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Kushnarova-Vakal A, Aalto R, Huovinen T, Wittfooth S, Lamminmäki U. Controlled labelling of tracer antibodies for time-resolved fluorescence-based immunoassays. Sci Rep 2024; 14:18113. [PMID: 39103434 PMCID: PMC11300886 DOI: 10.1038/s41598-024-69294-7] [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: 05/15/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024] Open
Abstract
Tracer antibodies, which are labelled with fluorescent or other type of reporter molecules, are widely employed in diagnostic immunoassays. Time-resolved fluorescence immunoassay (TRFIA), recognized as one of the most sensitive immunoassay techniques, utilizes tracers labelled with lanthanide ion (Ln) chelates. The conventional approach for conjugating isothiocyanate (ITC) Ln-chelates to antibodies involves random chemical targeting of the primary amino group of Lys residues, requiring typically overnight exposure to an elevated pH of 9-9.3 and leading to heterogeneity. Moreover, efforts to enhance the sensitivity of the assays by introducing a higher number of Ln-chelates per tracer antibody are associated with an elevated risk of targeting critical amino acid residues in the binding site, compromising the binding properties of the antibody. Herein, we report a method to precisely label recombinant antibodies with a defined number of Ln-chelates in a well-controlled manner by employing the SpyTag/SpyCatcher protein ligation technology. We demonstrate the functionality of the method with a full-length recombinant antibody (IgG) as well as an antibody fragment by producing site-specifically labelled antibodies for TRFIA for cardiac troponin I (cTnI) detection with a significant improvement in assay sensitivity compared to that with conventionally labelled tracer antibodies. Overall, our data clearly illustrates the benefits of the site-specific labelling strategy for generating high-performing tracer antibodies for TRF immunoassays.
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Affiliation(s)
- Anastasiia Kushnarova-Vakal
- Department of Life Technologies, University of Turku, 20520, Turku, Finland.
- InFLAMES Research Flagship, University of Turku, 20014, Turku, Finland.
| | - Rami Aalto
- Department of Life Technologies, University of Turku, 20520, Turku, Finland
- Tyks Laboratories, Clinical Chemistry, Turku University Hospital, 20521, Turku, Finland
| | - Tuomas Huovinen
- Department of Life Technologies, University of Turku, 20520, Turku, Finland
| | - Saara Wittfooth
- Department of Life Technologies, University of Turku, 20520, Turku, Finland
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, 20520, Turku, Finland.
- InFLAMES Research Flagship, University of Turku, 20014, Turku, Finland.
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2
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Gavade A, Nagraj AK, Patel R, Pais R, Dhanure P, Scheele J, Seiz W, Patil J. Understanding the Specific Implications of Amino Acids in the Antibody Development. Protein J 2024; 43:405-424. [PMID: 38724751 DOI: 10.1007/s10930-024-10201-4] [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] [Accepted: 04/21/2024] [Indexed: 06/01/2024]
Abstract
As the demand for immunotherapy to treat and manage cancers, infectious diseases and other disorders grows, a comprehensive understanding of amino acids and their intricate role in antibody engineering has become a prime requirement. Naturally produced antibodies may not have the most suitable amino acids at the complementarity determining regions (CDR) and framework regions, for therapeutic purposes. Therefore, to enhance the binding affinity and therapeutic properties of an antibody, the specific impact of certain amino acids on the antibody's architecture must be thoroughly studied. In antibody engineering, it is crucial to identify the key amino acid residues that significantly contribute to improving antibody properties. Therapeutic antibodies with higher binding affinity and improved functionality can be achieved through modifications or substitutions with highly suitable amino acid residues. Here, we have indicated the frequency of amino acids and their association with the binding free energy in CDRs. The review also analyzes the experimental outcome of two studies that reveal the frequency of amino acids in CDRs and provides their significant correlation between the outcomes. Additionally, it discusses the various bond interactions within the antibody structure and antigen binding. A detailed understanding of these amino acid properties should assist in the analysis of antibody sequences and structures needed for designing and enhancing the overall performance of therapeutic antibodies.
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Affiliation(s)
- Akshata Gavade
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Anil Kumar Nagraj
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Riya Patel
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Roylan Pais
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Pratiksha Dhanure
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | | | | | - Jaspal Patil
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India.
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Li W, Lin H, Huang Z, Xie S, Zhou Y, Gong R, Jiang Q, Xiang C, Huang J. DOTAD: A Database of Therapeutic Antibody Developability. Interdiscip Sci 2024:10.1007/s12539-024-00613-2. [PMID: 38530613 DOI: 10.1007/s12539-024-00613-2] [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: 08/13/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 03/28/2024]
Abstract
The development of therapeutic antibodies is an important aspect of new drug discovery pipelines. The assessment of an antibody's developability-its suitability for large-scale production and therapeutic use-is a particularly important step in this process. Given that experimental assays to assess antibody developability in large scale are expensive and time-consuming, computational methods have been a more efficient alternative. However, the antibody research community faces significant challenges due to the scarcity of readily accessible data on antibody developability, which is essential for training and validating computational models. To address this gap, DOTAD (Database Of Therapeutic Antibody Developability) has been built as the first database dedicated exclusively to the curation of therapeutic antibody developability information. DOTAD aggregates all available therapeutic antibody sequence data along with various developability metrics from the scientific literature, offering researchers a robust platform for data storage, retrieval, exploration, and downloading. In addition to serving as a comprehensive repository, DOTAD enhances its utility by integrating a web-based interface that features state-of-the-art tools for the assessment of antibody developability. This ensures that users not only have access to critical data but also have the convenience of analyzing and interpreting this information. The DOTAD database represents a valuable resource for the scientific community, facilitating the advancement of therapeutic antibody research. It is freely accessible at http://i.uestc.edu.cn/DOTAD/ , providing an open data platform that supports the continuous growth and evolution of computational methods in the field of antibody development.
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Affiliation(s)
- Wenzhen Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Hongyan Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Ziru Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Shiyang Xie
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yuwei Zhou
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Rong Gong
- School of Computer Science and Technology, Aba Teachers University, Aba, 623002, China
| | - Qianhu Jiang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - ChangCheng Xiang
- School of Computer Science and Technology, Aba Teachers University, Aba, 623002, China.
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China.
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, 611844, China.
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4
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Yaghoobizadeh F, Roayaei Ardakani M, Ranjbar MM, Khosravi M, Galehdari H. Development of a potent recombinant scFv antibody against the SARS-CoV-2 by in-depth bioinformatics study: Paving the way for vaccine/diagnostics development. Comput Biol Med 2024; 170:108091. [PMID: 38295473 DOI: 10.1016/j.compbiomed.2024.108091] [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: 05/09/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND The SARS-CoV-2 has led to a worldwide disaster. Thus, developing prophylactics/therapeutics is required to overcome this public health issue. Among these, producing the anti-SARS-CoV-2 single-chain variable fragment (scFv) antibodies has attracted a significant attention. Accordingly, this study aims to address this question: Is it possible to bioinformatics-based design of a potent anti-SARS-CoV-2 scFv as an alternative to current production approaches? METHOD Using the complexed SARS-CoV-2 spike-antibodies, two sets analyses were performed: (1) B-cell epitopes (BCEs) prediction in the spike receptor-binding domain (RBD) region as a parameter for antibody screening; (2) the computational analysis of antibodies variable domains (VH/VL). Based on these primary screenings, and docking/binding affinity rating, one antibody was selected. The protein-protein interactions (PPIs) among the selected antibody-epitope complex were predicted and its epitope conservancy was also evaluated. Thereafter, some elements were added to the final scFv: (1) the PelB signal peptide; (2) a GSGGGGS linker to connect the VH-VL. Finally, this scFv was analyzed/optimized using various web servers. RESULTS Among the antibody library, only one met the various criteria for being an efficient scFv candidate. Moreover, no interaction was predicted between its paratope and RBD hot-spot residues of SARS-CoV-2 variants-of-Concern (VOCs). CONCLUSIONS Herein, a step-by-step bioinformatics platform has been introduced to bypass some barriers of traditional antibody production approaches. Based on existing literature, the current study is one of the pioneer works in the field of bioinformatics-based scFv production. This scFv may be a good candidate for diagnostics/therapeutics design against the SARS-CoV-2 as an emerging aggressive pathogen.
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Affiliation(s)
- Fatemeh Yaghoobizadeh
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, 6135783151, Iran.
| | - Mohammad Roayaei Ardakani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, 6135783151, Iran.
| | | | - Mohammad Khosravi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, 6135783151, Iran.
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, 6135783151, Iran.
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5
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Cheng LD, Li P, Lin YC, Hu HX, Zhang Y, Li HF, Huang J, Tan L, Ma N, Xia DY. Monoclonal neutralizing antibodies against SARS-COV-2 S protein. Am J Transl Res 2024; 16:681-689. [PMID: 38463597 PMCID: PMC10918147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/17/2023] [Indexed: 03/12/2024]
Abstract
Novel coronavirus pneumonia, also known as coronavirus disease 2019 (COVID-19), is caused by sub-severe acute respiratory syndrome type 2 coronavirus (SARS-CoV-2) infection. The spike (S) protein of SARS-CoV-2 binds to angiotensin-converting enzyme 2 (ACE2) receptors widely expressed on the surface of human cells leading to life-threatening respiratory infections. A serious hazard to human health is posed by the lack of particular treatment medications for this virus infection. We advocate the creation of high-affinity antibodies using the receptor binding domain (RBD) of S protein as a specific antigenic epitope to develop a drug that can precisely target therapy COVID-19 because SARS-CoV-2 infection of the host cells is dependent on S protein binding to ACE2. Finally, we obtained high-affinity antibodies 14F4HL and 14E3HL that have high affinity with RBD and well-drug-forming properties, suitable for further humanization studies. Thus, monoclonal antibodies that neutralize the S protein were identified in our study, which may provide new insights for the development of COVID-19 therapeutic drugs.
