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1.
J Agric Food Chem ; 72(26): 14967-14974, 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38957086

ABSTRACT

Nanobodies (Nbs) serve as powerful tools in immunoassays. However, their small size and monovalent properties pose challenges for practical application. Multimerization emerges as a significant strategy to address these limitations, enhancing the utilization of nanobodies in immunoassays. Herein, we report the construction of a Salmonella-specific fenobody (Fb) through the fusion of a nanobody to ferritin, resulting in a self-assembled 24-valent nanocage-like structure. The fenobody exhibits a 35-fold increase in avidity compared to the conventional nanobody while retaining good thermostability and specificity. Leveraging this advancement, three ELISA modes were designed using Fb as the capture antibody, along with unmodified Nb422 (FbNb-ELISA), biotinylated Nb422 (FbBio-ELISA), and phage-displayed Nb422 (FbP-ELISA) as the detection antibody, respectively. Notably, the FbNb-ELISA demonstrates a detection limit (LOD) of 3.56 × 104 CFU/mL, which is 16-fold lower than that of FbBio-ELISA and similar to FbP-ELISA. Moreover, a fenobody and nanobody sandwich chemiluminescent enzyme immunoassay (FbNb-CLISA) was developed by replacing the TMB chromogenic substrate with luminal, resulting in a 12-fold reduction in the LOD. Overall, the ferritin-displayed technology represents a promising methodology for enhancing the detection performance of nanobody-based sandwich ELISAs, thereby expanding the applicability of Nbs in food detection and other fields requiring multivalent modification.


Subject(s)
Enzyme-Linked Immunosorbent Assay , Ferritins , Salmonella , Single-Domain Antibodies , Ferritins/immunology , Ferritins/chemistry , Ferritins/genetics , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/genetics , Single-Domain Antibodies/immunology , Salmonella/immunology , Salmonella/genetics , Enzyme-Linked Immunosorbent Assay/methods , Limit of Detection , Antibody Affinity , Antibodies, Bacterial/immunology , Immunoassay/methods
2.
Elife ; 132024 Jul 24.
Article in English | MEDLINE | ID: mdl-39046772

ABSTRACT

Antimicrobial resistance (AMR) poses a significant threat to human health. Although vaccines have been developed to combat AMR, it has proven challenging to associate specific vaccine antigens with AMR. Bacterial plasmids play a crucial role in the transmission of AMR. Our recent research has identified a group of bacterial plasmids (specifically, IncHI plasmids) that encode large molecular mass proteins containing bacterial immunoglobulin-like domains. These proteins are found on the external surface of the bacterial cells, such as in the flagella or conjugative pili. In this study, we show that these proteins are antigenic and can protect mice from infection caused by an AMR Salmonella strain harboring one of these plasmids. Furthermore, we successfully generated nanobodies targeting these proteins, that were shown to interfere with the conjugative transfer of IncHI plasmids. Considering that these proteins are also encoded in other groups of plasmids, such as IncA/C and IncP2, targeting them could be a valuable strategy in combating AMR infections caused by bacteria harboring different groups of AMR plasmids. Since the selected antigens are directly linked to AMR itself, the protective effect extends beyond specific microorganisms to include all those carrying the corresponding resistance plasmids.


Subject(s)
Drug Resistance, Bacterial , Plasmids , Animals , Plasmids/genetics , Mice , Drug Resistance, Bacterial/genetics , Bacterial Proteins/genetics , Bacterial Proteins/immunology , Bacterial Proteins/metabolism , Anti-Bacterial Agents/pharmacology , Single-Domain Antibodies/immunology , Single-Domain Antibodies/genetics , Single-Domain Antibodies/pharmacology , Antigens, Bacterial/immunology , Antigens, Bacterial/genetics , Female , Salmonella/genetics , Salmonella/immunology , Salmonella/drug effects , Immunoglobulins/genetics , Immunoglobulins/immunology , Mice, Inbred BALB C
3.
J Agric Food Chem ; 72(29): 16368-16377, 2024 Jul 24.
Article in English | MEDLINE | ID: mdl-38979948

ABSTRACT

In planta expression of recombinant antibodies has been proposed as a strategy for herbicide resistance but is not well advanced yet. Here, an atrazine nanobody gene fused with a green fluorescent protein tag was transformed to Arabidopsis thaliana, which was confirmed with PCR, ELISA, and immunoblotting. High levels of nanobody accumulation were observed in the nucleus, cytoderm, and cytosol. The nanobody expressed in the plant had similar affinity, sensitivity, and selectivity as that expressed in Escherichia coli. The T3 homozygous line showed resistance in a dose-dependent manner up to 380 g ai/ha of atrazine, which is approximately one-third of the recommended field application rate. This is the first report of utilizing a nanobody in plants against herbicides. The results suggest that utilizing a high-affinity herbicide nanobody gene rather than increasing the expression of nanobodies in plants may be a technically viable approach to acquire commercial herbicide-resistant crops and could be a useful tool to study plant physiology.


