Search

Many difficulties related to using antibodies in diagnostic and therapeutic applications can sometimes be circumvented by using smaller, less complex single domain antibodies based on variable heavy chain (VH) domain constructs such as camelid VHH domains. However, VH domains have their own limitations, including an increased tendency to aggregate. VH domains often contain hydrophobic residues within their complementarity-determining regions (CDRs) that facilitate binding to target antigens but can also mediate VH domain aggregation, which is a concern for therapeutic applications since this can trigger immune responses. In this study, we engineered the human VH-1Ba domain to improve its stability and solubility by introducing charged amino acids in the VH domain framework region and CDRH1. We followed two strategies to improve the stability and solubility of VH domains. First, we introduced positive and negatively charged amino acids in the framework region of an autonomous human VH domain (VH-B1a) and observed the effect of framework net charge on VH domain refolding, stability, and solubility. Introducing positive charge into the VH-B1a framework increased its thermostability but slightly lowered its refolding ability and solubility. We were not able to obtain correctly folded negatively charged (-VH) VH domains. Second, we introduced a series of positive and negatively charged amino acids in the CDRH1 loop of near-neutral (VH-B1a) and positively charged (+VH) VH domains, and observed their effect on expression, refolding, stability, and solubility. For both the VH-B1a and +VH domains, we observed a decrease in melting temperature (Tm) and room temperature solubility as more negative or positive charged amino acids were added to the CDRH1. The VH-B1a domain had higher room temperature solubility for negative and slightly positive CDRH1 net charges. The + VH domain had higher Tms for all CDRH1 net charges and was better able to tolerate the adverse effects of adding positive charge to CDRH1. We observed a similar response in refolding and solubility of VH-B1a and +VH in response to changes in CDRH1 net charge after temperature-induced denaturation for negative and neutral CDRH1s. We observed a positional effect with a single Lys (31K) and double Lys (31, 32 KK) substitutions in CDRH1, which promoted VH-B1a aggregation and was partially overcome by the +VH domain. In summary, this study provides information for designing VH domains with improved biophysical properties and a +VH domain that will be useful for applications where positive surface charge and CDRH1 are desirable., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The microsomal epoxide hydrolase (mEH) is important in the detoxification of carcinogens in the liver and other tissues but is also a blood biomarker of hepatitis and liver cancer. Improved analytical methods are needed for the study of its role in the metabolism of xenobiotics and endogenous roles as a blood biomarker of diseases. The development of a double nanobody sandwich ELISA offers significant improvements over traditional polyclonal or monoclonal antibody-based assays, enhancing both the homogeneity and the stability of assay production. This study focuses on selecting and optimizing nanobody pairs for detecting human mEH. Four high-affinity nanobodies were identified and tested for thermal stability. Combinations of these nanobodies were evaluated, revealing that the MQ4-MQ30 pair achieved the best performance with a limit of detection (LOD) of 1 ng/mL. Additionally, polyHRP was also employed for signal amplification, enhancing detection capabilities despite challenges related to the small size and single epitope recognition of the nanobodies. Comparative studies using microplates and NHS@MF membranes were also performed. The superior performance of the NHS@MF membranes highlighted their potential as a promising alternative for point-of-care testing. The assay exhibited high specificity for human mEH and minimal cross-reactivity with related enzymes and effectively addressed matrix effects in plasma and tissue samples. These findings underscore the potential of double nanobody sandwich ELISAs for reliable and sensitive biomarker detection.

Immunoassays have become essential tools for detecting infectious viruses. However, traditional monoclonal antibody-dependent immunoassays are costly, fragile, and unstable, especially in complex media. To overcome these challenges, we have developed cost-effective, robust, and high-affinity nanobodies as alternatives to monoclonal antibodies for rapid detection applications. We engineered dual-epitope nanobody (NB) pairs and incorporated them into a sandwich immunosensor design to detect transmitted rotaviruses in rectal swabs and wastewater samples. To further enhance sensitivity, we synthesized an advanced two-dimensional material, MXenes@CNTs@AuNPs, which offers an extensive specific surface area that supports the enrichment and immobilization of NBs. This integration with catalase-modified magnetic probes facilitates signal generation. Subsequently, our sensor achieved a detection limit of 0.0207 pg/mL for the rotavirus VP6 antigen, significantly outperforming commercial antigen kits with a sensitivity enhancement of 3.77 × 10 5 -fold. The exceptional sensor performance extended to specificity, repeatability, stability, and accuracy across various sample types, establishing it as a promising tool for rotavirus detection. This research outlines a viable strategy for creating a robust and ultrasensitive analytical nanoprobe, thereby addressing the critical need for efficient and reliable viral detection methods in various environments.

The recent advancements on membrane protein degraders (MPDs) have broadened the applicability of proteolysis-targeting chimeras (PROTACs) beyond intracellular proteins to include the previously "undruggable" cell-surface targets. However, the potential toxicity of MPDs caused by undesired off-target degradation poses a significant challenge to clinical deployment, mirroring concerns associated with PROTACs. Here, we introduce a conditionally activatable membrane protein degrader (Pro-MPD), which leverages the specificity and high affinity of biparatopic nanobodies combined with a tumor microenvironment-activated cell-penetrating peptide (Pro-CPP) to achieve on-target activated internalization and degradation of PD-L1 within tumor sites. This modularly designed Pro-MPD demonstrated a high target degradation efficiency and T cell reactivation, as well as sustained inhibition of tumor growth in xenograft models, highlighting its potential as a safer and highly efficient MPD for in vivo applications. Our work provides a general strategy for the development of conditionally activatable MPDs, which offers a new avenue for reducing the undesired systemic toxicity of MPDs due to the off-tumor degradation.

Many proteins, especially eukaryotic proteins, membrane proteins and protein complexes, are challenging to study because they are difficult to purify in their native state without disrupting the interactions with their partners. Hence, our lab developed a novel purification technique employing Nanobodies® (Nbs). This technique, called nanobody exchange chromatography (NANEX), utilises an immobilised low-affinity Nb to capture the target protein, which is subsequently eluted - along with its interaction partners - by introducing a high-affinity Nb. In line with the growing trend towards studying proteins in smaller sample sizes, the present study validates miniaturisation of NANEX in a packed bed microfluidic (μNANEX) chip. This μNANEX setup integrates up to five submicroliter silicon chips, enabling fully automated and reproducible purifications within minutes. Additionally, a digital twin model of the μNANEX column, which accurately predicts the effect of the reaction kinetics and mass transfer on the elution peaks, has been validated over a broad range of experimental conditions. The effectiveness of the method is demonstrated with Nbs binding to the green fluorescent protein (GFP), allowing streamlined purification of any GFP fusion protein from biological samples. Specifically, we used μNANEX to purify 0.1-1 μg of GFP-fused yeast proteins from 20 μL crude lysate and identified their interaction partners via mass spectrometry, showing that μNANEX purification preserves protein complexes.

In this study, we aimed to develop nanobodies targeting receptor tyrosine kinase-like orphan receptor 1 (ROR1) for cancer diagnosis and therapy. We immunized alpacas with ROR1, extracted RNA from their blood, and converted it to complementary DNA (cDNA) to amplify the VHH (variable domain of heavy-chain antibodies) sequence. This sequence was used to construct a phage library with a capacity of 8 ×10 8 . Screening identified a high-affinity nanobody, HCAbs1, which binds effectively to ROR1. ELISA and surface plasmon resonance analyses revealed HCAbs1's binding affinities to ROR1 at 4.42 and 12.9 nM, respectively. Functional tests showed HCAbs1 could reduce extracellular signal-regulated kinase (ERK) phosphorylation levels induced by Wnt5a in ROR1-transfected cells. Our findings highlight the potential of HCAbs1 nanobodies in diagnosing and treating cancers through targeting ROR1., (© 2024 International Union of Biochemistry and Molecular Biology, Inc.)

