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Nur A, Lai JY, Ch'ng ACW, Choong YS, Wan Isa WYH, Lim TS. A review of in vitro stochastic and non-stochastic affinity maturation strategies for phage display derived monoclonal antibodies. Int J Biol Macromol 2024; 277:134217. [PMID: 39069045 DOI: 10.1016/j.ijbiomac.2024.134217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
Monoclonal antibodies identified using display technologies like phage display occasionally suffers from a lack of affinity making it unsuitable for application. This drawback is circumvented with the application of affinity maturation. Affinity maturation is an essential step in the natural evolution of antibodies in the immune system. The evolution of molecular based methods has seen the development of various mutagenesis approaches. This allows for the natural evolutionary process during somatic hypermutation to be replicated in the laboratories for affinity maturation to fine-tune the affinity and selectivity of antibodies. In this review, we will discuss affinity maturation strategies for mAbs generated through phage display systems. The review will highlight various in vitro stochastic and non-stochastic affinity maturation approaches that includes but are not limited to random mutagenesis, site-directed mutagenesis, and gene synthesis.
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Affiliation(s)
- Alia Nur
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Wan Yus Haniff Wan Isa
- School of Medical Sciences, Department of Medicine, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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2
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Wang WC, Chang J, Lee CH, Chiang YW, Leu SJ, Mao YC, Chiang JR, Yang CK, Wu CJ, Yang YY. Phage display-derived alpaca nanobodies as potential therapeutics for Naja atra snake envenomation. Appl Environ Microbiol 2024; 90:e0012124. [PMID: 38980046 PMCID: PMC11337809 DOI: 10.1128/aem.00121-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024] Open
Abstract
Naja atra, the Chinese cobra, is a major cause of snake envenomation in Asia, causing hundreds of thousands of clinical incidents annually. The current treatment, horse serum-derived antivenom, has unpredictable side effects and presents manufacturing challenges. This study focused on developing new-generation snake venom antidotes by using microbial phage display technology to derive nanobodies from an alpaca immunized with attenuated N. atra venom. Following confirmation of the immune response in the alpaca, we amplified VHH genes from isolated peripheral blood mononuclear cells and constructed a phage display VHH library of 1.0 × 107 transformants. After four rounds of biopanning, the enriched phages exhibited increased binding activity to N. atra venom. Four nanobody clones with high binding affinities were selected: aNAH1, aNAH6, aNAH7, and aNAH9. Specificity testing against venom from various snake species, including two Southeast Asian cobra species, revealed nanobodies specific to the genus Naja. An in vivo mouse venom neutralization assay demonstrated that all nanobodies prolonged mouse survival and aNAH6 protected 66.6% of the mice from the lethal dosage. These findings highlight the potential of phage display-derived nanobodies as valuable antidotes for N. atra venom, laying the groundwork for future applications in snakebite treatment.IMPORTANCEChinese cobra venom bites present a formidable medical challenge, and current serum treatments face unresolved issues. Our research applied microbial phage display technology to obtain a new, effective, and cost-efficient treatment approach. Despite interest among scientists in utilizing this technology to screen alpaca antibodies against toxins, the available literature is limited. This study makes a significant contribution by introducing neutralizing antibodies that are specifically tailored to Chinese cobra venom. We provide a comprehensive and unbiased account of the antibody construction process, accompanied by thorough testing of various nanobodies and an assessment of cross-reactivity with diverse snake venoms. These nanobodies represent a promising avenue for targeted antivenom development that bridges microbiology and biotechnology to address critical health needs.
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Affiliation(s)
- Wei-Chu Wang
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Jungshan Chang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
- International Master/Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chi-Hsin Lee
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Core Laboratory of Antibody Generation and Research, Taipei Medical University, Taipei, Taiwan
| | - Yu-Wei Chiang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Biology and Anatomy, National Defense Medical Center, Taipei, Taiwan
- Foundation for Poison Control, Taipei, Taiwan
| | - Sy-Jye Leu
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yan-Chiao Mao
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- School of Medicine, National Defense Medical Centre, Taipei, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- Division of Clinical Toxicology, Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jen-Ron Chiang
- Bioproduction Plants, National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Chun-Kai Yang
- Interdisciplinary Research on Ecology and Sustainability, National Dong Hwa University, Hualien, Taiwan
| | - Chao-Jung Wu
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yi-Yuan Yang
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Core Laboratory of Antibody Generation and Research, Taipei Medical University, Taipei, Taiwan
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3
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Schardt JS, Sivaneri NS, Tessier PM. Monoclonal Antibody Generation Using Single B Cell Screening for Treating Infectious Diseases. BioDrugs 2024; 38:477-486. [PMID: 38954386 DOI: 10.1007/s40259-024-00667-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2024] [Indexed: 07/04/2024]
Abstract
The screening of antigen-specific B cells has been pivotal for biotherapeutic development for over four decades. Conventional antibody discovery strategies, including hybridoma technology and single B cell screening, remain widely used based on their simplicity, accessibility, and proven track record. Technological advances and the urgent demand for infectious disease applications have shifted paradigms in single B cell screening, resulting in increased throughput and decreased time and labor, ultimately enabling the rapid identification of monoclonal antibodies with desired biological and biophysical properties. Herein, we provide an overview of conventional and emergent single B cell screening approaches and highlight their potential strengths and weaknesses. We also detail the impact of innovative technologies-including miniaturization, microfluidics, multiplexing, and deep sequencing-on the recent identification of broadly neutralizing antibodies for infectious disease applications. Overall, the coronavirus disease 2019 (COVID-19) pandemic has reinvigorated efforts to improve the efficiency of monoclonal antibody discovery, resulting in the broad application of innovative antibody discovery methodologies for treating a myriad of infectious diseases and pathological conditions.
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Affiliation(s)
- John S Schardt
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Neelan S Sivaneri
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Peter M Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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4
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Ribeiro R, Moreira JN, Goncalves J. Development of a new affinity maturation protocol for the construction of an internalizing anti-nucleolin antibody library. Sci Rep 2024; 14:10608. [PMID: 38719911 PMCID: PMC11079059 DOI: 10.1038/s41598-024-61230-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
Over the last decades, monoclonal antibodies have substantially improved the treatment of several conditions. The continuous search for novel therapeutic targets and improvements in antibody's structure, demands for a constant optimization of their development. In this regard, modulation of an antibody's affinity to its target has been largely explored and culminated in the discovery and optimization of a variety of molecules. It involves the creation of antibody libraries and selection against the target of interest. In this work, we aimed at developing a novel protocol to be used for the affinity maturation of an antibody previously developed by our group. An antibody library was constructed using an in vivo random mutagenesis approach that, to our knowledge, has not been used before for antibody development. Then, a cell-based phage display selection protocol was designed to allow the fast and simple screening of antibody clones capable of being internalized by target cells. Next generation sequencing coupled with computer analysis provided an extensive characterization of the created library and post-selection pool, that can be used as a guide for future antibody development. With a single selection step, an enrichment in the mutated antibody library, given by a decrease in almost 50% in sequence diversity, was achieved, and structural information useful in the study of the antibody-target interaction in the future was obtained.
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Affiliation(s)
- Rita Ribeiro
- CNC-Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine (Polo 1), University of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Lisbon, Portugal
- Univ Coimbra-University of Coimbra, CIBB, Faculty of Pharmacy, Coimbra, Portugal
| | - João N Moreira
- CNC-Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine (Polo 1), University of Coimbra, Coimbra, Portugal.
- Univ Coimbra-University of Coimbra, CIBB, Faculty of Pharmacy, Coimbra, Portugal.
| | - João Goncalves
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Lisbon, Portugal.
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5
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Lee HE, Cho AH, Hwang JH, Kim JW, Yang HR, Ryu T, Jung Y, Lee S. Development, High-Throughput Profiling, and Biopanning of a Large Phage Display Single-Domain Antibody Library. Int J Mol Sci 2024; 25:4791. [PMID: 38732011 PMCID: PMC11083953 DOI: 10.3390/ijms25094791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Immunoglobulin G-based monoclonal antibodies (mAbs) have been effective in treating various diseases, but their large molecular size can limit their penetration of tissue and efficacy in multifactorial diseases, necessitating the exploration of alternative forms. In this study, we constructed a phage display library comprising single-domain antibodies (sdAbs; or "VHHs"), known for their small size and remarkable stability, using a total of 1.6 × 109 lymphocytes collected from 20 different alpacas, resulting in approximately 7.16 × 1010 colonies. To assess the quality of the constructed library, next-generation sequencing-based high-throughput profiling was performed, analyzing approximately 5.65 × 106 full-length VHH sequences, revealing 92% uniqueness and confirming the library's diverse composition. Systematic characterization of the library revealed multiple sdAbs with high affinity for three therapeutically relevant antigens. In conclusion, our alpaca sdAb phage display library provides a versatile resource for diagnostics and therapeutics. Furthermore, the library's vast natural VHH antibody repertoire offers insights for generating humanized synthetic sdAb libraries, further advancing sdAb-based therapeutics.
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Affiliation(s)
- Hee Eon Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Ah Hyun Cho
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Jae Hyeon Hwang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Ji Woong Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Ha Rim Yang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Taehoon Ryu
- ATG Lifetech Inc., Seoul 08507, Republic of Korea; (T.R.); (Y.J.)
| | - Yushin Jung
- ATG Lifetech Inc., Seoul 08507, Republic of Korea; (T.R.); (Y.J.)
| | - Sukmook Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
- Department of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul 02707, Republic of Korea
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Song BPC, Lai JY, Lim TS. Generation of a Naïve Human scFv Phage Display Library and Panning Selection. Methods Mol Biol 2024; 2793:21-40. [PMID: 38526721 DOI: 10.1007/978-1-0716-3798-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Phage display antibody libraries have been successfully used as the essential tool to produce monoclonal antibodies against a plethora of targets ranging from diseases to native biologically important proteins as well as small molecules. It is well documented that diverse antibody genes are the major genetic source for the construction of a high-quality antibody library and selection of high-affinity antibodies. Naïve antibody libraries are derived using the IgM repertoire of healthy donors obtained from B-cells isolated from human peripheral blood mononuclear cell (PBMC). Single-chain fragment variable (scFv) is a routinely used format due to its smaller size and preference for phage display. The process involves the use of a two-step cloning method for library construction. The protocol also covers the biopanning process for target positive clone selection.
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Affiliation(s)
- Brenda Pei Chui Song
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang, Malaysia.
