Article
Multidisciplinary Sciences
Ruiqi Huang, Gabrielle Warner Jenkins, Yunjeong Kim, Robyn L. Stanfield, Amrinder Singh, Maria Martinez-Yamout, Gerard J. Kroon, Jonathan L. Torres, Abigail M. Jackson, Abigail Kelley, Namir Shaabani, Baisen Zeng, Michael Bacica, Wen Chen, Christopher Warner, Jasmina Radoicic, Joongho Joh, Krishani Dinali Perera, Huldah Sang, Tae Kim, Jianxiu Yao, Fangzhu Zhao, Devin Sokd, Dennis R. Burton, Jeff Allen, William Harriman, Waithaka Mwangi, Donghoon Chung, John R. Teijaro, Andrew B. Ward, H. Jane Dyson, Peter E. Wright, Ian A. Wilson, Kyeong-Ok Chang, Duncan Mcgregor, Vaughn V. Smider
Summary: Antibodies derived from cows have the potential to be a new class of therapeutics, capable of neutralizing various SARS-CoV-2 variants and providing protection against disease.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Virology
Kazuya Nagano, Yasuo Tsutsumi
Summary: Antibody drugs with high affinity and specificity are effective for intractable diseases, such as cancers and autoimmune diseases. The recent breakthrough in antibody drugs is largely due to the contribution of phage display technology.
Article
Biochemistry & Molecular Biology
Xuelian Bai, Moonseon Jang, Nam Ju Lee, Thi Thu Ha Nguyen, Mooyoung Jung, Jeong Yeon Hwang, Hyunbo Shim
Summary: Antibody discovery by phage display involves two phases, the binding phase and the amplification phase. The amplification efficiency of antibody fragments varies widely among different sequences, leading to diminished efficiency of antibody isolation. In this study, a novel synthetic scFv library with diversities aimed at improved amplification efficiency was designed and constructed. CDR sequences were analyzed to design the new library, and a machine learning method was used to predict potential fast-amplified sequences. The new library performed better in terms of binders isolated, unique sequences, and binder enrichment compared to the previous generation library.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Medicinal
Tomofumi Nakada-Masuta, Hiroyuki Takeda, Kazuhisa Uchida
Summary: In this study, a selection method for VNAR antibodies combining selection pressures and next-generation sequencing (NGS) analysis was investigated. The VNARs obtained under specific selection pressures showed higher reactivity and possessed physicochemical properties that reflected their respective selection pressures. This study enhances our understanding of VNAR properties and provides guidance for the screening of high-quality VNAR clones.
Review
Microbiology
Ana S. S. Andre, Isa Moutinho, Joana N. R. Dias, Frederico Aires-da-Silva
Summary: The discovery of hybridoma technology and the development of phage display technology have opened a new era in antibody research and clinical development. Over the past thirty years, display selection technologies such as phage display have been widely promoted as ideal alternatives to traditional methods, with significant advancements in design, construction, and selection of antibody libraries. With the emergence of new therapeutic antibodies, phage display is expected to continue playing a central role, especially in challenging cases. In vivo phage display methods offer an advantage over conventional in vitro procedures for generating therapeutic antibodies against difficult targets and unmet medical needs.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Seyedeh Zahra Bahojb Mahdavi, Fatemeh Oroojalian, Shirin Eyvazi, Maryam Hejazi, Behzad Baradaran, Nasser Pouladi, Mohammad Reza Tohidkia, Ahad Mokhtarzadeh, Serge Muyldermans
Summary: Antibodies, as therapeutic and diagnostic molecules, play a crucial role in disease treatment, especially in cancer therapy. Alternative approaches, such as display selection technologies, have been developed to overcome the limitations of traditional hybridoma technology. These methods, including phage display, bacterial display, and yeast display, enable the screening and generation of high affinity antibodies with low immunogenicity risk. Understanding the basics of each method is important for antibody design suitable for different diseases, including cancer.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Mohammad Ridhuan Mohd Ali, Jia Siang Sum, Nurul Najian Aminuddin Baki, Yee Siew Choong, Nur Asyura Nor Amdan, Fairuz Amran, Theam Soon Lim
Summary: This study aimed to develop specific monoclonal antibodies against LipL21 antigen for future use in rapid and accurate immunoassay for leptospirosis. The generated monoclonal antibody against rLipL21 will be evaluated as a detection reagent for the diagnosis of human leptospirosis in a future study.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biotechnology & Applied Microbiology
Jingru Liang, Hang Dong, Fei Xu, Baowei Li, Haimei Li, Limei Chen, Mei Li, Yingchu Liu, Guosheng Jiang, Jinhua Dong
Summary: In this study, a monoclonal antibody named ESC9 was developed, and an immunosensor called ESC9 Quenchbody (Q-body) was generated for rapid and sensitive detection of estradiol. The ESC9 Q-body showed potential for clinical applications due to its excellent detection speed and sensitivity.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Medicinal
Tiange Gao, Chenxi Lou, Yan Wang, Haifang Wang, Aoneng Cao
Summary: It has been found that the CDR fragments of antibodies can be grafted onto gold nanoparticles to create artificial antibodies called Goldbodies, which maintain the same binding specificity as the original antibodies but have better stability. This study successfully created two anti-CA Goldbodies by predicting and reconstructing the CDR3 regions through sequence alignment of two anti-carbonic anhydrase (CA) antibodies, one with a known complex structure and the other without. The results showed that both Goldbodies can bind to CA simultaneously, indicating the possibility of developing artificial antibodies by directly grafting and conformationally reconstructing predicted CDR3 regions.