Human neutrophil elastase (hNE), a serine protease released by neutrophils during inflammation, plays a major role in the pathophysiology of several conditions especially in inflammatory lung diseases. Its inhibition constitutes, therefore, a promising therapeutic strategy to combat these diseases. In this work, we characterized the in vitro properties of a VHH (i.e., the antigen binding domain of camelid heavy chain-only antibodies), referred to as NbE201. This VHH is able to inhibit tightly, selectively and competitively both human and murine elastases with the inhibition constants (K i ) of 4.1 ± 0.9 nM and 36.8 ± 3.9 nM, respectively. The IC 50 for the inhibition of the hydrolysis of elastin is in the same range to that of alpha-1 antitrypsin (i.e., the main endogenous inhibitor of hNE also used in the clinic) and 14 times better than that of Sivelestat (i.e., the 2nd clinically approved hNE inhibitor). The X-ray crystal structure of the NbE201-hNE complex reveals that the Complementarity Determining Regions CDR1 and CDR3 of the VHH bind into the substrate binding pocket of hNE and prevent the access to small or macromolecular substrates. They do not, however, bind deep enough into the pocket to be hydrolyzed. NbE201 is highly stable towards oxidation, deamidation, and chemical or thermal denaturation. NbE201 is therefore likely to tolerate manufacturing processes during drug development. These results highlight the high potential of NbE201 as a (pre)clinical tool to diagnose and treat diseases associated with excessive hNE activity, and for fundamental research to better understand the role of hNE in these conditions., (© 2024 The Protein Society.)

Salmonella-related foodborne infections are commonly caused by the serovars of S. Typhimurium, which can be detected using antibody-based immunoassays. The monovalent variable domain of the camelid heavy chain antibody (VHH) performs excellently in constructing multivalent VHH variants, which generally exhibit higher affinities with antigens and consequently enhance the assay sensitivity. In this study, the divalent variants of VHHs (diVHHs) targeting S. Typhimurium were generated by encoding the monovalent VHH genes assembled in tandem with a flexible linker peptide (G 4 S) 2 . Soluble diVHHs were produced in a prokaryotic expression system and purified with a yield of 4.22 mg/L. Benefiting from their stability and antigen-binding abilities towards tested Salmonella serovars, diVHH-based immunoassays were developed. The diVHH-based sandwich immunoassay, using diVHH as capture antibody, exhibited a detection limit of 1.04×10 2 CFU/mL and enabled as low as 10 CFU/mL S. Typhimurium to be detected after 6 h of enrichment in lettuce. Furthermore, this assay can be applied to spiked lettuce, chicken, and pork samples, showing acceptable recoveries ranging from 83 to 106%. This study presented feasible strategies for VHH multivalence and established a superior sensitivity VHH-based immunoassay for monitoring and analyzing Salmonella contamination in food., Competing Interests: Declarations. Conflict of interest: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature.)

Research on camelid-derived single-domain antibodies (sdAbs) has demonstrated their significant utility in diverse biotechnological applications, including therapy and diagnostic. This is largely due to their relative simplicity as monomeric proteins, ranging from 12 to 15 kDa, in contrast to immunoglobulin G (IgG) antibodies, which are glycosylated heterotetramers of 150-160 kDa. Single-domain antibodies exhibit high conformational stability and adopt the typical immunoglobulin domain fold, consisting of a two-layer sandwich of 7-9 antiparallel beta-strands. They contain three loops, known as complementary-determining regions (CDRs), which are assembled on the sdAb surface and are responsible for antigen recognition. The single-domain antibody examined in this study, sdAb-mrh-IgG, was engineered to recognize IgG from rats, mice, but it also weakly recognizes IgG from humans (Pleiner et al. 2018). A search of the Protein Data Bank revealed only one NMR structure of a single-domain antibody, which is unrelated to sdAb-mrh-IgG. The NMR chemical shift assignments of sdAb-mrh-IgG will be utilized to study its molecular dynamics and interactions with antigens in solution, which is fundamental for the rational design of novel single-domain antibodies., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Branched ubiquitin (Ub) chains constitute a sizable fraction of Ub polymers in human cells. Despite their abundance, our understanding of branched Ub function in cell signaling has been stunted by the absence of accessible methods and tools. Here we identify cellular branched-chain-specific binding proteins and devise approaches to probe K48-K63-branched Ub function. We establish a method to monitor cleavage of linkages within complex Ub chains and unveil ATXN3 and MINDY as debranching enzymes. We engineer a K48-K63 branch-specific nanobody and reveal the molecular basis of its specificity in crystal structures of nanobody-branched Ub chain complexes. Using this nanobody, we detect increased K48-K63-Ub branching following valosin-containing protein (VCP)/p97 inhibition and after DNA damage. Together with our discovery that multiple VCP/p97-associated proteins bind to or debranch K48-K63-linked Ub, these results suggest a function for K48-K63-branched chains in VCP/p97-related processes., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

G-protein-coupled receptors (GPCRs) are key regulators of human physiology and are the targets of many small-molecule research compounds and therapeutic drugs. While most of these ligands bind to their target GPCR with high affinity, selectivity is often limited at the receptor, tissue and cellular levels. Antibodies have the potential to address these limitations but their properties as GPCR ligands remain poorly characterized. Here, using protein engineering, pharmacological assays and structural studies, we develop maternally selective heavy-chain-only antibody ('nanobody') antagonists against the angiotensin II type I receptor and uncover the unusual molecular basis of their receptor antagonism. We further show that our nanobodies can simultaneously bind to angiotensin II type I receptor with specific small-molecule antagonists and demonstrate that ligand selectivity can be readily tuned. Our work illustrates that antibody fragments can exhibit rich and evolvable pharmacology, attesting to their potential as next-generation GPCR modulators., Competing Interests: Competing interests: A.C.K., C.M., L.M.W., D.P.S. and M.A.S. are co-inventors on a patent application for AT1R blocking nanobodies. A.C.K. is a cofounder and consultant for biotechnology companies Tectonic Therapeutic and Seismic Therapeutic, and also for the Institute for Protein Innovation, a nonprofit research institute. L.M.W. is a scientific advisor for Septerna. D.P.S. is a Septerna employee. C.M. is a Sanofi employee. P.B. holds patents and provisional patent applications in the field of engineered T-cell therapies and protein design. The other authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Pathogens constantly evolve and can develop mutations that evade host immunity and treatment. Addressing these escape mechanisms requires targeting evolutionarily conserved vulnerabilities, as mutations in these regions often impose fitness costs. We introduce adaptive multi-epitope targeting with enhanced avidity (AMETA), a modular and multivalent nanobody platform that conjugates potent bispecific nanobodies to a human immunoglobulin M (IgM) scaffold. AMETA can display 20+ nanobodies, enabling superior avidity binding to multiple conserved and neutralizing epitopes. By leveraging multi-epitope SARS-CoV-2 nanobodies and structure-guided design, AMETA constructs exponentially enhance antiviral potency, surpassing monomeric nanobodies by over a million-fold. These constructs demonstrate ultrapotent, broad, and durable efficacy against pathogenic sarbecoviruses, including Omicron sublineages, with robust preclinical results. Structural analysis through cryoelectron microscopy and modeling has uncovered multiple antiviral mechanisms within a single construct. At picomolar to nanomolar concentrations, AMETA efficiently induces inter-spike and inter-virus cross-linking, promoting spike post-fusion and striking viral disarmament. AMETA's modularity enables rapid, cost-effective production and adaptation to evolving pathogens., Competing Interests: Declaration of interests Y.X. and Y.S. are co-inventors on a provisional patent of AMETA technology filed by Icahn School of Medicine at Mount Sinai. The A.G.-S. laboratory has received research support from GSK, Pfizer, Senhwa Biosciences, Kenall Manufacturing, Blade Therapeutics, Avimex, Johnson & Johnson, Dynavax, 7Hills Pharma, Pharmamar, ImmunityBio, Accurius, Nanocomposix, Hexamer, N-fold LLC, Model Medicines, Atea Pharma, Applied Biological Laboratories, and Merck, outside of the reported work. A.G.-S. has consulting agreements for the following companies involving cash and/or stock: Castlevax, Amovir, Vivaldi Biosciences, Contrafect, 7Hills Pharma, Avimex, Pagoda, Accurius, Esperovax, Applied Biological Laboratories, Pharmamar, CureLab Oncology, CureLab Veterinary, Synairgen, Paratus, Pfizer, and Prosetta, outside of the reported work. A.G.-S. has been an invited speaker in meeting events organized by Seqirus, Janssen, Abbott, and AstraZeneca. A.G.-S. is an inventor of patents and patent applications on the use of antivirals and vaccines for the treatment and prevention of virus infections and cancer, owned by the Icahn School of Medicine at Mount Sinai, New York, outside of the reported work. Y.X. and Y.S. are co-inventors on a patent of Nbs filed by Univ. of Pittsburgh. Y.S. is a co-founder of Antenna Biotech Inc., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Efficiently predicting the paratope holds immense potential for enhancing antibody design, treating cancers and other serious diseases, and advancing personalized medicine. Although traditional methods are highly accurate, they are often time-consuming, labor-intensive, and reliant on 3D structures, restricting their broader use. On the other hand, machine learning-based methods, besides relying on structural data, entail descriptor computation, consideration of diverse physicochemical properties, and feature engineering. Here, we develop a deep learning-assisted prediction method for paratope identification, relying solely on amino acid sequences and being antigen-agnostic. Built on the ProtTrans architecture, and utilizing pre-trained protein and antibody language models, we extract efficient embeddings for predicting paratope. By incorporating positional encoding for Complementarity Determining Regions, our model gains a deeper structural understanding, achieving remarkable performance with a 0.904 ROC AUC, 0.701 F1-score, and 0.585 MCC on benchmark datasets. In addition to yielding accurate antibody paratope predictions, our method exhibits strong performance in predicting nanobody paratope, achieving a ROC AUC of 0.912 and a PR AUC of 0.665 on the nanobody dataset. Notably, our approach outperforms structure-based prediction methods, boasting a PR AUC of 0.731. Various conducted ablation studies, which elaborate on the impact of each part of the model on the prediction task, show that the improvement in prediction performance by applying CDR positional encoding together with CNNs depends on the specific protein and antibody language models used. These results highlight the potential of our method to advance disease understanding and aid in the discovery of new diagnostics and antibody therapies., Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable., (© 2024. The Author(s).)

