Research progress on unique paratope structure, antigen binding modes, and systematic mutagenesis strategies of single-domain antibodies

Nanoscale warriors against viral invaders: a comprehensive review of Nanobodies as potential antiviral therapeutics

Viral infections remain a significant global health threat, with emerging and reemerging viruses causing epidemics and pandemics. Despite advancements in antiviral therapies, the development of effective treatments is often hindered by challenges, such as viral resistance and the emergence of new strains. In this context, the development of novel therapeutic modalities is essential to combat notorious viruses. While traditional monoclonal antibodies are widely used for the treatment of several diseases, nanobodies derived from heavy chain-only antibodies have emerged as promising "nanoscale warriors" against viral infections. Nanobodies possess unique structural properties that enhance their ability to recognize diverse epitopes. Their small size also imparts properties, such as improved bioavailability, solubility, stability, and proteolytic resistance, making them an ideal class of therapeutics for viral infections. In this review, we discuss the role of nanobodies as antivirals against various viruses. Techniques used for developing nanobodies, delivery strategies are covered, and the challenges and opportunities associated with their use as antiviral therapies are discussed. We also offer insights into the future of nanobody-based antiviral research to support the development of new strategies for managing viral infections.

Screening and Interaction Analysis of Shark-Derived Nanobodies against Crayfish Major Allergen Pro c 2

Pro c 2 (arginine kinase) is a major allergen in crayfish (Procambarus clarkii). Shark-derived variable domains of new antigen receptors (VNARs) have advantages in developing allergen detection and immunotherapy. This study constructed a VNAR domain library from Chiloscyllium plagiosum immunized with Pro c 2. Three VNARs (VNAR-11, VNAR-20, and VNAR-29) against Pro c 2 obtained by screening the library were expressed in the HEK293F cells, fusing with the immunoglobulin (Ig) G1 Fc fragment (VNAR-Fc-11, VNAR-Fc-29, and VNAR-Fc-20). The VNAR-Fc fusions bound to Pro c 2 with an affinity KD ranging from 0.2131 ∼ 465.3 μM, with the ability to inhibit patients' IgE binding to Pro c 2. VNAR-20 and VNAR-29 displayed more stable binding with Pro c 2 during molecular dynamics simulation. The binding sites of the VNARs are distributed in the conserved IgE epitopes of arginine kinase. These achievements indicate the application potential of VNARs in allergen detection and allergy therapeutics.

Impact of Noncanonical Disulfide Bond on Thermal Resistance and Binding Affinity of Shark-Derived Single-Domain Antibodies

Single-domain antibodies (sdAbs) often exhibit superior thermal stability compared to traditional antibodies. Efforts are currently focused on enhancing their structural robustness and thermal refolding ability through protein engineering to achieve greater thermal properties and functionality in practical applications. Thermal aggregation is a key factor hindering the reversible thermal denaturation of sdAbs. While studies have explored the role of noncanonical disulfide bonds in camelid-derived VHH aggregation, research on thermal aggregation in shark-derived sdAbs (also known as VNARs) remains scarce, limiting their potential for further optimization. In this study, the role of noncanonical disulfide bonds in VNAR structural robustness, aggregation, and affinity has been simultaneously investigated. Enzyme-linked immunosorbent assay (ELISA), circular dichroism, and intrinsic fluorescence were carried out to compare thermal antigen-binding stability, refolding abilities, and melting temperatures of four wild VNARs B7, 1N9, 2E6, and 2E11 specific for different antigens. Meanwhile, nano differential scanning fluorimetry (nanoDSF) was applied, for the first time, to monitor the thermal aggregation of VNARs. Notably, 2E11, which lacked the noncanonical disulfide bond, demonstrated impressive performance in many aspects. When alanine mutation was engineered to remove the CDR1-CDR3 disulfide bond in 2E6, its refolding rate was increased, and thermal aggregation was prevented significantly. Furthermore, 2E6 exhibited enhanced thermal antigen-binding stability despite reduced structural robustness and affinity. This study provides deeper insights and theoretical support for improving VNAR biophysical properties, with potential applications in enhancing immunoassay performance.

Construction and validation of a synthetic phage-displayed nanobody library

Nanobodies derived from camelids and sharks offer unique advantages in therapeutic applications due to their ability to bind to epitopes that were previously inaccessible. Traditional methods of nanobody development face challenges such as ethical concerns and antigen toxicity. Our study presents a synthetic, phagedisplayed nanobody library using trinucleotide-directed mutagenesis technology, which allows precise amino acid composition in complementarity-determining regions (CDRs), with a focus on CDR3 diversity. This approach avoids common problems such as frameshift mutations and stop codon insertions associated with other synthetic antibody library construction methods. By analyzing FDA-approved nanobodies and Protein Data Bank sequences, we designed sub-libraries with different CDR3 lengths and introduced amino acid substitutions to improve solubility. The validation of our library through the successful isolation of nanobodies against targets such as PD-1, ATXN1 and STAT3 demonstrates a versatile and ethical platform for the development of high specificity and affinity nanobodies and represents a significant advance in biotechnology.

