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Journal articles on the topic 'Antibody-Libraries'

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Author: Grafiati

Published: 1 April 2023

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1

Vaughan, T. J., A. J. Williams, K. Pritchard, J. K. Osbourn, A. R. Pope, J. C. Earnshaw, J. McCafferty, J. Wilton, and K. S. Johnson. "Human antibody libraries." Immunotechnology 2, no. 1 (February 1996): 72–73. http://dx.doi.org/10.1016/1380-2933(96)80683-x.

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2

Valadon, Philippe, Sonia M. Pérez-Tapia, Renae S. Nelson, Omar U. Guzmán-Bringas, Hugo I. Arrieta-Oliva, Keyla M. Gómez-Castellano, Mary Ann Pohl, and Juan C. Almagro. "ALTHEA Gold Libraries™: antibody libraries for therapeutic antibody discovery." mAbs 11, no. 3 (February 26, 2019): 516–31. http://dx.doi.org/10.1080/19420862.2019.1571879.

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3

Lou, Kai-Jye. "Fab libraries for antibody discovery." Science-Business eXchange 3, no. 44 (November 2010): 1314. http://dx.doi.org/10.1038/scibx.2010.1314.

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4

Benhar, Itai. "Design of synthetic antibody libraries." Expert Opinion on Biological Therapy 7, no. 5 (May 2007): 763–79. http://dx.doi.org/10.1517/14712598.7.5.763.

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5

Bradbury, Andrew R. M., and James D. Marks. "Antibodies from phage antibody libraries." Journal of Immunological Methods 290, no. 1-2 (July 2004): 29–49. http://dx.doi.org/10.1016/j.jim.2004.04.007.

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6

Rader, Christoph, and Carlos F. Barbas. "Phage display of combinatorial antibody libraries." Current Opinion in Biotechnology 8, no. 4 (August 1997): 503–8. http://dx.doi.org/10.1016/s0958-1669(97)80075-4.

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7

Little, Melvyn, Frank Breitling, Stefan Dübel, Patrick Fuchs, and Michael Braunagel. "Human antibody libraries in Escherichia coli." Journal of Biotechnology 41, no. 2-3 (July 1995): 187–95. http://dx.doi.org/10.1016/0168-1656(95)00022-i.

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8

Zhou, Heyue, Yan-Liang Zhang, Guodi Lu, Henry Ji, and Charles P. Rodi. "Recombinant antibody libraries and selection technologies." New Biotechnology 28, no. 5 (September 2011): 448–52. http://dx.doi.org/10.1016/j.nbt.2011.03.013.

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9

Hoogenboom, Hennie R. "Selecting and screening recombinant antibody libraries." Nature Biotechnology 23, no. 9 (September 2005): 1105–16. http://dx.doi.org/10.1038/nbt1126.

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10

Catcott, Kalli C., Molly A. McShea, Carl Uli Bialucha, Kathy L. Miller, Stuart W. Hicks, Parmita Saxena, Thomas G. Gesner, et al. "Microscale screening of antibody libraries as maytansinoid antibody-drug conjugates." mAbs 8, no. 3 (January 11, 2016): 513–23. http://dx.doi.org/10.1080/19420862.2015.1134408.

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11

Bowley, D. R., T. M. Jones, D. R. Burton, and R. A. Lerner. "Libraries against libraries for combinatorial selection of replicating antigen-antibody pairs." Proceedings of the National Academy of Sciences 106, no. 5 (January 12, 2009): 1380–85. http://dx.doi.org/10.1073/pnas.0812291106.

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12

Dantas-Barbosa, Carmela, Marcelo de Macedo Brigido, and Andrea Queiroz Maranhao. "Antibody Phage Display Libraries: Contributions to Oncology." International Journal of Molecular Sciences 13, no. 5 (May 4, 2012): 5420–40. http://dx.doi.org/10.3390/ijms13055420.

