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Probing the Antigenicity of HCV Envelope Glycoproteins by Phage Display Antibody Technology. Methods Mol Biol 2019. [PMID: 30593640 DOI: 10.1007/978-1-4939-8976-8_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The envelope glycoproteins E1 and E2 of hepatitis C virus form a heterodimeric complex on the viral surface. They are the targets of neutralizing antibodies and are being investigated as potential vaccine antigens. Because of the high level of cysteine residues and N-glycosylation sites in the polypeptide sequences, it is technically challenging to produce pure, folded recombinant E1, E2, and E1E2 complex for downstream analysis. In this chapter, the methods we used to isolate a panel of human antibodies specific to diverse antigenic regions on the glycoproteins are discussed. The antibodies have been found to be valuable reagents for the study of HCV envelope glycoproteins, including the determination of the first E2 core domain structure.
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Mattes DS, Jung N, Weber LK, Bräse S, Breitling F. Miniaturized and Automated Synthesis of Biomolecules-Overview and Perspectives. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806656. [PMID: 31033052 DOI: 10.1002/adma.201806656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Chemical synthesis is performed by reacting different chemical building blocks with defined stoichiometry, while meeting additional conditions, such as temperature and reaction time. Such a procedure is especially suited for automation and miniaturization. Life sciences lead the way to synthesizing millions of different oligonucleotides in extremely miniaturized reaction sites, e.g., pinpointing active genes in whole genomes, while chemistry advances different types of automation. Recent progress in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging could match miniaturized chemical synthesis with a powerful analytical tool to validate the outcome of many different synthesis pathways beyond applications in the life sciences. Thereby, due to the radical miniaturization of chemical synthesis, thousands of molecules can be synthesized. This in turn should allow ambitious research, e.g., finding novel synthesis routes or directly screening for photocatalysts. Herein, different technologies are discussed that might be involved in this endeavor. A special emphasis is given to the obstacles that need to be tackled when depositing tiny amounts of materials to many different extremely miniaturized reaction sites.
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Affiliation(s)
- Daniela S Mattes
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nicole Jung
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Laura K Weber
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Frank Breitling
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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Lee ACL, Harris JL, Khanna KK, Hong JH. A Comprehensive Review on Current Advances in Peptide Drug Development and Design. Int J Mol Sci 2019; 20:ijms20102383. [PMID: 31091705 PMCID: PMC6566176 DOI: 10.3390/ijms20102383] [Citation(s) in RCA: 353] [Impact Index Per Article: 70.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 11/16/2022] Open
Abstract
Protein-protein interactions (PPIs) execute many fundamental cellular functions and have served as prime drug targets over the last two decades. Interfering intracellular PPIs with small molecules has been extremely difficult for larger or flat binding sites, as antibodies cannot cross the cell membrane to reach such target sites. In recent years, peptides smaller size and balance of conformational rigidity and flexibility have made them promising candidates for targeting challenging binding interfaces with satisfactory binding affinity and specificity. Deciphering and characterizing peptide-protein recognition mechanisms is thus central for the invention of peptide-based strategies to interfere with endogenous protein interactions, or improvement of the binding affinity and specificity of existing approaches. Importantly, a variety of computation-aided rational designs for peptide therapeutics have been developed, which aim to deliver comprehensive docking for peptide-protein interaction interfaces. Over 60 peptides have been approved and administrated globally in clinics. Despite this, advances in various docking models are only on the merge of making their contribution to peptide drug development. In this review, we provide (i) a holistic overview of peptide drug development and the fundamental technologies utilized to date, and (ii) an updated review on key developments of computational modeling of peptide-protein interactions (PepPIs) with an aim to assist experimental biologists exploit suitable docking methods to advance peptide interfering strategies against PPIs.
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Affiliation(s)
- Andy Chi-Lung Lee
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 333, Taiwan.
- Department of Radiation Oncology, Chang Gung Memorial Hospital, Linkou 333, Taiwan.
| | | | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
| | - Ji-Hong Hong
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 333, Taiwan.
- Department of Radiation Oncology, Chang Gung Memorial Hospital, Linkou 333, Taiwan.
