Isolation of monomeric human V(H)s by a phage selection

A single-domain antibody library based on a stability-engineered human VH3 scaffold

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.

Sequence tolerance of immunoglobulin variable domain framework regions to noncanonical intradomain disulfide linkages

Most immunoglobulin (Ig) domains bear only a single highly conserved canonical intradomain, inter-β-sheet disulfide linkage formed between Cys23-Cys104, and incorporation of rare noncanonical disulfide linkages at other locations can enhance Ig domain stability. Here, we exhaustively surveyed the sequence tolerance of Ig variable (V) domain framework regions (FRs) to noncanonical disulfide linkages. Starting from a destabilized VH domain lacking a Cys23-Cys104 disulfide linkage, we generated and screened phage-displayed libraries of engineered VHs, bearing all possible pairwise combinations of Cys residues in neighboring β-strands of the Ig fold FRs. This approach identified seven novel Cys pairs in VH FRs (Cys4-Cys25, Cys4-Cys118, Cys5-Cys120, Cys6-Cys119, Cys22-Cys88, Cys24-Cys86, and Cys45-Cys100; the international ImMunoGeneTics information system numbering), whose presence rescued domain folding and stability. Introduction of a subset of these noncanonical disulfide linkages (three intra-β-sheet: Cys4-Cys25, Cys22-Cys88, and Cys24-Cys86, and one inter-β-sheet: Cys6-Cys119) into a diverse panel of VH, VL, and VHH domains enhanced their thermostability and protease resistance without significantly impacting expression, solubility, or binding to cognate antigens. None of the noncanonical disulfide linkages identified were present in the natural human VH repertoire. These data reveal an unexpected permissiveness of Ig V domains to noncanonical disulfide linkages at diverse locations in FRs, absent in the human repertoire, whose presence is compatible with antigen recognition and improves domain stability. Our work represents the most complete assessment to date of the role of engineered noncanonical disulfide bonding within FRs in Ig V domain structure and function.

Increased migration and motility in XIAP-null cells mediated by the C-RAF protein kinase

The product encoded by the X-linked inhibitor of apoptosis (XIAP) gene is a multi-functional protein which not only controls caspase-dependent cell death, but also participates in inflammatory signalling, copper homeostasis, response to hypoxia and control of cell migration. Deregulation of XIAP, either by elevated expression or inherited genetic deletion, is associated with several human disease states. Reconciling XIAP-dependent signalling pathways with its role in disease progression is essential to understand how XIAP promotes the progression of human pathologies. In this study we have created a panel of genetically modified XIAP-null cell lines using TALENs and CRISPR/Cas9 to investigate the functional outcome of XIAP deletion. Surprisingly, in our genetically modified cells XIAP deletion had no effect on programmed cell death, but instead the primary phenotype we observed was a profound increase in cell migration rates. Furthermore, we found that XIAP-dependent suppression of cell migration was dependent on XIAPdependent control of C-RAF levels, a protein kinase which controls cell signalling pathways that regulate the cytoskeleton. These results suggest that XIAP is not necessary for control of the apoptotic signalling cascade, however it does have a critical role in controlling cell migration and motility that cannot be compensated for in XIAP-knockout cells.

Structure- and sequence-based design of synthetic single-domain antibody libraries

Single-domain antibody fragments known as VHH have emerged in the pharmaceutical industry as useful biotherapeutics. These molecules, which are naturally produced by camelids, share the characteristics of high affinity and specificity with traditional human immunoglobulins, while consisting of only a single heavy chain. Currently, the most common method for generating VHH is via animal immunization, which can be costly and time-consuming. Here we describe the development of a synthetic VHH library for in vitro selection of single domain binders. We combine structure-based design and next-generation sequencing analysis to build a library with characteristics that closely mimic the natural repertoire. To validate the performance of our synthetic library, we isolated VHH against three model antigens (soluble mouse PD-1 ectodomain, amyloid-β peptide, and MrgX1 GPCR) of different sizes and characteristics. We were able to isolate diverse binders targeting different epitopes with high affinity (as high as 5 nM) against all three targets. We then show that anti-mPD-1 binders have functional activity in a receptor blocking assay.

