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Fernández‐Quintero ML, Guarnera E, Musil D, Pekar L, Sellmann C, Freire F, Sousa RL, Santos SP, Freitas MC, Bandeiras TM, Silva MMS, Loeffler JR, Ward AB, Harwardt J, Zielonka S, Evers A. On the humanization of VHHs: Prospective case studies, experimental and computational characterization of structural determinants for functionality. Protein Sci 2024; 33:e5176. [PMID: 39422475 PMCID: PMC11487682 DOI: 10.1002/pro.5176] [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: 07/04/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 10/19/2024]
Abstract
The humanization of camelid-derived variable domain heavy chain antibodies (VHHs) poses challenges including immunogenicity, stability, and potential reduction of affinity. Critical to this process are complementarity-determining regions (CDRs), Vernier and Hallmark residues, shaping the three-dimensional fold and influencing VHH structure and function. Additionally, the presence of non-canonical disulfide bonds further contributes to conformational stability and antigen binding. In this study, we systematically humanized two camelid-derived VHHs targeting the natural cytotoxicity receptor NKp30. Key structural positions in Vernier and Hallmark regions were exchanged with residues from the most similar human germline sequences. The resulting variants were characterized for binding affinities, yield, and purity. Structural binding modes were elucidated through crystal structure determination and AlphaFold2 predictions, providing insights into differences in binding affinity. Comparative structural and molecular dynamics characterizations of selected variants were performed to rationalize their functional properties and elucidate the role of specific sequence motifs in antigen binding. Furthermore, systematic analyses of next-generation sequencing (NGS) and Protein Data Bank (PDB) data was conducted, shedding light on the functional significance of Hallmark motifs and non-canonical disulfide bonds in VHHs in general. Overall, this study provides valuable insights into the structural determinants governing the functional properties of VHHs, offering a roadmap for their rational design, humanization, and optimization for therapeutic applications.
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Affiliation(s)
- Monica L. Fernández‐Quintero
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Enrico Guarnera
- Antibody Discovery and Protein EngineeringMerck Healthcare KGaADarmstadtGermany
| | - Djordje Musil
- Structural Biology and BiophysicsMerck Healthcare KGaADarmstadtGermany
| | - Lukas Pekar
- Antibody Discovery and Protein EngineeringMerck Healthcare KGaADarmstadtGermany
| | - Carolin Sellmann
- Antibody Discovery and Protein EngineeringMerck Healthcare KGaADarmstadtGermany
| | - Filipe Freire
- iBET, Instituto de Biologia Experimental e TecnológicaOeirasPortugal
| | - Raquel L. Sousa
- iBET, Instituto de Biologia Experimental e TecnológicaOeirasPortugal
| | - Sandra P. Santos
- iBET, Instituto de Biologia Experimental e TecnológicaOeirasPortugal
| | - Micael C. Freitas
- iBET, Instituto de Biologia Experimental e TecnológicaOeirasPortugal
| | | | | | - Johannes R. Loeffler
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Julia Harwardt
- Antibody Discovery and Protein EngineeringMerck Healthcare KGaADarmstadtGermany
| | - Stefan Zielonka
- Antibody Discovery and Protein EngineeringMerck Healthcare KGaADarmstadtGermany
- Institute for Organic Chemistry and BiochemistryTechnical University of DarmstadtDarmstadtGermany
| | - Andreas Evers
- Antibody Discovery and Protein EngineeringMerck Healthcare KGaADarmstadtGermany
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2
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Hu Y, Huo L, Chen W, Shen J, Wang W. Resistance-based directed evolution of nanobodies for higher affinity in prokaryotes. Biochim Biophys Acta Gen Subj 2024; 1868:130710. [PMID: 39245149 DOI: 10.1016/j.bbagen.2024.130710] [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: 08/15/2024] [Revised: 08/30/2024] [Accepted: 09/03/2024] [Indexed: 09/10/2024]
Abstract
A prokaryotic resistance-based directed evolution system leveraging protein-fragment complementation assay (PCA) was devised, and its proficiency in detecting protein-protein interactions and discriminating varying degrees of binding affinity was demonstrated by two well-characterized protein pairs. Furthermore, we constructed a random mutant library based on the GBPR36K/E45K mutant, characterized by almost no affinity towards EGFP. This library was subjected to PCA-based prokaryotic directed evolution, resulting in the isolation of back-mutated variants. In summary, we have established an expedited, cost-effective, and structural information-independent PCA-based prokaryotic directed evolution platform for nanobody affinity maturation, featuring tunable screening stringency via modulation of antibiotic concentrations.
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Affiliation(s)
- Yue Hu
- Institute for Medical Biology & Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for Biotechnology of the State Ethnic Affairs Commission, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China
| | - Li Huo
- Institute for Medical Biology & Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for Biotechnology of the State Ethnic Affairs Commission, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China
| | - Weiwei Chen
- Institute for Medical Biology & Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for Biotechnology of the State Ethnic Affairs Commission, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China
| | - Jinhua Shen
- Institute for Medical Biology & Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for Biotechnology of the State Ethnic Affairs Commission, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China.
| | - Wenyi Wang
- Institute for Medical Biology & Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China & Key Laboratory for Biotechnology of the State Ethnic Affairs Commission, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei 430074, PR China.
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3
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Cheng G, Ding Q, Sun Y, Zhang Y, Zhang W, Li G. Electrochemiluminescence resonance energy transfer detection of HBsAg based on Co doped 3D porous luminol-based conjugates and quencher UiO-66-NH 2@Au. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124574. [PMID: 38838601 DOI: 10.1016/j.saa.2024.124574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
An electrochemiluminescence (ECL) biosensor based on ECL resonance energy transfer (ECL-RET) was designed to sensitively detect hepatitis B virus surface antigen (HBsAg). In this ECL-RET system, luminol was employed as ECL donor, and gold nanoparticles functionalized zirconium organoskeleton (UiO-66-NH2@Au) was prepared and served as ECL acceptor. The UiO-66-NH2@Au possessed an ultraviolet-visible (UV-vis) absorption between 400 nm and 500 nm, and the absorption spectra overlapped with the ECL spectrum of luminol. Furthermore, Graphene oxide-poly(aniline-luminol)-cobalt nanoparticles conjugates (GO-PALu-Co) was prepared to optimize the ECL behavior through the catalysis of Cobalt nanoparticles and served as a stable 3D porous film to load capture probe primary antibody (Ab1). Based on the ECL-RET biosensing method, the UiO-66-NH2@Au-labeled Ab2 and target HBsAg could pair with primary antibody Ab1 to form sandwich-type structure, and the ECL signal of GO-PALu-Co was quenched. Under optimized experimental conditions, the ECL-RET analytical method represented eminent analytical performance for HBsAg detection with a wide linear relationship from 2.2 × 10-13 to 2.2 × 10-5 mg/mL, and a detection limit of 9 × 10-14 mg/mL (S/N = 3), with spiked sample recoveries ranging from 97.27 % to 102.73 %. The constructed sensor has good stability, reproducibility, and specificity. It can be used to detect HBsAg in human serum and has the potential to be used for the sensitive detection of other disease biomarkers.
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Affiliation(s)
- Gaoxing Cheng
- Xinjiang Key Laboratory of Energy Storage and Photoelectrocatalytic Materials, School of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi, Xinjiang 830054, China
| | - Qiaoyu Ding
- Xinjiang Key Laboratory of Energy Storage and Photoelectrocatalytic Materials, School of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi, Xinjiang 830054, China
| | - Yue Sun
- Xinjiang Key Laboratory of Energy Storage and Photoelectrocatalytic Materials, School of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi, Xinjiang 830054, China
| | - Yanhui Zhang
- Xinjiang Key Laboratory of Energy Storage and Photoelectrocatalytic Materials, School of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi, Xinjiang 830054, China
| | - Wanwan Zhang
- Xinjiang Key Laboratory of Energy Storage and Photoelectrocatalytic Materials, School of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi, Xinjiang 830054, China
| | - Guixin Li
- Xinjiang Key Laboratory of Energy Storage and Photoelectrocatalytic Materials, School of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi, Xinjiang 830054, China.
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4
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Yu J, Kumar A, Zhang X, Martin C, Van Holsbeeck K, Raia P, Koehl A, Laeremans T, Steyaert J, Manglik A, Ballet S, Boland A, Stoeber M. Structural basis of μ-opioid receptor targeting by a nanobody antagonist. Nat Commun 2024; 15:8687. [PMID: 39384768 PMCID: PMC11464722 DOI: 10.1038/s41467-024-52947-6] [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: 12/16/2023] [Accepted: 09/24/2024] [Indexed: 10/11/2024] Open
Abstract
The μ-opioid receptor (μOR), a prototypical G protein-coupled receptor (GPCR), is the target of opioid analgesics such as morphine and fentanyl. Due to the severe side effects of current opioid drugs, there is considerable interest in developing novel modulators of μOR function. Most GPCR ligands today are small molecules, however biologics, including antibodies and nanobodies, represent alternative therapeutics with clear advantages such as affinity and target selectivity. Here, we describe the nanobody NbE, which selectively binds to the μOR and acts as an antagonist. We functionally characterize NbE as an extracellular and genetically encoded μOR ligand and uncover the molecular basis for μOR antagonism by determining the cryo-EM structure of the NbE-μOR complex. NbE displays a unique ligand binding mode and achieves μOR selectivity by interactions with the orthosteric pocket and extracellular receptor loops. Based on a β-hairpin loop formed by NbE that deeply protrudes into the μOR, we design linear and cyclic peptide analogs that recapitulate NbE's antagonism. The work illustrates the potential of nanobodies to uniquely engage with GPCRs and describes lower molecular weight μOR ligands that can serve as a basis for therapeutic developments.
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MESH Headings
- Receptors, Opioid, mu/metabolism
- Receptors, Opioid, mu/chemistry
- Receptors, Opioid, mu/antagonists & inhibitors
- Single-Domain Antibodies/chemistry
- Single-Domain Antibodies/metabolism
- Single-Domain Antibodies/pharmacology
- Humans
- Cryoelectron Microscopy
- Ligands
- HEK293 Cells
- Animals
- Protein Binding
- Binding Sites
- Models, Molecular
- Analgesics, Opioid/pharmacology
- Analgesics, Opioid/chemistry
- Analgesics, Opioid/metabolism
- Peptides, Cyclic/chemistry
- Peptides, Cyclic/metabolism
- Peptides, Cyclic/pharmacology
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Affiliation(s)
- Jun Yu
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Amit Kumar
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Xuefeng Zhang
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Charlotte Martin
- Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kevin Van Holsbeeck
- Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Pierre Raia
- Department of Plant Sciences, University of Geneva, Geneva, Switzerland
| | - Antoine Koehl
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | | | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Steven Ballet
- Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Andreas Boland
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
| | - Miriam Stoeber
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland.
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5
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Zhang Y, Kuang X, Yi J, Sun T, Guo Q, Gu H, Xu H. Revolutionizing the capture efficiency of ultrasensitive digital ELISA via an antibody oriented-immobilization strategy. J Mater Chem B 2024; 12:10041-10053. [PMID: 39257162 DOI: 10.1039/d4tb01141d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Bead-based digital ELISA, the most sensitive protein quantification method, has drawn much attention to exploring ultra-low abundance biomarkers in the life sciences and clinical applications. However, its major challenge refers to the low antigen capture efficiency in the immunoreaction process due to the low probability of collision between the deficient concentration of the analytes and the captured antibody-immobilized on the beads. Here, we achieved significantly improved reaction efficiency in the digital signal formation by fixing the orientation of antibodies and revealed the kinetic mechanism for the first time. A facile and fast antibody conjugation strategy that formed boronate ester complexes was designed to retain the uniform orientation of antibodies with controllable antibody density. Remarkably, the oriented immobilized antibody exhibited stronger antigen-binding capacity and faster antigen-binding speed compared to randomly immobilized antibodies, with capture efficiency increasing approximately 14-fold at 15 μg of antibody per 1 mg microbeads (0.035 antibody nm-2) under 0.5 h incubation. Combined with theoretical analysis, we verified that the improved capture efficiency of the oriented antibodies mainly originated from the considerable rise in the binding rate constant (kon) rather than the increase in antigen-binding sites, which further prominently decreased the limit of detection (LoD) in a shorter incubation time compared with the randomly immobilized antibody. In conclusion, the antibody oriented conjugation method effectively overcomes the low capture efficiency challenge of bead-based digital ELISA. It paves a promising way for further improving the digital immunoassay performance and promotes the early diagnosis of diseases by recognizing more ultra-low abundance significant biomarkers.
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Affiliation(s)
- Yutong Zhang
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Xiaojun Kuang
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Jingwei Yi
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Tong Sun
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Qingsheng Guo
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Hongchen Gu
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Hong Xu
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China.
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6
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Qin S, Liu Y, He G, Yang J, Zeng F, Lu Q, Wang M, He B, Song Y. Spatiotemporal Delivery of Dual Nanobodies by Engineered Probiotics to Reverse Tumor Immunosuppression via Targeting Tumor-Derived Exosomes. ACS NANO 2024; 18:26858-26871. [PMID: 39308426 DOI: 10.1021/acsnano.4c08117] [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: 10/02/2024]
Abstract
The anti-PD-L1 and its bispecific antibodies have exhibited durable antitumor immunity but still elicit immunosuppression mainly caused by tumor-derived exosomes (TDEs), leading to difficulty in clinical transformation. Herein, engineered Escherichia coli Nissle 1917 (EcN) coexpressing anti-PD-L1 and anti-CD9 nanobodies (EcN-Nb) are developed and decorated with zinc-based metal-organic frameworks (MOFs) loaded with indocyanine green (ICG), to generate EcN-Nb-ZIF-8CHO-ICG (ENZC) for spatiotemporal lysis of bacteria for immunotherapy. The tumor-homing hybrid system can specifically release nanobodies in response to near-infrared (NIR) radiation, thereby targeting TDEs and changing their biological distribution, remodeling tumor-associated macrophages to M1 states, activating more effective and cytotoxic T lymphocytes, and finally, leading to the inhibition of tumor proliferation and metastasis. Altogether, the microfluidic-enabled MOF-modified engineered probiotics target TDEs and activate the antitumor immune response in a spatiotemporally manipulated manner, offering promising TDE-targeted immune therapy.
