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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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2
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Nemecz D, Nowak WA, Nemecz Á. VHH Nanobody Versatility against Pentameric Ligand-Gated Ion Channels. J Med Chem 2024; 67:8502-8518. [PMID: 38829690 PMCID: PMC11181324 DOI: 10.1021/acs.jmedchem.4c00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/17/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
Pentameric ligand-gated ion channels provide rapid chemical-electrical signal transmission between cells in the central and peripheral nervous system. Their dysfunction is associated with many nervous system disorders. They are composed of five identical (homomeric receptors) or homologous (heteromeric receptors) subunits. VHH nanobodies, or single-chain antibodies, are the variable domain, VHH, of antibodies that are composed of the heavy chain only from camelids. Their unique structure results in many specific biochemical and biophysical properties that make them an excellent alternative to conventional antibodies. This Perspective explores the published VHH nanobodies which have been isolated against pentameric ligand-gated ion channel subfamilies. It outlines the genetic and chemical modifications available to alter nanobody function. An assessment of the available functional and structural data indicate that it is feasible to create therapeutic agents and impart, through their modification, a given desired modulatory effect of its target receptor for current stoichiometric-specific VHH nanobodies.
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Affiliation(s)
- Dorota Nemecz
- Biochemistry
Department, Nicolaus Copernicus University
in Torun, 87-100 Torun, Poland
| | - Weronika A. Nowak
- Biochemistry
Department, Nicolaus Copernicus University
in Torun, 87-100 Torun, Poland
| | - Ákos Nemecz
- Biochemistry
Department, Nicolaus Copernicus University
in Torun, 87-100 Torun, Poland
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3
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Leighton PA, Ching K, Reynolds K, Vuong CN, Zeng B, Zhang Y, Gupta A, Morales J, Rivera GS, Srivastava DB, Cotter R, Pedersen D, Collarini E, Izquierdo S, van de Lavoir MC, Harriman W. Chickens with a Truncated Light Chain Transgene Express Single-Domain H Chain-Only Antibodies. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1744-1753. [PMID: 38629917 PMCID: PMC11102025 DOI: 10.4049/jimmunol.2300617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 03/22/2024] [Indexed: 05/20/2024]
Abstract
H chain-only Igs are naturally produced in camelids and sharks. Because these Abs lack the L chain, the Ag-binding domain is half the size of a traditional Ab, allowing this type of Ig to bind to targets in novel ways. Consequently, the H chain-only single-domain Ab (sdAb) structure has the potential to increase the repertoire and functional range of an active humoral immune system. The majority of vertebrates use the standard heterodimeric (both H and L chains) structure and do not produce sdAb format Igs. To investigate if other animals are able to support sdAb development and function, transgenic chickens (Gallus gallus) were designed to produce H chain-only Abs by omitting the L chain V region and maintaining only the LC region to serve as a chaperone for Ab secretion from the cell. These birds produced 30-50% normal B cell populations within PBMCs and readily expressed chicken sequence sdAbs. Interestingly, the H chains contained a spontaneous CH1 deletion. Although no isotype switching to IgY or IgA occurred, the IgM repertoire was diverse, and immunization with a variety of protein immunogens rapidly produced high and specific serum titers. mAbs of high affinity were efficiently recovered by single B cell screening. In in vitro functional assays, the sdAbs produced by birds immunized against SARS-CoV-2 were also able to strongly neutralize and prevent viral replication. These data suggest that the truncated L chain design successfully supported sdAb development and expression in chickens.
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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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5
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Tripathy RK, Pande AH. Molecular and functional insight into anti-EGFR nanobody: Theranostic implications for malignancies. Life Sci 2024; 345:122593. [PMID: 38554946 DOI: 10.1016/j.lfs.2024.122593] [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: 01/09/2024] [Revised: 02/27/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
Targeted therapy and imaging are the most popular techniques for the intervention and diagnosis of cancer. A potential therapeutic target for the treatment of cancer is the epidermal growth factor receptor (EGFR), primarily for glioblastoma, lung, and breast cancer. Over-production of ligand, transcriptional up-regulation due to autocrine/paracrine signalling, or point mutations at the genomic locus may contribute to the malfunction of EGFR in malignancies. This exploit makes use of EGFR, an established biomarker for cancer diagnostics and treatment. Despite considerable development in the last several decades in making EGFR inhibitors, they are still not free from limitations like toxicity and a short serum half-life. Nanobodies and antibodies share similar binding properties, but nanobodies have the additional advantage that they can bind to antigenic epitopes deep inside the target that conventional antibodies are unable to access. For targeted therapy, anti-EGFR nanobodies can be conjugated to various molecules such as drugs, peptides, toxins and photosensitizers. These nanobodies can be designed as novel immunoconjugates using the universal modular antibody-based platform technology (UniCAR). Furthermore, Anti-EGFR nanobodies can be expressed in neural stem cells and visualised by effective fluorescent and radioisotope labelling.
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Affiliation(s)
- Rajan K Tripathy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, (Mohali) 160062, Punjab, India
| | - Abhay H Pande
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, (Mohali) 160062, Punjab, India.
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Yuan M, Wang W, Hawes I, Han J, Yao Z, Bertaina A. Advancements in γδT cell engineering: paving the way for enhanced cancer immunotherapy. Front Immunol 2024; 15:1360237. [PMID: 38576617 PMCID: PMC10991697 DOI: 10.3389/fimmu.2024.1360237] [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: 12/22/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
Comprising only 1-10% of the circulating T cell population, γδT cells play a pivotal role in cancer immunotherapy due to their unique amalgamation of innate and adaptive immune features. These cells can secrete cytokines, including interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α), and can directly eliminate tumor cells through mechanisms like Fas/FasL and antibody-dependent cell-mediated cytotoxicity (ADCC). Unlike conventional αβT cells, γδT cells can target a wide variety of cancer cells independently of major histocompatibility complex (MHC) presentation and function as antigen-presenting cells (APCs). Their ability of recognizing antigens in a non-MHC restricted manner makes them an ideal candidate for allogeneic immunotherapy. Additionally, γδT cells exhibit specific tissue tropism, and rapid responsiveness upon reaching cellular targets, indicating a high level of cellular precision and adaptability. Despite these capabilities, the therapeutic potential of γδT cells has been hindered by some limitations, including their restricted abundance, unsatisfactory expansion, limited persistence, and complex biology and plasticity. To address these issues, gene-engineering strategies like the use of chimeric antigen receptor (CAR) T therapy, T cell receptor (TCR) gene transfer, and the combination with γδT cell engagers are being explored. This review will outline the progress in various engineering strategies, discuss their implications and challenges that lie ahead, and the future directions for engineered γδT cells in both monotherapy and combination immunotherapy.
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Affiliation(s)
| | - Wenjun Wang
- *Correspondence: Wenjun Wang, ; Alice Bertaina,
| | | | | | | | - Alice Bertaina
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University, School of Medicine, Stanford, CA, United States
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Dhehibi A, Terrak M, Seddik MM, Hammadi M, Salhi I. Development of a bispecific Nanobody anti-F17 fimbria as a potential therapeutic tool. Protein Expr Purif 2024; 215:106411. [PMID: 38056514 DOI: 10.1016/j.pep.2023.106411] [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: 10/26/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
Pathogenic strains of Escherichia coli F17+ are associated with various intestinal and extra-intestinal pathologies, including diarrhea, and result in significant animal mortality. These infections rely on the expression of virulence factors, such as F17 fimbriae, for adhesion. F17 fimbriae form a protective layer on the surface of E. coli bacteria, consisting of a major structural subunit, F17A, and a minor functional subunit, F17G. Because of the evolution of bacterial resistance, conventional antibiotic treatments have limited efficacy. Therefore, there is a pressing need to develop novel therapeutic tools. In this study, we cloned and produced the F17G protein. We then immunized a camel with the purified F17G protein and constructed a VHH library consisting of 2 × 109 clones. The library was then screened against F17G protein using phage display technology. Through this process, we identified an anti-F17G nanobody that was subsequently linked, via a linker, to an anti-F17A nanobody, resulting in the creation of an effective bispecific nanobody. Comprehensive characterization of this bispecific nanobody demonstrated excellent production, specific binding capacity to both recombinant forms of the two F17 antigens and the E. coli F17+ strain, remarkable stability in camel serum, and superior resistance to pepsin protease. The successful generation of this bispecific nanobody with excellent production, specific binding capacity and stability highlights its potential as a valuable tool for fighting infections caused by pathogenic E. coli F17+ strain.
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Affiliation(s)
- Asma Dhehibi
- Livestock and Wildlife Laboratory (LR16IRA04), Arid Lands Institute (I.R.A), University of Gabès, Médenine, 4119, Tunisia.
| | - Mohammed Terrak
- InBioS-Centre for Protein Engineering, University of Liege, B-4000, Liege, Belgium
| | - Mabrouk-Mouldi Seddik
- Livestock and Wildlife Laboratory (LR16IRA04), Arid Lands Institute (I.R.A), University of Gabès, Médenine, 4119, Tunisia
| | - Mohamed Hammadi
- Livestock and Wildlife Laboratory (LR16IRA04), Arid Lands Institute (I.R.A), University of Gabès, Médenine, 4119, Tunisia
| | - Imed Salhi
- Livestock and Wildlife Laboratory (LR16IRA04), Arid Lands Institute (I.R.A), University of Gabès, Médenine, 4119, Tunisia
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8
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Sun M, Wang C, Luo H, Chen Y, Qu G, Chen J, Li L, Zhang M, Xue Q. Development and characterization of a novel nanobody with SRMV neutralizing activity. Microb Cell Fact 2024; 23:45. [PMID: 38341572 PMCID: PMC10858559 DOI: 10.1186/s12934-024-02311-6] [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: 08/27/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Peste des petits ruminants (PPR) is an acute, contact infectious disease caused by the small ruminant morbillivirus (SRMV), and its morbidity in goats and sheep can be up to 100% with significant mortality. Nanobody generated from camelid animals such as alpaca has attracted wide attention because of its unique advantages compared with conventional antibodies. The main objective of this study was to produce specific nanobodies against SRMV and identify its characteristics. To obtain the coding gene of SRMV-specific nanobodies, we first constructed an immune phage-displayed library from the VHH repertoire of alpaca that was immunized with SRMV-F and -H proteins. By using phage display technology, the target antigen-specific VHHs can be obtained after four consecutive rounds of biopanning. Results showed that the size of this VHH library was 2.26 × 1010 CFU/mL and the SRMV-F and -H specific phage particles were greatly enriched after four rounds of biopanning. The positive phage clones were selected and sequenced, and total of five independent different sequences of SRMV-specific nanobodies were identified. Subsequently, the DNA fragments of the five nanobodies were cloned into E. coli BL21(DE3), respectively, and three of them were successfully expressed and purified. Specificity and affinity towards inactivated SRMV of these purified nanobodies were then evaluated using the ELISA method. Results demonstrated that NbSRMV-1-1, NbSRMV-2-10, and NbSRMV-1-21 showed no cross-reactivity with other antigens, such as inactivated BTV, inactivated FMDV, His-tag labeled protein, and BSA. The ELISA titer of these three nanobodies against inactivated SRMV was up to 1:1000. However, only NbSRMV-1-21 displayed SRMV neutralizing activity at a maximum dilution of 1:4. The results indicate that the nanobodies against SRMV generated in this study could be useful in future applications. This study provided a novel antibody tool and laid a foundation for the treatment and detection of SRMV.
