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Advances in Single Domain-Based Antibodies
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Advances in Single Domain-Based Antibodies

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Immunology".

Deadline for manuscript submissions: closed (15 September 2023) | Viewed by 34165

Special Issue Editor

Dr. Sergei V. Tillib

E-Mail Website
Guest Editor
Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.
Interests: molecular immunology; single-domain antibody; phage display; medical diagnostics; immunotherapy; vaccine development

Special Issue Information

Dear Colleagues,

Almost 30 years have passed since the pioneer discovery of heavy-chain-only antibodies in camelids and the development of a very efficient technique for generation of new single-domain antigen-binding molecules (“nanobodies”, sdAbs) by R. Hammers’ group (Hamers-Casterman et al., 1993). This discovery established a solid base for the exponential growth of many very different and successful applications of the technology in recent years to solve actual problems of fundamental science, biotechnology, and medicine.

This Special Issue on “Single Domain-Based Antibodies” aims to highlight recent advances, promises, and challenges in the field of a variety of actual issues related to generation, formatting, and different new applications of single-domain antibodies and their derivatives.

Potential topics include but are not limited to the following:

  • sdAbs for an analysis of biomarkers associated with a cancer or another disease development;
  • Making di- and multimeric sdAb-derivatives as well as sdAb-conjugates and immunotoxins with a special focus on site-specific attachment of effector molecules;
  • sdAbs to fight infections (broadly neutralizing nanobodies or nanobody cocktails, virus-retaining inhalable constructs, new types of vaccines);
  • New efficient methods for the generation of sdAbs with required features (high specificity for a particular antigenic epitope, conformation capture, pH-dependent recognition, for specific inhibition of a ligand–receptor pair or an enzyme/toxin, etc.);
  • Bispecific sdAb-constructs facilitating connections of cytotoxic cells of the immune system with cancer cells or blocking cytokines in a tissue-specific manner;
  • sdAbs-based intrabodies and tracers for in vivo fluorescence imaging and image-guided surgery;
  • Anti-idiotypic sdAbs mimicking certain epitopes of various target antigens, mimicking natural enzymes;
  • New sdAb-based promising substances for theranostics and therapeutics.

Dr. Sergei V. Tillib
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • single-domain antibody
  • nanobody
  • early diagnosis
  • biomarker
  • neutralizing nanobodies
  • conjugate
  • immunotoxin
  • conformation capture
  • pH-dependent recognition
  • bispecific and multimeric constructs
  • intrabody
  • tracer
  • anti-idiotypic antibody
  • theranostics
  • preventive medicine

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Published Papers (5 papers)

