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Seo Y, Zhou A, Nguyen TH, Wei N. Yeast Surface-Displayed Quenchbody as a Novel Whole-Cell Biosensor for One-Step Detection of Influenza A (H1N1) Virus. ACS Synth Biol 2024; 13:2926-2937. [PMID: 39256183 DOI: 10.1021/acssynbio.4c00317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Timely surveillance of airborne pathogens is essential to preventing the spread of infectious diseases and safeguard human health. Methods for sensitive, efficient, and cost-effective detection of airborne viruses are needed. With advances in synthetic biology, whole-cell biosensors have emerged as promising platforms for environmental monitoring and medical diagnostics. However, the current design paradigm of whole-cell biosensors is mostly based on intracellular detection of analytes that can transport across the cell membrane, which presents a critical challenge for viral pathogens and large biomolecules. To address this challenge, we developed a new type of whole-cell biosensor by expressing and displaying VHH-based quenchbody (Q-body) on the surface of the yeast Saccharomyces cerevisiae for simple one-step detection of influenza A (H1N1) virus. Seventeen VHH antibody fragments targeting the hemagglutinin protein H1N1-HA were displayed on the yeast cells and screened for the H1N1-HA binding affinity. The functionally displayed VHHs were selected to create surface-displayed Q-body biosensors. The surface-displayed Q-body exhibiting the highest quenching and dequenching efficiency was identified. The biosensor quantitatively detected H1N1-HA in a range from 0.5 to 16 μg/mL, with a half-maximal concentration of 2.60 μg/mL. The biosensor exhibited high specificity for H1N1-HA over other hemagglutinin proteins from various influenza A virus subtypes. Moreover, the biosensor succeeded in detecting the H1N1 virus at concentrations from 2.4 × 104 to 1.5 × 107 PFU/mL. The results from this study demonstrated a new whole-cell biosensor design that circumvents the need for transport of analytes into biosensor cells, enabling efficient detection of the target virus particles.
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Affiliation(s)
- Yoonjoo Seo
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, Urbana, Illinois 61801, United States
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, Urbana, Illinois 61801, United States
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, Urbana, Illinois 61801, United States
| | - Na Wei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, Urbana, Illinois 61801, United States
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2
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Heidari MM, Shirazi EA, Cheraghi SF, Shahshahani R, Rahnama T, Khatami M. CDR grafting and site-directed mutagenesis approach for the generation and affinity maturation of Anti-CD20 nanobody. Mol Biol Rep 2024; 51:751. [PMID: 38874667 DOI: 10.1007/s11033-024-09684-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/29/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Recently, new and advanced techniques have been adopted to design and produce nanobodies, which are used in diagnostic and immunotherapy treatments. Traditionally, nanobodies are prepared from camelid immune libraries that require animal treatments. However, such approaches require large library sizes and complicated selection procedures. The current study has employed CDR grafting and site-directed mutagenesis techniques to create genetically engineered nanobodies against the tumor marker CD20 (anti-CD20 nanobodies) used in leukemia treatment. METHODS AND RESULTS In this study, we utilized the swapping method to graft CDRs from the VH Rituximab antibody to VHH CDRs. We aimed to enhance the binding affinity of the nanobodies by substituting the amino acids (Y101R-Y102R-Y107R) in the VHH-CDR3. To assess the binding capacity of the mutated nanobodies, we conducted an ELISA test. Moreover, through flow cytometry analysis, we compared the fluorescence intensity of the grafted CD20 and mutant nanobodies with that of the commercially available human anti-CD20 in Raji cells. The results showed a significant difference in the fluorescence intensity of the grafted nanobodies and mutant nanobodies when compared to the commercially available human anti-CD20. CONCLUSION The approach we followed in this study makes it possible to create multiple anti-CD20 nanobodies with varying affinities without the need for extensive selection efforts. Additionally, our research has demonstrated that computational tools are highly reliable in designing functional nanobodies.
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Affiliation(s)
| | | | | | | | - Tina Rahnama
- Department of Biology, Yazd University, Yazd, Iran
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3
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Ben Abderrazek R, Hamdi E, Piccirilli A, Dhaouadi S, Muyldermans S, Perilli M, Bouhaouala-Zahar B. Camel-Derived Nanobodies as Potent Inhibitors of New Delhi Metallo-β-Lactamase-1 Enzyme. Molecules 2024; 29:1431. [PMID: 38611711 PMCID: PMC11013165 DOI: 10.3390/molecules29071431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/14/2024] Open
Abstract
The injudicious usage of antibiotics during infections caused by Gram-negative bacteria leads to the emergence of β-lactamases. Among them, the NDM-1 enzyme poses a serious threat to human health. Developing new antibiotics or inhibiting β-lactamases might become essential to reduce and prevent bacterial infections. Nanobodies (Nbs), the smallest antigen-binding single-domain fragments derived from Camelidae heavy-chain-only antibodies, targeting enzymes, are innovative alternatives to develop effective inhibitors. The biopanning of an immune VHH library after phage display has helped to retrieve recombinant antibody fragments with high inhibitory activity against recombinant-NDM-1 enzyme. Nb02NDM-1, Nb12NDM-1, and Nb17NDM-1 behaved as uncompetitive inhibitors against NDM-1 with Ki values in the nM range. Remarkably, IC50 values of 25.0 nM and 8.5 nM were noted for Nb02NDM-1 and Nb17NDM-1, respectively. The promising inhibition of NDM-1 by Nbs highlights their potential application in combating particular Gram-negative infections.