Evaluation of a noncanonical Cys40-Cys55 disulfide linkage for stabilization of single-domain antibodies

Incorporation of noncanonical disulfide linkages into single-domain antibodies (sdAbs) has been shown to enhance thermostability and other properties. Here, we evaluated the effects of introducing a novel disulfide linkage formed between Cys residues at IMGT positions 40 and 55 on the melting temperatures (T _m s), reversibility of thermal unfolding, solubility, and antigen-binding affinities of three types of sdAbs (V_H H, V_H , and V_L domains). The Cys40-Cys55 disulfide linkage was tolerated by 9/9 V_H Hs, 12/12 V_H s, and 2/11 V_L s tested and its formation was confirmed by mass spectrometry. Using circular dichroism, we found that the Cys40-Cys55 disulfide linkage increased sdAb T _m by an average of 10.0°C (range: 0-21.8°C). However, enhanced thermostability came at the cost of a partial loss of refolding ability upon thermal denaturation as well as, for some sdAbs, significantly decreased solubility and antigen-binding affinity. Thus, Cys40/Cys55 can be added to the panel of known locations for introducing stabilizing noncanonical disulfide linkages into antibody variable domains, although its effects should be tested empirically for individual sdAbs.

Physicochemical improvement of rabbit derived single-domain antibodies by substitutions with amino acids conserved in camelid antibodies

Recently, we showed that immunized rabbit heavy chain variable regions (rVHs) can have strong antigen binding activity comparable to that of the camelid variable domain of the heavy chain of heavy chain antibody (VHH). These rVHs lack the light chain variable regions (rVLs), which exist in the authentic Fab format; thus, molecular surfaces at the interface region of rVHs are exposed to solvent. This physical feature may change physicochemical properties, such as causing reduced stability. By overcoming potential physicochemical issues through engineering the interface region, rVHs could become more useful as single-domain antibodies. In this study, we substituted amino acid residues conserved at the interface region of rVHs with those of VHHs. These substitutions included V37F, involving substitution of a residue in the hydrophobic core with a bulkier hydrophobic amino acid, and G44E/L45R, involving double substitutions of highly exposed residues with more hydrophilic ones. As expected, biophysical and structural characterizations showed that the V37F substitution markedly enhanced the thermal stability through increased hydrophobic packing, while G44E/L45R substitutions greatly reduced hydrophobicity of the interface. The quadruple substitutions of V37F/G44E/L45R/F91Y resulted in not only enhancements of thermal stability and reduction in hydrophobicity, both in an additive manner, but also synergistic improvement of purification yield. This quadruple mutant exhibited greatly reduced non-specific binding with improved colloidal stability owing to the reduced hydrophobicity. The approach used in this study should further enhance the utility of rVHs and promote research and development of single-domain antibodies.

Stability-Diversity Tradeoffs Impose Fundamental Constraints on Selection of Synthetic Human VH/VL Single-Domain Antibodies from In Vitro Display Libraries

Human autonomous V_H/V_L single-domain antibodies (sdAbs) are attractive therapeutic molecules, but often suffer from suboptimal stability, solubility and affinity for cognate antigens. Most commonly, human sdAbs have been isolated from in vitro display libraries constructed via synthetic randomization of rearranged V_H/V_L domains. Here, we describe the design and characterization of three novel human V_H/V_L sdAb libraries through a process of: (i) exhaustive biophysical characterization of 20 potential V_H/V_L sdAb library scaffolds, including assessment of expression yield, aggregation resistance, thermostability and tolerance to complementarity-determining region (CDR) substitutions; (ii) in vitro randomization of the CDRs of three V_H/V_L sdAb scaffolds, with tailored amino acid representation designed to promote solubility and expressibility; and (iii) systematic benchmarking of the three V_H/V_L libraries by panning against five model antigens. We isolated ≥1 antigen-specific human sdAb against four of five targets (13 V_Hs and 7 V_Ls in total); these were predominantly monomeric, had antigen-binding affinities ranging from 5 nM to 12 µM (average: 2–3 µM), but had highly variable expression yields (range: 0.1–19 mg/L). Despite our efforts to identify the most stable V_H/V_L scaffolds, selection of antigen-specific binders from these libraries was unpredictable (overall success rate for all library-target screens: ~53%) with a high attrition rate of sdAbs exhibiting false positive binding by ELISA. By analyzing V_H/V_L sdAb library sequence composition following selection for monomeric antibody expression (binding to protein A/L followed by amplification in bacterial cells), we found that some V_H/V_L sdAbs had marked growth advantages over others, and that the amino acid composition of the CDRs of this set of sdAbs was dramatically restricted (bias toward Asp and His and away from aromatic and hydrophobic residues). Thus, CDR sequence clearly dramatically impacts the stability of human autonomous V_H/V_L immunoglobulin domain folds, and sequence-stability tradeoffs must be taken into account during the design of such libraries.