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Affiliation(s)
- Miao Sun
- Department of Viral Biologics, China Institute of Veterinary Drug Control, Beijing, China
| | - Changjiang Wang
- Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Huaye Luo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Yanfei Chen
- Department of Viral Biologics, China Institute of Veterinary Drug Control, Beijing, China
| | - Guanggang Qu
- Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Jian Chen
- Department of Viral Biologics, China Institute of Veterinary Drug Control, Beijing, China
| | - Ling Li
- Department of Viral Biologics, China Institute of Veterinary Drug Control, Beijing, China
| | - Min Zhang
- Tech-Bank Food Corporation Limited, Nanjing, China
| | - Qinghong Xue
- Department of Viral Biologics, China Institute of Veterinary Drug Control, Beijing, China.
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Beckers CJ, Mrestani A, Komma F, Dannhäuser S. Versatile Endogenous Editing of GluRIIA in Drosophila melanogaster. Cells 2024; 13:323. [PMID: 38391936 PMCID: PMC10887371 DOI: 10.3390/cells13040323] [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: 01/15/2024] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Glutamate receptors at the postsynaptic side translate neurotransmitter release from presynapses into postsynaptic excitation. They play a role in many forms of synaptic plasticity, e.g., homeostatic scaling of the receptor field, activity-dependent synaptic plasticity and the induction of presynaptic homeostatic potentiation (PHP). The latter process has been extensively studied at Drosophila melanogaster neuromuscular junctions (NMJs). The genetic removal of the glutamate receptor subunit IIA (GluRIIA) leads to an induction of PHP at the synapse. So far, mostly imprecise knockouts of the GluRIIA gene have been utilized. Furthermore, mutated and tagged versions of GluRIIA have been examined in the past, but most of these constructs were not expressed under endogenous regulatory control or involved the mentioned imprecise GluRIIA knockouts. We performed CRISPR/Cas9-assisted gene editing at the endogenous locus of GluRIIA. This enabled the investigation of the endogenous expression pattern of GluRIIA using tagged constructs with an EGFP and an ALFA tag for super-resolution immunofluorescence imaging, including structured illumination microscopy (SIM) and direct stochastic optical reconstruction microscopy (dSTORM). All GluRIIA constructs exhibited full functionality and PHP could be induced by philanthotoxin at control levels. By applying hierarchical clustering algorithms to analyze the dSTORM data, we detected postsynaptic receptor cluster areas of ~0.15 µm2. Consequently, our constructs are suitable for ultrastructural analyses of GluRIIA.
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Affiliation(s)
- Constantin J. Beckers
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, D-97070 Würzburg, Germany
| | - Achmed Mrestani
- Department of Neurology, University of Leipzig Medical Center, D-04103 Leipzig, Germany;
- Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Medical Faculty, Leipzig University, D-04103 Leipzig, Germany
| | - Fabian Komma
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, D-97070 Würzburg, Germany
| | - Sven Dannhäuser
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, D-97070 Würzburg, Germany
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Wang C, Lai AY, Baiu DC, Smith KA, Odorico JS, Wilson K, Schreiber T, de Silva S, Gumperz JE. Analysis of Butyrophilin-Mediated Activation of γδ T Cells from Human Spleen. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:284-294. [PMID: 37991420 DOI: 10.4049/jimmunol.2300588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/02/2023] [Indexed: 11/23/2023]
Abstract
There is considerable interest in therapeutically engaging human γδ T cells. However, due to the unique TCRs of human γδ T cells, studies from animal models have provided limited directly applicable insights, and human γδ T cells from key immunological tissues remain poorly characterized. In this study, we investigated γδ T cells from human spleen tissue. Compared to blood, where Vδ2+Vγ9+ T cells are the dominant subset, splenic γδ T cells included a variety of TCR types, with Vδ1+ T cells typically being the most frequent. Intracellular cytokine staining revealed that IFN-γ was produced by a substantial fraction of splenic γδ T cells, IL-17A by a small fraction, and IL-4 was minimal. Primary splenic γδ T cells frequently expressed NKG2D (NK group 2 member D) and CD16, whereas expression of DNAM-1 (DNAX accessory molecule 1), CD28, PD-1, TIGIT, and CD94 varied according to subset, and there was generally little expression of natural cytotoxicity receptors, TIM-3, LAG-3, or killer Ig-like receptors. In vitro expansion was associated with marked changes in expression of these activating and inhibitory receptors. Analysis of functional responses of spleen-derived Vδ2+Vγ9+, Vδ1+Vγ9+, and Vδ1+Vγ9- T cell lines to recombinant butyrophilin BTN2A1 and BTN3A1 demonstrated that both Vδ2+Vγ9+ and Vδ1+Vγ9+ T cells were capable of responding to the extracellular domain of BTN2A1, whereas the addition of BTN3A1 only markedly enhanced the responses of Vδ2+Vγ9+ T cells. Conversely, Vδ1+Vγ9+ T cells appeared more responsive than Vδ2+Vγ9+ T cells to TCR-independent NKG2D stimulation. Thus, despite shared recognition of BTN2A1, differential effects of BTN3A1 and coreceptors may segregate target cell responses of Vδ2+Vγ9+ and Vδ1+Vγ9+ T cells.
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Affiliation(s)
- Chunyan Wang
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | | | - Dana C Baiu
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Kelsey A Smith
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Jon S Odorico
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | | | | | | | - Jenny E Gumperz
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI
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11
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Babamohamadi M, Mohammadi N, Faryadi E, Haddadi M, Merati A, Ghobadinezhad F, Amirian R, Izadi Z, Hadjati J. Anti-CTLA-4 nanobody as a promising approach in cancer immunotherapy. Cell Death Dis 2024; 15:17. [PMID: 38191571 PMCID: PMC10774412 DOI: 10.1038/s41419-023-06391-x] [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: 06/21/2023] [Revised: 11/25/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024]
Abstract
Cancer is one of the most common diseases and causes of death worldwide. Since common treatment approaches do not yield acceptable results in many patients, developing innovative strategies for effective treatment is necessary. Immunotherapy is one of the promising approaches that has been highly regarded for preventing tumor recurrence and new metastases. Meanwhile, inhibiting immune checkpoints is one of the most attractive methods of cancer immunotherapy. Cytotoxic T lymphocyte-associated protein-4 (CTLA-4) is an essential immune molecule that plays a vital role in cell cycle modulation, regulation of T cell proliferation, and cytokine production. This molecule is classically expressed by stimulated T cells. Inhibition of overexpression of immune checkpoints such as CTLA-4 receptors has been confirmed as an effective strategy. In cancer immunotherapy, immune checkpoint-blocking drugs can be enhanced with nanobodies that target immune checkpoint molecules. Nanobodies are derived from the variable domain of heavy antibody chains. These small protein fragments have evolved entirely without a light chain and can be used as a powerful tool in imaging and treating diseases with their unique structure. They have a low molecular weight, which makes them smaller than conventional antibodies while still being able to bind to specific antigens. In addition to low molecular weight, specific binding to targets, resistance to temperature, pH, and enzymes, high ability to penetrate tumor tissues, and low toxicity make nanobodies an ideal approach to overcome the disadvantages of monoclonal antibody-based immunotherapy. In this article, while reviewing the cellular and molecular functions of CTLA-4, the structure and mechanisms of nanobodies' activity, and their delivery methods, we will explain the advantages and challenges of using nanobodies, emphasizing immunotherapy treatments based on anti-CTLA-4 nanobodies.
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Affiliation(s)
- Mehregan Babamohamadi
- Department of Biology, School of Natural Sciences, University of Tabriz, Tabriz, Iran
- Stem Cell and Regenerative Medicine Innovation Center, Tehran University of Medical Sciences, Tehran, Iran
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Nastaran Mohammadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Elham Faryadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Maryam Haddadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhossein Merati
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Medical Laboratory Sciences, School of Paramedical, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Farbod Ghobadinezhad
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Roshanak Amirian
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Zhila Izadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Jamshid Hadjati
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Selmi R, Mamlouk A, Belkahia H, Ben Yahia H, Abdelaali H, Jemli MH, Ben Said M, Messadi L. Serological and molecular survey of brucellosis and chlamydiosis in dromedary camels from Tunisia. Comp Immunol Microbiol Infect Dis 2024; 104:102098. [PMID: 38007988 DOI: 10.1016/j.cimid.2023.102098] [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: 08/25/2023] [Revised: 11/02/2023] [Accepted: 11/13/2023] [Indexed: 11/28/2023]
Abstract
The present sero-epidemiological survey was designed and conducted to scrutinize the current status of camel-related brucellosis and chlamydiosis in Tunisia. Whole blood and serum samples were collected from 470 dromedaries (Camelus dromedarius) from eight different Tunisian governorates. Serum samples were subjected to indirect enzyme-linked immunosorbent assay (iELISA). The detection of Brucella and Chlamydia DNA was performed using conventional PCR targeting the bcsp-31 and 16 S rRNA gene, respectively. Overall, 10/470(2.12%) and 27/470 (5.75%) camels were revealed seropositive to Brucella and Chlamydia, respectively. Multivariate logistic regression analysis showed different risk factors associated with these infections. Meaningful high rates of seropositivity of brucellosis (9.5%; p = 0.000; OR=64.193) and chlamydiosis (22.6%; p = 0.000; OR=42.860) were noted among camels showing previous abortions in particular for aged females. Besides, Chlamydia seropositivity is significantly important during winter (12.5%; p = 0.009; OR= 27.533), and in camels raised in small farms (11.4%, p = 0.000, OR=86.052). Molecular analysis revealed no positivity from all analyzed blood samples. These findings indicate the involvement of camels in the epidemiology of these abortive infectious diseases. This raises awareness and serious public health concern for infectious camel diseases in order to develop further diagnostic improvements and effective control strategies.
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Affiliation(s)
- Rachid Selmi
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, LR16AGR01, University of Manouba, Manouba, Tunisia; Ministry of National Defense, General Directorate of Military Health, Military Center of Veterinary Medicine, Tunis, Tunisia.
| | - Aymen Mamlouk
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, LR16AGR01, University of Manouba, Manouba, Tunisia
| | - Hanene Belkahia
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, LR16AGR01, University of Manouba, Manouba, Tunisia
| | - Houcine Ben Yahia
- Ministry of National Defense, General Directorate of Military Health, Military Center of Veterinary Medicine, Tunis, Tunisia
| | - Hedi Abdelaali
- Ministry of National Defense, General Directorate of Military Health, Military Center of Veterinary Medicine, Tunis, Tunisia
| | - Mohamed-Habib Jemli
- Laboratory of Parasitology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, Manouba, Tunisia
| | - Mourad Ben Said
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, LR16AGR01, University of Manouba, Manouba, Tunisia; Department of Basic Sciences, Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, Manouba, Tunisia
| | - Lilia Messadi
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, LR16AGR01, University of Manouba, Manouba, Tunisia
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13
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Campbell E, Luxton T, Kohl D, Goodchild SA, Walti C, Jeuken LJC. Chimeric Protein Switch Biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:1-35. [PMID: 38273207 DOI: 10.1007/10_2023_241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Rapid detection of protein and small-molecule analytes is a valuable technique across multiple disciplines, but most in vitro testing of biological or environmental samples requires long, laborious processes and trained personnel in laboratory settings, leading to long wait times for results and high expenses. Fusion of recognition with reporter elements has been introduced to detection methods such as enzyme-linked immunoassays (ELISA), with enzyme-conjugated secondary antibodies removing one of the many incubation and wash steps. Chimeric protein switch biosensors go further and provide a platform for homogenous mix-and-read assays where long wash and incubation steps are eradicated from the process. Chimeric protein switch biosensors consist of an enzyme switch (the reporter) coupled to a recognition element, where binding of the analyte results in switching the activity of the reporter enzyme on or off. Several chimeric protein switch biosensors have successfully been developed for analytes ranging from small molecule drugs to large protein biomarkers. There are two main formats of chimeric protein switch biosensor developed, one-component and multi-component, and these formats exhibit unique advantages and disadvantages. Genetically fusing a recognition protein to the enzyme switch has many advantages in the production and performance of the biosensor. A range of immune and synthetic binding proteins have been developed as alternatives to antibodies, including antibody mimetics or antibody fragments. These are mainly small, easily manipulated proteins and can be genetically fused to a reporter for recombinant expression or manipulated to allow chemical fusion. Here, aspects of chimeric protein switch biosensors will be reviewed with a comparison of different classes of recognition elements and switching mechanisms.
