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Wei Y, Li G, Wang Z, Qian K, Zhang S, Zhang L, Lei C, Hu S. Development and characterization of a novel neutralizing scFv vectored immunoprophylaxis against botulinum toxin type A. J Drug Target 2024; 32:213-222. [PMID: 38164940 DOI: 10.1080/1061186x.2023.2301418] [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: 05/17/2023] [Accepted: 10/18/2023] [Indexed: 01/03/2024]
Abstract
Botulinum toxin is a protein toxin secreted by Clostridium botulinum that is strongly neurotoxic. Due to its characteristics of being super toxic, quick acting, and difficult to prevent, the currently reported antiviral studies focusing on monoclonal antibodies have limited effectiveness. Therefore, for the sake of effectively prevention and treatment of botulism and to maintain country biosecurity as well as the health of the population, in this study, we intend to establish a single chain antibody (scFv) targeting the carboxyl terminal binding functional domain of the botulinum neurotoxin heavy chain (BONT/AHc) of botulinum neurotoxin type A, and explore the value of a new passive immune method in antiviral research which based on adeno-associated virus (AAV) mediated vector immunoprophylaxis (VIP) strategy. The scFv small-molecular single-chain antibody sequenced, designed, constructed, expressed and purified by hybridoma has high neutralising activity and affinity level, which can lay a good foundation for the modification and development of antibody engineering drugs. In vivo experiments, AAV-mediated scFv engineering drug has good anti-BONT/A toxin neutralisation ability, has advantages of simple operation, stable expression and good efficacy, and may be one of the effective treatment strategies for long-term prevention and protection of BONT/A botulinum neurotoxin.
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Affiliation(s)
- Yongpeng Wei
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
- Hepatic Surgery Department V, The Third Affiliated Hospital, Second Military Medical University, Shanghai, China
| | - Guangyao Li
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
- Department of Biomedical Engineering, College of Basic Medical Sciences, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Zhuo Wang
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
- Hepatic Surgery Department V, The Third Affiliated Hospital, Second Military Medical University, Shanghai, China
| | - Kewen Qian
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
- Department of Biomedical Engineering, College of Basic Medical Sciences, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Shuyi Zhang
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
| | - Lingling Zhang
- Department of Central Laboratory, Clinical Research Center of Changhai Hospital, Shanghai, China
| | - Changhai Lei
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
| | - Shi Hu
- Department of Biomedical Engineering, College of Basic Medical Sciences, Naval Medical University (Second Military Medical University), Shanghai, China
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2
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Marino SF, Daumke O. Structure-based humanization of a therapeutic antibody for multiple myeloma. J Mol Med (Berl) 2024; 102:1151-1161. [PMID: 39052065 PMCID: PMC11358308 DOI: 10.1007/s00109-024-02470-4] [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: 11/08/2023] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024]
Abstract
The optimal efficacy of xenogeneically generated proteins intended for application in humans requires that their own antigenicity be minimized. This necessary adaptation of antibodies to a humanized version poses challenges since modifications even distant from the binding sites can greatly influence antigen recognition and this is the primary feature that must be maintained during all modifications. Current strategies often rely on grafting and/or randomization/selection to arrive at a humanized variant retaining the binding properties of the original molecule. However, in terms of speed and efficiency, rationally directed approaches can be superior, provided the requisite structural information is available. We present here a humanization procedure based on the high-resolution X-ray structure of a chimaeric IgG against a marker for multiple myeloma. Based on in silico modelling of humanizing amino acid substitutions identified from sequence alignments, we devised a straightforward cloning procedure to rapidly evaluate the proposed sequence changes. Careful inspection of the structure allowed the identification of a potentially problematic amino acid change that indeed disrupted antigen binding. Subsequent optimization of the antigen binding loop sequences resulted in substantial recovery of binding affinity lost in the completely humanized antibody. X-ray structures of the humanized and optimized variants demonstrate that the antigen binding mode is preserved, with surprisingly few direct contacts to antibody atoms. These results underline the importance of structural information for the efficient optimization of protein therapeutics. KEY MESSAGES: Structure-based humanization of an IgG against BCMA, a marker for Multiple Myeloma. Identification of problematic mutations and unexpected modification sites. Structures of the modified IgG-antigen complexes verified predictions. Provision of humanized high-affinity IgGs against BCMA for therapeutic applications.
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Affiliation(s)
- Stephen F Marino
- Max Delbrück Centrum for Molecular Medicine, Robert-Rössle-Straße 10, 13125, Berlin, Germany.
- German Federal Institute for Risk Assessment, Max-Dohrn-Strasse 8-10, 10589, Berlin, Germany.
| | - Oliver Daumke
- Max Delbrück Centrum for Molecular Medicine, Robert-Rössle-Straße 10, 13125, Berlin, Germany
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Nguyen NM, Nakao K, Kobayashi R, Taniguchi H, Yokoyama F, Horiuchi JI, Kumada Y. Generation of rabbit single-chain variable fragments with different physicochemical and biological properties by complementary determining region-grafting technology. J Biosci Bioeng 2024:S1389-1723(24)00198-1. [PMID: 39198103 DOI: 10.1016/j.jbiosc.2024.07.009] [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: 05/16/2024] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 09/01/2024]
Abstract
In this study, we have demonstrated a complementary-determining region (CDR) grafting technology for the generation of rabbit scFvs with different antigen recognition and physicochemical properties. The antigen-binding affinity of the CDR-grafted anti-CRP scFv, C1R/B1R (V1), which was generated by the CDR/framework region (CDR/FR) definition based on the traditional numbering rule, was insufficient when compared to that of the original clone, C1R, suggesting that the amino acid residues outside the original CDRs might significantly contribute to antigen recognition in rabbit scFvs. We redefined new CDRs and FRs to maintain antigen-binding affinities through the extension of multiple amino acid residues for CDRH1 and CDRH2, based on the amino acid sequence alignments of rabbit scFvs isolated from phage libraries. The new version successfully maintained the antigen binding affinity. CDR-grafted scFvs possessing a common CDR sequence and different FR sequences were successfully generated based on this new CDR/FR definition, and their physicochemical properties were further investigated. The antigen-binding activities of rabbit scFvs on Maxisorp varied between the tested clones in sandwich ELISA, supporting the idea that the combination of CDR with different FRs might change the physicochemical properties of scFvs on a solid material. The CDR-grafted scFvs possessing a frame sequence of anti-CRP scFv C2R maintained the ability to bind to protein L and were successfully purified. Expression titers showed improved solubility by diminishing the amount of insoluble scFvs. Thus, the method developed in this study is promising for generating alternatives with strict antigen binding recognition and different physicochemical properties.
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Affiliation(s)
- Ngoc Minh Nguyen
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kiichi Nakao
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Ryo Kobayashi
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Haruka Taniguchi
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Fuki Yokoyama
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Jun-Ichi Horiuchi
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yoichi Kumada
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
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Sada R, Yamamoto H, Matsumoto S, Harada A, Kikuchi A. Newly developed humanized anti-CKAP4 antibody suppresses pancreatic cancer growth by inhibiting DKK1-CKAP4 signaling. Cancer Sci 2024. [PMID: 39118263 DOI: 10.1111/cas.16278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 08/10/2024] Open
Abstract
Cytoskeleton-associated protein 4 (CKAP4) is a cell surface receptor for Dickkopf 1 (DKK1), a secreted protein. The DKK1-CKAP4 pathway is activated in various malignant tumors, including pancreatic, lung, esophageal, and liver cancers, to promote tumor growth. Thus, CKAP4 has been expected to represent a novel molecular target of cancer therapy. Recombinant mouse anti-CKAP4 antibodies were generated based on an original mouse antibody (3F11-2B10) and inhibited DKK1-CKAP4 signaling and xenograft tumor formation induced by pancreatic cancer cells, which was comparable with 3F11-2B10. From the 3F11-2B10 nucleotide sequence, humanized anti-CKAP4 antibody (Hv1Lt1) was subsequently developed. The binding affinity of Hv1Lt1 for CKAP4 was superior to that of 3F11-2B10. Hv1Lt1 inhibited DKK1 binding to CKAP4, AKT activity, and sphere formation of pancreatic cancer cells, which was comparable with 3F11-2B10. Hv1Lt1 also suppressed xenograft tumor formation induced by human pancreatic cancer cells and tumor growth in murine cancer models, in which murine pancreatic cancer organoids were orthotopically transplanted into the pancreas. In resected tumor samples from mice treated with Hv1Lt1, anti-tumor immune reactions were modulated and cytotoxic T cells were highly infiltrated in the tumor microenvironment. Additionally, combination of Hv1Lt1 and other chemotherapy drugs exhibited stronger effects compared with monotherapy. These results suggest that Hv1Lt1 represents a promising anti-cancer therapy.
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Affiliation(s)
- Ryota Sada
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Hideki Yamamoto
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Health Care Sciences, Jikei University of Health Care Sciences, Osaka, Japan
| | - Shinji Matsumoto
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Akikazu Harada
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Akira Kikuchi
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
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Zhang T, Yang D, Tang L, Hu Y. Current development of severe acute respiratory syndrome coronavirus 2 neutralizing antibodies (Review). Mol Med Rep 2024; 30:148. [PMID: 38940338 PMCID: PMC11228696 DOI: 10.3892/mmr.2024.13272] [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: 02/26/2024] [Accepted: 05/21/2024] [Indexed: 06/29/2024] Open
Abstract
The coronavirus disease 2019 pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) seriously affected global public health security. Studies on vaccines, neutralizing antibodies (NAbs) and small molecule antiviral drugs are currently ongoing. In particular, NAbs have emerged as promising therapeutic agents due to their well‑defined mechanism, high specificity, superior safety profile, ease of large‑scale production and simultaneous application for both prevention and treatment of viral infection. Numerous NAb therapeutics have entered the clinical research stages, demonstrating promising therapeutic and preventive effects. These agents have been used for outbreak prevention and control under urgent authorization processes. The present review summarizes the molecular targets of SARS‑CoV‑2‑associated NAbs and screening and identification techniques for NAb development. Moreover, the current shortcomings and challenges that persist with the use of NAbs are discussed. The aim of the present review is to offer a reference for the development of NAbs for any future emergent infectious diseases, including SARS‑CoV‑2.
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Affiliation(s)
- Tong Zhang
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Di Yang
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Liang Tang
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yu Hu
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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Li D, Pucci F, Rooman M. Prediction of Paratope-Epitope Pairs Using Convolutional Neural Networks. Int J Mol Sci 2024; 25:5434. [PMID: 38791470 PMCID: PMC11121317 DOI: 10.3390/ijms25105434] [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: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Antibodies play a central role in the adaptive immune response of vertebrates through the specific recognition of exogenous or endogenous antigens. The rational design of antibodies has a wide range of biotechnological and medical applications, such as in disease diagnosis and treatment. However, there are currently no reliable methods for predicting the antibodies that recognize a specific antigen region (or epitope) and, conversely, epitopes that recognize the binding region of a given antibody (or paratope). To fill this gap, we developed ImaPEp, a machine learning-based tool for predicting the binding probability of paratope-epitope pairs, where the epitope and paratope patches were simplified into interacting two-dimensional patches, which were colored according to the values of selected features, and pixelated. The specific recognition of an epitope image by a paratope image was achieved by using a convolutional neural network-based model, which was trained on a set of two-dimensional paratope-epitope images derived from experimental structures of antibody-antigen complexes. Our method achieves good performances in terms of cross-validation with a balanced accuracy of 0.8. Finally, we showcase examples of application of ImaPep, including extensive screening of large libraries to identify paratope candidates that bind to a selected epitope, and rescoring and refining antibody-antigen docking poses.
