databases is displayed in our tables. Considerable part of the text deals with the searches for common conserved or functionally convergent protein regions and subgraphs of conserved interaction networks, new outstanding trends and clinically interesting results. In agreement with the presented data and relationships, virtual interactomic tools improve our scientific knowledge, help us to formulate working hypotheses, and they frequently also mediate variously important in silico simulations.
Collapse
Affiliation(s)
- Jaroslav Kubrycht
- Department of Physiology, Second Medical School, Charles University, 150 00 Prague, Czech Republic
| | - Karel Sigler
- Laboratory of Cell Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic
| | - Pavel Souček
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
| |
Collapse
|
88
|
Matochko WL, Chu K, Jin B, Lee SW, Whitesides GM, Derda R. Deep sequencing analysis of phage libraries using Illumina platform. Methods 2012; 58:47-55. [PMID: 22819855 DOI: 10.1016/j.ymeth.2012.07.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 07/11/2012] [Indexed: 11/25/2022] Open
Abstract
This paper presents an analysis of phage-displayed libraries of peptides using Illumina. We describe steps for the preparation of short DNA fragments for deep sequencing and MatLab software for the analysis of the results. Screening of peptide libraries displayed on the surface of bacteriophage (phage display) can be used to discover peptides that bind to any target. The key step in this discovery is the analysis of peptide sequences present in the library. This analysis is usually performed by Sanger sequencing, which is labor intensive and limited to examination of a few hundred phage clones. On the other hand, Illumina deep-sequencing technology can characterize over 10(7) reads in a single run. We applied Illumina sequencing to analyze phage libraries. Using PCR, we isolated the variable regions from M13KE phage vectors from a phage display library. The PCR primers contained (i) sequences flanking the variable region, (ii) barcodes, and (iii) variable 5'-terminal region. We used this approach to examine how diversity of peptides in phage display libraries changes as a result of amplification of libraries in bacteria. Using HiSeq single-end Illumina sequencing of these fragments, we acquired over 2×10(7) reads, 57 base pairs (bp) in length. Each read contained information about the barcode (6bp), one complimentary region (12bp) and a variable region (36bp). We applied this sequencing to a model library of 10(6) unique clones and observed that amplification enriches ∼150 clones, which dominate ∼20% of the library. Deep sequencing, for the first time, characterized the collapse of diversity in phage libraries. The results suggest that screens based on repeated amplification and small-scale sequencing identify a few binding clones and miss thousands of useful clones. The deep sequencing approach described here could identify under-represented clones in phage screens. It could also be instrumental in developing new screening strategies, which can preserve diversity of phage clones and identify ligands previously lost in phage display screens.
Collapse
Affiliation(s)
- Wadim L Matochko
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | | | | | | | | | | |
Collapse
|
89
|
PepMapper: a collaborative web tool for mapping epitopes from affinity-selected peptides. PLoS One 2012; 7:e37869. [PMID: 22701536 PMCID: PMC3360666 DOI: 10.1371/journal.pone.0037869] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/26/2012] [Indexed: 01/13/2023] Open
Abstract
Epitope mapping from affinity-selected peptides has become popular in epitope prediction, and correspondingly many Web-based tools have been developed in recent years. However, the performance of these tools varies in different circumstances. To address this problem, we employed an ensemble approach to incorporate two popular Web tools, MimoPro and Pep-3D-Search, together for taking advantages offered by both methods so as to give users more options for their specific purposes of epitope-peptide mapping. The combined operation of Union finds as many associated peptides as possible from both methods, which increases sensitivity in finding potential epitopic regions on a given antigen surface. The combined operation of Intersection achieves to some extent the mutual verification by the two methods and hence increases the likelihood of locating the genuine epitopic region on a given antigen in relation to the interacting peptides. The Consistency between Intersection and Union is an indirect sufficient condition to assess the likelihood of successful peptide-epitope mapping. On average from 27 tests, the combined operations of PepMapper outperformed either MimoPro or Pep-3D-Search alone. Therefore, PepMapper is another multipurpose mapping tool for epitope prediction from affinity-selected peptides. The Web server can be freely accessed at: http://informatics.nenu.edu.cn/PepMapper/
Collapse
|