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7
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Song BPC, Ch'ng ACW, Lim TS. Review of phage display: A jack-of-all-trades and master of most biomolecule display. Int J Biol Macromol 2024; 256:128455. [PMID: 38013083 DOI: 10.1016/j.ijbiomac.2023.128455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Phage display was first described by George P. Smith when it was shown that virus particles were capable of presenting foreign proteins on their surface. The technology has paved the way for the evolution of various biomolecules presentation and diverse selection strategies. This unique feature has been applied as a versatile platform for numerous applications in drug discovery, protein engineering, diagnostics, and vaccine development. Over the decades, the limits of biomolecules displayed on phage particles have expanded from peptides to proteomes and even alternative scaffolds. This has allowed phage display to be viewed as a versatile display platform to accommodate various biomolecules ranging from small peptides to larger proteomes which has significantly impacted advancements in the biomedical industry. This review will explore the vast array of biomolecules that have been successfully employed in phage display technology in biomedical research.
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Affiliation(s)
- Brenda Pei Chui Song
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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8
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Vu SH, Pham HH, Pham TTP, Le TT, Vo MC, Jung SH, Lee JJ, Nguyen XH. Adoptive NK Cell Therapy - a Beacon of Hope in Multiple Myeloma Treatment. Front Oncol 2023; 13:1275076. [PMID: 38023191 PMCID: PMC10656693 DOI: 10.3389/fonc.2023.1275076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Major advances in the treatment of multiple myeloma (MM) have been achieved by effective new agents such as proteasome inhibitors, immunomodulatory drugs, or monoclonal antibodies. Despite significant progress, MM remains still incurable and, recently, cellular immunotherapy has emerged as a promising treatment for relapsed/refractory MM. The emergence of chimeric antigen receptor (CAR) technology has transformed immunotherapy by enhancing the antitumor functions of T cells and natural killer (NK) cells, leading to effective control of hematologic malignancies. Recent advancements in gene delivery to NK cells have paved the way for the clinical application of CAR-NK cell therapy. CAR-NK cell therapy strategies have demonstrated safety, tolerability, and substantial efficacy in treating B cell malignancies in various clinical settings. However, their effectiveness in eliminating MM remains to be established. This review explores multiple approaches to enhance NK cell cytotoxicity, persistence, expansion, and manufacturing processes, and highlights the challenges and opportunities associated with CAR-NK cell therapy against MM. By shedding light on these aspects, this review aims to provide valuable insights into the potential of CAR-NK cell therapy as a promising approach for improving the treatment outcomes of MM patients.
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Affiliation(s)
- Son Hai Vu
- Hi-Tech Center and Vinmec-VinUni Institute of Immunology, Vinmec Healthcare System, Hanoi, Vietnam
| | - Ha Hong Pham
- Hi-Tech Center and Vinmec-VinUni Institute of Immunology, Vinmec Healthcare System, Hanoi, Vietnam
| | - Thao Thi Phuong Pham
- Hi-Tech Center and Vinmec-VinUni Institute of Immunology, Vinmec Healthcare System, Hanoi, Vietnam
| | - Thanh Thien Le
- Hi-Tech Center and Vinmec-VinUni Institute of Immunology, Vinmec Healthcare System, Hanoi, Vietnam
| | - Manh-Cuong Vo
- Research Center for Cancer Immunotherapy, Chonnam National University Hwasun Hospital, Hwasun, Jeollanamdo, Republic of Korea
| | - Sung-Hoon Jung
- Research Center for Cancer Immunotherapy, Chonnam National University Hwasun Hospital, Hwasun, Jeollanamdo, Republic of Korea
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital and Chonnam National University Medical School, Hwasun, Jeollanamdo, Republic of Korea
| | - Je-Jung Lee
- Research Center for Cancer Immunotherapy, Chonnam National University Hwasun Hospital, Hwasun, Jeollanamdo, Republic of Korea
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital and Chonnam National University Medical School, Hwasun, Jeollanamdo, Republic of Korea
| | - Xuan-Hung Nguyen
- Hi-Tech Center and Vinmec-VinUni Institute of Immunology, Vinmec Healthcare System, Hanoi, Vietnam
- College of Health Sciences, VinUniversity, Hanoi, Vietnam
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9
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Longsompurana P, Rungrotmongkol T, Plongthongkum N, Wangkanont K, Wolschann P, Poo-arporn RP. Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2. PLoS One 2023; 18:e0293263. [PMID: 37874836 PMCID: PMC10597523 DOI: 10.1371/journal.pone.0293263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
The COVID-19 pandemic has created an urgent need for effective therapeutic and diagnostic strategies to manage the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the emergence of numerous variants of concern (VOCs) has made it challenging to develop targeted therapies that are broadly specific in neutralizing the virus. In this study, we aimed to develop neutralizing nanobodies (Nbs) using computational techniques that can effectively neutralize the receptor-binding domain (RBD) of SARS-CoV-2 VOCs. We evaluated the performance of different protein-protein docking programs and identified HDOCK as the most suitable program for Nb/RBD docking with high accuracy. Using this approach, we designed 14 novel Nbs with high binding affinity to the VOC RBDs. The Nbs were engineered with mutated amino acids that interacted with key amino acids of the RBDs, resulting in higher binding affinity than human angiotensin-converting enzyme 2 (ACE2) and other viral RBDs or haemagglutinins (HAs). The successful development of these Nbs demonstrates the potential of molecular modeling as a low-cost and time-efficient method for engineering effective Nbs against SARS-CoV-2. The engineered Nbs have the potential to be employed in RBD-neutralizing assays, facilitating the identification of novel treatment, prevention, and diagnostic strategies against SARS-CoV-2.
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Affiliation(s)
- Phoomintara Longsompurana
- Biological Engineering Program, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Nongluk Plongthongkum
- Biological Engineering Program, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Kittikhun Wangkanont
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Peter Wolschann
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Rungtiva P. Poo-arporn
- Biological Engineering Program, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
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10
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Li J, Kang G, Wang J, Yuan H, Wu Y, Meng S, Wang P, Zhang M, Wang Y, Feng Y, Huang H, de Marco A. Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization. Int J Biol Macromol 2023; 247:125733. [PMID: 37423452 DOI: 10.1016/j.ijbiomac.2023.125733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Routinely screened antibody fragments usually require further in vitro maturation to achieve the desired biophysical properties. Blind in vitro strategies can produce improved ligands by introducing random mutations into the original sequences and selecting the resulting clones under more and more stringent conditions. Rational approaches exploit an alternative perspective that aims first at identifying the specific residues potentially involved in the control of biophysical mechanisms, such as affinity or stability, and then to evaluate what mutations could improve those characteristics. The understanding of the antigen-antibody interactions is instrumental to develop this process the reliability of which, consequently, strongly depends on the quality and completeness of the structural information. Recently, methods based on deep learning approaches critically improved the speed and accuracy of model building and are promising tools for accelerating the docking step. Here, we review the features of the available bioinformatic instruments and analyze the reports illustrating the result obtained with their application to optimize antibody fragments, and nanobodies in particular. Finally, the emerging trends and open questions are summarized.
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Affiliation(s)
- Jiaqi Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Guangbo Kang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jiewen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Haibin Yuan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yili Wu
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and the Affiliated Kangning Hospital, Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Wenzhou Medical University, Oujiang Laboratory, Wenzhou, Zhejiang 325035, China
| | - Shuxian Meng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Ping Wang
- New Technology R&D Department, Tianjin Modern Innovative TCM Technology Company Limited, Tianjin 300392, China
| | - Miao Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; China Resources Biopharmaceutical Company Limited, Beijing 100029, China
| | - Yuli Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Tianjin Pharmaceutical Da Ren Tang Group Corporation Limited, Traditional Chinese Pharmacy Research Institute, Tianjin Key Laboratory of Quality Control in Chinese Medicine, Tianjin 300457, China; State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China
| | - Yuanhang Feng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - He Huang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia.
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11
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Fetse J, Kandel S, Mamani UF, Cheng K. Recent advances in the development of therapeutic peptides. Trends Pharmacol Sci 2023; 44:425-441. [PMID: 37246037 PMCID: PMC10330351 DOI: 10.1016/j.tips.2023.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/30/2023]
Abstract
Peptides have unique characteristics that make them highly desirable as therapeutic agents. The physicochemical and proteolytic stability profiles determine the therapeutic potential of peptides. Multiple strategies to enhance the therapeutic profile of peptides have emerged. They include chemical modifications, such as cyclization, substitution with d-amino acids, peptoid formation, N-methylation, and side-chain halogenation, and incorporation in delivery systems. There have been recent advances in approaches to discover peptides having these modifications to attain desirable therapeutic properties. We critically review these recent advancements in therapeutic peptide development.
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Affiliation(s)
- John Fetse
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO 64108, USA
| | - Sashi Kandel
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO 64108, USA
| | - Umar-Farouk Mamani
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO 64108, USA
| | - Kun Cheng
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO 64108, USA.
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12
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Huang CY, Lok YY, Lin CH, Lai SL, Wu YY, Hu CY, Liao CB, Ho CH, Chou YP, Hsu YH, Lo YH, Chern E. Highly reliable GIGA-sized synthetic human therapeutic antibody library construction. Front Immunol 2023; 14:1089395. [PMID: 37180155 PMCID: PMC10174300 DOI: 10.3389/fimmu.2023.1089395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/12/2023] [Indexed: 05/15/2023] Open
Abstract
Background Monoclonal antibodies (mAbs) and their derivatives are the fastest expanding category of pharmaceuticals. Efficient screening and generation of appropriate therapeutic human antibodies are important and urgent issues in the field of medicine. The successful in vitro biopanning method for antibody screening largely depends on the highly diverse, reliable and humanized CDR library. To rapidly obtain potent human antibodies, we designed and constructed a highly diverse synthetic human single-chain variable fragment (scFv) antibody library greater than a giga in size by phage display. Herein, the novel TIM-3-neutralizing antibodies with immunomodulatory functions derived from this library serve as an example to demonstrate the library's potential for biomedical applications. Methods The library was designed with high stability scaffolds and six complementarity determining regions (CDRs) tailored to mimic human composition. The engineered antibody sequences were optimized for codon usage and subjected to synthesis. The six CDRs with variable length CDR-H3s were individually subjected to β-lactamase selection and then recombined for library construction. Five therapeutic target antigens were used for human antibody generation via phage library biopanning. TIM-3 antibody activity was verified by immunoactivity assays. Results We have designed and constructed a highly diverse synthetic human scFv library named DSyn-1 (DCB Synthetic-1) containing 2.5 × 1010 phage clones. Three selected TIM-3-recognizing antibodies DCBT3-4, DCBT3-19, and DCBT3-22 showed significant inhibition activity by TIM-3 reporter assays at nanomolar ranges and binding affinities in sub-nanomolar ranges. Furthermore, clone DCBT3-22 was exceptionally superior with good physicochemical property and a purity of more than 98% without aggregation. Conclusion The promising results illustrate not only the potential of the DSyn-1 library for biomedical research applications, but also the therapeutic potential of the three novel fully human TIM-3-neutralizing antibodies.