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Zambrano-Mila MS, Sánchez Blacio KE, Santiago Vispo N. Peptide Phage Display: Molecular Principles and Biomedical Applications. Ther Innov Regul Sci 2019. [DOI: 10.1177/2168479019837624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Marlon S. Zambrano-Mila
- School of Biological Sciences and Engineering, Yachay Tech University, San Miguel de Urcuquí, Ecuador
| | | | - Nelson Santiago Vispo
- School of Biological Sciences and Engineering, Yachay Tech University, San Miguel de Urcuquí, Ecuador
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Single-Chain Variable Fragment Antibody of Vascular Cell Adhesion Molecule 1 as a Molecular Imaging Probe for Colitis Model Rabbit Investigation. CONTRAST MEDIA & MOLECULAR IMAGING 2019; 2019:2783519. [PMID: 30804723 PMCID: PMC6360587 DOI: 10.1155/2019/2783519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 10/27/2018] [Accepted: 11/12/2018] [Indexed: 12/18/2022]
Abstract
Vascular cell adhesion molecule-1 (VCAM-1) can be a promising target for colitis study because of its critical role in inflammation development. Single-chain variable fragment (scFv) antibody presents fast blood clearance when served as an imaging probe. We applied the probe of 99mTc-scFv-VCAM-1 to colitis rabbit to examine its imaging performance. The colitis model rabbit was prepared, and a typical inflammatory lesion was confirmed in the colon. The probe of 99mTc-scFv-VCAM-1 was synthesized and injected into the model animal before imaging examination. Scintigraphy detected colitis lesions in both SPECT planar and SPECT/CT fused images, with higher target-to-nontarget ratios in the model group (2.71 ± 0.31) than those in the control group (1.12 ± 0.10). Biodistribution study determined tracer uptake in different organs, and autoradiography (ARG) confirmed probe accumulation in colon lesions. The uptake ratio of the model colon to the control colon was 4.71 ± 0.61 in quantitative analysis of the ARG regions of interest. Stronger VCAM-1 expression in the model colon than that in the control colon was confirmed by western blotting and immunohistochemistry. Our imaging study indicates molecular imaging with scFv-VCAM-1 as a promising way for inflammatory bowel disease diagnosis and evaluation.
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Hu FJ, Volk AL, Persson H, Säll A, Borrebaeck C, Uhlen M, Rockberg J. Combination of phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity binders. N Biotechnol 2018; 45:80-88. [DOI: 10.1016/j.nbt.2017.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/28/2017] [Accepted: 07/31/2017] [Indexed: 10/19/2022]
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Domingo-Calap P, Delgado-Martínez J. Bacteriophages: Protagonists of a Post-Antibiotic Era. Antibiotics (Basel) 2018; 7:E66. [PMID: 30060506 PMCID: PMC6163168 DOI: 10.3390/antibiotics7030066] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 12/31/2022] Open
Abstract
Despite their long success for more than half a century, antibiotics are currently under the spotlight due to the emergence of multidrug-resistant bacteria. The development of new alternative treatments is of particular interest in the fight against bacterial resistance. Bacteriophages (phages) are natural killers of bacteria and are an excellent tool due to their specificity and ecological safety. Here, we highlight some of their advantages and drawbacks as potential therapeutic agents. Interestingly, phages are not only attractive from a clinical point of view, but other areas, such as agriculture, food control, or industry, are also areas for their potential application. Therefore, we propose phages as a real alternative to current antibiotics.
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Affiliation(s)
- Pilar Domingo-Calap
- Department of Genetics, Universitat de València, 46100 Burjassot, Valencia, Spain.
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Valencia, Spain.
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Spicer CD, Jumeaux C, Gupta B, Stevens MM. Peptide and protein nanoparticle conjugates: versatile platforms for biomedical applications. Chem Soc Rev 2018; 47:3574-3620. [PMID: 29479622 PMCID: PMC6386136 DOI: 10.1039/c7cs00877e] [Citation(s) in RCA: 283] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Peptide- and protein-nanoparticle conjugates have emerged as powerful tools for biomedical applications, enabling the treatment, diagnosis, and prevention of disease. In this review, we focus on the key roles played by peptides and proteins in improving, controlling, and defining the performance of nanotechnologies. Within this framework, we provide a comprehensive overview of the key sequences and structures utilised to provide biological and physical stability to nano-constructs, direct particles to their target and influence their cellular and tissue distribution, induce and control biological responses, and form polypeptide self-assembled nanoparticles. In doing so, we highlight the great advances made by the field, as well as the challenges still faced in achieving the clinical translation of peptide- and protein-functionalised nano-drug delivery vehicles, imaging species, and active therapeutics.
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Affiliation(s)
- Christopher D Spicer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, Stockholm, Sweden.