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Research

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23 pages, 4262 KiB  
Article
Anti-Idiotypic Nanobodies Mimicking an Epitope of the Needle Protein of the Chlamydial Type III Secretion System for Targeted Immune Stimulation
by Ekaterina A. Koroleva, Oksana S. Goryainova, Tatiana I. Ivanova, Marina V. Rutovskaya, Naylia A. Zigangirova and Sergei V. Tillib
Int. J. Mol. Sci. 2024, 25(4), 2047; https://doi.org/10.3390/ijms25042047 - 7 Feb 2024
Cited by 1 | Viewed by 1561
Abstract
The development of new approaches and drugs for effective control of the chronic and complicated forms of urogenital chlamydia caused by Chlamydia trachomatis, which is suspected to be one of the main causes of infertility in both women and men, is an [...] Read more.
The development of new approaches and drugs for effective control of the chronic and complicated forms of urogenital chlamydia caused by Chlamydia trachomatis, which is suspected to be one of the main causes of infertility in both women and men, is an urgent task. We used the technology of single-domain antibody (nanobody) generation both for the production of targeting anti-chlamydia molecules and for the subsequent acquisition of anti-idiotypic nanobodies (ai-Nbs) mimicking the structure of a given epitope of the pathogen (the epitope of the Chlamydial Type III Secretion System Needle Protein). In a mouse model, we have shown that the obtained ai-Nbs are able to induce a narrowly specific humoral immune response in the host, leading to the generation of intrinsic anti-Chlamydia antibodies, potentially therapeutic, specifically recognizing a given antigenic epitope of Chlamydia. The immune sera derived from mice immunized with ai-Nbs are able to suppress chlamydial infection in vitro. We hypothesize that the proposed method of the creation and use of ai-Nbs, which mimic and present to the host immune system exactly the desired region of the antigen, create a fundamentally new universal approach to generating molecular structures as a part of specific vaccine for the targeted induction of immune response, especially useful in cases where it is difficult to prepare an antigen preserving the desired epitope in its native conformation. Full article
(This article belongs to the Special Issue Advances in Single Domain-Based Antibodies)
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13 pages, 2250 KiB  
Article
Macroporous Epoxy-Based Monoliths Functionalized with Anti-CD63 Nanobodies for Effective Isolation of Extracellular Vesicles in Urine
by Julia Neumair, Claudia D’Ercole, Matteo De March, Martin Elsner, Michael Seidel and Ario de Marco
Int. J. Mol. Sci. 2023, 24(7), 6131; https://doi.org/10.3390/ijms24076131 - 24 Mar 2023
Cited by 6 | Viewed by 2534
Abstract
Extracellular vesicles (EVs) have enormous potential for the implementation of liquid biopsy and as effective drug delivery means, but the fulfilment of these expectations requires overcoming at least two bottlenecks relative to their purification, namely the finalization of reliable and affordable protocols for: [...] Read more.
Extracellular vesicles (EVs) have enormous potential for the implementation of liquid biopsy and as effective drug delivery means, but the fulfilment of these expectations requires overcoming at least two bottlenecks relative to their purification, namely the finalization of reliable and affordable protocols for: (i) EV sub-population selective isolation and (ii) the scalability of their production/isolation from complex biological fluids. In this work, we demonstrated that these objectives can be achieved by a conceptually new affinity chromatography platform composed of a macroporous epoxy monolith matrix functionalized with anti-CD63 nanobodies with afflux of samples and buffers regulated through a pump. Such a system successfully captured and released integral EVs from urine samples and showed negligible unspecific binding for circulating proteins. Additionally, size discrimination of eluted EVs was achieved by different elution approaches (competitive versus pH-dependent). The physical characteristics of monolith material and the inexpensive production of recombinant nanobodies make scaling-up the capture unit feasible and affordable. Additionally, the availability of nanobodies for further specific EV biomarkers will allow for the preparation of monolithic affinity filters selective for different EV subclasses. Full article
(This article belongs to the Special Issue Advances in Single Domain-Based Antibodies)
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17 pages, 2456 KiB  
Article
Targeted Phagocytosis Induction for Cancer Immunotherapy via Bispecific MerTK-Engaging Antibodies
by Stefania C. Carrara, Jan P. Bogen, David Fiebig, Julius Grzeschik, Björn Hock and Harald Kolmar
Int. J. Mol. Sci. 2022, 23(24), 15673; https://doi.org/10.3390/ijms232415673 - 10 Dec 2022
Cited by 1 | Viewed by 3648
Abstract
The Tyro, Axl, and MerTK receptors (TAMRs) play a significant role in the clearance of apoptotic cells. In this work, the spotlight was set on MerTK, as it is one of the prominent TAMRs expressed on the surface of macrophages and dendritic cells. [...] Read more.
The Tyro, Axl, and MerTK receptors (TAMRs) play a significant role in the clearance of apoptotic cells. In this work, the spotlight was set on MerTK, as it is one of the prominent TAMRs expressed on the surface of macrophages and dendritic cells. MerTK-specific antibodies were previously isolated from a transgenic rat-derived immune library with suitable biophysical properties. Further characterisation resulted in an agonistic MerTK antibody that led to phospho AKT activation in a dose-dependent manner. In this proof-of-concept study, a MerTK-specific antibody, MerK28, was combined with tandem, biparatopic EGFR-binding VHH camelid antibody domains (7D9G) in different architectures to generate bispecific antibodies with the capacity to bind EGFR and MerTK simultaneously. The bispecific molecules exhibited appropriate binding properties with regard to both targets in their soluble forms as well as to cells, which resulted in the engagement of macrophage-like THP-1 cells with epidermoid carcinoma A431 cells. Furthermore, targeted phagocytosis in co-culture experiments was observed only with the bispecific variants and not the parental MerTK-binding antibody. This work paves the way for the generation of bispecific macrophage-engaging antibodies for targeted phagocytosis harnessing the immune-modulating roles of MerTK in immunotherapy. Full article
(This article belongs to the Special Issue Advances in Single Domain-Based Antibodies)
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Review