The tripartite ATP-independent periplasmic (TRAP) transporters enable Vibrio cholerae and Haemophilus influenzae to acquire sialic acid, aiding their colonization of human hosts. This process depends on SiaP, a substrate-binding protein (SBP) that captures and delivers sialic acid to the transporter. We identified 11 nanobodies that bind specifically to the SiaP proteins from H. influenzae (HiSiaP) and V. cholerae (VcSiaP). Two nanobodies inhibited sialic acid binding. Detailed structural and biophysical studies of one nanobody-SBP complex revealed an allosteric inhibition mechanism, preventing ligand binding and releasing pre-bound sialic acid. A hydrophobic surface pocket of the SBP is crucial for the allosteric mechanism and for the conformational rearrangement that occurs upon binding of sialic acid to the SBP. Our findings provide new clues regarding the mechanism of TRAP transporters, as well as potential starting points for novel drug design approaches to starve these human pathogens of important host-derived molecules., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

We developed a nanobody-based homogeneous bioluminescent immunosensor to achieve a one-pot detection for point-of-care testing (POCT). This immunosensor was named BRET nano Q-body as its emission color changes via bioluminescence resonance energy transfer (BRET) upon antigen addition. NanoLuc luciferase and a cysteine-containing tag were fused to the N-terminus of the nanobody, which was labeled with a fluorescent dye via thiol-maleimide Michael addition. The nanobody employed in this proof-of-principle experiment recognizes methotrexate (MTX), a chemotherapeutic agent. After optimizing the fluorescent dye and linker, the BRET nano Q-body dose-dependently exhibited a greater than 7-fold increase in emission ratio (TAMRA/NanoLuc). Moreover, we found its superior thermostability endurance in organic solvents, reducing agents, and detergents due to the robust structure of nanobody, as well as accommodation in biological fluids, such as milk, serum, and whole blood without dilution, with limits of detection of 0.50, 1.6, and 3.7 nM, respectively. Furthermore, the BRET nano Q-body was subjected to lyophilization and fabricated into a paper device, which markedly improved its portability and enabled more than one month of storage at 25 °C. The paper device also performed appropriate functions in the biological fluids without any dilution and can be used for on-site therapeutic drug monitoring of MTX. Altogether, we developed a powerful tool, the BRET nano Q-body, for POCT, and demonstrated its applicability in several biological fluids. In addition, we confirmed the feasibility of paper devices, which are expected to be transformative for in situ detection in therapeutic, diagnostic, and environmental applications.

Background: Our previously described a nanobody precisely targeting CTLA-4 and demonstrated that it can promote the antitumor response of adoptive T cells. Here we examined whether fusing it to the IgG1 Fc region would induce stronger, longer-lasting T-cell immune responses after exposure to the dendritic-tumor cell fusions., Methods: The fusion of nanobody to Fc region was overexpressed in E. coli . Next, the proliferation, activation and cytotoxicity of the CD8 + T cells stimulated by the fusion protein and dendritic-tumor cell fusions was assessed in vitro, and the antitumor activity was evaluated in nude mice bearing xenografts of each type of solid tumor., Results: Proliferation, activation and cytotoxicity of CD8 + T cells in vitro were significantly greater in the presence of the fusion protein than those in other groups. Consistently, different types of xenografts growth were significantly slower and animal survival significantly longer when the injected CD8 + T cells had been activated in vitro in the presence of the fusion protein., Conclusion: Fusing our anti-CTLA-4 nanobody to the IgG1 Fc region potentiates its ability to induce strong, persistent CD8 + T cell responses against solid tumors in mice. This fusion strategy has the potential to realize clinical transformation and application to clinical treatment., Competing Interests: The authors report no competing interests related to this work., (© 2024 Li et al.)

Tauopathies are neurodegenerative diseases that involve tau misfolding and aggregation in the brain. These diseases, including Alzheimer's disease (AD), are some of the least understood and most difficult to treat neurodegenerative disorders. Antibodies and antibody fragments that target tau oligomers, which are especially toxic forms of tau, are promising options for immunotherapies and diagnostic tools for tauopathies. In this study, we have developed conformational, tau oligomer-specific nanobodies, or single-domain antibodies. We demonstrate that these nanobodies, OT2.4 and OT2.6, are highly specific for tau oligomers relative to tau monomers and fibrils. We used epitope mapping to verify that these nanobodies bind to discontinuous epitopes on tau and to support the idea that they interact with a conformation present in the oligomeric, and not monomeric or fibrillar, forms of tau. We show that these nanobodies interact with tau oligomers in brain samples from AD patients and from healthy older adults with primary age-related tauopathy. Our results demonstrate the potential of these nanobodies as tau oligomer-specific binding reagents and future tauopathy therapeutics and diagnostics.