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Kalimuthu K, Lubin BC, Bazylevich A, Gellerman G, Shpilberg O, Luboshits G, Firer MA. Gold nanoparticles stabilize peptide-drug-conjugates for sustained targeted drug delivery to cancer cells. J Nanobiotechnology 2018; 16:34. [PMID: 29602308 PMCID: PMC5877385 DOI: 10.1186/s12951-018-0362-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/21/2018] [Indexed: 11/12/2022] Open
Abstract
Background Peptide-drug-conjugates (PDCs) are being developed as an effective strategy to specifically deliver cytotoxic drugs to cancer cells. However one of the challenges to their successful application is the relatively low stability of peptides in the blood, liver and kidneys. Since AuNPs seem to have a longer plasma half-life than PDCs, one approach to overcoming this problem would be to conjugate the PDCs to gold nanoparticles (AuNPs), as these have demonstrated favorable physico-chemical and safety properties for drug delivery systems. We set out to test whether PEG coated-AuNPs could provide a suitable platform for the non-covalent loading of pre-formed PDCs and whether this modification would affect the bioavailability of the PDCs and their cytotoxicity toward target cancer cells. Methods Peptides specifically internalized by A20 murine lymphoma cells were isolated from a phage library displaying 7mer linear peptides. Peptide specificity was validated by flow cytometry and confocal microscopy. PDCs were synthesized containing a selected peptide (P4) and either chlorambucil (Chlor), melphalan (Melph) or bendamustine (Bend). Gold nanoparticles were sequentially coated with citrate, PEG-6000 and then PDC (PDC-PEG-AuNP). The physico-chemical properties of the coated particles were analyzed by electrophoresis, TEM, UV–VIS and FTIR. Stability of free and PDC-coated AuNP was determined. Results Biopanning of the phage library resulted in discovery of several novel peptides that internalized into A20 cells. One of these (P4) was used to synthesize PDCs containing either Chlor, Melph or Bend. All three PDCs specifically killed A20 target cells, however they had short half-lives ranging from 10.6 to 15.4 min. When coated to PEG-AuNPs, the half-lives were extended to 21.0–22.3 h. The PDC-PEG-AuNPs retained cytotoxicity towards the target cells. Moreover, whereas pre-incubation for 24 h of free PDCs almost completely abolished their cytotoxic activity, the PDC-PEG-AuNPs were still active even after 72 h pre-incubation. Conclusions Peptide-drug-conjugates hold potential for improving the target efficacy of chemotherapeutic drugs, however their short half-lives may limit their application. This hurdle can be overcome by easily conjugating them to gold nanoparticles. This conjugation also opens up the possibility of developing slow release formulations of targeted drug delivery systems containing PDCs. Electronic supplementary material The online version of this article (10.1186/s12951-018-0362-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Bat-Chen Lubin
- Dept. Chemical Engineering, Ariel University, 40700, Ariel, Israel.,Eastern R&D Center, Ariel, 40700, Israel
| | | | - Gary Gellerman
- Dept. Chemical Sciences, Ariel University, 40700, Ariel, Israel
| | - Ofer Shpilberg
- Tel Aviv & Pre-Med Faculty, Assuta Medical Center, Institute of Hematology, Ariel University, 40700, Ariel, Israel
| | - Galia Luboshits
- Dept. Chemical Engineering, Ariel University, 40700, Ariel, Israel
| | - Michael A Firer
- Dept. Chemical Engineering, Ariel University, 40700, Ariel, Israel. .,Ariel Center for Applied Cancer Research, Ariel University, 40700, Ariel, Israel.
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60
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Utilization of phage display to identify antigenic regions in the PCV2 capsid protein for the evaluation of serological responses in mice and pigs. Arch Virol 2018; 163:1877-1887. [PMID: 29589172 DOI: 10.1007/s00705-018-3816-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 02/07/2018] [Indexed: 10/17/2022]
Abstract
Porcine circovirus 2 (PCV2) is associated with a series of swine diseases. There is a great interest in improving our understanding of the immunology of PCV2, especially the properties of the viral capsid protein Cap-PCV2 and how they relate to the immunogenicity of the virus and the subsequent development of vaccines. Phage display screening has been widely used to study binding affinities for target proteins. The aim of this study was to use phage display screening to identify antigenic peptides in the PCV2 capsid protein. After the selection of peptides, five of them presented similarity to sequences found in cap-PCV2, and four peptides were synthesized and used for immunization in mice: 51-CTFGYTIKRTVT-62 (PS14), 127-CDNFVTKATALTY-138 (PS34), 164-CKPVLDSTIDY-173 (PC12), and 79-CFLPPGGGSNT-88 (PF1). Inoculation with the PC12 peptide led to the highest production of antibodies. Furthermore, we used the PC12 peptide as an antigen to examine the humoral response of swine serum by ELISA. The sensitivity and specificity of this assay was 88.9% and 92.85%, respectively. Altogether, characterization of immunogenic epitopes in the capsid protein of PCV2 may contribute to the improvement of vaccines and diagnostics.
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Abstract
In this report, we describe an efficient way to generate libraries of macrocyclic glycopeptides in one step by reacting phage-displayed libraries of peptides with dichloro-oxime derivatives. We showed that the reactions do not interfere with the ability of phage to replicate in bacteria. The reactions are site-selective for phage-displayed peptides and they do not modify any other proteins of phage. The technology described in this report will be instrumental for genetic selection of macrocyclic glycopeptides for diverse glycan-binding proteins.
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Affiliation(s)
- Simon Ng
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
| | - Ratmir Derda
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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62
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Peptide Derivatives of Erythropoietin in the Treatment of Neuroinflammation and Neurodegeneration. THERAPEUTIC PROTEINS AND PEPTIDES 2018; 112:309-357. [DOI: 10.1016/bs.apcsb.2018.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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63
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A computational approach for designing D-proteins with non-canonical amino acid optimised binding affinity. PLoS One 2017; 12:e0187524. [PMID: 29108013 PMCID: PMC5673230 DOI: 10.1371/journal.pone.0187524] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 10/21/2017] [Indexed: 01/08/2023] Open
Abstract
Redesigning protein surface topology to improve target binding holds great promise in the search for highly selective therapeutics. While significant binding improvements can be achieved using natural amino acids, the introduction of non-canonical residues vastly increases sequence space and thus the chance to significantly out-compete native partners. The potency of protein inhibitors can be further enhanced by synthesising mirror image, D-amino versions. This renders them non-immunogenic and makes them highly resistant to proteolytic degradation. Current experimental design methods often preclude the use of D-amino acids and non-canonical amino acids for a variety of reasons. To address this, we build an in silico pipeline for D-protein designs featuring non-canonical amino acids. For a test scaffold we use an existing D-protein inhibitor of VEGF: D-RFX001. We benchmark the approach by recapitulating previous experimental optimisation with canonical amino acids. Subsequent incorporation of non-canonical amino acids allows designs that are predicted to improve binding affinity by up to -7.18 kcal/mol.