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Affiliation(s)
- Lin-Dong Cheng
- Graduate School, Hebei North UniversityZhangjiakou 075000, Hebei, China
| | - Ping Li
- Graduate School, Wannan Medical CollegeWuhu 241000, Anhui, China
| | - Yan-Chen Lin
- Graduate School, Hebei North UniversityZhangjiakou 075000, Hebei, China
| | - Hui-Xiu Hu
- Graduate School, Hebei North UniversityZhangjiakou 075000, Hebei, China
| | - Ying Zhang
- Graduate School, Hebei North UniversityZhangjiakou 075000, Hebei, China
| | - Hou-Feng Li
- Graduate School, Hebei North UniversityZhangjiakou 075000, Hebei, China
| | - Jing Huang
- Graduate School, Wannan Medical CollegeWuhu 241000, Anhui, China
| | - Li Tan
- Department of Anesthesiology, Chongqing University Cancer HospitalChongqing 400030, China
| | - Ning Ma
- Department of Clinical Laboratory, 905th Hospital of PLAShanghai 200052, China
| | - Deng-Yun Xia
- Department of Anesthesiology, The First Affiliated Hospital of Hebei North UniversityZhangjiakou 075000, Hebei, China
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Tawfeeq C, Song J, Khaniya U, Madej T, Wang J, Youkharibache P, Abrol R. Towards a structural and functional analysis of the immunoglobulin-fold proteome. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 138:135-178. [PMID: 38220423 DOI: 10.1016/bs.apcsb.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The immunoglobulin fold (Ig fold) domain is a super-secondary structural motif consisting of a sandwich with two layers of β-sheets that is present in many proteins with very diverse biological functions covering a wide range of physiological processes. This domain presents a modular architecture built with β strands connected by variable length loops that has a highly conserved structural core of four β-strands and quite variable β-sheet extensions in the two sandwich layers that enable both divergent and convergent evolutionary mechanisms in the known Ig fold proteome. The central role of this Ig fold's structural plasticity in the evolutionary success of antibodies in our immune system is well established. Nature has also utilized this Ig fold in all domains of life in many different physiological contexts that go way beyond the immune system. Here we will present a structural and functional overview of the utilization of the Ig fold in different biological processes and in different cellular contexts to highlight some of the innumerable ways that this structural motif can interact in multidomain proteins to enable their diversity of functions. This includes shareable specific protein structure visualizations behind those functions that serve as starting points for further explorations of the biomolecular interactions spanning the Ig fold proteome. This overview also highlights how this Ig fold is being utilized through natural adaptation, engineering, and even building from scratch for a range of biotechnological applications.
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Affiliation(s)
- Caesar Tawfeeq
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, United States
| | - James Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Umesh Khaniya
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Thomas Madej
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Philippe Youkharibache
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, United States.
| | - Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, United States.
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7
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Fernández-Quintero ML, Pomarici ND, Fischer ALM, Hoerschinger VJ, Kroell KB, Riccabona JR, Kamenik AS, Loeffler JR, Ferguson JA, Perrett HR, Liedl KR, Han J, Ward AB. Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines. Antibodies (Basel) 2023; 12:67. [PMID: 37873864 PMCID: PMC10594513 DOI: 10.3390/antib12040067] [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: 09/05/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Antibodies and other new antibody-like formats have emerged as one of the most rapidly growing classes of biotherapeutic proteins. Understanding the structural features that drive antibody function and, consequently, their molecular recognition is critical for engineering antibodies. Here, we present the structural architecture of conventional IgG antibodies alongside other formats. We emphasize the importance of considering antibodies as conformational ensembles in solution instead of focusing on single-static structures because their functions and properties are strongly governed by their dynamic nature. Thus, in this review, we provide an overview of the unique structural and dynamic characteristics of antibodies with respect to their antigen recognition, biophysical properties, and effector functions. We highlight the numerous technical advances in antibody structure prediction and design, enabled by the vast number of experimentally determined high-quality structures recorded with cryo-EM, NMR, and X-ray crystallography. Lastly, we assess antibody and vaccine design strategies in the context of structure and dynamics.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nancy D. Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna-Lena M. Fischer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Katharina B. Kroell
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Jakob R. Riccabona
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna S. Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James A. Ferguson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailee R. Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Sheng Z, Bimela JS, Wang M, Li Z, Guo Y, Ho DD. An optimized thermodynamics integration protocol for identifying beneficial mutations in antibody design. Front Immunol 2023; 14:1190416. [PMID: 37275896 PMCID: PMC10235760 DOI: 10.3389/fimmu.2023.1190416] [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: 03/20/2023] [Accepted: 04/28/2023] [Indexed: 06/07/2023] Open
Abstract
Accurate identification of beneficial mutations is central to antibody design. Many knowledge-based (KB) computational approaches have been developed to predict beneficial mutations, but their accuracy leaves room for improvement. Thermodynamic integration (TI) is an alchemical free energy algorithm that offers an alternative technique for identifying beneficial mutations, but its performance has not been evaluated. In this study, we developed an efficient TI protocol with high accuracy for predicting binding free energy changes of antibody mutations. The improved TI method outperforms KB methods at identifying both beneficial and deleterious mutations. We observed that KB methods have higher accuracies in predicting deleterious mutations than beneficial mutations. A pipeline using KB methods to efficiently exclude deleterious mutations and TI to accurately identify beneficial mutations was developed for high-throughput mutation scanning. The pipeline was applied to optimize the binding affinity of a broadly sarbecovirus neutralizing antibody 10-40 against the circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron variant. Three identified beneficial mutations show strong synergy and improve both binding affinity and neutralization potency of antibody 10-40. Molecular dynamics simulation revealed that the three mutations improve the binding affinity of antibody 10-40 through the stabilization of an altered binding mode with increased polar and hydrophobic interactions. Above all, this study presents an accurate and efficient TI-based approach for optimizing antibodies and other biomolecules.
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Affiliation(s)
- Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Jude S. Bimela
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Zhiteng Li
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
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Chauhan VM, Pantazes RJ. MutDock: A computational docking approach for fixed-backbone protein scaffold design. Front Mol Biosci 2022; 9:933400. [PMID: 36106019 PMCID: PMC9465448 DOI: 10.3389/fmolb.2022.933400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Despite the successes of antibodies as therapeutic binding proteins, they still face production and design challenges. Alternative binding scaffolds of smaller size have been developed to overcome these issues. A subset of these alternative scaffolds recognizes target molecules through mutations to a set of surface resides, which does not alter their backbone structures. While the computational design of antibodies for target epitopes has been explored in depth, the same has not been done for alternative scaffolds. The commonly used dock-and-mutate approach for binding proteins, including antibodies, is limited because it uses a constant sequence and structure representation of the scaffold. Docking fixed-backbone scaffolds with a varied group of surface amino acids increases the chances of identifying superior starting poses that can be improved with subsequent mutations. In this work, we have developed MutDock, a novel computational approach that simultaneously docks and mutates fixed backbone scaffolds for binding a target epitope by identifying a minimum number of hydrogen bonds. The approach is broadly divided into two steps. The first step uses pairwise distance alignment of hydrogen bond-forming areas of scaffold residues and compatible epitope atoms. This step considers both native and mutated rotamers of scaffold residues. The second step mutates clashing variable interface residues and thermodynamically unfavorable residues to create additional strong interactions. MutDock was used to dock two scaffolds, namely, Affibodies and DARPins, with ten randomly selected antigens. The energies of the docked poses were minimized and binding energies were compared with docked poses from ZDOCK and HADDOCK. The top MutDock poses consisted of higher and comparable binding energies than the top ZDOCK and HADDOCK poses, respectively. This work contributes to the discovery of novel binders based on smaller-sized, fixed-backbone protein scaffolds.
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10
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Non-covalent Fc-Fab interactions significantly alter internal dynamics of an IgG1 antibody. Sci Rep 2022; 12:9321. [PMID: 35661134 PMCID: PMC9167292 DOI: 10.1038/s41598-022-13370-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
The fragment-antigen-binding arms (Fab1 and Fab2) in a canonical immunoglobulin G (IgG) molecule have identical sequences and hence are always expected to exhibit symmetric conformations and dynamics. Using long all atom molecular simulations of a human IgG1 crystal structure 1HZH, we demonstrate that the translational and rotational dynamics of Fab1 and Fab2 also strongly depend on their interactions with each other and with the fragment-crystallizable (Fc) region. We show that the Fab2 arm in the 1HZH structure is non-covalently bound to the Fc region via long-lived hydrogen bonds, involving its light chain and both heavy chains of the Fc region. These highly stable interactions stabilize non-trivial conformer states with constrained fluctuations. We observe subtle modifications in Fab1 dynamics in response to Fab2-Fc interactions that points to novel allosteric interactions between the Fab arms. These results yield novel insights into the inter- and intra-fragment motions of immunoglobulins which could help us better understand the relation between their structure and function.
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11
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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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12
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Rodriguez-Urretavizcaya B, Pascual N, Pastells C, Martin-Gomez MT, Vilaplana L, Marco MP. Diagnosis and Stratification of Pseudomonas aeruginosa Infected Patients by Immunochemical Quantitative Determination of Pyocyanin From Clinical Bacterial Isolates. Front Cell Infect Microbiol 2022; 11:786929. [PMID: 34970510 PMCID: PMC8712664 DOI: 10.3389/fcimb.2021.786929] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/12/2021] [Indexed: 12/04/2022] Open
Abstract
The development of a highly sensitive, specific, and reliable immunochemical assay to detect pyocyanin (PYO), one of the most important virulence factors (VFs) of Pseudomonas aeruginosa, is here reported. The assay uses a high-affinity monoclonal antibody (mAb; C.9.1.9.1.1.2.2.) raised against 1-hydroxyphenazine (1-OHphz) hapten derivatives (PC1; a 1:1 mixture of 9-hydroxy- and 6-hydroxy-phenazine-2-carobxylic acids). Selective screening using PYO and 1-OHphz on several cloning cycles allowed the selection of a clone able to detect PYO at low concentration levels. The microplate-based ELISA developed is able to achieve a limit of detection (LoD) of 0.07 nM, which is much lower than the concentrations reported to be found in clinical samples (130 μM in sputa and 2.8 μM in ear secretions). The ELISA has allowed the investigation of the release kinetics of PYO and 1-OHphz (the main metabolite of PYO) of clinical isolates obtained from P. aeruginosa-infected patients and cultured in Mueller–Hinton medium. Significant differences have been found between clinical isolates obtained from patients with an acute or a chronic infection (~6,000 nM vs. ~8 nM of PYO content, respectively) corroborated by the analysis of PYO/1-OHphz levels released by 37 clinical isolates obtained from infected patients at different stages. In all cases, the levels of 1-OHphz were much lower than those of PYO (at the highest levels 6,000 nM vs. 300 nM for PYO vs. 1-OHphz, respectively). The results found point to a real potential of PYO as a biomarker of P. aeruginosa infection and the possibility to use such VF also as a biomarker for patient stratification[2] and for an effective management of these kinds of infections.