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Affiliation(s)
- Dong Li
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (D.L.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (D.L.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (D.L.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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7
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Gordon GL, Raybould MIJ, Wong A, Deane CM. Prospects for the computational humanization of antibodies and nanobodies. Front Immunol 2024; 15:1399438. [PMID: 38812514 PMCID: PMC11133524 DOI: 10.3389/fimmu.2024.1399438] [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: 03/11/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
To be viable therapeutics, antibodies must be tolerated by the human immune system. Rational approaches to reduce the risk of unwanted immunogenicity involve maximizing the 'humanness' of the candidate drug. However, despite the emergence of new discovery technologies, many of which start from entirely human gene fragments, most antibody therapeutics continue to be derived from non-human sources with concomitant humanization to increase their human compatibility. Early experimental humanization strategies that focus on CDR loop grafting onto human frameworks have been critical to the dominance of this discovery route but do not consider the context of each antibody sequence, impacting their success rate. Other challenges include the simultaneous optimization of other drug-like properties alongside humanness and the humanization of fundamentally non-human modalities such as nanobodies. Significant efforts have been made to develop in silico methodologies able to address these issues, most recently incorporating machine learning techniques. Here, we outline these recent advancements in antibody and nanobody humanization, focusing on computational strategies that make use of the increasing volume of sequence and structural data available and the validation of these tools. We highlight that structural distinctions between antibodies and nanobodies make the application of antibody-focused in silico tools to nanobody humanization non-trivial. Furthermore, we discuss the effects of humanizing mutations on other essential drug-like properties such as binding affinity and developability, and methods that aim to tackle this multi-parameter optimization problem.
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Affiliation(s)
| | | | | | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
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Parkinson J, Wang W. For antibody sequence generative modeling, mixture models may be all you need. Bioinformatics 2024; 40:btae278. [PMID: 38652603 PMCID: PMC11093529 DOI: 10.1093/bioinformatics/btae278] [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: 01/29/2024] [Revised: 04/02/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024] Open
Abstract
MOTIVATION Antibody therapeutic candidates must exhibit not only tight binding to their target but also good developability properties, especially low risk of immunogenicity. RESULTS In this work, we fit a simple generative model, SAM, to sixty million human heavy and seventy million human light chains. We show that the probability of a sequence calculated by the model distinguishes human sequences from other species with the same or better accuracy on a variety of benchmark datasets containing >400 million sequences than any other model in the literature, outperforming large language models (LLMs) by large margins. SAM can humanize sequences, generate new sequences, and score sequences for humanness. It is both fast and fully interpretable. Our results highlight the importance of using simple models as baselines for protein engineering tasks. We additionally introduce a new tool for numbering antibody sequences which is orders of magnitude faster than existing tools in the literature. AVAILABILITY AND IMPLEMENTATION All tools developed in this study are available at https://github.com/Wang-lab-UCSD/AntPack.
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Affiliation(s)
- Jonathan Parkinson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, United States
- MAP Bioscience, La Jolla, CA 92093, United States
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, United States
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359, United States
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Gallo E. The rise of big data: deep sequencing-driven computational methods are transforming the landscape of synthetic antibody design. J Biomed Sci 2024; 31:29. [PMID: 38491519 PMCID: PMC10943851 DOI: 10.1186/s12929-024-01018-5] [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: 10/16/2023] [Accepted: 03/05/2024] [Indexed: 03/18/2024] Open
Abstract
Synthetic antibodies (Abs) represent a category of artificial proteins capable of closely emulating the functions of natural Abs. Their in vitro production eliminates the need for an immunological response, streamlining the process of Ab discovery, engineering, and development. These artificially engineered Abs offer novel approaches to antigen recognition, paratope site manipulation, and biochemical/biophysical enhancements. As a result, synthetic Abs are fundamentally reshaping conventional methods of Ab production. This mirrors the revolution observed in molecular biology and genomics as a result of deep sequencing, which allows for the swift and cost-effective sequencing of DNA and RNA molecules at scale. Within this framework, deep sequencing has enabled the exploration of whole genomes and transcriptomes, including particular gene segments of interest. Notably, the fusion of synthetic Ab discovery with advanced deep sequencing technologies is redefining the current approaches to Ab design and development. Such combination offers opportunity to exhaustively explore Ab repertoires, fast-tracking the Ab discovery process, and enhancing synthetic Ab engineering. Moreover, advanced computational algorithms have the capacity to effectively mine big data, helping to identify Ab sequence patterns/features hidden within deep sequencing Ab datasets. In this context, these methods can be utilized to predict novel sequence features thereby enabling the successful generation of de novo Ab molecules. Hence, the merging of synthetic Ab design, deep sequencing technologies, and advanced computational models heralds a new chapter in Ab discovery, broadening our comprehension of immunology and streamlining the advancement of biological therapeutics.
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Affiliation(s)
- Eugenio Gallo
- Department of Medicinal Chemistry, Avance Biologicals, 950 Dupont Street, Toronto, ON, M6H 1Z2, Canada.
- Department of Protein Engineering, RevivAb, Av. Ipiranga, 6681, Partenon, Porto Alegre, RS, 90619-900, Brazil.
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Liu Z, Kim D, Kang S, Jung JU. A Detailed Protocol for Constructing a Human Single-Chain Variable Fragment (scFv) Library and Downstream Screening via Phage Display. Methods Protoc 2024; 7:13. [PMID: 38392687 PMCID: PMC10893473 DOI: 10.3390/mps7010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
The development of monoclonal antibodies (mAbs) represents a significant milestone in both basic research and clinical applications due to their target specificity and versatility in therapeutic and diagnostic applications. The innovative strategy of mAb screening, utilizing phage display, facilitates the in vitro screening of antibodies with high affinity to target antigens. The single-chain variable fragment (scFv) is a subset of mAb derivatives, known for its high binding affinity and smaller size-just one-third of that of human IgG. This report outlines a detailed and comprehensive procedure for constructing a scFv phagemid library derived from human patients, followed by screening via phage display affinity selection. The protocol utilizes 348 primer combinations spanning the entire human antibody repertoire to minimize sequence bias and maintain library diversity during polymerase chain reaction (PCR) for scFv generation, resulting in a library size greater than 1 × 108. Furthermore, we describe a high-throughput phage display screening protocol using enzyme-linked immunosorbent assay (ELISA) to evaluate more than 1200 scFv candidates. The generation of a highly diverse scFv library, coupled with the implementation of a phage display screening methodology, is expected to provide a valuable resource for researchers in pursuit of scFvs with high affinity for target antigens, thus advancing both research and clinical endeavors.
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Affiliation(s)
- Ziyi Liu
- Cancer Biology Department, Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (Z.L.); (D.K.); (S.K.)
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Dokyun Kim
- Cancer Biology Department, Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (Z.L.); (D.K.); (S.K.)
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Seokmin Kang
- Cancer Biology Department, Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (Z.L.); (D.K.); (S.K.)
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jae U. Jung
- Cancer Biology Department, Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (Z.L.); (D.K.); (S.K.)
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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11
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Wei J, Li J, Zong F, Xiao ZX, Cao Y. Computational Analysis of B-Cell Receptor (BCR) Immune Repertoires with Abalign. Curr Protoc 2024; 4:e1002. [PMID: 38406972 DOI: 10.1002/cpz1.1002] [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] [Indexed: 02/27/2024]
Abstract
The widespread application of high-throughput sequencing technology has generated massive sequences of B-cell receptor (BCR) immune repertoires. Computational analysis of these data has gained significant attention due to the increasing importance of immunotherapy and precision medicine. It not only reveals the diversity and dynamic changes in immune responses, contributing to the study of associated diseases, but also provides valuable information for immunodiagnostics and drug development. Recently, we introduced a BCR-specific multiple sequence alignment (MSA) method along with a comprehensive platform software called Abalign, which stands out as an excellent choice for analyzing BCR immune repertoires due to its unique high-throughput processing capability. It offers ultra-fast MSA functionality and a wide range of analytical features, including BCR/antibody extraction, clonal grouping, lineage tree construction, mutation profiling, diversity statistics, VJ gene assignment, antibody humanization, and more. Importantly, users can perform these analyses using the graphical user interface without any programming skills or scripts. In this article, we present a series of protocols that integrate Abalign's analysis modules into a cohesive workflow. This step-by-step workflow provides detailed instructions for software installation, data preparation, and comprehensive analysis of BCR immune repertoires. This workflow facilitates the efficient acquisition of comprehensive results in profiling BCR immune repertoires, offering insights into the impacts of infectious diseases, allergies, autoimmune disorders, tumor immunology, and antibody drugs. Abalign is freely available at http://cao.labshare.cn/abalign/. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Resource preparation Basic Protocol 2: Analyzing BCR immune repertoires Support Protocol 1: Aiding antibody humanization Support Protocol 2: Constructing B-cell lineage trees Alternate Protocol: Running with Linux command line Basic Protocol 3: Comparing BCR immune repertoires.
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Affiliation(s)
- Jiachen Wei
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Junxian Li
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fanjie Zong
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhi-Xiong Xiao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
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12
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Kirkland ME, Patfield S, Hughes AC, Hernlem B, He X. A novel Shiga toxin 2a neutralizing antibody therapeutic with low immunogenicity and high efficacy. Antimicrob Agents Chemother 2024; 68:e0059823. [PMID: 38047751 PMCID: PMC10777836 DOI: 10.1128/aac.00598-23] [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: 05/09/2023] [Accepted: 10/18/2023] [Indexed: 12/05/2023] Open
Abstract
Shiga toxin-producing Escherichia coli infections are difficult to treat due to the risk of antibiotic-induced stress upregulating the production of toxins, medical treatment is consequently limited to supportive care to prevent the development of hemolytic uremic syndrome (HUS). Here, we introduce a potentially therapeutic humanized mouse monoclonal antibody (Hu-mAb 2-5) targeting Stx2a, the most common Shiga toxin subtype identified from outbreaks. We demonstrate that Hu-mAb 2-5 has low immunogenicity in healthy adults ex vivo and high neutralizing efficacy in vivo, protecting mice from mortality and HUS-related tissue damage.
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Affiliation(s)
- Marina E. Kirkland
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
- U.S. Department of Energy, Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Stephanie Patfield
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
| | - Anna C. Hughes
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
| | - Bradley Hernlem
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
| | - Xiaohua He
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
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13
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Tennenhouse A, Khmelnitsky L, Khalaila R, Yeshaya N, Noronha A, Lindzen M, Makowski EK, Zaretsky I, Sirkis YF, Galon-Wolfenson Y, Tessier PM, Abramson J, Yarden Y, Fass D, Fleishman SJ. Computational optimization of antibody humanness and stability by systematic energy-based ranking. Nat Biomed Eng 2024; 8:30-44. [PMID: 37550425 PMCID: PMC10842793 DOI: 10.1038/s41551-023-01079-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 07/13/2023] [Indexed: 08/09/2023]
Abstract
Conventional methods for humanizing animal-derived antibodies involve grafting their complementarity-determining regions onto homologous human framework regions. However, this process can substantially lower antibody stability and antigen-binding affinity, and requires iterative mutational fine-tuning to recover the original antibody properties. Here we report a computational method for the systematic grafting of animal complementarity-determining regions onto thousands of human frameworks. The method, which we named CUMAb (for computational human antibody design; available at http://CUMAb.weizmann.ac.il ), starts from an experimental or model antibody structure and uses Rosetta atomistic simulations to select designs by energy and structural integrity. CUMAb-designed humanized versions of five antibodies exhibited similar affinities to those of the parental animal antibodies, with some designs showing marked improvement in stability. We also show that (1) non-homologous frameworks are often preferred to highest-homology frameworks, and (2) several CUMAb designs that differ by dozens of mutations and that use different human frameworks are functionally equivalent.