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64
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Zhu L, Guo Y, Wang L, Fan X, Xiong X, Fang K, Xu D. Construction of ultrasonic nanobubbles carrying CAIX polypeptides to target carcinoma cells derived from various organs. J Nanobiotechnology 2017; 15:63. [PMID: 28962657 PMCID: PMC5622542 DOI: 10.1186/s12951-017-0307-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/23/2017] [Indexed: 01/01/2023] Open
Abstract
Background Ultrasound molecular imaging is a novel diagnostic approach for tumors, whose key link is the construction of targeted ultrasound contrast agents. However, available targeted ultrasound contrast agents for molecular imaging of tumors are only achieving imaging in blood pool or one type tumor. No targeted ultrasound contrast agents have realized targeted ultrasound molecular imaging of tumor parenchymal cells in a variety of solid tumors so far. Carbonic anhydrase IX (CAIX) is highly expressed on cell membranes of various malignant solid tumors, so it’s a good target for ultrasound molecular imaging. Here, targeted nanobubbles carrying CAIX polypeptides for targeted binding to a variety of malignant tumors were constructed, and targeted binding ability and ultrasound imaging effect in different types of tumors were evaluated. Results The mean diameter of lipid targeted nanobubbles was (503.7 ± 78.47) nm, and the polypeptides evenly distributed on the surfaces of targeted nanobubbles, which possessed the advantages of homogenous particle size, high stability, and good safety. Targeted nanobubbles could gather around CAIX-positive cells (786-O and Hela cells), while they cannot gather around CAIX-negative cells (BxPC-3 cells) in vitro, and the affinity of targeted nanobubbles to CAIX-positive cells were significantly higher than that to CAIX-negative cells (P < 0.05). Peak intensity and duration time of targeted nanobubbles and blank nanobubbles were different in CAIX-positive transplanted tumor tissues in vivo (P < 0.05). Moreover, targeted nanobubbles in CAIX-positive transplanted tumor tissues produced higher peak intensity and longer duration time than those in CAIX-negative transplanted tumor tissues (P < 0.05). Finally, immunofluorescence not only confirmed targeted nanobubbles could pass through blood vessels to enter in tumor tissue spaces, but also clarified imaging differences of targeted nanobubbles in different types of transplanted tumor tissues. Conclusions Targeted nanobubbles carrying CAIX polypeptides can specifically enhance ultrasound imaging in CAIX-positive transplanted tumor tissues and could potentially be used in early diagnosis of a variety of solid tumors derived from various organs. Electronic supplementary material The online version of this article (doi:10.1186/s12951-017-0307-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lianhua Zhu
- Department of Ultrasound, Southwest Hospital, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Yanli Guo
- Department of Ultrasound, Southwest Hospital, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China.
| | - Luofu Wang
- Department of Urology, Daping Hospital, Third Military Medical University, 10 Changjiang Zhi Road, Yuzhong District, Chongqing, 400038, China
| | - Xiaozhou Fan
- Department of Ultrasound, Southwest Hospital, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Xingyu Xiong
- Department of Ultrasound, Southwest Hospital, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Kejing Fang
- Department of Ultrasound, Southwest Hospital, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Dan Xu
- Department of Ultrasound, Southwest Hospital, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
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Bashari O, Redko B, Cohen A, Luboshits G, Gellerman G, Firer MA. Discovery of peptide drug carrier candidates for targeted multi-drug delivery into prostate cancer cells. Cancer Lett 2017; 408:164-173. [PMID: 28888997 DOI: 10.1016/j.canlet.2017.08.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 08/23/2017] [Accepted: 08/28/2017] [Indexed: 11/24/2022]
Abstract
Metastatic castration-resistant prostate cancer (mCRPC) remains essentially incurable. Targeted Drug Delivery (TDD) systems may overcome the limitations of current mCRPC therapies. We describe the use of strict criteria to isolate novel prostate cancer cell targeting peptides that specifically deliver drugs into target cells. Phage from a libraries displaying 7mer peptides were exposed to PC-3 cells and only internalized phage were recovered. The ability of these phage to internalize into other prostate cancer cells (LNCaP, DU-145) was validated. The displayed peptides of selected phage clones were synthesized and their specificity for target cells was validated in vitro and in vivo. One peptide (P12) which specifically targeted PC-3 tumors in vivo was incorporated into mono-drug (Chlorambucil, Combretastatin or Camptothecin) and dual-drug (Chlorambucil/Combretastatin or Chlorambucil/Camptothecin) PDCs and the cytotoxic efficacy of these conjugates for target cells was tested. Conjugation of P12 into dual-drug PDCs allowed discovery of new drug combinations with synergistic effects. The use of strict selection criteria can lead to discovery of novel peptides for use as drug carriers for TDD. PDCs represent an effective alternative to current modes of free drug chemotherapy for prostate cancer.