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Affiliation(s)
- Rahma Ben Abderrazek
- Laboratoire des Biomolécules Venins et Applications Théranostiques, Institut Pasteur Tunis, 13 Place Pasteur, Tunisie Université Tunis El Manar, B.P N 93, Tunis 1068, Tunisia; (E.H.); (S.D.); (B.B.-Z.)
| | - Emna Hamdi
- Laboratoire des Biomolécules Venins et Applications Théranostiques, Institut Pasteur Tunis, 13 Place Pasteur, Tunisie Université Tunis El Manar, B.P N 93, Tunis 1068, Tunisia; (E.H.); (S.D.); (B.B.-Z.)
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell’Aquila, Via Veteoio Coppito, 67100 L’Aquila, Italy; (A.P.); (M.P.)
| | - Alessandra Piccirilli
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell’Aquila, Via Veteoio Coppito, 67100 L’Aquila, Italy; (A.P.); (M.P.)
| | - Sayda Dhaouadi
- Laboratoire des Biomolécules Venins et Applications Théranostiques, Institut Pasteur Tunis, 13 Place Pasteur, Tunisie Université Tunis El Manar, B.P N 93, Tunis 1068, Tunisia; (E.H.); (S.D.); (B.B.-Z.)
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleenlaan, 9, 1050 Brussels, Belgium;
| | - Mariagrazia Perilli
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell’Aquila, Via Veteoio Coppito, 67100 L’Aquila, Italy; (A.P.); (M.P.)
| | - Balkiss Bouhaouala-Zahar
- Laboratoire des Biomolécules Venins et Applications Théranostiques, Institut Pasteur Tunis, 13 Place Pasteur, Tunisie Université Tunis El Manar, B.P N 93, Tunis 1068, Tunisia; (E.H.); (S.D.); (B.B.-Z.)
- Faculté de Médecine de Tunis, Université Tunis El Manar, B.P N 93, Tunis 1068, Tunisia
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Martins C, Diharce J, Nadaradjane AA, de Brevern AG. Evaluation of the Potential Impact of In Silico Humanization on V HH Dynamics. Int J Mol Sci 2023; 24:14586. [PMID: 37834033 PMCID: PMC10572902 DOI: 10.3390/ijms241914586] [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: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
Camelids have the peculiarity of having classical antibodies composed of heavy and light chains as well as single-chain antibodies. They have lost their light chains and one heavy-chain domain. This evolutionary feature means that their terminal heavy-chain domain, VH, called VHH here, has no partner and forms an independent domain. The VHH is small and easy to express alone; it retains thermodynamic and interaction properties. Consequently, VHHs have garnered significant interest from both biotechnological and pharmaceutical perspectives. However, due to their origin in camelids, they cannot be used directly on humans. A humanization step is needed before a possible use. However, changes, even in the constant parts of the antibodies, can lead to a loss of quality. A dedicated tool, Llamanade, has recently been made available to the scientific community. In a previous paper, we already showed the different types of VHH dynamics. Here, we have selected a representative VHH and tested two humanization hypotheses to accurately assess the potential impact of these changes. This example shows that despite the non-negligible change (1/10th of residues) brought about by humanization, the effect is not drastic, and the humanized VHH retains conformational properties quite similar to those of the camelid VHH.
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Affiliation(s)
- Carla Martins
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
| | - Aravindan Arun Nadaradjane
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
| | - Alexandre G. de Brevern
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
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Li J, Kang G, Wang J, Yuan H, Wu Y, Meng S, Wang P, Zhang M, Wang Y, Feng Y, Huang H, de Marco A. Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization. Int J Biol Macromol 2023; 247:125733. [PMID: 37423452 DOI: 10.1016/j.ijbiomac.2023.125733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Routinely screened antibody fragments usually require further in vitro maturation to achieve the desired biophysical properties. Blind in vitro strategies can produce improved ligands by introducing random mutations into the original sequences and selecting the resulting clones under more and more stringent conditions. Rational approaches exploit an alternative perspective that aims first at identifying the specific residues potentially involved in the control of biophysical mechanisms, such as affinity or stability, and then to evaluate what mutations could improve those characteristics. The understanding of the antigen-antibody interactions is instrumental to develop this process the reliability of which, consequently, strongly depends on the quality and completeness of the structural information. Recently, methods based on deep learning approaches critically improved the speed and accuracy of model building and are promising tools for accelerating the docking step. Here, we review the features of the available bioinformatic instruments and analyze the reports illustrating the result obtained with their application to optimize antibody fragments, and nanobodies in particular. Finally, the emerging trends and open questions are summarized.