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13

Jara-Acevedo, Ricardo, Paula Diez, Maria Gonzalez-Gonzalez, Rosa Degano, Nieves Ibarrola, Rafael Gongora, Alberto Orfao, and Manuel Fuentes. "Methods for Selecting Phage Display Antibody Libraries." Current Pharmaceutical Design 22, no. 43 (January 11, 2017): 6490–99. http://dx.doi.org/10.2174/1381612822666161007153127.

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14

Clackson, Tim, Hennie R. Hoogenboom, Andrew D. Griffiths, and Greg Winter. "Making antibody fragments using phage display libraries." Nature 352, no. 6336 (August 1991): 624–28. http://dx.doi.org/10.1038/352624a0.

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15

Wright, Michael J., and Mahendra P. Deonarain. "Phage display of chelating recombinant antibody libraries." Molecular Immunology 44, no. 11 (April 2007): 2860–69. http://dx.doi.org/10.1016/j.molimm.2007.01.026.

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16

Cobaugh, Christian W., Juan C. Almagro, Mark Pogson, Brent Iverson, and George Georgiou. "Synthetic Antibody Libraries Focused Towards Peptide Ligands." Journal of Molecular Biology 378, no. 3 (May 2008): 622–33. http://dx.doi.org/10.1016/j.jmb.2008.02.037.

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17

Appel, Jon R., Jaime Buencamino, Richard A. Houghten, and Clemencia Pinilla. "Exploring antibody polyspecificity using synthetic combinatorial libraries." Molecular Diversity 2, no. 1-2 (October 1996): 29–34. http://dx.doi.org/10.1007/bf01718697.

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18

Rader, Christoph. "Antibody libraries in drug and target discovery." Drug Discovery Today 6, no. 1 (January 2001): 36–43. http://dx.doi.org/10.1016/s1359-6446(00)01595-6.

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19

Paull, Michael L., and Patrick S. Daugherty. "Mapping serum antibody repertoires using peptide libraries." Current Opinion in Chemical Engineering 19 (March 2018): 21–26. http://dx.doi.org/10.1016/j.coche.2017.12.001.

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20

Harel Inbar, Noa, and Itai Benhar. "Selection of antibodies from synthetic antibody libraries." Archives of Biochemistry and Biophysics 526, no. 2 (October 2012): 87–98. http://dx.doi.org/10.1016/j.abb.2011.12.028.

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21

Buckler, David R., Albert Park, Malini Viswanathan, Rene M. Hoet, and Robert C. Ladner. "Screening isolates from antibody phage-display libraries." Drug Discovery Today 13, no. 7-8 (April 2008): 318–24. http://dx.doi.org/10.1016/j.drudis.2007.10.012.

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22

Zhao, Aizhi, Mohammad R. Tohidkia, Donald L. Siegel, George Coukos, and Yadollah Omidi. "Phage antibody display libraries: a powerful antibody discovery platform for immunotherapy." Critical Reviews in Biotechnology 36, no. 2 (November 14, 2014): 276–89. http://dx.doi.org/10.3109/07388551.2014.958978.

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23

Soon Lim, Theam, and Soo Khim Chan. "Immune Antibody Libraries: Manipulating The Diverse Immune Repertoire for Antibody Discovery." Current Pharmaceutical Design 22, no. 43 (January 11, 2017): 6480–89. http://dx.doi.org/10.2174/1381612822666160923111924.

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24

Batonick, Melissa, Erika G. Holland, Valeria Busygina, Dawn Alderman, Brian K. Kay, Michael P. Weiner, and Margaret M. Kiss. "Platform for high-throughput antibody selection using synthetically-designed antibody libraries." New Biotechnology 33, no. 5 (September 2016): 565–73. http://dx.doi.org/10.1016/j.nbt.2015.11.005.

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25

Almagro, Juan C., Martha Pedraza-Escalona, Hugo Iván Arrieta, and Sonia Mayra Pérez-Tapia. "Phage Display Libraries for Antibody Therapeutic Discovery and Development." Antibodies 8, no. 3 (August 23, 2019): 44. http://dx.doi.org/10.3390/antib8030044.