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Affiliation(s)
- Chao-Yang Huang
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Ying-Yung Lok
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Chia-Hui Lin
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Szu-Liang Lai
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Yen-Yu Wu
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Chih-Yung Hu
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Chu-Bin Liao
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Chen-Hsuan Ho
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Yu-Ping Chou
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Yi-Hsuan Hsu
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Yu-Hsun Lo
- Development Center for Biotechnology, New Taipei City, Taiwan
| | - Edward Chern
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- *Correspondence: Edward Chern,
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13
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Svilenov HL, Arosio P, Menzen T, Tessier P, Sormanni P. Approaches to expand the conventional toolbox for discovery and selection of antibodies with drug-like physicochemical properties. MAbs 2023; 15:2164459. [PMID: 36629855 PMCID: PMC9839375 DOI: 10.1080/19420862.2022.2164459] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
Antibody drugs should exhibit not only high-binding affinity for their target antigens but also favorable physicochemical drug-like properties. Such drug-like biophysical properties are essential for the successful development of antibody drug products. The traditional approaches used in antibody drug development require significant experimentation to produce, optimize, and characterize many candidates. Therefore, it is attractive to integrate new methods that can optimize the process of selecting antibodies with both desired target-binding and drug-like biophysical properties. Here, we summarize a selection of techniques that can complement the conventional toolbox used to de-risk antibody drug development. These techniques can be integrated at different stages of the antibody development process to reduce the frequency of physicochemical liabilities in antibody libraries during initial discovery and to co-optimize multiple antibody features during early-stage antibody engineering and affinity maturation. Moreover, we highlight biophysical and computational approaches that can be used to predict physical degradation pathways relevant for long-term storage and in-use stability to reduce the need for extensive experimentation.
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Affiliation(s)
- Hristo L. Svilenov
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Gent, Belgium
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Tim Menzen
- Coriolis Pharma Research GmbH, Martinsried, 82152, Germany
| | - Peter Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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14
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Dai Z, Saksena SD, Horny G, Banholzer C, Ewert S, Gifford DK. Ultra-high-diversity factorizable libraries for efficient therapeutic discovery. Genome Res 2022; 32:1787-1794. [PMID: 35738900 PMCID: PMC9528983 DOI: 10.1101/gr.276593.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 06/22/2022] [Indexed: 01/13/2023]
Abstract
The successful discovery of novel biological therapeutics by selection requires highly diverse libraries of candidate sequences that contain a high proportion of desirable candidates. Here we propose the use of computationally designed factorizable libraries made of concatenated segment libraries as a method of creating large libraries that meet an objective function at low cost. We show that factorizable libraries can be designed efficiently by representing objective functions that describe sequence optimality as an inner product of feature vectors, which we use to design an optimization method we call stochastically annealed product spaces (SAPS). We then use this approach to design diverse and efficient libraries of antibody CDR-H3 sequences with various optimized characteristics.
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Affiliation(s)
- Zheng Dai
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sachit D Saksena
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Geraldine Horny
- Novartis Institutes for BioMedical Research (NIBR), CH-4056 Basel, Switzerland
| | - Christine Banholzer
- Novartis Institutes for BioMedical Research (NIBR), CH-4056 Basel, Switzerland
| | - Stefan Ewert
- Novartis Institutes for BioMedical Research (NIBR), CH-4056 Basel, Switzerland
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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15
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Li L, Wu S, Si Y, Li H, Yin X, Peng D. Single-chain fragment variable produced by phage display technology: Construction, selection, mutation, expression, and recent applications in food safety. Compr Rev Food Sci Food Saf 2022; 21:4354-4377. [PMID: 35904244 DOI: 10.1111/1541-4337.13018] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 01/28/2023]
Abstract
Immunoassays are reliable, efficient, and accurate methods for the analysis of small-molecule harmful substances (such as pesticides, veterinary drugs, and biological toxins) that may be present in food. However, traditional polyclonal and monoclonal antibodies are limited by animal hosts and hinder further development of immunoassays. With the gradual application of phage display technology as an efficient in vitro selection technology, the single-chain fragment variable (scFv) now provides an exciting alternative to traditional antibodies. Efficiently constructed scFv source libraries and specifically designed biopanning schemes can now yield scFvs possessing specific recognition capabilities. A rational mutation strategy further enhances the affinity of scFv, and allows it to reach a level that cannot be achieved by immunization. Finally, appropriate prokaryotic expression measures ensure stable and efficient production of scFv. Therefore, when developing excellent scFvs, it is necessary to focus on three key aspects of this process that include screening, mutation, and expression. In this review, we analyze in detail the preparation and affinity improvement process for scFv and provide insights into the research progress and development trend of scFv-based immunoassay methods for monitoring small-molecule harmful substances.
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Affiliation(s)
- Long Li
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shuangmin Wu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yu Si
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Huaming Li
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaoyang Yin
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dapeng Peng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei, China.,Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, Guangdong, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
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16
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Czarnecka M, Weichelt U, Rödiger S, Hanack K. Novel Anti Double-Stranded Nucleic Acids Full-Length Recombinant Camelid Heavy-Chain Antibody for the Detection of miRNA. Int J Mol Sci 2022; 23:ijms23116275. [PMID: 35682952 PMCID: PMC9181593 DOI: 10.3390/ijms23116275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 11/24/2022] Open
Abstract
The discovery that certain diseases have specific miRNA signatures which correspond to disease progression opens a new biomarker category. The detection of these small non-coding RNAs is performed routinely using body fluids or tissues with real-time PCR, next-generation sequencing, or amplification-based miRNA assays. Antibody-based detection systems allow an easy onset handling compared to PCR or sequencing and can be considered as alternative methods to support miRNA diagnostic in the future. In this study, we describe the generation of a camelid heavy-chain-only antibody specifically recognizing miRNAs to establish an antibody-based detection method. The generation of nucleic acid-specific binders is a challenge. We selected camelid binders via phage display, expressed them as VHH as well as full-length antibodies, and characterized the binding to several miRNAs from a signature specific for dilated cardiomyopathy. The described workflow can be used to create miRNA-specific binders and establish antibody-based detection methods to provide an additional way to analyze disease-specific miRNA signatures.
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Affiliation(s)
- Malgorzata Czarnecka
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; (M.C.); (U.W.)
| | - Ulrike Weichelt
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; (M.C.); (U.W.)
| | - Stefan Rödiger
- Faculty of Health Sciences Brandenburg, Brandenburg University of Technology, Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany;
| | - Katja Hanack
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; (M.C.); (U.W.)
- Correspondence: ; Tel.: +49-3319-775-348
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17
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Laeremans T, Sands ZA, Claes P, De Blieck A, De Cesco S, Triest S, Busch A, Felix D, Kumar A, Jaakola VP, Menet C. Accelerating GPCR Drug Discovery With Conformation-Stabilizing VHHs. Front Mol Biosci 2022; 9:863099. [PMID: 35677880 PMCID: PMC9170359 DOI: 10.3389/fmolb.2022.863099] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/22/2022] [Indexed: 01/19/2023] Open
Abstract
The human genome encodes 850 G protein-coupled receptors (GPCRs), half of which are considered potential drug targets. GPCRs transduce extracellular stimuli into a plethora of vital physiological processes. Consequently, GPCRs are an attractive drug target class. This is underlined by the fact that approximately 40% of marketed drugs modulate GPCRs. Intriguingly 60% of non-olfactory GPCRs have no drugs or candidates in clinical development, highlighting the continued potential of GPCRs as drug targets. The discovery of small molecules targeting these GPCRs by conventional high throughput screening (HTS) campaigns is challenging. Although the definition of success varies per company, the success rate of HTS for GPCRs is low compared to other target families (Fujioka and Omori, 2012; Dragovich et al., 2022). Beyond this, GPCR structure determination can be difficult, which often precludes the application of structure-based drug design approaches to arising HTS hits. GPCR structural studies entail the resource-demanding purification of native receptors, which can be challenging as they are inherently unstable when extracted from the lipid matrix. Moreover, GPCRs are flexible molecules that adopt distinct conformations, some of which need to be stabilized if they are to be structurally resolved. The complexity of targeting distinct therapeutically relevant GPCR conformations during the early discovery stages contributes to the high attrition rates for GPCR drug discovery programs. Multiple strategies have been explored in an attempt to stabilize GPCRs in distinct conformations to better understand their pharmacology. This review will focus on the use of camelid-derived immunoglobulin single variable domains (VHHs) that stabilize disease-relevant pharmacological states (termed ConfoBodies by the authors) of GPCRs, as well as GPCR:signal transducer complexes, to accelerate drug discovery. These VHHs are powerful tools for supporting in vitro screening, deconvolution of complex GPCR pharmacology, and structural biology purposes. In order to demonstrate the potential impact of ConfoBodies on translational research, examples are presented of their role in active state screening campaigns and structure-informed rational design to identify de novo chemical space and, subsequently, how such matter can be elaborated into more potent and selective drug candidates with intended pharmacology.
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18
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Assessment of Therapeutic Antibody Developability by Combinations of In Vitro and In Silico Methods. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2313:57-113. [PMID: 34478132 DOI: 10.1007/978-1-0716-1450-1_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although antibodies have become the fastest-growing class of therapeutics on the market, it is still challenging to develop them for therapeutic applications, which often require these molecules to withstand stresses that are not present in vivo. We define developability as the likelihood of an antibody candidate with suitable functionality to be developed into a manufacturable, stable, safe, and effective drug that can be formulated to high concentrations while retaining a long shelf life. The implementation of reliable developability assessments from the early stages of antibody discovery enables flagging and deselection of potentially problematic candidates, while focussing available resources on the development of the most promising ones. Currently, however, thorough developability assessment requires multiple in vitro assays, which makes it labor intensive and time consuming to implement at early stages. Furthermore, accurate in vitro analysis at the early stage is compromised by the high number of potential candidates that are often prepared at low quantities and purity. Recent improvements in the performance of computational predictors of developability potential are beginning to change this scenario. Many computational methods only require the knowledge of the amino acid sequences and can be used to identify possible developability issues or to rank available candidates according to a range of biophysical properties. Here, we describe how the implementation of in silico tools into antibody discovery pipelines is increasingly offering time- and cost-effective alternatives to in vitro experimental screening, thus streamlining the drug development process. We discuss in particular the biophysical and biochemical properties that underpin developability potential and their trade-offs, review various in vitro assays to measure such properties or parameters that are predictive of developability, and give an overview of the growing number of in silico tools available to predict properties important for antibody development, including the CamSol method developed in our laboratory.