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Affiliation(s)
- O Bashari
- Dept. Chemical Engineering, Ariel University, Ariel, 40700, Israel.
| | - B Redko
- Dept. Chemical Sciences, Ariel University, Ariel, 40700, Israel.
| | - A Cohen
- Dept. Chemical Engineering, Ariel University, Ariel, 40700, Israel.
| | - G Luboshits
- Dept. Chemical Engineering, Ariel University, Ariel, 40700, Israel.
| | - G Gellerman
- Dept. Chemical Sciences, Ariel University, Ariel, 40700, Israel.
| | - M A Firer
- Dept. Chemical Engineering, Ariel University, Ariel, 40700, Israel.
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66
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Henninot A, Collins JC, Nuss JM. The Current State of Peptide Drug Discovery: Back to the Future? J Med Chem 2017; 61:1382-1414. [PMID: 28737935 DOI: 10.1021/acs.jmedchem.7b00318] [Citation(s) in RCA: 655] [Impact Index Per Article: 93.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Over the past decade, peptide drug discovery has experienced a revival of interest and scientific momentum, as the pharmaceutical industry has come to appreciate the role that peptide therapeutics can play in addressing unmet medical needs and how this class of compounds can be an excellent complement or even preferable alternative to small molecule and biological therapeutics. In this Perspective, we give a concise description of the recent progress in peptide drug discovery in a holistic manner, highlighting enabling technological advances affecting nearly every aspect of this field: from lead discovery, to synthesis and optimization, to peptide drug delivery. An emphasis is placed on describing research efforts to overcome the inherent weaknesses of peptide drugs, in particular their poor pharmacokinetic properties, and how these efforts have been critical to the discovery, design, and subsequent development of novel therapeutics.
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Affiliation(s)
- Antoine Henninot
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - James C Collins
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - John M Nuss
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
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67
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Alfaleh MA, Jones ML, Howard CB, Mahler SM. Strategies for Selecting Membrane Protein-Specific Antibodies using Phage Display with Cell-Based Panning. Antibodies (Basel) 2017; 6:E10. [PMID: 31548525 PMCID: PMC6698842 DOI: 10.3390/antib6030010] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/05/2017] [Accepted: 07/07/2017] [Indexed: 12/14/2022] Open
Abstract
Membrane proteins are attractive targets for monoclonal antibody (mAb) discovery and development. Although several approved mAbs against membrane proteins have been isolated from phage antibody libraries, the process is challenging, as it requires the presentation of a correctly folded protein to screen the antibody library. Cell-based panning could represent the optimal method for antibody discovery against membrane proteins, since it allows for presentation in their natural conformation along with the appropriate post-translational modifications. Nevertheless, screening antibodies against a desired antigen, within a selected cell line, may be difficult due to the abundance of irrelevant organic molecules, which can potentially obscure the antigen of interest. This review will provide a comprehensive overview of the different cell-based phage panning strategies, with an emphasis placed on the optimisation of four critical panning conditions: cell surface antigen presentation, non-specific binding events, incubation time, and temperature and recovery of phage binders.
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Affiliation(s)
- Mohamed A Alfaleh
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia.
- Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Martina L Jones
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Christopher B Howard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia.
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia.
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68
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Abstract
Codon usage is one of the factors influencing recombinant protein expression. We were interested in the codon usage of an antibody Fab fragment gene exhibiting extreme toxicity in the E. coli host. The toxic synthetic human Fab gene contained domains optimized by the “one amino acid-one codon” method. We redesigned five segments of the Fab gene with a “codon harmonization” method described by Angov et al. and studied the effects of these changes on cell viability, Fab yield and display on filamentous phage using different vectors and bacterial strains. The harmonization considerably reduced toxicity, increased Fab expression from negligible levels to 10 mg/l, and restored the display on phage. Testing the impact of the individual redesigned segments revealed that the most significant effects were conferred by changes in the constant domain of the light chain. For some of the Fab gene variants, we also observed striking differences in protein yields when cloned from a chloramphenicol resistant vector into an identical vector, except with ampicillin resistance. In conclusion, our results show that the expression of a heterodimeric secretory protein can be improved by harmonizing selected DNA segments by synonymous codons and reveal additional complexity involved in heterologous protein expression.
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69
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Cunningham AD, Qvit N, Mochly-Rosen D. Peptides and peptidomimetics as regulators of protein-protein interactions. Curr Opin Struct Biol 2017; 44:59-66. [PMID: 28063303 PMCID: PMC5496809 DOI: 10.1016/j.sbi.2016.12.009] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/03/2016] [Accepted: 12/16/2016] [Indexed: 01/16/2023]
Abstract
Protein-protein interactions are essential for almost all intracellular and extracellular biological processes. Regulation of protein-protein interactions is one strategy to regulate cell fate in a highly selective manner. Specifically, peptides are ideal candidates for inhibition of protein-protein interactions because they can mimic a protein surface to effectively compete for binding. Additionally, peptides are synthetically accessible and can be stabilized by chemical modifications. In this review, we survey screening and rational design methods for identifying peptides to inhibit protein-protein interactions, as well as methods for stabilizing peptides to effectively mimic protein surfaces. In addition, we discuss recent applications of peptides to regulate protein-protein interactions for both basic research and therapeutic purposes.