Subject(s)
Arabidopsis , Atrazine , Herbicide Resistance , Herbicides , Plants, Genetically Modified , Single-Domain Antibodies , Atrazine/pharmacology , Herbicides/pharmacology , Arabidopsis/genetics , Arabidopsis/immunology , Arabidopsis/metabolism , Arabidopsis/drug effects , Herbicide Resistance/genetics , Plants, Genetically Modified/genetics , Plants, Genetically Modified/immunology , Single-Domain Antibodies/genetics , Single-Domain Antibodies/pharmacology , Single-Domain Antibodies/immunology
4.
Sci Rep ; 14(1): 17747, 2024 Jul 31.
Article in English | MEDLINE | ID: mdl-39085444

ABSTRACT

Using conventional immunoglobulin G (IgG) molecules as therapeutic agents presents several well-known disadvantages owing to their large size and structural complexity, negatively impacting development and production efficiency. Single-domain antibodies (sdAbs) are the smallest functional antibody format (~ 15 kDa) and represent a viable alternative to IgG in many applications. However, unlike natural single-domain antibodies, such as camelid VHH, the variable domains of conventional antibodies show poor physicochemical properties when expressed as sdAbs. This report identified stable sdAb variants of human VH3-23 from a framework region 2-randomized human VH library by phage display selection under thermal challenge. Synthetic complementarity determining region diversity was introduced to one of the selected variants with high thermal stability, expression level, and monomeric content to construct a human VH sdAb library. The library was validated by panning against a panel of antigens, and target-specific binders were identified and characterized for their affinity and biophysical properties. The results of this study suggest that a synthetic sdAb library based on a stability-engineered human VH scaffold could be a facile source of high-quality sdAb for many practical applications.


Subject(s)
Complementarity Determining Regions , Peptide Library , Protein Engineering , Protein Stability , Single-Domain Antibodies , Humans , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/genetics , Single-Domain Antibodies/immunology , Protein Engineering/methods , Complementarity Determining Regions/chemistry , Complementarity Determining Regions/immunology , Complementarity Determining Regions/genetics , Immunoglobulin Heavy Chains/chemistry , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Heavy Chains/immunology , Immunoglobulin G/chemistry , Immunoglobulin G/immunology
5.
Methods Mol Biol ; 2824: 135-146, 2024.
Article in English | MEDLINE | ID: mdl-39039411

ABSTRACT

Compared with traditional antibodies, nanobodies from camelids have various advantages, including small molecular weight, high affinity, low immunogenicity, convenient production through genetic engineering, etc. Here we combined next-generation sequencing (NGS) with proteomics technology based on affinity purification-mass spectrometry (AP-MS) and bioinformatics analysis to high-throughput screen monoclonal nanobodies from camels immunized with surface glycoprotein (glycoprotein N, Gn) of severe fever with thrombocytopenia syndrome virus and fulfilled production of the screened anti-Gn monoclonal nanobody with high affinity by genetic engineering. The innovative high-throughput technical route developed here could also be expanded to the production of neutralizing nanobodies specific for Rift Valley fever virus.


Subject(s)
Antibodies, Neutralizing , High-Throughput Nucleotide Sequencing , Proteomics , Single-Domain Antibodies , High-Throughput Nucleotide Sequencing/methods , Animals , Proteomics/methods , Single-Domain Antibodies/genetics , Single-Domain Antibodies/immunology , Single-Domain Antibodies/isolation & purification , Antibodies, Neutralizing/immunology , Camelus , Antibodies, Viral/immunology , High-Throughput Screening Assays/methods , Mass Spectrometry/methods
6.
Nat Commun ; 15(1): 4728, 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38830864

ABSTRACT

Due to their exceptional solubility and stability, nanobodies have emerged as powerful building blocks for research tools and therapeutics. However, their generation in llamas is cumbersome and costly. Here, by inserting an engineered llama immunoglobulin heavy chain (IgH) locus into IgH-deficient mice, we generate a transgenic mouse line, which we refer to as 'LamaMouse'. We demonstrate that LamaMice solely express llama IgH molecules without association to Igκ or λ light chains. Immunization of LamaMice with AAV8, the receptor-binding domain of the SARS-CoV-2 spike protein, IgE, IgG2c, and CLEC9A enabled us to readily select respective target-specific nanobodies using classical hybridoma and phage display technologies, single B cell screening, and direct cloning of the nanobody-repertoire into a mammalian expression vector. Our work shows that the LamaMouse represents a flexible and broadly applicable platform for a facilitated selection of target-specific nanobodies.