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19
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Yang Y, Nian S, Li L, Wen X, Liu Q, Zhang B, Lan Y, Yuan Q, Ye Y. Fully human recombinant antibodies against EphA2 from a multi-tumor patient immune library suitable for tumor-targeted therapy. Bioengineered 2021; 12:10379-10400. [PMID: 34709992 PMCID: PMC8810047 DOI: 10.1080/21655979.2021.1996807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Enhanced EphA2 expression is observed in a variety of epithelial-derived malignancies and is an important target for anti-tumor therapy. Currently, Therapeutic monoclonal antibodies against immune checkpoints have shown good efficacy for tumor treatment. In this study, we constructed an immune single-chain fragment variable (scFv) library using peripheral blood mononuclear cells (PBMCs) from 200 patients with a variety of malignant tumors. High affinity scFvs against EphA2 can be easily screened from the immune library using phage display technology. Anti-EphA2 scFvs can be modified into any form of recombinant antibody, including scFv-Fc and full-length IgG1 antibodies, and the recombinant antibody affinity was improved following modification. Among the modified anti-EphA2 antibodies the affinity of 77-IgG1 was significantly increased, reaching a pmol affinity level (10−12). We further demonstrated the binding activity of recombinant antibodies to the EphA2 protein, tumor cells, and tumor tissues using macromolecular interaction techniques, flow cytometry and immunohistochemistry. Most importantly, both the constructed scFvs-Fc, as well as the IgG1 antibodies against EphA2 were able to inhibit the growth of tumor cells to some extent. These results suggest that the immune libraries from patients with malignant tumors are more likely to screen for antibodies with high affinity and therapeutic effect. The constructed fully human scFv immune library has broad application prospects for specific antibody screening. The screened scFv-Fc and IgG1 antibodies against EphA2 can be used for the further study of tumor immunotherapy.
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Affiliation(s)
- Yaqi Yang
- Public Center of Experimental Technology, The school of Basic medical science, Southwest medical university, Luzhou, Sichuan Province, 646000, China
| | - Siji Nian
- Public Center of Experimental Technology, The school of Basic medical science, Southwest medical university, Luzhou, Sichuan Province, 646000, China
| | - Lin Li
- Public Center of Experimental Technology, The school of Basic medical science, Southwest medical university, Luzhou, Sichuan Province, 646000, China
| | - Xue Wen
- Public Center of Experimental Technology, The school of Basic medical science, Southwest medical university, Luzhou, Sichuan Province, 646000, China.,Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Sichuan 646000, P.R. China
| | - Qin Liu
- Public Center of Experimental Technology, The school of Basic medical science, Southwest medical university, Luzhou, Sichuan Province, 646000, China
| | - Bo Zhang
- Public Center of Experimental Technology, The school of Basic medical science, Southwest medical university, Luzhou, Sichuan Province, 646000, China
| | - Yu Lan
- Public Center of Experimental Technology, The school of Basic medical science, Southwest medical university, Luzhou, Sichuan Province, 646000, China
| | - Qing Yuan
- Public Center of Experimental Technology, The school of Basic medical science, Southwest medical university, Luzhou, Sichuan Province, 646000, China
| | - Yingchun Ye
- Public Center of Experimental Technology, The school of Basic medical science, Southwest medical university, Luzhou, Sichuan Province, 646000, China
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20
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Shin C, Kim SS, Jo YH. Extending traditional antibody therapies: Novel discoveries in immunotherapy and clinical applications. Mol Ther Oncolytics 2021; 22:166-179. [PMID: 34514097 PMCID: PMC8416972 DOI: 10.1016/j.omto.2021.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Immunotherapy has been well regarded as one of the safer and antigen-specific anti-cancer treatments compared to first-generation chemotherapy. Since Coley's discovery, researchers focused on engineering novel antibody-based therapies. Including artificial and modified antibodies, such as antibody fragments, antibody-drug conjugates, and synthetic mimetics, the variety of immunotherapy has been rapidly expanding in the last few decades. Genetic and chemical modifications to monoclonal antibody have been brought into academia, in vivo trials, and clinical applications. Here, we have looked around antibodies overall. First, we elucidate the antibody structure and its cytotoxicity mechanisms. Second, types of therapeutic antibodies are presented. Additionally, there is a summarized list of US Food and Drug Administration (FDA)-approved therapeutic antibodies and recent clinical trials. This review provides a comprehensive overview of both the general function of therapeutic antibodies and a few main variations in development, including recent advent with the proposed mechanism of actions, and we introduce types of therapeutic antibodies, clinical trials, and approved commercial immunotherapeutic drugs.
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Affiliation(s)
- Charles Shin
- Chadwick International, Incheon 22002, Republic of Korea
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sung Soo Kim
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yong Hwa Jo
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
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21
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Klangprapan S, Weng CC, Huang WT, Li YK, Choowongkomon K. Selection and Characterization of a Single-Chain Variable Fragment against Porcine Circovirus Type 2 Capsid and Impedimetric Immunosensor Development. ACS OMEGA 2021; 6:24233-24243. [PMID: 34568701 PMCID: PMC8459408 DOI: 10.1021/acsomega.1c03894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Porcine circovirus type 2 (PCV2) is the primary causative agent of porcine circovirus-associated disease (PCVAD) that causes huge global economic losses for the swine industry. Effective strategies or rapid detection of PCV2 in pig are essential to control PCVAD. Here, single-chain variable fragments (scFvs) were selected and characterized against the PCV2 capsid using phage display technology. Phage scFv clones were selected from the human scFv phagemid library (Tomlinson I + J) for direct panning against the PCV2 capsid. Eighty-four monoclonal phage scFvs were individually tested for binding to the PCV2 capsid by ELISA. Eight scFv clones showed significant binding to the PCV2 capsid and only three clones (clone nos. 13, 37, and 81) contained both VHCDRs and VLCDRs in the sequence. Clone scFv no. 81 had the highest reactivity to the PCV2 capsid and was constructed in the pET22b (+) expression vector. The recombinant was transformed to Escherichia coli BL21(DE3) for expression and purification. The scFv showed appropriate affinity to the PCV2 capsid by western blot analysis. Kinetics of scFv and the PCV2 capsid were determined using surface plasmon resonance and showed binding affinity in the nanomolar range (K D = 57.2 nM). Our scFv was first applied in the development of an impedimetric immunosensor for PCV2 capsid detection, and results showed that impedance increased with increasing PCV2 capsid expression with limit of detection = 114 nM. Findings demonstrated that our scFv has potential for use as a receptor for biosensor devices.
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Affiliation(s)
- Supaporn Klangprapan
- Genetic Engineering Interdisciplinary Program, Graduate School, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand
| | - Chang-Ching Weng
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Wan-Ting Huang
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Yaw-Kuen Li
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
- Center for Emergent Functional Matter Science, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand
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22
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de Brito PM, Saruga A, Cardoso M, Goncalves J. Methods and cell-based strategies to produce antibody libraries: current state. Appl Microbiol Biotechnol 2021; 105:7215-7224. [PMID: 34524471 DOI: 10.1007/s00253-021-11570-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 11/24/2022]
Abstract
Antibodies are critical components of the adaptive immune system, whose therapeutic applications have been growing exponentially in the last years. Discovery and development of therapeutic antibodies encompasses in vivo immunization, synthetic libraries, and surface display methodologies. To overcome some of their limitations, several platforms in higher eukaryotic cells have been developed. Moreover, these platforms aim to replicate in the bench both primary and secondary antibody diversification mechanisms that occur in vivo. Here, we describe the latest strategies that have been used to mirror both naïve and affinity-maturated antibody repertoire. KEY POINTS: • Therapeutic antibodies are one of the most promising classes of drugs to fight diseases. • Antibodies discovered through hybridoma or display technologies require further engineering. • Innovative antibody discovery platforms in higher eukaryotic cells have been developed.
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Affiliation(s)
- Paula Matos de Brito
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal
| | - Andreia Saruga
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.,INESC MN - Instituto de Engenharia de Sistemas e Computadores - Microsystems and Nanotecnologies, R. Alves Redol 9, 1000-029, Lisbon, Portugal
| | - Miguel Cardoso
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal
| | - Joao Goncalves
- Faculty of Pharmacy, iMed.ULisboa - Research Institute for Medicines, University of Lisbon, Av. Professor Gama Pinto, 1649-019, Lisbon, Portugal.
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Zhang Y, Thangam R, You SH, Sultonova RD, Venu A, Min JJ, Hong Y. Engineering Calreticulin-Targeting Monobodies to Detect Immunogenic Cell Death in Cancer Chemotherapy. Cancers (Basel) 2021; 13:2801. [PMID: 34199835 PMCID: PMC8200062 DOI: 10.3390/cancers13112801] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 12/26/2022] Open
Abstract
Surface-exposed calreticulin (ecto-CRT) plays a crucial role in the phagocytic removal of apoptotic cells during immunotherapy. Ecto-CRT is an immunogenic signal induced in response to treatment with chemotherapeutic agents such as doxorubicin (DOX) and mitoxantrone (MTX), and two peptides (KLGFFKR (Integrin-α) and GQPMYGQPMY (CRT binding peptide 1, Hep-I)) are known to specifically bind CRT. To engineer CRT-specific monobodies as agents to detect immunogenic cell death (ICD), we fused these peptide sequences at the binding loops (BC and FG) of human fibronectin domain III (FN3). CRT-specific monobodies were purified from E. coli by affinity chromatography. Using these monobodies, ecto-CRT was evaluated in vitro, in cultured cancer cell lines (CT-26, MC-38, HeLa, and MDA-MB-231), or in mice after anticancer drug treatment. Monobodies with both peptide sequences (CRT3 and CRT4) showed higher binding to ecto-CRT than those with a single peptide sequence. The binding affinity of the Rluc8 fusion protein-engineered monobodies (CRT3-Rluc8 and CRT4-Rluc8) to CRT was about 8 nM, and the half-life in serum and tumor tissue was about 12 h. By flow cytometry and confocal immunofluorescence of cancer cell lines, and by in vivo optical bioluminescence imaging of tumor-bearing mice, CRT3-Rluc8 and CRT4-Rluc8 bound specifically to ecto-CRT and effectively detected pre-apoptotic cells after treatment with ICD-inducing agents (DOX and MTX) but not a non-ICD-inducing agent (gemcitabine). Using CRT-specific monobodies, it is possible to detect ecto-CRT induction in cancer cells in response to drug exposure. This technique may be used to predict the therapeutic efficiency of chemo- and immuno-therapeutics early during anticancer treatment.
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Affiliation(s)
- Ying Zhang
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
| | - Ramar Thangam
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
- Department of Materials Science & Engineering, Korea University, Seoul 02841, Korea
| | - Sung-Hwan You
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
| | - Rukhsora D. Sultonova
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
| | - Akhil Venu
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
| | - Jung-Joon Min
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
- Department of Microbiology, Chonnam National University Medical School, Hwasun 58128, Korea
| | - Yeongjin Hong
- Department of Nuclear Medicine, Institute for Molecular Imaging and Theranostics, Hwasun Hospital, Chonnam National University Medical School, Hwasun 58128, Korea; (Y.Z.); (R.T.); (S.-H.Y.); (R.D.S.); (A.V.)