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Phage display technology has played a key role in the remarkable progress of discovering and optimizing antibodies for diverse applications, particularly antibody-based drugs. This technology was initially developed by George Smith in the mid-1980s and applied by John McCafferty and Gregory Winter to antibody engineering at the beginning of 1990s. Here, we compare nine phage display antibody libraries published in the last decade, which represent the state of the art in the discovery and development of therapeutic antibodies using phage display. We first discuss the quality of the libraries and the diverse types of antibody repertoires used as substrates to build the libraries, i.e., naïve, synthetic, and semisynthetic. Second, we review the performance of the libraries in terms of the number of positive clones per panning, hit rate, affinity, and developability of the selected antibodies. Finally, we highlight current opportunities and challenges pertaining to phage display platforms and related display technologies.

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26

Wollacott, Andrew M., Chonghua Xue, Qiuyuan Qin, June Hua, Tanggis Bohnuud, Karthik Viswanathan, and Vijaya B. Kolachalama. "Quantifying the nativeness of antibody sequences using long short-term memory networks." Protein Engineering, Design and Selection 32, no. 7 (July 2019): 347–54. http://dx.doi.org/10.1093/protein/gzz031.

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Abstract Antibodies often undergo substantial engineering en route to the generation of a therapeutic candidate with good developability properties. Characterization of antibody libraries has shown that retaining native-like sequence improves the overall quality of the library. Motivated by recent advances in deep learning, we developed a bi-directional long short-term memory (LSTM) network model to make use of the large amount of available antibody sequence information, and use this model to quantify the nativeness of antibody sequences. The model scores sequences for their similarity to naturally occurring antibodies, which can be used as a consideration during design and engineering of libraries. We demonstrate the performance of this approach by training a model on human antibody sequences and show that our method outperforms other approaches at distinguishing human antibodies from those of other species. We show the applicability of this method for the evaluation of synthesized antibody libraries and humanization of mouse antibodies.

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27

Tohidkia, Mohammad Reza, Jaleh Barar, Farzad Asadi, and Yadollah Omidi. "Molecular considerations for development of phage antibody libraries." Journal of Drug Targeting 20, no. 3 (September 27, 2011): 195–208. http://dx.doi.org/10.3109/1061186x.2011.611517.

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28

Bonvin, Pauline, Sophie Venet, Marie Kosco-Vilbois, and Nicolas Fischer. "Purpose-Oriented Antibody Libraries Incorporating Tailored CDR3 Sequences." Antibodies 4, no. 2 (May 20, 2015): 103–22. http://dx.doi.org/10.3390/antib4020103.

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29

Jespers, L., T. P. Bonnert, and G. Winter. "Selection of optical biosensors from chemisynthetic antibody libraries." Protein Engineering Design and Selection 17, no. 10 (November 10, 2004): 709–13. http://dx.doi.org/10.1093/protein/gzh083.

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30

Janda, Kim D., Lee-Chiang Lo, Chih-Hung L. Lo, Mui-Mui Sim, Ruo Wang, Chi-Huey Wong, and Richard A. Lerner. "Chemical Selection for Catalysis in Combinatorial Antibody Libraries." Science 275, no. 5302 (February 14, 1997): 945–48. http://dx.doi.org/10.1126/science.275.5302.945.

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31

Gong, Bing, Scott A. Lesley, and Peter G. Schultz. "A chromogenic assay for screening large antibody libraries." Journal of the American Chemical Society 114, no. 4 (February 1992): 1486–87. http://dx.doi.org/10.1021/ja00030a056.

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32

Kelly, Ryan L., Doris Le, Jessie Zhao, and K. Dane Wittrup. "Reduction of Nonspecificity Motifs in Synthetic Antibody Libraries." Journal of Molecular Biology 430, no. 1 (January 2018): 119–30. http://dx.doi.org/10.1016/j.jmb.2017.11.008.

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33

Tanaka, T. "De novo production of diverse intracellular antibody libraries." Nucleic Acids Research 31, no. 5 (March 1, 2003): 23e—23. http://dx.doi.org/10.1093/nar/gng023.