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Affiliation(s)
- Jiaqi Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Guangbo Kang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jiewen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Haibin Yuan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yili Wu
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and the Affiliated Kangning Hospital, Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Wenzhou Medical University, Oujiang Laboratory, Wenzhou, Zhejiang 325035, China
| | - Shuxian Meng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Ping Wang
- New Technology R&D Department, Tianjin Modern Innovative TCM Technology Company Limited, Tianjin 300392, China
| | - Miao Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; China Resources Biopharmaceutical Company Limited, Beijing 100029, China
| | - Yuli Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Tianjin Pharmaceutical Da Ren Tang Group Corporation Limited, Traditional Chinese Pharmacy Research Institute, Tianjin Key Laboratory of Quality Control in Chinese Medicine, Tianjin 300457, China; State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China
| | - Yuanhang Feng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - He Huang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia.
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Lee YC, Lai GH, Lin TY, Tseng TS, Tsai TH, Chen WC, Lee CC, Tsai KC. Development of anti-aflatoxin B1 nanobodies from a novel mutagenesis-derived synthetic library for traditional Chinese medicine and foods safety testing. J Biol Eng 2023; 17:30. [PMID: 37095503 PMCID: PMC10127376 DOI: 10.1186/s13036-023-00350-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/17/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND The main commercially available methods for detecting small molecules of mycotoxins in traditional Chinese medicine (TCM) and functional foods are enzyme-linked immunosorbent assay and mass spectrometry. Regarding the development of diagnostic antibody reagents, effective methods for the rapid preparation of specific monoclonal antibodies are inadequate. METHODS In this study, a novel synthetic phage-displayed nanobody Golden Glove (SynaGG) library with a glove-like cavity configuration was established using phage display technology in synthetic biology. We applied this unique SynaGG library on the small molecule aflatoxin B1 (AFB1), which has strong hepatotoxicity, to isolate specific nanobodies with high affinity for AFB1. RESULT These nanobodies exhibit no cross-reactivity with the hapten methotrexate, which is recognized by the original antibody template. By binding to AFB1, two nanobodies can neutralize AFB1-induced hepatocyte growth inhibition. Using molecular docking, we found that the unique non-hypervariable complementarity-determining region 4 (CDR4) loop region of the nanobody was involved in the interaction with AFB1. Specifically, the CDR4's positively charged amino acid arginine directed the binding interaction between the nanobody and AFB1. We then rationally optimized the interaction between AFB1 and the nanobody by mutating serine at position 2 into valine. The binding affinity of the nanobody to AFB1 was effectively improved, and this result supported the use of molecular structure simulation for antibody optimization. CONCLUSION In summary, this study revealed that the novel SynaGG library, which was constructed through computer-aided design, can be used to isolate nanobodies that specifically bind to small molecules. The results of this study could facilitate the development of nanobody materials to detect small molecules for the rapid screening of TCM materials and foods in the future.
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Affiliation(s)
- Yu-Ching Lee
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Gar-Hwa Lai
- Department of Orthopedics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Tsai-Yu Lin
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Tsung-Hsun Tsai
- Department of Psychiatry, Kaohsiung Armed Forces General Hospital, Kaohsiung, Taiwan
| | - Wang-Chuan Chen
- The School of Chinese Medicine for Post Baccalaureate, I-Shou University, Kaohsiung, Taiwan
- Department of Chinese Medicine, E-Da Hospital, Kaohsiung, Taiwan
| | - Cheng-Chung Lee
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Keng-Chang Tsai
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, No. 155-1, Sec. 2, Linong St., Beitou District, Taipei, 11221, Taiwan.
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General Trends of the Camelidae Antibody V HHs Domain Dynamics. Int J Mol Sci 2023; 24:ijms24054511. [PMID: 36901942 PMCID: PMC10003728 DOI: 10.3390/ijms24054511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Conformational flexibility plays an essential role in antibodies' functional and structural stability. They facilitate and determine the strength of antigen-antibody interactions. Camelidae express an interesting subtype of single-chain antibody, named Heavy Chain only Antibody. They have only one N-terminal Variable domain (VHH) per chain, composed of Frameworks (FRs) and Complementarity Determining regions (CDRs) like their VH and VL counterparts in IgG. Even when expressed independently, VHH domains display excellent solubility and (thermo)stability, which helps them to retain their impressive interaction capabilities. Sequence and structural features of VHH domains contributing to these abilities have already been studied compared to classical antibodies. To have the broadest view and understand the changes in dynamics of these macromolecules, large-scale molecular dynamics simulations for a large number of non-redundant VHH structures have been performed for the first time. This analysis reveals the most prevalent movements in these domains. It reveals the four main classes of VHHs dynamics. Diverse local changes were observed in CDRs with various intensities. Similarly, different types of constraints were observed in CDRs, while FRs close to CDRs were sometimes primarily impacted. This study sheds light on the changes in flexibility in different regions of VHH that may impact their in silico design.