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Affiliation(s)
- Barbara Rodriguez-Urretavizcaya
- Nanobiotechnology for Diagnostics (Nb4D), Institute of Advanced Chemistry of Catalonia, Institute for Advanced Chemistry of Catalonia (IQAC)-Spanish National Research Council (CSIC), Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Nuria Pascual
- Nanobiotechnology for Diagnostics (Nb4D), Institute of Advanced Chemistry of Catalonia, Institute for Advanced Chemistry of Catalonia (IQAC)-Spanish National Research Council (CSIC), Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Carme Pastells
- Nanobiotechnology for Diagnostics (Nb4D), Institute of Advanced Chemistry of Catalonia, Institute for Advanced Chemistry of Catalonia (IQAC)-Spanish National Research Council (CSIC), Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | | | - Lluïsa Vilaplana
- Nanobiotechnology for Diagnostics (Nb4D), Institute of Advanced Chemistry of Catalonia, Institute for Advanced Chemistry of Catalonia (IQAC)-Spanish National Research Council (CSIC), Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Maria-Pilar Marco
- Nanobiotechnology for Diagnostics (Nb4D), Institute of Advanced Chemistry of Catalonia, Institute for Advanced Chemistry of Catalonia (IQAC)-Spanish National Research Council (CSIC), Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
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13
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Boehringer HR, O'Farrell BJ. Lateral Flow Assays in Infectious Disease Diagnosis. Clin Chem 2021; 68:52-58. [PMID: 34969115 PMCID: PMC9383164 DOI: 10.1093/clinchem/hvab194] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/17/2021] [Indexed: 11/23/2022]
Abstract
Background Lateral flow immunoassays are widely used as diagnostic tests in many applications in human and other diagnostic areas. Assays for human applications have been commercially available since the 1980s and initially were primarily used to identify pregnancy by measuring human chorionic gonadotropin in urine and serum/plasma. Content The first infectious disease lateral flow assays were commercialized in the late 1980s identifying the presence of Group A Streptococcus pyogenes collected with throat swabs; innumerable other applications followed in the intervening decades. The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) pandemic has brought a vast number of new assays for which emergency use authorization (EUA) has been requested in the USA. These assays have been designed for detection of the antibody response to an infection and viral antigens in respiratory samples. In view of the onslaught of new tests, this review will focus on the use of rapid lateral flow immunoassays for infectious diseases. Principles of lateral flow assays and approaches to the production of high-sensitivity point-of-care assays are presented. Market trends, customer requirements, and future directions of lateral flow assay technology and its applications in the infectious disease diagnostic space are discussed. Summary Lateral flow immunoassays play an important role in infectious disease diagnostics. Advancements in technology have led to improved performance of these assays and acceptance by professional users. With the advent of the SARS-CoV-2 pandemic, the market has reached new levels requiring hundreds of millions of tests per year for professional and even home use.
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14
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Nawab DH. Vaccinal antibodies: Fc antibody engineering to improve the antiviral antibody response and induce vaccine-like effects. Hum Vaccin Immunother 2021; 17:5532-5545. [PMID: 34844516 PMCID: PMC8903937 DOI: 10.1080/21645515.2021.1985891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 09/21/2021] [Indexed: 10/19/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic highlights the urgent clinical need for efficient virus therapies and vaccines. Although the functional importance of antibodies is indisputable in viral infections, there are still significant unmet needs that require vast improvements in antibody-based therapeutics. The IgG Fc domain can be engineered to produce antibodies with tailored and potent responses that will meet these clinical demands. Engaging Fc receptors (FcRs) to perform effector functions as cytotoxicity, phagocytosis, complement activation, intracellular neutralization and controlling antibody persistence. Furthermore, it produces vaccine-like effects by activating signals to stimulate T-cell responses, have proven to be required for protection, as neutralization alone does not off the full protection capacity of antibodies. This review highlights antiviral Fc functions and FcRs' contributions in linking innate and adaptive immunity against viral threats. Moreover, it provides the latest Fc engineering strategies to improve the safety and efficacy of human antiviral antibodies and vaccines.
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Affiliation(s)
- Dhuha H Nawab
- Pharmacy Department, Ministry of Health, Saudi Arabia
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15
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Vimer S, Ben-Nissan G, Marty M, Fleishman SJ, Sharon M. Direct-MS analysis of antibody-antigen complexes. Proteomics 2021; 21:e2000300. [PMID: 34310051 PMCID: PMC8595693 DOI: 10.1002/pmic.202000300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/04/2021] [Accepted: 07/15/2021] [Indexed: 11/05/2022]
Abstract
In recent decades, antibodies (Abs) have attracted the attention of academia and the biopharmaceutical industry due to their therapeutic properties and versatility in binding a vast spectrum of antigens. Different engineering strategies have been developed for optimizing Ab specificity, efficacy, affinity, stability and production, enabling systematic screening and analysis procedures for selecting lead candidates. This quality assessment is critical but usually demands time-consuming and labor-intensive purification procedures. Here, we harnessed the direct-mass spectrometry (direct-MS) approach, in which the analysis is carried out directly from the crude growth media, for the rapid, structural characterization of designed Abs. We demonstrate that properties such as stability, specificity and interactions with antigens can be defined, without the need for prior purification.
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Affiliation(s)
- Shay Vimer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Marty
- Department of Chemistry & Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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16
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Lengfeld J, Zhang H, Stoesz S, Murali R, Pass F, Greene MI, Goel PN, Grover P. Challenges in Detection of Serum Oncoprotein: Relevance to Breast Cancer Diagnostics. BREAST CANCER-TARGETS AND THERAPY 2021; 13:575-593. [PMID: 34703307 PMCID: PMC8524259 DOI: 10.2147/bctt.s331844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/02/2021] [Indexed: 11/23/2022]
Abstract
Breast cancer is a highly prevalent malignancy that shows improved outcomes with earlier diagnosis. Current screening and monitoring methods have improved survival rates, but the limitations of these approaches have led to the investigation of biomarker evaluation to improve early diagnosis and treatment monitoring. The enzyme-linked immunosorbent assay (ELISA) is a specific and robust technique ideally suited for the quantification of protein biomarkers from blood or its constituents. The continued clinical relevancy of this assay format will require overcoming specific technical challenges, including the ultra-sensitive detection of trace biomarkers and the circumventing of potential assay interference due to the expanding use of monoclonal antibody (mAb) therapeutics. Approaches to increasing the sensitivity of ELISA have been numerous and include employing more sensitive substrates, combining ELISA with the polymerase chain reaction (PCR), and incorporating nanoparticles as shuttles for detection antibodies and enzymes. These modifications have resulted in substantial boosts in the ability to detect extremely low levels of protein biomarkers, with some systems reliably detecting antigen at sub-femtomolar concentrations. Extensive utilization of mAb therapies in oncology has presented an additional contemporary challenge for ELISA, particularly when both therapeutic and assay antibodies target the same protein antigen. Resolution of issues such as epitope overlap and steric hindrance requires a rational approach to the design of diagnostic antibodies that takes advantage of modern antibody generation pipelines, epitope binning techniques and computational methods to strategically target biomarker epitopes. This review discusses technical strategies in ELISA implemented to date and their feasibility to address current constraints on sensitivity and problems with interference in the clinical setting. The impact of these recent advancements will depend upon their transformation from research laboratory protocols into facile, reliable detection systems that can ideally be replicated in point-of-care devices to maximize utilization and transform both the diagnostic and therapeutic monitoring landscape.
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Affiliation(s)
- Justin Lengfeld
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Hongtao Zhang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven Stoesz
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Research Division of Immunology; Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Franklin Pass
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Mark I Greene
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peeyush N Goel
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Payal Grover
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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17
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Rangnoi K, Rüker F, Wozniak-Knopp G, Cvak B, O’Kennedy R, Yamabhai M. Binding Characteristic of Various Antibody Formats Against Aflatoxins. ACS OMEGA 2021; 6:25258-25268. [PMID: 34632185 PMCID: PMC8495687 DOI: 10.1021/acsomega.1c03044] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
The application of recombinant antibodies for the analysis of foods and food contaminants is now a major focus, given their capacity to be engineered to tailor their specificity, enhance their stability, and modify their structural formats to fit the desired analytical platform. In this study, human scFv antibody fragments generated against aflatoxin B1 (AFB1) were selected as the model antibody to explore the effect of antibody formats on their binding activity and to evaluate their potential use as immunoreagents for food contaminant analysis. Four human scFv antibody fragments against aflatoxin B1 (AFB1), previously isolated and engineered by chain shuffling, were converted into various formats, that is, scFv-AP fusions, scFv-Fc, and whole IgG molecules. The result indicated that the effects of the antibody format on the binding property varied, depending on the sequence of scFv. For all of the scFv clones, the scFv-AP fusion format showed the highest sensitivity by competitive ELISA, while the effects on the binding activity after conversion to scFv-Fc or IgG format varied, depending on the amino acid sequence of the antibodies. The sAFH-3e3 antibodies that showed the best performance by competitive ELISA were selected for further investigation. The sAFH-3e3 was converted to the scFv-GFP format and tested by fluorescence-linked immunosorbent assay (FLISA), which showed that its binding property was equivalent to those of scFv-Fc and IgG formats. The potential applications of the sAFH-3e3 in a rapid test kit format based on ELISA (scFv-AP) and in a lateral flow immunochromatography assay (LFIA) (IgG) were demonstrated. A comparison of methods for the extraction of AFB1 from matrices for use with these assay formats indicated that PBS and TBST are better than 70% methanol.
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Affiliation(s)
- Kuntalee Rangnoi
- Molecular
Biotechnology Laboratory, School of Biotechnology, Institute of Agriculture
Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Florian Rüker
- Institute
of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences,
Vienna (BOKU), Muthgasse 18, Vienna A-1190, Austria
| | - Gordana Wozniak-Knopp
- Institute
of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences,
Vienna (BOKU), Muthgasse 18, Vienna A-1190, Austria
| | - Barbara Cvak
- Romer
Labs Division Holding GmbH, Technopark 5, Tulln 3430, Austria
| | - Richard O’Kennedy
- School
of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin 9 D09 DX63, Ireland
| | - Montarop Yamabhai
- Molecular
Biotechnology Laboratory, School of Biotechnology, Institute of Agriculture
Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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18
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Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021; 50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.
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Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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19
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Passeri L, Marta F, Bassi V, Gregori S. Tolerogenic Dendritic Cell-Based Approaches in Autoimmunity. Int J Mol Sci 2021; 22:8415. [PMID: 34445143 PMCID: PMC8395087 DOI: 10.3390/ijms22168415] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022] Open
Abstract
Dendritic cells (DCs) dictate the outcomes of tissue-specific immune responses. In the context of autoimmune diseases, DCs instruct T cells to respond to antigens (Ags), including self-Ags, leading to organ damage, or to becoming regulatory T cells (Tregs) promoting and perpetuating immune tolerance. DCs can acquire tolerogenic properties in vitro and in vivo in response to several stimuli, a feature that opens the possibility to generate or to target DCs to restore tolerance in autoimmune settings. We present an overview of the different subsets of human DCs and of the regulatory mechanisms associated with tolerogenic (tol)DC functions. We review the role of DCs in the induction of tissue-specific autoimmunity and the current approaches exploiting tolDC-based therapies or targeting DCs in vivo for the treatment of autoimmune diseases. Finally, we discuss limitations and propose future investigations for improving the knowledge on tolDCs for future clinical assessment to revert and prevent autoimmunity. The continuous expansion of tolDC research areas will lead to improving the understanding of the role that DCs play in the development and treatment of autoimmunity.