Subject(s)
Camelids, New World , Immunoglobulin Heavy Chains , Mice, Transgenic , Single-Domain Antibodies , Spike Glycoprotein, Coronavirus , Animals , Single-Domain Antibodies/genetics , Single-Domain Antibodies/immunology , Camelids, New World/immunology , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Heavy Chains/immunology , Mice , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/chemistry , Lectins, C-Type/metabolism , Lectins, C-Type/immunology , Lectins, C-Type/genetics , SARS-CoV-2/immunology , SARS-CoV-2/genetics , Immunoglobulin E/immunology , Humans , Dependovirus/genetics , Dependovirus/immunology , Immunoglobulin G/immunology , COVID-19/immunology , B-Lymphocytes/immunology
7.
Biochemistry (Mosc) ; 89(5): 933-941, 2024 May.
Article in English | MEDLINE | ID: mdl-38880653

ABSTRACT

Technology of production of single-domain antibodies (NANOBODY® molecules, also referred to as nanoantibodies, nAb, or molecules based on other stable protein structures) and their derivatives to solve current problems in biomedicine is becoming increasingly popular. Indeed, the format of one small, highly soluble protein with a stable structure, fully functional in terms of specific recognition, is very convenient as a module for creating multivalent, bi-/oligo-specific genetically engineered targeting molecules and structures. Production of nAb in periplasm of E. coli bacterium is a very convenient and fairly universal way to obtain analytical quantities of nAb for the initial study of the properties of these molecules and selection of the most promising nAb variants. The situation is more complicated with production of bi- and multivalent derivatives of the initially selected nAbs under the same conditions. In this work, extended linker sequences (52 and 86 aa) between the antigen-recognition modules in the cloned expression constructs were developed and applied in order to increase efficiency of production of bispecific nanoantibodies (bsNB) in the periplasm of E. coli bacteria. Three variants of model bsNBs described in this study were produced in the periplasm of bacteria and isolated in soluble form with preservation of functionality of all the protein domains. If earlier our attempts to produce bsNB in the periplasm with traditional linkers no longer than 30 aa were unsuccessful, the extended linkers used here provided a significantly more efficient production of bsNB, comparable in efficiency to the traditional production of original monomeric nAbs. The use of sufficiently long linkers could presumably be useful for increasing efficiency of production of other bsNBs and similar molecules in the periplasm of E. coli bacteria.


Subject(s)
Antibodies, Bispecific , Escherichia coli , Periplasm , Single-Domain Antibodies , Escherichia coli/genetics , Escherichia coli/metabolism , Periplasm/metabolism , Antibodies, Bispecific/biosynthesis , Antibodies, Bispecific/immunology , Antibodies, Bispecific/genetics , Single-Domain Antibodies/genetics , Single-Domain Antibodies/immunology , Single-Domain Antibodies/chemistry , Antigens/immunology
8.
Mol Biol Rep ; 51(1): 751, 2024 Jun 14.
Article in English | MEDLINE | ID: mdl-38874667

ABSTRACT

BACKGROUND: Recently, new and advanced techniques have been adopted to design and produce nanobodies, which are used in diagnostic and immunotherapy treatments. Traditionally, nanobodies are prepared from camelid immune libraries that require animal treatments. However, such approaches require large library sizes and complicated selection procedures. The current study has employed CDR grafting and site-directed mutagenesis techniques to create genetically engineered nanobodies against the tumor marker CD20 (anti-CD20 nanobodies) used in leukemia treatment. METHODS AND RESULTS: In this study, we utilized the swapping method to graft CDRs from the VH Rituximab antibody to VHH CDRs. We aimed to enhance the binding affinity of the nanobodies by substituting the amino acids (Y101R-Y102R-Y107R) in the VHH-CDR3. To assess the binding capacity of the mutated nanobodies, we conducted an ELISA test. Moreover, through flow cytometry analysis, we compared the fluorescence intensity of the grafted CD20 and mutant nanobodies with that of the commercially available human anti-CD20 in Raji cells. The results showed a significant difference in the fluorescence intensity of the grafted nanobodies and mutant nanobodies when compared to the commercially available human anti-CD20. CONCLUSION: The approach we followed in this study makes it possible to create multiple anti-CD20 nanobodies with varying affinities without the need for extensive selection efforts. Additionally, our research has demonstrated that computational tools are highly reliable in designing functional nanobodies.