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Nadaradjane AA, Diharce J, Rebehmed J, Cadet F, Gardebien F, Gelly JC, Etchebest C, de Brevern AG. Quality assessment of V HH models. J Biomol Struct Dyn 2023; 41:13287-13301. [PMID: 36752327 DOI: 10.1080/07391102.2023.2172613] [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: 10/13/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023]
Abstract
Heavy Chain Only Antibodies are specific to Camelid species. Despite the lack of the light chain variable domain, their heavy chain variable domain (VH) domain, named VHH or nanobody, has promising potential applications in research and therapeutic fields. The structural study of VHH is therefore of great interest. Unfortunately, considering the huge amount of sequences that might be produced, only about one thousand of VHH experimental structures are publicly available in the Protein Data Bank, implying that structural model prediction of VHH is a necessary alternative to obtaining 3D information besides its sequence. The present study aims to assess and compare the quality of predictions from different modelling methodologies. Established comparative & homology modelling approaches to recent Deep Learning-based modelling strategies were applied, i.e. Modeller using single or multiple structural templates, ModWeb, SwissModel (with two evaluation schema), RoseTTAfold, AlphaFold 2 and NanoNet. The prediction accuracy was evaluated using RMSD, TM-score, GDT-TS, GDT-HA and Protein Blocks distance metrics. Besides the global structure assessment, we performed specific analyses of Frameworks and CDRs structures. We observed that AlphaFold 2 and especially NanoNet performed better than the other evaluated softwares. Importantly, we performed molecular dynamics simulations of an experimental structure and a NanoNet predicted model of a VHH in order to compare the global structural flexibility and local conformations using Protein Blocks. Despite rather similar structures, substantial differences in dynamical properties were observed, which underlies the complexity of the task of model evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aravindan Arun Nadaradjane
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Joseph Rebehmed
- Department of Computer Science and Mathematics, Lebanese, American University, Beirut, Lebanon
| | - Frédéric Cadet
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
- Artificial Intelligence Department, PEACCEL, Paris, France
| | - Fabrice Gardebien
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
| | - Jean-Christophe Gelly
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Catherine Etchebest
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Alexandre G de Brevern
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
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9
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Abstract
The immune systems protect vertebrates from foreign molecules or antigens, and antibodies are important mediators of this system. The sequences and structural features of antibodies vary depending on species. Many of antibodies from vertebrates, including camelids, have both heavy and light chain variable domains, but camelids also have antibodies that lack the light chains. In antibodies that lack light chains, the C-terminal variable region is called the VHH domain. Antibodies recognize antigens through six complementarity-determining regions (CDRs). The third CDR of the heavy chain (CDR-H3) is at the center of the antigen-binding site and is diverse in terms of sequence and structure. Due to the importance of antibodies in basic science as well as in medical applications, there have been many studies of CDR-H3s of antibodies that possess both light and heavy chains. However, nature of CDR-H3s of single-domain VHH antibodies is less well studied. In this chapter, we describe current knowledge of sequence-structure-function correlations of single-domain VHH antibodies with emphasis on CDR-H3. Based on the 370 crystal structures in the Protein Data Bank, we also attempt structural classification of CDR-H3 in single-domain VHH antibodies and discuss lessons learned from the ever-increasing number of the structures.
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Affiliation(s)
- Daisuke Kuroda
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Kouhei Tsumoto
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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Wang M, Wei L, Xiang H, Ren B, Liu X, Jiang L, Yang N, Shi J. A megadiverse naïve library derived from numerous camelids for efficient and rapid development of VHH antibodies. Anal Biochem 2022; 657:114871. [PMID: 36108795 DOI: 10.1016/j.ab.2022.114871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 07/20/2022] [Accepted: 08/17/2022] [Indexed: 11/01/2022]
Abstract
The field of antibody development is under pressure to meet rising demands for speed, cost-effectiveness, efficacy, reliability, and large-scale production. It is costly and time-consuming to immunize animals and build a single-domain antibody (sdAb) library for each target. Using the variable domain (VHH) of heavy-chain only antibodies (HcAbs) derived from blood samples of 75 non-immunized camelid animals (51 alpacas, 13 llamas, 11 Bactrian camels), and spleens from two Bactrian camels, a naïve sdAb library with extensive megadiversity and reusability was constructed. The library was evaluated using next-generation DNA sequencing (NGS) and was found to contain hundreds of billions of unique clones. To confirm the availability of target-specific VHHs, a naive library was screened for a variety of targets. At least two VHH candidates were extracted for each target using a 20-day selection pipeline. Some binders had ultrahigh potencies, with binding affinities in the nanomolar range. This naïve library, in particular, offers the possibility of acquiring unique antibodies targeting antigens of interest with low feasible dissociation constant (kD) without the time, effort, and price associated in producing antibodies in animals via antigen injection. Overall, the study shows that the megadiverse naïve library provides a rapid, adaptable, and easy platform for antibody creation, emphasizing its therapeutic and diagnostic implications.