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34

Lerner, Richard A. "Combinatorial antibody libraries: new advances, new immunological insights." Nature Reviews Immunology 16, no. 8 (July 4, 2016): 498–508. http://dx.doi.org/10.1038/nri.2016.67.

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35

Kato, Mieko, and Yoshiro Hanyu. "Single-step colony assay for screening antibody libraries." Journal of Biotechnology 255 (August 2017): 1–8. http://dx.doi.org/10.1016/j.jbiotec.2017.06.010.

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36

Yamazoe, Sayumi, Jason M. Hogan, Sean M. West, Xiaodi A. Deng, Srikanth Kotapati, Xiang Shao, Patrick Holder, et al. "High-Throughput Platform to Identify Antibody Conjugation Sites from Antibody–Drug Conjugate Libraries." Bioconjugate Chemistry 31, no. 4 (March 16, 2020): 1199–208. http://dx.doi.org/10.1021/acs.bioconjchem.0c00146.

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37

Lim, Bee Nar, Gee Jun Tye, Yee Siew Choong, Eugene Boon Beng Ong, Asma Ismail, and Theam Soon Lim. "Principles and application of antibody libraries for infectious diseases." Biotechnology Letters 36, no. 12 (September 12, 2014): 2381–92. http://dx.doi.org/10.1007/s10529-014-1635-x.

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38

Collet, T. A., P. Roben, R. O'Kennedy, C. F. Barbas, D. R. Burton, and R. A. Lerner. "A binary plasmid system for shuffling combinatorial antibody libraries." Proceedings of the National Academy of Sciences 89, no. 21 (November 1, 1992): 10026–30. http://dx.doi.org/10.1073/pnas.89.21.10026.

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39

Zebedee, S. L., C. F. Barbas, Y. L. Hom, R. H. Caothien, R. Graff, J. DeGraw, J. Pyati, R. LaPolla, D. R. Burton, and R. A. Lerner. "Human combinatorial antibody libraries to hepatitis B surface antigen." Proceedings of the National Academy of Sciences 89, no. 8 (April 15, 1992): 3175–79. http://dx.doi.org/10.1073/pnas.89.8.3175.

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40

Baecher-AIIan, C. M., K. Santora, S. Sarantopoulos, W. Den, S. R. Sompuram, A. M. Cevallos, N. Bhat, H. Ward, and J. Sharon. "Generation of a Polyclonal Fab Phage Display Library to the Protozoan Parasite Cryptosporidium parvum." Combinatorial Chemistry & High Throughput Screening 2, no. 6 (December 1999): 319–25. http://dx.doi.org/10.2174/1386207302666220205231512.

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We had developed a technology for creation of recombinant polyclonal antibody libraries, standardized perpetual mixtures of polyclonal whole antibodies for which the genes are available and can be altered as desired. We report here the first phase of generating a polyclonal antibody library to Cryptosporidium parvum, a protozoan parasite that causes severe disease in AIDS patients, for which there is no effective treatment. BALB/c mice, immunized by neonatal oral infection with oocysts followed by intraperitoneal immunization with a sporozoite/oocyst preparation of C. parvum, were used for construction of a Fab phage display library in a specially designed bidirectional vector. This library was selected for reactivity to an oocyst/sporozoite preparation, and was shown to be antigen-specific and diverse. Following mass transfer of the selected variable region gene pairs to appropriate mammalian expression vectors, such anti-C. parvum Fab phage display libraries could be used to develop chimeric polyclonal antibody libraries, with mouse variable regions and human constant regions, for passive immunotherapy of C. parvum infection.

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41

Pranomphon, Ranya, Witsanu Srila, and Montarop Yamabhai. "Generation of recombinant scFv antibody against Ochratoxin A (OTA)." Indonesian Journal of Biotechnology 22, no. 2 (February 13, 2018): 107. http://dx.doi.org/10.22146/ijbiotech.31121.