A Novel Affinity Tag, ABTAG, and Its Application to the Affinity Screening of Single-Domain Antibodies Selected by Phage Display

ABTAG is a camelid single-domain antibody (sdAb) that binds to bovine serum albumin (BSA) with low picomolar affinity. In surface plasmon resonance (SPR) analyses using BSA surfaces, bound ABTAG can be completely dissociated from the BSA surfaces at low pH, over multiple cycles, without any reduction in the capacity of the BSA surfaces to bind ABTAG. A moderate throughput, SPR-based, antibody screening assay exploiting the unique features of ABTAG is described. Anti-carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) sdAbs were isolated from a phage-displayed sdAb library derived from the heavy chain antibody repertoire of a llama immunized with CEACAM6. Following one or two rounds of panning, enriched clones were expressed as ABTAG fusions in microtiter plate cultures. The sdAb-ABTAG fusions from culture supernatants were captured on BSA surfaces and CEACAM6 antigen was then bound to the captured molecules. The SPR screening method gives a read-out of relative expression levels of the fusion proteins and kinetic and affinity constants for CEACAM6 binding by the captured molecules. The library was also panned and screened by conventional methods and positive clones were subcloned and expressed for SPR analysis. Compared to conventional panning and screening, the SPR-based ABTAG method yielded a considerably higher diversity of binders, some with affinities that were three orders of magnitude higher affinity than those identified by conventional panning.

A Rational Engineering Strategy for Designing Protein A-Binding Camelid Single-Domain Antibodies

Staphylococcal protein A (SpA) and streptococcal protein G (SpG) affinity chromatography are the gold standards for purifying monoclonal antibodies (mAbs) in therapeutic applications. However, camelid VHH single-domain Abs (sdAbs or VHHs) are not bound by SpG and only sporadically bound by SpA. Currently, VHHs require affinity tag-based purification, which limits their therapeutic potential and adds considerable complexity and cost to their production. Here we describe a simple and rapid mutagenesis-based approach designed to confer SpA binding upon a priori non-SpA-binding VHHs. We show that SpA binding of VHHs is determined primarily by the same set of residues as in human mAbs, albeit with an unexpected degree of tolerance to substitutions at certain core and non-core positions and some limited dependence on at least one residue outside the SpA interface, and that SpA binding could be successfully introduced into five VHHs against three different targets with no adverse effects on expression yield or antigen binding. Next-generation sequencing of llama, alpaca and dromedary VHH repertoires suggested that species differences in SpA binding may result from frequency variation in specific deleterious polymorphisms, especially Ile57. Thus, the SpA binding phenotype of camelid VHHs can be easily modulated to take advantage of tag-less purification techniques, although the frequency with which this is required may depend on the source species.

An update on antibody-based immunotherapies for Clostridium difficile infection

Clostridium difficile continues to be one of the most prevalent hospital-acquired bacterial infections in the developed world, despite the recent introduction of a novel and effective antibiotic agent (fidaxomicin). Alternative approaches under investigation to combat the anaerobic Gram-positive bacteria include fecal transplantation therapy, vaccines, and antibody-based immunotherapies. In this review, we catalog the recent advances in antibody-based approaches under development and in the clinic for the treatment of C. difficile infection. By and large, inhibitory antibodies that recognize the primary C. difficile virulence factors, toxin A and toxin B, are the most popular passive immunotherapies under investigation. We provide a detailed summary of the toxin epitopes recognized by various antitoxin antibodies and discuss general trends on toxin inhibition efficacy. In addition, antibodies to other C. difficile targets, such as surface-layer proteins, binary toxin, motility factors, and adherence and colonization factors, are introduced in this review.

(99m) Tc-labeled tetramer and pentamer of single-domain antibody for targeting epidermal growth factor receptor in xenografted tumors

The single-domain antibody EG2 can be fused with right-handed coiled-coil (RHCC) and human cartilage oligomeric matrix protein (COMP), to form the multivalent antibodies EG2-RHCC and EG2-COMP. We labeled these two antibodies with (99m) Tc and assessed their targeting efficiency for epidermal growth factor receptor (EGFR). Cell binding, uptake, efflux, and blocking studies were performed with EGFR high- and/or low-expressing cells with (99m) Tc-labeled EG2-RHCC or EG2-COMP. Single photon-emission computed tomography (SPECT) imaging and biodistribution studies were further carried out. Both (99m) Tc-EG2-RHCC and (99m) Tc-EG2-COMP can specially bind to EGFR in vitro. SPECT imaging showed that A431, which expresses high levels of EGFR, was clearly visible 6 h after (99m) Tc-EG2-COMP injection; however, it was not detectable after administration of (99m) Tc-EG2-RHCC. Uptake of both antibodies by the non-EGFR-secreting OCM-1 tumors was low. EG2-COMP shows promise in identifying EGFR over-expression in tumors; however, EG2-RHCC may not be suitable for targeting EGFR in vivo.