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Affiliation(s)
- Shurong Qin
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Yuta Liu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Guanzhong He
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Jingjing Yang
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Fei Zeng
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Qianglan Lu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Meng Wang
- Department of Gastric and Hernia Surgery, Nanjing University Medical School Affiliated Drum Tower Hospital, Nanjing 210023, China
| | - Bangshun He
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Yujun Song
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
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7
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Jiang D, Chen R, Wang L, Xu G. Screening, expression and anti-tumor functional identification of anti-LAG-3 nanobodies. Protein Expr Purif 2024; 222:106522. [PMID: 38851552 DOI: 10.1016/j.pep.2024.106522] [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: 04/22/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024]
Abstract
OBJECTIVE To screen and obtain specific anti-lymphocyte activation gene-3 (LAG3) nanobody sequences, purify and express recombinant anti-LAG3 nanobody, and verify its effect on promoting T cells to kill tumor cells. METHODS Based on the camel derived natural nanobody phage display library constructed by the research group, the biotinylated LAG3 antigen was used as the target, and the anti-LAG3 nanobody sequences were screened by biotin-streptavidin liquid phase screening, phage-ELISA and sequencing. The sequence-conjμgated human IgG1 Fc fragment was obtained, the recombinant anti-LAG3 nanobody expression vector was constructed, the expression of the recombinant anti-LAG3 nanobody was induced by IPTG and purified, and the characteristics and functions of the recombinant anti-LAG3 nanobody were verified by SDS-PAGE, Western blot, cytotoxicity assay, etc. RESULTS: One anti-LAG3 nanobody sequence was successfully screened, and the corresponding recombinant anti-LAG3 nanobody-expressing bacteria were constructed. The results of SDS-PAGE, Western blot and cytotoxicity assay showed that the recombinant anti-LAG3 nanobody was successfully expressed, which was specific, and it could promote the killing ability of T cells against tumor cells, and the optimal concentration was 200 μg/mL. CONCLUSION The recombinant anti-LAG3 nanobody screened and expressed has specific and auxiliary anti-tumor cell effects, which lays a foundation for its subsequent application.
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Affiliation(s)
- Dan Jiang
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, Guangdong, 523808, China
| | - Rui Chen
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, Guangdong, 523808, China
| | - Liyan Wang
- Ningxia Chinese Medicine Research Centre, Yinchuan, Ningxia, 750000, China
| | - Guangxian Xu
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, Guangdong, 523808, China.
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8
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Slavny P, Hegde M, Doerner A, Parthiban K, McCafferty J, Zielonka S, Hoet R. Advancements in mammalian display technology for therapeutic antibody development and beyond: current landscape, challenges, and future prospects. Front Immunol 2024; 15:1469329. [PMID: 39381002 PMCID: PMC11459229 DOI: 10.3389/fimmu.2024.1469329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 09/04/2024] [Indexed: 10/10/2024] Open
Abstract
The evolving development landscape of biotherapeutics and their growing complexity from simple antibodies into bi- and multi-specific molecules necessitates sophisticated discovery and engineering platforms. This review focuses on mammalian display technology as a potential solution to the pressing challenges in biotherapeutic development. We provide a comparative analysis with established methodologies, highlighting key aspects of mammalian display technology, including genetic engineering, construction of display libraries, and its pivotal role in hit selection and/or developability engineering. The review delves into the mechanisms underpinning developability-driven selection via mammalian display and their broader implications. Applications beyond antibody discovery are also explored, alongside advancements towards function-first screening technologies, precision genome engineering and AI/ML-enhanced libraries, situating them in the context of mammalian display. Overall, the review provides a comprehensive overview of the current mammalian display technology landscape, underscores the expansive potential of the technology for biotherapeutic development, addresses the critical challenges for the full realisation of this potential, and examines advances in related disciplines that might impact the future application of mammalian display technologies.
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Affiliation(s)
- Peter Slavny
- Discovery & Engineering Division, Iontas Ltd./FairJourney Biologics, Cambridge, United Kingdom
| | - Manjunath Hegde
- Technology Division, Iontas/FairJourney Biologics, Cambridge, United Kingdom
| | - Achim Doerner
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Kothai Parthiban
- Discovery & Engineering Division, Iontas Ltd./FairJourney Biologics, Cambridge, United Kingdom
| | - John McCafferty
- Maxion Therapeutics, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stefan Zielonka
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Rene Hoet
- Technology Division, Iontas/FairJourney Biologics, Cambridge, United Kingdom
- Technology Division, FairJourney Biologics, Porto, Portugal
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9
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Saleem MZ, Jahangir GZ, Saleem A, Zulfiqar A, Khan KA, Ercisli S, Ali B, Saleem MH, Saleem A. Production Technologies for Recombinant Antibodies: Insights into Eukaryotic, Prokaryotic, and Transgenic Expression Systems. Biochem Genet 2024:10.1007/s10528-024-10911-5. [PMID: 39287779 DOI: 10.1007/s10528-024-10911-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 09/05/2024] [Indexed: 09/19/2024]
Abstract
Recombinant antibodies, a prominent class of recombinant proteins, are witnessing substantial growth in research and diagnostics. Recombinant antibodies are being produced employing diverse hosts ranging from highly complex eukaryotes, for instance, mammalian cell lines (and insects, fungi, yeast, etc.) to unicellular prokaryotic models like gram-positive and gram-negative bacteria. This review delves into these production methods, highlighting approaches like antibody phage display that employs bacteriophages for gene library creation. Recent studies emphasize monoclonal antibody generation through hybridoma technology, utilizing hybridoma cells from myeloma and B-lymphocytes. Transgenic plants and animals have emerged as sources for polyclonal and monoclonal antibodies, with transgenic animals preferred due to their human-like post-translational modifications and reduced immunogenicity risk. Chloroplast expression offers environmental safety by preventing transgene contamination in pollen. Diverse production technologies, such as stable cell pools and clonal cell lines, are available, followed by purification via techniques like affinity chromatography. The burgeoning applications of recombinant antibodies in medicine have led to their large-scale industrial production.
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Affiliation(s)
| | | | - Ammara Saleem
- Institute of Botany, University of the Punjab, Lahore, Pakistan.
| | - Asma Zulfiqar
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Khalid Ali Khan
- Applied College, Center of Bee Research and its Products, Unit of Bee Research and Honey Production, and Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, 61413, Abha, Saudi Arabia
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, 25240, Erzurum, Türkiye
- HGF Agro, Ata Teknokent, 25240, Erzurum, Türkiye
| | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- School of Science, Western Sydney University, Penrith, 2751, Australia
| | - Muhammad Hamzah Saleem
- Office of Academic Research, Office of VP for Research & Graduate Studies, Qatar University, 2713, Doha, Qatar
| | - Aroona Saleem
- Applied College, Center of Bee Research and its Products, Unit of Bee Research and Honey Production, and Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, 61413, Abha, Saudi Arabia.
- Department of Microbiology, Dr. Ikram-Ul-Haq Institute of Industrial Biotechnology (IIIB), Government College University, Lahore, 54000, Pakistan.
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10
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Szupryczyński K, Czeleń P, Jeliński T, Szefler B. What is the Reason That the Pharmacological Future of Chemotherapeutics in the Treatment of Lung Cancer Could Be Most Closely Related to Nanostructures? Platinum Drugs in Therapy of Non-Small and Small Cell Lung Cancer and Their Unexpected, Possible Interactions. The Review. Int J Nanomedicine 2024; 19:9503-9547. [PMID: 39296940 PMCID: PMC11410046 DOI: 10.2147/ijn.s469217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/19/2024] [Indexed: 09/21/2024] Open
Abstract
Over the course of several decades, anticancer treatment with chemotherapy drugs for lung cancer has not changed significantly. Unfortunately, this treatment prolongs the patient's life only by a few months, causing many side effects in the human body. It has also been proven that drugs such as Cisplatin, Carboplatin, Oxaliplatin and others can react with other substances containing an aromatic ring in which the nitrogen atom has a free electron group in its structure. Thus, such structures may have a competitive effect on the nucleobases of DNA. Therefore, scientists are looking not only for new drugs, but also for new alternative ways of delivering the drug to the cancer site. Nanotechnology seems to be a great hope in this matter. Creating a new nanomedicine would reduce the dose of the drug to an absolute minimum, and thus limit the toxic effect of the drug; it would allow for the exclusion of interactions with competitive compounds with a structure similar to nucleobases; it would also permit using the so-called targeted treatment and bypassing healthy cells; it would allow for the introduction of other treatment options, such as radiotherapy directly to the cancer site; and it would provide diagnostic possibilities. This article is a review that aims to systematize the knowledge regarding the anticancer treatment of lung cancer, but not only. It shows the clear possibility of interactions of chemotherapeutics with compounds competitive to the nitrogenous bases of DNA. It also shows the possibilities of using nanostructures as potential Platinum drug carriers, and proves that nanomedicine can easily become a new medicinal product in personalized medicine.
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Affiliation(s)
- Kamil Szupryczyński
- Doctoral School of Medical and Health Sciences, Faculty of Pharmacy, Collegium Medicum, Nicolaus, Copernicus University, Bydgoszcz, Poland
| | - Przemysław Czeleń
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Tomasz Jeliński
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Beata Szefler
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
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11
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Lilja J, Kaivola J, Conway JRW, Vuorio J, Parkkola H, Roivas P, Dibus M, Chastney MR, Varila T, Jacquemet G, Peuhu E, Wang E, Pentikäinen U, Martinez D Posada I, Hamidi H, Najumudeen AK, Sansom OJ, Barsukov IL, Abankwa D, Vattulainen I, Salmi M, Ivaska J. SHANK3 depletion leads to ERK signalling overdose and cell death in KRAS-mutant cancers. Nat Commun 2024; 15:8002. [PMID: 39266533 PMCID: PMC11393128 DOI: 10.1038/s41467-024-52326-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 09/03/2024] [Indexed: 09/14/2024] Open
Abstract
The KRAS oncogene drives many common and highly fatal malignancies. These include pancreatic, lung, and colorectal cancer, where various activating KRAS mutations have made the development of KRAS inhibitors difficult. Here we identify the scaffold protein SH3 and multiple ankyrin repeat domain 3 (SHANK3) as a RAS interactor that binds active KRAS, including mutant forms, competes with RAF and limits oncogenic KRAS downstream signalling, maintaining mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) activity at an optimal level. SHANK3 depletion breaches this threshold, triggering MAPK/ERK signalling hyperactivation and MAPK/ERK-dependent cell death in KRAS-mutant cancers. Targeting this vulnerability through RNA interference or nanobody-mediated disruption of the SHANK3-KRAS interaction constrains tumour growth in vivo in female mice. Thus, inhibition of SHANK3-KRAS interaction represents an alternative strategy for selective killing of KRAS-mutant cancer cells through excessive signalling.
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Affiliation(s)
- Johanna Lilja
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Jasmin Kaivola
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - James R W Conway
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Joni Vuorio
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Hanna Parkkola
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Pekka Roivas
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
- Institute of Biomedicine, University of Turku, FI-20520, Turku, Finland
| | - Michal Dibus
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Megan R Chastney
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Taru Varila
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, FI-20520, Turku, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
- InFLAMES Research Flagship Center, Åbo Akademi University, FI-20520, Turku, Finland
| | - Emilia Peuhu
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
- Institute of Biomedicine, Cancer Research Laboratory FICAN West, University of Turku, FI-20520, Turku, Finland
| | - Emily Wang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Ulla Pentikäinen
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
- Institute of Biomedicine, University of Turku, FI-20520, Turku, Finland
| | | | - Hellyeh Hamidi
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Arafath K Najumudeen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- CRUK Scotland Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Owen J Sansom
- CRUK Scotland Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Igor L Barsukov
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniel Abankwa
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
- Department of Life Sciences and Medicine, University of Luxembourg, 4365, Esch- sur-Alzette, Luxembourg
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Marko Salmi
- Institute of Biomedicine, University of Turku, FI-20520, Turku, Finland
- MediCity Research Laboratory, University of Turku, FI-20520, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, FI-20520, Turku, Finland
| | - Johanna Ivaska
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, FI-20520, Turku, Finland.
- Department of Life Technologies, University of Turku, Turku, Finland.
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, FI-00014, Helsinki, Finland.
- Western Finnish Cancer Center, University of Turku, Turku, FI-20520, Finland.
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12
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Nagraj AK, Shukla M, Kulkarni M, Patil P, Borgave M, Banerjee SK. Reversal of carbapenem resistance in Pseudomonas aeruginosa by camelid single domain antibody fragment (VHH) against the C4-dicarboxylate transporter. J Antibiot (Tokyo) 2024; 77:612-626. [PMID: 38886486 DOI: 10.1038/s41429-024-00748-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 05/06/2024] [Accepted: 05/18/2024] [Indexed: 06/20/2024]
Abstract
Antimicrobial resistance is emerging as the new healthcare crisis necessitating the development of newer classes of drugs using non-traditional approaches. Pseudomonas aeruginosa, one of the most common pathogens involved in nosocomial infections, is extremely difficult to treat even with the last resort frontline drug, the carbapenems. As the pathogen has the ability to acquire resistance to new small-molecule antibiotics, being deployed, a novel biological approach has been tried using antibody fragments in combination with carbapenems and β-lactams as adjunct therapy for an enduring solution to the problem. In this study, we developed a camelid antibody fragment (VHH) library against P. aeruginosa and isolated a highly potent hit, PsC23. Mass spectrometry identified the target to be a component of the C4-dicarboxylate transporter that feeds metabolites to the glyoxylate shunt particularly under conditions of oxidative stress. PsC23 is bacteriostatic at a concentration of 1.66 µM (25 µg ml-1) and shows a synergistic effect with both the classes of drugs at an effective concentration of 100-200 nM (1.5-3.0 µg ml-1) when co administered with them. In combination with meropenem the VHH completely cleared the infection from a neutropenic mouse with a carbapenem-resistant P. aeruginosa systemic infection. Blocking the glyoxylate shunt by PsC23 resulted in disruption of energy transduction due to a respiratory shift to the oxygen-depleted TCA cycle causing inhibition of efflux and increased free radical generation from carbapenems and β-lactams exerting a strong bactericidal effect that reversed the resistance to multiple unrelated drugs.