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Affiliation(s)
- Ariel Tennenhouse
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lev Khmelnitsky
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Razi Khalaila
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Yeshaya
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ashish Noronha
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Moshit Lindzen
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Emily K Makowski
- Biointerfaces Institute and Departments of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ira Zaretsky
- Antibody Engineering Unit, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Peter M Tessier
- Biointerfaces Institute and Departments of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yosef Yarden
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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14
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Zhuang W, Zhang W, Xie L, Wang L, Li Y, Wang Z, Zhang A, Qiu H, Feng J, Zhang B, Hu Y. Generation and Characterization of SORT1-Targeted Antibody-Drug Conjugate for the Treatment of SORT1-Positive Breast Tumor. Int J Mol Sci 2023; 24:17631. [PMID: 38139459 PMCID: PMC10743877 DOI: 10.3390/ijms242417631] [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: 11/08/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Antibody-drug conjugates (ADCs) have greatly improved the outcomes of advanced breast tumors. However, the treatment of breast tumors with existing ADCs is still hindered by many issues, such as tumor antigen heterogeneity and drug resistance. Therefore, ADCs against new targets would provide options for the treatment of these challenges. Sortilin-1 (SORT1) may be a promising target for ADC as it is upregulated in breast cancer. To evaluate the possibility of SORT1 as an ADC target, a humanized antibody_8D302 with high affinity against SORT1 was generated. Additionally, 8D302 was conjugated with MMAE and DXd to generate two ADCs_8D302-MMAE and 8D302-DXd, respectively. Both 8D302-MMAE and 8D302-DXd showed effective cytotoxicity against SORT1 positive breast tumor cell lines and induced bystander killing. Consequently, 8D302-MMAE showed relatively better anti-tumor activity than 8D302-DXd both in vitro and in vivo, but 8D302-DXd had superior safety profile and pharmacokinetics profile over 8D302-MMAE. Furthermore, SORT1 induced faster internalization and lysosomal trafficking of antibodies and had a higher turnover compared with HER2. Also, 8D302-DXd exhibited superior cell cytotoxicity and tumor suppression over trastuzumab-DXd, a HER2-targeted ADC. We hypothesize that the high turnover of SORT1 enables SORT1-targeted ADC to be a powerful agent for the treatment of SORT1-positive breast tumor.
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Affiliation(s)
- Weiliang Zhuang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; (W.Z.); (L.W.)
- China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China; (W.Z.); (L.X.); (Y.L.); (Z.W.); (A.Z.); (H.Q.); (J.F.)
| | - Wei Zhang
- China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China; (W.Z.); (L.X.); (Y.L.); (Z.W.); (A.Z.); (H.Q.); (J.F.)
| | - Liping Xie
- China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China; (W.Z.); (L.X.); (Y.L.); (Z.W.); (A.Z.); (H.Q.); (J.F.)
| | - Lei Wang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; (W.Z.); (L.W.)
| | - Yuan Li
- China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China; (W.Z.); (L.X.); (Y.L.); (Z.W.); (A.Z.); (H.Q.); (J.F.)
| | - Ziyu Wang
- China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China; (W.Z.); (L.X.); (Y.L.); (Z.W.); (A.Z.); (H.Q.); (J.F.)
| | - Ao Zhang
- China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China; (W.Z.); (L.X.); (Y.L.); (Z.W.); (A.Z.); (H.Q.); (J.F.)
| | - Haitao Qiu
- China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China; (W.Z.); (L.X.); (Y.L.); (Z.W.); (A.Z.); (H.Q.); (J.F.)
| | - Jun Feng
- China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China; (W.Z.); (L.X.); (Y.L.); (Z.W.); (A.Z.); (H.Q.); (J.F.)
| | - Baohong Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; (W.Z.); (L.W.)
| | - Youjia Hu
- China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Shanghai 201203, China; (W.Z.); (L.X.); (Y.L.); (Z.W.); (A.Z.); (H.Q.); (J.F.)
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15
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Gulyak EL, Alferova VA, Korshun VA, Sapozhnikova KA. Introduction of Carbonyl Groups into Antibodies. Molecules 2023; 28:7890. [PMID: 38067618 PMCID: PMC10707781 DOI: 10.3390/molecules28237890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Antibodies and their derivatives (scFv, Fabs, etc.) represent a unique class of biomolecules that combine selectivity with the ability to target drug delivery. Currently, one of the most promising endeavors in this field is the development of molecular diagnostic tools and antibody-based therapeutic agents, including antibody-drug conjugates (ADCs). To meet this challenge, it is imperative to advance methods for modifying antibodies. A particularly promising strategy involves the introduction of carbonyl groups into the antibody that are amenable to further modification by biorthogonal reactions, namely aliphatic, aromatic, and α-oxo aldehydes, as well as aliphatic and aryl-alkyl ketones. In this review, we summarize the preparation methods and applications of site-specific antibody conjugates that are synthesized using this approach.
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Affiliation(s)
| | | | | | - Ksenia A. Sapozhnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.L.G.); (V.A.A.); (V.A.K.)
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16
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Ormundo LF, Barreto CT, Tsuruta LR. Development of Therapeutic Monoclonal Antibodies for Emerging Arbovirus Infections. Viruses 2023; 15:2177. [PMID: 38005854 PMCID: PMC10675117 DOI: 10.3390/v15112177] [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: 09/11/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Antibody-based passive immunotherapy has been used effectively in the treatment and prophylaxis of infectious diseases. Outbreaks of emerging viral infections from arthropod-borne viruses (arboviruses) represent a global public health problem due to their rapid spread, urging measures and the treatment of infected individuals to combat them. Preparedness in advances in developing antivirals and relevant epidemiological studies protect us from damage and losses. Immunotherapy based on monoclonal antibodies (mAbs) has been shown to be very specific in combating infectious diseases and various other illnesses. Recent advances in mAb discovery techniques have allowed the development and approval of a wide number of therapeutic mAbs. This review focuses on the technological approaches available to select neutralizing mAbs for emerging arbovirus infections and the next-generation strategies to obtain highly effective and potent mAbs. The characteristics of mAbs developed as prophylactic and therapeutic antiviral agents for dengue, Zika, chikungunya, West Nile and tick-borne encephalitis virus are presented, as well as the protective effect demonstrated in animal model studies.
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Affiliation(s)
- Leonardo F. Ormundo
- Biopharmaceuticals Laboratory, Instituto Butantan, São Paulo 05503-900, Brazil; (L.F.O.); (C.T.B.)
- The Interunits Graduate Program in Biotechnology, University of São Paulo, São Paulo 05503-900, Brazil
| | - Carolina T. Barreto
- Biopharmaceuticals Laboratory, Instituto Butantan, São Paulo 05503-900, Brazil; (L.F.O.); (C.T.B.)
- The Interunits Graduate Program in Biotechnology, University of São Paulo, São Paulo 05503-900, Brazil
| | - Lilian R. Tsuruta
- Biopharmaceuticals Laboratory, Instituto Butantan, São Paulo 05503-900, Brazil; (L.F.O.); (C.T.B.)
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17
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Thran M, Pönisch M, Danz H, Horscroft N, Ichtchenko K, Tzipori S, Shoemaker CB. Co-administration of an effector antibody enhances the half-life and therapeutic potential of RNA-encoded nanobodies. Sci Rep 2023; 13:14632. [PMID: 37670025 PMCID: PMC10480410 DOI: 10.1038/s41598-023-41092-7] [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: 05/30/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023] Open
Abstract
The incidence of Clostridioides difficile infection (CDI) and associated mortality have increased rapidly worldwide in recent years. Therefore, it is critical to develop new therapies for CDI. Here we report on the development of mRNA-LNPs encoding camelid-derived VHH-based neutralizing agents (VNAs) targeting toxins A and/or B of C. difficile. In preclinical models, intravenous administration of the mRNA-LNPs provided serum VNA levels sufficient to confer protection of mice against severe disease progression following toxin challenge. Furthermore, we employed an mRNA-LNP encoded effector antibody, a molecular tool designed to specifically bind an epitopic tag linked to the VNAs, to prolong VNA serum half-life. Co-administration of VNA-encoding mRNA-LNPs and an effector antibody, either provided as recombinant protein or encoded by mRNA-LNP, increased serum VNA half-life in mice and in gnotobiotic piglets. Prolonged serum half-life was associated with higher concentrations of serum VNA and enhanced prophylactic protection of mice in challenge models.
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Affiliation(s)
| | | | - Hillary Danz
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, 01536, USA
| | | | - Konstantin Ichtchenko
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, 01536, USA
| | - Charles B Shoemaker
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, 01536, USA.
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18
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Arslan M, Uluçay T, Kale S, Kalyoncu S. Engineering of conserved residues near antibody heavy chain complementary determining region 3 (HCDR3) improves both affinity and stability. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140915. [PMID: 37059314 DOI: 10.1016/j.bbapap.2023.140915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023]
Abstract
Affinity and stability are crucial parameters in antibody development and engineering approaches. Although improvement in both metrics is desirable, trade-offs are almost unavoidable. Heavy chain complementarity determining region 3 (HCDR3) is the best-known region for antibody affinity but its impact on stability is often neglected. Here, we present a mutagenesis study of conserved residues near HCDR3 to elicit the role of this region in the affinity-stability trade-off. These key residues are positioned around the conserved salt bridge between VH-K94 and VH-D101 which is crucial for HCDR3 integrity. We show that the additional salt bridge at the stem of HCDR3 (VH-K94:VH-D101:VH-D102) has an extensive impact on this loop's conformation, therefore simultaneous improvement in both affinity and stability. We find that the disruption of π-π stacking near HCDR3 (VH-Y100E:VL-Y49) at the VH-VL interface cause an irrecoverable loss in stability even if it improves the affinity. Molecular simulations of putative rescue mutants exhibit complex and often non-additive effects. We confirm that our experimental measurements agree with the molecular dynamic simulations providing detailed insights for the spatial orientation of HCDR3. VH-V102 right next to HCDR3 salt bridge might be an ideal candidate to overcome affinity-stability trade-off.
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Affiliation(s)
- Merve Arslan
- Izmir Biomedicine and Genome Center, Balçova, 35340 Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, 35340 Izmir, Turkey
| | - Tuğçe Uluçay
- Izmir Biomedicine and Genome Center, Balçova, 35340 Izmir, Turkey
| | - Seyit Kale
- Izmir Biomedicine and Genome Center, Balçova, 35340 Izmir, Turkey
| | - Sibel Kalyoncu
- Izmir Biomedicine and Genome Center, Balçova, 35340 Izmir, Turkey.
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19
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Qian L, Lin X, Gao X, Khan RU, Liao JY, Du S, Ge J, Zeng S, Yao SQ. The Dawn of a New Era: Targeting the "Undruggables" with Antibody-Based Therapeutics. Chem Rev 2023. [PMID: 37186942 DOI: 10.1021/acs.chemrev.2c00915] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The high selectivity and affinity of antibodies toward their antigens have made them a highly valuable tool in disease therapy, diagnosis, and basic research. A plethora of chemical and genetic approaches have been devised to make antibodies accessible to more "undruggable" targets and equipped with new functions of illustrating or regulating biological processes more precisely. In this Review, in addition to introducing how naked antibodies and various antibody conjugates (such as antibody-drug conjugates, antibody-oligonucleotide conjugates, antibody-enzyme conjugates, etc.) work in therapeutic applications, special attention has been paid to how chemistry tools have helped to optimize the therapeutic outcome (i.e., with enhanced efficacy and reduced side effects) or facilitate the multifunctionalization of antibodies, with a focus on emerging fields such as targeted protein degradation, real-time live-cell imaging, catalytic labeling or decaging with spatiotemporal control as well as the engagement of antibodies inside cells. With advances in modern chemistry and biotechnology, well-designed antibodies and their derivatives via size miniaturization or multifunctionalization together with efficient delivery systems have emerged, which have gradually improved our understanding of important biological processes and paved the way to pursue novel targets for potential treatments of various diseases.