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Affiliation(s)
- Laura Passeri
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (L.P.); (F.M.); (V.B.)
- San Raffaele Scientific Institute IRCCS, University Vita-Salute San Raffaele, 20132 Milan, Italy
| | - Fortunato Marta
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (L.P.); (F.M.); (V.B.)
| | - Virginia Bassi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (L.P.); (F.M.); (V.B.)
- San Raffaele Scientific Institute IRCCS, University Vita-Salute San Raffaele, 20132 Milan, Italy
| | - Silvia Gregori
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (L.P.); (F.M.); (V.B.)
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20
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Brilhante-da-Silva N, de Oliveira Sousa RM, Arruda A, Dos Santos EL, Marinho ACM, Stabeli RG, Fernandes CFC, Pereira SDS. Camelid Single-Domain Antibodies for the Development of Potent Diagnosis Platforms. Mol Diagn Ther 2021; 25:439-456. [PMID: 34146333 DOI: 10.1007/s40291-021-00533-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2021] [Indexed: 11/26/2022]
Abstract
The distinct biophysical and pharmaceutical properties of camelid single-domain antibodies, referred to as VHHs or nanobodies, are associated with their nanometric dimensions, elevated stability, and antigen recognition capacity. These biomolecules can circumvent a number of diagnostic system limitations, especially those related to the size and stability of conventional immunoglobulins currently used in enzyme-linked immunosorbent assays and point-of-care, electrochemical, and imaging assays. In these formats, VHHs are directionally conjugated to different molecules, such as metallic nanoparticles, small peptides, and radioisotopes, which demonstrates their comprehensive versatility. Thus, the application of VHHs in diagnostic systems range from the identification of cancer cells to the detection of degenerative disease biomarkers, viral antigens, bacterial toxins, and insecticides. The improvements of sensitivity and specificity are among the central benefits resulting from the use of VHHs, which are indispensable parameters for high-quality diagnostics. Therefore, this review highlights the main biotechnological advances related to camelid single-domain antibodies and their use in in vitro and in vivo diagnostic approaches for human health.
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Affiliation(s)
- Nairo Brilhante-da-Silva
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, Fiocruz, Unidade Rondônia, Porto Velho, RO, 76812-245, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, Brazil
| | - Rosa Maria de Oliveira Sousa
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, Fiocruz, Unidade Rondônia, Porto Velho, RO, 76812-245, Brazil
| | - Andrelisse Arruda
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, Fiocruz, Unidade Rondônia, Porto Velho, RO, 76812-245, Brazil
| | - Eliza Lima Dos Santos
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, Fiocruz, Unidade Rondônia, Porto Velho, RO, 76812-245, Brazil
| | - Anna Carolina Machado Marinho
- Plataforma de Desenvolvimento de Anticorpos e Nanocorpos, Fundação Oswaldo Cruz, Fiocruz Ceará, Eusebio, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Rodrigo Guerino Stabeli
- Plataforma Bi-institucional de Medicina Translacional.Fundação Oswaldo Cruz-USP, Ribeirão Preto, São Paulo, Brazil
| | - Carla Freire Celedonio Fernandes
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, Brazil
- Plataforma de Desenvolvimento de Anticorpos e Nanocorpos, Fundação Oswaldo Cruz, Fiocruz Ceará, Eusebio, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Soraya Dos Santos Pereira
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, Fiocruz, Unidade Rondônia, Porto Velho, RO, 76812-245, Brazil.
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, Brazil.
- Programa de Pós-graduação em Biologia Experimental, Universidade Federal de Rondônia, Porto Velho, Brazil.
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21
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Xi Z, Liu X, Lin R, Persons JD, Ilina TV, Li W, Dimitrov DS, Ishima R. The reduced form of the antibody CH2 domain. Protein Sci 2021; 30:1895-1903. [PMID: 34107549 DOI: 10.1002/pro.4142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022]
Abstract
Among the immunoglobulin domains, the CH2 domain has the lowest thermal stability, which also depends on amino acid sequence and buffer conditions. To further identify factors that influence CH2 folding and stability, we characterized the domain in the reduced form using differential scanning fluorimetry and nuclear magnetic resonance. We show that the CH2 domain can fold, similarly to the disulfide-bridged form, without forming a disulfide-bridge, even though the protein contains two Cys residues. Although the reduced form exhibits thermal stability more than 15°C lower than the disulfide-bridged form, it does not undergo immediate full oxidization. To explain this phenomenon, we compared CH2 oxidization at different conditions and demonstrate a need for significant fluctuation of the folded conformation to enhance CH2 disulfide-bridge formation. We conclude that, since CH2 can be purified as a folded, semi-stable, reduced protein that can coexist with the oxidized form, verification of the level of oxidization at each step is critical in CH2 engineering studies.
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Affiliation(s)
- Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Xianglei Liu
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rui Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Gastroenterology and Hepatology, Tianjin Medical University, General Hospital, Tianjin, China
| | - John D Persons
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Wei Li
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dimiter S Dimitrov
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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22
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Cassedy A, Parle-McDermott A, O’Kennedy R. Virus Detection: A Review of the Current and Emerging Molecular and Immunological Methods. Front Mol Biosci 2021; 8:637559. [PMID: 33959631 PMCID: PMC8093571 DOI: 10.3389/fmolb.2021.637559] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Viruses are ubiquitous in the environment. While many impart no deleterious effects on their hosts, several are major pathogens. This risk of pathogenicity, alongside the fact that many viruses can rapidly mutate highlights the need for suitable, rapid diagnostic measures. This review provides a critical analysis of widely used methods and examines their advantages and limitations. Currently, nucleic-acid detection and immunoassay methods are among the most popular means for quickly identifying viral infection directly from source. Nucleic acid-based detection generally offers high sensitivity, but can be time-consuming, costly, and require trained staff. The use of isothermal-based amplification systems for detection could aid in the reduction of results turnaround and equipment-associated costs, making them appealing for point-of-use applications, or when high volume/fast turnaround testing is required. Alternatively, immunoassays offer robustness and reduced costs. Furthermore, some immunoassay formats, such as those using lateral-flow technology, can generate results very rapidly. However, immunoassays typically cannot achieve comparable sensitivity to nucleic acid-based detection methods. Alongside these methods, the application of next-generation sequencing can provide highly specific results. In addition, the ability to sequence large numbers of viral genomes would provide researchers with enhanced information and assist in tracing infections.
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Affiliation(s)
- A. Cassedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | | | - R. O’Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
- Hamad Bin Khalifa University, Doha, Qatar
- Qatar Foundation, Doha, Qatar
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23
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Mahmoudinobar F, Britton D, Montclare JK. Protein-based lateral flow assays for COVID-19 detection. Protein Eng Des Sel 2021; 34:gzab010. [PMID: 33991088 PMCID: PMC8194834 DOI: 10.1093/protein/gzab010] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022] Open
Abstract
To combat the enduring and dangerous spread of COVID-19, many innovations to rapid diagnostics have been developed based on proteinprotein interactions of the SARS-CoV-2 spike and nucleocapsid proteins to increase testing accessibility. These antigen tests have most prominently been developed using the lateral flow assay (LFA) test platform which has the benefit of administration at point-of-care, delivering quick results, lower cost, and does not require skilled personnel. However, they have gained criticism for an inferior sensitivity. In the last year, much attention has been given to creating a rapid LFA test for detection of COVID-19 antigens that can address its high limit of detection while retaining the advantages of rapid antibodyantigen interaction. In this review, a summary of these proteinprotein interactions as well as the challenges, benefits, and recent improvements to protein based LFA for detection of COVID-19 are discussed.
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Affiliation(s)
- Farbod Mahmoudinobar
- Department of Chemical and Biomolecular Engineering New York University Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering New York University Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering New York University Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Chemistry New York University, New York, NY 10003, USA
- Department of Biomaterials New York University College of Dentistry, New York, NY 10010, USA
- Department of Radiology New York University Langone Health, New York, NY 10016, USA
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24
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Liu C, Kobashigawa Y, Yamauchi S, Fukuda N, Sato T, Masuda T, Ohtsuki S, Morioka H. Convenient method of producing cyclic single-chain Fv antibodies by split-intein-mediated protein ligation and chaperone co-expression. J Biochem 2021; 168:257-263. [PMID: 32275752 DOI: 10.1093/jb/mvaa042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Single-chain Fv (scFv) is a recombinant antibody in which the variable regions of the heavy chain (VH) and light chain (VL) are connected by a short flexible polypeptide linker. Compared with monoclonal antibodies, scFvs have the advantages of low-cost production using Escherichia coli and easy genetic manipulation. ScFvs are, therefore, regarded as useful modules for producing next-generation medical antibodies. The practical use of scFvs has been limited due to their aggregation propensity mediated by interchain VH-VL interactions. To overcome this problem, we recently reported a cyclic scFv whose N-terminus and C-terminus were connected by sortase A-mediated ligation. Preparation of cyclic scFv is, however, a time-consuming process. To accelerate the application study of cyclic scFv, we developed a method to produce cyclic scFv by the combined use of a protein ligation technique based on protein trans-splicing reaction (PTS) by split intein and a chaperone co-expression system. This method allows for the preparation of active cyclic scFv from the cytoplasm of E. coli. The present method was applied to the production of cyclic 73MuL9-scFv, a GA-pyridine antibody, as a kind of advanced glycation end-product. These findings are expected to evoke further application study of cyclic scFv.
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Affiliation(s)
| | | | | | | | - Takashi Sato
- Department of Analytical and Biophysical Chemistry
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
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25
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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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26
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Ma H, Ó'Fágáin C, O'Kennedy R. Antibody stability: A key to performance - Analysis, influences and improvement. Biochimie 2020; 177:213-225. [PMID: 32891698 DOI: 10.1016/j.biochi.2020.08.019] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 02/01/2023]
Abstract
An antibody's stability greatly influences its performance (i.e. its specificity and affinity). Thus, stability is a major issue for researchers and manufacturers, especially with the increasing use of antibodies in therapeutics, diagnostics and rapid analytical platforms. Here we review antibody stability under five headings: (i) measurement techniques; (ii) stability issues in expression and production (expression, proteolysis, aggregation); (iii) effects of antibody format and engineering on stability and (iv) formulation, drying and storage conditions. We consider more than 100 sources, including patents, and conclude with (v) recommendations to promote antibody stability.