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Affiliation(s)
- Anna D Cunningham
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA 94305-5174, USA
| | - Nir Qvit
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA 94305-5174, USA.
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA 94305-5174, USA.
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70
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Abstract
Molecular imaging allows for the visualization of changes at the cellular level in diseases such as cancer. A successful molecular imaging agent must rely on disease-selective targets and ligands that specifically interact with those targets. Unfortunately, the translation of novel target-specific ligands into the clinic has been frustratingly slow with limitations including the complex design and screening approaches for ligand identification, as well as their subsequent optimization into useful imaging agents. This review focuses on combinatorial library approaches towards addressing these two challenges, with particular focus on phage display and one-bead one-compound (OBOC) libraries. Both of these peptide-based techniques have proven successful in identifying new ligands for cancer-specific targets and some of the success stories will be highlighted. New developments in screening methodology and sequencing technology have pushed the bounds of phage display and OBOC even further, allowing for even faster and more robust discovery of novel ligands. The combination of multiple high-throughput technologies will not only allow for more accurate identification, but also faster affinity maturation, while overall streamlining the process of translating novel ligands into clinical imaging agents.
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71
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TLR4/MD2 specific peptides stalled in vivo LPS-induced immune exacerbation. Biomaterials 2017; 126:49-60. [PMID: 28254693 DOI: 10.1016/j.biomaterials.2017.02.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/15/2017] [Accepted: 02/17/2017] [Indexed: 12/22/2022]
Abstract
Negative regulation of Toll-like receptor-4 (TLR4) is anticipated to control the pathogen-induced exaggerated immune response. However, effective TLR4 antagonists with scarce off-target effects are yet to be developed. To fill this void, we sought to design small peptide-inhibitors of the TLR4/MD2-LPS interaction. Here we report novel TLR4-antagonistic peptides (TAP), identified through phage display, endowed with the LPS-induced proinflammation inhibition, and confirmed in mice. TAPs-attributed TLR4-antagonism were initially evaluated through NF-κB inhibition in HEK-blue hTLR4 and RAW264.7 cells, and further reinforced by the downregulation of MAPKs (mitogen-activated protein kinases), NF-κB, interleukin 6, and suppression of the oxidative-stress products and iNOS in macrophages and human peripheral blood mononuclear cells (hPBMCs). Among these, TAP2 specifically halted the TLR4, but not other TLRs signaling, which was further confirmed by the biophysical kinetic assay. Finally, TAP2 diminished LPS-elicited systemic cytokine response in vivo, suggesting that TAPs, specifically TAP2, have the potential to treat TLR4-mediated immune ailments.
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72
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Short peptides interfering with signaling pathways as new therapeutic tools for cancer treatment. Future Med Chem 2017; 9:199-221. [PMID: 28111982 DOI: 10.4155/fmc-2016-0189] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Short peptides have many advantages, such as low molecular weight, selectivity for a specific target, organelles or cells with minimal toxicity. We describe properties of short peptides, which interfere with communication networks in tumor cells and within microenvironment of malignant gliomas, the most common brain tumors. We focus on ligand/receptor axes and intracellular signaling pathways critical for gliomagenesis that could be targeted with interfering peptides. We review structures and efficacy of organelle-specific and cell-penetrating peptides and describe diverse chemical modifications increasing proteolytic stability and protecting synthetic peptides against degradation. We report results of application of short peptides in glioma therapy clinical trials, their rises and falls. The most advanced examples of therapeutics such as short interfering peptides combined with cell-penetrating peptides that show good effectiveness in disease models are presented. It is foreseen that identification of peptides with better clinical properties may improve their success rates in clinical trials.
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73
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Quinn CM, Polenova T. Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy. Q Rev Biophys 2017; 50:e1. [PMID: 28093096 PMCID: PMC5483179 DOI: 10.1017/s0033583516000159] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as human immunodeficiency virus 1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology.