Targeting surface-layer proteins with single-domain antibodies: a potential therapeutic approach against Clostridium difficile-associated disease

Clostridium difficile is a leading cause of death from gastrointestinal infections in North America. Antibiotic therapy is effective, but the high incidence of relapse and the rise in hypervirulent strains warrant the search for novel treatments. Surface layer proteins (SLPs) cover the entire C. difficile bacterial surface, are composed of high-molecular-weight (HMW) and low-molecular-weight (LMW) subunits, and mediate adherence to host cells. Passive and active immunization against SLPs has enhanced hamster survival, suggesting that antibody-mediated neutralization may be an effective therapeutic strategy. Here, we isolated a panel of SLP-specific single-domain antibodies (V_HHs) using an immune llama phage display library and SLPs isolated from C. difficile hypervirulent strain QCD-32g58 (027 ribotype) as a target antigen. Binding studies revealed a number of V_HHs that bound QCD-32g58 SLPs with high affinity (K_D = 3–6 nM) and targeted epitopes located on the LMW subunit of the SLP. The V_HHs demonstrated melting temperatures as high as 75 °C, and a few were resistant to the gastrointestinal protease pepsin at physiologically relevant concentrations. In addition, we demonstrated the binding specificity of the V_HHs to the major C. difficile ribotypes by whole cell ELISA, where all V_HHs were found to bind 001 and 027 ribotypes, and a subset of antibodies were found to be broadly cross-reactive in binding cells representative of 012, 017, 023, and 078 ribotypes. Finally, we showed that several of the V_HHs inhibited C. difficile QCD-32g58 motility in vitro. Targeting SLPs with V_HHs may be a viable therapeutic approach against C. difficile-associated disease.

Antibody light chain variable domains and their biophysically improved versions for human immunotherapy

We set out to gain deeper insight into the potential of antibody light chain variable domains (V_Ls) as immunotherapeutics. To this end, we generated a naïve human V_L phage display library and, by using a method previously shown to select for non-aggregating antibody heavy chain variable domains (V_Hs), we isolated a diversity of V_L domains by panning the library against B cell super-antigen protein L. Eight domains representing different germline origins were shown to be non-aggregating at concentrations as high as 450 µM, indicating V_L repertoires are a rich source of non-aggregating domains. In addition, the V_Ls demonstrated high expression yields in E. coli, protein L binding and high reversibility of thermal unfolding. A side-by-side comparison with a set of non-aggregating human V_Hs revealed that the V_Ls had similar overall profiles with respect to melting temperature (T_m), reversibility of thermal unfolding and resistance to gastrointestinal proteases. Successful engineering of a non-canonical disulfide linkage in the core of V_Ls did not compromise the non-aggregation state or protein L binding properties. Furthermore, the introduced disulfide bond significantly increased their T_ms, by 5.5–17.5 °C, and pepsin resistance, although it somewhat reduced expression yields and subtly changed the structure of V_Ls. Human V_Ls and engineered versions may make suitable therapeutics due to their desirable biophysical features. The disulfide linkage-engineered V_Ls may be the preferred therapeutic format because of their higher stability, especially for oral therapy applications that necessitate high resistance to the stomach’s acidic pH and pepsin.

Human recombinant domain antibodies against multiple sclerosis antigenic peptide CSF114(Glc)

Multiple sclerosis (MS) is a chronic auto-immune disease characterized by a damage to the myelin component of the central nervous system. Self-antigens created by aberrant glycosylation have been described to be a key component in the formation of auto-antibodies. CSF114(Glc) is a synthetic glucopeptide detecting in vitro MS-specific auto-antibodies, and it is actively used in diagnostics and research to monitor and quantify MS-associated Ig levels. We reasoned that antibodies raised against this probe could have been relevant for MS. We therefore screened a human Domain Antibody library against CSF114(Glc) using magnetic separation as a panning method. We obtained and described several clones, and the one with the highest signals was produced as a 6×His-tagged protein to properly study the binding properties as a soluble antibody. By surface plasmon resonance measurements, we evidenced that our clone recognized CSF114(Glc) with high affinity and specific for the glucosylated peptide. Kinetic parameters of peptide-clone interaction were calculated obtaining a value of KD in the nanomolar range. Harboring a human framework, this antibody should be very well tolerated by human immune system and may represent a valuable tool for MS diagnosis and therapy, paving the way to new research strategies.