Subject(s)
Antibody Affinity , Antigens, CD20 , Complementarity Determining Regions , Mutagenesis, Site-Directed , Rituximab , Single-Domain Antibodies , Single-Domain Antibodies/genetics , Single-Domain Antibodies/immunology , Mutagenesis, Site-Directed/methods , Antigens, CD20/immunology , Antigens, CD20/genetics , Antigens, CD20/metabolism , Humans , Rituximab/pharmacology , Complementarity Determining Regions/genetics , Complementarity Determining Regions/immunology , Cell Line, Tumor , Animals
9.
Protein Expr Purif ; 222: 106522, 2024 Oct.
Article in English | MEDLINE | ID: mdl-38851552

ABSTRACT

OBJECTIVE: To screen and obtain specific anti-lymphocyte activation gene-3 (LAG3) nanobody sequences, purify and express recombinant anti-LAG3 nanobody, and verify its effect on promoting T cells to kill tumor cells. METHODS: Based on the camel derived natural nanobody phage display library constructed by the research group, the biotinylated LAG3 antigen was used as the target, and the anti-LAG3 nanobody sequences were screened by biotin-streptavidin liquid phase screening, phage-ELISA and sequencing. The sequence-conjµgated human IgG1 Fc fragment was obtained, the recombinant anti-LAG3 nanobody expression vector was constructed, the expression of the recombinant anti-LAG3 nanobody was induced by IPTG and purified, and the characteristics and functions of the recombinant anti-LAG3 nanobody were verified by SDS-PAGE, Western blot, cytotoxicity assay, etc. RESULTS: One anti-LAG3 nanobody sequence was successfully screened, and the corresponding recombinant anti-LAG3 nanobody-expressing bacteria were constructed. The results of SDS-PAGE, Western blot and cytotoxicity assay showed that the recombinant anti-LAG3 nanobody was successfully expressed, which was specific, and it could promote the killing ability of T cells against tumor cells, and the optimal concentration was 200 µg/mL. CONCLUSION: The recombinant anti-LAG3 nanobody screened and expressed has specific and auxiliary anti-tumor cell effects, which lays a foundation for its subsequent application.


Subject(s)
Lymphocyte Activation Gene 3 Protein , Single-Domain Antibodies , Single-Domain Antibodies/genetics , Single-Domain Antibodies/immunology , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/biosynthesis , Single-Domain Antibodies/pharmacology , Humans , Antigens, CD/genetics , Antigens, CD/immunology , Antigens, CD/metabolism , Antigens, CD/biosynthesis , Recombinant Proteins/genetics , Recombinant Proteins/biosynthesis , Recombinant Proteins/immunology , Recombinant Proteins/chemistry , Animals , Peptide Library , Camelus/immunology , Camelus/genetics , Cell Line, Tumor , Escherichia coli/genetics , T-Lymphocytes/immunology , Gene Expression
10.
Food Chem ; 455: 139684, 2024 Oct 15.
Article in English | MEDLINE | ID: mdl-38833869

ABSTRACT

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 109 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 R2 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.


Subject(s)
Coumaphos , Single-Domain Antibodies , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/immunology , Single-Domain Antibodies/genetics , Coumaphos/chemistry , Coumaphos/immunology , Enzyme-Linked Immunosorbent Assay , Tandem Mass Spectrometry , Food Contamination/analysis , Peptide Library
11.
Protein Expr Purif ; 221: 106501, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38782081