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Affiliation(s)
| | | | | | - Pratik Patil
- AbGenics Life Sciences Pvt. Ltd, Pune, 411045, India
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13
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Dierick E, Callens C, Bloch Y, Savvides SN, Hark S, Pelzer S, Ducatelle R, Van Immerseel F, Goossens E. Clostridium perfringens chitinases, key enzymes during early stages of necrotic enteritis in broiler chickens. PLoS Pathog 2024; 20:e1012560. [PMID: 39283899 PMCID: PMC11426533 DOI: 10.1371/journal.ppat.1012560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 09/26/2024] [Accepted: 09/03/2024] [Indexed: 09/27/2024] Open
Abstract
The interaction between bacteria and the intestinal mucus is crucial during the early pathogenesis of many enteric diseases in mammals. A critical step in this process employed by both commensal and pathogenic bacteria focuses on the breakdown of the protective layer presented by the intestinal mucus by mucolytic enzymes. C. perfringens type G, the causative agent of necrotic enteritis in broilers, produces two glycosyl hydrolase family 18 chitinases, ChiA and ChiB, which display distinct substrate preferences. Whereas ChiB preferentially processes linear substrates such as chitin, ChiA prefers larger and more branched substrates, such as carbohydrates presented by the chicken intestinal mucus. Here, we show via crystal structures of ChiA and ChiB in the apo and ligand-bound forms that the two enzymes display structural features that explain their substrate preferences providing a structural blueprint for further interrogation of their function and inhibition. This research focusses on the roles of ChiA and ChiB in bacterial proliferation and mucosal attachment, two processes leading to colonization and invasion of the gut. ChiA and ChiB, either supplemented or produced by the bacteria, led to a significant increase in C. perfringens growth. In addition to nutrient acquisition, the importance of chitinases in bacterial attachment to the mucus layer was shown using an in vitro binding assay of C. perfringens to chicken intestinal mucus. Both an in vivo colonization trial and a necrotic enteritis trial were conducted, demonstrating that a ChiA chitinase mutant strain was less capable to colonize the intestine and was hampered in its disease-causing ability as compared to the wild-type strain. Our findings reveal that the pathogen-specific chitinases produced by C. perfringens type G strains play a fundamental role during colonization, suggesting their potential as vaccine targets.
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Affiliation(s)
- Evelien Dierick
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Chana Callens
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Yehudi Bloch
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Current address: European Molecular Biology Laboratory, EMBL Hamburg, c/o DESY, Hamburg, Germany
| | - Savvas N. Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Sarah Hark
- Evonik Operations GmbH, Nutrition & Care, Halle, Westfalen, Germany
| | - Stefan Pelzer
- Evonik Operations GmbH, Nutrition & Care, Halle, Westfalen, Germany
| | - Richard Ducatelle
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Filip Van Immerseel
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evy Goossens
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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14
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Fridy PC, Farrell RJ, Molloy KR, Keegan S, Wang J, Jacobs EY, Li Y, Trivedi J, Sehgal V, Fenyö D, Wu Z, Chait BT, Rout MP. A new generation of nanobody research tools using improved mass spectrometry-based discovery methods. J Biol Chem 2024; 300:107623. [PMID: 39098531 PMCID: PMC11401214 DOI: 10.1016/j.jbc.2024.107623] [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: 03/13/2024] [Revised: 07/01/2024] [Accepted: 07/22/2024] [Indexed: 08/06/2024] Open
Abstract
Single-domain antibodies ("nanobodies") derived from the variable region of camelid heavy-chain only antibody variants have proven to be widely useful tools for research, therapeutic, and diagnostic applications. In addition to traditional display techniques, methods to generate nanobodies using direct detection by mass spectrometry and DNA sequencing have been highly effective. However, certain technical challenges have limited widespread application. We have optimized a new pipeline for this approach that greatly improves screening sensitivity, depth of antibody coverage, antigen compatibility, and overall hit rate and affinity. We have applied this improved methodology to generate significantly higher affinity nanobody repertoires against widely used targets in biological research-i.e., GFP, tdTomato, GST, and mouse, rabbit, and goat immunoglobulin G. We have characterized these reagents in affinity isolations and tissue immunofluorescence microscopy, identifying those that are optimal for these particularly demanding applications, and engineering dimeric constructs for ultra-high affinity. This study thus provides new nanobody tools directly applicable to a wide variety of research problems, and improved techniques enabling future nanobody development against diverse targets.
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Affiliation(s)
- Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Ryan J Farrell
- Laboratory of Brain Development and Repair, The Rockefeller University, New York, New York, USA; Department of Biochemistry, Weill Cornell Medicine, New York, New York, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Sarah Keegan
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Erica Y Jacobs
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA; Chemistry Department, St John's University, Queens, New York, USA
| | - Yinyin Li
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Jill Trivedi
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Viren Sehgal
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York, USA
| | - Zhuhao Wu
- Laboratory of Brain Development and Repair, The Rockefeller University, New York, New York, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA.
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15
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Hennigan JN, Menacho-Melgar R, Sarkar P, Golovsky M, Lynch MD. Scalable, robust, high-throughput expression & purification of nanobodies enabled by 2-stage dynamic control. Metab Eng 2024; 85:116-130. [PMID: 39059674 PMCID: PMC11408108 DOI: 10.1016/j.ymben.2024.07.012] [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: 02/05/2024] [Revised: 05/16/2024] [Accepted: 07/24/2024] [Indexed: 07/28/2024]
Abstract
Nanobodies are single-domain antibody fragments that have garnered considerable use as diagnostic and therapeutic agents as well as research tools. However, obtaining pure VHHs, like many proteins, can be laborious and inconsistent. High level cytoplasmic expression in E. coli can be challenging due to improper folding and insoluble aggregation caused by reduction of the conserved disulfide bond. We report a systems engineering approach leveraging engineered strains of E. coli, in combination with a two-stage process and simplified downstream purification, enabling improved, robust, soluble cytoplasmic nanobody expression, as well as rapid cell autolysis and purification. This approach relies on the dynamic control over the reduction potential of the cytoplasm, incorporates lysis enzymes for purification, and can also integrate dynamic expression of protein folding catalysts. Collectively, the engineered system results in more robust growth and protein expression, enabling efficient scalable nanobody production, and purification from high throughput microtiter plates, to routine shake flask cultures and larger instrumented bioreactors. We expect this system will expedite VHH development.
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Affiliation(s)
| | | | - Payel Sarkar
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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16
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Morez M, Lara Ordóñez AJ, Melnyk P, Liberelle M, Lebègue N, Taymans JM. Leucine-rich repeat kinase 2 (LRRK2) inhibitors for Parkinson's disease: a patent review of the literature to date. Expert Opin Ther Pat 2024; 34:773-788. [PMID: 39023243 DOI: 10.1080/13543776.2024.2378076] [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: 04/26/2024] [Accepted: 07/04/2024] [Indexed: 07/20/2024]
Abstract
INTRODUCTION Nearly two decades after leucine rich repeat kinase 2 (LRRK2) was discovered as a genetic determinant of Parkinson's disease (PD), LRRK2 has emerged a priority therapeutic target in PD and inhibition of its activity is hypothesized to be beneficial. AREAS COVERED LRRK2 targeting agents, in particular kinase inhibitors and agents reducing LRRK2 expression show promise in model systems and have progressed to phase I and phase II clinical testing for PD. Several additional targeting strategies for LRRK2 are emerging, based on promoting specific 'healthy' LRRK2 quaternary structures, heteromeric complexes and conformations. EXPERT OPINION It can be expected that LRRK2 targeting strategies may proceed to phase III clinical testing for PD in the next five years, allowing the field to discover the real clinical value of LRRK2 targeting strategies.
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Affiliation(s)
- Margaux Morez
- University Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | | | - Patricia Melnyk
- University Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Maxime Liberelle
- University Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Nicolas Lebègue
- University Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Jean-Marc Taymans
- University Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
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17
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Nakakido M, Kinoshita S, Tsumoto K. Development of novel humanized VHH synthetic libraries based on physicochemical analyses. Sci Rep 2024; 14:19533. [PMID: 39174623 PMCID: PMC11341556 DOI: 10.1038/s41598-024-70513-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 08/19/2024] [Indexed: 08/24/2024] Open
Abstract
Due to the high affinity and specificity of antibodies toward antigens, various antibody-based applications have been developed. Recently, variable antigen-binding domains of heavy-chain antibodies (VHH) have become an attractive alternative to conventional fragment antibodies due to their unique molecular characteristics. As an antibody-generating strategy, synthetic VHH libraries (including humanized VHH libraries) have been developed using distinct strategies to constrain the diversity of amino acid sequences. In this study, we designed and constructed several novel synthetic humanized VHH libraries based on biophysical analyses conducted using the complementarity determining region-grafting method and comprehensive sequence analyses of VHHs deposited in the protein data bank. We obtained VHHs from the libraries, and hit clones exhibited considerable thermal stability. We also found that VHHs from distinct libraries tended to have different epitopes. Based on our results, we propose a strategy for generating humanized VHHs with distinct epitopes toward various antigens by utilizing our library combinations.
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Affiliation(s)
- Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Seisho Kinoshita
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
- Laboratory of Medical Proteomics, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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18
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Hashimoto-Tane A, Bowman EP, Sakuma M, Yoneda N, Yugi K, de Waal Malefyt R, Saito T. Dissociation of LAG-3 inhibitory cluster from TCR microcluster by immune checkpoint blockade. Front Immunol 2024; 15:1444424. [PMID: 39234253 PMCID: PMC11371725 DOI: 10.3389/fimmu.2024.1444424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 07/24/2024] [Indexed: 09/06/2024] Open
Abstract
Lymphocyte activation gene (Lag)-3 is an inhibitory co-receptor and target of immune checkpoint inhibitor (ICI) therapy for cancer. The dynamic behavior of Lag-3 was analyzed at the immune synapse upon T-cell activation to elucidate the Lag-3 inhibitory mechanism. Lag-3 formed clusters and co-localized with T-cell receptor microcluster (TCR-MC) upon T-cell activation similar to PD-1. Lag-3 blocking antibodies (Abs) inhibited the co-localization between Lag-3 and TCR-MC without inhibiting Lag-3 cluster formation. Lag-3 also inhibited MHC-II-independent stimulation and Lag-3 Ab, which did not block MHC-II binding could still block Lag-3's inhibitory function, suggesting that the Lag-3 Ab blocks the Lag-3 inhibitory signal by dissociating the co-assembly of TCR-MC and Lag-3 clusters. Consistent with the combination benefit of PD-1 and Lag-3 Abs to augment T-cell responses, bispecific Lag-3/PD-1 antagonists effectively inhibited both cluster formation and co-localization of PD-1 and Lag-3 with TCR-MC. Therefore, Lag-3 inhibits T-cell activation at TCR-MC, and the target of Lag-3 ICI is to dissociate the co-localization of Lag-3 with TCR-MC.
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Affiliation(s)
- Akiko Hashimoto-Tane
- Laboratory of Cell Signaling, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Edward P Bowman
- Department of Oncology, Merck & Co., Inc., Rahway, NJ, United States
| | - Machie Sakuma
- Laboratory of Cell Signaling, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Natsumi Yoneda
- Laboratory of Cell Signaling, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsuyuki Yugi
- Laboratory of Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Takashi Saito
- Laboratory of Cell Signaling, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Cell Signaling, Immunology Frontier of Immunology, Osaka University, Suita, Japan
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19
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Jia Q, Ren H, Zhang S, Yang H, Gao S, Fan R. Preparation and Application of Clostridium perfringens Alpha Toxin Nanobodies. Vet Sci 2024; 11:381. [PMID: 39195835 PMCID: PMC11360521 DOI: 10.3390/vetsci11080381] [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: 07/25/2024] [Revised: 08/16/2024] [Accepted: 08/18/2024] [Indexed: 08/29/2024] Open
Abstract
All subtypes of Clostridium perfringens (C. perfringens) produce the alpha toxin (CPA), which can cause enteritis or enterotoxemia in lambs, cattle, pigs, and horses, as well as traumatic clostridial myonecrosis in humans and animals. CPA acts on cell membranes, ultimately leading to endocytosis and cell death. Therefore, the neutralization of CPA is crucial for the prevention and treatment of diseases caused by C. perfringens. In this study, utilizing CPA as an antigen, a nanobody (CPA-VHH) with a half-life of 2.9 h, an affinity constant (KD) of 0.9 nmol/L, and good stability below 60 °C was prepared from a natural nanobody library from alpacas. The biological activity analysis of CPA-VHH revealed its ability to effectively neutralize the phospholipase and hemolytic activity of CPA at a 15-fold ratio. In Vero cells, 9.8 μg/mL CPA-VHH neutralized the cytotoxicity of CPA at two times the half-maximal inhibitory concentration (IC50). In a mouse model, 35.7 ng/g body weight (BW) of CPA-VHH neutralized 90% of the lethality caused by a 2× median lethal dose (LD50) of CPA. It was found that CPA-VHH protected 80% of mice within 30 min at 2 × LD50 CPA, but this dropped below 50% after 2 h and to 0% after 4 h. Rescue trials indicated that using CPA-VHH within 30 min post-infection with 2 × LD50 CPA achieved an 80% rescue rate, which decreased to 10% after 2 h. Furthermore, CPA-VHH effectively mitigated the reduction in the expression levels of zonula occludens-1 (ZO-1), Occludin, and Claudin-1, while also attenuating the upregulation of the pro-inflammatory cytokines interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-7 (IL-7), interleukin-8 (IL-8), tumor necrosis factor α (TNF-α), and interferon-γ (IFN-γ) induced by CPA infection. Overall, this study has identified a specific nanobody, CPA-VHH, that effectively neutralizes CPA toxins in vitro and in animal models, providing a new tool for inhibiting the pathogenicity resulting from these toxins and laying an important foundation for the development of new anti-C. perfringens toxin-related therapeutic products.
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Affiliation(s)
| | | | | | | | | | - Ruiwen Fan
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (Q.J.); (H.R.); (S.Z.); (H.Y.); (S.G.)