The optimization of antibodies to attain the desired levels of affinity and specificity holds great promise for the development of next generation therapeutics. This study delves into the refinement and engineering of complementarity-determining regions (CDRs) through in silico affinity maturation followed by binding validation using isothermal titration calorimetry (ITC) and pseudovirus-based neutralization assays. Specifically, it focuses on engineering CDRs targeting the epitopes of receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. A structure-guided virtual library of 112 single mutations in CDRs was generated and screened against RBD to select the potential affinity-enhancing mutations. Protein-protein docking analysis identified 32 single mutants of which nine mutants were selected for molecular dynamics (MD) simulations. Subsequently, biophysical ITC studies provided insights into binding affinity, and consistent with in silico findings, six mutations that demonstrated better binding affinity than native nanobody were further tested in vitro for neutralization activity against SARS-CoV-2 pseudovirus. Leu106Thr mutant was found to be most effective in virus-neutralization with IC 50 values of ∼0.03 μM, as compared to the native nanobody (IC 50 ∼0.77 μM). Thus, in this study, the developed computational pipeline guided by structure-aided interface profiles and thermodynamic analysis holds promise for the streamlined development of antibody-based therapeutic interventions against emerging variants of SARS-CoV-2 and other infectious pathogens., Competing Interests: Declaration of competing interest We declare that we have no conflicts of interest in the authorship or publication of this contribution., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Bovine milk exosomes (BmExo) have been identified as versatile nanovesicles for anti-cancer drugs delivery due to their natural availability and biocompatibility. However, tumor-specific delivery based on BmExo often requires post-isolation modifications of the membrane surface with active-targeting ligands. In this study, we report an alternative approach to functionalize BmExo with nanobody combining facile chemical modification and Sortase A-mediated site-specific ligation, as demonstrated by the development of an epidermal growth factor receptor (EGFR)-targeted drug delivery system. The BmExo membrane was first coated with a diglycine-containing amphiphile molecule, NH 2 -GG-PEG2000-DSPE, by hydrophobic insertion. The diglycine as nucleophiles displayed on the membrane enabled the subsequent ligation of the EGFR nanobody (7D12) by Sortase A (SrtA)-mediated site-specific transpeptidation. The successful construction of BmExo-7D12 was confirmed by Western blotting analysis, electron microscopy, and dynamic light scattering (DLS). As a demonstration model, BmExo-7D12 loaded with the chemotherapeutic drug doxorubicin (Dox) was shown to be able to deliver Dox to cancer cells in response to the expression of EGFR as manifested by immunocytochemistry and flow cytometry analysis. Finally, the cytotoxicity assay showed that BmExo-7D12-Dox was more effective in killing tumor cells with high EGFR expression while significantly reduced the non-specific toxicity to EGFR negative cells. In conclusion, these results demonstrate that 7D12-functionalized BmExo can serve as a target-specific delivery system for Dox to selectively kill EGFR-expressing tumor cells. This approach should prove to be versatile and efficient for the generation of protein-ligands modified BmExo., (© 2024 Wiley-VCH GmbH.)

Although tumor immunotherapy has achieved significant success in recent years, tackling solid tumors remains a formidable challenge. Here, we present an approach that utilizes outer membrane vesicles (OMVs) from bacterial cells as scaffolds to engage immune cells in solid tumor immunotherapy. Two types of nanobodies targeting CD47/SIRPα and PD-1/PD-L1 pathways were simultaneously conjugated onto the surfaces of the OMVs in divalent and trivalent forms using orthogonal SpyCatcher-SpyTag and SnoopCatcher-SnoopTag chemistry. This resulted in the generation of an OMV-based nanosized immune cell engager (OMV-NICE) with dual-targeting abilities. In vitro assays confirmed the retention of the function of the two nanobodies on the OMV-NICE, as evidenced by the synergistically enhanced macrophage phagocytosis and T cell cytotoxicity against tumor cells. In vivo studies using a B16-F10 melanoma mouse model also revealed the superior antitumor activity of OMV-NICE compared to those of unconjugated nanobodies and OMVs alone. Subsequent mechanistic investigations further supported the enhanced recruitment of macrophages and T cells to the tumor region by OMV-NICE. Overall, this work expands the current repertoire of immune cell engagers, and the developed OMV-NICE platform holds great promise for broad applications, particularly in solid tumor immunotherapy.

Protein-nanoparticle interactions play a crucial role in both biomedical applications and the biosafety assessment of nanomaterials. Here, we found that nanobodies can induce citrate-capped gold nanoparticles (AuNPs) to aggregate into large clusters. Subsequently, we explored the mechanism behind this aggregation and proposed the "gold nucleation mechanism" to explain this phenomenon. Building on this observation, we developed a one-step label-free colorimetric method based on nanobody-induced AuNP aggregation. When nanobodies bind to target bacteria, spatial hindrance occurs, preventing further AuNPs aggregation. This alteration in surface plasmon resonance properties results in visible color changes. As an example, we present a simple and sensitive "mix-and-read" chromogenic immunosensor for Cronobacter sakazakii ( C. sakazakii ). The experiment can be completed within 20 min, with a visual detection limit of 10 3 CFU/mL and a quantitative detection limit of 136 CFU/mL. Importantly, our method exhibits no cross-reactivity with other bacterial species. This strategy harnesses the excellent properties of nanobodies and the optical characteristics of AuNPs for direct and rapid detection of foodborne pathogen.

Siglec-9 is a promising immune checkpoint molecule, and therapeutics targeting Siglec-9 have the potential to augment anti-tumor immunity. Here, we generated a bispecific antibody, named as aSE4-1-Fc, by fusing two distinct alpaca derived nanobodies, which can simultaneously target the extracellular Ig variable (V)-set domain and C2-set domains of murine Siglec-9 (also known as Siglec-E) with high affinity. In vivo studies showed that aSE4-1-Fc was better than its component antibodies in inhibiting tumor growth/metastasis, and Siglec-E blockade using aSE4-1-Fc generated protective anti-tumor T cell memory. Furthermore, the combination of aSE4-1-Fc with anti-PD-L1 therapy greatly improved the antitumor effects by augmenting both T and NK cells. Taken together, this study emphasizes the importance of Siglec-9 as a potential cancer therapeutic target, demonstrates the synergistic effect of co-inhibition of Siglec-9 and PD-L1, and may have implications for developing engineered antibodies targeting Siglec-9 with enhanced therapeutic efficacy., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Tengchuan Jin has patent pending to Tengchuan Jin, Dan Zhao. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

SARS-CoV-2 and its variants continue to pose a significant threat to public health. Nanobodies (Nbs) that inhibit the interaction between the receptor-binding domain (RBD) of the spike protein and the host cell receptor angiotensin-converting enzyme 2 (ACE2) are promising drug candidates. In this study, we report the discovery and structural characterization of a potent Nb that targets the RBD. By screening a phage display alpaca naive Nbs library using the RBD as bait, we identified sixteen candidate Nbs. Of these, nine exhibited nanomolar to micromolar binding affinity and strong neutralizing activity against pseudotyped SARS-CoV-2 viruses, with NbS4 showing the highest neutralization potency. The crystal structure of the SARS-CoV-2 RBD in complex with NbS4 revealed that this Nb binds to a site partially overlapping the ACE2 binding region. Importantly, the key binding residues of NbS4 in the RBD are conserved across most known variants, making it a promising candidate for COVID-19 treatment., Competing Interests: Declaration of competing interest The authors have no conflicts of interest to declare., (Copyright © 2024 Elsevier B.V. All rights reserved.)

A column-free immunoaffinity purification (CFIP) technique for sample preparation of aflatoxin B 1 (AFB 1 ) was developed using an AFB 1 -specific nanobody (named G8) and an elastin-like polypeptide (ELP). The reversible phase transition between liquid and solid in response to temperature changes was exhibited by the ELP which was derived from human elastin. The G8 was tagged with ELPs of various lengths (20, 40, 60, and 80 repeat units) at the C-terminus using recursive directional ligation (RDL). Coding sequences were then subcloned into pET30a at the multiple cloning sites. Bioactive recombinant proteins were produced by expressing them as inclusion bodies in Escherichia coli BL21 (DE3), then dissolved and refolded. Analysis by indirect competitive enzyme-linked immunosorbent assay (icELISA) and transition temperature (T t ) measurement confirmed that the refolded G8-ELPs preserved the ability to recognize AFB 1 as well as phase transition when the temperature rose above T t . To establish the optimal conditions for cleaning AFB 1 , the effects of various parameters on recovery were investigated. The recovery in ELISA tests was 95 ± 3.67% under the optimized CFIP workflow. Furthermore, the CFIP-prepared samples were applied for high-performance liquid chromatography (HPLC) detection. The recovery in the CFIP-HPLC test ranged from 54 ± 1.86% to 98 ± 3.58% for maize, rice, soy sauce, and vegetable oil samples. To the best of our knowledge, this is the first report combining the function of both nanobody and ELP to develop a cleanup technique for small molecules in a complex matrix. The CFIP for the sample pretreatment was easy to use and inexpensive. In contrast to conventional immunosensitivity materials, the reagent utilized in the CFIP was entirely biosynthesized without any chemical coupling reactions. This suggests that the nanobody-ELP may serve as a useful dual-functional reagent for the development of sample cleaning or purification methods., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature.)