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27 pages, 2090 KiB  
Review
Single-Domain Antibodies—Novel Tools to Study and Treat Allergies
by Ines Zettl, Clarissa Bauernfeind, Jessica Kollárová and Sabine Flicker
Int. J. Mol. Sci. 2024, 25(14), 7602; https://doi.org/10.3390/ijms25147602 - 11 Jul 2024
Viewed by 2146
Abstract
IgE-mediated allergies represent a major health problem in the modern world. Apart from allergen-specific immunotherapy (AIT), the only disease-modifying treatment, researchers focus on biologics that target different key molecules such as allergens, IgE, or type 2 cytokines to ameliorate allergic symptoms. Single-domain antibodies, [...] Read more.
IgE-mediated allergies represent a major health problem in the modern world. Apart from allergen-specific immunotherapy (AIT), the only disease-modifying treatment, researchers focus on biologics that target different key molecules such as allergens, IgE, or type 2 cytokines to ameliorate allergic symptoms. Single-domain antibodies, or nanobodies, are the newcomers in biotherapeutics, and their huge potential is being investigated in various research fields since their discovery 30 years ago. While they are dominantly applied for theranostics of cancer and treatment of infectious diseases, nanobodies have become increasingly substantial in allergology over the last decade. In this review, we discuss the prerequisites that we consider to be important for generating useful nanobody-based drug candidates for treating allergies. We further summarize the available research data on nanobodies used as allergen monitoring and detection probes and for therapeutic approaches. We reflect on the limitations that have to be addressed during the development process, such as in vivo half-life and immunogenicity. Finally, we speculate about novel application formats for allergy treatment that might be available in the future. Full article
(This article belongs to the Special Issue Advances in Single Domain-Based Antibodies)
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22 pages, 2663 KiB  
Review
NANOBODIES®: A Review of Diagnostic and Therapeutic Applications
by Bo-kyung Jin, Steven Odongo, Magdalena Radwanska and Stefan Magez
Int. J. Mol. Sci. 2023, 24(6), 5994; https://doi.org/10.3390/ijms24065994 - 22 Mar 2023
Cited by 136 | Viewed by 23567
Abstract
NANOBODY® (a registered trademark of Ablynx N.V) molecules (Nbs), also referred to as single domain-based VHHs, are antibody fragments derived from heavy-chain only IgG antibodies found in the Camelidae family. Due to their small size, simple structure, high antigen binding affinity, and [...] Read more.
NANOBODY® (a registered trademark of Ablynx N.V) molecules (Nbs), also referred to as single domain-based VHHs, are antibody fragments derived from heavy-chain only IgG antibodies found in the Camelidae family. Due to their small size, simple structure, high antigen binding affinity, and remarkable stability in extreme conditions, Nbs possess the potential to overcome several of the limitations of conventional monoclonal antibodies. For many years, Nbs have been of great interest in a wide variety of research fields, particularly in the diagnosis and treatment of diseases. This has culminated with the approval of the world’s first Nb based drug (Caplacizumab) in 2018 with others following, and more on the way. This review will provide an overview, with examples, of (i) the structure and advantages of Nbs compared to conventional monoclonal antibodies, (ii) methods used to generate and produce antigen-specific Nbs, (iii) applications for diagnostics, and (iv) ongoing clinical trials for Nb therapeutics as well as promising candidates for clinical development. Full article
(This article belongs to the Special Issue Advances in Single Domain-Based Antibodies)
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