Directed evolution of human heavy chain variable domain (VH) using in vivo protein fitness filter

Human immunoglobulin heavy chain variable domains (VH) are promising scaffolds for antigen binding. However, VH is an unstable and aggregation-prone protein, hindering its use for therapeutic purposes. To evolve the VH domain, we performed in vivo protein solubility selection that linked antibiotic resistance to the protein folding quality control mechanism of the twin-arginine translocation pathway of E. coli. After screening a human germ-line VH library, 95% of the VH proteins obtained were identified as VH3 family members; one VH protein, MG2x1, stood out among separate clones expressing individual VH variants. With further screening of combinatorial framework mutation library of MG2x1, we found a consistent bias toward substitution with tryptophan at the position of 50 and 58 in VH. Comparison of the crystal structures of the VH variants revealed that those substitutions with bulky side chain amino acids filled the cavity in the VH interface between heavy and light chains of the Fab arrangement along with the increased number of hydrogen bonds, decreased solvation energy, and increased negative charge. Accordingly, the engineered VH acquires an increased level of thermodynamic stability, reversible folding, and soluble expression. The library built with the VH variant as a scaffold was qualified as most of VH clones selected randomly were expressed as soluble form in E. coli regardless length of the combinatorial CDR. Furthermore, a non-aggregation feature of the selected VH conferred a free of humoral response in mice, even when administered together with adjuvant. As a result, this selection provides an alternative directed evolution pathway for unstable proteins, which are distinct from conventional methods based on the phage display.

Optimal charged mutations in the complementarity-determining regions that prevent domain antibody aggregation are dependent on the antibody scaffold

Therapeutic antibodies need to be highly resistant to aggregation due to the high concentrations required for subcutaneous delivery and the potential immunogenicity of antibody aggregates. Human antibody fragments-such as single-domain antibodies (VH or VL)-are typically much less soluble than full-length antibodies. Nevertheless, some aggregation-resistant VH domains have been discovered that are negatively charged at neutral pH and/or enriched in negatively charged residues within the complementarity-determining regions (CDRs). To better understand how to engineer diverse domain antibodies to resist aggregation, we have investigated the solubilizing activity of positively and negatively charged mutations within hydrophobic CDRs of multiple VH scaffolds that differ in their net charge. We find that negatively charged mutations inserted near the edges of hydrophobic CDRs are more effective than positively charged ones at inhibiting aggregation for VH scaffolds that are negatively or near-neutrally charged. In contrast, positively charged CDR mutations prevent aggregation better than negatively charged ones for a VH scaffold that is highly positively charged. Our findings suggest that the net charge of the antibody scaffold is a key determinant of the optimal CDR mutations for preventing aggregation. We expect that our findings will improve the design of aggregation-resistant antibodies with single- and multidomain scaffolds.

Single-domain antibodies and their utility

Engineered monoclonal antibody fragments have gained market attention due to their versatility and tailor-made potential and are now considered to be an important part of future immunobiotherapeutics. Single-domain antibodies (sdAbs), also known as nanobodies, are derived from VHHs [variable domains (V) of heavy-chain-only antibodies (HCAb)] of camelid heavy-chain antibodies. These nature-made sdAbs are well suited for various applications due to their favorable characteristics such as small size, ease of genetic manipulation, high affinity and solubility, overall stability, resistance to harsh conditions (e.g., low pH, high temperature), and low immunogenicity. Most importantly, sdAbs have the feature of penetrating into cavities and recognizing hidden epitopes normally inaccessible to conventional antibodies, mainly due to their protruding CDR3/H3 loops. In this unit, we will present and discuss comprehensive and step-by-step protocols routinely practiced in our laboratory for isolating sdAbs from immunized llamas (or other members of the Camelidae family) against target antigens using phage-display technology. Expression, purification, and characterization of the isolated sdAbs will then be described, followed by presentation of several examples of applications of sdAbs previously characterized in our laboratory and elsewhere.

Design of synthetic autonomous VH domain libraries and structural analysis of a VH domain bound to vascular endothelial growth factor

We compared the capacity of an autonomous heavy chain variable (VH) domain (VH-B1a) to support diversity within its antigen-binding site relative to the conventional antigen-binding fragment (Fab) from which it was derived. We find that VH-B1a can tolerate significant diversity within all three complementarity-determining regions (CDRs) and also within framework 3, and thus, VH-B1a and the Fab are similar in terms of the regions of the antigen-binding site that can tolerate diversity without compromising stability. We constructed libraries of synthetic VH domains and isolated binders with moderate affinity for vascular endothelial growth factor (VEGF) from a library in which only CDR3 was randomized. One binder was subjected to affinity maturation to derive an autonomous VH domain (VH-V1a) that recognized both human and mouse VEGF with high affinity (KD=16nM or 10nM, respectively). Structural analysis revealed that VH-V1a binds to an epitope that is distinct from the epitopes of a natural VEGF receptor and six different anti-VEGF Fabs. Moreover, VH-V1a recognizes VEGF by using an unusual paratope consisting predominantly of CDR3 but with significant contributions from framework residues within the former light chain interface. These results suggest that VH-B1a and other autonomous VH domains may be useful scaffolds to support both conventional libraries with antigen-binding sites built from the three CDR loops and, also, nonconventional libraries with antigen-binding sites built from CDR3 and the former light chain interface.