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Affiliation(s)
- Meiniang Wang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Likun Wei
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China; Biotechnology and Health Centre, City University of Hong Kong, Shenzhen Research Institute, Shenzhen, China
| | - Haitao Xiang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Bingzhao Ren
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiaopan Liu
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Lin Jiang
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Naibo Yang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; Complete Genomics, Inc., 2904 Orchard Parkway, San Jose, CA, 95134, USA.
| | - Jiahai Shi
- Synthetic Biology Translational Research Programmes, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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11
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Vishwakarma P, Vattekatte AM, Shinada N, Diharce J, Martins C, Cadet F, Gardebien F, Etchebest C, Nadaradjane AA, de Brevern AG. V HH Structural Modelling Approaches: A Critical Review. Int J Mol Sci 2022; 23:3721. [PMID: 35409081 PMCID: PMC8998791 DOI: 10.3390/ijms23073721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/20/2022] Open
Abstract
VHH, i.e., VH domains of camelid single-chain antibodies, are very promising therapeutic agents due to their significant physicochemical advantages compared to classical mammalian antibodies. The number of experimentally solved VHH structures has significantly improved recently, which is of great help, because it offers the ability to directly work on 3D structures to humanise or improve them. Unfortunately, most VHHs do not have 3D structures. Thus, it is essential to find alternative ways to get structural information. The methods of structure prediction from the primary amino acid sequence appear essential to bypass this limitation. This review presents the most extensive overview of structure prediction methods applied for the 3D modelling of a given VHH sequence (a total of 21). Besides the historical overview, it aims at showing how model software programs have been shaping the structural predictions of VHHs. A brief explanation of each methodology is supplied, and pertinent examples of their usage are provided. Finally, we present a structure prediction case study of a recently solved VHH structure. According to some recent studies and the present analysis, AlphaFold 2 and NanoNet appear to be the best tools to predict a structural model of VHH from its sequence.
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Affiliation(s)
- Poonam Vishwakarma
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-75015 Paris, France; (P.V.); (A.M.V.); (J.D.); (C.M.); (C.E.); (A.A.N.)
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-97715 Saint Denis Messag, France; (F.C.); (F.G.)
| | - Akhila Melarkode Vattekatte
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-75015 Paris, France; (P.V.); (A.M.V.); (J.D.); (C.M.); (C.E.); (A.A.N.)
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-97715 Saint Denis Messag, France; (F.C.); (F.G.)
| | | | - Julien Diharce
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-75015 Paris, France; (P.V.); (A.M.V.); (J.D.); (C.M.); (C.E.); (A.A.N.)
| | - Carla Martins
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-75015 Paris, France; (P.V.); (A.M.V.); (J.D.); (C.M.); (C.E.); (A.A.N.)
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-97715 Saint Denis Messag, France; (F.C.); (F.G.)
| | - Frédéric Cadet
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-97715 Saint Denis Messag, France; (F.C.); (F.G.)
- PEACCEL, Artificial Intelligence Department, Square Albin Cachot, F-75013 Paris, France
| | - Fabrice Gardebien
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-97715 Saint Denis Messag, France; (F.C.); (F.G.)
| | - Catherine Etchebest
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-75015 Paris, France; (P.V.); (A.M.V.); (J.D.); (C.M.); (C.E.); (A.A.N.)
| | - Aravindan Arun Nadaradjane
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-75015 Paris, France; (P.V.); (A.M.V.); (J.D.); (C.M.); (C.E.); (A.A.N.)
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-97715 Saint Denis Messag, France; (F.C.); (F.G.)
| | - Alexandre G. de Brevern
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-75015 Paris, France; (P.V.); (A.M.V.); (J.D.); (C.M.); (C.E.); (A.A.N.)
- INSERM UMR_S 1134, BIGR, DSIMB Team, Université de Paris and Université de la Réunion, F-97715 Saint Denis Messag, France; (F.C.); (F.G.)
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12
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Golcuk M, Hacisuleyman A, Erman B, Yildiz A, Gur M. Binding Mechanism of Neutralizing Nanobodies Targeting SARS-CoV-2 Spike Glycoprotein. J Chem Inf Model 2021; 61:5152-5160. [PMID: 34581563 PMCID: PMC8491549 DOI: 10.1021/acs.jcim.1c00695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Indexed: 12/25/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters human cells upon binding of its spike (S) glycoproteins to ACE2 receptors. Several nanobodies neutralize SARS-CoV-2 infection by binding to the receptor-binding domain (RBD) of the S protein, but how their binding antagonizes S-ACE2 interactions is not well understood. Here, we identified interactions between the RBD and nanobodies H11-H4, H11-D4, and Ty1 by performing all-atom molecular dynamics simulations. H11-H4 and H11-D4 can bind to RBD without overlapping with ACE2. H11-H4, and to a lesser extent H11-D4, binding dislocates ACE2 from its binding site due to electrostatic repulsion. In comparison, Ty1 overlaps with ACE2 on RBD and has a similar binding strength to ACE2. Mutations in the Alpha variant of SARS-CoV-2 had a minor effect in RBD binding strengths of ACE2 and nanobodies, but reduced the ability of H11-H4 and H11-D4 to dislocate ACE2 from RBD. In comparison, the Beta variant weakened the RBD binding strengths of H11-H4 and H11-D4, which were less effective to dislocate ACE2 binding. Unexpectedly, mutations in Beta strengthened Ty1 binding to RBD, suggesting that this nanobody may be more effective to neutralize the Beta variant of SARS-CoV-2.