Article
Immunology
Ahmad Najafi, Reza Valadan, Hossein Asgarian-Omran, Alireza Rafiei, Mohsen Tehrani
Summary: In this study, a recombinant phage was generated using the phage display method to select monoclonal phages that can react with the dimerization domain of HER2 receptor. Functional tests confirmed their specificity and anti-tumor properties.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Review
Chemistry, Multidisciplinary
Michael A. Firer, Galia Luboshits
Summary: The development and clinical efficacy of ADCs have attracted significant interest in academia and industry, with ten ADCs having received FDA approval. These drugs specifically deliver cytotoxic agents to target cells, showing promise in providing long-term clinical benefits for patients with hematological malignancies.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Article
Biochemical Research Methods
Eeva-Christine Brockmann, Mikko Pyykko, Heidi Hannula, Kamran Khan, Urpo Lamminmaki, Tuomas Huovinen
Summary: This study discusses the impact of loop length variation on the structural diversity of antibody libraries. Introducing loop length variation in specific antibody fragments can enhance affinity, especially in CDR-L1 and CDR-H2 loops. The results lay the foundation for developing novel synthetic antibody libraries with unique loop length combinations.
Review
Virology
Renato Kaylan Alves Franca, Igor Cabral Studart, Marcus Rafael Lobo Bezerra, Larissa Queiroz Pontes, Antonio Marcos Aires Barbosa, Marcelo Macedo Brigido, Gilvan Pessoa Furtado, Andrea Queiroz Maranhao
Summary: The search for innovative anti-cancer drugs remains challenging, but antibodies have proven to be a valuable asset in successful cancer therapy. The traditional hybridoma technology has limitations, necessitating alternative approaches like humanizing murine monoclonal antibodies. Phage Display libraries offer an innovative tool for antibody selection, allowing the in vitro selection of antibodies directed towards cancer antigens.
Article
Food Science & Technology
Janne Leivo, Markus Vehniainen, Urpo Lamminmaki
Summary: The use of synthetic antibody libraries and phage displays allows for efficient generation of specific antibodies against a wide range of targets, particularly those that are difficult to target. In this study, anti-idiotype antibodies with unique binding properties were successfully generated from synthetic antibody libraries for deoxynivalenol mycotoxin, leading to the development of specific assays for its detection.
Article
Medicine, Research & Experimental
Andre Azevedo Reis Teixeira, Michael Frank Erasmus, Sara D'Angelo, Leslie Naranjo, Fortunato Ferrara, Camila Leal-Lopes, Oliver Durrant, Cecile Galmiche, Aleardo Morelli, Anthony Scott-Tucker, Andrew Raymon Morton Bradbury
Summary: This paper introduces a new antibody library format that generates high-affinity binders with drug-like developability properties directly from initial selections, reducing the need for further engineering or affinity maturation. This innovative design is expected to accelerate drug development processes by reducing the failure rate of leads due to poor antibody affinities and developability.