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Affiliation(s)
- Emma Campbell
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Timothy Luxton
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Declan Kohl
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | | | - Christoph Walti
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
| | - Lars J C Jeuken
- School of Biomedical Sciences, University of Leeds, Leeds, UK.
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
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14
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Guo X, Wu Y, Xue Y, Xie N, Shen G. Revolutionizing cancer immunotherapy: unleashing the potential of bispecific antibodies for targeted treatment. Front Immunol 2023; 14:1291836. [PMID: 38106416 PMCID: PMC10722299 DOI: 10.3389/fimmu.2023.1291836] [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: 09/10/2023] [Accepted: 11/08/2023] [Indexed: 12/19/2023] Open
Abstract
Recent progressions in immunotherapy have transformed cancer treatment, providing a promising strategy that activates the immune system of the patient to find and eliminate cancerous cells. Bispecific antibodies, which engage two separate antigens or one antigen with two distinct epitopes, are of tremendous concern in immunotherapy. The bi-targeting idea enabled by bispecific antibodies (BsAbs) is especially attractive from a medical standpoint since most diseases are complex, involving several receptors, ligands, and signaling pathways. Several research look into the processes in which BsAbs identify different cancer targets such angiogenesis, reproduction, metastasis, and immune regulation. By rerouting cells or altering other pathways, the bispecific proteins perform effector activities in addition to those of natural antibodies. This opens up a wide range of clinical applications and helps patients with resistant tumors respond better to medication. Yet, further study is necessary to identify the best conditions where to use these medications for treating tumor, their appropriate combination partners, and methods to reduce toxicity. In this review, we provide insights into the BsAb format classification based on their composition and symmetry, as well as the delivery mode, focus on the action mechanism of the molecule, and discuss the challenges and future perspectives in BsAb development.
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Affiliation(s)
- Xiaohan Guo
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yi Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Ying Xue
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Na Xie
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Guobo Shen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
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15
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Frecot DI, Froehlich T, Rothbauer U. 30 years of nanobodies - an ongoing success story of small binders in biological research. J Cell Sci 2023; 136:jcs261395. [PMID: 37937477 DOI: 10.1242/jcs.261395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
A milestone in the field of recombinant binding molecules was achieved 30 years ago with the discovery of single-domain antibodies from which antigen-binding variable domains, better known as nanobodies (Nbs), can be derived. Being only one tenth the size of conventional antibodies, Nbs feature high affinity and specificity, while being highly stable and soluble. In addition, they display accessibility to cryptic sites, low off-target accumulation and deep tissue penetration. Efficient selection methods, such as (semi-)synthetic/naïve or immunized cDNA libraries and display technologies, have facilitated the isolation of Nbs against diverse targets, and their single-gene format enables easy functionalization and high-yield production. This Review highlights recent advances in Nb applications in various areas of biological research, including structural biology, proteomics and high-resolution and in vivo imaging. In addition, we provide insights into intracellular applications of Nbs, such as live-cell imaging, biosensors and targeted protein degradation.
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Affiliation(s)
- Desiree I Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Reutlingen, Germany
| | - Theresa Froehlich
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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16
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Prado NDR, Brilhante-Da-Silva N, Sousa RMO, Morais MSDS, Roberto SA, Luiz MB, Assis LCD, Marinho ACM, Araujo LFLD, Pontes RDS, Stabeli RG, Fernandes CFC, Pereira SDS. Single-domain antibodies applied as antiviral immunotherapeutics. J Virol Methods 2023; 320:114787. [PMID: 37516366 DOI: 10.1016/j.jviromet.2023.114787] [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: 12/12/2022] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Viral infections have been the cause of high mortality rates throughout different periods in history. Over the last two decades, outbreaks caused by zoonotic diseases and transmitted by arboviruses have had a significant impact on human health. The emergence of viral infections in different parts of the world encourages the search for new inputs to fight pathologies of viral origin. Antibodies represent the predominant class of new drugs developed in recent years and approved for the treatment of various human diseases, including cancer, autoimmune and infectious diseases. A promising group of antibodies are single-domain antibodies derived from camelid heavy chain immunoglobulins, or VHHs, are biomolecules with nanometric dimensions and unique pharmaceutical and biophysical properties that can be used in the diagnosis and immunotherapy of viral infections. For viral neutralization to occur, VHHs can act in different stages of the viral cycle, including the actual inhibition of infection, to hindering viral replication or assembly. This review article addresses advances involving the use of VHHs in therapeutic propositions aimed to battle different viruses that affect human health.
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Affiliation(s)
- Nidiane Dantas Reis Prado
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, FIOCRUZ, unidade Rondônia, Porto Velho, RO, Brazil
| | - Nairo Brilhante-Da-Silva
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, FIOCRUZ, unidade Rondônia, Porto Velho, RO, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, RJ, Brazil
| | - Rosa Maria Oliveira Sousa
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, FIOCRUZ, unidade Rondônia, Porto Velho, RO, Brazil
| | | | - Sibele Andrade Roberto
- Plataforma Bi-institucional de Medicina Translacional, Fundação Oswaldo Cruz-USP, Ribeirão Preto, SP, Brazil
| | - Marcos Barros Luiz
- Instituto Federal de Rondônia Campus Guajará-Mirim, IFRO, Guajará-Mirim, RO, Brazil
| | - Livia Coelho de Assis
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, RJ, Brazil; Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz, Fiocruz unidade Ceará, Eusebio, CE, Brazil
| | - Anna Carolina M Marinho
- Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz, Fiocruz unidade Ceará, Eusebio, CE, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Luiz Felipe Lemes de Araujo
- Plataforma Bi-institucional de Medicina Translacional, Fundação Oswaldo Cruz-USP, Ribeirão Preto, SP, Brazil; Programa de Pós-Graduação em Imunologia Básica e Aplicada, Universidade de São Paulo, USP, Ribeirão Preto, SP, Brazil
| | - Rafael de Souza Pontes
- Plataforma Bi-institucional de Medicina Translacional, Fundação Oswaldo Cruz-USP, Ribeirão Preto, SP, Brazil; Programa de Pós-Graduação em Imunologia Básica e Aplicada, Universidade de São Paulo, USP, Ribeirão Preto, SP, Brazil
| | - Rodrigo Guerino Stabeli
- Plataforma Bi-institucional de Medicina Translacional, Fundação Oswaldo Cruz-USP, Ribeirão Preto, SP, Brazil
| | - Carla Freire Celedonio Fernandes
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, RJ, Brazil; Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz, Fiocruz unidade Ceará, Eusebio, CE, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Soraya Dos Santos Pereira
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, FIOCRUZ, unidade Rondônia, Porto Velho, RO, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, RJ, Brazil; Programa de Pós-graduação em Biologia Experimental, Universidade Federal de Rondônia, UNIR, Porto Velho, RO, Brazil.
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17
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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18
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De Fauw K, Umelo IA, Teng X, Vlyminck S, Rivera G, Brigé A, Delangle A. Theoretical charge plots as a tool for targeted and accelerated ion exchange chromatography method development of NANOBODY Ⓡ molecules. J Chromatogr A 2023; 1705:464137. [PMID: 37356365 DOI: 10.1016/j.chroma.2023.464137] [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: 03/15/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/27/2023]
Abstract
NANOBODYⓇ molecules are an innovative class of biotherapeutics based on heavy chain only VHH immunoglobulins. Much like canonical antibodies, they are prone to the formation of charge variants and other post-translational modifications, which can potentially impact their critical quality attributes. Therefore, establishing high-resolution product-specific methods, such as IEX chromatography, is essential for evaluating the purity of these molecules. However, due to the lower surface charge of NANOBODYⓇ molecules, their charge-based elution behavior can differ considerably from that of classical antibodies, resulting in a more extensive method development set-up for these smaller molecules. Using an initial pH screening gradient based on theoretical protein charge plots, we investigated the IEX retention behavior of eight NANOBODYⓇ molecules with a wide range of pI values (pI 5.0 to 10.0). Our findings reveal that the charge-based chromatographic behavior of NANOBODYⓇ molecules cannot be solely attributed to the isoelectric point (pI) of the protein. Rather, a molecule-specific charge threshold was identified as a critical parameter for NANOBODYⓇ molecule retention. Furthermore, the protein charge plot also showed that NANOBODYⓇ molecule elution can be characterized by a charge plateau where the net charge of the protein remains constant over a certain pH range (∼ pH 5.5 to pH 8.0), further challenging the paradigm that elution pH and pI are fixed values. The application of this theoretical approach using protein charge plots to define NANOBODYⓇ molecule charge threshold and charge plateau parameters, can reduce overall IEX method development turnaround time by at least 2-fold.
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Affiliation(s)
- Ken De Fauw
- Sanofi Large Molecules Research, NANOBODY(Ⓡ) Research Platform, Analytics, Technologiepark 21, 9052 Zwijnaarde (Ghent), Belgium
| | - Ijeoma A Umelo
- Sanofi Large Molecules Research, NANOBODY(Ⓡ) Research Platform, Analytics, Technologiepark 21, 9052 Zwijnaarde (Ghent), Belgium
| | - Xia Teng
- Sanofi Large Molecules Research, NANOBODY(Ⓡ) Research Platform, Analytics, Technologiepark 21, 9052 Zwijnaarde (Ghent), Belgium
| | - Silke Vlyminck
- Sanofi Large Molecules Research, NANOBODY(Ⓡ) Research Platform, Analytics, Technologiepark 21, 9052 Zwijnaarde (Ghent), Belgium
| | - Gustavo Rivera
- Sanofi Large Molecules Research, NANOBODY(Ⓡ) Research Platform, Analytics, Technologiepark 21, 9052 Zwijnaarde (Ghent), Belgium
| | - Ann Brigé
- Sanofi Large Molecules Research, NANOBODY(Ⓡ) Research Platform, Analytics, Technologiepark 21, 9052 Zwijnaarde (Ghent), Belgium
| | - Aurélie Delangle
- Sanofi Large Molecules Research, NANOBODY(Ⓡ) Research Platform, Analytics, Technologiepark 21, 9052 Zwijnaarde (Ghent), Belgium.