ABSTRACT

Nanobodies are single-variable domain antibodies with excellent properties, which are evolving as versatile tools to guide cognate antigens in vitro and in vivo for biological research, diagnosis, and treatment. Given their simple structure, nanobodies are readily produced in multiple systems. However, selecting an appropriate expression system is crucial because different conditions might cause proteins to produce different folds or post-translational modifications (PTMs), and these differences often result in different functions. At present, the strategies of PTMs are rarely reported. The GFP nanobody can specifically target the GFP protein. Here, we engineered a GFP nanobody fused with 6 × His tag and Fc tag, respectively, and expressed in bacteria and mammalian cells. The 6 × His-GFP-nanobody was produced from Escherichia coli at high yields and the pull-down assay indicated that it can precipitate the GFP protein. Meanwhile, the Fc-GFP-nanobody can be expressed in HEK293T cells, and the co-immunoprecipitation experiment can trace and target the GFP-tagged protein in vivo. Furthermore, some different PTMs in antigen-binding regions have been identified after using mass spectrometry (MS) to analyze the GFP nanobodies, which are expressed in prokaryotes and eukaryotes. In this study, a GFP nanobody was designed, and its binding ability was verified by using the eukaryotic and prokaryotic protein expression systems. In addition, this GFP nanobody was transformed into a useful instrument for more in-depth functional investigations of GFP fusion proteins. MS was further used to explore the reason for the difference in binding ability, providing a novel perspective for the study of GFP nanobodies and protein expression purification.


Subject(s)
Escherichia coli , Green Fluorescent Proteins , Protein Processing, Post-Translational , Recombinant Fusion Proteins , Single-Domain Antibodies , Humans , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Green Fluorescent Proteins/chemistry , Single-Domain Antibodies/genetics , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/biosynthesis , Single-Domain Antibodies/isolation & purification , Single-Domain Antibodies/immunology , HEK293 Cells , Escherichia coli/genetics , Escherichia coli/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/isolation & purification , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/biosynthesis , Protein Engineering/methods , Gene Expression
12.
Int J Mol Sci ; 25(9)2024 Apr 27.
Article in English | MEDLINE | ID: mdl-38732011

ABSTRACT

Immunoglobulin G-based monoclonal antibodies (mAbs) have been effective in treating various diseases, but their large molecular size can limit their penetration of tissue and efficacy in multifactorial diseases, necessitating the exploration of alternative forms. In this study, we constructed a phage display library comprising single-domain antibodies (sdAbs; or "VHHs"), known for their small size and remarkable stability, using a total of 1.6 × 109 lymphocytes collected from 20 different alpacas, resulting in approximately 7.16 × 1010 colonies. To assess the quality of the constructed library, next-generation sequencing-based high-throughput profiling was performed, analyzing approximately 5.65 × 106 full-length VHH sequences, revealing 92% uniqueness and confirming the library's diverse composition. Systematic characterization of the library revealed multiple sdAbs with high affinity for three therapeutically relevant antigens. In conclusion, our alpaca sdAb phage display library provides a versatile resource for diagnostics and therapeutics. Furthermore, the library's vast natural VHH antibody repertoire offers insights for generating humanized synthetic sdAb libraries, further advancing sdAb-based therapeutics.


Subject(s)
Camelids, New World , Peptide Library , Single-Domain Antibodies , Single-Domain Antibodies/genetics , Single-Domain Antibodies/immunology , Single-Domain Antibodies/chemistry , Animals , Camelids, New World/immunology , High-Throughput Nucleotide Sequencing , Humans , Antibodies, Monoclonal/immunology , Antibodies, Monoclonal/genetics , High-Throughput Screening Assays/methods , Antibody Affinity , Cell Surface Display Techniques/methods
13.
Antiviral Res ; 226: 105898, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38692413

ABSTRACT

SARS-CoV-2 continues to threaten human health, antibody therapy is one way to control the infection. Because new SARS-CoV-2 mutations are constantly emerging, there is an urgent need to develop broadly neutralizing antibodies to block the viral entry into host cells. VNAR from sharks is the smallest natural antigen binding domain, with the advantages of small size, flexible paratopes, good stability, and low manufacturing cost. Here, we used recombinant SARS-CoV-2 Spike-RBD to immunize sharks and constructed a VNAR phage display library. VNAR R1C2, selected from the library, efficiently binds to the RBD domain and blocks the infection of ACE2-positive cells by pseudovirus. Next, homologous bivalent VNARs were constructed through the tandem fusion of two R1C2 units, which enhanced both the affinity and neutralizing activity of R1C2. R1C2 was predicted to bind to a relatively conserved region within the RBD. By introducing mutations at four key binding sites within the CDR3 and HV2 regions of R1C2, the affinity and neutralizing activity of R1C2 were significantly improved. Furthermore, R1C2 also exhibits an effective capacity of binding to the Omicron variants (BA.2 and XBB.1). Together, these results suggest that R1C2 could serve as a valuable candidate for preventing and treating SARS-CoV-2 infections.