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Affiliation(s)
- Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xuefen Lin
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xue Gao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Rizwan Ullah Khan
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jia-Yu Liao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shubo Du
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544
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20
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Jiang J, Yang G, Ma F. Fluorescence coupling strategies in fluorescence-activated droplet sorting (FADS) for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Biotechnol Adv 2023; 66:108173. [PMID: 37169102 DOI: 10.1016/j.biotechadv.2023.108173] [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: 01/11/2023] [Revised: 04/17/2023] [Accepted: 05/06/2023] [Indexed: 05/13/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a powerful tool for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Fluorescence coupling strategies (FCSs) are key to the development of new FADS methods through their coupling of analyte properties such as concentration, activities, and affinity with fluorescence signals. Over the last decade, a series of FCSs have been developed, greatly expanding applications of FADS. Here, we review recent advances in FCS for different analyte types, providing a critical comparison of the available FCSs and further classification into four categories according to their principles. We also summarize successful FADS applications employing FCSs in enzymes, metabolites, and antibodies. Further, we outline possible future developments in this area.
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Affiliation(s)
- Jingjie Jiang
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fuqiang Ma
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
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21
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Chen L, Lu J, Wang R, Huang Y, Yu Y, Du P, Guo J, Wang X, Jiang Y, Cheng K, Zheng T, Yang Z. Humanization and characterization of a murine monoclonal neutralizing antibody against human adenovirus 7. Virology 2023; 583:36-44. [PMID: 37104921 DOI: 10.1016/j.virol.2023.04.008] [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: 02/04/2023] [Revised: 04/07/2023] [Accepted: 04/21/2023] [Indexed: 04/29/2023]
Abstract
Human adenovirus type 7 (HAdV7) is commonly associated with febrile acute respiratory disease (ARD) outbreaks. We have reported that 10G12, a mouse monoclonal antibody (mAb) specifically recognizing and neutralizing HAdV7, is a promising candidate for humanization. In this study, we engineered the six variants of 10G12 with increased degree of humanization and investigated their biological activity. The humanized monoclonal antibody (mAb) 10G12-M2 was shown to retain the parental antibody's high binding affinity, specificity and potent efficacy of viral suppression. The mAb 10G12-M2 recognized a conformational neutralization epitope of the hexon protein. Complex structure-based molecular docking simulation showed that the hexon protein formed several interactions with 10G12-M2, including hydrogen bonds and salt bridges interaction. Physicochemical properties analysis of 10G12-M2 demonstrated that it is stable and desirable lead candidate. In general, 10G12-M2 had excellent biological activity after humanization combined with the potential for use in prophylactic or therapeutic applications against HAdV7.
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Affiliation(s)
- Lei Chen
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Jiansheng Lu
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Rong Wang
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Ying Huang
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Yunzhou Yu
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Peng Du
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Jiazheng Guo
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Xi Wang
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Yujia Jiang
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Kexuan Cheng
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Tao Zheng
- Beijing Institute of Biotechnology, Beijing, 100071, China.
| | - Zhixin Yang
- Beijing Institute of Biotechnology, Beijing, 100071, China.
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22
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Transgenic HA-1-Specific CD8 + T-Lymphocytes Selectively Target Leukemic Cells. Cancers (Basel) 2023; 15:cancers15051592. [PMID: 36900382 PMCID: PMC10000933 DOI: 10.3390/cancers15051592] [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: 01/31/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
A significant share of allogeneic hematopoietic stem cell transplantations (allo-HSCT) results in the relapse of malignant disease. The T cell immune response to minor histocompatibility antigens (MiHAs) promotes a favorable graft-versus-leukemia response. The immunogenic MiHA HA-1 is a promising target for leukemia immunotherapy, as it is predominantly expressed in hematopoietic tissues and presented by the common HLA A*02:01 allele. Adoptive transfer of HA-1-specific modified CD8+ T cells could complement allo-HSCT from HA-1- donors to HA-1+ recipients. Using bioinformatic analysis and a reporter T cell line, we discovered 13 T cell receptors (TCRs) specific for HA-1. Their affinities were measured by the response of the TCR-transduced reporter cell lines to HA-1+ cells. The studied TCRs showed no cross-reactivity to the panel of donor peripheral mononuclear blood cells with 28 common HLA alleles. CD8+ T cells after endogenous TCR knock out and introduction of transgenic HA-1-specific TCR were able to lyse hematopoietic cells from HA-1+ patients with acute myeloid, T-, and B-cell lymphocytic leukemia (n = 15). No cytotoxic effect was observed on cells from HA-1- or HLA-A*02-negative donors (n = 10). The results support the use of HA-1 as a target for post-transplant T cell therapy.
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23
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Chen X, Chen LC, Khericha M, Meng X, Salvestrini E, Shafer A, Iyer N, Alag AS, Ding Y, Nicolaou DM, Chen YY. Rational Protein Design Yields a CD20 CAR with Superior Antitumor Efficacy Compared with CD19 CAR. Cancer Immunol Res 2023; 11:150-163. [PMID: 36409926 PMCID: PMC9898126 DOI: 10.1158/2326-6066.cir-22-0504] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/29/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022]
Abstract
Chimeric antigen receptors (CAR) are fusion proteins whose functional domains are often connected in a plug-and-play manner to generate multiple CAR variants. However, CARs with highly similar sequences can exhibit dramatic differences in function. Thus, approaches to rationally optimize CAR proteins are critical to the development of effective CAR T-cell therapies. Here, we report that as few as two amino-acid changes in nonsignaling domains of a CAR were able to significantly enhance in vivo antitumor efficacy. We demonstrate juxtamembrane alanine insertion and single-chain variable fragment sequence hybridization as two strategies that could be combined to maximize CAR functionality, and describe a CD20 CAR that outperformed the CD19 CAR in antitumor efficacy in preclinical in vitro and in vivo assays. Precise changes in the CAR sequence drove dramatically different transcriptomic profiles upon antigen stimulation, with the most efficacious CAR inducing an enrichment in highly functional memory T cells upon antigen stimulation. These findings underscore the importance of sequence-level optimization to CAR T-cell function, and the protein-engineering strategy described here may be applied to the development of additional CARs against diverse antigens. See related Spotlight by Scheller and Hudecek, p. 142.
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Affiliation(s)
- Ximin Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California
| | - Laurence C Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California
| | - Mobina Khericha
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California
| | - Xiangzhi Meng
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California
| | - Emma Salvestrini
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California
| | - Amanda Shafer
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California
| | - Neha Iyer
- Department of Bioengineering, University of California Los Angeles, California
| | - Anya S Alag
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California
| | - Yunfeng Ding
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California
| | - Demetri M Nicolaou
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California
| | - Yvonne Y Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California.,Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California.,Parker Institute for Cancer Immunotherapy at UCLA, University of California Los Angeles, Los Angeles, California
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24
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Evers A, Malhotra S, Bolick WG, Najafian A, Borisovska M, Warszawski S, Fomekong Nanfack Y, Kuhn D, Rippmann F, Crespo A, Sood V. SUMO: In Silico Sequence Assessment Using Multiple Optimization Parameters. Methods Mol Biol 2023; 2681:383-398. [PMID: 37405660 DOI: 10.1007/978-1-0716-3279-6_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
To select the most promising screening hits from antibody and VHH display campaigns for subsequent in-depth profiling and optimization, it is highly desirable to assess and select sequences on properties beyond only their binding signals from the sorting process. In addition, developability risk criteria, sequence diversity, and the anticipated complexity for sequence optimization are relevant attributes for hit selection and optimization. Here, we describe an approach for the in silico developability assessment of antibody and VHH sequences. This method not only allows for ranking and filtering multiple sequences with regard to their predicted developability properties and diversity, but also visualizes relevant sequence and structural features of potentially problematic regions and thereby provides rationales and starting points for multi-parameter sequence optimization.
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Affiliation(s)
- Andreas Evers
- Computational Chemistry & Biologics (CCB), Merck Healthcare KGaA, Darmstadt, Germany.
| | - Shipra Malhotra
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
| | | | - Ahmad Najafian
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
| | - Maria Borisovska
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
| | | | | | - Daniel Kuhn
- Computational Chemistry & Biologics (CCB), Merck Healthcare KGaA, Darmstadt, Germany
| | - Friedrich Rippmann
- Computational Chemistry & Biologics (CCB), Merck Healthcare KGaA, Darmstadt, Germany
| | - Alejandro Crespo
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
| | - Vanita Sood
- Computational Chemistry & Biologics (CCB), EMD Serono, Billerica, MA, USA
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25
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Maleki R, Rahimpour A, Rajabibazl M. Construction and evaluation of wild and mutant ofatumumab scFvs against the human CD20 antigen. Prep Biochem Biotechnol 2023; 53:239-246. [PMID: 35579623 DOI: 10.1080/10826068.2022.2073598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Several monoclonal antibodies targeting the CD20 have been produced and Ofatumumab is a case in point. Although whole antibodies target cancer cells effectively, their applications are restricted in some ways. Single-chain fragment variable antibodies, rather than employing the entire structure of antibodies, have proven a practical approach for creating completely functional antigen-binding fragments. In current research, the DNA coding sequence of VL and VH of the wild and mutant forms of ofatumumab were joined with a flexible linker (GGGGS)3 separately. Using the E. coli BL21 (DE3) expression system, the VL-linker-VH genes were cloned into the pET-28 a (+), and the associated recombinant proteins were produced. Purified and refolded scFvs (scFv-C and scFv-V3) represented a concentration of around 0.7 mg/ml from 1 L of initial E. coli culture with a molecular weight of about 27 kDa. Affinity measurement disclosed anti-CD20 scFv-V3 possesses a higher affinity constant compared to anti-CD20 scFv-C. The recombinant scFvs exclusively attach to Raji cells but not to Jurkat cells, according to a cell-ELISA analysis. The MTT test signified anti-CD20 scFvs could affect cell viability in Raji cells but had no impact on Jurkat cells and also, Raji cells viability was affected more significantly by anti-CD20 scFv-V3.
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Affiliation(s)
- Reza Maleki
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azam Rahimpour
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Rajabibazl
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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26
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Pascual N, Belecciu T, Schmidt S, Nakisa A, Huang X, Woldring D. Single-Cell B-Cell Sequencing to Generate Natively Paired scFab Yeast Surface Display Libraries. Methods Mol Biol 2023; 2681:175-212. [PMID: 37405649 DOI: 10.1007/978-1-0716-3279-6_11] [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] [Indexed: 07/06/2023]
Abstract
The immune cell profiling capabilities of single-cell RNA sequencing (scRNA-seq) are powerful tools that can be applied to the design of theranostic monoclonal antibodies (mAbs). Using scRNA-seq to determine natively paired B-cell receptor (BCR) sequences of immunized mice as a starting point for design, this method outlines a simplified workflow to express single-chain antibody fragments (scFabs) on the surface of yeast for high-throughput characterization and further refinement with directed evolution experiments. While not extensively detailed in this chapter, this method easily accommodates the implementation of a growing body of in silico tools that improve affinity and stability among a range of other developability criteria (e.g., solubility and immunogenicity).
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Affiliation(s)
- Nathaniel Pascual
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
| | - Theodore Belecciu
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
| | - Sam Schmidt
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
| | - Athar Nakisa
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Xuefei Huang
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Daniel Woldring
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA.
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA.
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27
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Mieczkowski C, Zhang X, Lee D, Nguyen K, Lv W, Wang Y, Zhang Y, Way J, Gries JM. Blueprint for antibody biologics developability. MAbs 2023; 15:2185924. [PMID: 36880643 PMCID: PMC10012935 DOI: 10.1080/19420862.2023.2185924] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Large-molecule antibody biologics have revolutionized medicine owing to their superior target specificity, pharmacokinetic and pharmacodynamic properties, safety and toxicity profiles, and amenability to versatile engineering. In this review, we focus on preclinical antibody developability, including its definition, scope, and key activities from hit to lead optimization and selection. This includes generation, computational and in silico approaches, molecular engineering, production, analytical and biophysical characterization, stability and forced degradation studies, and process and formulation assessments. More recently, it is apparent these activities not only affect lead selection and manufacturability, but ultimately correlate with clinical progression and success. Emerging developability workflows and strategies are explored as part of a blueprint for developability success that includes an overview of the four major molecular properties that affect all developability outcomes: 1) conformational, 2) chemical, 3) colloidal, and 4) other interactions. We also examine risk assessment and mitigation strategies that increase the likelihood of success for moving the right candidate into the clinic.