- Department of Microbiology, Chonnam National University Medical School, Hwasun 58128, Korea
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24
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Lim CC, Chan SK, Lim YY, Ishikawa Y, Choong YS, Nagaoka Y, Lim TS. Development and structural characterisation of human scFv targeting MDM2 spliced variant MDM2 15kDa. Mol Immunol 2021; 135:191-203. [PMID: 33930714 DOI: 10.1016/j.molimm.2021.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/09/2021] [Accepted: 04/18/2021] [Indexed: 01/10/2023]
Abstract
The murine double minute 2 (MDM2) protein is a major negative regulator of the tumour suppressor protein p53. Under normal conditions, MDM2 constantly binds to p53 transactivation domain and/or ubiquinates p53 via its role as E3 ubiquitin ligase to promote p53 degradation as well as nuclear export to maintain p53 levels in cells. Meanwhile, amplification of MDM2 and appearance of MDM2 spliced variants occur in many tumours and normal tissues making it a prognostic indicator for human cancers. The mutation or deletion of p53 protein in half of human cancers inactivates its tumour suppressor activity. However, cancers with wild type p53 have its function effectively inhibited through direct interaction with MDM2 oncoprotein. Here, we described the construction of a MDM2 spliced variant (rMDM215kDa) consisting of SWIB/MDM2 domain and its central region for antibody generation. Biopanning with a human naïve scFv library generated four scFv clones specific to rMDM215kDa. Additionally, the selected scFv clones were able to bind to the recombinant full length MDM2 (rMDM2-FL). Computational prediction showed that the selected scFv clones potentially bind to exon 7-8 of MDM2 while leaving the MDM2/SWIB domain free for p53 interaction. The developed antibodies exhibit good specificity can be further investigated for downstream biomedical and research applications.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Yee Ying Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Yuya Ishikawa
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho Suita, Osaka, 564-8680, Japan
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Yasuo Nagaoka
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho Suita, Osaka, 564-8680, Japan
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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Xu P, Ghosh S, Gul AR, Bhamore JR, Park JP, Park TJ. Screening of specific binding peptides using phage-display techniques and their biosensing applications. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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26
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Kulenkampff K, Wolf Perez AM, Sormanni P, Habchi J, Vendruscolo M. Quantifying misfolded protein oligomers as drug targets and biomarkers in Alzheimer and Parkinson diseases. Nat Rev Chem 2021; 5:277-294. [PMID: 37117282 DOI: 10.1038/s41570-021-00254-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Protein misfolding and aggregation are characteristic of a wide range of neurodegenerative disorders, including Alzheimer and Parkinson diseases. A hallmark of these diseases is the aggregation of otherwise soluble and functional proteins into amyloid aggregates. Although for many decades such amyloid deposits have been thought to be responsible for disease progression, it is now increasingly recognized that the misfolded protein oligomers formed during aggregation are, instead, the main agents causing pathological processes. These oligomers are transient and heterogeneous, which makes it difficult to detect and quantify them, generating confusion about their exact role in disease. The lack of suitable methods to address these challenges has hampered efforts to investigate the molecular mechanisms of oligomer toxicity and to develop oligomer-based diagnostic and therapeutic tools to combat protein misfolding diseases. In this Review, we describe methods to quantify misfolded protein oligomers, with particular emphasis on diagnostic applications as disease biomarkers and on therapeutic applications as target biomarkers. The development of these methods is ongoing, and we discuss the challenges that remain to be addressed to establish measurement tools capable of overcoming existing limitations and to meet present needs.
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Sivaccumar J, Sandomenico A, Vitagliano L, Ruvo M. Monoclonal Antibodies: A Prospective and Retrospective View. Curr Med Chem 2021; 28:435-471. [PMID: 32072887 DOI: 10.2174/0929867327666200219142231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Monoclonal Antibodies (mAbs) represent one of the most important classes of biotherapeutic agents. They are used to cure many diseases, including cancer, autoimmune diseases, cardiovascular diseases, angiogenesis-related diseases and, more recently also haemophilia. They can be highly varied in terms of format, source, and specificity to improve efficacy and to obtain more targeted applications. This can be achieved by leaving substantially unchanged the basic structural components for paratope clustering. OBJECTIVES The objective was to trace the most relevant findings that have deserved prestigious awards over the years, to report the most important clinical applications and to emphasize their latest emerging therapeutic trends. RESULTS We report the most relevant milestones and new technologies adopted for antibody development. Recent efforts in generating new engineered antibody-based formats are briefly reviewed. The most important antibody-based molecules that are (or are going to be) used for pharmacological practice have been collected in useful tables. CONCLUSION The topics here discussed prove the undisputed role of mAbs as innovative biopharmaceuticals molecules and as vital components of targeted pharmacological therapies.
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Affiliation(s)
- Jwala Sivaccumar
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
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Broad specificity of immune helminth scFv library to identify monoclonal antibodies targeting Strongyloides. Sci Rep 2021; 11:2502. [PMID: 33510342 PMCID: PMC7843650 DOI: 10.1038/s41598-021-82125-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022] Open
Abstract
Antibodies have different chemical properties capable of targeting a diverse nature of antigens. Traditionally, immune antibody libraries are perceived to be disease-specific with a skewed repertoire. The complexity during the generation of a combinatorial antibody library allows for a skewed but diverse repertoire to be generated. Strongyloides stercoralis is a parasite that causes strongyloidiasis, a potentially life-threatening disease with a complex diagnosis that impedes effective control and treatment of the disease. This study describes the isolation of monoclonal antibodies against S. stercoralis NIE recombinant protein using an immune antibody phage display library derived from lymphatic filaria-infected individuals. The isolated antibody clones showed both lambda and kappa light chains gene usage, with diverse amino acid distributions. Structural analysis showed that electropositivity and the interface area could determine the binding affinity of the clones with NIE. The successful identification of S. stercoralis antibodies from the filarial immune library highlights the breadth of antibody gene diversification in an immune antibody library that can be applied for closely related infections.
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Abstract
Even after more than 30 years since its discovery, there is no cure for HIV-1 infection. Combination antiretroviral therapy (cART) is currently the only HIV-1 infection management option in clinics. Despite its success in suppressing viral replication and converting HIV-1 from a lethal infection to a chronic and manageable disease, cART treatment is life long and long-term use can result in major drawbacks such as high cost, multiple side effects, and an increase in the development of multidrug-resistant escape mutants. Recently, antibody-based anti-HIV-1 treatment has emerged as a potential alternative therapeutic modality for HIV-1 treatment and cure strategies. These antibody-based anti-HIV-1 treatments comprising either receptor-targeting antibodies or broad neutralizing antibodies (bNAbs) are currently being developed and evaluated in clinical trials. These antibodies have demonstrated potent antiviral effects against multiple strains of HIV-1, and shown promise for prevention, maintenance, and prolonged remission of HIV-1 infection. This review gives an update on the current status of these antibody-based treatments for HIV-1, discusses their mechanism of action and the challenges in developing them, providing insight for their development as novel clinical therapies against HIV-1 infection.
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Affiliation(s)
- Wanwisa Promsote
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Megan E DeMouth
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cassandra G Almasri
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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Soler MA, Medagli B, Wang J, Oloketuyi S, Bajc G, Huang H, Fortuna S, de Marco A. Effect of Humanizing Mutations on the Stability of the Llama Single-Domain Variable Region. Biomolecules 2021; 11:biom11020163. [PMID: 33530572 PMCID: PMC7911018 DOI: 10.3390/biom11020163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 11/24/2022] Open
Abstract
In vivo clinical applications of nanobodies (VHHs) require molecules that induce minimal immunoresponse and therefore possess sequences as similar as possible to the human VH domain. Although the relative sequence variability in llama nanobodies has been used to identify scaffolds with partially humanized signature, the transformation of the Camelidae hallmarks in the framework2 still represents a major problem. We assessed a set of mutants in silico and experimentally to elucidate what is the contribution of single residues to the VHH stability and how their combinations affect the mutant nanobody stability. We described at molecular level how the interaction among residues belonging to different structural elements enabled a model llama nanobody (C8WT, isolated from a naïve library) to be functional and maintain its stability, despite the analysis of its primary sequence would classify it as aggregation-prone. Five chimeras formed by grafting CDRs isolated from different nanobodies into C8WT scaffold were successfully expressed as soluble proteins and both tested clones preserved their antigen binding specificity. We identified a nanobody with human hallmarks that seems suitable for humanizing selected camelid VHHs by grafting heterologous CDRs in its scaffold and could serve for the preparation of a synthetic library of human-like single domains.
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Affiliation(s)
- Miguel A. Soler
- CONCEPT Lab, Italian Institute of Technology (IIT), 16152 Genova, Italy
- Correspondence: (M.A.S.); (A.d.M.); Tel.: +386-05-3315295 (A.d.M.); Fax: +386-05-90-99-722 (A.d.M.)
| | - Barbara Medagli
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy; (B.M.); (S.F.)
| | - Jiewen Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China; (J.W.); (H.H.)
| | - Sandra Oloketuyi
- Lab of Environmental and Life Sciences, University of Nova Gorica, 5000 Rožna Dolina-Nova Gorica, Slovenia;
| | - Gregor Bajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - He Huang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China; (J.W.); (H.H.)
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy; (B.M.); (S.F.)
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, 5000 Rožna Dolina-Nova Gorica, Slovenia;
- Correspondence: (M.A.S.); (A.d.M.); Tel.: +386-05-3315295 (A.d.M.); Fax: +386-05-90-99-722 (A.d.M.)