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20
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Sun Y, Martinez-Ramos C, Chen E, Osawa Y, Zhang H. A General Method to Screen Nanobodies for Cytochrome P450 Enzymes from a Yeast Surface Display Library. Biomedicines 2024; 12:1863. [PMID: 39200327 PMCID: PMC11351928 DOI: 10.3390/biomedicines12081863] [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: 07/26/2024] [Revised: 08/08/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
The availability of yeast surface display nanobody (Nb) libraries offers a convenient way to acquire antigen-specific nanobodies that may be useful for protein structure-function studies and/or therapeutic applications, complementary to the conventional method of acquiring nanobodies through immunization in camelids. In this study, we developed a general approach to select nanobodies for cytochrome P450 enzymes from a highly diverse yeast display library. We tested our method on three P450 enzymes including CYP102A1, neuronal nitric oxide synthase (nNOS), and the complex of CYP2B4:POR, using a novel streamlined approach where biotinylated P450s were bound to fluorescent-labeled streptavidin for Nb screening. The Nb-antigen binders were selectively enriched using magnetic-activated cell sorting (MACS) and fluorescence-activated cell sorting (FACS). After two rounds of MACS, the population of positive binders was enriched by >5-fold compared to the naïve library. The subsequent FACS selection, with a gating of 0.1%, identified 634, 270, and 215 positive binders for CYP102A1, nNOS, and CYP2B4:POR, respectively. The positive binders for CYP102A1 were further triaged based on EC50 determined at various antigen concentrations. DNA sequencing of the top 30 binders of CYP102A1 resulted in 26 unique clones, 8 of which were selected for over-expression and characterization. They were found to inhibit CYP102A1-catalyzed oxidation of omeprazole with IC50 values in the range of 0.16-2.8 µM. These results validate our approach and may be applied to other protein targets for the effective selection of specific nanobodies.
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Affiliation(s)
- Yudong Sun
- Department of Pharmacology, The University of Michigan Medical School, Ann Arbor, MI 48109, USA; (Y.S.); (C.M.-R.); (Y.O.)
| | - Cristian Martinez-Ramos
- Department of Pharmacology, The University of Michigan Medical School, Ann Arbor, MI 48109, USA; (Y.S.); (C.M.-R.); (Y.O.)
| | - Eugene Chen
- Internal Medicine, The University of Michigan Medical School, Ann Arbor, MI 48109, USA;
| | - Yoichi Osawa
- Department of Pharmacology, The University of Michigan Medical School, Ann Arbor, MI 48109, USA; (Y.S.); (C.M.-R.); (Y.O.)
| | - Haoming Zhang
- Department of Pharmacology, The University of Michigan Medical School, Ann Arbor, MI 48109, USA; (Y.S.); (C.M.-R.); (Y.O.)
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21
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Zhu L, Huang B, Wang X, Ni F, Ao M, Wang R, Zheng B, Chen C, Xue J, Zhu L, Yang C, Shi L, Geng S, Hu J, Yang M, Zhang D, Yang P, Li M, Li Y, Hu Q, Ye S, Zheng P, Wei H, Wu Z, Zhang L, Wang Y, Liu Y, Wu X. Highly potent and broadly neutralizing anti-CD4 trimeric nanobodies inhibit HIV-1 infection by inducing CD4 conformational alteration. Nat Commun 2024; 15:6961. [PMID: 39138183 PMCID: PMC11322561 DOI: 10.1038/s41467-024-51414-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 08/06/2024] [Indexed: 08/15/2024] Open
Abstract
Despite advancements in antiretroviral therapy (ART) suppressing HIV-1 replication, existing antiviral drugs pose limitations, including lifelong medication, frequent administration, side effects and viral resistance, necessitating novel HIV-1 treatment approaches. CD4, pivotal for HIV-1 entry, poses challenges for drug development due to neutralization and cytotoxicity concerns. Nevertheless, Ibalizumab, the sole approved CD4-specific antibody for HIV-1 treatment, reignites interest in exploring alternative anti-HIV targets, emphasizing CD4's potential value for effective drug development. Here, we explore anti-CD4 nanobodies, particularly Nb457 from a CD4-immunized alpaca. Nb457 displays high potency and broad-spectrum activity against HIV-1, surpassing Ibalizumab's efficacy. Strikingly, engineered trimeric Nb457 nanobodies achieve complete inhibition against live HIV-1, outperforming Ibalizumab and parental Nb457. Structural analysis unveils Nb457-induced CD4 conformational changes impeding viral entry. Notably, Nb457 demonstrates therapeutic efficacy in humanized female mouse models. Our findings highlight anti-CD4 nanobodies as promising HIV-1 therapeutics, with potential implications for advancing clinical treatment against this global health challenge.
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Affiliation(s)
- Linjing Zhu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, P.R. China
- Abrev Biotechnology Co. Ltd., Nanjing, P.R. China
| | - Bilian Huang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China
| | - Xiangyao Wang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life sciences, Tianjin University, Tianjin, P.R. China
| | - Fengfeng Ni
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P.R. China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijin, P.R. China
| | - Mingjun Ao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, P. R. China
| | - Ruoke Wang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, P.R. China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, P. R. China
| | - Chen Chen
- Department of Infection, Nanjing Hospital Affiliated to Nanjing university of Chinese Medicine, Nanjing, P.R. China
| | - Jing Xue
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Lin Zhu
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Chenbo Yang
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Lingen Shi
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China
| | - Shengya Geng
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China
- MOE Key Laboratory of Model Animals for Disease Study, Medical School, Nanjing University, Nanjing, P.R. China
| | - Jiaqian Hu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China
| | - Mengshi Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Doudou Zhang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China
| | - Ping Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Miaomiao Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P.R. China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijin, P.R. China
| | - Yuncheng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P.R. China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijin, P.R. China
| | - Qinxue Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life sciences, Tianjin University, Tianjin, P.R. China
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, P.R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, P. R. China
| | - Hongxia Wei
- Department of Infection, Nanjing Hospital Affiliated to Nanjing university of Chinese Medicine, Nanjing, P.R. China
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China.
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, P.R. China.
- School of Life Sciences, Ningxia University, Yinchuan, Ningxia, P.R. China.
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, P.R. China.
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, P.R. China.
| | - Yaxin Wang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life sciences, Tianjin University, Tianjin, P.R. China.
| | - Yalan Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P.R. China.
- Hubei Jiangxia Laboratory, Wuhan, P.R. China.
| | - Xilin Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China.
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, P.R. China.
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, P.R. China.
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22
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Goldman ER, Sugiharto VA, Shriver-Lake LC, Garcia AM, Wu SJ, Jenkins SA, Chen HW. A single domain antibody-based Luminex assay for the detection of SARS-CoV-2 in clinical samples. Front Immunol 2024; 15:1446095. [PMID: 39192985 PMCID: PMC11347438 DOI: 10.3389/fimmu.2024.1446095] [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: 06/09/2024] [Accepted: 07/25/2024] [Indexed: 08/29/2024] Open
Abstract
Within the past decade, single domain antibodies (sdAbs) have been recognized as unique affinity binding reagents that can be tailored for performance in a variety of immunoassay formats. Luminex MagPlex color-coded magnetic microspheres provide a high-throughput platform that enables multiplexed immunoassays. We developed a MagPlex bead-based assay for the detection of SARS-CoV-2, using sdAbs against SARS-CoV-2 nucleocapsid (N) protein in which we engineered the sdAb capture reagents to orient them on the beads. The oriented sdAbs provided an increase in sensitivity over randomly oriented sdAbs for samples of N diluted in buffer, which also translated into better detection of SARS-CoV-2 in clinical samples. We assessed the specificity of the assay by examining seasonal coronavirus clinical samples. In summary, we provide a proof-of-concept that a bead-based assay using sdAbs to detect SARS-CoV-2 is feasible and future research combining it with other sdAb-coated beads that can detect other viruses may provide a useful diagnostic tool.
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Affiliation(s)
- Ellen R. Goldman
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States
| | - Victor A. Sugiharto
- Diagnostic and Surveillance Department, Naval Medical Research Command, Silver Spring, MD, United States
- Henry M. Jackson Foundation, Bethesda, MD, United States
| | - Lisa C. Shriver-Lake
- Center for Biomolecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States
| | - Andrew M. Garcia
- Diagnostic and Surveillance Department, Naval Medical Research Command, Silver Spring, MD, United States
- Leidos Inc., Reston, VA, United States
| | - Shuenn-Jue Wu
- Diagnostic and Surveillance Department, Naval Medical Research Command, Silver Spring, MD, United States
| | - Sarah A. Jenkins
- Diagnostic and Surveillance Department, Naval Medical Research Command, Silver Spring, MD, United States
| | - Hua-Wei Chen
- Diagnostic and Surveillance Department, Naval Medical Research Command, Silver Spring, MD, United States
- Henry M. Jackson Foundation, Bethesda, MD, United States
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23
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Zhang T, Yang D, Tang L, Hu Y. Current development of severe acute respiratory syndrome coronavirus 2 neutralizing antibodies (Review). Mol Med Rep 2024; 30:148. [PMID: 38940338 PMCID: PMC11228696 DOI: 10.3892/mmr.2024.13272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/21/2024] [Indexed: 06/29/2024] Open
Abstract
The coronavirus disease 2019 pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) seriously affected global public health security. Studies on vaccines, neutralizing antibodies (NAbs) and small molecule antiviral drugs are currently ongoing. In particular, NAbs have emerged as promising therapeutic agents due to their well‑defined mechanism, high specificity, superior safety profile, ease of large‑scale production and simultaneous application for both prevention and treatment of viral infection. Numerous NAb therapeutics have entered the clinical research stages, demonstrating promising therapeutic and preventive effects. These agents have been used for outbreak prevention and control under urgent authorization processes. The present review summarizes the molecular targets of SARS‑CoV‑2‑associated NAbs and screening and identification techniques for NAb development. Moreover, the current shortcomings and challenges that persist with the use of NAbs are discussed. The aim of the present review is to offer a reference for the development of NAbs for any future emergent infectious diseases, including SARS‑CoV‑2.
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Affiliation(s)
- Tong Zhang
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Di Yang
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Liang Tang
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yu Hu
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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24
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Medina Pérez VM, Baselga M, Schuhmacher AJ. Single-Domain Antibodies as Antibody-Drug Conjugates: From Promise to Practice-A Systematic Review. Cancers (Basel) 2024; 16:2681. [PMID: 39123409 PMCID: PMC11311928 DOI: 10.3390/cancers16152681] [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: 06/26/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Antibody-drug conjugates (ADCs) represent potent cancer therapies that deliver highly toxic drugs to tumor cells precisely, thus allowing for targeted treatment and significantly reducing off-target effects. Despite their effectiveness, ADCs can face limitations due to acquired resistance and potential side effects. OBJECTIVES This study focuses on advances in various ADC components to improve both the efficacy and safety of these agents, and includes the analysis of several novel ADC formats. This work assesses whether the unique features of VHHs-such as their small size, enhanced tissue penetration, stability, and cost-effectiveness-make them a viable alternative to conventional antibodies for ADCs and reviews their current status in ADC development. METHODS Following PRISMA guidelines, this study focused on VHHs as components of ADCs, examining advancements and prospects from 1 January 2014 to 30 June 2024. Searches were conducted in PubMed, Cochrane Library, ScienceDirect and LILACS using specific terms related to ADCs and single-domain antibodies. Retrieved articles were rigorously evaluated, excluding duplicates and non-qualifying studies. The selected peer-reviewed articles were analyzed for quality and synthesized to highlight advancements, methods, payloads, and future directions in ADC research. RESULTS VHHs offer significant advantages for drug conjugation over conventional antibodies due to their smaller size and structure, which enhance tissue penetration and enable access to previously inaccessible epitopes. Their superior stability, solubility, and manufacturability facilitate cost-effective production and expand the range of targetable antigens. Additionally, some VHHs can naturally cross the blood-brain barrier or be easily modified to favor their penetration, making them promising for targeting brain tumors and metastases. Although no VHH-drug conjugates (nADC or nanoADC) are currently in the clinical arena, preclinical studies have explored various conjugation methods and linkers. CONCLUSIONS While ADCs are transforming cancer treatment, their unique mechanisms and associated toxicities challenge traditional views on bioavailability and vary with different tumor types. Severe toxicities, often linked to compound instability, off-target effects, and nonspecific blood cell interactions, highlight the need for better understanding. Conversely, the rapid distribution, tumor penetration, and clearance of VHHs could be advantageous, potentially reducing toxicity by minimizing prolonged exposure. These attributes make single-domain antibodies strong candidates for the next generation of ADCs, potentially enhancing both efficacy and safety.
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Affiliation(s)
- Víctor Manuel Medina Pérez
- Molecular Oncology Group, Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain;
| | - Marta Baselga
- Molecular Oncology Group, Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain;
| | - Alberto J. Schuhmacher
- Molecular Oncology Group, Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain;
- Fundación Aragonesa para la Investigación y el Desarrollo (ARAID), 50018 Zaragoza, Spain
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25
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Prieto A, Miró L, Margolles Y, Bernabeu M, Salguero D, Merino S, Tomas J, Corbera JA, Perez-Bosque A, Huttener M, Fernández LÁ, Juarez A. Targeting plasmid-encoded proteins that contain immunoglobulin-like domains to combat antimicrobial resistance. eLife 2024; 13:RP95328. [PMID: 39046772 PMCID: PMC11268884 DOI: 10.7554/elife.95328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to human health. Although vaccines have been developed to combat AMR, it has proven challenging to associate specific vaccine antigens with AMR. Bacterial plasmids play a crucial role in the transmission of AMR. Our recent research has identified a group of bacterial plasmids (specifically, IncHI plasmids) that encode large molecular mass proteins containing bacterial immunoglobulin-like domains. These proteins are found on the external surface of the bacterial cells, such as in the flagella or conjugative pili. In this study, we show that these proteins are antigenic and can protect mice from infection caused by an AMR Salmonella strain harboring one of these plasmids. Furthermore, we successfully generated nanobodies targeting these proteins, that were shown to interfere with the conjugative transfer of IncHI plasmids. Considering that these proteins are also encoded in other groups of plasmids, such as IncA/C and IncP2, targeting them could be a valuable strategy in combating AMR infections caused by bacteria harboring different groups of AMR plasmids. Since the selected antigens are directly linked to AMR itself, the protective effect extends beyond specific microorganisms to include all those carrying the corresponding resistance plasmids.