Solubility and stability engineering of human VH domains

Solubility and stability are amongst the factors contributing to the therapeutic efficacy of biologics. Human antibody heavy chain variable domains, VHs, are one class of biologics; improving VH biophysical properties is the focus of significant protein engineering efforts. Here, we describe an efficacy engineering approach which involves the introduction of a disulfide linkage in the VH core and which improves both VH solubility and stability. More specifically, we describe protocols for generation of disulfide engineered human VHs and their characterization in terms of disulfide linkage formation, non-aggregation, and stability. Our solubility/stability engineering approach may be applied to other VHs.

Disulfide linkage engineering for improving biophysical properties of human VH domains

To enhance their therapeutic potential, human antibody heavy chain variable domains (V(H)s) would benefit from increased thermostability. The highly conserved disulfide linkage that connects Cys23 and Cys104 residues in the core of V(H) domains is crucial to their stability and function. It has previously been shown that the introduction of a second disulfide linkage can increase the thermostability of camelid heavy-chain antibody variable domains (V(H)Hs). Using four model domains we demonstrate that this strategy is also applicable to human V(H) domains. The introduced disulfide linkage, formed between Cys54 and Cys78 residues, increased the thermostability of V(H)s by 14-18°C. In addition, using a novel hexa-histidine capture technology, circular dichroism, turbidity, size exclusion chromatography and multiangle light scattering measurements, we demonstrate reduced V(H) aggregation in domains with the Cys54-Cys78 disulfide linkage. However, we also found that the engineered disulfide linkage caused conformational changes, as indicated by reduced binding of the V(H)s to protein A. This indicates that it may be prudent to use the synthetic V(H) libraries harboring the engineered disulfide linkage before screening for affinity reagents. Such strategies may increase the number of thermostable binders.

Crystal structure of a human single domain antibody dimer formed through V(H)-V(H) non-covalent interactions

Single-domain antibodies (sdAbs) derived from human V_H are considered to be less soluble and prone to aggregate which makes it difficult to determine the crystal structures. In this study, we isolated and characterized two anti-human epidermal growth factor receptor-2 (HER2) sdAbs, Gr3 and Gr6, from a synthetic human V_H phage display library. Size exclusion chromatography and surface plasmon resonance analyses demonstrated that Gr3 is a monomer, but that Gr6 is a strict dimer. To understand this different molecular behavior, we solved the crystal structure of Gr6 to 1.6 Å resolution. The crystal structure revealed that the homodimer assembly of Gr6 closely mimics the V_H-V_L heterodimer of immunoglobulin variable domains and the dimerization interface is dominated by hydrophobic interactions.

Characterization of single-domain antibodies with an engineered disulfide bond

Camelidae single-domain antibodies (VHHs) represent a unique class of emerging therapeutics. Similar to other recombinant antibody fragments (e.g., Fabs, scFvs), VHHs are amenable to library screening and selection, but benefit from superior intrinsic biophysical properties such as high refolding efficiency, high solubility, no tendency for aggregation, resistance to proteases and chemical denaturants, and high expression, making them ideal agents for antibody-based drug design. Despite these favorable biophysical characteristics, further improvements to VHH stability are desirable when considering applications in adverse environments like high heat, low humidity, pH extremes, and the acidic, protease-rich gastrointestinal tract. Recently, the introduction of a disulfide bond into the hydrophobic core of camelid VHHs increased antibody thermal and conformational stability. Here, we present additional protocols for characterizing the effects of the introduced disulfide bond on a panel of llama VHHs. Specifically, we employ mass spectrometry fingerprinting analysis of VHH peptides to confirm the presence of the introduced disulfide bond, size exclusion chromatography, and surface plasmon resonance to examine the effects on aggregation state and target affinity, and circular dichroism spectroscopy and protease digestion assays to assess the effects on thermal and proteolytic stability. The disulfide bond stabilization strategy can be incorporated into antibody library design and should lead to hyperstabilized single-domain antibodies (VHHs, VHs), and possibly Fabs and scFvs, if selection pressures such as denaturants or proteases are introduced during antibody selection.