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Azevedo Reis Teixeira A, Erasmus MF, D’Angelo S, Naranjo L, Ferrara F, Leal-Lopes C, Durrant O, Galmiche C, Morelli A, Scott-Tucker A, Bradbury ARM. Drug-like antibodies with high affinity, diversity and developability directly from next-generation antibody libraries. MAbs 2021; 13:1980942. [PMID: 34850665 PMCID: PMC8654478 DOI: 10.1080/19420862.2021.1980942] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 11/09/2022] Open
Abstract
Therapeutic antibodies must have "drug-like" properties. These include high affinity and specificity for the intended target, biological activity, and additional characteristics now known as "developability properties": long-term stability and resistance to aggregation when in solution, thermodynamic stability to prevent unfolding, high expression yields to facilitate manufacturing, low self-interaction, among others. Sequence-based liabilities may affect one or more of these characteristics. Improving the stability and developability of a lead antibody is typically achieved by modifying its sequence, a time-consuming process that often results in reduced affinity. Here we present a new antibody library format that yields high-affinity binders with drug-like developability properties directly from initial selections, reducing the need for further engineering or affinity maturation. The innovative semi-synthetic design involves grafting natural complementarity-determining regions (CDRs) from human antibodies into scaffolds based on well-behaved clinical antibodies. HCDR3s were amplified directly from B cells, while the remaining CDRs, from which all sequence liabilities had been purged, were replicated from a large next-generation sequencing dataset. By combining two in vitro display techniques, phage and yeast display, we were able to routinely recover a large number of unique, highly developable antibodies against clinically relevant targets with affinities in the subnanomolar to low nanomolar range. We anticipate that the designs and approaches presented here will accelerate the drug development process by reducing the failure rate of leads due to poor antibody affinities and developability.Abbreviations: AC-SINS: affinity-capture self-interaction nanoparticle spectroscopy; CDR: complementarity-determining region; CQA: critical quality attribute; ELISA: enzyme-linked immunoassay; FACS: fluorescence-activated cell sorting; Fv: fragment variable; GM-CSF: granulocyte-macrophage colony-stimulating factor; HCDR3: heavy chain CDR3; IFN2a: interferon α-2; IL6: interleukin-6; MACS: magnetic-activated cell sorting; NGS: next generation sequencing; PCR: polymerase chain reaction; SEC: size-exclusion chromatography; SPR: surface plasmon resonance; TGFβ-R2: transforming growth factor β-R2; VH: variable heavy; VK: variable kappa; VL: variable light; Vl: variable lambda.
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Lai JY, Lim TS. Infectious disease antibodies for biomedical applications: A mini review of immune antibody phage library repertoire. Int J Biol Macromol 2020; 163:640-648. [PMID: 32650013 PMCID: PMC7340592 DOI: 10.1016/j.ijbiomac.2020.06.268] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/21/2020] [Accepted: 06/28/2020] [Indexed: 12/18/2022]
Abstract
Antibody phage display is regarded as a critical tool for the development of monoclonal antibodies for infectious diseases. The different classes of antibody libraries are classified based on the source of repertoire used to generate the libraries. Immune antibody libraries are generated from disease infected host or immunization against an infectious agent. Antibodies derived from immune libraries are distinct from those derived from naïve libraries as the host's in vivo immune mechanisms shape the antibody repertoire to yield high affinity antibodies. As the immune system is constantly evolving in accordance to the health state of an individual, immune libraries can offer more than just infection-specific antibodies but also antibodies derived from the memory B-cells much like naïve libraries. The combinatorial nature of the gene cloning process would give rise to a combination of natural and un-natural antibody gene pairings in the immune library. These factors have a profound impact on the coverage of immune antibody libraries to target both disease-specific and non-disease specific antigens. This review looks at the diverse nature of antibody responses for immune library generation and discusses the extended potential of a disease-specified immune library in the context of phage display.
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Affiliation(s)
- Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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33
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Zarei B, Javidan Z, Fatemi E, Rahimi Jamnani F, Khatami S, Khalaj V. Targeting c-Met on gastric cancer cells through a fully human fab antibody isolated from a large naive phage antibody library. Daru 2020; 28:221-235. [PMID: 32193747 PMCID: PMC7238820 DOI: 10.1007/s40199-020-00334-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/14/2020] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The aberrant Hepatocyte growth factor (HGF)/ mesenchymal-epithelial transition factor (c-Met) signaling pathway in various malignancies and its correlation with tumor invasion and poor prognosis has validated c-Met as a compelling therapeutic target. Up to now, several monoclonal antibodies and small molecule inhibitors targeting c-Met have been introduced with different outcomes, none are yet clinically approved. Toward the generation of novel fully human anti-c-Met molecules, we generated a large naïve Fab antibody library using phage display technology, which subsequently screened for novel Fabs against c-Met. METHODS A phage library, with a functional size of 5.5 × 1010 individual antibody clones, was prepared using standard protocols and screened for c-Met-specific Fabs by successive rounds of panning. A panel of Fabs targeting c-Met were isolated, from which four clones were selected and further characterized by DNA sequencing. The c-Met binding ability of our selected Fabs was evaluated by c-Met ELISA assay and flow cytometry techniques. RESULTS Among the confirmed anti-c-Met Fabs, clone C16, showed the highest affinity (Kaff: 0.3 × 109 M-1), and 63% binding to MKN45 cells (a human gastric adenocarcinoma cell-line) as compared to c-Met negative T47D cell-line (9.03%). CONCLUSION Together, our study presents a single-pot antibody library, as a valuable source for finding a range of antigen-specific Fab antibodies, and also, a fully human, high affinity and specific anti c-Met Fab antibody, C16, which has the potential of developing as a therapeutic or chemotherapeutic delivery agent for killing c-Met-positive tumor cells.
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Affiliation(s)
- Bahareh Zarei
- Medical Biotechnology Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Zahra Javidan
- Medical Biotechnology Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Elnaz Fatemi
- Medical Biotechnology Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Rahimi Jamnani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research,
Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Shohreh Khatami
- Biochemistry Department, Pasteur Institute of Iran, Tehran, Iran
| | - Vahid Khalaj
- Medical Biotechnology Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran, Iran
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Warszawski S, Borenstein Katz A, Lipsh R, Khmelnitsky L, Ben Nissan G, Javitt G, Dym O, Unger T, Knop O, Albeck S, Diskin R, Fass D, Sharon M, Fleishman SJ. Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces. PLoS Comput Biol 2019; 15:e1007207. [PMID: 31442220 PMCID: PMC6728052 DOI: 10.1371/journal.pcbi.1007207] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 09/05/2019] [Accepted: 06/21/2019] [Indexed: 11/18/2022] Open
Abstract
Antibodies developed for research and clinical applications may exhibit suboptimal stability, expressibility, or affinity. Existing optimization strategies focus on surface mutations, whereas natural affinity maturation also introduces mutations in the antibody core, simultaneously improving stability and affinity. To systematically map the mutational tolerance of an antibody variable fragment (Fv), we performed yeast display and applied deep mutational scanning to an anti-lysozyme antibody and found that many of the affinity-enhancing mutations clustered at the variable light-heavy chain interface, within the antibody core. Rosetta design combined enhancing mutations, yielding a variant with tenfold higher affinity and substantially improved stability. To make this approach broadly accessible, we developed AbLIFT, an automated web server that designs multipoint core mutations to improve contacts between specific Fv light and heavy chains (http://AbLIFT.weizmann.ac.il). We applied AbLIFT to two unrelated antibodies targeting the human antigens VEGF and QSOX1. Strikingly, the designs improved stability, affinity, and expression yields. The results provide proof-of-principle for bypassing laborious cycles of antibody engineering through automated computational affinity and stability design.
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Affiliation(s)
- Shira Warszawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Rosalie Lipsh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lev Khmelnitsky
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gabriel Javitt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Orly Dym
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | - Orli Knop
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shira Albeck
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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Kumar R, Parray HA, Shrivastava T, Sinha S, Luthra K. Phage display antibody libraries: A robust approach for generation of recombinant human monoclonal antibodies. Int J Biol Macromol 2019; 135:907-918. [PMID: 31170490 DOI: 10.1016/j.ijbiomac.2019.06.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/02/2019] [Accepted: 06/02/2019] [Indexed: 12/29/2022]
Abstract
Monoclonal antibodies (mAbs) and their derivatives have achieved remarkable success as medicine, targeting both diagnostic and therapeutic applications associated with communicable and non-communicable diseases. In the last 3 to 4 decades, tremendous success has been manifested in the field of cancer therapy, autoimmune diseases, cardiovascular and infectious diseases. MAbs are the fastest growing class of biopharmaceuticals, with more than 25 derivatives are in clinical use and 7 of these have been isolated through phage display technology. Phage display technology has gained impetus in the field of medical and health sciences, as a large repertoire of diverse recombinant antibodies, targeting various antigens have been generated in a short span of time. A prominent number of phage display derived antibodies are already approved for therapy and significant numbers are currently in clinical trials. In this review we have discussed the various strategies employed for generation of monoclonal antibodies; their advantages, limitations and potential therapeutic applications. We also discuss the potential of phage display antibody libraries in isolation of monoclonal antibodies.
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Affiliation(s)
- Rajesh Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India; Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India.
| | - Hilal Ahmed Parray
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Tripti Shrivastava
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Subrata Sinha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
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Sakhnini LI, Greisen PJ, Wiberg C, Bozoky Z, Lund S, Wolf Perez AM, Karkov HS, Huus K, Hansen JJ, Bülow L, Lorenzen N, Dainiak MB, Pedersen AK. Improving the Developability of an Antigen Binding Fragment by Aspartate Substitutions. Biochemistry 2019; 58:2750-2759. [DOI: 10.1021/acs.biochem.9b00251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laila I. Sakhnini
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
- Department of Pure and Applied Biochemistry, Lund University, 223 62 Lund, Sweden
| | - Per J. Greisen
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Charlotte Wiberg
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Zoltan Bozoky
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Søren Lund
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | | | - Hanne S. Karkov
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Kasper Huus
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | | | - Leif Bülow
- Department of Pure and Applied Biochemistry, Lund University, 223 62 Lund, Sweden
| | - Nikolai Lorenzen
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Maria B. Dainiak
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Anja K. Pedersen
- Chemistry, Manufacturing and Control, Novo Nordisk A/S, 2820 Gentofte, Denmark
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Targeting the MHC Ligandome by Use of TCR-Like Antibodies. Antibodies (Basel) 2019; 8:antib8020032. [PMID: 31544838 PMCID: PMC6640717 DOI: 10.3390/antib8020032] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/11/2022] Open
Abstract
Monoclonal antibodies (mAbs) are valuable as research reagents, in diagnosis and in therapy. Their high specificity, the ease in production, favorable biophysical properties and the opportunity to engineer different properties make mAbs a versatile class of biologics. mAbs targeting peptide–major histocompatibility molecule (pMHC) complexes are often referred to as “TCR-like” mAbs, as pMHC complexes are generally recognized by T-cell receptors (TCRs). Presentation of self- and non-self-derived peptide fragments on MHC molecules and subsequent activation of T cells dictate immune responses in health and disease. This includes responses to infectious agents or cancer but also aberrant responses against harmless self-peptides in autoimmune diseases. The ability of TCR-like mAbs to target specific peptides presented on MHC allows for their use to study peptide presentation or for diagnosis and therapy. This extends the scope of conventional mAbs, which are generally limited to cell-surface or soluble antigens. Herein, we review the strategies used to generate TCR-like mAbs and provide a structural comparison with the analogous TCR in pMHC binding. We further discuss their applications as research tools and therapeutic reagents in preclinical models as well as challenges and limitations associated with their use.