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19
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M Morris N, A Blee J, Hauert S. Global parameter optimisation and sensitivity analysis of antivenom pharmacokinetics and pharmacodynamics. Toxicon 2023; 232:107206. [PMID: 37356552 DOI: 10.1016/j.toxicon.2023.107206] [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: 03/14/2023] [Revised: 06/05/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
In recent years it has become possible to design snakebite antivenoms with diverse pharmacokinetic properties. Owing to the pharmacokinetic variability of venoms, the choice of antivenom scaffold may influence a treatment's neutralisation coverage. Computation offers a useful medium through which to assess the pharmacokinetics and pharmacodynamics of envenomation-treatment systems, as antivenoms with identical neutralising capacities can be simulated. In this study, we simulate envenomation and treatment with a variety of antivenoms, to define the properties of effective antivenoms. Systemic envenomation and treatment were described using a two-compartment pharmacokinetic model. Treatment of Naja sumatrana and Cryptelytrops purpureomaculatus envenomation was simulated with a set of 200,000 theoretical antivenoms across 10 treatment time delays. These two venoms are well-characterised and have differing pharmacokinetic properties. The theoretical antivenom set varied across molecular weight, dose, kon, koff, and valency. The best and worst treatments were identified using an area under the curve metric, and a global sensitivity analysis was performed to quantify the influence of the input parameters on treatment outcome. The simulations show that scaffolds of diverse molecular formats can be effective. Molecular weight and valency have a negligible direct impact on treatment outcome, however low molecular weight scaffolds offer more flexibility across the other design parameters, particularly when treatment is delayed. The simulations show kon to primarily mediate treatment efficacy, with rates above 105 M-1s-1 required for the most effective treatments. koff has the greatest impact on the performance of less effective scaffolds. While the same scaffold preferences for improved treatment are seen for both model snakes, the parameter bounds for C. purpureomaculatus envenomation are more constrained. This paper establishes a computational framework for the optimisation of antivenom design.
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Affiliation(s)
- Natalie M Morris
- Department of Engineering Mathematics, Ada Lovelace Building, University of Bristol, University Walk, Bristol, BS8 1TW, UK.
| | - Johanna A Blee
- Department of Engineering Mathematics, Ada Lovelace Building, University of Bristol, University Walk, Bristol, BS8 1TW, UK.
| | - Sabine Hauert
- Department of Engineering Mathematics, Ada Lovelace Building, University of Bristol, University Walk, Bristol, BS8 1TW, UK.
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20
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Śledź M, Wojciechowska A, Zagożdżon R, Kaleta B. In Situ Programming of CAR-T Cells: A Pressing Need in Modern Immunotherapy. Arch Immunol Ther Exp (Warsz) 2023; 71:18. [PMID: 37419996 PMCID: PMC10329070 DOI: 10.1007/s00005-023-00683-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
Chimeric antigen receptor-T (CAR-T) cell-based therapy has become a successful option for treatment of numerous hematological malignancies, but also raises hope in a range of non-malignant diseases. However, in a traditional approach, generation of CAR-T cells is associated with the separation of patient's lymphocytes, their in vitro modification, and expansion and infusion back into patient's bloodstream. This classical protocol is complex, time-consuming, and expensive. Those problems could be solved by successful protocols to produce CAR-T cells, but also CAR-natural killer cells or CAR macrophages, in situ, using viral platforms or non-viral delivery systems. Moreover, it was demonstrated that in situ CAR-T induction may be associated with reduced risk of the most common toxicities associated with CAR-T therapy, such as cytokine release syndrome, immune effector cell-associated neurotoxicity syndrome, and "on-target, off-tumor" toxicity. This review aims to summarize the current state-of-the-art and future perspectives for the in situ-produced CAR-T cells. Indeed, preclinical work in this area, including animal studies, raises hope for prospective translational development and validation in practical medicine of strategies for in situ generation of CAR-bearing immune effector cells.
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Affiliation(s)
- Marta Śledź
- Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland
| | | | - Radosław Zagożdżon
- Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Beata Kaleta
- Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland.
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21
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Hurley K, Cao M, Huang H, Wang Y. Targeted Alpha Therapy (TAT) with Single-Domain Antibodies (Nanobodies). Cancers (Basel) 2023; 15:3493. [PMID: 37444603 DOI: 10.3390/cancers15133493] [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: 05/30/2023] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
The persistent threat of cancer necessitates the development of improved and more efficient therapeutic strategies that limit damage to healthy tissues. Targeted alpha therapy (TαT), a novel form of radioimmuno-therapy (RIT), utilizes a targeting vehicle, commonly antibodies, to deliver high-energy, but short-range, alpha-emitting particles specifically to cancer cells, thereby reducing toxicity to surrounding normal tissues. Although full-length antibodies are often employed as targeting vehicles for TαT, their high molecular weight and the presence of an Fc-region lead to a long blood half-life, increased bone marrow toxicity, and accumulation in other tissues such as the kidney, liver, and spleen. The discovery of single-domain antibodies (sdAbs), or nanobodies, naturally occurring in camelids and sharks, has introduced a novel antigen-specific vehicle for molecular imaging and TαT. Given that nanobodies are the smallest naturally occurring antigen-binding fragments, they exhibit shorter relative blood half-lives, enhanced tumor uptake, and equivalent or superior binding affinity and specificity. Nanobody technology could provide a viable solution for the off-target toxicity observed with full-length antibody-based TαT. Notably, the pharmacokinetic properties of nanobodies align better with the decay characteristics of many short-lived α-emitting radionuclides. This review aims to encapsulate recent advancements in the use of nanobodies as a vehicle for TαT.
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Affiliation(s)
- Kate Hurley
- Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
| | - Meiyun Cao
- Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
| | - Haiming Huang
- Research Center, Forlong Biotechnology Inc., Suzhou 215004, China
| | - Yi Wang
- Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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22
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Shapiro MB, Boucher J, Brousseau A, Dehkharghani A, Gabriel J, Kamat V, Patil K, Gao F, Walker J, Kelly R, Souders CA. Alpaca single B cell interrogation and heavy-chain-only antibody discovery on an optofluidic platform. Antib Ther 2023; 6:211-223. [PMID: 37680350 PMCID: PMC10481890 DOI: 10.1093/abt/tbad018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/02/2023] [Accepted: 08/13/2023] [Indexed: 09/09/2023] Open
Abstract
In vivo VHH discovery approaches have been limited by the lack of methodologies for camelid B cell interrogation. Here, we report a novel application of the Beacon® optofluidic platform to the discovery of heavy-chain-only antibodies by screening alpaca B cells. Methods for alpaca B cell enrichment, culture, IgG2/3 detection, and sequencing were developed and used to discover target-specific VHH from an alpaca immunized with prostate-specific membrane antigen (PSMA) or a second target. PSMA-specific hits were expressed as VHH-Fc and characterized using label-free techniques. Anti-PSMA IgG2/3 titer plateaued on day 153, when on-Beacon IgG2/3 secretion and target binding rates peaked. Of 13 recombinantly expressed VHH-Fc, all but one bound with nanomolar affinity, and five were successfully humanized. Repertoire sequencing uncovered additional variants within the clonal lineages of the validated hits. The establishment of this workflow extends the powerful Beacon technology to enable rapid VHH discovery directly from natural camelid immune repertoires.
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Affiliation(s)
- Mariya B Shapiro
- Twist Biopharma Solutions, Twist Bioscience Corporation, Quincy, MA 02169, USA
| | - Jacqueline Boucher
- Twist Biopharma Solutions, Twist Bioscience Corporation, Quincy, MA 02169, USA
| | - Anna Brousseau
- Twist Biopharma Solutions, Twist Bioscience Corporation, Quincy, MA 02169, USA
| | - Amin Dehkharghani
- Twist Biopharma Solutions, Twist Bioscience Corporation, Quincy, MA 02169, USA
| | - Justin Gabriel
- Twist Biopharma Solutions, Twist Bioscience Corporation, Quincy, MA 02169, USA
| | - Vishal Kamat
- Twist Biopharma Solutions, Twist Bioscience Corporation, Quincy, MA 02169, USA
| | - Ketan Patil
- Twist Biopharma Solutions, Twist Bioscience Corporation, Quincy, MA 02169, USA
- Department of Molecular and Cell Biology, Gennao Bio, Hopewell, NJ 08534, USA
| | - Feng Gao
- Twist Biopharma Solutions, Twist Bioscience Corporation, Quincy, MA 02169, USA
| | - Jennifer Walker
- Twist Biopharma Solutions, Twist Bioscience Corporation, Quincy, MA 02169, USA
| | - Ryan Kelly
- Twist Biopharma Solutions, Twist Bioscience Corporation, Quincy, MA 02169, USA
| | - Colby A Souders
- Twist Biopharma Solutions, Twist Bioscience Corporation, Quincy, MA 02169, USA
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23
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Pawlowski KD, Duffy JT, Tiwari A, Zannikou M, Balyasnikova IV. Bi-Specific Killer Cell Engager Enhances NK Cell Activity against Interleukin-13 Receptor Alpha-2 Positive Gliomas. Cells 2023; 12:1716. [PMID: 37443750 PMCID: PMC10340194 DOI: 10.3390/cells12131716] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
Glioblastoma (GBM) is a lethal brain tumor with limited therapeutic options. Bi-specific killer cell engagers (BiKEs) are novel immunotherapies designed to engage natural killer (NK) cells against cancer. We designed a BiKE molecule consisting of a single-domain CD16 antibody, an interleukin-15 linker, and a single-chain variable antibody against the glioma-associated antigen interleukin 13 receptor alpha 2 (IL13Rα2). Recombinant BiKE protein was expressed in HEK cells and purified. Flow cytometric analysis of co-cultures of peripheral blood-derived NK cells with GBM6 and GBM39 patient-derived xenograft lines revealed significantly increased activation of NK cells (CD25+CD69+) and increased glioma cell killing following BiKE treatment compared to controls (n = 4, p < 0.01). Glioma cell killing was also confirmed via immunofluorescence staining for cleaved caspase-3 (p < 0.05). In vivo, intracranial delivery of NK cells with BiKE extended median survival in mice bearing GBM6 (p < 0.01) and GBM12 (p < 0.01) tumors compared to controls. Finally, histological analysis of brain tissues revealed a higher frequency of peritumoral NK cells in mice treated with BiKE than with NK cells alone (p < 0.05). In conclusion, we demonstrate that a BiKE generated in a mammalian expression system is functional in augmenting NK cell targeting of IL13Rα2-positive gliomas.
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Affiliation(s)
- Kristen D. Pawlowski
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60611, USA
- Rush Medical College, Rush University Medical Center, Chicago, IL 60612, USA
| | - Joseph T. Duffy
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60611, USA
| | - Arushi Tiwari
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60611, USA
| | - Markella Zannikou
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60611, USA
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24
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Zhao Y, Yang J, Niu Q, Wang J, Jing M, Guan G, Liu M, Luo J, Yin H, Liu Z. Identification and Characterization of Nanobodies from a Phage Display Library and Their Application in an Immunoassay for the Sensitive Detection of African Swine Fever Virus. J Clin Microbiol 2023; 61:e0119722. [PMID: 37154731 PMCID: PMC10281114 DOI: 10.1128/jcm.01197-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 04/15/2023] [Indexed: 05/10/2023] Open
Abstract
African swine fever (ASF) is one of the most lethal and devastating diseases of domestic and wild swine. The continual spread and frequent outbreaks of ASF have seriously threatened the pig and pig-related industries, causing great socioeconomic losses at unprecedented proportions. Although ASF has been documented for a century, no effective vaccine or antiviral treatment is currently available. Nanobodies (Nbs) derived from heavy-chain-only antibodies in camelids have been discovered to be effective as therapeutics and robust biosensors in imaging and diagnostic applications. In the present study, a high-quality phage display library containing specific Nbs raised against ASFV proteins was successfully constructed, and 19 nanobodies specific to ASFV p30 were preliminarily identified by phage display technology. After extensive evaluation, nanobodies Nb17 and Nb30 were employed as immunosensors and applied to develop a sandwich enzyme-linked immunosorbent assay (ELISA) for the detection of ASFV in clinical specimens. This immunoassay showed a detection limit of approximately 1.1 ng/mL target protein and 102.5 hemadsorption (HAD50/mL) of ASFV and exhibited high specificity with no cross-reaction with the other porcine viruses tested. The performances of the newly developed assay and a commercial kit in testing 282 clinical swine samples were very similar (93.62% agreement). However, the novel sandwich Nb-ELISA showed higher sensitivity than the commercial kit when serial dilutions of ASFV-positive samples were tested. The present study describes a valuable alternative technique for the detection and surveillance of ASF in endemic regions. Furthermore, additional nanobodies specific to ASFV may be developed using the generated VHH library and employed in different biotechnology fields.