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Affiliation(s)
- Hui Ma
- School of Biotechnology, Dublin City University, Dublin 9, D09 V2O9, Ireland
| | - Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Dublin 9, D09 V2O9, Ireland.
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Dublin 9, D09 V2O9, Ireland; Qatar Foundation, Research Complex, And Hamad Bin Khalifa University, Education City, Doha, Qatar
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27
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Ahangarzadeh S, Payandeh Z, Arezumand R, Shahzamani K, Yarian F, Alibakhshi A. An update on antiviral antibody-based biopharmaceuticals. Int Immunopharmacol 2020; 86:106760. [PMID: 32645633 PMCID: PMC7336121 DOI: 10.1016/j.intimp.2020.106760] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/15/2020] [Accepted: 06/26/2020] [Indexed: 02/08/2023]
Abstract
Due to the vastness of the science virology, it is no longer an offshoot solely of the microbiology. Viruses have become as the causative agents of major epidemics throughout history. Many therapeutic strategies have been used for these microorganisms, and in this way the recognizing of potential targets of viruses is of particular importance for success. For decades, antibodies and antibody fragments have occupied a significant body of the treatment approaches against infectious diseases. Because of their high affinity, they can be designed and engineered against a variety of purposes, mainly since antibody fragments such as scFv, nanobody, diabody, and bispecific antibody have emerged owing to their small size and interesting properties. In this review, we have discussed the antibody discovery and molecular and biological design of antibody fragments as inspiring therapeutic and diagnostic agents against viral targets.
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Affiliation(s)
- Shahrzad Ahangarzadeh
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zahra Payandeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Roghaye Arezumand
- Department of Medical Biotechnology and Molecular Science, North Khorasan University of Medical Science, Bojnurd, Iran
| | - Kiana Shahzamani
- Isfahan Gastroenterology and Hepatology Research Center (IGHRC), Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Yarian
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Abbas Alibakhshi
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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28
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Pyo A, You SH, Sik Kim H, Young Kim J, Min JJ, Kim DY, Hong Y. Production of 64Cu-labeled monobody for imaging of human EphA2-expressing tumors. Bioorg Med Chem Lett 2020; 30:127262. [PMID: 32527560 DOI: 10.1016/j.bmcl.2020.127262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/20/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
We previously reported on the monobody E1, which specifically targets the tumor marker hEphA2. In this study, we labeled NOTA-conjugated E1 with 64Cu (64Cu-NOTA-E1) and evaluated biologic characteristics. The uptake of 64Cu-NOTA-E1 in PC3 cells (a human prostate cancer cell line) with high expression of hEphA2 increased in a time-dependent manner. In PC3 xenograft mice, 64Cu-NOTA-E1 injected via the tail vein allowed visualization of tumors on positron emission tomography after 1 h and the highest uptake measured at 24 h post-injection. By contrast, the radioactivity of other tissues either did not increase or decreased over 24 h. This indicates that 64Cu-NOTA-E1 has high tumor uptake and retention, with rapid clearance, and low background values in other tissues. Therefore, 64Cu-NOTA-E1 should be suitable as a novel PET imaging agent for hEphA2-expressing tumors.
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Affiliation(s)
- Ayoung Pyo
- Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea
| | - Sung-Hwan You
- Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea
| | - Hyeon Sik Kim
- Medical Photonics Research Center, Korea Photonics Technology Institute, Gwangju, Republic of Korea
| | - Jung Young Kim
- Division of RI-Convergence Research, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Jung-Joon Min
- Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea
| | - Dong-Yeon Kim
- Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea.
| | - Yeongjin Hong
- Department of Microbiology, Chonnam National University Medical School, Hwasun, Republic of Korea.
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29
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Yehl K, Lemire S, Yang AC, Ando H, Mimee M, Torres MDT, de la Fuente-Nunez C, Lu TK. Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phage Tail Fiber Mutagenesis. Cell 2020; 179:459-469.e9. [PMID: 31585083 DOI: 10.1016/j.cell.2019.09.015] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 06/24/2019] [Accepted: 09/10/2019] [Indexed: 01/21/2023]
Abstract
The rapid emergence of antibiotic-resistant infections is prompting increased interest in phage-based antimicrobials. However, acquisition of resistance by bacteria is a major issue in the successful development of phage therapies. Through natural evolution and structural modeling, we identified host-range-determining regions (HRDRs) in the T3 phage tail fiber protein and developed a high-throughput strategy to genetically engineer these regions through site-directed mutagenesis. Inspired by antibody specificity engineering, this approach generates deep functional diversity while minimizing disruptions to the overall tail fiber structure, resulting in synthetic "phagebodies." We showed that mutating HRDRs yields phagebodies with altered host-ranges, and select phagebodies enable long-term suppression of bacterial growth in vitro, by preventing resistance appearance, and are functional in vivo using a murine model. We anticipate that this approach may facilitate the creation of next-generation antimicrobials that slow resistance development and could be extended to other viral scaffolds for a broad range of applications.
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Affiliation(s)
- Kevin Yehl
- Synthetic Biology Group, MIT Synthetic Biology Center, The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA
| | - Sébastien Lemire
- Synthetic Biology Group, MIT Synthetic Biology Center, The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA
| | - Andrew C Yang
- Synthetic Biology Group, MIT Synthetic Biology Center, The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Hiroki Ando
- Synthetic Biology Group, MIT Synthetic Biology Center, The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA
| | - Mark Mimee
- Synthetic Biology Group, MIT Synthetic Biology Center, The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA
| | - Marcelo Der Torossian Torres
- Synthetic Biology Group, MIT Synthetic Biology Center, The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA
| | - Cesar de la Fuente-Nunez
- Synthetic Biology Group, MIT Synthetic Biology Center, The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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30
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Cnudde T, Lakhrif Z, Bourgoin J, Boursin F, Horiot C, Henriquet C, di Tommaso A, Juste MO, Jiacomini IG, Dimier-Poisson I, Pugnière M, Mévélec MN, Aubrey N. Exploration and Modulation of Antibody Fragment Biophysical Properties by Replacing the Framework Region Sequences. Antibodies (Basel) 2020; 9:E9. [PMID: 32326443 PMCID: PMC7344962 DOI: 10.3390/antib9020009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023] Open
Abstract
In order to increase the successful development of recombinant antibodies and fragments, it seems fundamental to enhance their expression and/or biophysical properties, such as the thermal, chemical, and pH stabilities. In this study, we employed a method bases on replacing the antibody framework region sequences, in order to promote more particularly single-chain Fragment variable (scFv) product quality. We provide evidence that mutations of the VH- C-C' loop might significantly improve the prokaryote production of well-folded and functional fragments with a production yield multiplied by 27 times. Additional mutations are accountable for an increase in the thermal (+19.6 °C) and chemical (+1.9 M) stabilities have also been identified. Furthermore, the hereby-produced fragments have shown to remain stable at a pH of 2.0, which avoids molecule functional and structural impairments during the purification process. Lastly, this study provides relevant information to the understanding of the relationship between the antibodies amino acid sequences and their respective biophysical properties.
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Affiliation(s)
- Thomas Cnudde
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
| | - Zineb Lakhrif
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
| | - Justine Bourgoin
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
| | - Fanny Boursin
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
| | - Catherine Horiot
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
| | - Corinne Henriquet
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM, U1194, Université Montpellier, ICM Institut Régional du Cancer, 34090 Montpellier, France
| | - Anne di Tommaso
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
| | | | - Isabella Gizzi Jiacomini
- Laboratório de Imunoquímica, Departamento de Patologia Básica, Universidade Federal do Paraná, Curitiba 81530, PR, Brazil
| | | | - Martine Pugnière
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM, U1194, Université Montpellier, ICM Institut Régional du Cancer, 34090 Montpellier, France
| | | | - Nicolas Aubrey
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
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31
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Mi P, Cabral H, Kataoka K. Ligand-Installed Nanocarriers toward Precision Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1902604. [PMID: 31353770 DOI: 10.1002/adma.201902604] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/04/2019] [Indexed: 05/20/2023]
Abstract
Development of drug-delivery systems that selectively target neoplastic cells has been a major goal of nanomedicine. One major strategy for achieving this milestone is to install ligands on the surface of nanocarriers to enhance delivery to target tissues, as well as to enhance internalization of nanocarriers by target cells, which improves accuracy, efficacy, and ultimately enhances patient outcomes. Herein, recent advances regarding the development of ligand-installed nanocarriers are introduced and the effect of their design on biological performance is discussed. Besides academic achievements, progress on ligand-installed nanocarriers in clinical trials is presented, along with the challenges faced by these formulations. Lastly, the future perspectives of ligand-installed nanocarriers are discussed, with particular emphasis on their potential for emerging precision therapies.
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Affiliation(s)
- Peng Mi
- Department of Radiology, Center for Medical Imaging, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, No.17 People's South Road, Chengdu, 610041, China
| | - Horacio Cabral
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kazunori Kataoka
- Innovation Center of Nanomedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
- Institute for Future Initiatives, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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32
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Makabe K. Molecular basis of flexible peptide recognition by an antibody. J Biochem 2020; 167:343-345. [PMID: 32027351 DOI: 10.1093/jb/mvaa017] [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: 01/15/2020] [Accepted: 01/19/2020] [Indexed: 11/12/2022] Open
Abstract
Antibodies can recognize various types of antigens with high specificity and affinity and peptide is one of their major targets. Understanding an antibody's molecular recognition mechanism for peptide is important for developing clones with a higher specificity and affinity. Here, the author reviews recent progresses in flexible peptide recognition by an antibody using several biophysical techniques, including X-ray crystallography, molecular dynamics simulations and calorimetric measurements. A set of two reports highlight the importance of intramolecular hydrogen bonds that form in an unbound flexible state. Such intramolecular hydrogen bonds restrict the fluctuation of the peptide and reduce the conformational entropy, resulting in the destabilization of the unbound state and increasing the binding affinity by increasing the free energy change. These detailed analyses will aid in the antibody design in the future.