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Ochratoxin A (OTA) is a mycotoxin commonly found in agricultural products and can accumulate in the blood and tissues after that consuming contaminated food. Recombinant single-chain antibody fragments (scFv) against OTA were selected from phage display libraries. After of one round of biopanning against BSA-conjugated OTA (OTA-BSA), 52 and 6 phage clones displaying scFv antibodies were isolated from human (Yamo I.3) and rabbit (Bozmix I.2) libraries. Two phage clones (one from each libraries, i.e., yOTA1e3 and bOTA2a9) showed binding to free toxin by competitive ELISA. The soluble scFv antibodies were produced by superinfecting phage clones into E. coli suppressor strain HB2151. The scFv genes from these two phage clones were sub-cloned into pKP300ΔIII vectors to generate scFv-AP fusions. The binding affinity (IC50) of antibody derived from human library was higher than those from rabbit library. The binding property of recombinant antibody in the form of scFv-AP was better than those of soluble scFv form. Cross-reactivity analysis indicated that the two recombinant antibodies did not cross-react with other soluble toxins, namely AFB1, DON, ZEN and FB. The ability to use the recombinant scFv-AP to detect contaminated toxins in agricultural product (corn) was demonstrated.

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42

Huang, Aric, Wei Jin, Ahmed S. Fahad, Brooklyn K. Mussman, Grazia Paola Nicchia, Bharat Madan, Matheus Oliveira de Souza, et al. "Strategies to Screen Anti-AQP4 Antibodies from Yeast Surface Display Libraries." Antibodies 11, no. 2 (June 5, 2022): 39. http://dx.doi.org/10.3390/antib11020039.

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A rapid and effective method to identify disease-specific antibodies from clinical patients is important for understanding autoimmune diseases and for the development of effective disease therapies. In neuromyelitis optica (NMO), the identification of antibodies targeting the aquaporin-4 (AQP4) membrane protein traditionally involves the labor-intensive and time-consuming process of single B-cell sorting, followed by antibody cloning, expression, purification, and analysis for anti-AQP4 activity. To accelerate patient-specific antibody discovery, we compared two unique approaches for screening anti-AQP4 antibodies from yeast antibody surface display libraries. Our first approach, cell-based biopanning, has strong advantages for its cell-based display of native membrane-bound AQP4 antigens and is inexpensive and simple to perform. Our second approach, FACS screening using solubilized AQP4 antigens, permits real-time population analysis and precision sorting for specific antibody binding parameters. We found that both cell-based biopanning and FACS screening were effective for the enrichment of AQP4-binding clones. These screening techniques will enable library-scale functional interrogation of large natively paired antibody libraries for comprehensive analysis of anti-AQP4 antibodies in clinical samples and for robust therapeutic discovery campaigns.

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43

Sblattero, Daniele, Fiorella Florian, Tarcisio Not, Alessandro Ventura, Andrew Bradbury, and Roberto Marzari. "Analyzing the peripheral blood antibody repertoire of a celiac disease patient using phage antibody libraries." Human Antibodies 9, no. 4 (March 1, 2000): 199–205. http://dx.doi.org/10.3233/hab-2000-9402.

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44

Kim, Ho San, Shyh-Ching Lo, Douglas J. Wear, Alexander Stojadinovic, Peter J. Weina, and Mina J. Izadjoo. "Improvement of anti-Burkholderia mouse monoclonal antibody from various phage-displayed single-chain antibody libraries." Journal of Immunological Methods 372, no. 1-2 (September 2011): 146–61. http://dx.doi.org/10.1016/j.jim.2011.07.009.

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45

Leivo, Janne, Markus Vehniäinen, and Urpo Lamminmäki. "Phage Display Selection of an Anti-Idiotype-Antibody with Broad-Specificity to Deoxynivalenol Mycotoxins." Toxins 13, no. 1 (December 28, 2020): 18. http://dx.doi.org/10.3390/toxins13010018.