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Affiliation(s)
- Alejandro Prieto
- Department of Genetics, Microbiology and Statistics, University of BarcelonaBarcelonaSpain
| | - Luïsa Miró
- Department of Biochemistry and Physiology, Universitat de BarcelonaBarcelonaSpain
- Institut de Nutrició i Seguretat Alimentària, Universitat de BarcelonaBarcelonaSpain
| | - Yago Margolles
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC)MadridSpain
| | - Manuel Bernabeu
- Department of Genetics, Microbiology and Statistics, University of BarcelonaBarcelonaSpain
| | - David Salguero
- Department of Genetics, Microbiology and Statistics, University of BarcelonaBarcelonaSpain
| | - Susana Merino
- Department of Genetics, Microbiology and Statistics, University of BarcelonaBarcelonaSpain
| | - Joan Tomas
- Department of Genetics, Microbiology and Statistics, University of BarcelonaBarcelonaSpain
| | - Juan Alberto Corbera
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria (ULPGC), Campus Universitario de ArucasLas PalmasSpain
| | - Anna Perez-Bosque
- Department of Biochemistry and Physiology, Universitat de BarcelonaBarcelonaSpain
- Institut de Nutrició i Seguretat Alimentària, Universitat de BarcelonaBarcelonaSpain
| | - Mario Huttener
- Department of Genetics, Microbiology and Statistics, University of BarcelonaBarcelonaSpain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC)MadridSpain
| | - Antonio Juarez
- Department of Genetics, Microbiology and Statistics, University of BarcelonaBarcelonaSpain
- Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and TechnologyBarcelonaSpain
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26
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Hansman GS, Kher G, Svirina AD, Tame JRH, Hartley-Tassell L, Irie H, Haselhorst T, von Itzstein M, Rudd PA, Pancera M. Development of a broad-spectrum therapeutic Fc-nanobody for human noroviruses. J Virol 2024; 98:e0070724. [PMID: 38953655 PMCID: PMC11264634 DOI: 10.1128/jvi.00707-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024] Open
Abstract
Human norovirus was discovered more than five decades ago and is a widespread cause of outbreaks of acute gastroenteritis. There are no approved vaccines or antivirals currently available. However, norovirus inhibitors, including capsid-specific monoclonal antibodies (Mabs) and nanobodies, have recently shown promising results. Several Mabs and nanobodies were found to inhibit norovirus replication using a human intestinal enteroid (HIE) culture system and/or could block norovirus attachment to histo-blood group antigen (HBGA) co-factors. In our pursuit to develop a single broad-spectrum norovirus therapeutic, we continued our analysis and development of a cross-reactive and HBGA interfering nanobody (NB26). To improve NB26 binding capacity and therapeutic potential, we conjugated NB26 onto a human IgG Fc domain (Fc-NB26). We confirmed that Fc-NB26 cross-reacts with genetically diverse GII genotype capsid protruding (P) domains (GII.8, GII.14, GII.17, GII.24, GII.26, and GII.NA1) using a direct enzyme-linked immunosorbent assay. Furthermore, X-ray crystallography structures of these P domains and structures of other GII genotypes reveal that the NB26 binding site is largely conserved, validating its broad reactivity. We showed that Fc-NB26 has ~100-fold higher affinity toward the norovirus P domain compared to native NB26. We also found that both NB26 and Fc-NB26 neutralize human norovirus replication in the HIE culture system. Furthermore, the mode of inhibition confirmed that like NB26, Fc-NB26 caused norovirus particle disassembly and aggregation. Overall, these new findings demonstrate that structural modifications to nanobodies can improve their therapeutic potential.IMPORTANCEDeveloping vaccines and antivirals against norovirus remains a challenge, mainly due to the constant genetic and antigenic evolution. Moreover, re-infection with genetically related and/or antigenic variants is not uncommon. We further developed our leading norovirus nanobody (NB26) that indirectly interfered with norovirus binding to HBGAs, by converting NB26 into a dimeric Fc-linked Nanobody (Fc-NB26). We found that Fc-NB26 had improved binding affinity and neutralization capacity compared with native NB26. Using X-ray crystallography, we showed this nanobody engaged highly conserved capsid residues among genetically diverse noroviruses. Development of such broadly reactive potent therapeutic nanobodies delivered as a slow-releasing prophylactic could be of exceptional value for norovirus outbreaks, especially for the prevention or treatment of severe acute gastroenteritis in high-risk groups such as the young, elderly, and immunocompromised.
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Affiliation(s)
- Grant S. Hansman
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Gargi Kher
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | | | - Jeremy R. H. Tame
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Lauren Hartley-Tassell
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Hiro Irie
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
- School of Environment and Science, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Penny A. Rudd
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
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27
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Dilly JJ, Morgan AL, Bedding MJ, Low JKK, Mackay JP, Conibear AC, Bhusal RP, Stone MJ, Franck C, Payne RJ. Tyrosine Sulfation Modulates the Binding Affinity of Chemokine-Targeting Nanobodies. ACS Chem Biol 2024; 19:1426-1432. [PMID: 38941516 DOI: 10.1021/acschembio.4c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Chemokines are an important family of small proteins integral to leukocyte recruitment during inflammation. Dysregulation of the chemokine-chemokine receptor axis is implicated in many diseases, and both chemokines and their cognate receptors have been the targets of therapeutic development. Analysis of the antigen-binding regions of chemokine-binding nanobodies revealed a sequence motif suggestive of tyrosine sulfation. Given the well-established importance of post-translational tyrosine sulfation of receptors for chemokine affinity, it was hypothesized that the sulfation of these nanobodies may contribute to chemokine binding and selectivity. Four nanobodies (16C1, 9F1, 11B1, and 11F2) were expressed using amber codon suppression to incorporate tyrosine sulfation. The sulfated variant of 16C1 demonstrated significantly improved chemokine binding compared to the non-sulfated counterpart, while the other nanobodies displayed equipotent or reduced affinity upon sulfation. The ability of tyrosine sulfation to modulate chemokine binding, both positively and negatively, could be leveraged for chemokine-targeted sulfo-nanobody therapeutics in the future.
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Affiliation(s)
- Joshua J Dilly
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alexandra L Morgan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Max J Bedding
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Anne C Conibear
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9/163, Wien 1060, Austria
| | - Ram Prasad Bhusal
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Martin J Stone
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Charlotte Franck
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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Zettl I, Bauernfeind C, Kollárová J, Flicker S. Single-Domain Antibodies-Novel Tools to Study and Treat Allergies. Int J Mol Sci 2024; 25:7602. [PMID: 39062843 PMCID: PMC11277559 DOI: 10.3390/ijms25147602] [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: 06/07/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
IgE-mediated allergies represent a major health problem in the modern world. Apart from allergen-specific immunotherapy (AIT), the only disease-modifying treatment, researchers focus on biologics that target different key molecules such as allergens, IgE, or type 2 cytokines to ameliorate allergic symptoms. Single-domain antibodies, or nanobodies, are the newcomers in biotherapeutics, and their huge potential is being investigated in various research fields since their discovery 30 years ago. While they are dominantly applied for theranostics of cancer and treatment of infectious diseases, nanobodies have become increasingly substantial in allergology over the last decade. In this review, we discuss the prerequisites that we consider to be important for generating useful nanobody-based drug candidates for treating allergies. We further summarize the available research data on nanobodies used as allergen monitoring and detection probes and for therapeutic approaches. We reflect on the limitations that have to be addressed during the development process, such as in vivo half-life and immunogenicity. Finally, we speculate about novel application formats for allergy treatment that might be available in the future.
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Affiliation(s)
- Ines Zettl
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Clarissa Bauernfeind
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria
- Center for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria
| | - Jessica Kollárová
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Sabine Flicker
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria
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Liao X, Wang J, Guo B, Bai M, Zhang Y, Yu G, Wang P, Wei J, Wang J, Yan X, Fan K, Wang Y. Enhancing Nanobody Immunoassays through Ferritin Fusion: Construction of a Salmonella-Specific Fenobody for Improved Avidity and Sensitivity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14967-14974. [PMID: 38957086 DOI: 10.1021/acs.jafc.4c03606] [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: 07/04/2024]
Abstract
Nanobodies (Nbs) serve as powerful tools in immunoassays. However, their small size and monovalent properties pose challenges for practical application. Multimerization emerges as a significant strategy to address these limitations, enhancing the utilization of nanobodies in immunoassays. Herein, we report the construction of a Salmonella-specific fenobody (Fb) through the fusion of a nanobody to ferritin, resulting in a self-assembled 24-valent nanocage-like structure. The fenobody exhibits a 35-fold increase in avidity compared to the conventional nanobody while retaining good thermostability and specificity. Leveraging this advancement, three ELISA modes were designed using Fb as the capture antibody, along with unmodified Nb422 (FbNb-ELISA), biotinylated Nb422 (FbBio-ELISA), and phage-displayed Nb422 (FbP-ELISA) as the detection antibody, respectively. Notably, the FbNb-ELISA demonstrates a detection limit (LOD) of 3.56 × 104 CFU/mL, which is 16-fold lower than that of FbBio-ELISA and similar to FbP-ELISA. Moreover, a fenobody and nanobody sandwich chemiluminescent enzyme immunoassay (FbNb-CLISA) was developed by replacing the TMB chromogenic substrate with luminal, resulting in a 12-fold reduction in the LOD. Overall, the ferritin-displayed technology represents a promising methodology for enhancing the detection performance of nanobody-based sandwich ELISAs, thereby expanding the applicability of Nbs in food detection and other fields requiring multivalent modification.
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Affiliation(s)
- Xingrui Liao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Jiamin Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Bing Guo
- College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengfan Bai
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Yao Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Gege Yu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Peng Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Juan Wei
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Jianlong Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Xiyun Yan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Kelong Fan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Nanozyme Laboratory in Zhongyuan, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan 451163, China
| | - Yanru Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shanxi 712100, China
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Hwang J, Jang IY, Bae E, Choi J, Kim JH, Lee SB, Kim JH, Lee JP, Jang HY, Kim HT, Lim JW, Yeom M, Jang E, Kim SE, Jeong HH, Kim JW, Seong SY, Song D, Na W. H1N1 nanobody development and therapeutic efficacy verification in H1N1-challenged mice. Biomed Pharmacother 2024; 176:116781. [PMID: 38805966 DOI: 10.1016/j.biopha.2024.116781] [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: 03/11/2024] [Revised: 05/08/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024] Open
Abstract
Influenza A virus causes numerous deaths and infections worldwide annually. Therefore, we have considered nanobodies as a potential treatment for patients with severe cases of influenza. We developed a nanobody that was expected to have protective efficacy against the A/California/04/2009 (CA/04; pandemic 2009 flu strain) and evaluated its therapeutic efficacy against CA/04 in mice experiments. This nanobody was derived from the immunization of the alpaca, and the inactivated CA/04 virus was used as an immunogen. We successfully generated a nanobody library through bio-panning, phage ELISA, and Bio-layer interferometry. Moreover, we confirmed that administering nanobodies after lethal doses of CA/04 reduced viral replication in the lungs and influenza-induced clinical signs in mice. These research findings will help to develop nanobodies as viral therapeutics for CA/04 and other infectious viruses.
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Affiliation(s)
- Jaehyun Hwang
- College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea; Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea
| | - In-Young Jang
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Eunseo Bae
- College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea; Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea
| | - Jaeseok Choi
- College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea; Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea
| | - Jeong Hwan Kim
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Sang Beum Lee
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Jong Hyun Kim
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Jae Pil Lee
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Ho Young Jang
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Hyoung Tae Kim
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea
| | - Jong-Woo Lim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Minjoo Yeom
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunhee Jang
- Research Center, HuVet bio, Inc., Seoul 05836, Republic of Korea
| | - Seong-Eun Kim
- Research Center, HuVet bio, Inc., Seoul 05836, Republic of Korea
| | - Hyoung Hwa Jeong
- Research Center, HuVet bio, Inc., Seoul 05836, Republic of Korea
| | - Jung Woo Kim
- Research Center, HuVet bio, Inc., Seoul 05836, Republic of Korea
| | - Seung-Yong Seong
- Shaperon R&D center, Shaperon, Inc., Seoul 06373, Republic of Korea.
| | - Daesub Song
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea.
| | - Woonsung Na
- Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea; Department of Oral Microbiology and Immunology, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea.
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Wang M, Ying T, Wu Y. Single-domain antibodies as therapeutics for solid tumor treatment. Acta Pharm Sin B 2024; 14:2854-2868. [PMID: 39027249 PMCID: PMC11252471 DOI: 10.1016/j.apsb.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/23/2024] [Accepted: 03/01/2024] [Indexed: 07/20/2024] Open
Abstract
Single-domain antibodies (sdAbs), initially identified in camelids or sharks and commonly referred to as nanobodies or VNARs, have emerged as a promising alternative to conventional therapeutic antibodies. These sdAbs have many superior physicochemical and pharmacological properties, including small size, good solubility and thermostability, easier accessible epitopes, and strong tissue penetration. However, the inherent challenges associated with the animal origin of sdAbs limit their clinical use. In recent years, various innovative humanization technologies, including complementarity-determining region (CDR) grafting or complete engineering of fully human sdAbs, have been developed to mitigate potential immunogenicity issues and enhance their compatibility. This review provides a comprehensive exploration of sdAbs, emphasizing their distinctive features and the progress in humanization methodologies. In addition, we provide an overview of the recent progress in developing drugs and therapeutic strategies based on sdAbs and their potential in solid tumor treatment, such as sdAb-drug conjugates, multispecific sdAbs, sdAb-based delivery systems, and sdAb-based cell therapy.