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Lim CC, Woo PCY, Lim TS. Development of a Phage Display Panning Strategy Utilizing Crude Antigens: Isolation of MERS-CoV Nucleoprotein human antibodies. Sci Rep 2019; 9:6088. [PMID: 30988390 PMCID: PMC6465254 DOI: 10.1038/s41598-019-42628-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 04/04/2019] [Indexed: 12/20/2022] Open
Abstract
Antibody phage display has been pivotal in the quest to generate human monoclonal antibodies for biomedical and research applications. Target antigen preparation is a main bottleneck associated with the panning process. This includes production complexity, downstream purification, quality and yield. In many instances, purified antigens are preferred for panning but this may not be possible for certain difficult target antigens. Here, we describe an improved procedure of affinity selection against crude or non-purified antigen by saturation of non-binders with blocking agents to promote positive binder enrichment termed as Yin-Yang panning. A naïve human scFv library with kappa light chain repertoire with a library size of 109 was developed. The improved Yin-Yang biopanning process was able to enrich monoclonal antibodies specific to the MERS-CoV nucleoprotein. Three unique monoclonal antibodies were isolated in the process. The Yin-Yang biopanning method highlights the possibility of utilizing crude antigens for the isolation of monoclonal antibodies by phage display.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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Lim CC, Choong YS, Lim TS. Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation. Int J Mol Sci 2019; 20:E1861. [PMID: 30991723 PMCID: PMC6515083 DOI: 10.3390/ijms20081861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
Antibodies leverage on their unique architecture to bind with an array of antigens. The strength of interaction has a direct relation to the affinity of the antibodies towards the antigen. In vivo affinity maturation is performed through multiple rounds of somatic hypermutation and selection in the germinal centre. This unique process involves intricate sequence rearrangements at the gene level via molecular mechanisms. The emergence of in vitro display technologies, mainly phage display and recombinant DNA technology, has helped revolutionize the way antibody improvements are being carried out in the laboratory. The adaptation of molecular approaches in vitro to replicate the in vivo processes has allowed for improvements in the way recombinant antibodies are designed and tuned. Combinatorial libraries, consisting of a myriad of possible antibodies, are capable of replicating the diversity of the natural human antibody repertoire. The isolation of target-specific antibodies with specific affinity characteristics can also be accomplished through modification of stringent protocols. Despite the ability to screen and select for high-affinity binders, some 'fine tuning' may be required to enhance antibody binding in terms of its affinity. This review will provide a brief account of phage display technology used for antibody generation followed by a summary of different combinatorial library characteristics. The review will focus on available strategies, which include molecular approaches, next generation sequencing, and in silico approaches used for antibody affinity maturation in both therapeutic and diagnostic applications.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
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Kravchenko Y, Ivanov SV, Kravchenko DS, Frolova EI, Chumakov SP. Combination of ribosome and phage display for fast selection of high affinity VHH antibody fragments. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Selection of antibodies using phage display involves the preliminary cloning of the repertoire of sequences encoding antigen-binding domains into phagemid, which is considered the bottleneck of the method, limiting the resulting diversity of libraries and leading to the loss of poorly represented variants before the start of the selection procedure. Selection in cell-free conditions using a ribosomal display is devoid from this drawback, however is highly sensitive to PCR artifacts and the RNase contamination. The aim of the study was to test the efficiency of a combination of both methods, including pre-selection in a cell-free system to enrich the source library, followed by cloning and final selection using phage display. This approach may eliminate the shortcomings of each method and increase the efficiency of selection. For selection, alpaca VHH antibody sequences suitable for building an immune library were used due to the lack of VL domains. Analysis of immune libraries from the genes of the VH3, VHH3 and VH4 families showed that the VHH antibodies share in the VH3 and VH4 gene groups is insignificant, and selection from the combined library is less effective than from the VHH3 family of sequences. We found that the combination of ribosomal and phage displays leads to a higher enrichment of high-affinity fragments and avoids the loss of the original diversity during cloning. The combined method allowed us to obtain a greater number of different high-affinity sequences, and all the tested VHH fragments were able to specifically recognize the target, including the total protein extracts of cell cultures.
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Affiliation(s)
- YuE Kravchenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - SV Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - DS Kravchenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - EI Frolova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - SP Chumakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Solemani Zadeh A, Grässer A, Dinter H, Hermes M, Schindowski K. Efficient Construction and Effective Screening of Synthetic Domain Antibody Libraries. Methods Protoc 2019; 2:mps2010017. [PMID: 31164599 PMCID: PMC6481084 DOI: 10.3390/mps2010017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/27/2019] [Accepted: 02/11/2019] [Indexed: 01/02/2023] Open
Abstract
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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Affiliation(s)
- Arghavan Solemani Zadeh
- Institute for Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
- Faculty of Medicine, Graduate School "Molecular Medicine", University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
- Faculty of Natural Sciences, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Alissa Grässer
- Institute for Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
- Faculty of Natural Sciences, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Heiko Dinter
- Institute for Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
| | - Maximilian Hermes
- Institute for Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
- Faculty of Natural Sciences, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Katharina Schindowski
- Institute for Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
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Jian JW, Chen HS, Chiu YK, Peng HP, Tung CP, Chen IC, Yu CM, Tsou YL, Kuo WY, Hsu HJ, Yang AS. Effective binding to protein antigens by antibodies from antibody libraries designed with enhanced protein recognition propensities. MAbs 2019; 11:373-387. [PMID: 30526270 PMCID: PMC6380391 DOI: 10.1080/19420862.2018.1550320] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Antibodies provide immune protection by recognizing antigens of diverse chemical properties, but elucidating the amino acid sequence-function relationships underlying the specificity and affinity of antibody-antigen interactions remains challenging. We designed and constructed phage-displayed synthetic antibody libraries with enriched protein antigen-recognition propensities calculated with machine learning predictors, which indicated that the designed single-chain variable fragment variants were encoded with enhanced distributions of complementarity-determining region (CDR) hot spot residues with high protein antigen recognition propensities in comparison with those in the human antibody germline sequences. Antibodies derived directly from the synthetic antibody libraries, without affinity maturation cycles comparable to those in in vivo immune systems, bound to the corresponding protein antigen through diverse conformational or linear epitopes with specificity and affinity comparable to those of the affinity-matured antibodies from in vivo immune systems. The results indicated that more densely populated CDR hot spot residues were sustainable by the antibody structural frameworks and could be accompanied by enhanced functionalities in recognizing protein antigens. Our study results suggest that synthetic antibody libraries, which are not limited by the sequences found in antibodies in nature, could be designed with the guidance of the computational machine learning algorithms that are programmed to predict interaction propensities to molecules of diverse chemical properties, leading to antibodies with optimal characteristics pertinent to their medical applications.
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Affiliation(s)
- Jhih-Wei Jian
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan.,b Institute of Biomedical Informatics, National Yang-Ming University , Taipei , Taiwan.,c Bioinformatics Program, Taiwan International Graduate Program , Institute of Information Science, Academia Sinica , Taipei , Taiwan
| | - Hong-Sen Chen
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Yi-Kai Chiu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Hung-Pin Peng
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Chao-Ping Tung
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Ing-Chien Chen
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Chung-Ming Yu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Yueh-Liang Tsou
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Wei-Ying Kuo
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Hung-Ju Hsu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - An-Suei Yang
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
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Ministro J, Manuel AM, Goncalves J. Therapeutic Antibody Engineering and Selection Strategies. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 171:55-86. [PMID: 31776591 DOI: 10.1007/10_2019_116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Antibody drugs became an increasingly important element of the therapeutic landscape. Their accomplishment has been driven by many unique properties, in particular by their very high specificity and selectivity, in contrast to the off-target liabilities of small molecules (SMs). Antibodies can bring additional functionality to the table with their ability to interact with the immune system, and this can be further manipulated with advances in antibody engineering.The expansion of strategies related to discovery technologies of monoclonal antibodies (mAbs) (phage display, yeast display, ribosome display, bacterial display, mammalian cell surface display, mRNA display, DNA display, transgenic animal, and human B cell derived) opened perspectives for the screening and the selection of therapeutic antibodies for, theoretically, any target from any kind of organism. Moreover, antibody engineering technologies were developed and explored to obtain chosen characteristics of selected leading candidates such as high affinity, low immunogenicity, improved functionality, improved protein production, improved stability, and others. This chapter contains an overview of discovery technologies, mainly display methods and antibody humanization methods for the selection of therapeutic humanized and human mAbs that appeared along the development of these technologies and thereafter. The increasing applications of these technologies will be highlighted in the antibody engineering area (affinity maturation, guided selection to obtain human antibodies) giving promising perspectives for the development of future therapeutics.
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Affiliation(s)
| | - Ana Margarida Manuel
- iMed - Research Institute for Medicines, Faculty of Pharmacy at University of Lisbon, Lisbon, Portugal
| | - Joao Goncalves
- iMed - Research Institute for Medicines, Faculty of Pharmacy at University of Lisbon, Lisbon, Portugal.
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Schröter C, Beck J, Krah S, Zielonka S, Doerner A, Rhiel L, Günther R, Toleikis L, Kolmar H, Hock B, Becker S. Selection of Antibodies with Tailored Properties by Application of High-Throughput Multiparameter Fluorescence-Activated Cell Sorting of Yeast-Displayed Immune Libraries. Mol Biotechnol 2018; 60:727-735. [PMID: 30076531 PMCID: PMC6132741 DOI: 10.1007/s12033-018-0109-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In this study, we present a multiparameter screening procedure for the identification of target-specific antibodies with prescribed properties. Based on B cell receptor gene repertoires from transgenic rats, yeast surface display libraries were generated, and high-affinity human antibodies were readily isolated. We demonstrate that specific desirable features, i.e., species' cross-reactivity and a broad epitope coverage can be integrated into the screening procedure using high-throughput fluorescence-activated cell sorting. We show that the applied screening stringencies translate directly into binding properties of isolated human antibody variants.
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Affiliation(s)
- Christian Schröter
- Antibody Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Jan Beck
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany.,Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Laura Rhiel
- Antibody Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Ralf Günther
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany
| | - Björn Hock
- Antibody Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Stefan Becker
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany.