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Affiliation(s)
- Koki Makabe
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
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33
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Busold S, Nagy NA, Tas SW, van Ree R, de Jong EC, Geijtenbeek TBH. Various Tastes of Sugar: The Potential of Glycosylation in Targeting and Modulating Human Immunity via C-Type Lectin Receptors. Front Immunol 2020; 11:134. [PMID: 32117281 PMCID: PMC7019010 DOI: 10.3389/fimmu.2020.00134] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/20/2020] [Indexed: 12/31/2022] Open
Abstract
C-type lectin receptors (CLRs) are important in several immune regulatory processes. These receptors recognize glycans expressed by host cells or by pathogens. Whereas pathogens are recognized through their glycans, which leads to protective immunity, aberrant cellular glycans are now increasingly recognized as disease-driving factors in cancer, auto-immunity, and allergy. The vast variety of glycan structures translates into a wide spectrum of effects on the immune system ranging from immune suppression to hyper-inflammatory responses. CLRs have distinct expression patterns on antigen presenting cells (APCs) controlling their role in immunity. CLRs can also be exploited to selectively target specific APCs, modulate immune responses and enhance antigen presentation. Here we will discuss the role of glycans and their receptors in immunity as well as potential strategies for immune modulation. A special focus will be given to different dendritic cell subsets as these APCs are crucial orchestrators of immune responses in infections, cancer, auto-immunity and allergies. Furthermore, we will highlight the potential use of nanoscale lipid bi-layer structures (liposomes) in targeted immunotherapy.
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Affiliation(s)
- Stefanie Busold
- Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Noémi A Nagy
- Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Sander W Tas
- Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands.,Department of Rheumatology and Clinical Immunology, Amsterdam University Medical Centers, Amsterdam Rheumatology and Immunology Center, University of Amsterdam, Amsterdam, Netherlands
| | - Ronald van Ree
- Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands.,Department of Otorhinolaryngology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Esther C de Jong
- Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
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Lu RM, Hwang YC, Liu IJ, Lee CC, Tsai HZ, Li HJ, Wu HC. Development of therapeutic antibodies for the treatment of diseases. J Biomed Sci 2020; 27:1. [PMID: 31894001 PMCID: PMC6939334 DOI: 10.1186/s12929-019-0592-z] [Citation(s) in RCA: 1046] [Impact Index Per Article: 261.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/18/2019] [Indexed: 12/13/2022] Open
Abstract
It has been more than three decades since the first monoclonal antibody was approved by the United States Food and Drug Administration (US FDA) in 1986, and during this time, antibody engineering has dramatically evolved. Current antibody drugs have increasingly fewer adverse effects due to their high specificity. As a result, therapeutic antibodies have become the predominant class of new drugs developed in recent years. Over the past five years, antibodies have become the best-selling drugs in the pharmaceutical market, and in 2018, eight of the top ten bestselling drugs worldwide were biologics. The global therapeutic monoclonal antibody market was valued at approximately US$115.2 billion in 2018 and is expected to generate revenue of $150 billion by the end of 2019 and $300 billion by 2025. Thus, the market for therapeutic antibody drugs has experienced explosive growth as new drugs have been approved for treating various human diseases, including many cancers, autoimmune, metabolic and infectious diseases. As of December 2019, 79 therapeutic mAbs have been approved by the US FDA, but there is still significant growth potential. This review summarizes the latest market trends and outlines the preeminent antibody engineering technologies used in the development of therapeutic antibody drugs, such as humanization of monoclonal antibodies, phage display, the human antibody mouse, single B cell antibody technology, and affinity maturation. Finally, future applications and perspectives are also discussed.
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Affiliation(s)
- Ruei-Min Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Yu-Chyi Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - I-Ju Liu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Chi-Chiu Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Han-Zen Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Hsin-Jung Li
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan. .,, 128 Academia Rd., Section 2, Nankang, Taipei, 11529, Taiwan.
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Lee JY, Dang K, Liu A, Alba BM. Automated buffer preparation using quaternary valve in fast performance liquid chromatography for protein purification from a cell membrane. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1136:121849. [PMID: 31841981 DOI: 10.1016/j.jchromb.2019.121849] [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: 04/21/2019] [Revised: 10/06/2019] [Indexed: 10/25/2022]
Abstract
There is a great need for high-throughput protein purification to produce protein molecules for research and therapeutics. Although there have been significant advancements made in automated multi-step chromatography and preparative in-process design-of-experiment (DOE) capabilities in commercial fast performance liquid chromatography (FPLC) instruments, almost all commercial FPLCs rely on a binary buffer mixing system, which hinders automated buffer preparation. Nevertheless, current-generation FPLCs are equipped with a quaternary mixer designed for limited in-line buffer preparation and preparative pH scouting DOE experiments. We decided to leverage the quaternary mixing capability by extending and re-programming AkTA Avant's quaternary valve into an automated in-process buffer preparation system to simplify automated purification requiring complex washing steps. We accomplished this by using two extra inlet valves, a sample valve, and versatile valve to split inputs of the quaternary valve into software-selectable stock solutions of pH buffers, salts, eluents, and additives. We also devised a new flow scheme to perform automated two-step chromatography using only one versatile valve. This was accomplished by using only stock parts and software to facilitate reproduction. To demonstrate the versatility and capability of the system, we purified a transmembrane protein that requires a detergent to stay soluble and needs an in-column, high-salt washing step to achieve high purity.
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Affiliation(s)
- Jonas Y Lee
- Department of Therapeutic Discovery, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA 94080, United States; Current address: Janssen Research and Development, 3210 Merryfield Row, San Diego, CA 92121, United States
| | - Khue Dang
- Department of Therapeutic Discovery, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA 94080, United States
| | - Alan Liu
- Department of Therapeutic Discovery, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA 94080, United States
| | - Benjamin M Alba
- Department of Therapeutic Discovery, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA 94080, United States.
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Nguyen QT, Yang J, Byun JW, Pyo HM, Park MY, Ku BK, Nah J, Ryoo S, Wee SH, Choi KS, Poo H. Development of Monoclonal Antibody Specific to Foot-and-Mouth Disease Virus Type A for Serodiagnosis. Pathogens 2019; 8:pathogens8040301. [PMID: 31861046 PMCID: PMC6963590 DOI: 10.3390/pathogens8040301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 11/16/2022] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious and economically devastating disease affecting cloven-hoofed livestock worldwide. FMD virus (FMDV) type A is one of the most common causes of FMD outbreaks among the seven FMDV serotypes, and its serological diagnosis is therefore important to confirm FMDV type A infection and to determine FMD vaccine efficacy. Here, we generated monoclonal antibodies (mAbs) specific to FMDV type A via hybridoma systems using an inactivated FMDV type A (A22/Iraq/1964) and found 4 monoclones (#29, #106, #108, and #109) with high binding reactivity to FMDV type A among 594 primary clones. In particular, the #106 mAb had a higher binding reactivity to the inactivated FMDV type A than the other mAbs and a commercial mAb. Moreover, the #106 mAb showed no cross-reactivity to inactivated FMDV type South African territories 1, 2, and 3, and low reactivity to inactivated FMDV type O (O1 Manisa). Importantly, the solid-phase competitive ELISA (SPCE) using horseradish peroxidase (HRP)-conjugated #106 mAb detected FMDV type A-specific Abs in sera from FMD type A-vaccinated cattle more effectively than a commercial SPCE. These results suggest that the newly developed FMDV type A-specific mAb might be useful for diagnostic approaches for detecting Abs against FMDV type A.
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Affiliation(s)
- Quyen Thi Nguyen
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (Q.T.N.); (J.Y.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Korea
| | - Jihyun Yang
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (Q.T.N.); (J.Y.)
| | - Jae-Won Byun
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Gyongsangbuk-do 39660, Korea; (J.-W.B.); (H.M.P.); (M.-Y.P.); (B.K.K.); (J.N.); (S.R.); (S.-H.W.); (K.-S.C.)
| | - Hyun Mi Pyo
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Gyongsangbuk-do 39660, Korea; (J.-W.B.); (H.M.P.); (M.-Y.P.); (B.K.K.); (J.N.); (S.R.); (S.-H.W.); (K.-S.C.)
| | - Mi-Young Park
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Gyongsangbuk-do 39660, Korea; (J.-W.B.); (H.M.P.); (M.-Y.P.); (B.K.K.); (J.N.); (S.R.); (S.-H.W.); (K.-S.C.)
| | - Bok Kyung Ku
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Gyongsangbuk-do 39660, Korea; (J.-W.B.); (H.M.P.); (M.-Y.P.); (B.K.K.); (J.N.); (S.R.); (S.-H.W.); (K.-S.C.)
| | - Jinju Nah
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Gyongsangbuk-do 39660, Korea; (J.-W.B.); (H.M.P.); (M.-Y.P.); (B.K.K.); (J.N.); (S.R.); (S.-H.W.); (K.-S.C.)
| | - Soyoon Ryoo
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Gyongsangbuk-do 39660, Korea; (J.-W.B.); (H.M.P.); (M.-Y.P.); (B.K.K.); (J.N.); (S.R.); (S.-H.W.); (K.-S.C.)
| | - Sung-Hwan Wee
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Gyongsangbuk-do 39660, Korea; (J.-W.B.); (H.M.P.); (M.-Y.P.); (B.K.K.); (J.N.); (S.R.); (S.-H.W.); (K.-S.C.)
| | - Kang-Seuk Choi
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Gyongsangbuk-do 39660, Korea; (J.-W.B.); (H.M.P.); (M.-Y.P.); (B.K.K.); (J.N.); (S.R.); (S.-H.W.); (K.-S.C.)
| | - Haryoung Poo
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (Q.T.N.); (J.Y.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Korea
- Correspondence: ; Tel.: +82-42-860-4157
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Wälchli R, Ressurreição M, Vogg S, Feidl F, Angelo J, Xu X, Ghose S, Jian Li Z, Le Saoût X, Souquet J, Broly H, Morbidelli M. Understanding mAb aggregation during low pH viral inactivation and subsequent neutralization. Biotechnol Bioeng 2019; 117:687-700. [PMID: 31784982 DOI: 10.1002/bit.27237] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/22/2019] [Accepted: 11/22/2019] [Indexed: 12/31/2022]
Abstract
Monoclonal antibodies (mAbs) and related recombinant proteins continue to gain importance in the treatment of a great variety of diseases. Despite significant advances, their manufacturing can still present challenges owing to their molecular complexity and stringent regulations with respect to product purity, stability, safety, and so forth. In this context, protein aggregates are of particular concern due to their immunogenic potential. During manufacturing, mAbs routinely undergo acidic treatment to inactivate viral contamination, which can lead to their aggregation and thereby to product loss. To better understand the underlying mechanism so as to propose strategies to mitigate the issue, we systematically investigated the denaturation and aggregation of two mAbs at low pH as well as after neutralization. We observed that at low pH and low ionic strength, mAb surface hydrophobicity increased whereas molecular size remained constant. After neutralization of acidic mAb solutions, the fraction of monomeric mAb started to decrease accompanied by an increase on average mAb size. This indicates that electrostatic repulsion prevents denatured mAb molecules from aggregation under acidic pH and low ionic strength, whereas neutralization reduces this repulsion and coagulation initiates. Limiting denaturation at low pH by d-sorbitol addition or temperature reduction effectively improved monomer recovery after neutralization. Our findings might be used to develop innovative viral inactivation procedures during mAb manufacturing that result in higher product yields.