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Affiliation(s)
- Mingkai Wang
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Department of Pulmonary and Critical Care Medicine, Department of Liver Surgery and Transplantation, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Engineering Research Center for Synthetic Immunology, Shanghai 200032, China
| | - Tianlei Ying
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Department of Pulmonary and Critical Care Medicine, Department of Liver Surgery and Transplantation, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Engineering Research Center for Synthetic Immunology, Shanghai 200032, China
| | - Yanling Wu
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Department of Pulmonary and Critical Care Medicine, Department of Liver Surgery and Transplantation, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Engineering Research Center for Synthetic Immunology, Shanghai 200032, China
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32
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Bastos-Soares EA, da Silva Morais MS, Funes-Huacca M, Sousa RMO, Brilhante-Da-Silva N, Roberto SA, Prado NDR, Dos Santos CND, Marinho ACM, Soares AM, Stabeli RG, Pereira SDS, Fernandes CFC. Single-Domain Antibody-Gold Nanoparticle Bioconjugates as Immunosensors for the Detection of Hantaviruses. Mol Diagn Ther 2024; 28:479-494. [PMID: 38796660 DOI: 10.1007/s40291-024-00713-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 05/28/2024]
Abstract
INTRODUCTION Hantavirus, a zoonotic pathogen, causes severe syndromes like hemorrhagic fever with renal syndrome (HFRS), sometimes fatal in humans. Considering the importance of detecting the hantavirus antigen, the construction of an immunosensor is essential. The structural and functional characteristics of camelid nanobodies (VHHs) encourage their application in the areas of nanobiotechnology, therapeutics, diagnostics, and basic research. Therefore, this study aimed to standardize stable bioconjugates using gold nanoparticles (AuNPs) and VHHs, in order to develop immunobiosensors for the diagnosis of hantavirus infection. METHODS Immobilized metal affinity chromatography (IMAC) was performed to obtain purified recombinant anti-hantavirus nucleocapsid nanobodies (anti-prNΔ85 VHH), while AuNPs were synthesized for bioconjugation. UV-visible spectrophotometry and transmission electron microscopy (TEM) analysis were employed to characterize AuNPs. RESULTS The bioconjugation stability parameters (VHH-AuNPs), analyzed by spectrophotometry, showed that the ideal pH value and VHH concentration were obtained at 7.4 and 50 μg/mL, respectively, after addition of 1 M NaCl, which induces AuNP aggregation. TEM performed before and after bioconjugation showed uniform, homogeneous, well-dispersed, and spherical AuNPs with an average diameter of ~ 14 ± 0.57 nm. Furthermore, high-resolution images revealed a thin white halo on the surface of the AuNPs, indicating the coating of the AuNPs with protein. A biosensor simulation test (dot blot-like [DB-like]) was performed in stationary phase to verify the binding and detection limits of the recombinant nucleocapsid protein from the Araucária hantavirus strain (prN∆85). DISCUSSION Using AuNPs/VHH bioconjugates, a specific interaction was detected between 5 and 10 min of reaction in a dose-dependent manner. It was observed that this test was sensitive enough to detect prNΔ85 at concentrations up to 25 ng/μL. Considering that nanostructured biological systems such as antibodies conjugated with AuNPs are useful tools for the development of chemical and biological sensors, the stability of the bioconjugate indicates proficiency in detecting antigens. The experimental results obtained will be used in a future immunospot assay or lateral flow immunochromatography analysis for hantavirus detection.
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Affiliation(s)
- Erika A Bastos-Soares
- Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Porto Velho, RO, Brazil
- Programa de Pós-graduação em Biologia Experimental, PGBIOEXP, Universidade Federal de Rondônia, UNIR, Porto Velho, RO, Brazil
| | - Michelle Suelen da Silva Morais
- Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Porto Velho, RO, Brazil
- Programa de Pós-graduação em Biologia Experimental, PGBIOEXP, Universidade Federal de Rondônia, UNIR, Porto Velho, RO, Brazil
| | - Maribel Funes-Huacca
- Departamento de Química, Universidade Federal de Rondônia, UNIR, Porto Velho, RO, Brazil
| | - Rosa Maria O Sousa
- Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Porto Velho, RO, Brazil
| | | | - Sibele Andrade Roberto
- Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Porto Velho, RO, Brazil
- Programa de Pós-graduação em Biologia Experimental, PGBIOEXP, Universidade Federal de Rondônia, UNIR, Porto Velho, RO, Brazil
| | | | | | - Anna C M Marinho
- Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Ceará, Eusébio, CE, Brazil
| | - Andreimar M Soares
- Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Porto Velho, RO, Brazil
- Centro Universitário São Lucas, UniSL, Porto Velho, RO, Brazil
- Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, RO, Brazil
- Programa de Pós-graduação em Biologia Experimental, PGBIOEXP, Universidade Federal de Rondônia, UNIR, Porto Velho, RO, Brazil
| | - Rodrigo G Stabeli
- Fundação Oswaldo Cruz, FIOCRUZ, Plataforma Bi-institucional de Medicina Translacional, Ribeirão Preto, SP, Brazil
| | - Soraya Dos Santos Pereira
- Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Porto Velho, RO, Brazil
- Programa de Pós-graduação em Biologia Experimental, PGBIOEXP, Universidade Federal de Rondônia, UNIR, Porto Velho, RO, Brazil
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Zeng J, Fang Y, Zhang Z, Lv Z, Wang X, Huang Q, Tian Z, Li J, Xu W, Zhu W, Yu J, Liu T, Qian Q. Antitumor activity of Z15-0-2, a bispecific nanobody targeting PD-1 and CTLA-4. Oncogene 2024; 43:2244-2252. [PMID: 38806619 PMCID: PMC11245388 DOI: 10.1038/s41388-024-03066-5] [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: 03/06/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024]
Abstract
The combination of programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte antigen 4 (CTLA-4) antibodies has potential for enhancing clinical efficacy. We described the development and antitumor activity of Z15-0, a bispecific nanobody targeting both the PD-1 and CTLA-4 pathways simultaneously. We designed and optimized the mRNA sequence encoding Z15-0, referred to as Z15-0-2 and through a series of in vitro and in vivo experiments, we established that the optimized Z15-0-2 mRNA sequence significantly increased the expression of the bispecific nanobody. Administration of Z15-0-2 mRNA to tumor-bearing mice led to greater inhibition of tumor growth compared to controls. In aggregate, we introduced a novel bispecific nanobody and have re-engineered it to boost expression of mRNA, representing a new drug development paradigm.
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Affiliation(s)
- Jianyao Zeng
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Yuan Fang
- Shanghai Cell Therapy Group Co., Ltd, Shanghai, 201805, China
| | - Zixuan Zhang
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Zhenzhen Lv
- Shanghai Cell Therapy Group Co., Ltd, Shanghai, 201805, China
| | - Xiaodie Wang
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Qian Huang
- Shanghai Cell Therapy Group Co., Ltd, Shanghai, 201805, China
| | - Zhidan Tian
- Shanghai Cell Therapy Group Co., Ltd, Shanghai, 201805, China
| | - Jiaguo Li
- Shanghai Cell Therapy Group Co., Ltd, Shanghai, 201805, China
| | - Wenfeng Xu
- Shanghai Cell Therapy Group Co., Ltd, Shanghai, 201805, China
| | - Weimin Zhu
- Shanghai Cell Therapy Group Co., Ltd, Shanghai, 201805, China
| | - Jing Yu
- Shanghai Cell Therapy Group Co., Ltd, Shanghai, 201805, China
| | - Tao Liu
- Shanghai Cell Therapy Group Co., Ltd, Shanghai, 201805, China.
| | - Qijun Qian
- School of Medicine, Shanghai University, Shanghai, 200444, China.
- Shanghai Cell Therapy Group Co., Ltd, Shanghai, 201805, China.
- Shanghai Mengchao Cancer Hospital, Shanghai University, Shanghai, 201805, China.
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Zhang Y, Wang T, Zhang P, Wan Y, Chang G, Xu X, Ruan F, Zhou T, Zhao Q, Zhang M, Wang X. Facile construction of sandwich ELISA based on double-nanobody for specific detection of α-hemolysin in food samples. Talanta 2024; 274:126021. [PMID: 38569370 DOI: 10.1016/j.talanta.2024.126021] [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: 10/10/2023] [Revised: 03/25/2024] [Accepted: 03/30/2024] [Indexed: 04/05/2024]
Abstract
α-hemolysin (Hla), a toxin secreted by Staphylococcus aureus (S. aureus), has been proved to be involved in the occurrence and aggravation of food poisoning. Hence, it is quite essential to establish its rapid detection methods to guarantee food safety. Sandwich ELISA based on nanobody is well known to be viable for toxins, but there is absence of nanobody against Hla, let alone a pair for it. Therefore, in this paper, we screened specific nanobodies by bio-panning and obtained the optimal nanobody pair for sandwich ELISA firstly. Then, RANbody, a novel nanobody owning both recognition and catalytic capability, is generated in a single step and at low cost through molecular recombination technology. Subsequently, sandwich ELISA was developed to detect Hla based on the nanobody and RANbody, that not only eliminated the use of secondary antibodies and animal-derived antibody, but also reduced detection time and cost, compared with traditional sandwich ELISA. Lastly, the performance has been evaluated, especially for specificity which showed no response to other hemolysins and a low limit of detection of 10 ng/mL. Besides, the proposed sandwich ELISA exhibits favorable feasibility and was successfully employed for the detection of Hla in milk and pork samples.
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Affiliation(s)
- Yao Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Ting Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Pengfei Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yangli Wan
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Guanhong Chang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xu Xu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Fuqian Ruan
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Ting Zhou
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Qin Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Min Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Xin Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Eshak F, Pion L, Scholler P, Nevoltris D, Chames P, Rondard P, Pin JP, Acher FC, Goupil-Lamy A. Epitope Identification of an mGlu5 Receptor Nanobody Using Physics-Based Molecular Modeling and Deep Learning Techniques. J Chem Inf Model 2024; 64:4436-4461. [PMID: 38423996 DOI: 10.1021/acs.jcim.3c01620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The world has witnessed a revolution in therapeutics with the development of biological medicines such as antibodies and antibody fragments, notably nanobodies. These nanobodies possess unique characteristics including high specificity and modulatory activity, making them promising candidates for therapeutic applications. Identifying their binding mode is essential for their development. Experimental structural techniques are effective to get such information, but they are expensive and time-consuming. Here, we propose a computational approach, aiming to identify the epitope of a nanobody that acts as an agonist and a positive allosteric modulator at the rat metabotropic glutamate receptor 5. We employed multiple structure modeling tools, including various artificial intelligence algorithms for epitope mapping. The computationally identified epitope was experimentally validated, confirming the success of our approach. Additional dynamics studies provided further insights on the modulatory activity of the nanobody. The employed methodologies and approaches initiate a discussion on the efficacy of diverse techniques for epitope mapping and later nanobody engineering.
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Affiliation(s)
- Floriane Eshak
- SPPIN CNRS UMR 8003, Université Paris Cité, 75006 Paris, France
| | - Léo Pion
- Institut de Génomique Fonctionnelle, Université Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Pauline Scholler
- Institut de Génomique Fonctionnelle, Université Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Damien Nevoltris
- Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 13009 Marseille, France
| | - Patrick Chames
- Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 13009 Marseille, France
| | - Philippe Rondard
- Institut de Génomique Fonctionnelle, Université Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle, Université Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | | | - Anne Goupil-Lamy
- BIOVIA Science Council, Dassault Systèmes, 78140 Vélizy-Villacoublay, France
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Badenhorst M, Windhorst AD, Beaino W. Navigating the landscape of PD-1/PD-L1 imaging tracers: from challenges to opportunities. Front Med (Lausanne) 2024; 11:1401515. [PMID: 38915766 PMCID: PMC11195831 DOI: 10.3389/fmed.2024.1401515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/20/2024] [Indexed: 06/26/2024] Open
Abstract
Immunotherapy targeted to immune checkpoint inhibitors, such as the program cell death receptor (PD-1) and its ligand (PD-L1), has revolutionized cancer treatment. However, it is now well-known that PD-1/PD-L1 immunotherapy response is inconsistent among patients. The current challenge is to customize treatment regimens per patient, which could be possible if the PD-1/PD-L1 expression and dynamic landscape are known. With positron emission tomography (PET) imaging, it is possible to image these immune targets non-invasively and system-wide during therapy. A successful PET imaging tracer should meet specific criteria concerning target affinity, specificity, clearance rate and target-specific uptake, to name a few. The structural profile of such a tracer will define its properties and can be used to optimize tracers in development and design new ones. Currently, a range of PD-1/PD-L1-targeting PET tracers are available from different molecular categories that have shown impressive preclinical and clinical results, each with its own advantages and disadvantages. This review will provide an overview of current PET tracers targeting the PD-1/PD-L1 axis. Antibody, peptide, and antibody fragment tracers will be discussed with respect to their molecular characteristics and binding properties and ways to optimize them.
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Affiliation(s)
- Melinda Badenhorst
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Radiology and Nuclear Medicine, De Boelelaan, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Albert D. Windhorst
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Radiology and Nuclear Medicine, De Boelelaan, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Wissam Beaino
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Radiology and Nuclear Medicine, De Boelelaan, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
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Paul S, Konig MF, Pardoll DM, Bettegowda C, Papadopoulos N, Wright KM, Gabelli SB, Ho M, van Elsas A, Zhou S. Cancer therapy with antibodies. Nat Rev Cancer 2024; 24:399-426. [PMID: 38740967 PMCID: PMC11180426 DOI: 10.1038/s41568-024-00690-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/29/2024] [Indexed: 05/16/2024]
Abstract
The greatest challenge in cancer therapy is to eradicate cancer cells with minimal damage to normal cells. Targeted therapy has been developed to meet that challenge, showing a substantially increased therapeutic index compared with conventional cancer therapies. Antibodies are important members of the family of targeted therapeutic agents because of their extraordinarily high specificity to the target antigens. Therapeutic antibodies use a range of mechanisms that directly or indirectly kill the cancer cells. Early antibodies were developed to directly antagonize targets on cancer cells. This was followed by advancements in linker technologies that allowed the production of antibody-drug conjugates (ADCs) that guide cytotoxic payloads to the cancer cells. Improvement in our understanding of the biology of T cells led to the production of immune checkpoint-inhibiting antibodies that indirectly kill the cancer cells through activation of the T cells. Even more recently, bispecific antibodies were synthetically designed to redirect the T cells of a patient to kill the cancer cells. In this Review, we summarize the different approaches used by therapeutic antibodies to target cancer cells. We discuss their mechanisms of action, the structural basis for target specificity, clinical applications and the ongoing research to improve efficacy and reduce toxicity.