Single domain antibodies with VH hallmarks are positively selected during panning of llama (Lama glama) naïve libraries

Independent variable domains with VH hallmarks have been repeatedly identified in immune and pre-immune VHH libraries. In some cases, stable independent VH domains have been also isolated in mouse and human recombinant antibody repertoires. However, we have come to realize that VHs were selected with a higher efficiency than VHHs during biopanning of a pre-immune (VHH) library. The biochemical and biophysical comparison did not indicate a presence of any feature that would favor the VH binders during the selection process. In contrast, selected VHHs seemed to be more stable than the VHs, ruling out the existence of a thermodynamically - favored VH sub-class. Therefore, we reasoned that a certain degree of thermodynamic instability may be beneficial for both displaying and expression of VH(H)s when the Sec-pathway is used for their secretion to avoid the cytoplasmic trapping of fast-folding polypeptides. Indeed, VHHs, but not VHs, were accumulated at higher concentrations when expressed fused to the dsbA leader peptide, a sequence that drives the linked polypeptides to the co-translational SRP secretion machinery. These data suggest that the thermodynamically favored VHHs can be lost during biopanning, as previously observed for DARPins and in contrast to the recombinant antibodies in scFv format.

Engineered single-domain antibodies with high protease resistance and thermal stability

The extreme pH and protease-rich environment of the upper gastrointestinal tract is a major obstacle facing orally-administered protein therapeutics, including antibodies. Through protein engineering, several Clostridium difficile toxin A-specific heavy chain antibody variable domains (V_HHs) were expressed with an additional disulfide bond by introducing Ala/Gly54Cys and Ile78Cys mutations. Mutant antibodies were compared to their wild-type counterparts with respect to expression yield, non-aggregation status, affinity for toxin A, circular dichroism (CD) structural signatures, thermal stability, protease resistance, and toxin A-neutralizing capacity. The mutant V_HHs were found to be well expressed, although with lower yields compared to wild-type counterparts, were non-aggregating monomers, retained low nM affinity for toxin A, albeit the majority showed somewhat reduced affinity compared to wild-type counterparts, and were capable of in vitro toxin A neutralization in cell-based assays. Far-UV and near-UV CD spectroscopy consistently showed shifts in peak intensity and selective peak minima for wild-type and mutant V_HH pairs; however, the overall CD profile remained very similar. A significant increase in the thermal unfolding midpoint temperature was observed for all mutants at both neutral and acidic pH. Digestion of the V_HHs with the major gastrointestinal proteases, at biologically relevant concentrations, revealed a significant increase in pepsin resistance for all mutants and an increase in chymotrypsin resistance for the majority of mutants. Mutant V_HH trypsin resistance was similar to that of wild-type V_HHs, although the trypsin resistance of one V_HH mutant was significantly reduced. Therefore, the introduction of a second disulfide bond in the hydrophobic core not only increases V_HH thermal stability at neutral pH, as previously shown, but also represents a generic strategy to increase V_HH stability at low pH and impart protease resistance, with only minor perturbations in target binding affinities. These are all desirable characteristics for the design of protein-based oral therapeutics.

Biotechnological applications of recombinant single-domain antibody fragments

BACKGROUND

Single-domain antibody fragments possess structural features, such as a small dimension, an elevated stability, and the singularity of recognizing epitopes non-accessible for conventional antibodies that make them interesting for several research and biotechnological applications.

RESULTS

The discovery of the single-domain antibody's potentials has stimulated their use in an increasing variety of fields. The rapid accumulation of articles describing new applications and further developments of established approaches has made it, therefore, necessary to update the previous reviews with a new and more complete summary of the topic.

CONCLUSIONS

Beside the necessary task of updating, this work analyses in detail some applicative aspects of the single-domain antibodies that have been overseen in the past, such as their efficacy in affinity chromatography, as co-crystallization chaperones, protein aggregation controllers, enzyme activity tuners, and the specificities of the unconventional single-domain fragments.