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Affiliation(s)
- Ruben Wälchli
- Department of Chemistry and Applied Biosciences, ETH Zurich, Institute for Chemical and Bioengineering, Zurich, Switzerland
| | - Mariana Ressurreição
- Department of Chemistry and Applied Biosciences, ETH Zurich, Institute for Chemical and Bioengineering, Zurich, Switzerland
| | - Sebastian Vogg
- Department of Chemistry and Applied Biosciences, ETH Zurich, Institute for Chemical and Bioengineering, Zurich, Switzerland
| | - Fabian Feidl
- Department of Chemistry and Applied Biosciences, ETH Zurich, Institute for Chemical and Bioengineering, Zurich, Switzerland
| | - James Angelo
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Devens, Massachusetts
| | - Xuankuo Xu
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Devens, Massachusetts
| | - Sanchayita Ghose
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Devens, Massachusetts
| | - Zheng Jian Li
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Devens, Massachusetts
| | - Xavier Le Saoût
- Biotech Process Sciences, Merck KGaA, Corsier-sur-Vevey, Vaud, Switzerland
| | - Jonathan Souquet
- Biotech Process Sciences, Merck KGaA, Corsier-sur-Vevey, Vaud, Switzerland
| | - Hervé Broly
- Biotech Process Sciences, Merck KGaA, Corsier-sur-Vevey, Vaud, Switzerland
| | - Massimo Morbidelli
- Department of Chemistry and Applied Biosciences, ETH Zurich, Institute for Chemical and Bioengineering, Zurich, Switzerland
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Liu C, Kobashigawa Y, Yamauchi S, Toyota Y, Teramoto M, Ikeguchi Y, Fukuda N, Sato T, Sato Y, Kimura H, Morioka H. Preparation of single-chain Fv antibodies in the cytoplasm of Escherichia coli by simplified and systematic chaperone optimization. J Biochem 2019; 166:455-462. [DOI: 10.1093/jb/mvz059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/13/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
A single-chain variable fragment (scFv) antibody is a recombinant protein in which a peptide linker connects the variable regions of the heavy chain and light chain. Due to its smaller molecular size, an scFv can be expressed using Escherichia coli. The presence of two disulphide bonds in the molecule often prevents expression of correctly folded scFv in the E. coli cytoplasm, making a refolding process necessary to regenerate scFv activity. The refolding process is time-consuming and requires large amounts of expensive reagents, such as guanidine hydrochloride, l-arginine and glutathione. Here, to conveniently obtain scFv proteins, we devised a simple and systematic method to optimize the co-expression of chaperone proteins and to combine them with specially engineered E. coli strains that permit the formation of stable disulphide bonds within the cytoplasm. Several scFv proteins were successfully obtained in a soluble form from E. coli cytoplasm. Thermal denaturation experiments and/or surface plasmon resonance measurements revealed that the thus-obtained scFvs possessed a stable tertiary structure and antigen-binding activity. The combined use of engineered E. coli with the simplified and systematic chaperone optimization can be useful for the production of scFv proteins.
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Affiliation(s)
- Chenjiang Liu
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yoshihiro Kobashigawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Soichiro Yamauchi
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yuya Toyota
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Manaka Teramoto
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yuka Ikeguchi
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Natsuki Fukuda
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Takashi Sato
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
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Cyclization of Single-Chain Fv Antibodies Markedly Suppressed Their Characteristic Aggregation Mediated by Inter-Chain VH-VL Interactions. Molecules 2019; 24:molecules24142620. [PMID: 31323851 PMCID: PMC6681014 DOI: 10.3390/molecules24142620] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 01/08/2023] Open
Abstract
Single-chain Fv (scFv) antibodies are recombinant proteins in which the variable regions of the heavy chain (VH) and light chain (VL) are connected by a short flexible polypeptide linker. ScFvs have the advantages of easy genetic manipulation and low-cost production using Escherichia coli compared with monoclonal antibodies, and are thus expected to be utilized as next-generation medical antibodies. However, the practical use of scFvs has been limited due to low homogeneity caused by their aggregation propensity mediated by inter-chain VH-VL interactions. Because the interactions between the VH and VL domains of antibodies are generally weak, individual scFvs are assumed to be in equilibrium between a closed state and an open state, in which the VH and VL domains are assembled and disassembled, respectively. This dynamic feature of scFvs triggers the formation of dimer, trimer, and larger aggregates caused by the inter-chain VH-VL interactions. To overcome this problem, the N-terminus and C-terminus were herein connected by sortase A-mediated ligation to produce a cyclic scFv. Open-closed dynamics and aggregation were markedly suppressed in the cyclic scFv, as judged from dynamic light scattering and high-speed atomic force microscopy analyses. Surface plasmon resonance and differential scanning fluorometry analysis revealed that neither the affinity for antigen nor the thermal stability was disrupted by the scFv cyclization. Generality was confirmed by applying the present method to several scFv proteins. Based on these results, cyclic scFvs are expected to be widely utilized in industrial and therapeutic applications.
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Lim CC, Choong YS, Lim TS. Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation. Int J Mol Sci 2019; 20:E1861. [PMID: 30991723 PMCID: PMC6515083 DOI: 10.3390/ijms20081861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
Antibodies leverage on their unique architecture to bind with an array of antigens. The strength of interaction has a direct relation to the affinity of the antibodies towards the antigen. In vivo affinity maturation is performed through multiple rounds of somatic hypermutation and selection in the germinal centre. This unique process involves intricate sequence rearrangements at the gene level via molecular mechanisms. The emergence of in vitro display technologies, mainly phage display and recombinant DNA technology, has helped revolutionize the way antibody improvements are being carried out in the laboratory. The adaptation of molecular approaches in vitro to replicate the in vivo processes has allowed for improvements in the way recombinant antibodies are designed and tuned. Combinatorial libraries, consisting of a myriad of possible antibodies, are capable of replicating the diversity of the natural human antibody repertoire. The isolation of target-specific antibodies with specific affinity characteristics can also be accomplished through modification of stringent protocols. Despite the ability to screen and select for high-affinity binders, some 'fine tuning' may be required to enhance antibody binding in terms of its affinity. This review will provide a brief account of phage display technology used for antibody generation followed by a summary of different combinatorial library characteristics. The review will focus on available strategies, which include molecular approaches, next generation sequencing, and in silico approaches used for antibody affinity maturation in both therapeutic and diagnostic applications.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
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Kuramochi T, Igawa T, Tsunoda H, Hattori K. Humanization and Simultaneous Optimization of Monoclonal Antibody. Methods Mol Biol 2019; 1904:213-230. [PMID: 30539472 DOI: 10.1007/978-1-4939-8958-4_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Antibody humanization is an essential technology for reducing the potential risk of immunogenicity associated with animal-derived antibodies and has been applied to a majority of the therapeutic antibodies on the market. For developing an antibody molecule as a pharmaceutical at the current biotechnology level, however, other properties also have to be considered in parallel with humanization in antibody generation and optimization. This section describes the critical properties of therapeutic antibodies that should be sufficiently qualified, including immunogenicity, binding affinity, physicochemical stability, expression in host cells and pharmacokinetics, and the basic methodologies of antibody engineering involved. By simultaneously optimizing the antibody molecule in light of these properties, it should prove possible to shorten the research and development period necessary to identify a highly qualified clinical candidate and consequently accelerate the start of the clinical trial.
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Affiliation(s)
| | - Tomoyuki Igawa
- Chugai Pharmabody Research Pte. Ltd., Singapore, Singapore
| | - Hiroyuki Tsunoda
- Research Division, Chugai Pharmaceutical, Kamakura, Kanagawa, Japan
| | - Kunihiro Hattori
- Research Division, Chugai Pharmaceutical, Kamakura, Kanagawa, Japan
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Xu Y, Wang D, Mason B, Rossomando T, Li N, Liu D, Cheung JK, Xu W, Raghava S, Katiyar A, Nowak C, Xiang T, Dong DD, Sun J, Beck A, Liu H. Structure, heterogeneity and developability assessment of therapeutic antibodies. MAbs 2018; 11:239-264. [PMID: 30543482 DOI: 10.1080/19420862.2018.1553476] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Increasing attention has been paid to developability assessment with the understanding that thorough evaluation of monoclonal antibody lead candidates at an early stage can avoid delays during late-stage development. The concept of developability is based on the knowledge gained from the successful development of approximately 80 marketed antibody and Fc-fusion protein drug products and from the lessons learned from many failed development programs over the last three decades. Here, we reviewed antibody quality attributes that are critical to development and traditional and state-of-the-art analytical methods to monitor those attributes. Based on our collective experiences, a practical workflow is proposed as a best practice for developability assessment including in silico evaluation, extended characterization and forced degradation using appropriate analytical methods that allow characterization with limited material consumption and fast turnaround time.
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Affiliation(s)
- Yingda Xu
- a Protein Analytics , Adimab , Lebanon , NH , USA
| | - Dongdong Wang
- b Analytical Department , Bioanalytix, Inc ., Cambridge , MA , USA
| | - Bruce Mason
- c Product Characterization , Alexion Pharmaceuticals, Inc ., New Haven , CT , USA
| | - Tony Rossomando
- c Product Characterization , Alexion Pharmaceuticals, Inc ., New Haven , CT , USA
| | - Ning Li
- d Analytical Chemistry , Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Dingjiang Liu
- e Formulation Development , Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Jason K Cheung
- f Pharmaceutical Sciences , MRL, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Wei Xu
- g Analytical Method Development , MRL, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Smita Raghava
- h Sterile Formulation Sciences , MRL, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Amit Katiyar
- i Analytical Development , Bristol-Myers Squibb , Pennington , NJ , USA
| | - Christine Nowak
- c Product Characterization , Alexion Pharmaceuticals, Inc ., New Haven , CT , USA
| | - Tao Xiang
- j Manufacturing Sciences , Abbvie Bioresearch Center , Worcester , MA , USA
| | - Diane D Dong
- j Manufacturing Sciences , Abbvie Bioresearch Center , Worcester , MA , USA
| | - Joanne Sun
- k Product development , Innovent Biologics , Suzhou Industrial Park , China
| | - Alain Beck
- l Analytical chemistry , NBEs, Center d'immunologie Pierre Fabre , St Julien-en-Genevois Cedex , France
| | - Hongcheng Liu
- c Product Characterization , Alexion Pharmaceuticals, Inc ., New Haven , CT , USA
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43
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Hageman T, Wei H, Kuehne P, Fu J, Ludwig R, Tao L, Leone A, Zocher M, Das TK. Impact of Tryptophan Oxidation in Complementarity-Determining Regions of Two Monoclonal Antibodies on Structure-Function Characterized by Hydrogen-Deuterium Exchange Mass Spectrometry and Surface Plasmon Resonance. Pharm Res 2018; 36:24. [PMID: 30536043 PMCID: PMC6290686 DOI: 10.1007/s11095-018-2545-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/18/2018] [Indexed: 12/16/2022]
Abstract
Purpose Tryptophan’s (Trp) unique hydrophobic and structural properties make it an important antigen binding motif when positioned in complementarity-determining regions (CDRs) of monoclonal antibodies (mAbs). Oxidation of Trp residues within the CDR can deleteriously impact antigen binding, particularly if the CDR conformation is altered. The goal of this study was to evaluate the conformational and functional impact of Trp oxidation for two mAb subtypes, which is essential in determining the structure-function relationship and establishing appropriate analytical control strategies during protein therapeutics development. Methods Selective Trp oxidation was induced by 2,2′-Azobis(2-amidinopropane) dihydrochloride (AAPH) treatment in the presence of free methionine (Met). The native and chemically oxidized mAbs were characterized by hydrogen-deuterium exchange mass spectrometry (HDX-MS) for conformational changes and surface plasmon resonance (SPR) for antigen-antibody binding. Results Treatment of mAbs with AAPH selectively oxidized solvent accessible Trp residues. Oxidation of Trp within or in proximity of CDRs increased conformational flexibility in variable domains and disrupted antigen binding. Conclusions Trp oxidation in CDRs can adversely impact mAbs’ conformation and antigen binding. Trp oxidation should be carefully evaluated as part of critical quality attribute assessments. Oxidation susceptible Trp should be closely monitored during process development for mAbs to establish appropriate analytical control for manufacturing of drug substance and drug product. Electronic supplementary material The online version of this article (10.1007/s11095-018-2545-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tyler Hageman
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, KS, USA.,Biologics Development, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ, 08534, USA
| | - Hui Wei
- Biologics Development, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ, 08534, USA.