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Affiliation(s)
- Yaru Zhao
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
- China Agricultural VET. BIO, Science and Technology Co., Ltd., Lanzhou, People’s Republic of China
| | - Jifei Yang
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Qingli Niu
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Jinming Wang
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Mengyao Jing
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Guiquan Guan
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Meng Liu
- Animal Husbandry and Veterinary Bureau of Dingxi City, Dingxi, Gansu, People’s Republic of China
| | - Jianxun Luo
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
| | - Hong Yin
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
| | - Zhijie Liu
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, People’s Republic of China
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, People’s Republic of China
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25
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Oghalaie A, Shoari A, Kazemi-Lomedasht F, Rahimi-Jamnani F, Mahboudi F, Ghaderi H, Hosseininejad-Chafi M, Moazzami R, Ashja Ardalan A, Piri-Gavgani S, Shahbazzadeh D, Behdani M. Development of polyclonal heavy chain antibodies targeting programmed death ligand-1. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2023; 14:323-328. [PMID: 37383651 PMCID: PMC10298837 DOI: 10.30466/vrf.2022.553274.3461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/27/2022] [Indexed: 06/30/2023]
Abstract
Programmed death ligand-1 (PD-L1, CD274 and B7-H1) has been described as a ligand for immune inhibitory receptor programmed death protein 1 (PD-1). With binding to PD-1 on activated T cells, PD-L1 can prevent T cell responses via motivating apoptosis. Consequently, it causes cancers immune evasion and helps the tumor growth; hence, PD-L1 is regarded as a therapeutic target for malignant cancers. The anti-PD-L1 monoclonal antibody targeting PD-1/PD-L1 immune checkpoint has attained remarkable outcomes in clinical application and has turned to one of the most prevalent anti-cancer drugs. The present study aimed to develop polyclonal heavy chain antibodies targeting PD-L1via Camelus dromedarius immunization. The extra-cellular domain of human PD-L1 (hPD-L1) protein was cloned, expressed, and purified. Afterwards, this recombinant protein was utilized as an antigen for camel immunization to acquire polyclonal camelid sera versus this protein. Our outcomes showed that hPD-L1 protein was effectively expressed in the prokaryotic system. The antibody-based techniques, such as enzyme-linked immunosorbent assay, western blotting, and flow cytometry displayed that the hPD-L1 protein was detected by generated polyclonal antibody. Due to the advantages of multi-epitope-binding ability, our study exhibited that camelid antibody is effective to be applied significantly for detection of PD-L1 protein in essential antibody-based studies.
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Affiliation(s)
- Akbar Oghalaie
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran;
| | - Alireza Shoari
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran;
| | - Fatemeh Kazemi-Lomedasht
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran;
| | - Fatemeh Rahimi-Jamnani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran;
| | | | - Hajarossadat Ghaderi
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran;
| | - Mohammad Hosseininejad-Chafi
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran;
| | - Reza Moazzami
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran;
| | - Arghavan Ashja Ardalan
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran;
| | - Somayeh Piri-Gavgani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran;
| | - Delavar Shahbazzadeh
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran;
| | - Mahdi Behdani
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran;
- Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran.
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26
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Arai T, Wada M, Nishiguchi H, Takimura Y, Ishii J. Inducer-free recombinant protein production in Trichoderma reesei: secretory production of endogenous enzymes and heterologous nanobodies using glucose as the sole carbon source. Microb Cell Fact 2023; 22:103. [PMID: 37208691 DOI: 10.1186/s12934-023-02109-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/28/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei has been used as a host organism for the production of lignocellulosic biomass-degrading enzymes. Although this microorganism has high potential for protein production, it has not yet been widely used for heterologous recombinant protein production. Transcriptional induction of the cellulase genes is essential for high-level protein production in T. reesei; however, glucose represses this transcriptional induction. Therefore, cellulose is commonly used as a carbon source for providing its degraded sugars such as cellobiose, which act as inducers to activate the strong promoters of the major cellulase (cellobiohydrolase 1 and 2 (cbh1 and cbh2) genes. However, replacement of cbh1 and/or cbh2 with a gene encoding the protein of interest (POI) for high productivity and occupancy of recombinant proteins remarkably impairs the ability to release soluble inducers from cellulose, consequently reducing the production of POI. To overcome this challenge, we first used an inducer-free biomass-degrading enzyme expression system, previously developed to produce cellulases and hemicellulases using glucose as the sole carbon source, for recombinant protein production using T. reesei. RESULTS We chose endogenous secretory enzymes and heterologous camelid small antibodies (nanobody) as model proteins. By using the inducer-free strain as a parent, replacement of cbh1 with genes encoding two intrinsic enzymes (aspartic protease and glucoamylase) and three different nanobodies (1ZVH, caplacizumab, and ozoralizumab) resulted in their high secretory productions using glucose medium without inducers such as cellulose. Based on signal sequences (carrier polypeptides) and protease inhibitors, additional replacement of cbh2 with the nanobody gene increased the percentage of POI to about 20% of total secreted proteins in T. reesei. This allowed the production of caplacizumab, a bivalent nanobody, to be increased to 9.49-fold (508 mg/L) compared to the initial inducer-free strain. CONCLUSIONS In general, whereas the replacement of major cellulase genes leads to extreme decrease in the degradation capacity of cellulose, our inducer-free system enabled it and achieved high secretory production of POI with increased occupancy in glucose medium. This system would be a novel platform for heterologous recombinant protein production in T. reesei.
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Affiliation(s)
- Toshiharu Arai
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, 640‑8580, Japan.
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Mayumi Wada
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, 640‑8580, Japan
| | - Hiroki Nishiguchi
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, 640‑8580, Japan
| | - Yasushi Takimura
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, 640‑8580, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
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27
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Manoutcharian K, Gevorkian G. Shark VNAR phage display libraries: An alternative source for therapeutic and diagnostic recombinant antibody fragments. FISH & SHELLFISH IMMUNOLOGY 2023; 138:108808. [PMID: 37169114 DOI: 10.1016/j.fsi.2023.108808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/02/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023]
Abstract
The development of recombinant antibody fragments as promising alternatives to full-length immunoglobulins offers vast opportunities for biomedicine. Antibody fragments have important advantages compared with conventional monoclonal antibodies that make them attractive for the biotech industry: superior stability and solubility, reduced immunogenicity, higher specificity and affinity, capacity to target the hidden epitope and cross the blood-brain barrier, the ability to refold after heat denaturation and inexpensive and easy large-scale production. Different antibody formats such as antigen-binding fragments (Fab), single-chain fragment variable (scFv) consisting of the antigen-binding domains of Ig heavy (VH) and light (VL) chain regions connected by a flexible peptide linker, single-domain antibody fragments (sdAbs) like camelid heavy-chain variable domains (VHHs) and shark variable new antigen receptor (VNARs), and bispecific antibodies (bsAbs) are currently being evaluated as diagnostics or therapeutics in preclinical studies and clinical trials. In the present review, we summarize and discuss studies on VNARs, the smallest recombinant antibody fragment, obtained after the screening of different types of phage display antibody libraries. Results published until March 2023 are discussed.
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Affiliation(s)
- Karen Manoutcharian
- Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico (UNAM), Mexico, DF, Mexico
| | - Goar Gevorkian
- Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico (UNAM), Mexico, DF, Mexico.
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28
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Mejias-Gomez O, Madsen AV, Skovgaard K, Pedersen LE, Morth JP, Jenkins TP, Kristensen P, Goletz S. A window into the human immune system: comprehensive characterization of the complexity of antibody complementary-determining regions in functional antibodies. MAbs 2023; 15:2268255. [PMID: 37876265 PMCID: PMC10601506 DOI: 10.1080/19420862.2023.2268255] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
The human immune system uses antibodies to neutralize foreign antigens. They are composed of heavy and light chains, both with constant and variable regions. The variable region has six hypervariable loops, also known as complementary-determining regions (CDRs) that determine antibody diversity and antigen specificity. Knowledge of their significance, and certain residues present in these areas, is vital for antibody therapeutics development. This study includes an analysis of more than 11,000 human antibody sequences from the International Immunogenetics information system (IMGT). The analysis included parameters such as length distribution, overall amino acid diversity, amino acid frequency per CDR and residue position within antibody chains. Overall, our findings confirm existing knowledge, such as CDRH3's high length diversity and amino acid variability, increased aromatic residue usage, particularly tyrosine, charged and polar residues like aspartic acid, serine, and the flexible residue glycine. Specific residue positions within each CDR influence these occurrences, implying a unique amino acid type distribution pattern. We compared amino acid type usage in CDRs and non-CDR regions, both in globular and transmembrane proteins, which revealed distinguishing features, such as increased frequency of tyrosine, serine, aspartic acid, and arginine. These findings should prove useful for future optimization, improvement of affinity, synthetic antibody library design, or the creation of antibodies de-novo in silico.
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Affiliation(s)
- Oscar Mejias-Gomez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas V. Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lasse E. Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - J. Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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Rossotti MA, Trempe F, van Faassen H, Hussack G, Arbabi-Ghahroudi M. Isolation and Characterization of Single-Domain Antibodies from Immune Phage Display Libraries. Methods Mol Biol 2023; 2702:107-147. [PMID: 37679618 DOI: 10.1007/978-1-0716-3381-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Naturally occurring heavy chain antibodies (HCAbs) in Camelidae species were a surprise discovery in 1993 by Hamers et al. Since that time, antibody fragments derived from HCAbs have garnered considerable attention by researchers and biotechnology companies. Due to their biophysico-chemical advantages over conventional antibody fragments, camelid single-domain antibodies (sdAbs, VHHs, nanobodies) are being increasingly utilized as viable immunotherapeutic modalities. Currently there are multiple VHH-based therapeutic agents in different phases of clinical trials in various formats such as bi- and multivalent, bi- and multi-specific, CAR-T, and antibody-drug conjugates. The first approved VHH, a bivalent humanized VHH (caplacizumab), was approved for treating rare blood clotting disorders in 2018 by the EMA and the FDA in 2019. This was followed by the approval of an anti-BCMA VHH-based CAR-T cell product in 2022 (ciltacabtagene autoleucel; CARVYKTI™) and more recently a trivalent antitumor necrosis factor alpha-based VHH drug (ozoralizumab; Nanozora®) in Japan for the treatment of rheumatoid arthritis. In this chapter we provide protocols describing the latest developments in isolating antigen-specific VHHs including llama immunization, construction of phage-displayed libraries, phage panning and screening of the soluble VHHs by ELISA, affinity measurements by surface plasmon resonance, functional cell binding by flow cytometry, and additional validation by immunoprecipitation. We present and discuss comprehensive, step-by-step methods for isolating and characterization of antigen-specific VHHs. This includes protocols for expression, biotinylation, purification, and characterization of the isolated VHHs. To demonstrate the feasibility of the entire strategy, we present examples of VHHs previously isolated and characterized in our laboratory.