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Affiliation(s)
- Carl Mieczkowski
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Xuejin Zhang
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Dana Lee
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Khanh Nguyen
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Wei Lv
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Yanling Wang
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Yue Zhang
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Jackie Way
- Department of Protein Sciences, Hengenix Biotech, Inc, Milpitas, CA, USA
| | - Jean-Michel Gries
- President, Discovery Research, Hengenix Biotech, Inc, Milpitas, CA, USA
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28
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Hicks D, Baehr C, Silva-Ortiz P, Khaimraj A, Luengas D, Hamid FA, Pravetoni M. Advancing humanized monoclonal antibody for counteracting fentanyl toxicity towards clinical development. Hum Vaccin Immunother 2022; 18:2122507. [PMID: 36194773 PMCID: PMC9746415 DOI: 10.1080/21645515.2022.2122507] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/19/2022] [Accepted: 09/04/2022] [Indexed: 12/15/2022] Open
Abstract
Innovative therapies to complement current treatments are needed to curb the growing incidence of fatal overdoses related to synthetic opioids. Murine and chimeric monoclonal antibodies (mAb) specific for fentanyl and its analogs have demonstrated pre-clinical efficacy in preventing and reversing drug-induced toxicity in rodent models. However, mAb-based therapeutics require extensive engineering as well as in vitro and in vivo characterization to advance to first-in-human clinical trials. Here, novel murine anti-fentanyl mAbs were selected for development based on affinity for fentanyl, and efficacy in counteracting the pharmacological effects of fentanyl in mice. Humanization and evaluation of mutations designed to eliminate predicted post-translational modifications resulted in two humanized mAbs that were effective at preventing fentanyl-induced pharmacological effects in rats. These humanized mAbs showed favorable biophysical properties with respect to aggregation and hydrophobicity by chromatography-based assays, and thermostability by dynamic scanning fluorimetry. These results collectively support that the humanized anti-fentanyl mAbs developed herein warrant further clinical development for treatment of fentanyl toxicity.
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Affiliation(s)
- Dustin Hicks
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Carly Baehr
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Pedro Silva-Ortiz
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Aaron Khaimraj
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Diego Luengas
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Fatima A. Hamid
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Marco Pravetoni
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
- School of Medicine, Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
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29
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Structural Investigation of Therapeutic Antibodies Using Hydroxyl Radical Protein Footprinting Methods. Antibodies (Basel) 2022; 11:antib11040071. [PMID: 36412837 PMCID: PMC9680451 DOI: 10.3390/antib11040071] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Commercial monoclonal antibodies are growing and important components of modern therapies against a multitude of human diseases. Well-known high-resolution structural methods such as protein crystallography are often used to characterize antibody structures and to determine paratope and/or epitope binding regions in order to refine antibody design. However, many standard structural techniques require specialized sample preparation that may perturb antibody structure or require high concentrations or other conditions that are far from the conditions conducive to the accurate determination of antigen binding or kinetics. We describe here in this minireview the relatively new method of hydroxyl radical protein footprinting, a solution-state method that can provide structural and kinetic information on antibodies or antibody-antigen interactions useful for therapeutic antibody design. We provide a brief history of hydroxyl radical footprinting, examples of current implementations, and recent advances in throughput and accessibility.
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30
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Walser M, Mayor J, Rothenberger S. Designed Ankyrin Repeat Proteins: A New Class of Viral Entry Inhibitors. Viruses 2022; 14:2242. [PMID: 36298797 PMCID: PMC9611651 DOI: 10.3390/v14102242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 08/08/2023] Open
Abstract
Designed ankyrin repeat proteins (DARPins) are engineered proteins comprising consensus designed ankyrin repeats as scaffold. Tightly packed repeats form a continuous hydrophobic core and a large groove-like solvent-accessible surface that creates a binding surface. DARPin domains recognizing a target of interest with high specificity and affinity can be generated using a synthetic combinatorial library and in vitro selection methods. They can be linked together in a single molecule to build multispecific and multifunctional proteins without affecting expression or function. The modular architecture of DARPins offers unprecedented possibilities of design and opens avenues for innovative antiviral strategies.
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Affiliation(s)
- Marcel Walser
- Molecular Partners AG, Wagistrasse 14, 8952 Zurich-Schlieren, Switzerland
| | - Jennifer Mayor
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
| | - Sylvia Rothenberger
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
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31
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Chouhan P, Singh S, Sharma V, Prajapati VK. Anti-IL-10 Antibody Humanization by SDR Grafting with Enhanced Affinity to Neutralize the Adverse Response of Interleukin-10. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10456-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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32
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Development and characterization of a camelid derived antibody targeting a linear epitope in the hinge domain of human PCSK9 protein. Sci Rep 2022; 12:12211. [PMID: 35842473 PMCID: PMC9288512 DOI: 10.1038/s41598-022-16453-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
PCSK9 is an effective target for lowering LDL-c. Previously, a camelid-human chimeric heavy chain antibody VHH-B11-Fc targeting human PCSK9 was designed. It had a potent hypolipidemic effect. However, the nanobody VHH-B11 interacts with PCSK9 at low affinity, while camelid VHH exhibits some immunogenicity. Moreover, the interacting epitope is yet to be identified, although VHH-B11 was shown to have distinct hPCSK9-binding epitopes for Evolocumab. This might impede the molecule’s progress from bench to bedside. In the present study, we designed various configurations to improve the affinity of VHH-B11 with hPCSK9 (< 10 nM) that in turn enhanced the druggability of VHH-B11-Fc. Then, 17 amino acids were specifically mutated to increase the degree of humanization of the nanobody VHH-B11. Using phage display and sequencing technology, the linear epitope “STHGAGW” (amino acids 447–452) was identified in the hinge region of PCSK9 as the interacting site between VHH-B11-Fc and hPCSK9. Unlike the interaction epitope of Evolocumab, located in the catalytic region of PCSK9, the binding epitope of VHH-B11 is located in the hinge region of PCSK9, which is rarely reported. These findings indicated that a specific mechanism underlying this interaction needs to be explored.
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33
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An effective strategy for the humanization of antibody fragments under an accelerated timeline. Int J Biol Macromol 2022; 216:465-474. [PMID: 35803408 DOI: 10.1016/j.ijbiomac.2022.06.195] [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: 05/11/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/22/2022]
Abstract
The use of monoclonal antibodies (mAbs) in therapy is gradually advancing and discussions entail its safety, rentability and effectiveness. To this date, around a hundred mAbs have been approved by the FDA for the treatment of various diseases. Aiming for their large-scale production, recombinant DNA technology is mainly employed, and antibodies can be expressed in various eukaryotic and prokaryotic systems. Moreover, considering their heterologous origin and potential immunogenicity, various strategies have been developed for mAb humanization, considering that around 50 % of commercial mAbs are humanized. Hence, we introduce LimAb7, a mouse mAb capable of binding and neutralizing brown spider's Loxosceles intermedia dermonecrotic toxins in vivo/in vitro. This antibody has been produced in mouse and humanized scFv and diabody formats, however results indicated losses in antigen-binding affinity, stability, and neutralizing ability. Intending to develop evolved, stable, and neutralizing antibody fragments, we report for the first time the design of humanized antibody V-domains produced as Fab fragments, against spider venom toxins. Improvements in constructs were observed regarding their physicochemical stability, target binding and binding pattern maintenance. As their neutralizing features remain to be characterized, we believe this data sheds new light on antibody humanization by producing a parental molecule in different recombinant formats.
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34
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Tsuji I, Vang F, Dominguez D, Karwal L, Sanjali A, Livengood JA, Davidson E, Fouch ME, Doranz BJ, Das SC, Dean HJ. Somatic Hypermutation and Framework Mutations of Variable Region Contribute to Anti-Zika Virus-Specific Monoclonal Antibody Binding and Function. J Virol 2022; 96:e0007122. [PMID: 35575481 PMCID: PMC9175631 DOI: 10.1128/jvi.00071-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
Zika virus (ZIKV) is a global public health concern due to its ability to cause congenital Zika syndrome and lack of approved vaccine, therapeutic, or other control measures. We discovered eight novel rabbit monoclonal antibodies (MAbs) that bind to distinct ZIKV envelope protein epitopes. The majority of the MAbs were ZIKV specific and targeted the lateral ridge of the envelope (E) protein domain III, while the MAb with the highest neutralizing activity recognized a putative quaternary epitope spanning E protein domains I and III. One of the non-neutralizing MAbs specifically recognized ZIKV precursor membrane protein (prM). Somatic hypermutation of immunoglobulin variable regions increases antibody affinity maturation and triggers antibody class switching. Negative correlations were observed between the somatic hypermutation rate of the immunoglobulin heavy-chain variable region and antibody binding parameters such as equilibrium dissociation constant, dissociation constant, and half-maximal effective concentration value of MAb binding to ZIKV virus-like particles. Complementarity-determining regions recognize the antigen epitopes and are scaffolded by canonical framework regions. Reversion of framework region amino acids to the rabbit germ line sequence decreased anti-ZIKV MAb binding activity of some MAbs. Thus, antibody affinity maturation, including somatic hypermutation and framework region mutations, contributed to the binding and function of these anti-ZIKV MAbs. IMPORTANCE ZIKV is a global health concern against which no vaccine or therapeutics are available. We characterized eight novel rabbit monoclonal antibodies recognizing ZIKV envelope and prM proteins and studied the relationship between somatic hypermutation of complementarity-determining regions, framework regions, mutations, antibody specificity, binding, and neutralizing activity. The results contribute to understanding structural features and somatic mutation pathways by which potent Zika virus-neutralizing antibodies can evolve, including the role of antibody framework regions.
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Affiliation(s)
- Isamu Tsuji
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | - Fue Vang
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | - David Dominguez
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | - Lovkesh Karwal
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | - Ankita Sanjali
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | - Jill A. Livengood
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | | | | | | | - Subash C. Das
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | - Hansi J. Dean
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
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35
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Ko D, Kim E, Shin EA, Nam SH, Yoon J, Lee JS, Lee Y, Park S, Ha K, Choi SY, Lee JW, Kim S. Therapeutic effects of TM4SF5-targeting chimeric and humanized monoclonal antibodies in hepatocellular and colon cancer models. Mol Ther Oncolytics 2022; 24:452-466. [PMID: 35211652 PMCID: PMC8841960 DOI: 10.1016/j.omto.2022.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/21/2022] [Indexed: 12/14/2022] Open
Abstract
The transmembrane 4 L six family member 5 (TM4SF5) is aberrantly expressed in hepatocellular and colorectal cancers, and has been implicated in tumor progression, suggesting that it could serve as a novel therapeutic target. Previously, we screened a murine antibody phage-display library to generate a novel monoclonal antibody, Ab27, that is specific to the extracellular loop 2 of TM4SF5. In this study, we evaluated the effects of chimeric Ab27 using cancer cells expressing endogenous TM4SF5 or stably overexpressing TM4SF5 in vivo and in vitro. Monotherapy with Ab27 significantly decreased tumor growth in liver and colon cancer xenograft models, including a sorafenib-resistant model, and decreased the phosphorylation of focal adhesion kinase (FAK), p27Kip1, and signal transducer and activator of transcription 3 (STAT3). No general Ab27 toxicity was observed in vivo. Combination treatment with Ab27 and sorafenib or doxorubicin exerted higher antitumor activity than monotherapy. In addition, we humanized the Ab27 sequence by the complementarity-determining region (CDR) grafting method. The humanized antibody Ab27-hz9 had reduced immunogenicity but exhibited target recognition and antitumor activity comparable with those of Ab27. Both Ab27 and Ab27-hz9 efficiently targeted tumor cells expressing TM4SF5 in vivo. These observations strongly support the further development of Ab27-hz9 as a novel therapeutic agent against liver and colorectal cancers.