Subject(s)
Antibodies, Neutralizing , Antibodies, Viral , COVID-19 , SARS-CoV-2 , Sharks , Single-Domain Antibodies , Spike Glycoprotein, Coronavirus , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/genetics , Animals , SARS-CoV-2/immunology , Single-Domain Antibodies/immunology , Single-Domain Antibodies/genetics , Humans , Sharks/immunology , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/immunology , COVID-19/virology , Binding Sites , Protein Binding , Peptide Library , HEK293 Cells , Mutation
14.
J Agric Food Chem ; 72(19): 10753-10771, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38706131

ABSTRACT

Food-borne biotoxins from microbes, plants, or animals contaminate unclean, spoiled, and rotten foods, posing significant health risks. Neutralizing such toxins is vital for human health, especially after food poisoning. Nanobodies (Nbs), a type of single-domain antibodies derived from the genetic cloning of a variable domain of heavy chain antibodies (VHHs) in camels, offer unique advantages in toxin neutralization. Their small size, high stability, and precise binding enable effective neutralization. The use of Nbs in neutralizing food-borne biotoxins offers numerous benefits, and their genetic malleability allows tailored optimization for diverse toxins. As nanotechnology continues to evolve and improve, Nbs are poised to become increasingly efficient and safer tools for toxin neutralization, playing a pivotal role in safeguarding human health and environmental safety. This review not only highlights the efficacy of these agents in neutralizing toxins but also proposes innovative solutions to address their current challenges. It lays a solid foundation for their further development in this crucial field and propels their commercial application, thereby contributing significantly to advancements in this domain.


Subject(s)
Single-Domain Antibodies , Animals , Single-Domain Antibodies/immunology , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/genetics , Humans , Food Contamination/analysis , Food Contamination/prevention & control , Antibodies, Neutralizing/immunology , Toxins, Biological/immunology , Foodborne Diseases/prevention & control , Foodborne Diseases/immunology , Camelus/immunology
15.
Signal Transduct Target Ther ; 9(1): 131, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38740785

ABSTRACT

Almost all the neutralizing antibodies targeting the receptor-binding domain (RBD) of spike (S) protein show weakened or lost efficacy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged or emerging variants, such as Omicron and its sub-variants. This suggests that highly conserved epitopes are crucial for the development of neutralizing antibodies. Here, we present one nanobody, N235, displaying broad neutralization against the SARS-CoV-2 prototype and multiple variants, including the newly emerged Omicron and its sub-variants. Cryo-electron microscopy demonstrates N235 binds a novel, conserved, cryptic epitope in the N-terminal domain (NTD) of the S protein, which interferes with the RBD in the neighboring S protein. The neutralization mechanism interpreted via flow cytometry and Western blot shows that N235 appears to induce the S1 subunit shedding from the trimeric S complex. Furthermore, a nano-IgM construct (MN235), engineered by fusing N235 with the human IgM Fc region, displays prevention via inducing S1 shedding and cross-linking virus particles. Compared to N235, MN235 exhibits varied enhancement in neutralization against pseudotyped and authentic viruses in vitro. The intranasal administration of MN235 in low doses can effectively prevent the infection of Omicron sub-variant BA.1 and XBB in vivo, suggesting that it can be developed as a promising prophylactic antibody to cope with the ongoing and future infection.


Subject(s)
Antibodies, Neutralizing , Antibodies, Viral , COVID-19 , Epitopes , Immunoglobulin M , SARS-CoV-2 , Single-Domain Antibodies , Spike Glycoprotein, Coronavirus , SARS-CoV-2/immunology , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/chemistry , Humans , Single-Domain Antibodies/immunology , Single-Domain Antibodies/genetics , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/pharmacology , Epitopes/immunology , Epitopes/genetics , Epitopes/chemistry , Animals , COVID-19/immunology , COVID-19/virology , Antibodies, Viral/immunology , Antibodies, Viral/chemistry , Antibodies, Neutralizing/immunology , Antibodies, Neutralizing/chemistry , Antibodies, Neutralizing/genetics , Immunoglobulin M/immunology , Immunoglobulin M/genetics , Mice , Protein Domains , Cryoelectron Microscopy
16.
J Med Virol ; 96(6): e29692, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38804172