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Affiliation(s)
- Suman Paul
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Maximilian F Konig
- Division of Rheumatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chetan Bettegowda
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Katharine M Wright
- Discovery Chemistry, Merck Research Laboratory, Merck and Co, West Point, PA, USA
| | - Sandra B Gabelli
- Discovery Chemistry, Merck Research Laboratory, Merck and Co, West Point, PA, USA.
| | - Mitchell Ho
- Antibody Engineering Program, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | | | - Shibin Zhou
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
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Figueroa GB, D'souza S, Pereira HS, Vasudeva G, Figueroa SB, Robinson ZE, Badmalia MD, Meier-Stephenson V, Corcoran JA, van Marle G, Ni Y, Urban S, Coffin CS, Patel TR. Development of a single-domain antibody to target a G-quadruplex located on the hepatitis B virus covalently closed circular DNA genome. J Med Virol 2024; 96:e29692. [PMID: 38804172 DOI: 10.1002/jmv.29692] [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: 01/11/2024] [Revised: 04/22/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
To achieve a virological cure for hepatitis B virus (HBV), innovative strategies are required to target the covalently closed circular DNA (cccDNA) genome. Guanine-quadruplexes (G4s) are a secondary structure that can be adopted by DNA and play a significant role in regulating viral replication, transcription, and translation. Antibody-based probes and small molecules have been developed to study the role of G4s in the context of the human genome, but none have been specifically made to target G4s in viral infection. Herein, we describe the development of a humanized single-domain antibody (S10) that can target a G4 located in the PreCore (PreC) promoter of the HBV cccDNA genome. MicroScale Thermophoresis demonstrated that S10 has a strong nanomolar affinity to the PreC G4 in its quadruplex form and a structural electron density envelope of the complex was determined using Small-Angle X-ray Scattering. Lentiviral transduction of S10 into HepG2-NTCP cells shows nuclear localization, and chromatin immunoprecipitation coupled with next-generation sequencing demonstrated that S10 can bind to the HBV PreC G4 present on the cccDNA. This research validates the existence of a G4 in HBV cccDNA and demonstrates that this DNA secondary structure can be targeted with high structural and sequence specificity using S10.
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Affiliation(s)
- Gerardo B Figueroa
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Simmone D'souza
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Higor S Pereira
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Gunjan Vasudeva
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Sara B Figueroa
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Zachary E Robinson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Maulik D Badmalia
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Vanessa Meier-Stephenson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jennifer A Corcoran
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Guido van Marle
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Yi Ni
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infection Research, Heidelberg University, Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infection Research, Heidelberg University, Heidelberg, Germany
| | - Carla S Coffin
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Trushar R Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
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Liu X, Wang Y, Sun L, Xiao G, Hou N, Chen J, Wang W, Xu X, Gu Y. Screening and optimization of shark nanobodies against SARS-CoV-2 spike RBD. Antiviral Res 2024; 226:105898. [PMID: 38692413 DOI: 10.1016/j.antiviral.2024.105898] [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: 01/01/2024] [Revised: 03/28/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
SARS-CoV-2 continues to threaten human health, antibody therapy is one way to control the infection. Because new SARS-CoV-2 mutations are constantly emerging, there is an urgent need to develop broadly neutralizing antibodies to block the viral entry into host cells. VNAR from sharks is the smallest natural antigen binding domain, with the advantages of small size, flexible paratopes, good stability, and low manufacturing cost. Here, we used recombinant SARS-CoV-2 Spike-RBD to immunize sharks and constructed a VNAR phage display library. VNAR R1C2, selected from the library, efficiently binds to the RBD domain and blocks the infection of ACE2-positive cells by pseudovirus. Next, homologous bivalent VNARs were constructed through the tandem fusion of two R1C2 units, which enhanced both the affinity and neutralizing activity of R1C2. R1C2 was predicted to bind to a relatively conserved region within the RBD. By introducing mutations at four key binding sites within the CDR3 and HV2 regions of R1C2, the affinity and neutralizing activity of R1C2 were significantly improved. Furthermore, R1C2 also exhibits an effective capacity of binding to the Omicron variants (BA.2 and XBB.1). Together, these results suggest that R1C2 could serve as a valuable candidate for preventing and treating SARS-CoV-2 infections.
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Affiliation(s)
- Xiaochun Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao, 266071, China
| | - Yanqing Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Lishan Sun
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Guokai Xiao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Ning Hou
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jin Chen
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Wei Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Ximing Xu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao, 266071, China.
| | - Yuchao Gu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
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Yamamoto K, Nagatoishi S, Nakakido M, Kuroda D, Tsumoto K. Functional insights of Tyr37 in framework region 2 directly contributing to the binding affinities and dissociation kinetics in single-domain V HH antibodies. Biochem Biophys Res Commun 2024; 709:149839. [PMID: 38564943 DOI: 10.1016/j.bbrc.2024.149839] [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: 03/10/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Single-domain VHH antibody is regarded as one of the promising antibody classes for therapeutic and diagnostic applications. VHH antibodies have amino acids in framework region 2 that are distinct from those in conventional antibodies, such as the Val37Phe/Tyr (V37F/Y) substitution. Correlations between the residue type at position 37 and the conformation of the CDR3 in VHH antigen recognition have been previously reported. However, few studies focused on the meaning of harboring two residue types in position 37 of VHH antibodies, and the concrete roles of Y37 have been little to be elucidated. Here, we investigated the functional states of position 37 in co-crystal structures and performed analyses of three model antibodies with either F or Y at position 37. Our analysis indicates that Y at position 37 enhances the dissociation rate, which is highly correlated with drug efficacy. Our findings help to explain the molecular mechanisms that distinguish VHH antibodies from conventional antibodies.
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Affiliation(s)
- Koichi Yamamoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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Rizk SS, Moustafa DM, ElBanna SA, Nour El-Din HT, Attia AS. Nanobodies in the fight against infectious diseases: repurposing nature's tiny weapons. World J Microbiol Biotechnol 2024; 40:209. [PMID: 38771414 PMCID: PMC11108896 DOI: 10.1007/s11274-024-03990-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024]
Abstract
Nanobodies are the smallest known antigen-binding molecules to date. Their small size, good tissue penetration, high stability and solubility, ease of expression, refolding ability, and negligible immunogenicity in the human body have granted them excellence over conventional antibodies. Those exceptional attributes of nanobodies make them promising candidates for various applications in biotechnology, medicine, protein engineering, structural biology, food, and agriculture. This review presents an overview of their structure, development methods, advantages, possible challenges, and applications with special emphasis on infectious diseases-related ones. A showcase of how nanobodies can be harnessed for applications including neutralization of viruses and combating antibiotic-resistant bacteria is detailed. Overall, the impact of nanobodies in vaccine design, rapid diagnostics, and targeted therapies, besides exploring their role in deciphering microbial structures and virulence mechanisms are highlighted. Indeed, nanobodies are reshaping the future of infectious disease prevention and treatment.
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Affiliation(s)
- Soha S Rizk
- Microbiology and Immunology Postgraduate Program, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Dina M Moustafa
- Department of Medical Sciences, Faculty of Dentistry, The British University in Egypt, El Sherouk City, Cairo, 11837, Egypt
| | - Shahira A ElBanna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Hanzada T Nour El-Din
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Ahmed S Attia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
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Esposito G, Hunashal Y, Percipalle M, Fogolari F, Venit T, Leonchiks A, Gunsalus KC, Piano F, Percipalle P. Assessing nanobody interaction with SARS-CoV-2 Nsp9. PLoS One 2024; 19:e0303839. [PMID: 38758765 PMCID: PMC11101046 DOI: 10.1371/journal.pone.0303839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
The interaction between SARS-CoV-2 non-structural protein Nsp9 and the nanobody 2NSP90 was investigated by NMR spectroscopy using the paramagnetic perturbation methodology PENELOP (Paramagnetic Equilibrium vs Nonequilibrium magnetization Enhancement or LOss Perturbation). The Nsp9 monomer is an essential component of the replication and transcription complex (RTC) that reproduces the viral gRNA for subsequent propagation. Therefore preventing Nsp9 recruitment in RTC would represent an efficient antiviral strategy that could be applied to different coronaviruses, given the Nsp9 relative invariance. The NMR results were consistent with a previous characterization suggesting a 4:4 Nsp9-to-nanobody stoichiometry with the occurrence of two epitope pairs on each of the Nsp9 units that establish the inter-dimer contacts of Nsp9 tetramer. The oligomerization state of Nsp9 was also analyzed by molecular dynamics simulations and both dimers and tetramers resulted plausible. A different distribution of the mapped epitopes on the tetramer surface with respect to the former 4:4 complex could also be possible, as well as different stoichiometries of the Nsp9-nanobody assemblies such as the 2:2 stoichiometry suggested by the recent crystal structure of the Nsp9 complex with 2NSP23 (PDB ID: 8dqu), a nanobody exhibiting essentially the same affinity as 2NSP90. The experimental NMR evidence, however, ruled out the occurrence in liquid state of the relevant Nsp9 conformational change observed in the same crystal structure.
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Affiliation(s)
- Gennaro Esposito
- Division of Science, New York University Abu Dhabi, Abu Dhabi, UAE
- Istituto Nazionale Biostrutture e Biosistemi, Roma, Italy
| | | | | | - Federico Fogolari
- Istituto Nazionale Biostrutture e Biosistemi, Roma, Italy
- Dipartimento di Scienze Matematiche, Informatiche e Fisiche, Università di Udine, Udine, Italy
| | - Tomas Venit
- Division of Science, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Kristin C. Gunsalus
- Department of Biology and Center Genomics System Biology, NYU, New York, New York, United States of America
- Center Genomics System Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Fabio Piano
- Department of Biology and Center Genomics System Biology, NYU, New York, New York, United States of America
- Center Genomics System Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Piergiorgio Percipalle
- Division of Science, New York University Abu Dhabi, Abu Dhabi, UAE
- Center Genomics System Biology, New York University Abu Dhabi, Abu Dhabi, UAE
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Wu Y, Zhu M, Sun B, Chen Y, Huang Y, Gai J, Li G, Li Y, Wan Y, Ma L. A humanized trivalent Nectin-4-targeting nanobody drug conjugate displays potent antitumor activity in gastric cancer. J Nanobiotechnology 2024; 22:256. [PMID: 38755613 PMCID: PMC11097425 DOI: 10.1186/s12951-024-02521-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Gastric cancer represents a highly lethal malignancy with an elevated mortality rate among cancer patients, coupled with a suboptimal postoperative survival prognosis. Nectin-4, an overexpressed oncological target for various cancers, has been exploited to create antibody-drug conjugates (ADCs) to treat solid tumors. However, there is limited research on Nectin-4 ADCs specifically for gastric cancer, and conventional immunoglobulin G (IgG)-based ADCs frequently encounter binding site barriers. Based on the excellent tumor penetration capabilities inherent in nanobodies (Nbs), we developed Nectin-4-targeting Nb drug conjugates (NDCs) for the treatment of gastric cancer. RESULTS An immunized phage display library was established and employed for the selection of Nectin-4-specific Nbs using phage display technology. Subsequently, these Nbs were engineered into homodimers to enhance Nb affinity. To prolong in vivo half-life and reduce immunogenicity, we fused an Nb targeting human serum albumin (HSA), resulting in the development of trivalent humanized Nbs. Further, we site-specifically conjugated a monomethyl auristatin E (MMAE) at the C-terminus of the trivalent Nbs, creating Nectin-4 NDC (huNb26/Nb26-Nbh-MMAE) with a drug-to-antibody ratio (DAR) of 1. Nectin-4 NDC demonstrated excellent in vitro cell-binding activities and cytotoxic efficacy against cells with high Nectin-4 expression. Subsequent administration of Nectin-4 NDC to mice bearing NCI-N87 human gastric cancer xenografts demonstrated rapid tissue penetration and high tumor uptake through in vivo imaging. Moreover, Nectin-4 NDC exhibited noteworthy dose-dependent anti-tumor efficacy in in vivo studies. CONCLUSION We have engineered a Nectin-4 NDC with elevated affinity and effective tumor uptake, further establishing its potential as a therapeutic agent for gastric cancer.
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Affiliation(s)
- Yue Wu
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Min Zhu
- Shanghai Novamab Biopharmaceuticals Co., Ltd., Shanghai, China
| | - Baihe Sun
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yongting Chen
- Graduate School of Xinxiang Medical University, Henan, China
| | - Yuping Huang
- Shanghai Novamab Biopharmaceuticals Co., Ltd., Shanghai, China
| | - Junwei Gai
- Shanghai Novamab Biopharmaceuticals Co., Ltd., Shanghai, China
| | - Guanghui Li
- Shanghai Novamab Biopharmaceuticals Co., Ltd., Shanghai, China
| | - Yanfei Li
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China.
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China.
| | - Yakun Wan
- Shanghai Novamab Biopharmaceuticals Co., Ltd., Shanghai, China.
| | - Linlin Ma
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China.
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China.
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Tillib SV, Goryainova OS. Extending Linker Sequences between Antigen-Recognition Modules Provides More Effective Production of Bispecific Nanoantibodies in the Periplasma of E. coli. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:933-941. [PMID: 38880653 DOI: 10.1134/s0006297924050134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/27/2024] [Accepted: 04/27/2024] [Indexed: 06/18/2024]
Abstract
Technology of production of single-domain antibodies (NANOBODY® molecules, also referred to as nanoantibodies, nAb, or molecules based on other stable protein structures) and their derivatives to solve current problems in biomedicine is becoming increasingly popular. Indeed, the format of one small, highly soluble protein with a stable structure, fully functional in terms of specific recognition, is very convenient as a module for creating multivalent, bi-/oligo-specific genetically engineered targeting molecules and structures. Production of nAb in periplasm of E. coli bacterium is a very convenient and fairly universal way to obtain analytical quantities of nAb for the initial study of the properties of these molecules and selection of the most promising nAb variants. The situation is more complicated with production of bi- and multivalent derivatives of the initially selected nAbs under the same conditions. In this work, extended linker sequences (52 and 86 aa) between the antigen-recognition modules in the cloned expression constructs were developed and applied in order to increase efficiency of production of bispecific nanoantibodies (bsNB) in the periplasm of E. coli bacteria. Three variants of model bsNBs described in this study were produced in the periplasm of bacteria and isolated in soluble form with preservation of functionality of all the protein domains. If earlier our attempts to produce bsNB in the periplasm with traditional linkers no longer than 30 aa were unsuccessful, the extended linkers used here provided a significantly more efficient production of bsNB, comparable in efficiency to the traditional production of original monomeric nAbs. The use of sufficiently long linkers could presumably be useful for increasing efficiency of production of other bsNBs and similar molecules in the periplasm of E. coli bacteria.