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Affiliation(s)
- Martin A Rossotti
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Frederic Trempe
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Mehdi Arbabi-Ghahroudi
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada.
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.
- Department of Biology, Carleton University, Ottawa, ON, Canada.
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30
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Banik SSR, Kushnir N, Doranz BJ, Chambers R. Breaking barriers in antibody discovery: harnessing divergent species for accessing difficult and conserved drug targets. MAbs 2023; 15:2273018. [PMID: 38050985 DOI: 10.1080/19420862.2023.2273018] [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: 05/31/2023] [Accepted: 10/16/2023] [Indexed: 12/07/2023] Open
Abstract
To exploit highly conserved and difficult drug targets, including multipass membrane proteins, monoclonal antibody discovery efforts increasingly rely on the advantages offered by divergent species such as rabbits, camelids, and chickens. Here, we provide an overview of antibody discovery technologies, analyze gaps in therapeutic antibodies that stem from the historic use of mice, and examine opportunities to exploit previously inaccessible targets through discovery now possible in alternate species. We summarize the clinical development of antibodies raised from divergent species, discussing how these animals enable robust immune responses against highly conserved binding sites and yield antibodies capable of penetrating functional pockets via long HCDR3 regions. We also discuss the value of pan-reactive molecules often produced by these hosts, and how these antibodies can be tested in accessible animal models, offering a faster path to clinical development.
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31
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Medagli B, Soler MA, De Zorzi R, Fortuna S. Antibody Affinity Maturation Using Computational Methods: From an Initial Hit to Small-Scale Expression of Optimized Binders. Methods Mol Biol 2023; 2552:333-359. [PMID: 36346602 DOI: 10.1007/978-1-0716-2609-2_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nanobodies (VHHs) are engineered fragments of the camelid single-chain immunoglobulins. The VHH domain contains the highly variable segments responsible for antigen recognition. VHHs can be easily produced as recombinant proteins. Their small size is a good advantage for in silico approaches. Computer methods represent a valuable strategy for the optimization and improvement of their binding affinity. They also allow for epitope selection offering the possibility to design new VHHs for regions of a target protein that are not naturally immunogenic. Here we present an in silico mutagenic protocol developed to improve the binding affinity of nanobodies together with the first step of their in vitro production. The method, already proven successful in improving the low Kd of a nanobody hit obtained by panning, can be employed for the ex novo design of antibody fragments against selected protein target epitopes.
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Affiliation(s)
- Barbara Medagli
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy.
| | - Miguel A Soler
- CONCEPT Lab, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Mathematics, Computer Science and Physics, University of Udine, Udine, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy.
- CONCEPT Lab, Istituto Italiano di Tecnologia, Genova, Italy.
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32
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Nguyen TD, Bordeau BM, Zhang Y, Mattle AG, Balthasar JP. Half-Life Extension and Biodistribution Modulation of Biotherapeutics via Red Blood Cell Hitch-Hiking with Novel Anti-Band 3 Single-Domain Antibodies. Int J Mol Sci 2022; 24:475. [PMID: 36613917 PMCID: PMC9820191 DOI: 10.3390/ijms24010475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Small therapeutic proteins are receiving increased interest as therapeutic drugs; however, their clinical success has been limited due to their rapid elimination. Here, we report a half-life extension strategy via strategy via red blood cell red blood cell (RBC) hitch-hiking. This manuscript details the development and characterization of novel anti-RBC single-domain antibodies (sdAbs), their genetic fusion to therapeutic antibody fragments (TAF) as bispecific fusion constructs, and their influence on TAF pharmacokinetics and biodistribution. Several sdAbs specific to the band 3 antigen were generated via phage-display technology. Binding affinity to RBCs was assessed via flow cytometry. Affinity maturation via random mutagenesis was carried out to improve the binding affinity of the sdAbs. Bi-specific constructs were generated by fusing the anti-RBC sdAbs with anti-tissue necrosis factor alpha (TNF-α) TAF via the use of a glycine-serine flexible linker, and assessments for binding were performed via enzyme-linked immunosorbent assay and flow cytometry. Pharmacokinetics of anti-RBC sdAbs and fusion constructs were evaluated following intravenous bolus dosing in mice at a 1 mg/kg dose. Two RBC-binding sdAbs, RB12 and RE8, were developed. These two clones showed high binding affinity to human RBC with an estimated KD of 17.7 nM and 23.6 nM and low binding affinity to mouse RBC with an estimated KD of 335 nM and 528 nM for RB12 and RE8, respectively. Two derivative sdAbs, RMA1, and RMC1, with higher affinities against mouse RBC, were generated via affinity maturation (KD of 66.9 nM and 30.3 nM, respectively). Pharmacokinetic investigations in mice demonstrated prolonged circulation half-life of an anti-RBC-TNF-α bispecific construct (75 h) compared to a non-RBC binding control (1.3 h). In summary, the developed anti-RBC sdAbs and fusion constructs have demonstrated high affinity in vitro, and sufficient half-life extension in vivo.
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Affiliation(s)
- Toan D. Nguyen
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Brandon M. Bordeau
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Yu Zhang
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Anna G. Mattle
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Joseph P. Balthasar
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
- 450 Pharmacy Building, Buffalo, NY 14214, USA
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Nguyen TD, Bordeau BM, Zhang Y, Mattle AG, Balthasar JP. Half-Life Extension and Biodistribution Modulation of Biotherapeutics via Red Blood Cell Hitch-Hiking with Novel Anti-Band 3 Single-Domain Antibodies. Int J Mol Sci 2022. [PMID: 36613917 DOI: 10.3390/ijms23179779/s1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
Small therapeutic proteins are receiving increased interest as therapeutic drugs; however, their clinical success has been limited due to their rapid elimination. Here, we report a half-life extension strategy via strategy via red blood cell red blood cell (RBC) hitch-hiking. This manuscript details the development and characterization of novel anti-RBC single-domain antibodies (sdAbs), their genetic fusion to therapeutic antibody fragments (TAF) as bispecific fusion constructs, and their influence on TAF pharmacokinetics and biodistribution. Several sdAbs specific to the band 3 antigen were generated via phage-display technology. Binding affinity to RBCs was assessed via flow cytometry. Affinity maturation via random mutagenesis was carried out to improve the binding affinity of the sdAbs. Bi-specific constructs were generated by fusing the anti-RBC sdAbs with anti-tissue necrosis factor alpha (TNF-α) TAF via the use of a glycine-serine flexible linker, and assessments for binding were performed via enzyme-linked immunosorbent assay and flow cytometry. Pharmacokinetics of anti-RBC sdAbs and fusion constructs were evaluated following intravenous bolus dosing in mice at a 1 mg/kg dose. Two RBC-binding sdAbs, RB12 and RE8, were developed. These two clones showed high binding affinity to human RBC with an estimated KD of 17.7 nM and 23.6 nM and low binding affinity to mouse RBC with an estimated KD of 335 nM and 528 nM for RB12 and RE8, respectively. Two derivative sdAbs, RMA1, and RMC1, with higher affinities against mouse RBC, were generated via affinity maturation (KD of 66.9 nM and 30.3 nM, respectively). Pharmacokinetic investigations in mice demonstrated prolonged circulation half-life of an anti-RBC-TNF-α bispecific construct (75 h) compared to a non-RBC binding control (1.3 h). In summary, the developed anti-RBC sdAbs and fusion constructs have demonstrated high affinity in vitro, and sufficient half-life extension in vivo.
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Affiliation(s)
- Toan D Nguyen
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Brandon M Bordeau
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Yu Zhang
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Anna G Mattle
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Joseph P Balthasar
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
- 450 Pharmacy Building, Buffalo, NY 14214, USA
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Construction of a Fab Library Merging Chains from Semisynthetic and Immune Origin, Suitable for Developing New Tools for Gluten Immunodetection in Food. Foods 2022; 12:foods12010149. [PMID: 36613365 PMCID: PMC9818130 DOI: 10.3390/foods12010149] [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: 11/04/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
The observed increase in the prevalence of gluten-related disorders has prompted the development of novel immunological systems for gluten detection in foodstuff. The innovation on these methods relies on the generation of new antibodies, which might alternatively be obtained by molecular evolution methods such as phage display. This work presents a novel approach for the generation of a Fab library by merging semi-synthetic heavy chains built-up from a pre-existent recombinant antibody fragment (dAb8E) with an immune light chain set derived from celiac donors. From the initial phage population (107 candidates) and after three rounds of selection and amplification, four different clones were isolated for further characterization. The phage Fab8E-4 presented the best features to be applied in an indirect ELISA for the detection of gluten in foods, resulting in improved specificity and sensitivity.
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Zettl I, Ivanova T, Zghaebi M, Rutovskaya MV, Ellinger I, Goryainova O, Kollárová J, Villazala-Merino S, Lupinek C, Weichwald C, Drescher A, Eckl-Dorna J, Tillib SV, Flicker S. Generation of high affinity ICAM-1-specific nanobodies and evaluation of their suitability for allergy treatment. Front Immunol 2022; 13:1022418. [DOI: 10.3389/fimmu.2022.1022418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022] Open
Abstract
The nasal cavity is an important site of allergen entry. Hence, it represents an organ where trans-epithelial allergen penetration and subsequent IgE-mediated allergic inflammation can potentially be inhibited. Intercellular adhesion molecule 1 (ICAM-1) is highly expressed on the surface of respiratory epithelial cells in allergic patients. It was identified as a promising target to immobilize antibody conjugates bispecific for ICAM-1 and allergens and thereby block allergen entry. We have previously characterized a nanobody specific for the major birch pollen allergen Bet v 1 and here we report the generation and characterization of ICAM-1-specific nanobodies. Nanobodies were obtained from a camel immunized with ICAM-1 and a high affinity binder was selected after phage display (Nb44). Nb44 was expressed as recombinant protein containing HA- and His-tags in Escherichia coli (E.coli) and purified via affinity chromatography. SDS-PAGE and Western blot revealed a single band at approximately 20 kDa. Nb44 bound to recombinant ICAM-1 in ELISA, and to ICAM-1 expressed on the human bronchial epithelial cell line 16HBE14o- as determined by flow cytometry. Experiments conducted at 4°C and at 37°C, to mimic physiological conditions, yielded similar percentages (97.2 ± 1.2% and 96.7 ± 1.5% out of total live cells). To confirm and visualize binding, we performed immunofluorescence microscopy. While Texas Red Dextran was rapidly internalized Nb44 remained localized on the cell surface. Additionally, we determined the strength of Nb44 and ICAM-1 interaction using surface plasmon resonance (SPR). Nb44 bound ICAM-1 with high affinity (10-10 M) and had slow off-rates (10-4 s-1). In conclusion, our results showed that the selected ICAM-1-specific nanobody bound ICAM-1 with high affinity and was not internalized. Thus, it could be further used to engineer heterodimers with allergen-specific nanobodies in order to develop topical treatments of pollen allergy.
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36
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Mazinani M, Rahbarizadeh F. CAR-T cell potency: from structural elements to vector backbone components. Biomark Res 2022; 10:70. [PMID: 36123710 PMCID: PMC9487061 DOI: 10.1186/s40364-022-00417-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 09/07/2022] [Indexed: 12/03/2022] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy, in which a patient’s own T lymphocytes are engineered to recognize and kill cancer cells, has achieved remarkable success in some hematological malignancies in preclinical and clinical trials, resulting in six FDA-approved CAR-T products currently available in the market. Once equipped with a CAR construct, T cells act as living drugs and recognize and eliminate the target tumor cells in an MHC-independent manner. In this review, we first described all structural modular of CAR in detail, focusing on more recent findings. We then pointed out behind-the-scene elements contributing to CAR expression and reviewed how CAR expression can be drastically affected by the elements embedded in the viral vector backbone.