ABSTRACT

To achieve a virological cure for hepatitis B virus (HBV), innovative strategies are required to target the covalently closed circular DNA (cccDNA) genome. Guanine-quadruplexes (G4s) are a secondary structure that can be adopted by DNA and play a significant role in regulating viral replication, transcription, and translation. Antibody-based probes and small molecules have been developed to study the role of G4s in the context of the human genome, but none have been specifically made to target G4s in viral infection. Herein, we describe the development of a humanized single-domain antibody (S10) that can target a G4 located in the PreCore (PreC) promoter of the HBV cccDNA genome. MicroScale Thermophoresis demonstrated that S10 has a strong nanomolar affinity to the PreC G4 in its quadruplex form and a structural electron density envelope of the complex was determined using Small-Angle X-ray Scattering. Lentiviral transduction of S10 into HepG2-NTCP cells shows nuclear localization, and chromatin immunoprecipitation coupled with next-generation sequencing demonstrated that S10 can bind to the HBV PreC G4 present on the cccDNA. This research validates the existence of a G4 in HBV cccDNA and demonstrates that this DNA secondary structure can be targeted with high structural and sequence specificity using S10.


Subject(s)
DNA, Circular , DNA, Viral , G-Quadruplexes , Hepatitis B virus , Single-Domain Antibodies , Humans , Hepatitis B virus/genetics , Hepatitis B virus/immunology , DNA, Circular/genetics , DNA, Viral/genetics , Hep G2 Cells , Single-Domain Antibodies/genetics , Single-Domain Antibodies/immunology , Single-Domain Antibodies/chemistry , Genome, Viral , Promoter Regions, Genetic , Virus Replication , Hepatitis B/virology
17.
Virol Sin ; 39(3): 478-489, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38588947

ABSTRACT

African swine fever virus (ASFV) poses a significant threat to the global swine industry. Currently, there are no effective vaccines or treatments available to combat ASFV infection in pigs. The primary means of controlling the spread of the disease is through rapid detection and subsequent elimination of infected pig. Recently, a lower virulent ASFV isolate with a deleted EP402R gene (CD2v-deleted) has been reported in China, which further complicates the control of ASFV infection in pig farms. Furthermore, an EP402R-deleted ASFV variant has been developed as a potential live attenuated vaccine candidate strain. Therefore, it is crucial to develop detection methods that can distinguish wild-type and EP402R-deleted ASFV infections. In this study, two recombinant ASFV-p72 and -CD2v proteins were expressed using a prokaryotic system and used to immunize Bactrian camels. Subsequently, eight nanobodies against ASFV-p72 and ten nanobodies against ASFV-CD2v were screened. Following the production of these nanobodies with horse radish peroxidase (HRP) fusion proteins, the ASFV-p72-Nb2-HRP and ASFV-CD2v-Nb22-HRP fusions were selected for the development of two competitive ELISAs (cELISAs) to detect anti-ASFV antibodies. The two cELISAs exhibited high sensitivity, good specificity, repeatability, and stability. The coincidence rate between the two cELISAs and commercial ELISA kits was 98.6% and 97.6%, respectively. Collectively, the two cELISA for detecting antibodies against ASFV demonstrated ease of operation, a low cost, and a simple production process. The two cELISAs could determine whether pigs were infected with wild-type or CD2v-deleted ASFV, and could play an important role in monitoring ASFV infections in pig farms.


Subject(s)
African Swine Fever Virus , African Swine Fever , Antibodies, Viral , Enzyme-Linked Immunosorbent Assay , Single-Domain Antibodies , African Swine Fever Virus/immunology , African Swine Fever Virus/genetics , Animals , Swine , African Swine Fever/diagnosis , African Swine Fever/immunology , African Swine Fever/virology , Antibodies, Viral/immunology , Enzyme-Linked Immunosorbent Assay/methods , Single-Domain Antibodies/immunology , Single-Domain Antibodies/genetics , Camelus , Sensitivity and Specificity , China , Capsid Proteins/immunology , Capsid Proteins/genetics , Viral Proteins/immunology , Viral Proteins/genetics
18.
Mol Ther ; 32(6): 1687-1700, 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38582966