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The use of synthetic antibody libraries and phage displays provides an efficient and robust method for the generation of antibodies against a wide range of targets with highly specific binding properties. As the in vitro selection conditions can be easily controlled, these methods enable the rapid generation of binders against difficult targets such as toxins and haptens. In this study, we used deoxynivalenol mycotoxin as a target to generate anti-idiotype-antibodies with unique binding properties from synthetic antibody libraries. The binding of the selected anti-idiotype antibodies can be efficiently inhibited with the addition of free isoforms of deoxynivalenol. The antibody was consecutively used to develop deoxynivalenol-specific ELISA and TRF-immunoassays, which can detect deoxynivalenol and two of the most common metabolic isoforms in the range of 78–115 ng/mL.

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46

Ling, Michael. "Large Antibody Display Libraries for Isolation of High-Affinity Antibodies." Combinatorial Chemistry & High Throughput Screening 6, no. 5 (August 1, 2003): 421–32. http://dx.doi.org/10.2174/138620703106298608.

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47

Schulz, Steven, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, and Olivier Rivoire. "Parameters and determinants of responses to selection in antibody libraries." PLOS Computational Biology 17, no. 3 (March 25, 2021): e1008751. http://dx.doi.org/10.1371/journal.pcbi.1008751.

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The sequences of antibodies from a given repertoire are highly diverse at few sites located on the surface of a genome-encoded larger scaffold. The scaffold is often considered to play a lesser role than highly diverse, non-genome-encoded sites in controlling binding affinity and specificity. To gauge the impact of the scaffold, we carried out quantitative phage display experiments where we compare the response to selection for binding to four different targets of three different antibody libraries based on distinct scaffolds but harboring the same diversity at randomized sites. We first show that the response to selection of an antibody library may be captured by two measurable parameters. Second, we provide evidence that one of these parameters is determined by the degree of affinity maturation of the scaffold, affinity maturation being the process by which antibodies accumulate somatic mutations to evolve towards higher affinities during the natural immune response. In all cases, we find that libraries of antibodies built around maturated scaffolds have a lower response to selection to other arbitrary targets than libraries built around germline-based scaffolds. We thus propose that germline-encoded scaffolds have a higher selective potential than maturated ones as a consequence of a selection for this potential over the long-term evolution of germline antibody genes. Our results are a first step towards quantifying the evolutionary potential of biomolecules.

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48

Ferrara, Fortunato, Chang-Yub Kim, Leslie A. Naranjo, and Andrew RM Bradbury. "Large scale production of phage antibody libraries using a bioreactor." mAbs 7, no. 1 (January 2, 2015): 26–31. http://dx.doi.org/10.4161/19420862.2015.989034.

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49

Solemani Zadeh, Arghavan, Alissa Grässer, Heiko Dinter, Maximilian Hermes, and Katharina Schindowski. "Efficient Construction and Effective Screening of Synthetic Domain Antibody Libraries." Methods and Protocols 2, no. 1 (February 14, 2019): 17. http://dx.doi.org/10.3390/mps2010017.

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Phage display is a powerful technique for drug discovery in biomedical research in particular for antibody libraries. But, several technical challenges are associated with the selection process. For instance, during the panning step, the successful elution of the phages bound to the antigen is critical in order to avoid losing the most promising binders. Here, we present an efficient protocol to establish, screen and select synthetic libraries of domain antibodies using phage display. We do not only present suitable solutions to the above-mentioned challenges to improve elution by 50-fold, but we also present a step by step in-depth protocol with miniaturized volumes and optimized procedures to save material, costs and time for a successful phage display with domain antibodies. Hence, this protocol improves the selection process for an efficient handling process. The here presented library is based on the variable domain (vNAR) of the naturally occurring novel antibody receptor (IgNAR) from cartilage fishes. Diversity was introduced in the Complementarity-Determining Region 3 (CDR3) of the antigen-binding site with different composition and length.

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50

Crameri, Andreas, Steve Cwirla, and Willem P. C. Stemmer. "Construction and evolution of antibody–phage libraries by DMA shuffling." Nature Medicine 2, no. 1 (January 1996): 100–102. http://dx.doi.org/10.1038/nm0196-100.

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