Article
Biochemistry & Molecular Biology
Swe-Htet Naing, Krishna M. Vukoti, Jason E. Drury, Jennifer L. Johnson, Sibel Kalyoncu, Shannon E. Hill, Matthew P. Torres, Raquel L. Lieberman
ACS CHEMICAL BIOLOGY
(2015)
Article
Biochemical Research Methods
Jennifer L. Johnson, Kevin C. Entzminger, Jeongmin Hyun, Sibel Kalyoncu, David P. Heaner, Ivan A. Morales, Aly Sheppard, James C. Gumbart, Jennifer A. Maynard, Raquel L. Lieberman
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2015)
Article
Biochemistry & Molecular Biology
Sibel Kalyoncu, David P. Heaner, Zohre Kurt, Casey M. Bethel, Chiamaka U. Ukachukwu, Srinivas Chakravarthy, Jim C. Spain, Raquel L. Lieberman
NATURE CHEMICAL BIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Swe-Htet Naing, Sibel Kalyoncu, David M. Smalley, Hyojung Kim, Xingjian Tao, Josh B. George, Alex P. Jonke, Ryan C. Oliver, Volker S. Urban, Matthew P. Torres, Raquel L. Lieberman
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Biotechnology & Applied Microbiology
Samuel D. Stimple, Sibel Kalyoncu, Alec A. Desai, Jesper E. Mogensen, Lotte T. Spang, Desiree J. Asgreen, Arne Staby, Peter M. Tessier
BIOTECHNOLOGY AND BIOENGINEERING
(2019)
Article
Biochemistry & Molecular Biology
Merve Arslan, Dilara Karadag, Sibel Kalyoncu
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2020)
Article
Biotechnology & Applied Microbiology
Wenjia Lou, Samuel D. Stimple, Alec A. Desai, Emily K. Makowski, Sibel Kalyoncu, Jesper E. Mogensen, Lotte T. Spang, Desiree J. Asgreen, Arne Staby, Karen Duus, Jan Amstrup, Yulei Zhang, Peter M. Tessier
Summary: Biologics such as peptides and proteins have attractive attributes, but are prone to aggregation. By developing conformation-specific antibodies, a sensitive immunoassay for detecting aggregates has been successfully created. These antibodies not only exhibit high conformational specificity, but also cross-react with amyloid fibrils formed by various polypeptides.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Multidisciplinary Sciences
Merve Arslan, Murat Karadag, Ebru Onal, Emine Gelinci, Gulcin Cakan-Akdogan, Sibel Kalyoncu
Summary: Single chain antibody fragments (scFvs) are widely used in diagnostics and therapeutics due to their small size and various engineering approaches. The design of the linker between the variable heavy and light chains of scFv plays a crucial role in its construction. The flexibility of the linker is determined by its length and sequence content, and flexible linkers such as glycine-serine (GS) are commonly preferred. However, repeated sequences in GS linkers can cause problems in PCR-based engineering and immunogenicity.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Sibel Kalyoncu, Semiramis Yilmaz, Ayca Zeybek Kuyucu, Dogu Sayili, Olcay Mert, Hakan Soyturk, Seyda Gullu, Huseyin Akinturk, Erhan Citak, Merve Arslan, Melda Guray Taskinarda, Ibrahim Oguzhan Tarman, Gizem Yilmazer Altun, Ceren Ozer, Ridvan Orkut, Aysegul Demirtas, Idil Tilmensagir, Umur Keles, Ceren Ulker, Gizem Aralan, Yavuz Mercan, Muge Ozkan, Hasan Onur Caglar, Gizem Arik, Mehmet Can Ucar, Muzaffer Yildirim, Tugce Canavar Yildirim, Dilara Karadag, Erhan Bal, Aybike Erdogan, Serif Senturk, Serdar Uzar, Hakan Enul, Cumhur Adiay, Fahriye Sarac, Arzu Tas Ekiz, Irem Abaci, Ozge Aksoy, Hivda Ulbegi Polat, Saban Tekin, Stefan Dimitrov, Aykut Ozkul, Gerhard Wingender, Ihsan Gursel, Mehmet Ozturk, Mehmet Inan
Summary: Recombinant protein-based SARS-CoV-2 vaccines are developed to address the vaccine equity gap, especially for low-/middle-income countries. The vaccine utilizes the receptor binding domain of the SARS-CoV-2 Delta Plus strain (RBD-DP) and has shown high immunogenicity with both antibody and T-cell responses. It also demonstrates strong neutralizing activity against different strains of the virus and provides effective protection in mouse models.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Merve Arslan, Tugce Ulucay, Seyit Kale, Sibel Kalyoncu
Summary: Based on a mutagenesis study of conserved residues near HCDR3, it was found that key residues positioned around the salt bridge between VH-K94 and VH-D101 have an extensive impact on the conformation of HCDR3, thus providing insights for simultaneously improving both affinity and stability of antibodies.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2023)
Article
Biochemistry & Molecular Biology
Deniz Dogan, Merve Arslan, Tugce Ulucay, Sibel Kalyoncu, Stefan Dimitrov, Seyit Kale
Summary: The study investigates the structural rearrangements of CENP-A nucleosomes resulting from antibody binding, showing that the antibodies can alter the dynamics of the nucleosomal core and indirectly affect the surrounding DNA. The binding of antibodies to the histone octamer surface is associated with conformational changes in CENP-A nucleosomes, indicating a more drastic impact compared to canonical nucleosomes. In addition, evidence suggests that the antibodies bind different octamer facades at varying affinities, revealing another level of complexity in DNA sequence regulation.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Meeting Abstract
Chemistry, Multidisciplinary
Samuel Stimple, Sibel Kalyoncu, Alec Desai, Jesper Mogensen, Lotte Spang, Desiree Asgreen, Arne Staby, Peter Tessier
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Review
Biology
Merve Arslan, Dilara Karadag, Sibel Kalyoncu
TURKISH JOURNAL OF BIOLOGY
(2019)