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Affiliation(s)
- Marzieh Mazinani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-111, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-111, Tehran, Iran. .,Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.
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Wang M, Wei L, Xiang H, Ren B, Liu X, Jiang L, Yang N, Shi J. A megadiverse naïve library derived from numerous camelids for efficient and rapid development of VHH antibodies. Anal Biochem 2022; 657:114871. [PMID: 36108795 DOI: 10.1016/j.ab.2022.114871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 07/20/2022] [Accepted: 08/17/2022] [Indexed: 11/01/2022]
Abstract
The field of antibody development is under pressure to meet rising demands for speed, cost-effectiveness, efficacy, reliability, and large-scale production. It is costly and time-consuming to immunize animals and build a single-domain antibody (sdAb) library for each target. Using the variable domain (VHH) of heavy-chain only antibodies (HcAbs) derived from blood samples of 75 non-immunized camelid animals (51 alpacas, 13 llamas, 11 Bactrian camels), and spleens from two Bactrian camels, a naïve sdAb library with extensive megadiversity and reusability was constructed. The library was evaluated using next-generation DNA sequencing (NGS) and was found to contain hundreds of billions of unique clones. To confirm the availability of target-specific VHHs, a naive library was screened for a variety of targets. At least two VHH candidates were extracted for each target using a 20-day selection pipeline. Some binders had ultrahigh potencies, with binding affinities in the nanomolar range. This naïve library, in particular, offers the possibility of acquiring unique antibodies targeting antigens of interest with low feasible dissociation constant (kD) without the time, effort, and price associated in producing antibodies in animals via antigen injection. Overall, the study shows that the megadiverse naïve library provides a rapid, adaptable, and easy platform for antibody creation, emphasizing its therapeutic and diagnostic implications.
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Affiliation(s)
- Meiniang Wang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Likun Wei
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China; Biotechnology and Health Centre, City University of Hong Kong, Shenzhen Research Institute, Shenzhen, China
| | - Haitao Xiang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Bingzhao Ren
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiaopan Liu
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Lin Jiang
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Naibo Yang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; Complete Genomics, Inc., 2904 Orchard Parkway, San Jose, CA, 95134, USA.
| | - Jiahai Shi
- Synthetic Biology Translational Research Programmes, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Development of a Bispecific Nanobody Targeting CD20 on B-Cell Lymphoma Cells and CD3 on T Cells. Vaccines (Basel) 2022; 10:vaccines10081335. [PMID: 36016223 PMCID: PMC9413575 DOI: 10.3390/vaccines10081335] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
B-cell lymphoma is a group of malignant proliferative diseases originating from lymphoid tissue with different clinical manifestations and biological characteristics. It can occur in any part of the body, accounting for more than 80% of all lymphomas. The present study aimed to construct bispecific single-domain antibodies against CD20 and CD3 and to evaluate their function in killing tumor cells in vitro. A Bactrian camel was immunized with a human CD20 extracellular peptide, and the VHH gene was cloned and ligated into a phagemid vector to construct the phage antibody display library. A phage antibody library with a size of 1.2 × 108 was successfully constructed, and the VHH gene insertion rate was 91.7%. Ninety-two individual clones were randomly picked and screened by phage ELISA. Six strains with the high binding ability to human CD20 were named 11, 30, 71, 72, 83, and 92, and induced expression and purification were performed to obtain soluble CD20 single-domain antibodies. The obtained single-domain antibodies could specifically bind to human CD20 polypeptide and cell surface-expressed CD20 molecules in ELISA, Western blot, and cell immunofluorescence assays. The anti-CD20/CD3 bispecific nanobody (BsNb) was successfully constructed by fusing the anti-CD20 VHH gene with the anti-CD3 VHH and the bispecific single-domain antibody was expressed, purified, and validated. Anti-CD20/CD3 BsNb can specifically bind CD20 molecules on the surface of human lymphoma Raji cells and CD3 molecules on the surface of T cells in flow cytometry analysis and effectively mediate peripheral blood mononuclear cells (PBMCs) target Raji cells with a killing efficiency of up to 30.4%, as measured by the lactate dehydrogenase (LDH) method. The release of hIFN-γ from PBMCs during incubation with anti-CD20/CD3 BsNb was significantly higher than that of the control group (p < 0.01). The anti-CD20/CD3 BsNb could maintain 80% binding activity after incubation with human serum at 37 °C for 48 h. These results indicated the strong antitumor effect of the constructed anti-CD20/CD3 BsNb and laid the foundation for the further development of antitumor agents and the clinical application of anti-CD20/CD3 BsNb.
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Stam JC, de Maat S, de Jong D, Arens M, van Lint F, Gharu L, van Roosmalen MH, Roovers RC, Strokappe NM, Wagner R, Kliche A, de Haard HJ, van Bergen En Henegouwen PM, Nijhuis M, Verrips CT. Directing HIV-1 for degradation by non-target cells, using bi-specific single-chain llama antibodies. Sci Rep 2022; 12:13413. [PMID: 35927444 PMCID: PMC9352707 DOI: 10.1038/s41598-022-15993-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022] Open
Abstract
While vaccination against HIV-1 has been so far unsuccessful, recently broadly neutralizing antibodies (bNAbs) against HIV-1 envelope glycoprotein were shown to induce long-term suppression in the absence of antiretroviral therapy in patients with antibody-sensitive viral reservoirs. The requirement of neutralizing antibodies indicates that the antibody mediated removal (clearance) of HIV-1 in itself is not efficient enough in these immune compromised patients. Here we present a novel, alternative approach that is independent of a functional immune system to clear HIV-1, by capturing the virus and redirecting it to non-target cells where it is internalized and degraded. We use bispecific antibodies with domains derived from small single chain Llama antibodies (VHHs). These bind with one domain to HIV-1 envelope proteins and with the other domain direct the virus to cells expressing epidermal growth factor receptor (EGFR), a receptor that is ubiquitously expressed in the body. We show that HIV envelope proteins, virus-like particles and HIV-1 viruses (representing HIV-1 subtypes A, B and C) are efficiently recruited to EGFR, internalized and degraded in the lysosomal pathway at low nM concentrations of bispecific VHHs. This directed degradation in non-target cells may provide a clearance platform for the removal of viruses and other unwanted agents from the circulation, including toxins, and may thus provide a novel method for curing.
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Affiliation(s)
- Jord C Stam
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands.
| | - Steven de Maat
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Dorien de Jong
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mathia Arens
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Fenna van Lint
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Lavina Gharu
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mark H van Roosmalen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands.,Intervet, Wim de Körverstraat 35, 5831 AN, Boxmeer, The Netherlands
| | - Rob C Roovers
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands.,LAVA Therapeutics, Yalelaan 60, 3584CM, Utrecht, The Netherlands
| | - Nika M Strokappe
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Ralf Wagner
- Molecular Microbiology and Gene Therapy, Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Alexander Kliche
- Molecular Microbiology and Gene Therapy, Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Hans J de Haard
- Argenx, Industriepark Zwijnaarde 7, 9052, Zwijnaarde, Belgium
| | - Paul M van Bergen En Henegouwen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Monique Nijhuis
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C Theo Verrips
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands.,QVQ Holding BV, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
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40
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Saura-Esteller J, de Jong M, King LA, Ensing E, Winograd B, de Gruijl TD, Parren PWHI, van der Vliet HJ. Gamma Delta T-Cell Based Cancer Immunotherapy: Past-Present-Future. Front Immunol 2022; 13:915837. [PMID: 35784326 PMCID: PMC9245381 DOI: 10.3389/fimmu.2022.915837] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/05/2022] [Indexed: 12/15/2022] Open
Abstract
γδ T-cells directly recognize and kill transformed cells independently of HLA-antigen presentation, which makes them a highly promising effector cell compartment for cancer immunotherapy. Novel γδ T-cell-based immunotherapies, primarily focusing on the two major γδ T-cell subtypes that infiltrate tumors (i.e. Vδ1 and Vδ2), are being developed. The Vδ1 T-cell subset is enriched in tissues and contains both effector T-cells as well as regulatory T-cells with tumor-promoting potential. Vδ2 T-cells, in contrast, are enriched in circulation and consist of a large, relatively homogeneous, pro-inflammatory effector T-cell subset. Healthy individuals typically harbor in the order of 50-500 million Vγ9Vδ2 T-cells in the peripheral blood alone (1-10% of the total CD3+ T-cell population), which can rapidly expand upon stimulation. The Vγ9Vδ2 T-cell receptor senses intracellular phosphorylated metabolites, which accumulate in cancer cells as a result of mevalonate pathway dysregulation or upon pharmaceutical intervention. Early clinical studies investigating the therapeutic potential of Vγ9Vδ2 T-cells were based on either ex vivo expansion and adoptive transfer or their systemic activation with aminobisphosphonates or synthetic phosphoantigens, either alone or combined with low dose IL-2. Immune-related adverse events (irAE) were generally \mild, but the clinical efficacy of these approaches provided overall limited benefit. In recent years, critical advances have renewed the excitement for the potential of Vγ9Vδ2 T-cells in cancer immunotherapy. Here, we review γδ T-cell-based therapeutic strategies and discuss the prospects of those currently evaluated in clinical studies in cancer patients as well as future therapies that might arise from current promising pre-clinical results.
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Affiliation(s)
- José Saura-Esteller
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Milon de Jong
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Lisa A. King
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | | | - Tanja D. de Gruijl
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Paul W. H. I. Parren
- LAVA Therapeutics, Utrecht, Netherlands
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Hans J. van der Vliet
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- LAVA Therapeutics, Utrecht, Netherlands
- *Correspondence: Hans J. van der Vliet, ;
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Macias LA, Wang X, Davies BW, Brodbelt JS. Mapping paratopes of nanobodies using native mass spectrometry and ultraviolet photodissociation. Chem Sci 2022; 13:6610-6618. [PMID: 35756525 PMCID: PMC9172568 DOI: 10.1039/d2sc01536f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/16/2022] [Indexed: 11/21/2022] Open
Abstract
Following immense growth and maturity of the field in the past decade, native mass spectrometry has garnered widespread adoption for the structural characterization of macromolecular complexes. Routine analysis of biotherapeutics by this technique has become commonplace to assist in the development and quality control of immunoglobulin antibodies. Concurrently, 193 nm ultraviolet photodissociation (UVPD) has been developed as a structurally sensitive ion activation technique capable of interrogating protein conformational changes. Here, UVPD was applied to probe the paratopes of nanobodies, a class of single-domain antibodies with an expansive set of applications spanning affinity reagents, molecular imaging, and biotherapeutics. Comparing UVPD sequence fragments for the free nanobodies versus nanobody·antigen complexes empowered assignment of nanobody paratopes and intermolecular salt-bridges, elevating the capabilities of UVPD as a new strategy for characterization of nanobodies. Ultraviolet photodissociation mass spectrometry is used to probe the paratopes of nanobodies, a class of single-domain antibodies, and to determine intersubunit salt-bridges and explore the nanobody·antigen interfaces.![]()
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Affiliation(s)
- Luis A Macias
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Xun Wang
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
| | - Bryan W Davies
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
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Marine-derived microbes and molecules for drug discovery. Inflamm Regen 2022; 42:18. [PMID: 35655291 PMCID: PMC9164490 DOI: 10.1186/s41232-022-00207-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 03/21/2022] [Indexed: 12/03/2022] Open
Abstract
Increasing attention has been paid to marine-derived biomolecules as sources of therapeutics for autoimmune diseases. Nagasaki Prefecture has many islands and is surrounded by seas, straits, gulfs, bays, and coves, giving it the second longest coastline in Japan after Hokkaido. We have collected more than 20,000 marine microbes and have been preparing an original marine microbial extract library, which contains small and mid-size biomolecules that may penetrate cell membranes and interfere with the intracellular protein–protein interaction involved in the development of autoinflammatory diseases such as familial Mediterranean fever. In addition, we have been developing an indoor shark farming system to prepare shark nanobodies that could be developed as potential therapeutic agents for autoimmune diseases. Sharks produce heavy-chain antibodies, called immunoglobulin new antigen receptors (IgNARs), consisting of one variable domain (VNAR) and five constant domains (CNAR); of these, VNAR can recognize a variety of foreign antigens. A VNAR single domain fragment, called a nanobody, can be expressed in Escherichia coli and has the properties of an ideal therapeutic candidate for autoimmune diseases. Shark nanobodies contain complementarity-determining regions that are formed through the somatic rearrangement of variable, diversity, and joining segments, with the segment end trimming and the N- and P-additions, as found in the variable domains of mammalian antibodies. The affinity and diversity of shark nanobodies are thus expected to be comparable to those of mammalian antibodies. In addition, shark nanobodies are physically robust and can be prepared inexpensively; as such, they may lead to the development of highly specific, stable, effective, and inexpensive biotherapeutics in the future. In this review, we first summarize the history of the development of conventional small molecule drugs and monoclonal antibody therapeutics for autoimmune diseases, and then introduce our drug discovery system at Nagasaki University, including the preparation of an original marine microbial extract library and the development of shark nanobodies.