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Affiliation(s)
- Sergei V Tillib
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Oksana S Goryainova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
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Machado Marinho AC, Chapeaurouge A, Dutra BM, Quintela BCSF, Pereira SS, Fernandes CFC. The role of venom proteomics and single-domain antibodies for antivenoms: Progress in snake envenoming treatment. Drug Discov Today 2024; 29:103967. [PMID: 38555033 DOI: 10.1016/j.drudis.2024.103967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Single-domain antibodies (sdAbs) hold promise for developing new biopharmaceuticals to treat neglected tropical diseases (NTDs), including snakebites, which are severe and occur frequently. In addition, limitations of conventional snakebite treatments, especially in terms of local action, and the global antivenom crisis incentivize the use of this biotechnological tool to design next-generation snakebite antivenoms. Conventional antivenoms for snakebite treatment are usually composed of immunoglobulin G or F(ab')2 fragments derived from the plasma of immunized animals. sdAbs, the smallest antigen-binding fragments, are derived from the variable domains of camelid heavy-chain antibodies. sdAbs may have some advantages over conventional antivenoms for local toxicity, such as better penetration into tissues due to their small size, and high solubility and affinity for venom antigens due to their unique antigen-binding loops and ability to access cryptic epitopes. We present an overview of current antivenom therapy in the context of sdAb development for toxin neutralization. Furthermore, strategies are presented for identifying snake venom's major toxins as well as for developing antisnake toxin sdAbs by employing proteomic tools for toxin neutralization.
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Affiliation(s)
- Anna Carolina Machado Marinho
- Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz Ceará, FIOCRUZ CE, Eusébio-CE, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Ceará, UFC, Fortaleza, Brazil
| | - Alexander Chapeaurouge
- Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz Ceará, FIOCRUZ CE, Eusébio-CE, Brazil
| | - Brunheld Maia Dutra
- Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz Ceará, FIOCRUZ CE, Eusébio-CE, Brazil
| | - Barbara Cibelle S F Quintela
- Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz Ceará, FIOCRUZ CE, Eusébio-CE, Brazil
| | - Soraya S Pereira
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz Rondônia, FIOCRUZ RO, Porto Velho-RO, Brazil
| | - Carla Freire C Fernandes
- Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz Ceará, FIOCRUZ CE, Eusébio-CE, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Ceará, UFC, Fortaleza, Brazil
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Jiang Y, Wang R, Guo J, Cheng K, Chen L, Wang X, Li Y, Du P, Gao C, Lu J, Yu Y, Yang Z. Isolation and characterization of Hc-targeting chimeric heavy chain antibodies neutralizing botulinum neurotoxin type B. Front Immunol 2024; 15:1380694. [PMID: 38779676 PMCID: PMC11109933 DOI: 10.3389/fimmu.2024.1380694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/11/2024] [Indexed: 05/25/2024] Open
Abstract
Background Botulinum neurotoxin (BoNT) produced by Clostridium botulinum is one of the most potent known toxins. Moreover, BoNT is classified as one of the most important biological warfare agents that threatens the biosafety of the world. Currently, the approved treatment for botulism in humans is the use of polyvalent horse serum antitoxins. However, they are greatly limited because of insufficient supply and adverse reactions. Thus, treatment of human botulism requires the development of effective toxin-neutralizing antibodies. Considering their advantages, neutralizing nanobodies will play an increasing role as BoNTs therapeutics. Methods Herein, neutralizing nanobodies binding to the heavy chain (Hc) domain of BoNT/B (BHc) were screened from a phage display library. Then, BoNT/B-specific clones were identified and fused with the human Fc fragment (hFc) to form chimeric heavy chain antibodies. Finally, the affinity, specificity, and neutralizing activity of antibodies against BoNT/B in vivo were evaluated. Results The B5-hFc, B9-hFc and B12-hFc antibodies demonstrated high affinity for BHc in the nanomolar range. The three antibodies were proven to have potent neutralizing activity against BoNT/B in vivo. Conclusion The results demonstrate that inhibiting toxin binding to the host receptor is an efficient strategy and the three antibodies could be used as candidates for the further development of drugs to prevent and treat botulism.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jiansheng Lu
- Beijing Institute of Biotechnology, Beijing, China
| | - Yunzhou Yu
- Beijing Institute of Biotechnology, Beijing, China
| | - Zhixin Yang
- Beijing Institute of Biotechnology, Beijing, China
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Mortelecque J, Zejneli O, Bégard S, Simões MC, ElHajjar L, Nguyen M, Cantrelle FX, Hanoulle X, Rain JC, Colin M, Gomes CM, Buée L, Landrieu I, Danis C, Dupré E. A selection and optimization strategy for single-domain antibodies targeting the PHF6 linear peptide within the tau intrinsically disordered protein. J Biol Chem 2024; 300:107163. [PMID: 38484799 PMCID: PMC11007443 DOI: 10.1016/j.jbc.2024.107163] [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: 07/19/2023] [Revised: 02/15/2024] [Accepted: 03/06/2024] [Indexed: 04/12/2024] Open
Abstract
The use of variable domain of the heavy-chain of the heavy-chain-only antibodies (VHHs) as disease-modifying biomolecules in neurodegenerative disorders holds promises, including targeting of aggregation-sensitive proteins. Exploitation of their clinical values depends however on the capacity to deliver VHHs with optimal physico-chemical properties for their specific context of use. We described previously a VHH with high therapeutic potential in a family of neurodegenerative diseases called tauopathies. The activity of this promising parent VHH named Z70 relies on its binding within the central region of the tau protein. Accordingly, we carried out random mutagenesis followed by yeast two-hybrid screening to obtain optimized variants. The VHHs selected from this initial screen targeted the same epitope as VHH Z70 as shown using NMR spectroscopy and had indeed improved binding affinities according to dissociation constant values obtained by surface plasmon resonance spectroscopy. The improved affinities can be partially rationalized based on three-dimensional structures and NMR data of three complexes consisting of an optimized VHH and a peptide containing the tau epitope. Interestingly, the ability of the VHH variants to inhibit tau aggregation and seeding could not be predicted from their affinity alone. We indeed showed that the in vitro and in cellulo VHH stabilities are other limiting key factors to their efficacy. Our results demonstrate that only a complete pipeline of experiments, here described, permits a rational selection of optimized VHH variants, resulting in the selection of VHH variants with higher affinities and/or acting against tau seeding in cell models.
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Affiliation(s)
- Justine Mortelecque
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Orgeta Zejneli
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France; Univ. Lille, Inserm, CHU-Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Séverine Bégard
- Univ. Lille, Inserm, CHU-Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Margarida C Simões
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Lea ElHajjar
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Marine Nguyen
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - François-Xavier Cantrelle
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Xavier Hanoulle
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | | | - Morvane Colin
- Univ. Lille, Inserm, CHU-Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Cláudio M Gomes
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Luc Buée
- Univ. Lille, Inserm, CHU-Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France.
| | - Isabelle Landrieu
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France.
| | - Clément Danis
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France; Univ. Lille, Inserm, CHU-Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Elian Dupré
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France.
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da Silva Gomes B, Cláudia Paiva-Santos A, Veiga F, Mascarenhas-Melo F. Beyond the adverse effects of the systemic route: Exploiting nanocarriers for the topical treatment of skin cancers. Adv Drug Deliv Rev 2024; 207:115197. [PMID: 38342240 DOI: 10.1016/j.addr.2024.115197] [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: 05/13/2023] [Revised: 12/21/2023] [Accepted: 02/02/2024] [Indexed: 02/13/2024]
Abstract
Skin cancer is a heterogeneous disease that can be divided into two main groups, melanoma and nonmelanoma skin cancers. Conventional therapies for skin cancer have numerous systemic side effects and a high recurrence rate. Topical treatment is an alternative approach, but drug permeability remains a challenge. Therefore, nanocarriers appear as important nanotechnology tools that reduces both the side effects and improves clinical outcomes. This is why they are attracting growing interest. In this review, scientific articles on the use of nanocarriers for the topical treatment of skin cancer were collected. Despite the promising results of the presented nanocarriers and considering that some of them are already on the market, there is an urgent need for investment in the development of manufacturing methods, as well as of suitable toxicological and regulatory evaluations, since the conventional methods currently used to develop these nanocarriers-based products are more time-consuming and expensive than conventional products.
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Affiliation(s)
- Beatriz da Silva Gomes
- Laboratory of Development and Drug Technologies, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Azinhaga Sta. Comba, 3000-548 Coimbra, Portugal.
| | - Ana Cláudia Paiva-Santos
- Laboratory of Development and Drug Technologies, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Azinhaga Sta. Comba, 3000-548 Coimbra, Portugal; University of Coimbra, LAQV-REQUIMTE, Department of Pharmaceutical Technology, Faculty of Pharmacy, Azinhaga Sta. Comba, 3000-548 Coimbra, Portugal.
| | - Francisco Veiga
- Laboratory of Development and Drug Technologies, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Azinhaga Sta. Comba, 3000-548 Coimbra, Portugal; University of Coimbra, LAQV-REQUIMTE, Department of Pharmaceutical Technology, Faculty of Pharmacy, Azinhaga Sta. Comba, 3000-548 Coimbra, Portugal.
| | - Filipa Mascarenhas-Melo
- University of Coimbra, LAQV-REQUIMTE, Department of Pharmaceutical Technology, Faculty of Pharmacy, Azinhaga Sta. Comba, 3000-548 Coimbra, Portugal; Higher School of Health, Polytechnic Institute of Guarda, Rua da Cadeia, 6300 - 307 Guarda, Portugal.
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Shang W, Hu X, Lin X, Li S, Xiong S, Huang B, Wang X. Iterative In Silico Screening for Optimizing Stable Conformation of Anti-SARS-CoV-2 Nanobodies. Pharmaceuticals (Basel) 2024; 17:424. [PMID: 38675386 PMCID: PMC11054880 DOI: 10.3390/ph17040424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Nanobodies (Nbs or VHHs) are single-domain antibodies (sdAbs) derived from camelid heavy-chain antibodies. Nbs have special and unique characteristics, such as small size, good tissue penetration, and cost-effective production, making Nbs a good candidate for the diagnosis and treatment of viruses and other pathologies. Identifying effective Nbs against COVID-19 would help us control this dangerous virus or other unknown variants in the future. Herein, we introduce an in silico screening strategy for optimizing stable conformation of anti-SARS-CoV-2 Nbs. Firstly, various complexes containing nanobodies were downloaded from the RCSB database, which were identified from immunized llamas. The primary docking between Nbs and the SARS-CoV-2 spike protein receptor-binding domain was performed through the ClusPro program, with the manual screening leaving the reasonable conformation to the next step. Then, the binding distances of atoms between the antigen-antibody interfaces were measured through the NeighborSearch algorithm. Finally, filtered nanobodies were acquired according to HADDOCK scores through HADDOCK docking the COVID-19 spike protein with nanobodies under restrictions of calculated molecular distance between active residues and antigenic epitopes less than 4.5 Å. In this way, those nanobodies with more reasonable conformation and stronger neutralizing efficacy were acquired. To validate the efficacy ranking of the nanobodies we obtained, we calculated the binding affinities (∆G) and dissociation constants (Kd) of all screened nanobodies using the PRODIGY web tool and predicted the stability changes induced by all possible point mutations in nanobodies using the MAESTROWeb server. Furthermore, we examined the performance of the relationship between nanobodies' ranking and their number of mutation-sensitive sites (Spearman correlation > 0.68); the results revealed a robust correlation, indicating that the superior nanobodies identified through our screening process exhibited fewer mutation hotspots and higher stability. This correlation analysis demonstrates the validity of our screening criteria, underscoring the suitability of these nanobodies for future development and practical implementation. In conclusion, this three-step screening strategy iteratively in silico greatly improved the accuracy of screening desired nanobodies compared to using only ClusPro docking or default HADDOCK docking settings. It provides new ideas for the screening of novel antibodies and computer-aided screening methods.
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Affiliation(s)
| | | | | | | | | | - Bingding Huang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China; (W.S.); (X.H.); (X.L.); (S.L.); (S.X.)
| | - Xin Wang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China; (W.S.); (X.H.); (X.L.); (S.L.); (S.X.)
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50
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Li S, Meng X, Li R, Huang B, Wang X. NanoBERTa-ASP: predicting nanobody paratope based on a pretrained RoBERTa model. BMC Bioinformatics 2024; 25:122. [PMID: 38515052 PMCID: PMC10956323 DOI: 10.1186/s12859-024-05750-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/18/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Nanobodies, also known as VHH or single-domain antibodies, are unique antibody fragments derived solely from heavy chains. They offer advantages of small molecules and conventional antibodies, making them promising therapeutics. The paratope is the specific region on an antibody that binds to an antigen. Paratope prediction involves the identification and characterization of the antigen-binding site on an antibody. This process is crucial for understanding the specificity and affinity of antibody-antigen interactions. Various computational methods and experimental approaches have been developed to predict and analyze paratopes, contributing to advancements in antibody engineering, drug development, and immunotherapy. However, existing predictive models trained on traditional antibodies may not be suitable for nanobodies. Additionally, the limited availability of nanobody datasets poses challenges in constructing accurate models. METHODS To address these challenges, we have developed a novel nanobody prediction model, named NanoBERTa-ASP (Antibody Specificity Prediction), which is specifically designed for predicting nanobody-antigen binding sites. The model adopts a training strategy more suitable for nanobodies, based on an advanced natural language processing (NLP) model called BERT (Bidirectional Encoder Representations from Transformers). To be more specific, the model utilizes a masked language modeling approach named RoBERTa (Robustly Optimized BERT Pretraining Approach) to learn the contextual information of the nanobody sequence and predict its binding site. RESULTS NanoBERTa-ASP achieved exceptional performance in predicting nanobody binding sites, outperforming existing methods, indicating its proficiency in capturing sequence information specific to nanobodies and accurately identifying their binding sites. Furthermore, NanoBERTa-ASP provides insights into the interaction mechanisms between nanobodies and antigens, contributing to a better understanding of nanobodies and facilitating the design and development of nanobodies with therapeutic potential. CONCLUSION NanoBERTa-ASP represents a significant advancement in nanobody paratope prediction. Its superior performance highlights the potential of deep learning approaches in nanobody research. By leveraging the increasing volume of nanobody data, NanoBERTa-ASP can further refine its predictions, enhance its performance, and contribute to the development of novel nanobody-based therapeutics. Github repository: https://github.com/WangLabforComputationalBiology/NanoBERTa-ASP.
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Affiliation(s)
- Shangru Li
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, China
| | - Xiangpeng Meng
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, China
| | - Rui Li
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, China
| | - Bingding Huang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, China.
| | - Xin Wang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, China.
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