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Affiliation(s)
- Caitlin M. Quinn
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
| | - Tatyana Polenova
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
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74
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Grzeschik J, Hinz SC, Könning D, Pirzer T, Becker S, Zielonka S, Kolmar H. A simplified procedure for antibody engineering by yeast surface display: Coupling display levels and target binding by ribosomal skipping. Biotechnol J 2016; 12. [DOI: 10.1002/biot.201600454] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/19/2016] [Accepted: 11/22/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry; Technische Universität Darmstadt; Darmstadt Germany
| | - Steffen C. Hinz
- Institute for Organic Chemistry and Biochemistry; Technische Universität Darmstadt; Darmstadt Germany
| | - Doreen Könning
- Institute for Organic Chemistry and Biochemistry; Technische Universität Darmstadt; Darmstadt Germany
| | - Thomas Pirzer
- Institute for Organic Chemistry and Biochemistry; Technische Universität Darmstadt; Darmstadt Germany
| | - Stefan Becker
- Protein Engineering and Antibody Technologies; Merck Serono, Merck KGaA; Darmstadt Germany
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry; Technische Universität Darmstadt; Darmstadt Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry; Technische Universität Darmstadt; Darmstadt Germany
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75
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O'Sullivan L, Buttimer C, McAuliffe O, Bolton D, Coffey A. Bacteriophage-based tools: recent advances and novel applications. F1000Res 2016; 5:2782. [PMID: 27990274 PMCID: PMC5133683 DOI: 10.12688/f1000research.9705.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2016] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages (phages) are viruses that infect bacterial hosts, and since their discovery over a century ago they have been primarily exploited to control bacterial populations and to serve as tools in molecular biology. In this commentary, we highlight recent diverse advances in the field of phage research, going beyond bacterial control using whole phage, to areas including biocontrol using phage-derived enzybiotics, diagnostics, drug discovery, novel drug delivery systems and bionanotechnology.
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Affiliation(s)
- Lisa O'Sullivan
- Department of Biological Sciences, Cork Institute of Technology, County Cork, Ireland
| | - Colin Buttimer
- Department of Biological Sciences, Cork Institute of Technology, County Cork, Ireland
| | - Olivia McAuliffe
- Biotechnology Department, Teagasc, Moorepark Food Research Centre, Fermoy, County Cork, Ireland
| | - Declan Bolton
- Division of Food Safety, Teagasc, Food Research Centre, Ashtown, County Dublin, Ireland
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, County Cork, Ireland
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76
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Rahbarnia L, Farajnia S, Babaei H, Majidi J, Veisi K, Ahmadzadeh V, Akbari B. Evolution of phage display technology: from discovery to application. J Drug Target 2016; 25:216-224. [DOI: 10.1080/1061186x.2016.1258570] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Leila Rahbarnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Babaei
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Majidi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Kamal Veisi
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tabriz, Iran
| | - Vahideh Ahmadzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahman Akbari
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, University Of Medical Sciences Tabriz, Tabriz, Iran
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77
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Corbi-Verge C, Garton M, Nim S, Kim PM. Strategies to Develop Inhibitors of Motif-Mediated Protein-Protein Interactions as Drug Leads. Annu Rev Pharmacol Toxicol 2016; 57:39-60. [PMID: 27618737 DOI: 10.1146/annurev-pharmtox-010716-104805] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein-protein interactions are fundamental for virtually all functions of the cell. A large fraction of these interactions involve short peptide motifs, and there has been increased interest in targeting them using peptide-based therapeutics. Peptides benefit from being specific, relatively safe, and easy to produce. They are also easy to modify using chemical synthesis and molecular biology techniques. However, significant challenges remain regarding the use of peptides as therapeutic agents. Identification of peptide motifs is difficult, and peptides typically display low cell permeability and sensitivity to enzymatic degradation. In this review, we outline the principal high-throughput methodologies for motif discovery and describe current methods for overcoming pharmacokinetic and bioavailability limitations.
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Affiliation(s)
- Carles Corbi-Verge
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; , , ,
| | - Michael Garton
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; , , ,
| | - Satra Nim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; , , ,
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; , , , .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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78
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Chiu ML, Gilliland GL. Engineering antibody therapeutics. Curr Opin Struct Biol 2016; 38:163-73. [PMID: 27525816 DOI: 10.1016/j.sbi.2016.07.012] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 02/07/2023]
Abstract
The successful introduction of antibody-based protein therapeutics into the arsenal of treatments for patients has within a few decades fostered intense innovation in the production and engineering of antibodies. Reviewed here are the methods currently used to produce antibodies along with how our knowledge of the structural and functional characterization of immunoglobulins has resulted in the engineering of antibodies to produce protein therapeutics with unique properties, both biological and biophysical, that are leading to novel therapeutic approaches. Antibody engineering includes the introduction of the antibody combining site (variable regions) into a host of architectures including bi and multi-specific formats that further impact the therapeutic properties leading to further advantages and successes in patient treatment.
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Affiliation(s)
- Mark L Chiu
- Janssen Research & Development LLC, 1400 McKean Road, Spring House, PA 19477, USA.
| | - Gary L Gilliland
- Janssen Research & Development LLC, 1400 McKean Road, Spring House, PA 19477, USA.
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79
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Ruiz-Gómez G, Hawkins JC, Philipp J, Künze G, Wodtke R, Löser R, Fahmy K, Pisabarro MT. Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics. PLoS One 2016; 11:e0154046. [PMID: 27123592 PMCID: PMC4849758 DOI: 10.1371/journal.pone.0154046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/07/2016] [Indexed: 12/25/2022] Open
Abstract
Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.