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Affiliation(s)
- Dongjoon Ko
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejon 34141, Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejon 34113, Korea
| | - Eunmi Kim
- Department of Pharmacy Research Institute of Pharmaceutical Sciences College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul 08826, Korea
| | - Eun-Ae Shin
- Department of Pharmacy Research Institute of Pharmaceutical Sciences College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul 08826, Korea
| | - Seo Hee Nam
- Department of Pharmacy Research Institute of Pharmaceutical Sciences College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul 08826, Korea
| | - Junghwa Yoon
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejon 34141, Korea
| | - Jin-Sook Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejon 34141, Korea
| | - Yunhee Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejon 34141, Korea
| | - Sora Park
- Antibody Drug Team at New Drug Development Center, Osong Medical Innovation Foundation, Osong 28160, Korea
| | - Kyungsoo Ha
- Drug Efficacy Evaluation Team at New Drug Development Center, Osong Medical Innovation Foundation, Osong 28160, Korea
| | - So-Young Choi
- Protein Drug Team at New Drug Development Center, Osong Medical Innovation Foundation, Osong 28160, Korea
| | - Jung Weon Lee
- Department of Pharmacy Research Institute of Pharmaceutical Sciences College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul 08826, Korea
| | - Semi Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejon 34141, Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejon 34113, Korea
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36
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Hsieh YC, Liao JM, Chuang KH, Ho KW, Hong ST, Liu HJ, Huang BC, Chen IJ, Liu YL, Wang JY, Tsai HL, Su YC, Wang YT, Cheng TL. A universal in silico V(D)J recombination strategy for developing humanized monoclonal antibodies. J Nanobiotechnology 2022; 20:58. [PMID: 35101043 PMCID: PMC8805405 DOI: 10.1186/s12951-022-01259-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/12/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Humanization of mouse monoclonal antibodies (mAbs) is crucial for reducing their immunogenicity in humans. However, humanized mAbs often lose their binding affinities. Therefore, an in silico humanization method that can prevent the loss of the binding affinity of mAbs is needed. METHODS We developed an in silico V(D)J recombination platform in which we used V(D)J human germline gene sequences to design five humanized candidates of anti-tumor necrosis factor (TNF)-α mAbs (C1-C5) by using different human germline templates. The candidates were subjected to molecular dynamics simulation. In addition, the structural similarities of their complementarity-determining regions (CDRs) to those of original mouse mAbs were estimated to derive the weighted interatomic root mean squared deviation (wRMSDi) value. Subsequently, the correlation of the derived wRMSDi value with the half maximal effective concentration (EC50) and the binding affinity (KD) of the humanized anti-TNF-α candidates was examined. To confirm whether our in silico estimation method can be used for other humanized mAbs, we tested our method using the anti-epidermal growth factor receptor (EGFR) a4.6.1, anti-glypican-3 (GPC3) YP9.1 and anti-α4β1 integrin HP1/2L mAbs. RESULTS The R2 value for the correlation between the wRMSDi and log(EC50) of the recombinant Remicade and those of the humanized anti-TNF-α candidates was 0.901, and the R2 value for the correlation between wRMSDi and log(KD) was 0.9921. The results indicated that our in silico V(D)J recombination platform could predict the binding affinity of humanized candidates and successfully identify the high-affinity humanized anti-TNF-α antibody (Ab) C1 with a binding affinity similar to that of the parental chimeric mAb (5.13 × 10-10). For the anti-EGFR a4.6.1, anti-GPC3 YP9.1, and anti-α4β1 integrin HP1/2L mAbs, the wRMSDi and log(EC50) exhibited strong correlations (R2 = 0.9908, 0.9999, and 0.8907, respectively). CONCLUSIONS Our in silico V(D)J recombination platform can facilitate the development of humanized mAbs with low immunogenicity and high binding affinities. This platform can directly transform numerous mAbs with therapeutic potential to humanized or even human therapeutic Abs for clinical use.
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Affiliation(s)
- Yuan-Chin Hsieh
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
- School of Medicine for International Students, I-Shou University, No.8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung, 82445, Taiwan
| | - Jun-Min Liao
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Kuo-Hsiang Chuang
- Graduate Institute of Pharmacognosy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
- Ph.D. Program for Clinical Drug Discovery From Botanical Herbs, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Kai-Wen Ho
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Shih-Ting Hong
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Hui-Ju Liu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Bo-Cheng Huang
- Institute of Biomedical Sciences, National Sun Yat-Sen University, 70 Lien-hai Road, Kaohsiung, 804, Taiwan
| | - I-Ju Chen
- School of Medicine, I-Shou University, No.8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung, 82445, Taiwan
| | - Yen-Ling Liu
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Jaw-Yuan Wang
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
- Department of Surgery, Faculty of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, No.100, Tzyou 1st Rd., Sanmin Dist., Kaohsiung, 80756, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Hsiang-Lin Tsai
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
- Department of Surgery, Faculty of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan
| | - Yu-Cheng Su
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, No. 1001, Daxue Rd. East Dist., Hsin-Chu, 300, Taiwan
| | - Yen-Tseng Wang
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan.
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan.
| | - Tian-Lu Cheng
- Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan.
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100 Shih-Chuan First Road, Kaohsiung, 80708, Taiwan.
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Aminabad ED, Mobed A, Hasanzadeh M, Hosseinpour Feizi MA, Safaralizadeh R, Seidi F. Sensitive immunosensing of α-synuclein protein in human plasma samples using gold nanoparticles conjugated with graphene: an innovative immuno-platform towards early stage identification of Parkinson's disease using point of care (POC) analysis. RSC Adv 2022; 12:4346-4357. [PMID: 35425437 PMCID: PMC8980998 DOI: 10.1039/d1ra06437a] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 02/16/2022] [Accepted: 01/16/2022] [Indexed: 12/18/2022] Open
Abstract
Parkinson's disease (PD) or simply Parkinson's is a long-term degenerative disorder of the central nervous system, which mainly affects the motor system. Consequently, the detection and quantification of related biomarkers play vital roles in the early-stage diagnosis of PD. In the present study, an innovative electrochemical immunosensor based on gold nanoparticle-modified graphene towards bioconjugation with biotinylated antibody (bioreceptor) was developed for the ultra-sensitive and specific monitoring of the alpha-synuclein (α-synuclein) protein. The synergistic effects between the gold nanoparticles (AuNPs) and graphene drastically enhanced the electrochemical activity of the resulting materials. The enhanced conductivity of the substrate together with the increase in its surface area improved the sensitivity and lowered the detection limit of the capture layer. For the first time, the α-synuclein protein was measured in human plasma samples using bioconjugated AuNP-Gr bioconjugated specific antibody with an acceptable linear range of 4 to 128 ng mL-1 and a lower limit of quantification (LLOQ) of 4 ng mL-1. Accordingly, it is expected that this diagnostic method may be produced in the near future for clinical applications and high-throughput screening of PD using point of care (POC) analysis.
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Affiliation(s)
- Esmaeil Darvish Aminabad
- Department of Biology, Faculty of Natural Sciences, Tabriz University Tabriz Iran
- Pharmaceutical Analysis Recent Center, Tabriz University of Medical Sciences Tabriz 51664 Iran
| | - Ahmad Mobed
- Pharmaceutical Analysis Recent Center, Tabriz University of Medical Sciences Tabriz 51664 Iran
- Physical Medicine and Rehabilitation Research Center, Tabriz University of Medical Sciences Tabriz Iran
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Recent Center, Tabriz University of Medical Sciences Tabriz 51664 Iran
| | | | - Reza Safaralizadeh
- Department of Biology, Faculty of Natural Sciences, Tabriz University Tabriz Iran
| | - Farzad Seidi
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University Nanjing 210037 China
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Niu Y, Chen J, Qiao Y. Epigenetic Modifications in Tumor-Associated Macrophages: A New Perspective for an Old Foe. Front Immunol 2022; 13:836223. [PMID: 35140725 PMCID: PMC8818998 DOI: 10.3389/fimmu.2022.836223] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 12/11/2022] Open
Abstract
Tumorigenesis is frequently accompanied by chronic inflammation, and the tumor microenvironment (TME) can be considered an ecosystem that consists of tumor cells, endotheliocytes, fibroblasts, immune cells and acellular components such as extracellular matrix. For tumor cells, their survival advantages are dependent on both genetic and epigenetic alterations, while other cells mainly present epigenetic modifications. Macrophages are the most plastic type of immune cells and undergo diverse epigenetic alterations in the TME. Some of these epigenetic modifications mitigate against cancer progression, and others accelerate this process. Due to the complex roles of macrophages in the TME, it is urgent to understand their epigenetic modifications associated with the TME. Here, we mainly summarize recent findings on TME-associated epigenetic alterations of tumor-associated macrophages (TAMs), including DNA methylation, posttranslational modifications of histone proteins, chromatin remodeling, and noncoding RNA-mediated epigenetic regulation. At the end of this review, we also discuss the translational potential of these epigenetic modifications for developing novel cancer therapies targeting TAMs.
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Affiliation(s)
- Yuqin Niu
- The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Jianxiang Chen
- School of Pharmacy, Department of Hepatology, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
- *Correspondence: Yiting Qiao, ; Jianxiang Chen,
| | - Yiting Qiao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- *Correspondence: Yiting Qiao, ; Jianxiang Chen,
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Abstract
Humanization of therapeutic antibodies derived from animal immunizations is often required to minimize immunogenicity risks in humans, which can cause potentially harmful and serious side effects and reduce antibody efficacy. Humanization is typically applied to conventional monoclonal antibodies derived in rodents as well as single-domain antibodies isolated from camelids and sharks (VHHs and VNARs). A streamlined protocol is described here for sequence humanization of camelid VHHs, which represent a promising biotherapeutic format with many desirable attributes. From human framework selection and complementarity-determining region grafting strategies to empirical scoring for prioritization of back-mutations, step-by-step instructions, and templates are provided along with bioinformatics resources to assist each step of the humanization process. Alternative approaches, warnings, and caveats are also presented.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada.
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.
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Prihoda D, Maamary J, Waight A, Juan V, Fayadat-Dilman L, Svozil D, Bitton DA. BioPhi: A platform for antibody design, humanization, and humanness evaluation based on natural antibody repertoires and deep learning. MAbs 2022; 14:2020203. [PMID: 35133949 PMCID: PMC8837241 DOI: 10.1080/19420862.2021.2020203] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/09/2021] [Indexed: 12/20/2022] Open
Abstract
Despite recent advances in transgenic animal models and display technologies, humanization of mouse sequences remains one of the main routes for therapeutic antibody development. Traditionally, humanization is manual, laborious, and requires expert knowledge. Although automation efforts are advancing, existing methods are either demonstrated on a small scale or are entirely proprietary. To predict the immunogenicity risk, the human-likeness of sequences can be evaluated using existing humanness scores, but these lack diversity, granularity or interpretability. Meanwhile, immune repertoire sequencing has generated rich antibody libraries such as the Observed Antibody Space (OAS) that offer augmented diversity not yet exploited for antibody engineering. Here we present BioPhi, an open-source platform featuring novel methods for humanization (Sapiens) and humanness evaluation (OASis). Sapiens is a deep learning humanization method trained on the OAS using language modeling. Based on an in silico humanization benchmark of 177 antibodies, Sapiens produced sequences at scale while achieving results comparable to that of human experts. OASis is a granular, interpretable and diverse humanness score based on 9-mer peptide search in the OAS. OASis separated human and non-human sequences with high accuracy, and correlated with clinical immunogenicity. BioPhi thus offers an antibody design interface with automated methods that capture the richness of natural antibody repertoires to produce therapeutics with desired properties and accelerate antibody discovery campaigns. The BioPhi platform is accessible at https://biophi.dichlab.org and https://github.com/Merck/BioPhi.