A prokaryotic resistance-based directed evolution system leveraging protein-fragment complementation assay (PCA) was devised, and its proficiency in detecting protein-protein interactions and discriminating varying degrees of binding affinity was demonstrated by two well-characterized protein pairs. Furthermore, we constructed a random mutant library based on the GBP R36K/E45K mutant, characterized by almost no affinity towards EGFP. This library was subjected to PCA-based prokaryotic directed evolution, resulting in the isolation of back-mutated variants. In summary, we have established an expedited, cost-effective, and structural information-independent PCA-based prokaryotic directed evolution platform for nanobody affinity maturation, featuring tunable screening stringency via modulation of antibiotic concentrations., Competing Interests: Declaration of competing interest There are no conflicts of interest to declare., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Nanobodies, derived from camelids and sharks, offer compact, single-variable heavy-chain antibodies with diverse biomedical potential. This review explores their generation methods, including display techniques on phages, yeast, or bacteria, and computational methodologies. Integrating experimental and computational approaches enhances understanding of nanobody structure and function. Future trends involve leveraging next-generation sequencing, machine learning, and artificial intelligence for efficient candidate selection and predictive modeling. The convergence of traditional and computational methods promises revolutionary advancements in precision biomedical applications such as targeted drug delivery and diagnostics. Embracing these technologies accelerates nanobody development, driving transformative breakthroughs in biomedicine and paving the way for precision medicine and biomedical innovation., (© 2024 The Author(s). Biotechnology and Bioengineering published by Wiley Periodicals LLC.)

Antibody pairs-based immunoassay platforms served as essential and effective tools in the field of pathogen detection. However, the cumbersome preparation and limited detection sensitivity of antibody pairs challenge in establishment of a highly sensitive detection platform. In this study, using COVID-19 testing as a case, we utilized readily accessible nanobodies as detection antibodies and further proposed an accurate design concept with a more scientific and efficient screening strategy to obtain ultrasensitive antibody pairs. We employed nanobodies capable of binding different antigenic epitopes of the nucleocapsid (NP) or receptor-binding domain (RBD) antigens sandwich as substitutes for monoclonal antibodies (mAbs) sandwich in fast detection formats and utilized time-resolved fluorescence (TRF) microspheres as the signal probe. Consequently, we developed a multi-epitope nanobody sandwich-based fluorescence lateral flow immunoassay (FLFA) strip. Our results suggest that the NP antigen had a detection limit of 12.01pg/mL, while the RBD antigen had a limit of 6.51 pg/mL using our FLFA strip. Based on double mAb sandwiches, the values presented herein demonstrated 4 to 32-fold enhancements in sensitivity, and 32 to 256-fold enhancements compared to commercially available antigen lateral flow assay kits. Furthermore, we demonstrated the excellent characteristics of the proposed test strip, including its specificity, stability, accuracy, and repeatability, which underscores its the prospective utility. Indeed, these findings indicate that our established screening strategy along with the multi-epitope nanobody sandwich mode provides an optimized strategy in the field of pathogen detection., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Macroporous three-dimensional (3D) framework structured melamine foam-based Enzyme-Linked Immunosorbent Assay (f-ELISA) biosensors were developed for rapid, reliable, sensitive, and on-site detection of trace amount of biomolecules and chemicals. Various ligands can be chemically immobilized onto the melamine foam, which brings in the possibility of working with antibodies, nanobodies, and peptides, respectively, as affinity probes for f-ELISA biosensors with improved stability. Different chemical reagents can be used to modify the foam materials, resulting in varied reactivities with antibodies, nanobodies, and peptides. As a result, the f-ELISA sensors produced from these modified foams exhibit varying levels of sensitivity and performance. This study demonstrated that the chemical reagents used for immobilizing antibodies, nanobodies, and peptides could affect the sensitivities of the f-ELISA sensors, and their storage stabilities under different temperatures varied depending on the sensing probes used, with f-ELISA sensors employing nanobodies as probes exhibiting the highest stability. This study not only showcases the versatility of the f-ELISA system but also opens new avenues for developing cost-effective, portable, and user-friendly diagnostic tools with optimized sensitivity and stability., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The ease of expression and engineering of single domain antibodies, known as nanobodies, make them attractive alternatives to conventional antibodies in point-of-care diagnostics such as lateral flow assays. In lateral flow assays, gold nanoparticle bioconjugates serve as labels which display affinity molecules on the gold surface. While examples of nanobody gold nanoparticle bioconjugates exist, few utilise the simple one-step approach of physisorption owing to undesirable nanoparticle aggregation and loss of functionality. Here we show that engineering nanobodies into multivalent structures can significantly enhance their functionality when physisorbed onto gold nanoparticles. This approach enables resulting bioconjugates to withstand multiple processing steps required for long-term nanoparticle storage within lateral flow assays. Specifically, we show that the trivalent version of VHHV nanobody (VHH3) against the S1 protein of SARS-CoV-2 can be immobilised onto gold nanoparticles through passive adsorption. Unlike its monovalent and bivalent nanobody counterparts, using VHHV3 preserves nanoparticle stability under salt stress, blocking, washing, and freeze-drying conditions while maintaining picomolar sensitivity to the S1 protein. We anticipate that this facile strategy is a significant advancement towards the integration of nanobodies in lateral flow assay development.

Apolipoprotein A1 (Apo-A1) is a well-recognized biomarker in tissues, closely associated with cardiovascular diseases such as atherosclerosis, coronary artery disease, and heart failure. However, existing methods for Apo-A1 determination are limited by costly equipment and intricate operational procedures. Given the distinct advantages of electrochemical immunosensors, including affordability and high sensitivity, along with the unique attributes of nanobodies (Nbs), such as enhanced specificity and better tissue permeability, we developed an electrochemical immunosensor for Apo-A1 detection utilizing Nb technology. In our study, Ce-MOF@AuNPs nanocomposites were synthesized by using ultrasonic methods and applied to modify a glassy carbon electrode. The Nb6, screened from an Apo-A1 immunized phage library, was immobilized onto the nanocomposite material, establishing a robust binding interaction with Apo-A1. The recorded peak current values demonstrated a logarithmic increase corresponding to Apo-A1 concentrations ranging from 1 to 100,000 pg/mL, with a detection limit of 36 fg/mL. Additionally, the developed immunosensors demonstrated high selectivity, good stability, and reproducibility. Our methodology was also effectively utilized for serum sample analysis, showing good performance in clinical assessments. This electrochemical immunosensor represents a promising tool for Apo-A1 detection, with significant potential for advancing cardiovascular disease diagnostics.