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Affiliation(s)
- Mert Golcuk
- Department of Mechanical Engineering,
Istanbul Technical University (ITU), 34437 Istanbul,
Turkey
| | - Aysima Hacisuleyman
- Institute of Bioengineering, Swiss
Federal Institute of Technology (EPFL), 1015 Lausanne,
Switzerland
| | - Burak Erman
- Chemical and Biological Engineering Department,
Koc University, 34450 Istanbul,
Turkey
| | - Ahmet Yildiz
- Physics Department, University of
California, Berkeley, California 94720, United
States
- Department of Molecular and Cell Biology,
University of California, Berkeley, California 94720,
United States
| | - Mert Gur
- Department of Mechanical Engineering,
Istanbul Technical University (ITU), 34437 Istanbul,
Turkey
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13
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Dhaouadi S, Ben Abderrazek R, Loustau T, Abou-Faycal C, Ksouri A, Erne W, Murdamoothoo D, Mörgelin M, Kungl A, Jung A, Ledrappier S, Benlasfar Z, Bichet S, Chiquet-Ehrismann R, Hendaoui I, Orend G, Bouhaouala-Zahar B. Novel Human Tenascin-C Function-Blocking Camel Single Domain Nanobodies. Front Immunol 2021; 12:635166. [PMID: 33790905 PMCID: PMC8006918 DOI: 10.3389/fimmu.2021.635166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/19/2021] [Indexed: 01/05/2023] Open
Abstract
The extracellular matrix (ECM) molecule Tenascin-C (TNC) is well-known to promote tumor progression by multiple mechanisms. However, reliable TNC detection in tissues of tumor banks remains limited. Therefore, we generated dromedary single-domain nanobodies Nb3 and Nb4 highly specific for human TNC (hTNC) and characterized the interaction with TNC by several approaches including ELISA, western blot, isothermal fluorescence titration and negative electron microscopic imaging. Our results revealed binding of both nanobodies to distinct sequences within fibronectin type III repeats of hTNC. By immunofluroescence and immunohistochemical imaging we observed that both nanobodies detected TNC expression in PFA and paraffin embedded human tissue from ulcerative colitis, solid tumors and liver metastasis. As TNC impairs cell adhesion to fibronectin we determined whether the nanobodies abolished this TNC function. Indeed, Nb3 and Nb4 restored adhesion of tumor and mesangial cells on a fibronectin/TNC substratum. We recently showed that TNC orchestrates the immune-suppressive tumor microenvironment involving chemoretention, causing tethering of CD11c+ myeloid/dendritic cells in the stroma. Here, we document that immobilization of DC2.4 dendritic cells by a CCL21 adsorbed TNC substratum was blocked by both nanobodies. Altogether, our novel TNC specific nanobodies could offer valuable tools for detection of TNC in the clinical practice and may be useful to inhibit the immune-suppressive and other functions of TNC in cancer and other diseases.
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Affiliation(s)
- Sayda Dhaouadi
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Rahma Ben Abderrazek
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Thomas Loustau
- Université Strasbourg, INSERM U1109 – The Tumor Microenvironment group, Hôpital Civil, Institut d'Hématologie et d'Immunologie, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Chérine Abou-Faycal
- Université Strasbourg, INSERM U1109 – The Tumor Microenvironment group, Hôpital Civil, Institut d'Hématologie et d'Immunologie, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Ayoub Ksouri
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - William Erne
- Université Strasbourg, INSERM U1109 – The Tumor Microenvironment group, Hôpital Civil, Institut d'Hématologie et d'Immunologie, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Devadarssen Murdamoothoo
- Université Strasbourg, INSERM U1109 – The Tumor Microenvironment group, Hôpital Civil, Institut d'Hématologie et d'Immunologie, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | | | - Andreas Kungl
- Institute of Pharmaceutical Sciences, Karl Franzens University Graz, Graz, Austria
- Antagonis Biotherapeutics GmbH, Graz, Austria
| | - Alain Jung
- Tumor Bank Centre Paul Strauss, Strasbourg, France
| | | | - Zakaria Benlasfar
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Sandrine Bichet
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Ismaïl Hendaoui
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Gertraud Orend
- Université Strasbourg, INSERM U1109 – The Tumor Microenvironment group, Hôpital Civil, Institut d'Hématologie et d'Immunologie, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Balkiss Bouhaouala-Zahar
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
- Faculté de Médecine de Tunis, Université Tunis el Manar, Tunis, Tunisia
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14
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Melarkode Vattekatte A, Shinada NK, Narwani TJ, Noël F, Bertrand O, Meyniel JP, Malpertuy A, Gelly JC, Cadet F, de Brevern AG. Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction. PeerJ 2020; 8:e8408. [PMID: 32185102 PMCID: PMC7061911 DOI: 10.7717/peerj.8408] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/16/2019] [Indexed: 12/28/2022] Open
Abstract
Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only three CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with their other important features, e.g., easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationship. In this study, sequence characteristics of VHH domains have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHH domains showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.