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Affiliation(s)
- David Prihoda
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czech Republic
- R&D Informatics Solutions, MSD Czech Republic S.r.o, Prague, Czech Republic
| | - Jad Maamary
- Predictive and Clinical Immunogenicity, Merck & Co., Inc, Kenilworth, New Jersey, USA
| | - Andrew Waight
- Discovery Biologics, Protein Sciences, MRL, Merck & Co., Inc, South San Francisco, CA, USA
| | - Veronica Juan
- Discovery Biologics, Protein Sciences, MRL, Merck & Co., Inc, South San Francisco, CA, USA
| | | | - Daniel Svozil
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czech Republic
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
| | - Danny A. Bitton
- R&D Informatics Solutions, MSD Czech Republic S.r.o, Prague, Czech Republic
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Abstract
Polyclonal immunoglobulin (Ig) preparations have been used for several decades for treatment of primary and secondary immunodeficiencies and for treatment of some infections and intoxications. This has demonstrated the importance of Igs, also called antibodies (Abs) for prevention and elimination of infections. Moreover, elucidation of the structure and functions of Abs has suggested that they might be useful for targeted treatment of several diseases, including cancers and autoimmune diseases. The development of technologies for production of specific monoclonal Abs (MAbs) in large amounts has led to the production of highly effective therapeutic antibodies (TAbs), a collective term for MAbs (MAbs) with demonstrated clinical efficacy in one or more diseases. The number of approved TAbs is currently around hundred, and an even larger number is under development, including several engineered and modified Ab formats. The use of TAbs has provided new treatment options for many severe diseases, but prediction of clinical effect is difficult, and many patients eventually lose effect, possibly due to development of Abs to the TAbs or to other reasons. The therapeutic efficacy of TAbs can be ascribed to one or more effects, including binding and neutralization of targets, direct cytotoxicity, Ab-dependent complement-dependent cytotoxicity, Ab-dependent cellular cytotoxicity or others. The therapeutic options for TAbs have been expanded by development of several new formats of TAbs, including bispecific Abs, single domain Abs, TAb-drug conjugates, and the use of TAbs for targeted activation of immune cells. Most promisingly, current research and development can be expected to increase the number of clinical conditions, which may benefit from TAbs.
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Affiliation(s)
- Gunnar Houen
- Department of Neurology, Rigshospitalet, Glostrup, Denmark.
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Generation of a Novel High-Affinity Antibody Binding to PCSK9 Catalytic Domain with Slow Dissociation Rate by CDR-Grafting, Alanine Scanning and Saturated Site-Directed Mutagenesis for Favorably Treating Hypercholesterolemia. Biomedicines 2021; 9:biomedicines9121783. [PMID: 34944600 PMCID: PMC8698692 DOI: 10.3390/biomedicines9121783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
Inhibition of proprotein convertase subtilisin/kexin type 9 (PCSK9) has become an attractive therapeutic strategy for lowering low-density lipoprotein cholesterol (LDL-C). In this study, a novel high affinity humanized IgG1 mAb (named h5E12-L230G) targeting the catalytic domain of human PCSK9 (hPCSK9) was generated by using CDR-grafting, alanine-scanning mutagenesis, and saturated site-directed mutagenesis. The heavy-chain constant region of h5E12-L230G was modified to eliminate the cytotoxic effector functions and mitigate the heterogeneity. The biolayer interferometry (BLI) binding assay and molecular docking study revealed that h5E12-L230G binds to the catalytic domain of hPCSK9 with nanomolar affinity (KD = 1.72 nM) and an extremely slow dissociation rate (koff, 4.84 × 10−5 s−1), which interprets its quite low binding energy (−54.97 kcal/mol) with hPCSK9. Additionally, h5E12-L230G elevated the levels of LDLR and enhanced the LDL-C uptake in HepG2 cells, as well as reducing the serum LDL-C and total cholesterol (TC) levels in hyperlipidemic mouse model with high potency comparable to the positive control alirocumab. Our data indicate that h5E12-L230G is a high-affinity anti-PCSK9 antibody candidate with an extremely slow dissociation rate for favorably treating hypercholesterolemia and relevant cardiovascular diseases.
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A mosquito AgTRIO monoclonal antibody reduces early Plasmodium infection of mice. Infect Immun 2021; 90:e0035921. [PMID: 34724388 DOI: 10.1128/iai.00359-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Malaria begins when an infected mosquito injects saliva containing Plasmodium sporozoites into the skin of a vertebrate host. Passive immunization of mice with mosquito AgTRIO antisera offers significant protection against Plasmodium infection of mice. Furthermore, passive transfer of both AgTRIO antisera and an anti-circumsporozoite protein monoclonal antibody provides synergistic protection. In this study, we generated monoclonal antibodies against AgTRIO to delineate the regions of AgTRIO associated with protective immunity. Monoclonal antibody 13F-1 markedly reduced Plasmodium infection in mice and recognized a region, VDDLMAKFN, in the carboxyl terminus of AgTRIO. 13F-1 is an IgG2a isotype monoclonal antibody and the Fc region is required for protection. These data will aid in the generation of future malaria vaccines that may include both pathogen and vector antigens.
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Huang B, Zhu L, Wei H, Shi H, Zhang D, Yuan H, Luan L, Zheng N, Xu S, Nawaz W, Hong Y, Wu X, Wu Z. Potent Neutralizing Humanized Antibody With Topical Therapeutic Potential Against HPV18-Related Cervical Cancer. Front Immunol 2021; 12:678318. [PMID: 34248960 PMCID: PMC8264373 DOI: 10.3389/fimmu.2021.678318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Cervical cancer caused by human papillomavirus (HPV) infections is the fourth most common cancer in women worldwide. Current prophylactic HPV vaccines have achieved promising success in preventing HPV infection. However, still 570,000 new cases were reported in 2018. The current primary treatment for the patient with cervical cancer is either surgery or chemoradiotherapy. Cervical cancer still lacks standard medical therapy. HPV18 induced cervical cancer has the worst prognosis and high mortality compared to other HPV infections. The development of HPV18 related with cervical malignancy requires the persistent infection of cervical-vaginal epithelium by HPV18 subtype, which can take years to transform the epithelium. This period of repeated infection provides a window for therapeutic intervention. Neutralizing antibodies formulated as topical agents that inhibit HPV18 infection should reduce the chance of cervical malignancy. We previously demonstrated that potent neutralizing anti-sera against HPV18 infection were induced by HPV18 viral like particle (VLP) generated in mammalian cells. We, therefore, isolated two potent neutralizing antibodies, 2A12 and 8H4, from over 3,810 hybridomas prepared from mice immunized with HPV18 VLP. 2A12 and 8H4 exhibited excellent potency, with 50% virus-inhibitory concentrations (IC50) of 0.4 and 0.9 ng/ml, respectively. Furthermore, 2A12 and 8H4 recognized distinct and non-overlapping quaternary epitopes and bound specifically with HPV18. Humanized 2A12 (Hu2A12) retained comparable neutralizing activity against HPV18 infection in various acidic pH settings and in hydrogel formulation with IC50 values of 0.04 to 0.77 ng/ml, indicating that Hu2A12 will be a promising candidate for clinical development as a topical vaginal biopharmaceutical agent against HPV18 infection.
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Affiliation(s)
- Bilian Huang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
| | - Linjing Zhu
- Department of Antibody, Abrev Biotechnology Co., Ltd., Nanjing, China
| | - Hongxia Wei
- Department of Infection, Nanjing Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Haixia Shi
- Department of Antibody, Y-Clone Medical Science Co. Ltd., Suzhou, China
| | - Doudou Zhang
- Department of Antibody, Abrev Biotechnology Co., Ltd., Nanjing, China
| | - Huanyun Yuan
- Department of Antibody, Abrev Biotechnology Co., Ltd., Nanjing, China
| | - Linlin Luan
- Department of Antibody, Abrev Biotechnology Co., Ltd., Nanjing, China
| | - Nan Zheng
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
| | - Shijie Xu
- Department of Antibody, Abrev Biotechnology Co., Ltd., Nanjing, China
| | - Waqas Nawaz
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
| | - Ying Hong
- Obstetrics and Gynecology Department, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xilin Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China.,Department of Antibody, Abrev Biotechnology Co., Ltd., Nanjing, China
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China.,School of Life Sciences, Ningxia University, Yinchuan, China.,Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China.,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, China
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45
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Marks C, Hummer AM, Chin M, Deane CM. Humanization of antibodies using a machine learning approach on large-scale repertoire data. Bioinformatics 2021; 37:4041-4047. [PMID: 34110413 PMCID: PMC8760955 DOI: 10.1093/bioinformatics/btab434] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/06/2021] [Accepted: 06/09/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Monoclonal antibody therapeutics are often produced from non-human sources (typically murine), and can therefore generate immunogenic responses in humans. Humanization procedures aim to produce antibody therapeutics that do not elicit an immune response and are safe for human use, without impacting efficacy. Humanization is normally carried out in a largely trial-and-error experimental process. We have built machine learning classifiers that can discriminate between human and non-human antibody variable domain sequences using the large amount of repertoire data now available. RESULTS Our classifiers consistently outperform the current best-in-class model for distinguishing human from murine sequences, and our output scores exhibit a negative relationship with the experimental immunogenicity of existing antibody therapeutics. We used our classifiers to develop a novel, computational humanization tool, Hu-mAb, that suggests mutations to an input sequence to reduce its immunogenicity. For a set of therapeutic antibodies with known precursor sequences, the mutations suggested by Hu-mAb show significant overlap with those deduced experimentally. Hu-mAb is therefore an effective replacement for trial-and-error humanization experiments, producing similar results in a fraction of the time. AVAILABILITY Hu-mAb (humanness scoring and humanization) is freely available to use at opig.stats.ox.ac.uk/webapps/humab. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Claire Marks
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Alissa M Hummer
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Mark Chin
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
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Elshiaty M, Schindler H, Christopoulos P. Principles and Current Clinical Landscape of Multispecific Antibodies against Cancer. Int J Mol Sci 2021; 22:5632. [PMID: 34073188 PMCID: PMC8198225 DOI: 10.3390/ijms22115632] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/07/2023] Open
Abstract
Building upon the resounding therapeutic success of monoclonal antibodies, and supported by accelerating progress in engineering methods, the field of multispecific therapeutic antibodies is growing rapidly. Over 140 different molecules are currently in clinical testing, with excellent results in recent phase 1-3 clinical trials for several of them. Multivalent bispecific IgG-modified formats predominate today, with a clear tendency for more target antigens and further increased valency in newer constructs. The strategies to augment anticancer efficacy are currently equally divided between disruption of multiple surface antigens, and additional redirection of cytotoxic T or NK lymphocytes against the tumor. Both effects complement other modern modalities, such as tyrosine kinase inhibitors and adoptive cell therapies, with which multispecifics are increasingly applied in combination or merged, for example, in the form of antibody producing CAR-T cells and oncolytics. While mainly focused on B-cell malignancies early on, the contemporary multispecific antibody sector accommodates twice as many trials against solid compared to hematologic cancers. An exciting emerging prospect is the targeting of intracellular neoantigens using T-cell receptor (TCR) fusion proteins or TCR-mimic antibody fragments. Considering the fact that introduction of PD-(L)1 inhibitors only a few years ago has already facilitated 5-year survival rates of 30-50% for per se highly lethal neoplasms, such as metastatic melanoma and non-small-cell lung carcinoma, the upcoming enforcement of current treatments with "next-generation" immunotherapeutics, offers a justified hope for the cure of some advanced cancers in the near future.
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Affiliation(s)
- Mariam Elshiaty
- Thoraxklinik and National Center for Tumor Diseases (NCT) at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.E.); (H.S.)
