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A novel phage-library-selected peptide inhibits human TNF-α binding to its receptors. Molecules 2014; 19:7255-68. [PMID: 24896264 PMCID: PMC6271742 DOI: 10.3390/molecules19067255] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/22/2014] [Accepted: 05/27/2014] [Indexed: 12/31/2022] Open
Abstract
We report the identification of a new human tumor necrosis factor-alpha (TNF-α) specific peptide selected by competitive panning of a phage library. Competitive elution of phages was obtained using the monoclonal antibody adalimumab, which neutralizes pro-inflammatory processes caused by over-production of TNF-α in vivo, and is used to treat severe symptoms of rheumatoid arthritis. The selected peptide was synthesized in monomeric and branched form and analyzed for binding to TNF-α and competition with adalimumab and TNF-α receptors. Results of competition with TNF-α receptors in surface plasmon resonance and melanoma cells expressing both TNF receptors make the peptide a candidate compound for the development of a novel anti-TNF-α drug.
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Strokappe N, Szynol A, Aasa-Chapman M, Gorlani A, Forsman Quigley A, Hulsik DL, Chen L, Weiss R, de Haard H, Verrips T. Llama antibody fragments recognizing various epitopes of the CD4bs neutralize a broad range of HIV-1 subtypes A, B and C. PLoS One 2012; 7:e33298. [PMID: 22438910 PMCID: PMC3305327 DOI: 10.1371/journal.pone.0033298] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 02/10/2012] [Indexed: 11/30/2022] Open
Abstract
Many of the neutralising antibodies, isolated to date, display limited activities against the globally most prevalent HIV-1 subtypes A and C. Therefore, those subtypes are considered to be an important target for antibody-based therapy. Variable domains of llama heavy chain antibodies (VHH) have some superior properties compared with classical antibodies. Therefore we describe the application of trimeric forms of envelope proteins (Env), derived from HIV-1 of subtype A and B/C, for a prolonged immunization of two llamas. A panel of VHH, which interfere with CD4 binding to HIV-1 Env were selected with use of panning. The results of binding and competition assays to various Env, including a variant with a stabilized CD4-binding state (gp120Ds2), cross-competition experiments, maturation analysis and neutralisation assays, enabled us to classify the selected VHH into three groups. The VHH of group I were efficient mainly against viruses of subtype A, C and B′/C. The VHH of group II resemble the broadly neutralising antibody (bnmAb) b12, neutralizing mainly subtype B and C viruses, however some had a broader neutralisation profile. A representative of the third group, 2E7, had an even higher neutralization breadth, neutralizing 21 out of the 26 tested strains belonging to the A, A/G, B, B/C and C subtypes. To evaluate the contribution of certain amino acids to the potency of the VHH a small set of the mutants were constructed. Surprisingly this yielded one mutant with slightly improved neutralisation potency against 92UG37.A9 (subtype A) and 96ZM651.02 (subtype C). These findings and the well-known stability of VHH indicate the potential application of these VHH as anti-HIV-1 microbicides.
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Affiliation(s)
- Nika Strokappe
- Biomolecular Imaging, Department Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Agnieszka Szynol
- Biomolecular Imaging, Department Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Marlèn Aasa-Chapman
- Division of Infection and Immunity, UCL/MRC Centre for Medical Molecular Virology, University College London, London, United Kingdom
| | - Andrea Gorlani
- Biomolecular Imaging, Department Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Anna Forsman Quigley
- Division of Infection and Immunity, UCL/MRC Centre for Medical Molecular Virology, University College London, London, United Kingdom
| | - David Lutje Hulsik
- Unit of Virus Host Cell Interactions (UVHCI), UMI 3265, Université Joseph Fourier-EMBL-CNRS, Grenoble, France
| | - Lei Chen
- Vaccine Research Centre, National Institute of Allergy and Infectious Diseases (NIAID), Nation Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Robin Weiss
- Division of Infection and Immunity, UCL/MRC Centre for Medical Molecular Virology, University College London, London, United Kingdom
| | - Hans de Haard
- Biomolecular Imaging, Department Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Theo Verrips
- Biomolecular Imaging, Department Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- * E-mail:
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Cloning antifungal single chain fragment variable antibodies by phage display and competitive panning elution. Anal Biochem 2009; 395:16-24. [DOI: 10.1016/j.ab.2009.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 07/08/2009] [Accepted: 08/02/2009] [Indexed: 11/19/2022]
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Abstract
New ligands for a variety of biological targets can be selected from biological or synthetic combinatorial peptide libraries. The use of different libraries to select novel peptides with potential therapeutic applications is reviewed. The possible combination of molecular diversity provided by combinatorial libraries and a rational approach derived from computational modeling is also considered. Advantages and disadvantages of different approaches are compared. Possible strategies to bypass loss of peptide bioactivity in the transition from ligand selection to in vivo use are discussed.