A new type of label-free electrochemical immunosensor for the high-sensitivity determination of parathion was developed based on the oriented immobilization of nanobody (VHH9) on a gold nanoparticle-loaded polyvinyl alcohol/citric acid nanofiber membrane-modified electrode. The morphology characterization and assembly process of the modified materials were investigated using scanning electron microscopy (SEM) and electrochemical impedance spectroscopy (EIS). Under the optimum conditions, the label-free electrochemical immunosensor for parathion exhibited a linear range of 0.0015-6400 ng/mL and a low detection limit of 0.48 pg/mL, the signal response of which was 10 times higher than that of the randomly immobilized VHH9. The immunosensor possessed high selectivity, good repeatability and reusability (keeping above 90% of its initial activity after repeating 8 times), and stability (remaining 90% after 9 weeks of storage). Finally, the average recoveries of parathion from food samples were 93.76-105.73% with the coefficient of variation being 2.65-6.85%, showing good correlation with UPLC (R 2  = 0.9950). Therefore, our nanobody immobilization protocol is simple and effective and proves the potential to be utilized as a promising candidate for sensing platform., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

Nanobodies (Nbs) are antibody fragments derived from heavy-chain-only IgG antibodies found in the Camelidae family as well as cartilaginous fish. Their unique structural and functional properties, such as their small size, the ability to be engineered for high antigen-binding affinity, stability under extreme conditions, and ease of production, have made them promising tools for diagnostics and therapeutics. This potential was realized in 2018 with the approval of caplacizumab, the world's first Nb-based drug. Currently, Nbs are being investigated in clinical trials for a broad range of treatments, including targeted therapies against PDL1 and Epidermal Growth Factor Receptor (EGFR), cardiovascular diseases, inflammatory conditions, and neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. They are also being studied for their potential for detecting and imaging autoimmune conditions and infectious diseases such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A variety of methods are now available to generate target-specific Nbs quickly and efficiently at low costs, increasing their accessibility. This article examines these diverse applications of Nbs and their promising roles. Only the most recent articles published in the last five years have been used to summarize the most advanced developments in the field., (© 2024. The Author(s).)

Cervical cancer ranks as the third most prevalent malignancy in women worldwide. The persistence of Human papillomavirus (HPV) infection stands out as the foremost risk factor for cervical cancer development. Among the numerous HPV subtypes, HPV16 infection emerges as the primary pathogenic determinant of cervical cancer. To date, no specific drugs have been approved. In this study, we engineered two high-affinity fusion protein targeting HPV16 L1 protein based on the alpaca-derived single-domain antibody 2C12 previously obtained in our laboratory. These two fusion proteins exhibited potent neutralizing activity against HPV16 pseudovirus with IC50 values of 7.8 nM and 6.5 nM, respectively. Molecular docking analysis revealed that 2C12 formed ten pairs of hydrogen bonds with HPV16 L1, among which Arg39 and Thr100 established multiple pairs of hydrogen bonds with HPV16 L1, indicating their crucial roles in antigen-antibody binding process. These structural and biological findings underscore the effective binding capacity of these fusion proteins to HPV16, leading to reduced viral load and providing valuable insights into therapeutic antibody and vaccine development against HPV 16 infection., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Bai et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Immune checkpoint blockade targeting the CD47/SIRPα axis represents an alluring avenue for cancer immunotherapy. However, the compromised efficacy and safety concerns in vivo of conventional anti-CD47 antibodies impede their wide clinical applications. Here we introduced a single type of high-mannose glycans into the nanobody against CD47 (HM-nCD47) and subsequently displayed HM-nCD47 on cellular vesicles (CVs) for enhanced cancer immunotherapy. In this platform, the CVs significantly improved the circulation time of HM-nCD47-CVs, the nCD47 enabled the blockade of the CD47/SIRPα axis, and the HM enhanced recognition of mannose-binding lectin, all synergistically activating the macrophage-mediated antitumor immunity. In both subcutaneous and metastatic murine tumor models, the HM-nCD47-CVs possessed significantly extended half-lives and increased accumulation at the tumor site, resulting in a remarkable macrophage-dependent inhibition of tumor growth, a transcriptomic remodeling of the immune response, and an increase in survival time. By integrating the chemical biology toolbox with cell membrane nanotechnology, the HM-nCD47-CVs represent a new immunotherapeutic platform for cancer and other diseases., (© 2024 Wiley-VCH GmbH.)

Rational design of novel antibody therapeutics against viral infections such as coronavirus relies on surface complementarity and high affinity for their effectiveness. Here, we explore an additional property of protein complexes, the intrinsic mechanical stability, in SARS-CoV-2 variants when complexed with a potent antibody. In this study, we utilized a recent implementation of the GōMartini 3 approach to investigate large conformational changes in protein complexes with a focus on the mechanostability of the receptor-binding domain (RBD) from WT, Alpha, Delta, and XBB.1.5 variants in complex with the H11-H4 nanobody. The analysis revealed moderate differences in mechanical stability among these variants. Also, we identified crucial residues in both the RBD and certain protein segments in the nanobody that contribute to this property. By performing pulling simulations and monitoring the presence of specific native and non-native contacts across the protein complex interface, we provided mechanistic insights into the dissociation process. Force-displacement profiles indicate a tensile force clamp mechanism associated with the type of protein complex. Our computational approach not only highlights the key mechanostable interactions that are necessary to maintain overall stability, but it also paves the way for the rational design of potent antibodies that are mechanostable and effective against emergent SARS-CoV-2 variants.

To break through the bottleneck in preparation of nanobody (Nb) for chemical contaminants induced by the difficulties in the synthesis of immunogen, complexity and unexpectable efficiency of immunization, a novel strategy to generate Nbs based on the designed synthetic Nb libraries with final size up to 10 9  cfu/mL was adopted and succeeded in selection of anti-coumaphos Nb A4. Furthermore, an affinity-matured mutant Nb 3G was obtained from the secondary library. Finally, an ic-ELISA was established with the limit of detection for coumaphos low to 1.90 ng/mL, 6.4-fold improved than the parent Nb A4, and the detection range from 3.06 to 15.77 ng/mL. Meanwhile, the recovery rate of vegetable samples was from 89.9% to 98.5%. Finally, the accuracy was testified by the standard UPLC-MS/MS method with R 2 up to 0.99. Overall, fully synthetic Nb libraries constructed in this work provided an alternative possibility to generate the specific Nbs for chemical contaminants., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Camelids produce a special type of antibody, known as V H Hs, that has lost the V L domain, providing a more optimised V H domain. This particular highly stable antibody domain has interesting properties for biotechnological development. Ordinarily, those molecules possess only one disulphide bridge, but surprisingly, at least a quarter of these V H Hs have a second one. Curiously, this does not seem to be essential for the stability and the function of this domain. In an attempt to characterise precisely the role and impact of this disulphide bridge at the molecular level, several in silico mutants of a V H H were created to disrupt this second disulphide bridge and those systems were submitted to molecular dynamics simulation. The loss of the second disulphide bridge leads to an increase in the flexibility of CDR1 and CDR3 and an unexpected rigidification of CDR2. Local conformational analysis shows local differences in the observed protein conformations. However, in fact, there is no exploration of new conformations but a change in the equilibrium between the different observed conformations. This explains why the interaction of V H Hs is not really affected by the presence or absence of this second bridge, but their rigidity is slightly reduced. Therefore, the additional disulphide bridge does not seem to be an essential part of V H Hs function.

In silico optimization of protein binding has received a great deal of attention in the recent years. Since in silico prefiltering of strong binders is fast and cheap compared to in vitro library screening methods, the advent of powerful hardware and advanced machine learning algorithms has made this strategy more accessible and preferred. These advances have already impacted the global response to pandemic threats. In this study, we proposed and tested a workflow for designing nanobodies targeting the SARS-CoV-2 spike protein receptor binding domain (S-RBD) using machine learning techniques complemented by molecular dynamics simulations. We evaluated the feasibility of this workflow using a test set of 3 different nanobodies and 2 different S-RBD variants, from in silico design and bacterial expression to binding assays of the designed nanobody mutants. We successfully designed nanobodies that were subsequently tested against both the wild-type (Wuhan type) and the delta variant S-RBD and found 2 of them to be stronger binders compared to the wild-type nanobody. We use this case study to describe both the strengths and weaknesses of this in silico assisted nanobody design strategy.