Anti-Inflammatory Efficacy of Nanobody Specific to β-Glucan on a Fungal Cell Wall in a Murine Model of Fungal Keratitis

Purpose: to explore the anti-inflammatory effects of a nanobody (Nb) specific to β-glucan on fungal keratitis (FK). Methods: in order to verify the therapeutic and anti-inflammatory efficacy of Nb in FK, the severity of inflammation was assessed with inflammatory scores, hematoxylin-eosin (HE) staining, and myeloperoxidase (MPO) assays. In corneas of mice of FK model and human corneal epithelial cells stimulated by fungal hyphae, real-time reverse transcriptase polymerase chain reaction, Western blot, and enzyme-linked immunosorbent assay were used to detect the expression levels of inflammatory cytokines and pattern recognition receptors (PRRs). In vivo, macrophages and neutrophils infiltration in the cornea stroma was detected by immunofluorescence (IFS) staining. Results: In murine models infected with Aspergillus fumigatus (A. fumigatus), Nb treatment could reduce the inflammatory scores. HE staining and MPO results showed Nb significantly alleviated corneal edema and reduced inflammatory cell infiltration 3 days post-infection. In addition, the expression levels of LOX-1 and Dectin-1 were significantly decreased in the Nb group in vivo. The expression of chemokines CCL2 and CXCL2 also decreased in the Nb group. Compared with the PBS group, the number of macrophages and neutrophils in the Nb group was significantly decreased, which was shown in IFS results. Moreover, Nb attenuated the expression of Dectin-1, LOX-1, and inflammatory mediators, including IL-6 and IL-8 in vitro. Conclusion: our study showed that Nb could alleviate FK by downregulating the expression of PRRs and inflammatory factors as well as reducing the infiltration of macrophages and neutrophils.

Nanobody in a Double "Y"-Shaped Assembly: A Promising Candidate for Lateral Flow Immunoassays

Derived from camelid heavy-chain antibodies, nanobodies (Nbs) are the smallest natural antibodies and are an ideal tool in biological studies because of their simple structure, high yield, and low cost. Nbs possess significant potential for developing highly specific and user-friendly diagnostic assays. Despite offering considerable advantages in detection applications, knowledge is limited regarding the exclusive use of Nbs in lateral flow immunoassay (LFIA) detection. Herein, we present a novel double "Y" architecture, achieved by using the SpyTag/SpyCatcher and Im7/CL7 systems. The double "Y" assemblies exhibited a significantly higher affinity for their epitopes, as particularly evident in the reduced dissociation rate. An LFIA employing double "Y" assemblies was effectively used to detect the severe acute respiratory syndrome coronavirus-2 N protein, with a detection limit of at least 500 pg/mL. This study helps broaden the array of tools available for the development of Nb-based diagnostic techniques.

Site-specifically radiolabeled nanobodies for imaging blood-brain barrier penetration and targeting in the brain

Nanobodies (Nbs) hold significant potential in molecular imaging due to their unique characteristics. However, there are challenges to overcome when it comes to brain imaging. To address these obstacles, collaborative efforts and interdisciplinary research are needed. This article aims to raise awareness and encourage collaboration among researchers from various fields to find solutions for effective brain imaging using Nbs. By fostering cooperation and knowledge sharing, we can make progress in overcoming the existing limitations and pave the way for improved molecular imaging techniques in the future.

A PD-L1xCD3 bispecific nanobody as a novel T-cell engager in treating PD-L1 overexpression melanoma

The development of Immune checkpoint blockade(ICB) therapy and BRAF- and MEK-targeted therapies has reshaped the survival outcomes of the patients with advanced melanoma. PD-1/PD-L1 blockade was an approved strategy in melanoma treatment. Here we design a PD-L1 xCD3 nanobody as a novel bispecific T cell engager (BiTE) in treating PD-L1 overexpression melanoma. BiTE PD-L1×CD3 Nb was predicted to bind near a large acidic surface on CD3-ε similar to UCHT1-scFv antibody based on alpha-fold and molecular docking. BiTE PD-L1×CD3 Nb and anti-CD3 Nb retained the ability to activate T cells to produce TNF-α and IFN-γ in a dose-dependent manner. The IC50 value of BiTE PD-L1×CD3 Nb was 4.208μg/mL. BiTE PD-L1×CD3 Nb showed obvious cytotoxic activity on both A375WT and A375PD-L1 related to PD-L1 expression level.

Biopanning, Heterologous Expression, and Characterization of a Shark-Derived Single-Domain Antibody Fusion Protein against Pancreatic Lipase

Nowadays, obesity severely impacts human health and is the fifth leading risk factor that leads to death globally. Pancreatic lipase (PL) inhibitors have attracted extensive attention owing to their role in effective prevention and treatment of obesity. Here, a shark-derived single-domain antibody fusion protein was used to inhibit PL for the first time. After biopanning, the heterologous expression system pET28a-SUMO-D2 was constructed using the method of double restriction enzyme digestion and T4 ligase to achieve the soluble expression of the PL-specific antibody gene D2. According to the calculation of protein concentration, the final expression of fusion protein PL-D2S was 1.183 mg per liter of Luria Bertani broth. The binding ability of the soluble fusion protein PL-D2S to PL was identified. Enzyme-linked immunosorbent assay results showed that the fusion protein PL-D2S exhibited a strong binding affinity to PL. The experimental results of PL inhibition of PL-D2S in vitro showed that the fusion protein could significantly inhibit the activity of PL, with an IC₅₀ of 404 μg/mL. Our study shows that the fusion protein PL-D2S is a potential PL inhibitor to prevent and treat obesity.