| | - Patrick Kuehne
- Biologics Development, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ, 08534, USA
| | - Jinmei Fu
- Biologics Development, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ, 08534, USA
| | - Richard Ludwig
- Biologics Development, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ, 08534, USA
| | - Li Tao
- Biologics Development, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ, 08534, USA
| | - Anthony Leone
- Biologics Development, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ, 08534, USA
| | - Marcel Zocher
- Biologics Development, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ, 08534, USA
| | - Tapan K Das
- Biologics Development, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ, 08534, USA
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44
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Yan X, Le XC, Zhang H. Antibody-Bridged Beacon for Homogeneous Detection of Small Molecules. Anal Chem 2018; 90:9667-9672. [DOI: 10.1021/acs.analchem.8b02510] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xiaowen Yan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - X. Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
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45
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Carter LM, Poty S, Sharma SK, Lewis JS. Preclinical optimization of antibody-based radiopharmaceuticals for cancer imaging and radionuclide therapy-Model, vector, and radionuclide selection. J Labelled Comp Radiopharm 2018; 61:611-635. [PMID: 29412489 PMCID: PMC6081268 DOI: 10.1002/jlcr.3612] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/19/2017] [Accepted: 01/16/2018] [Indexed: 12/25/2022]
Abstract
Intact antibodies and their truncated counterparts (eg, Fab, scFv fragments) are generally exquisitely specific and selective vectors, enabling recognition of individual cancer-associated molecular phenotypes against a complex and dynamic biomolecular background. Complementary alignment of these advantages with unique properties of radionuclides is a defining paradigm in both radioimmunoimaging and radioimmunotherapy, which remain some of the most adept and promising tools for cancer diagnosis and treatment. This review discusses how translational potency can be maximized through rational selection of antibody-nuclide couples for radioimmunoimaging/therapy in preclinical models.
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Affiliation(s)
- Lukas M Carter
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sophie Poty
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sai Kiran Sharma
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jason S Lewis
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Departments of Radiology and Pharmacology, Weill Cornell Medical College, New York, New York, USA
- Radiochemistry and Molecular Imaging Probes Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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46
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Qian Y, Chen Z, Huang X, Wang X, Xu X, Kirov S, Ludwig R, Qian NX, Ravi K, Tao L, Borys MC, Li ZJ. Early identification of unusually clustered mutations and root causes in therapeutic antibody development. Biotechnol Bioeng 2018; 115:2377-2382. [PMID: 29777592 DOI: 10.1002/bit.26728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 04/29/2018] [Accepted: 05/17/2018] [Indexed: 11/08/2022]
Abstract
This study reports findings of an unusual cluster of mutations spanning 22 bp (base pairs) in a monoclonal antibody expression vector. It was identified by two orthogonal methods: mass spectrometry on expressed protein and next-generation sequencing (NGS) on the plasmid DNA. While the initial NGS analysis confirmed the designed sequence modification, intact mass analysis detected an additional mass of the antibody molecule expressed in CHO cells. The extra mass was eventually found to be associated with unmatched nucleotides in a distal region by checking full-length sequence alignment plots. Interestingly, the complementary sequence of the mutated sequence was a reverse sequence of the original sequence and flanked by two 10-bp reverse-complementary sequences, leading to an undesirable DNA recombination. The finding highlights the necessity of rigorous examination of expression vector design and early monitoring of molecule integrity at both DNA and protein levels to prevent clones from having sequence variants during cell line development.
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Affiliation(s)
- Yueming Qian
- Product Development, Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, Massachusetts
| | - Zhiqiang Chen
- Product Development, Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, Massachusetts
| | - Xin Huang
- Research and Development, Bristol-Myers Squibb Company, Pennington, New Jersey
| | - Xuning Wang
- Research and Development, Bristol-Myers Squibb Company, Pennington, New Jersey
| | - Xuankuo Xu
- Product Development, Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, Massachusetts
| | - Stefan Kirov
- Research and Development, Bristol-Myers Squibb Company, Pennington, New Jersey
| | - Richard Ludwig
- Product Development, Global Product Development and Supply, Bristol-Myers Squibb Company, Pennington, New Jersey
| | - Nan-Xin Qian
- Product Development, Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, Massachusetts
| | - Kandasamy Ravi
- Research and Development, Bristol-Myers Squibb Company, Pennington, New Jersey
| | - Li Tao
- Product Development, Global Product Development and Supply, Bristol-Myers Squibb Company, Pennington, New Jersey
| | - Michael C Borys
- Product Development, Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, Massachusetts
| | - Zheng Jian Li
- Product Development, Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, Massachusetts
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47
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Abstract
During the development of monoclonal antibodies (mAbs) and other therapeutic proteins, immunogenicity, in particular the induction of anti-drug antibodies (ADAs), is an important concern, and thus immunogenicity assessment is a requirement for their approval. Establishment of appropriate methods for detecting and characterizing ADAs is necessary for immunogenicity assessment, but the lack of commonly available reference standards makes it difficult to compare and evaluate the methods. It is also difficult to compare the data with those obtained by other methods or facilities without reference standards. Here, we developed a panel of ADAs against anti-CD20 rituximab (Rituxan®, MabThera®); the panel consisted of eight clones of recombinant human-rat chimeric mAbs that target rituximab. The anti-rituximab mAbs showed different binding properties (specificity, epitope and affinity), and different neutralization potencies for CD20 binding, complement-dependent cytotoxicity and antibody-dependent cell-mediated cytotoxicity. The molecular size of the immune complex consisting of rituximab and the anti-rituximab mAb differed among the clones, and was well correlated with their level of Fcγ-receptor activation. These results suggest that the ADAs chosen for the newly developed panel are suitable surrogates for human ADAs, which exhibit different potential to affect the efficacy and safety of rituximab. Next, we used this panel to compare several ADA-detecting assays and revealed that the assays had different abilities to detect the ADAs with different binding characteristics. We conclude that our panel of ADAs against rituximab will be useful for the future development and characterization of assays for immunogenicity assessment.
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Affiliation(s)
- Minoru Tada
- a Division of Biological Chemistry and Biologicals , National Institute of Health Sciences , Kawasaki, Kanagawa , Japan
| | - Takuo Suzuki
- a Division of Biological Chemistry and Biologicals , National Institute of Health Sciences , Kawasaki, Kanagawa , Japan
| | - Akiko Ishii-Watabe
- a Division of Biological Chemistry and Biologicals , National Institute of Health Sciences , Kawasaki, Kanagawa , Japan
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48
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Chang HJ, Mayonove P, Zavala A, De Visch A, Minard P, Cohen-Gonsaud M, Bonnet J. A Modular Receptor Platform To Expand the Sensing Repertoire of Bacteria. ACS Synth Biol 2018; 7:166-175. [PMID: 28946740 PMCID: PMC5880506 DOI: 10.1021/acssynbio.7b00266] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Engineered
bacteria promise to revolutionize diagnostics and therapeutics,
yet many applications are precluded by the limited number of detectable
signals. Here we present a general framework to engineer synthetic
receptors enabling bacterial cells to respond to novel ligands. These
receptors are activated via ligand-induced dimerization
of a single-domain antibody fused to monomeric DNA-binding domains
(split-DBDs). Using E. coli as a model system,
we engineer both transmembrane and cytosolic receptors using a VHH
for ligand detection and demonstrate the scalability of our platform
by using the DBDs of two different transcriptional regulators. We
provide a method to optimize receptor behavior by finely tuning protein
expression levels and optimizing interdomain linker regions. Finally,
we show that these receptors can be connected to downstream synthetic
gene circuits for further signal processing. The general nature of
the split-DBD principle and the versatility of antibody-based detection
should support the deployment of these receptors into various hosts
to detect ligands for which no receptor is found in nature.
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Affiliation(s)
- Hung-Ju Chang
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Pauline Mayonove
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Agustin Zavala
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Angelique De Visch
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Philippe Minard
- Institute
for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Martin Cohen-Gonsaud
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Jerome Bonnet
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
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49
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Leong SW, Lim TS, Ismail A, Choong YS. Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC protein. J Mol Recognit 2017; 31:e2695. [PMID: 29230887 DOI: 10.1002/jmr.2695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/13/2017] [Accepted: 11/19/2017] [Indexed: 01/10/2023]
Abstract
With the development of de novo binders for protein targets from non-related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single-chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking "disembodied" amino acid residues against TolC surface. Next, scFv scaffolds were selected from Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural protein-antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of antigen-based detection agents for typhoid diagnostics.
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Affiliation(s)
- Siew Wen Leong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Asma Ismail
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Penang, Malaysia
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50
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Expression and characterization of a recombinant porcinized antibody against the E2 protein of classical swine fever virus. Appl Microbiol Biotechnol 2017; 102:961-970. [DOI: 10.1007/s00253-017-8647-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/13/2017] [Accepted: 11/13/2017] [Indexed: 10/18/2022]
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