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Affiliation(s)
- Akhila Melarkode Vattekatte
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Faculté des Sciences et Technologies, Saint Denis, La Réunion, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Nicolas Ken Shinada
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Discngine SAS, Paris, France
| | - Tarun J Narwani
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Floriane Noël
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,PSL Research University, INSERM, UMR 932, Institut Curie, Paris, France.,Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Olivier Bertrand
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France
| | | | | | - Jean-Christophe Gelly
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,IBL, Paris, France
| | - Frédéric Cadet
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Faculté des Sciences et Technologies, Saint Denis, La Réunion, France.,Peaccel, Protein Engineering Accelerator, Paris, France
| | - Alexandre G de Brevern
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Faculté des Sciences et Technologies, Saint Denis, La Réunion, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,IBL, Paris, France
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15
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Li Z, Zhang M, Zheng S, Song Y, Cheng X, Yu D, Du L, Ren L, Han H, Zhao Y. Genetic removal of the CH1 exon leads to the production of hypofunctional heavy chain-only IgG2a in rats. Transgenic Res 2020; 29:199-213. [PMID: 32078126 DOI: 10.1007/s11248-020-00189-9] [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: 11/26/2019] [Accepted: 01/04/2020] [Indexed: 12/01/2022]
Abstract
Despite great values in many applications, heavy chain-only antibodies (HcAbs) are naturally only produced in camelids and sharks, which are not easy to access and handle. Production of the type of antibodies in small laboratory animals would remarkably facilitate their applications. We previously reported a mouse line in which the CH1 exon of mouse γ1 was deleted that could express heavy chain-only IgG1 antibodies. However, these mice showed an extremely weak IgG1 response to specific antigens when immunized, and we could only achieve single VH domains with low affinity to antigens using these mice. One possibility is that the mouse germline VH repertoire was not sufficient to support the expression of functional heavy chain-only antibodies. In this study, we report the generation of a rat line in which the CH1 exon of the γ2a gene was removed and the γ1 and γ2b genes were silenced. Although the genetically modified rats expressed heavy chain-only IgG2a, they also exhibited a very weak IgG2a response to antigen immunization. Panning of a phage library constructed using IgG2a VH segments amplified from immunized rats identified antigen-specific single VH antibodies, which also exhibited much lower affinity than that of commercial mAbs. Together with our previous report, this study suggests that the simple genetic removal of the CH1 exon does not guarantee the successful expression of functional heavy chain-only antibodies.
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Affiliation(s)
- Zhenrong Li
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Ming Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Shunan Zheng
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yu Song
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xueqian Cheng
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Di Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lijuan Du
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Liming Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Haitang Han
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, People's Republic of China.
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, People's Republic of China.
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16
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Huang C, Li D, Ren J, Ji F, Jia L. Generation and Application of Fluorescent Anti-Human β2-Microglobulin VHHs via Amino Modification. Molecules 2019; 24:E2600. [PMID: 31319525 PMCID: PMC6680903 DOI: 10.3390/molecules24142600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/07/2019] [Accepted: 07/14/2019] [Indexed: 01/21/2023] Open
Abstract
The functionalization of VHHs enables their application in almost every aspect of biomedical inquiry. Amino modification remains a common strategy for protein functionalization, though is considered to be inferior to site-specific methods and cause protein property changes. In this paper, four anti-β2M VHHs were selected and modified on the amino group by NHS-Fluo. The impacts of amino modification on these VHHs were drastically different, and among all th examples, the modified NB-1 maintained the original stability, bioactivity and homogeneity of unmodified NB-1. Specific recognition of VHHs targeting β2M detected by fluorescence imaging explored the possible applications of VHHs. Via this study, we successfully functionalized the anti-β2M VHHs through amino modification and the results are able to instruct the simple and fast functionalization of VHHs in biomedical researches.
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Affiliation(s)
- Chundong Huang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China
| | - Da Li
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China.