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Affiliation(s)
- Chiara Falciani
- Department of Molecular Biology, University of Siena, I-53100 Siena, Italy
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Han ZY, Wu KC, He FT, Han QL, Nie YZ, Han Y, Liu XN, Zheng JY, Xu MH, Lin T, Fan DM. Screening and identification of mimotope of gastric cancer associated antigen MGb1-Ag. World J Gastroenterol 2003; 9:1920-4. [PMID: 12970876 PMCID: PMC4656644 DOI: 10.3748/wjg.v9.i9.1920] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: Using a monoclonal antibody against gastric cancer antigen named MGb1 to screen a phage-displayed random peptide library fused with coat protein pIII in order to get some information on mimotopes.
METHODS: Through affinity enrichment and ELISA screening, positive clones of phages were amplified. 10 phage clones were selected after three rounds of biopanning and the ability of specific binding of the positive phage clones to MGb1-Ab were detected by ELISA assay (DNA sequencing was performed and the amino acid sequences were deduced) By blocking test, specificity of the mimic phage epitopes was identified.
RESULTS: There were approximately 200 times of enrichment about the titer of bound phages after three rounds of biopanning procedures. DNA of 10 phage clones after the third biopanning was assayed and the result showed that the positive clones had a specific binding activity to MGb1-Ab and a weak ability of binding to control mAb or to mouse IgG. DNA sequencing of 10 phage clones was performed and the amino acid sequences were deduced. According to the homology of the amino acid sequences of the displayed peptides, most of the phage clones had motifs of H(x)Q or L(x)S. And these 10 phage clones could also partly inhibit the binding of MGb1-Ab to gastric cancer cell KATO-III. The percentage of blocking was from (21.0 ± 1.6)% to (39.0 ± 2.7)%.
CONCLUSION: Motifs of H(x)Q and L(x)S selected and identified show a high homology in the mimic epitopes of gastric cancer associated antigen. There may be one or more clones which can act as candidates of tumor vaccines.
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Affiliation(s)
- Zhe-Yi Han
- Institute of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
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Bracci L, Pini A, Bernini A, Lelli B, Ricci C, Scarselli M, Niccolai N, Neri P. Biochemical filtering of a protein-protein docking simulation identifies the structure of a complex between a recombinant antibody fragment and alpha-bungarotoxin. Biochem J 2003; 371:423-7. [PMID: 12519078 PMCID: PMC1223289 DOI: 10.1042/bj20021369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2002] [Revised: 01/02/2003] [Accepted: 01/09/2003] [Indexed: 11/17/2022]
Abstract
The structural characterization of a complex of alpha-bungarotoxin with a recombinant antibody fragment that mimics the acetylcholine receptor was achieved using docking simulation procedures. To drive the computer simulation towards a limited set of solutions with biological significance, a filter, incorporating general considerations of antigen-antibody interactions, specificity of the selected antibody fragment and results from alpha-bungarotoxin epitope mapping, was adopted. Two similar structures were obtained for the complex, both of them stabilized by cation-pi and hydrophobic interactions due to tyrosilyl residues of the antibody fragment. Site-directed mutagenesis studies, removing each of the latter aromatic residues and causing full inactivation of the interaction process between the antibody fragment and the neurotoxin, support the validity of the calculated structure of the complex.
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Affiliation(s)
- Luisa Bracci
- Department of Molecular Biology, University of Siena, Via Fiorentina 1, I-53100 Siena, Italy.
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Abstract
We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Scarselli M, Spiga O, Ciutti A, Bernini A, Bracci L, Lelli B, Lozzi L, Calamandrei D, Di Maro D, Klein S, Niccolai N. NMR structure of alpha-bungarotoxin free and bound to a mimotope of the nicotinic acetylcholine receptor. Biochemistry 2002; 41:1457-63. [PMID: 11814338 DOI: 10.1021/bi011012f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A combinatorial library approach was used to produce synthetic peptides mimicking the snake neurotoxin binding site of nicotinic receptors. Among the sequences, which inhibited binding of alpha-bungarotoxin to muscle and neuronal nicotinic receptors, HRYYESSLPWYPD, a 14-amino acid peptide with considerably higher toxin-binding affinity than the other synthesized peptides, was selected, and the structure of its complex with the toxin was analyzed by NMR. Comparison of the solution structure of the free toxin and its complex with this peptide indicated that complex formation induced extensive conformational rearrangements mainly at finger II and the carboxy terminus of the protein. The peptidyl residues P10 and Y4 seemed to be critical for peptide folding and complex stability, respectively. The latter residue of the peptide strongly interacted with the protein by entering a small pocket delimited by D30, C33, S34, R36, and V39 toxin side chains.
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Affiliation(s)
- Maria Scarselli
- Department of Molecular Biology and Biomolecular Structure Research Center, University of Siena, Italy
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