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Generation and characterization of novel recombinant anti-hERG1 scFv antibodies for cancer molecular imaging. Oncotarget 2018; 9:34972-34989. [PMID: 30405887 PMCID: PMC6201861 DOI: 10.18632/oncotarget.26200] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/21/2018] [Indexed: 01/12/2023] Open
Abstract
Modern molecular imaging techniques have greatly improved tumor detection and post-treatment follow-up of cancer patients. In this context, antibody-based imaging is rapidly becoming the gold standard, since it combines the unique specificity of antibodies with the sensitivity of the different imaging technologies. The aim of this study was to generate and characterize antibodies in single chain Fragment variable (scFv) format directed to an emerging cancer biomarker, the human ether-à-go-go-related gene-1 (hERG1) potassium channel, and to obtain a proof of concept for their potential use for in vivo molecular imaging. The anti-hERG1scFv was generated from a full length monoclonal antibody and then mutagenized, substituting a Phenylalanine residue in the third framework of the VH domain with a Cysteine residue. The resulting scFv-hERG1-Cys showed much higher stability and protein yield, increased affinity and more advantageous binding kinetics, compared to the “native” anti-hERG1scFv. The scFv-hERG1-Cys was hence chosen and characterized: it showed a good binding to the native hERG1 antigen expressed on cells, was stable in serum and displayed a fast pharmacokinetic profile once injected intravenously in nude mice. The calculated half-life was 3.1 hours and no general toxicity or cardiac toxic effects were detected. Finally, the in vivo distribution of an Alexa Fluor 750 conjugated scFv-hERG1-Cys was evaluated both in healthy and tumor-bearing nude mice, showing a good tumor-to-organ ratio, ideal for visualizing hERG1-expressing tumor masses in vivo. In conclusion, the scFv-hERG1-Cys possesses features which make it a suitable tool for application in cancer molecular imaging.
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Antibody-Mediated Therapy against HIV/AIDS: Where Are We Standing Now? J Pathog 2018; 2018:8724549. [PMID: 29973995 PMCID: PMC6009031 DOI: 10.1155/2018/8724549] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/10/2018] [Accepted: 04/26/2018] [Indexed: 11/17/2022] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) cases are on the rise globally. To date, there is still no effective measure to eradicate the causative agent, human immunodeficiency virus (HIV). Highly active antiretroviral therapy (HAART) is being used in HIV/AIDS management, but it results in long-term medication and has major drawbacks such as multiple side effects, high cost, and increasing the generation rate of escape mutants. In addition, HAART does not control HIV-related complications, and hence more medications and further management are required. With this, other alternatives are urgently needed. In the past, small-molecule inhibitors have shown potent antiviral effects, and some of them are now being evaluated in clinical trials. The challenges in developing these small molecules for clinical use include the off-target effect, poor stability, and low bioavailability. On the other hand, antibody-mediated therapy has emerged as an important therapeutic modality for anti-HIV therapeutics development. Many antiviral antibodies, namely, broad neutralizing antibodies (bnAbs) against multiple strains of HIV, have shown promising effects in vitro and in animal studies; further studies are ongoing in clinical trials to evaluate their uses in clinical applications. This short review aims to discuss the current development of therapeutic antibodies against HIV and the challenges in adopting them for clinical use.
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47
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Huang G, Zhong Z, Miersch S, Sidhu SS, Hou SC, Wu D. Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity. J Vis Exp 2018:57357. [PMID: 29782009 PMCID: PMC6101057 DOI: 10.3791/57357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Demand for monoclonal antibodies (mAbs) in basic research and medicine is increasing yearly. Hybridoma technology has been the dominant method for mAb development since its first report in 1975. As an alternative technology, phage display methods for mAb development are increasingly attractive since Humira, the first phage-derived antibody and one of the best-selling mAbs, was approved for clinical treatment of rheumatoid arthritis in 2002. As a non-animal based mAb development technology, phage display bypasses antigen immunogenicity, humanization, and animal maintenance that are required from traditional hybridoma technology based antibody development. In this protocol, we describe a method for construction of synthetic phage-displayed Fab libraries with diversities of 109-1010 obtainable with a single electroporation. This protocol consists of: 1) high-efficiency electro-competent cell preparation; 2) extraction of uracil-containing single-stranded DNA (dU-ssDNA); 3) Kunkel's method based oligonucleotide-directed mutagenesis; 4) electroporation and calculation of library size; 5) protein A/L-based enzyme-linked immunosorbent assay (ELISA) for folding and functional diversity evaluation; and 6) DNA sequence analysis of diversity.
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Affiliation(s)
- Ganggang Huang
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University
| | - Zhenwei Zhong
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University
| | - Shane Miersch
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto; Department of Molecular Genetics, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto
| | - Sachdev S Sidhu
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University; Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto; Department of Molecular Genetics, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto
| | - Shin-Chen Hou
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University;
| | - Donghui Wu
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University;
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Adolf-Bryfogle J, Kalyuzhniy O, Kubitz M, Weitzner BD, Hu X, Adachi Y, Schief WR, Dunbrack RL. RosettaAntibodyDesign (RAbD): A general framework for computational antibody design. PLoS Comput Biol 2018; 14:e1006112. [PMID: 29702641 PMCID: PMC5942852 DOI: 10.1371/journal.pcbi.1006112] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 05/09/2018] [Accepted: 04/02/2018] [Indexed: 01/12/2023] Open
Abstract
A structural-bioinformatics-based computational methodology and framework have been developed for the design of antibodies to targets of interest. RosettaAntibodyDesign (RAbD) samples the diverse sequence, structure, and binding space of an antibody to an antigen in highly customizable protocols for the design of antibodies in a broad range of applications. The program samples antibody sequences and structures by grafting structures from a widely accepted set of the canonical clusters of CDRs (North et al., J. Mol. Biol., 406:228-256, 2011). It then performs sequence design according to amino acid sequence profiles of each cluster, and samples CDR backbones using a flexible-backbone design protocol incorporating cluster-based CDR constraints. Starting from an existing experimental or computationally modeled antigen-antibody structure, RAbD can be used to redesign a single CDR or multiple CDRs with loops of different length, conformation, and sequence. We rigorously benchmarked RAbD on a set of 60 diverse antibody-antigen complexes, using two design strategies-optimizing total Rosetta energy and optimizing interface energy alone. We utilized two novel metrics for measuring success in computational protein design. The design risk ratio (DRR) is equal to the frequency of recovery of native CDR lengths and clusters divided by the frequency of sampling of those features during the Monte Carlo design procedure. Ratios greater than 1.0 indicate that the design process is picking out the native more frequently than expected from their sampled rate. We achieved DRRs for the non-H3 CDRs of between 2.4 and 4.0. The antigen risk ratio (ARR) is the ratio of frequencies of the native amino acid types, CDR lengths, and clusters in the output decoys for simulations performed in the presence and absence of the antigen. For CDRs, we achieved cluster ARRs as high as 2.5 for L1 and 1.5 for H2. For sequence design simulations without CDR grafting, the overall recovery for the native amino acid types for residues that contact the antigen in the native structures was 72% in simulations performed in the presence of the antigen and 48% in simulations performed without the antigen, for an ARR of 1.5. For the non-contacting residues, the ARR was 1.08. This shows that the sequence profiles are able to maintain the amino acid types of these conserved, buried sites, while recovery of the exposed, contacting residues requires the presence of the antigen-antibody interface. We tested RAbD experimentally on both a lambda and kappa antibody-antigen complex, successfully improving their affinities 10 to 50 fold by replacing individual CDRs of the native antibody with new CDR lengths and clusters.
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Affiliation(s)
- Jared Adolf-Bryfogle
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, United States of America
- Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA, United States of America
- The Scripps Research Institute, La Jolla, CA, United States of America
| | - Oleks Kalyuzhniy
- The Scripps Research Institute, La Jolla, CA, United States of America
- IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, United States of America
| | - Michael Kubitz
- The Scripps Research Institute, La Jolla, CA, United States of America
| | - Brian D. Weitzner
- Department of Biochemistry, University of Washington, Seattle, WA, United States of America
- Institute for Protein Design, University of Washington, Seattle, WA, United States of America
| | - Xiaozhen Hu
- The Scripps Research Institute, La Jolla, CA, United States of America
| | - Yumiko Adachi
- IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, United States of America
| | - William R. Schief
- The Scripps Research Institute, La Jolla, CA, United States of America
- IAVI Neutralizing Antibody Center at TSRI, La Jolla, CA, United States of America
| | - Roland L. Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, United States of America
- * E-mail:
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49
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Wang B, DeKosky BJ, Timm MR, Lee J, Normandin E, Misasi J, Kong R, McDaniel JR, Delidakis G, Leigh KE, Niezold T, Choi CW, Viox EG, Fahad A, Cagigi A, Ploquin A, Leung K, Yang ES, Kong WP, Voss WN, Schmidt AG, Moody MA, Ambrozak DR, Henry AR, Laboune F, Ledgerwood JE, Graham BS, Connors M, Douek DC, Sullivan NJ, Ellington AD, Mascola JR, Georgiou G. Functional interrogation and mining of natively paired human V H:V L antibody repertoires. Nat Biotechnol 2018; 36:152-155. [PMID: 29309060 PMCID: PMC5801115 DOI: 10.1038/nbt.4052] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/06/2017] [Indexed: 01/12/2023]
Abstract
We present a technology to screen natively-paired human antibody repertoires from millions of B cells. Libraries of natively-paired variable region heavy and light (VH:VL) amplicons are expressed in a yeast display platform that is optimized for human Fab surface expression. Using our method we identify HIV-1 broadly neutralizing antibodies (bNAbs) from an HIV-1 slow progressor and high-affinity neutralizing antibodies against Ebola virus glycoprotein and influenza hemagglutinin.
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Affiliation(s)
- Bo Wang
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Brandon J DeKosky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA.,Department of Chemical & Petroleum Engineering, The University of Kansas, Lawrence, Kansas, USA.,Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas, USA
| | - Morgan R Timm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Jiwon Lee
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Erica Normandin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Jonathan R McDaniel
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - George Delidakis
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Kendra E Leigh
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Thomas Niezold
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Chang W Choi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Elise G Viox
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Ahmed Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas, USA
| | - Alberto Cagigi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Aurélie Ploquin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Wing-Pui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - William N Voss
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Aaron G Schmidt
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical School, Durham, North Carolina, USA.,Department of Pediatrics, Duke University Medical School, Durham, North Carolina, USA
| | - David R Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Farida Laboune
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Julie E Ledgerwood
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Mark Connors
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - George Georgiou
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA.,Department of Bioengineering, The University of Texas at Austin, Austin, Texas, USA
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50
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Abstract
This protocol describes the processes involved in the generation of human antibody libraries in Fab format. The antibody repertoire is derived from peripheral blood mononucleocytes focusing on different immunoglobulin isotypes. A two-step cloning process was used to generate a diverse human Fab library for subsequent selection by phage display. The method can be applied for the generation of both naive and immune antibody libraries. The naive repertoire allows for the library to be applied for the generation of human monoclonal antibodies against a broad range of target antigens making it a useful resource for antibody generation. However, the immune repertoire will be focused against target antigens from a particular disease. The protocol will focus on the generation of the library including the panning process.
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Affiliation(s)
- Noorsharmimi Omar
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia. .,Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Minden, Penang, Malaysia.
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