ABSTRACT

Deep-learning-based methods for protein structure prediction have achieved unprecedented accuracy, yet their utility in the engineering of protein-based binders remains constrained due to a gap between the ability to predict the structures of candidate proteins and the ability toprioritize proteins by their potential to bind to a target. To bridge this gap, we introduce Automated Pairwise Peptide-Receptor Analysis for Screening Engineered proteins (APPRAISE), a method for predicting the target-binding propensity of engineered proteins. After generating structural models of engineered proteins competing for binding to a target using an established structure prediction tool such as AlphaFold-Multimer or ESMFold, APPRAISE performs a rapid (under 1 CPU second per model) scoring analysis that takes into account biophysical and geometrical constraints. As proof-of-concept cases, we demonstrate that APPRAISE can accurately classify receptor-dependent vs. receptor-independent adeno-associated viral vectors and diverse classes of engineered proteins such as miniproteins targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike, nanobodies targeting a G-protein-coupled receptor, and peptides that specifically bind to transferrin receptor or programmed death-ligand 1 (PD-L1). APPRAISE is accessible through a web-based notebook interface using Google Colaboratory (https://tiny.cc/APPRAISE). With its accuracy, interpretability, and generalizability, APPRAISE promises to expand the utility of protein structure prediction and accelerate protein engineering for biomedical applications.


Subject(s)
Protein Binding , Protein Engineering , SARS-CoV-2 , Protein Engineering/methods , Humans , SARS-CoV-2/metabolism , SARS-CoV-2/genetics , Models, Molecular , Spike Glycoprotein, Coronavirus/metabolism , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/chemistry , Protein Conformation , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/genetics , Single-Domain Antibodies/metabolism , Deep Learning , COVID-19/virology , B7-H1 Antigen/metabolism , B7-H1 Antigen/genetics , B7-H1 Antigen/chemistry , Dependovirus/genetics , Genetic Vectors/chemistry , Genetic Vectors/genetics , Genetic Vectors/metabolism
19.
Protein Expr Purif ; 219: 106485, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38642863

ABSTRACT

BACKGROUND: Rational design of synthetic phage-displayed libraries requires the identification of the most appropriate positions for randomization using defined amino acid sets to recapitulate the natural occurrence. The present study uses position-specific scoring matrixes (PSSMs) for identifying and randomizing Camelidae nanobody (VHH) CDR3. The functionality of a synthetic VHH repertoire designed by this method was tested for discovering new VHH binders to recombinant coagulation factor VII (rfVII). METHODS: Based on PSSM analysis, the CDR3 of cAbBCII10 VHH framework was identified, and a set of amino acids for the substitution of each PSSM-CDR3 position was defined. Using the Rosetta design SwiftLib tool, the final repertoire was back-translated to a degenerate nucleotide sequence. A synthetic phage-displayed library was constructed based on this repertoire and screened for anti-rfVII binders. RESULTS: A synthetic phage-displayed VHH library with 1 × 108 variants was constructed. Three VHH binders to rfVII were isolated from this library with estimated dissociation constants (KD) of 1 × 10-8 M, 5.8 × 10-8 M and 2.6 × 10-7 M. CONCLUSION: PSSM analysis is a simple and efficient way to design synthetic phage-displayed libraries.


Subject(s)
Computational Biology , Peptide Library , Single-Domain Antibodies , Single-Domain Antibodies/genetics , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/immunology , Animals , Camelidae/genetics , Camelidae/immunology , Factor VII/genetics , Factor VII/chemistry , Factor VII/immunology , Recombinant Proteins/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/immunology , Amino Acid Sequence
20.
Microb Cell Fact ; 23(1): 124, 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38689251

ABSTRACT

BACKGROUND: Having a simple and fast dividing organism capable of producing and exposing at its surface or secreting functional complex biomolecules with disulphide bridges is of great interest. The mycoplasma bacterial genus offers a set of relevant properties that make it an interesting chassis for such purposes, the main one being the absence of a cell wall. However, due to their slow growth, they have rarely been considered as a potential platform in this respect. This notion may be challenged with the recent discovery of Mycoplasma feriruminatoris, a species with a dividing time close to that of common microbial workhorses. So far, no tools for heterologous protein expression nor secretion have been described for it. RESULTS: The work presented here develops the fast-dividing M. feriruminatoris as a tool for secreting functional biomolecules of therapeutic interest that could be used for screening functional mutants as well as potentially for protein-protein interactions. Based on RNAseq, quantitative proteomics and promoter sequence comparison we have rationally designed optimal promoter sequences. Then, using in silico analysis, we have identified putative secretion signals that we validated using a luminescent reporter. The potential of the resulting secretion cassette has been shown with set of active clinically relevant proteins (interleukins and nanobodies). CONCLUSIONS: We have engineered Mycoplasma feriruminatoris for producing and secreting functional proteins of medical interest.


Subject(s)
Bacterial Proteins , Mycoplasma , Mycoplasma/metabolism , Mycoplasma/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Promoter Regions, Genetic , Proteomics , Single-Domain Antibodies/metabolism , Single-Domain Antibodies/genetics
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