Unlike most other picornaviruses, foot-and-mouth disease (FMD) intact virions (146S) dissociate easily into small pentameric subunits (12S). This causes a dramatically decreased immunogenicity by a mechanism that remains elusive. Here, we present the high-resolution structures of 12S (3.2 Å) and its immune complex of a single-domain antibody (VHH) targeting the particle interior (3.2 Å), as well as two 146S-specific VHHs complexed to distinct sites on the 146S capsid surface (3.6 Å and 2.9 Å). The antigenic landscape of 146S is depicted using 13 known FMD virus-antibody complexes. Comparison of the immunogenicity of 146S and 12S in pigs, focusing on the resulting antigenic sites and incorporating structural analysis, reveals that dissociation of 146S leads to structural alteration and destruction of multiple epitopes, resulting in significant differences in antibody profiles/lineages induced by 12S and 146S. Furthermore, 146S generates higher synergistic neutralizing antibody titers compared to 12S, whereas both particles induce similar total FMD virus specific antibody titers. This study can guide the structure-based rational design of novel multivalent and broad-spectrum recombinant vaccines for protection against FMD., (© 2024. The Author(s).)

Fluorescence microscopy has long been a transformative technique in biological sciences. Nevertheless, most implementations are limited to a few targets, which have been revealed using primary antibodies and fluorescently conjugated secondary antibodies. Super-resolution techniques such as Exchange-PAINT and, more recently, SUM-PAINT have increased multiplexing capabilities, but they require specialized equipment, software, and knowledge. To enable multiplexing for any imaging technique in any laboratory, we developed NanoPlex, a streamlined method based on conventional antibodies revealed by engineered secondary nanobodies that allow the selective removal of fluorescence signals. We develop three complementary signal removal strategies: OptoPlex (light-induced), EnzyPlex (enzymatic), and ChemiPlex (chemical). We showcase NanoPlex reaching 21 targets for 3D confocal analyses and 5-8 targets for dSTORM and STED super-resolution imaging. NanoPlex has the potential to revolutionize multi-target fluorescent imaging methods, potentially redefining the multiplexing capabilities of antibody-based assays., (© 2024. The Author(s).)

The μ-opioid receptor (μOR), a prototypical G protein-coupled receptor (GPCR), is the target of opioid analgesics such as morphine and fentanyl. Due to the severe side effects of current opioid drugs, there is considerable interest in developing novel modulators of μOR function. Most GPCR ligands today are small molecules, however biologics, including antibodies and nanobodies, represent alternative therapeutics with clear advantages such as affinity and target selectivity. Here, we describe the nanobody NbE, which selectively binds to the μOR and acts as an antagonist. We functionally characterize NbE as an extracellular and genetically encoded μOR ligand and uncover the molecular basis for μOR antagonism by determining the cryo-EM structure of the NbE-μOR complex. NbE displays a unique ligand binding mode and achieves μOR selectivity by interactions with the orthosteric pocket and extracellular receptor loops. Based on a β-hairpin loop formed by NbE that deeply protrudes into the μOR, we design linear and cyclic peptide analogs that recapitulate NbE's antagonism. The work illustrates the potential of nanobodies to uniquely engage with GPCRs and describes lower molecular weight μOR ligands that can serve as a basis for therapeutic developments., (© 2024. The Author(s).)

The melanocortin receptor 4 (MC4R) belongs to the melanocortin receptor family of G-protein coupled receptors and is a key switch in the leptin-melanocortin molecular axis that controls hunger and satiety. Brain-produced hormones such as α-melanocyte-stimulating hormone (agonist) and agouti-related peptide (inverse agonist) regulate the molecular communication of the MC4R axis but are promiscuous for melanocortin receptor subtypes and induce a wide array of biological effects. Here, we use a chimeric construct of conformation-selective, nanobody-based binding domain (a ConfoBody Cb80) and active state-stabilized MC4R-β2AR hybrid for efficient de novo discovery of a sequence diverse panel of MC4R-specific, potent and full agonistic nanobodies. We solve the active state MC4R structure in complex with the full agonistic nanobody pN162 at 3.4 Å resolution. The structure shows a distinct interaction with pN162 binding deeply in the orthosteric pocket. MC4R peptide agonists, such as the marketed setmelanotide, lack receptor selectivity and show off-target effects. In contrast, the agonistic nanobody is highly specific and hence can be a more suitable agent for anti-obesity therapeutic intervention via MC4R., (© 2024. The Author(s).)

The anti-PD-L1 and its bispecific antibodies have exhibited durable antitumor immunity but still elicit immunosuppression mainly caused by tumor-derived exosomes (TDEs), leading to difficulty in clinical transformation. Herein, engineered Escherichia coli Nissle 1917 (EcN) coexpressing anti-PD-L1 and anti-CD9 nanobodies (EcN-Nb) are developed and decorated with zinc-based metal-organic frameworks (MOFs) loaded with indocyanine green (ICG), to generate EcN-Nb-ZIF-8 CHO -ICG (ENZC) for spatiotemporal lysis of bacteria for immunotherapy. The tumor-homing hybrid system can specifically release nanobodies in response to near-infrared (NIR) radiation, thereby targeting TDEs and changing their biological distribution, remodeling tumor-associated macrophages to M1 states, activating more effective and cytotoxic T lymphocytes, and finally, leading to the inhibition of tumor proliferation and metastasis. Altogether, the microfluidic-enabled MOF-modified engineered probiotics target TDEs and activate the antitumor immune response in a spatiotemporally manipulated manner, offering promising TDE-targeted immune therapy.

Ryanodine receptors (RyRs) are large Ca 2+ release channels residing in the endoplasmic or sarcoplasmic reticulum membrane. Three isoforms of RyRs have been identified in mammals, the disfunction of which has been associated with a series of life-threatening diseases. The need for large amounts of native tissue or eukaryotic cell cultures limits advances in structural studies of RyRs. Here, we report a method that utilizes nanobodies to purify RyRs from only 5 mg of total protein. The purification process, from isolated membranes to cryo-EM grade protein, is achieved within 4 h on the bench, yielding protein usable for cryo-EM analysis. This is demonstrated by solving the structures of rabbit RyR1, solubilized in detergent, reconstituted into lipid nanodiscs or liposomes, and bovine RyR2 reconstituted in nanodisc, and mouse RyR2 in detergent. The reported method facilitates structural studies of RyRs directed toward drug development and is useful in cases where the amount of starting material is limited., Competing Interests: Conflict of interests The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