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17
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Keller BM, Maier J, Secker KA, Egetemaier SM, Parfyonova Y, Rothbauer U, Traenkle B. Chromobodies to Quantify Changes of Endogenous Protein Concentration in Living Cells. Mol Cell Proteomics 2018; 17:2518-2533. [PMID: 30228193 DOI: 10.1074/mcp.tir118.000914] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/04/2018] [Indexed: 11/06/2022] Open
Abstract
Understanding cellular processes requires the determination of dynamic changes in the concentration of genetically nonmodified, endogenous proteins, which, to date, is commonly accomplished by end-point assays in vitro Molecular probes such as fluorescently labeled nanobodies (chromobodies, CBs) are powerful tools to visualize the dynamic subcellular localization of endogenous proteins in living cells. Here, we employed the dependence of intracellular levels of chromobodies on the amount of their endogenous antigens, a phenomenon, which we termed antigen-mediated CB stabilization (AMCBS), for simultaneous monitoring of time-resolved changes in the concentration and localization of native proteins. To improve the dynamic range of AMCBS we generated turnover-accelerated CBs and demonstrated their application in visualization and quantification of fast reversible changes in antigen concentration upon compound treatment by quantitative live-cell imaging. We expect that this broadly applicable strategy will enable unprecedented insights into the dynamic regulation of proteins, e.g. during cellular signaling, cell differentiation, or upon drug action.
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Affiliation(s)
| | - Julia Maier
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany
| | - Kathy-Ann Secker
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany
| | | | - Yana Parfyonova
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany; Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany.
| | - Bjoern Traenkle
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany.
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18
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A Novel Nanobody Targeting Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Receptor-Binding Domain Has Potent Cross-Neutralizing Activity and Protective Efficacy against MERS-CoV. J Virol 2018; 92:JVI.00837-18. [PMID: 29950421 PMCID: PMC6146697 DOI: 10.1128/jvi.00837-18] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/25/2018] [Indexed: 12/22/2022] Open
Abstract
Therapeutic development is critical for preventing and treating continual MERS-CoV infections in humans and camels. Because of their small size, nanobodies (Nbs) have advantages as antiviral therapeutics (e.g., high expression yield and robustness for storage and transportation) and also potential limitations (e.g., low antigen-binding affinity and fast renal clearance). Here, we have developed novel Nbs that specifically target the receptor-binding domain (RBD) of MERS-CoV spike protein. They bind to a conserved site on MERS-CoV RBD with high affinity, blocking RBD's binding to MERS-CoV receptor. Through engineering a C-terminal human Fc tag, the in vivo half-life of the Nbs is significantly extended. Moreover, the Nbs can potently cross-neutralize the infections of diverse MERS-CoV strains isolated from humans and camels. The Fc-tagged Nb also completely protects humanized mice from lethal MERS-CoV challenge. Taken together, our study has discovered novel Nbs that hold promise as potent, cost-effective, and broad-spectrum anti-MERS-CoV therapeutic agents. The newly emerged Middle East respiratory syndrome coronavirus (MERS-CoV) continues to infect humans and camels, calling for efficient, cost-effective, and broad-spectrum strategies to control its spread. Nanobodies (Nbs) are single-domain antibodies derived from camelids and sharks and are potentially cost-effective antivirals with small size and great expression yield. In this study, we developed a novel neutralizing Nb (NbMS10) and its human-Fc-fused version (NbMS10-Fc), both of which target the MERS-CoV spike protein receptor-binding domain (RBD). We further tested their receptor-binding affinity, recognizing epitopes, cross-neutralizing activity, half-life, and efficacy against MERS-CoV infection. Both Nbs can be expressed in yeasts with high yield, bind to MERS-CoV RBD with high affinity, and block the binding of MERS-CoV RBD to the MERS-CoV receptor. The binding site of the Nbs on the RBD was mapped to be around residue Asp539, which is part of a conserved conformational epitope at the receptor-binding interface. NbMS10 and NbMS10-Fc maintained strong cross-neutralizing activity against divergent MERS-CoV strains isolated from humans and camels. Particularly, NbMS10-Fc had significantly extended half-life in vivo; a single-dose treatment of NbMS10-Fc exhibited high prophylactic and therapeutic efficacy by completely protecting humanized mice from lethal MERS-CoV challenge. Overall, this study proves the feasibility of producing cost-effective, potent, and broad-spectrum Nbs against MERS-CoV and has produced Nbs with great potentials as anti-MERS-CoV therapeutics. IMPORTANCE Therapeutic development is critical for preventing and treating continual MERS-CoV infections in humans and camels. Because of their small size, nanobodies (Nbs) have advantages as antiviral therapeutics (e.g., high expression yield and robustness for storage and transportation) and also potential limitations (e.g., low antigen-binding affinity and fast renal clearance). Here, we have developed novel Nbs that specifically target the receptor-binding domain (RBD) of MERS-CoV spike protein. They bind to a conserved site on MERS-CoV RBD with high affinity, blocking RBD's binding to MERS-CoV receptor. Through engineering a C-terminal human Fc tag, the in vivo half-life of the Nbs is significantly extended. Moreover, the Nbs can potently cross-neutralize the infections of diverse MERS-CoV strains isolated from humans and camels. The Fc-tagged Nb also completely protects humanized mice from lethal MERS-CoV challenge. Taken together, our study has discovered novel Nbs that hold promise as potent, cost-effective, and broad-spectrum anti-MERS-CoV therapeutic agents.
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