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Gaudreault F, Corbeil CR, Purisima EO, Sulea T. Coevolved Canonical Loops Conformations of Single-Domain Antibodies: A Tale of Three Pockets Playing Musical Chairs. Front Immunol 2022; 13:884132. [PMID: 35720356 PMCID: PMC9203998 DOI: 10.3389/fimmu.2022.884132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Single-domain antibodies (sdAbs) are a promising class of biotherapeutics with unique structural traits within their paratope region. The distribution of canonical conformations explored by their complementarity determining region (CDR) loops differs to some extent from conventional two-chain Fv fragments of monoclonal antibodies (mAbs). In this study, we explored in detail the canonical structures of sdAb CDR-H1 and CDR-H2 loops and compared those with mAbs from the IGHV3 and IGHV1 gene families. We surveyed the antibody structures catalogued in SAbDab and clustered the CDR canonical loops in Cartesian space. While most of the sdAb clusters were sub-populations of previously defined canonical Fv conformations of CDR-H1 and CDR-H2, our stricter clustering approach defined narrower clusters in sequence-space. Meticulous visual inspection of sub-populations allowed a clearer understanding of sequence-structure relationships. The packing densities within structural pockets contacted by CDR-H1 and CDR-H2 canonical conformations were analyzed on the premise that these pockets cannot be left vacant as they would leave exposed supportive hydrophobic residues. The fine resolution of the canonical clusters defined here revealed unique signatures within these pockets, including distinct structural complementarities between CDR-H1 and CDR-H2 canonical clusters, which could not be perceived with the previous coarser clusters. We highlight examples where a single residue change in CDR-H1 sequence is sufficient to induce a dramatic population shift in CDR-H2 conformation. This suggests that preferences in combining CDR-H1 and CDR-H2 emerged naturally during antibody evolution, leading to preferred sets of conserved amino acids at key positions in the framework as well as within the CDR loops. We outline a game of musical chairs that is necessary to maintain the integrity of the antibody structures that arose during evolution. Our study also provides refined CDR-H1 and CDR-H2 structural templates for sdAb homology modeling that could be leveraged for improved antibody design.
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Eguchi RR, Choe CA, Huang PS. Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation. PLoS Comput Biol 2022; 18:e1010271. [PMID: 35759518 PMCID: PMC9269947 DOI: 10.1371/journal.pcbi.1010271] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/08/2022] [Accepted: 06/01/2022] [Indexed: 12/26/2022] Open
Abstract
While deep learning models have seen increasing applications in protein science, few have been implemented for protein backbone generation—an important task in structure-based problems such as active site and interface design. We present a new approach to building class-specific backbones, using a variational auto-encoder to directly generate the 3D coordinates of immunoglobulins. Our model is torsion- and distance-aware, learns a high-resolution embedding of the dataset, and generates novel, high-quality structures compatible with existing design tools. We show that the Ig-VAE can be used with Rosetta to create a computational model of a SARS-CoV2-RBD binder via latent space sampling. We further demonstrate that the model’s generative prior is a powerful tool for guiding computational protein design, motivating a new paradigm under which backbone design is solved as constrained optimization problem in the latent space of a generative model. Many essential biochemical processes are governed by protein-protein interactions (PPIs), and our ability to make binding proteins that modulate PPIs is crucial to the creation of therapeutics and the study of cell-signaling. One critical aspect of PPI design is to capture protein conformational flexibility. Deep generative models are a class of mathematical models that are able to synthesize novel data from a finite set of training examples. Here, we make advances in computational protein design methodology by developing a deep generative model that creates protein backbones adopting the immunoglobulin fold, which is found in natural binding proteins such as antibodies. While generative models have been powerful in tasks such as image generation, using them to create proteins has remained a challenge. We solve this problem with a new model that allows for the direct generation of novel 3D molecules and show that they are of high chemical accuracy. Generated structures work well with existing protein design methods such as Rosetta, providing access to a large collection of novel immunoglobulin structures. Finally, we present a new protein design framework, called “generative design,” that shows how deep generative models such as ours can be applied to virtually any protein design problem.
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Affiliation(s)
- Raphael R. Eguchi
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Christian A. Choe
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- * E-mail:
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Camelid Single-Domain Antibodies: Promises and Challenges as Lifesaving Treatments. Int J Mol Sci 2022; 23:ijms23095009. [PMID: 35563400 PMCID: PMC9100996 DOI: 10.3390/ijms23095009] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 02/07/2023] Open
Abstract
Since the discovery of camelid heavy-chain antibodies in 1993, there has been tremendous excitement for these antibody domains (VHHs/sdAbs/nanobodies) as research tools, diagnostics, and therapeutics. Commercially, several patents were granted to pioneering research groups in Belgium and the Netherlands between 1996–2001. Ablynx was established in 2001 with the aim of exploring the therapeutic applications and development of nanobody drugs. Extensive efforts over two decades at Ablynx led to the first approved nanobody drug, caplacizumab (Cablivi) by the EMA and FDA (2018–2019) for the treatment of rare blood clotting disorders in adults with acquired thrombotic thrombocytopenic purpura (TPP). The relatively long development time between camelid sdAb discovery and their entry into the market reflects the novelty of the approach, together with intellectual property restrictions and freedom-to-operate issues. The approval of the first sdAb drug, together with the expiration of key patents, may open a new horizon for the emergence of camelid sdAbs as mainstream biotherapeutics in the years to come. It remains to be seen if nanobody-based drugs will be cheaper than traditional antibodies. In this review, I provide critical perspectives on camelid sdAbs and present the promises and challenges to their widespread adoption as diagnostic and therapeutic agents.
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Shoari A, Tahmasebi M, Khodabakhsh F, Cohan RA, Oghalaie A, Behdani M. Angiogenic biomolecules specific nanobodies application in cancer imaging and therapy; review and updates. Int Immunopharmacol 2022; 105:108585. [DOI: 10.1016/j.intimp.2022.108585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/18/2022] [Accepted: 01/25/2022] [Indexed: 11/05/2022]
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Camouflaged liposomes by 11A4-nanobody for co-delivery of cisplatin and nitroxoline in breast cancer tumors: An in vitro/in vivo study. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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X-ray Crystal Structure Analysis of VHH-Protein Antigen Complexes. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2446:513-530. [PMID: 35157291 DOI: 10.1007/978-1-0716-2075-5_26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
VHHs are antigen-binding domains cloned from heavy-chain antibodies found in camelids. These proteins have generated considerable interest in a variety of applications as research reagents, crystallization chaperones, and therapeutics. The evolutionary adaptations of VHHs have resulted in biophysical properties and antigen-binding modalities which are distinct from those of conventional antibodies. A detailed molecular analysis of VHH interactions with their cognate protein antigens is valuable for understanding structure-function relationships and for protein engineering. The majority of VHHs bind to folded proteins and thus recognize discontinuous three-dimensional epitopes. While multiple approaches exist for dissecting the interaction between a protein antigen and a VHH, X-ray crystallography remains the highest resolution method available. Here, we provide an updated procedure for determining and analyzing the X-ray structure of a VHH in complex with a protein antigen. We describe the recombinant expression and purification of VHHs and protein antigens, purification and analysis of protein complexes, crystallization, and optimization, X-ray structure determination by molecular replacement, and analysis of the complex.
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The Therapeutic Effect of an Anti-TNF-α/HSA/IL-6R Triple-Specific Fusion Protein Under Experimental Septic Conditions. Inflammation 2022; 45:919-928. [PMID: 35059921 PMCID: PMC8776363 DOI: 10.1007/s10753-021-01595-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 11/05/2022]
Abstract
Sepsis caused by a dysregulated host response to infection is a life-threatening disease that can lead to organ dysfunction. Due to its unclear and complex mechanism, effective medicine for the treatment of sepsis is urgently required. The extensive release of cytokines and other mediators like TNF-α and interleukin-6 (IL-6) play critical roles in the development of sepsis. The present study aims to evaluate the potential protective effects of an anti-TNF-α/HSA/IL-6R triple-specific fusion protein (TAL-6) under septic experimental conditions. The anti-TNF-α/HSA/IL-6R triple-specific fusion protein (TAL-6), which links three published single domain antibodies, was designed and constructed in our lab. High purity fusion proteins were obtained with high binding affinity for TNF-α (94.75 pM), human serum albumin (1.83 nM) and IL-6R (2.29 nM). TAL-6 protected mouse fibroblast fibrosarcoma cells (L929) from apoptosis induced by TNF-α, establishing that the expressed fusion proteins can selectively interact with TNF-α in vitro. In vivo, the survival rate of cecal ligation and puncture (CLP) was notably increased in the group with TAL-6 treatment and significantly higher compared with the single-targeted IL-6R and TNF-α fusion protein at the same dose. After treatment with TAL-6, the serum levels of TNF-α, IL-1β, and IL-6 were significantly decreased, and sepsis-induced pathological injuries in the kidney were remarkably attenuated. TAL-6 is therefore a potential candidate for the development of new drugs against sepsis in human.
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Abstract
Humanization of therapeutic antibodies derived from animal immunizations is often required to minimize immunogenicity risks in humans, which can cause potentially harmful and serious side effects and reduce antibody efficacy. Humanization is typically applied to conventional monoclonal antibodies derived in rodents as well as single-domain antibodies isolated from camelids and sharks (VHHs and VNARs). A streamlined protocol is described here for sequence humanization of camelid VHHs, which represent a promising biotherapeutic format with many desirable attributes. From human framework selection and complementarity-determining region grafting strategies to empirical scoring for prioritization of back-mutations, step-by-step instructions, and templates are provided along with bioinformatics resources to assist each step of the humanization process. Alternative approaches, warnings, and caveats are also presented.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada.
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.
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