This study introduces an efficient on-column refolding and purification method for preparing nanobodies (Nbs) expressed as inclusion bodies and fusion proteins. The HisTrap TM FF system was successfully employed for the purification of the fusion protein FN1-ΔI-CM-2D5. The intein ΔI-CM cleavage activity was activated at 42 °C, followed by incubation for 4 h. Leveraging the remarkable thermal stability of Nbs, 2D5 was further purified through heat treatment at 80 °C for 1h. This method yielded up to 107.2 mg of pure 2D5 with a purity of 99.2 % from just 1L of bacterial culture grown in a shaker flask. Furthermore, this approach successfully restored native secondary structure and affinity of 2D5. Additionally, the platform was effectively applied to the refolding and purification of a polystyrene-binding nanobody (B2), which exhibited limited expression in the periplasmic and cytoplasmic spaces of E. coli. This endeavor resulted in the isolation of 53.2 mg of pure B2 Nb with a purity exceeding 99.5 % from the same volume of bacterial culture. Significantly, this approach restored the native secondary structure of the Nbs, highlighting its potential for addressing challenges associated with expressing complex Nbs in E. coli. Overall, this innovative platform provides a scientifically rigorous and reproducible method for the efficient preparation of Nbs, offering a valuable tool for antibody research and development., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Recombinant adeno-associated viruses (rAAVs) have been extensively studied for decades as carriers for delivering therapeutic genes. However, designing rAAV vectors with selective tropism for specific cell types and tissues has remained challenging. Here, we introduce a strategy for redirecting rAAV by attaching nanobodies with desired tropism at specific sites, effectively replacing the original tropism. To demonstrate this concept, we initially modified the genetic code of rAAV2 to introduce an azido-containing unnatural amino acid at a precise site within the capsid protein. Following a screening process, we identified a critical site (N587+1) where the introduction of unnatural amino acid eliminated the natural tropism of rAAV2. Subsequently, we successfully redirected rAAV2 by conjugating various nanobodies at the N587+1 site, using click and SpyTag-Spycatcher chemistries to form nanobody-AAV conjugates (NACs). By investigating the relationship between NACs quantity and effect and optimizing the linker between rAAV2 and the nanobody using a cathepsin B-susceptible valine-citrulline (VC) dipeptide, we significantly improved gene delivery efficiency both in vitro and in vivo. This enhancement can be attributed to the facilitated endosomal escape of rAAV2. Our method offers an exciting avenue for the rational modification of rAAV2 as a retargeting vehicle, providing a convenient platform for precisely engineering various rAAV2 vectors for both basic research and therapeutic applications. STATEMENT OF SIGNIFICANCE: AAVs hold great promise in the treatment of genetic diseases, but their clinical use has been limited by off-target transduction and efficiency. Here, we report a strategy to construct NACs by conjugating a nanobody or scFv to an rAAV capsid site, specifically via biorthogonal click chemistry and a spy-spycatcher reaction. We explored the structure-effect and quantity-effect relationships of NACs and then optimized the transduction efficiency by introducing a valine-citrulline peptide linker. This approach provides a biocompatible method for rational modification of rAAV as a retargeting platform without structural disruption of the virus or alteration of the binding capacity of the nanobody, with potential utility across a broad spectrum of applications in targeted imaging and gene delivery., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.)

Objective: To screen and obtain specific anti-lymphocyte activation gene-3 (LAG3) nanobody sequences, purify and express recombinant anti-LAG3 nanobody, and verify its effect on promoting T cells to kill tumor cells., Methods: Based on the camel derived natural nanobody phage display library constructed by the research group, the biotinylated LAG3 antigen was used as the target, and the anti-LAG3 nanobody sequences were screened by biotin-streptavidin liquid phase screening, phage-ELISA and sequencing. The sequence-conjμgated human IgG1 Fc fragment was obtained, the recombinant anti-LAG3 nanobody expression vector was constructed, the expression of the recombinant anti-LAG3 nanobody was induced by IPTG and purified, and the characteristics and functions of the recombinant anti-LAG3 nanobody were verified by SDS-PAGE, Western blot, cytotoxicity assay, etc. RESULTS: One anti-LAG3 nanobody sequence was successfully screened, and the corresponding recombinant anti-LAG3 nanobody-expressing bacteria were constructed. The results of SDS-PAGE, Western blot and cytotoxicity assay showed that the recombinant anti-LAG3 nanobody was successfully expressed, which was specific, and it could promote the killing ability of T cells against tumor cells, and the optimal concentration was 200 μg/mL., Conclusion: The recombinant anti-LAG3 nanobody screened and expressed has specific and auxiliary anti-tumor cell effects, which lays a foundation for its subsequent application., Competing Interests: Declaration of competing interest We do not have any recognized conflicting economic interests or personal relationships that influence the research presented in this paper., (Copyright © 2024. Published by Elsevier Inc.)

Targeted therapies have revolutionized traditional cancer treatments by precisely targeting tumor cells, enhancing efficacy and safety. Despite this advancement, the proportion of cancer patients eligible for such therapies remains low due to the absence of suitable targets. Here, we investigate whether the translocation of the immunogenic cell death (ICD) marker calreticulin (CALR) from the endoplasmic reticulum (ER) to the cell surface following ICD induction can serve as a target for targeted therapies. To target CALR, a nanobody Nb215 identified from a naïve VHH phage library with high binding affinity to both human and mouse CALR was employed to engineer probiotic EcN 1917. Our results demonstrated that CALR nanobody-modified EcN-215 coupled with the photothermal dye indocyanine green (ICG) was able to exert NIR-II imaging-guide photothermal therapy (PTT). Moreover, PTT with EcN-215/ICG can reshape the tumor microenvironment by enhancing the infiltration of CD45 + CD3 + T cells and CD11b + F4/80 + macrophages. Furthermore, the antitumor activity of CALR-targeted EcN-215/ICG is synergistically enhanced by blocking CD47-SIRPα axis. Collectively, our study provides a proof of concept for CALR-targeted therapy. Given that CALR translocation can be induced by various anticancer therapies across numerous tumor cell lines, CALR-targeted therapies hold promise as a novel approach for treating multiple types of cancers., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

In this work, with parathion, a typical forbidden organophosphate pesticide as target drug, an enhanced nanobody-driven bioluminescent immunoassay based on the engineered split-nanoluciferase (NanoLuc) was proposed. Concretely, through labeling 11S and β10, two split-NanoLuc units onto the anti-parathion nanobody (Nb) VHH9 and the artificial antigen H1 coupled with carrier protein ovalbumin (H1-OVA) respectively, an NanoLuc Binary Technology (NanoBiT) system was firstly developed in the form of homogeneous immunoassay, in which the luminescence signal was produced by the reassembled NanoLuc after the combination of the 11S-fused VHH9 and β10-labeled H1-OVA. Subsequently, in order to enhance the signal-to-noise (S/N) ratio, a novel strategy of splitting 11S into two smaller subunits Δ11S and β9 was adopted so then an NanoLuc Ternary Technology (NanoTeT) system based on tri-part components of β9-fused VHH9, β10-labeled H1-OVA and Δ11S was successfully established. The results showed that the maximum half inhibition concentration (IC 50 ) for parathion can be as low as 2.04 ng/mL, 3.2-fold and 4.2-fold improved than that of the NanoBiT system and indirect competitive enzyme-linked immunosorbent assay (ic-ELISA). Meanwhile, the detection range was from 0.19 ng/mL to 22.11 ng/mL. More importantly, this method required simply a one-step incubation with all reagents mixed together, and the total time used in detection was only 10 min, 7-fold faster than ic-ELISA. Finally, the average recoveries for vegetable samples were from 84.8% to 122% with the coefficient of variance (CV) below 15%. Overall, this study provides a new platform for homogeneous immunoassay of the small-molecule contaminants., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Microcystin-LR (MC-LR), a toxic cyanobacterial toxin in freshwater, poses significant health and ecological risks due to its ability to induce cell apoptosis and liver damage. Sensitive detection of MC-LR is crucial for public health and water safety. In this work, we engineered a multivalent bifunctional nanobody (A2.3-C4-SBP) by fusing the anti-MC-LR nanobody gene (A2.3) with self-assembling peptides (C4) and a streptavidin-binding peptide (SBP). A2.3-C4-SBP was directionally immobilized on the ELISA microplate via streptavidin-mediated to develop a multivalent bifunctional nanobody-based chemiluminescent immunoassay (MBN-CLIA) for MC-LR detection in lake water. The IC 50 of the A2.3-C4-SBP heptamer based CLIA was 5.80 ng/mL, and the LOD (IC 10 ) was 0.33 ng/mL, which were 9.51-fold and 1.82-fold lower, respectively, than those of the A2.3-SBP monomer based CLIA. Additionally, the IC 50 and LOD were 1.26-fold and 1.82-fold lower, respectively, than those of the A2.3-C4-SBP heptamer without streptavidin-mediated directional immobilization. In summary, this work developed a sensitive, rapid and simple immunoassay for the detection of MC-LR in lake water based on multivalent bifunctional nanobodies. Furthermore, the proposed combined strategy of nanobody multimerization and directed immobilization is simple to operate and has great potential to improve the sensitivity and signal amplification of various immunoassays., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)