- Translational Lung Cancer Center Heidelberg, Member of the German Center for Lung Research (DZL), 69126 Heidelberg, Germany
| | - Hannah Schindler
- Thoraxklinik and National Center for Tumor Diseases (NCT) at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.E.); (H.S.)
- Translational Lung Cancer Center Heidelberg, Member of the German Center for Lung Research (DZL), 69126 Heidelberg, Germany
| | - Petros Christopoulos
- Thoraxklinik and National Center for Tumor Diseases (NCT) at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.E.); (H.S.)
- Translational Lung Cancer Center Heidelberg, Member of the German Center for Lung Research (DZL), 69126 Heidelberg, Germany
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Yasui H, Nishinaga Y, Taki S, Takahashi K, Isobe Y, Shimizu M, Koike C, Taki T, Sakamoto A, Katsumi K, Ishii K, Sato K. Near-infrared photoimmunotherapy targeting GPR87: Development of a humanised anti-GPR87 mAb and therapeutic efficacy on a lung cancer mouse model. EBioMedicine 2021; 67:103372. [PMID: 33993055 PMCID: PMC8138482 DOI: 10.1016/j.ebiom.2021.103372] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/25/2021] [Accepted: 04/16/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND GPR87 is a G-protein receptor that is specifically expressed in tumour cells, such as lung cancer, and rarely expressed in normal cells. GPR87 is a promising target for cancer therapy, but its ligand is controversial. Near-infrared photoimmunotherapy (NIR-PIT) is a novel cancer therapy in which a photosensitiser, IRDye700DX (IR700), binds to antibodies and specifically destroys target cells by irradiating them with near-infrared-light. Here, we aimed to develop a NIR-PIT targeting GPR87. METHODS We evaluated the expression of GPR87 in resected specimens of lung cancer and malignant pleural mesothelioma (MPM) resected at Nagoya University Hospital using immunostaining. Humanised anti-GPR87 antibody (huGPR87) was generated by introducing CDRs from mouse anti-GPR87 antibody generated by standard hybridoma method. HuGPR87 was conjugated with IR700 and the therapeutic effect of NIR-PIT was evaluated in vitro and in vivo using lung cancer or MPM cell lines. FINDINGS Among the surgical specimens, 54% of lung cancer and 100% of MPM showed high expression of GPR87. It showed therapeutic effects on lung cancer and MPM cell lines in vitro, and showed therapeutic effects in multiple models in vivo. INTERPRETATION These results suggest that NIR-PIT targeting GPR87 is a promising therapeutic approach for the treatment of thoracic cancer. FUNDING This research was supported by the Program for Developing Next-generation Researchers (Japan Science and Technology Agency), KAKEN (18K15923, 21K07217, JSPS), FOREST-Souhatsu, CREST (JST).
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Affiliation(s)
- Hirotoshi Yasui
- Respiratory Medicine, Nagoya University Graduate School of Medicine, 65, Tsurumai-cho, Showa-ku, Nagoya 466-8560, Aichi, Japan
| | - Yuko Nishinaga
- Respiratory Medicine, Nagoya University Graduate School of Medicine, 65, Tsurumai-cho, Showa-ku, Nagoya 466-8560, Aichi, Japan
| | - Shunichi Taki
- Respiratory Medicine, Nagoya University Graduate School of Medicine, 65, Tsurumai-cho, Showa-ku, Nagoya 466-8560, Aichi, Japan
| | - Kazuomi Takahashi
- Respiratory Medicine, Nagoya University Graduate School of Medicine, 65, Tsurumai-cho, Showa-ku, Nagoya 466-8560, Aichi, Japan
| | - Yoshitaka Isobe
- Respiratory Medicine, Nagoya University Graduate School of Medicine, 65, Tsurumai-cho, Showa-ku, Nagoya 466-8560, Aichi, Japan
| | - Misae Shimizu
- Nagoya University Institute for Advanced Research, Advanced Analytical and Diagnostic Imaging Center (AADIC) / Medical Engineering Unit (MEU), B3 Unit, 65, Tsurumai-cho, Showa-ku, Nagoya 466-8560, Aichi, Japan
| | - Chiaki Koike
- Nagoya University Institute for Advanced Research, Advanced Analytical and Diagnostic Imaging Center (AADIC) / Medical Engineering Unit (MEU), B3 Unit, 65, Tsurumai-cho, Showa-ku, Nagoya 466-8560, Aichi, Japan
| | - Tetsuro Taki
- Department of Pathology, Nagoya University Graduate School of Medicine, 65, Tsurumai-cho, Showa-ku, Nagoya 466-8560, Aichi, Japan
| | - Aya Sakamoto
- Perseus Proteomics, Inc., 4-7-6, Komaba 153-0041, Meguro-ku, Tokyo, Japan
| | - Keiko Katsumi
- Perseus Proteomics, Inc., 4-7-6, Komaba 153-0041, Meguro-ku, Tokyo, Japan
| | - Keisuke Ishii
- Perseus Proteomics, Inc., 4-7-6, Komaba 153-0041, Meguro-ku, Tokyo, Japan
| | - Kazuhide Sato
- Respiratory Medicine, Nagoya University Graduate School of Medicine, 65, Tsurumai-cho, Showa-ku, Nagoya 466-8560, Aichi, Japan; Nagoya University Institute for Advanced Research, Advanced Analytical and Diagnostic Imaging Center (AADIC) / Medical Engineering Unit (MEU), B3 Unit, 65, Tsurumai-cho, Showa-ku, Nagoya 466-8560, Aichi, Japan; FOREST- Souhatsu, CREST, JST; Nagoya University Institute for Advanced Research, S-YLC, Furo-cho, Chikusa-ku, Nagoya 464-8601, Aichi,, Japan.
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Peplau E, De Rose F, Eichinger A, Reder S, Mittelhäuser M, Scafetta G, Schwaiger M, Weber WA, Bartolazzi A, D'Alessandria C, Skerra A. Effective rational humanization of a PASylated anti-galectin-3 Fab for the sensitive PET imaging of thyroid cancer in vivo. Sci Rep 2021; 11:7358. [PMID: 33795750 PMCID: PMC8016950 DOI: 10.1038/s41598-021-86641-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The lack of a non-invasive test for malignant thyroid nodules makes the diagnosis of thyroid cancer (TC) challenging. Human galectin-3 (hGal3) has emerged as a promising target for medical TC imaging and diagnosis because of its exclusive overexpression in malignant thyroid tissues. We previously developed a human-chimeric αhGal3 Fab fragment derived from the rat monoclonal antibody (mAb) M3/38 with optimized clearance characteristics using PASylation technology. Here, we describe the elucidation of the hGal3 epitope recognized by mAb M3/38, X-ray crystallographic analysis of its complex with the chimeric Fab and, based on the three-dimensional structure, the rational humanization of the Fab by CDR grafting. Four CDR-grafted versions were designed using structurally most closely related fully human immunoglobulin VH/VL regions of which one-employing the acceptor framework regions of the HIV-1 neutralizing human antibody m66-showed the highest antigen affinity. By introducing two additional back-mutations to the rodent donor sequence, an affinity toward hGal3 indistinguishable from the chimeric Fab was achieved (KD = 0.34 ± 0.02 nM in SPR). The PASylated humanized Fab was site-specifically labelled with the fluorescent dye Cy7 and applied for the immuno-histochemical staining of human tissue sections representative for different TCs. The same protein was conjugated with the metal chelator Dfo, followed by radiolabelling with 89Zr(IV). The resulting protein tracer allowed the highly sensitive and specific PET/CT imaging of orthotopic tumors in mice, which was confirmed by quantitative analysis of radiotracer accumulation. Thus, the PASylated humanized αhGal3 Fab offers clinical potential for the diagnostic imaging of TC.
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Affiliation(s)
- Emanuel Peplau
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising (Weihenstephan), Germany
| | - Francesco De Rose
- Klinikum rechts der Isar, Nuclear Medicine Department, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Andreas Eichinger
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising (Weihenstephan), Germany
| | - Sybille Reder
- Klinikum rechts der Isar, Nuclear Medicine Department, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Markus Mittelhäuser
- Klinikum rechts der Isar, Nuclear Medicine Department, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Giorgia Scafetta
- Pathology Research Laboratory, Sant'Andrea Hospital, University Sapienza, via di Grottarossa 1035, 00189, Rome, Italy
| | - Markus Schwaiger
- Klinikum rechts der Isar, Nuclear Medicine Department, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Wolfgang A Weber
- Klinikum rechts der Isar, Nuclear Medicine Department, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Armando Bartolazzi
- Pathology Research Laboratory, Cancer Center Karolinska, Karolinska Hospital, 17176, Stockholm, Sweden
- Pathology Research Laboratory, Sant'Andrea Hospital, University Sapienza, via di Grottarossa 1035, 00189, Rome, Italy
| | - Calogero D'Alessandria
- Klinikum rechts der Isar, Nuclear Medicine Department, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising (Weihenstephan), Germany.
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Ulitzka M, Carrara S, Grzeschik J, Kornmann H, Hock B, Kolmar H. Engineering therapeutic antibodies for patient safety: tackling the immunogenicity problem. Protein Eng Des Sel 2021; 33:5944198. [PMID: 33128053 DOI: 10.1093/protein/gzaa025] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022] Open
Abstract
Established monoclonal antibodies (mAbs) allow treatment of cancers, autoimmune diseases and other severe illnesses. Side effects either arise due to interaction with the target protein and its biology or result from of the patient's immune system reacting to the foreign protein. This immunogenic reaction against therapeutic antibodies is dependent on various factors. The presence of non-human sequences can trigger immune responses as well as chemical and post-translational modifications of the antibody. However, even fully human antibodies can induce immune response through T cell epitopes or aggregates. In this review, we briefly describe, how therapeutic antibodies can interact with the patient's immune system and summarize recent advancements in protein engineering and in silico methods to reduce immunogenicity of therapeutic monoclonal antibodies.
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Affiliation(s)
- Michael Ulitzka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany.,Ferring Darmstadt Labs, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Stefania Carrara
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany.,Ferring Darmstadt Labs, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Julius Grzeschik
- Ferring Darmstadt Labs, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Henri Kornmann
- Ferring International Center S.A., Chemin de la Vergognausaz 50, CH-1162 Saint-Prex, Switzerland
| | - Björn Hock
- Ferring International Center S.A., Chemin de la Vergognausaz 50, CH-1162 Saint-Prex, Switzerland
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
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Moraes JZ, Hamaguchi B, Braggion C, Speciale ER, Cesar FBV, Soares GDFDS, Osaki JH, Pereira TM, Aguiar RB. Hybridoma technology: is it still useful? CURRENT RESEARCH IN IMMUNOLOGY 2021; 2:32-40. [PMID: 35492397 PMCID: PMC9040095 DOI: 10.1016/j.crimmu.2021.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/15/2022] Open
Abstract
The isolation of single monoclonal antibodies (mAbs) against a given antigen was only possible with the introduction of the hybridoma technology, which is based on the fusion of specific B lymphocytes with myeloma cells. Since then, several mAbs were described for therapeutic, diagnostic, and research purposes. Despite being an old technique with low complexity, hybridoma-based strategies have limitations that include the low efficiency on B lymphocyte-myeloma cell fusion step, and the need to use experimental animals. In face of that, several methods have been developed to improve mAb generation, ranging from changes in hybridoma technique to the advent of completely new technologies, such as the antibody phage display and the single B cell antibody ones. In this review, we discuss the hybridoma technology along with emerging mAb isolation approaches, taking into account their advantages and limitations. Finally, we explore the usefulness of the hybridoma technology nowadays. Hybridoma technology is the most popular technique to obtain monoclonal antibodies. Hybridoma technology variants include B cell and stereospecific targeting protocols. Phage display and single B cell methods are hybridoma technology alternatives.
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