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Affiliation(s)
- Gloria Ruiz-Gómez
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg, Dresden, Germany
- * E-mail: (GRG); (MTB)
| | - John C. Hawkins
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg, Dresden, Germany
| | - Jenny Philipp
- Helmholtz-Zentrum Dresden Rossendorf, Institute of Resource Ecology, Dresden, Germany
| | - Georg Künze
- Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Robert Wodtke
- Helmholtz-Zentrum Dresden Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Reik Löser
- Helmholtz-Zentrum Dresden Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden Rossendorf, Institute of Resource Ecology, Dresden, Germany
| | - M. Teresa Pisabarro
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg, Dresden, Germany
- * E-mail: (GRG); (MTB)
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80
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Rhoden JJ, Dyas GL, Wroblewski VJ. A Modeling and Experimental Investigation of the Effects of Antigen Density, Binding Affinity, and Antigen Expression Ratio on Bispecific Antibody Binding to Cell Surface Targets. J Biol Chem 2016; 291:11337-47. [PMID: 27022022 DOI: 10.1074/jbc.m116.714287] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Indexed: 12/19/2022] Open
Abstract
Despite the increasing number of multivalent antibodies, bispecific antibodies, fusion proteins, and targeted nanoparticles that have been generated and studied, the mechanism of multivalent binding to cell surface targets is not well understood. Here, we describe a conceptual and mathematical model of multivalent antibody binding to cell surface antigens. Our model predicts that properties beyond 1:1 antibody:antigen affinity to target antigens have a strong influence on multivalent binding. Predicted crucial properties include the structure and flexibility of the antibody construct, the target antigen(s) and binding epitope(s), and the density of antigens on the cell surface. For bispecific antibodies, the ratio of the expression levels of the two target antigens is predicted to be critical to target binding, particularly for the lower expressed of the antigens. Using bispecific antibodies of different valencies to cell surface antigens including MET and EGF receptor, we have experimentally validated our modeling approach and its predictions and observed several nonintuitive effects of avidity related to antigen density, target ratio, and antibody affinity. In some biological circumstances, the effect we have predicted and measured varied from the monovalent binding interaction by several orders of magnitude. Moreover, our mathematical framework affords us a mechanistic interpretation of our observations and suggests strategies to achieve the desired antibody-antigen binding goals. These mechanistic insights have implications in antibody engineering and structure/activity relationship determination in a variety of biological contexts.
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Affiliation(s)
- John J Rhoden
- From the Department of Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285
| | - Gregory L Dyas
- From the Department of Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285
| | - Victor J Wroblewski
- From the Department of Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285
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81
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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.
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82
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Sagona AP, Grigonyte AM, MacDonald PR, Jaramillo A. Genetically modified bacteriophages. Integr Biol (Camb) 2016; 8:465-74. [DOI: 10.1039/c5ib00267b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Applications of genetically modified bacteriophages.
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Affiliation(s)
- Antonia P. Sagona
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences
- University of Warwick
- Coventry
- UK
| | - Aurelija M. Grigonyte
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences
- University of Warwick
- Coventry
- UK
- Synthetic Biology Centre for Doctoral Training
| | - Paul R. MacDonald
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences
- University of Warwick
- Coventry
- UK
- MOAC DTC
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences
- University of Warwick
- Coventry
- UK
- iSSB
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83
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Spain E, Gilgunn S, Sharma S, Adamson K, Carthy E, O'Kennedy R, Forster RJ. Detection of prostate specific antigen based on electrocatalytic platinum nanoparticles conjugated to a recombinant scFv antibody. Biosens Bioelectron 2015; 77:759-66. [PMID: 26513282 DOI: 10.1016/j.bios.2015.10.058] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/09/2015] [Accepted: 10/19/2015] [Indexed: 01/12/2023]
Abstract
Highly sensitive and label free detection of prostate specific antigen (PSA) still remains a challenge in prostate cancer diagnosis. In this paper, we propose a sensitive electrochemical immunosensor based on electrocatalytic platinum nanoparticles conjugated to a recombinant scFv antibody. Gold disc electrodes functionalised with a l-Cysteine (Cys) self-assembled monolayer (SAM) were used to covalently bind PSA specific monoclonal antibody (anti-PSA) using N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide and N-hydroxysuccinimide (EDC/NHS) chemistry. Immunosensing was completed using sandwich-type immunoreaction of the PSA-antigen (1-30 ng/mL) between anti-PSA immobilized on the l-Cys modified electrode using label free electrochemical impedance (EIS) technique. Furthermore, highly specific in-house generated scFv fragments as receptor proteins were utilised for one step site-directed immobilisation on the surface of platinum nanoparticles (PtNPs). To improve the sensitivity of the immunoassay, these scFV labelled electrocatalytic PtNPs were then used for covalent hybridisation to the PSA modified electrode and then applied in a hybridisation assay to determine the concentration of the PSA by measuring the faradaic current associated with reduction of peroxide in solution. Semi-log plots of the PSA concentration vs. faradaic current are linear from 1 to 30 ng/mL and pM concentrations can be detected without the need for molecular, e.g., PCR or NASBA, amplification.
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Affiliation(s)
- Elaine Spain
- Biomedical Diagnostic Institute, Dublin City University, Dublin 9, Ireland; School of Chemical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland.
| | - Sarah Gilgunn
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Shikha Sharma
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Kellie Adamson
- School of Chemical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Eadaoin Carthy
- School of Chemical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Robert J Forster
- School of Chemical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
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