Neutralization of Clostridium difficile toxin A with single-domain antibodies targeting the cell receptor binding domain

Clostridium difficile is a leading cause of nosocomial infection in North America and a considerable challenge to healthcare professionals in hospitals and nursing homes. The gram-positive bacterium produces two high molecular weight exotoxins, toxin A (TcdA) and toxin B (TcdB), which are the major virulence factors responsible for C. difficile-associated disease and are targets for C. difficile-associated disease therapy. Here, recombinant single-domain antibody fragments (V(H)Hs), which specifically target the cell receptor binding domains of TcdA or TcdB, were isolated from an immune llama phage display library and characterized. Four V(H)Hs (A4.2, A5.1, A20.1, and A26.8), all shown to recognize conformational epitopes, were potent neutralizers of the cytopathic effects of toxin A on fibroblast cells in an in vitro assay. The neutralizing potency was further enhanced when V(H)Hs were administered in paired or triplet combinations at the same overall V(H)H concentration, suggesting recognition of nonoverlapping TcdA epitopes. Biacore epitope mapping experiments revealed that some synergistic combinations consisted of V(H)Hs recognizing overlapping epitopes, an indication that factors other than mere epitope blocking are responsible for the increased neutralization. Further binding assays revealed TcdA-specific V(H)Hs neutralized toxin A by binding to sites other than the carbohydrate binding pocket of the toxin. With favorable characteristics such as high production yield, potent toxin neutralization, and intrinsic stability, these V(H)Hs are attractive systemic therapeutics but are more so as oral therapeutics in the destabilizing environment of the gastrointestinal tract.

Site-directed mutagenesis for improving biophysical properties of VH domains

Recombinant antibody fragments are significant therapeutic and diagnostic reagents. As such, their efficacy depends heavily on their affinities and biophysical properties. Thus, mutagenesis approaches have been extensively applied to recombinant antibodies to improve their affinity, stability, and solubility. Among the existing recombinant antibody variants, human V(H) domains stand out as the ones with the general need of solubility engineering at some point during their development; this solubility engineering step transforms V(H)s into nonaggregating, functional entities, rendering them useful as therapeutic and diagnostic reagents. Here, we present one of several approaches that have been employed to develop nonaggregating human V(H) domains. We apply an in vitro site-directed mutagenesis approach to an aggregating human V(H) domain by means of a splice overlap extension technique. The resultant mutant V(H)s are nonaggregating in contrast to the parent wild type V(H) and less prone to aggregation following thermal unfolding.

Toxin-specific antibodies for the treatment of Clostridium difficile: current status and future perspectives

Therapeutic agents targeting bacterial virulence factors are gaining interest as non-antibiotic alternatives for the treatment of infectious diseases. Clostridium difficile is a Gram-positive pathogen that produces two primary virulence factors, enterotoxins A and B (TcdA and TcdB), which are responsible for Clostridium difficile-associated disease (CDAD) and are targets for CDAD therapy. Antibodies specific for TcdA and TcdB have been shown to effectively treat CDAD and prevent disease relapse in animal models and in humans. This review summarizes the various toxin-specific antibody formats and strategies under development, and discusses future directions for CDAD immunotherapy, including the use of engineered antibody fragments with robust biophysical properties for systemic and oral delivery.

A novel promiscuous class of camelid single-domain antibody contributes to the antigen-binding repertoire

It is well established that, in addition to conventional Abs, camelids (such as Camelus dromedarius and Lama glama) possess unique homodimeric H chain Abs (HCAbs) devoid of L chains. The Ag-binding site of these HCAbs consists of a single variable domain, referred to as VHH. It is widely accepted that these VHHs, with distinct framework-2 imprints evolved within the V(H) clan III-family 3, are exclusively present on HCAbs. In this study, we report the finding of a distinct leader signal sequence linked to variable genes displaying a high degree of homology to the clan II, human VH(4) family that contributes to the HCAb Ag-binding diversity. Although the VHH framework-2 imprints are clearly absent, their VH(4)-D-JH recombination products can be rearranged to the H chains of both classical and HCAbs. This suggests that for these V domains the presence of a L chain to constitute the Ag-binding site is entirely optional. As such, the capacity of this promiscuous VH(4) family to participate in two distinct Ab formats significantly contributes to the breadth of the camelid Ag-binding repertoire. This was illustrated by the isolation of stable, dendritic cell-specific VH(4) single domains from a VH(4)-HCAb phage display library. The high degree of homology with human VH(4) sequences is promising in that it may circumvent the need for "humanization" of such single-domain Abs in therapeutic applications.

Single-domain antibody-nanoparticles: promising architectures for increased staphylococcus aureus detection specificity and sensitivity

Because antibodies are highly target-specific and nanoparticles possess diverse, material-dependent properties that can be exploited in order to label and potentially identify biomolecules, the development of antibody-nanoparticle conjugates (nanoconjugates) has huge potential in biodiagnostics. Here, we describe a novel superparamagnetic nanoconjugate, one whose recognition component is a single-domain antibody. It is highly active toward its target Staphylococcus aureus, displays long shelf life, lacks cross-reactivity inherent to traditional homologue whole antibodies, and captures a few dozen S. aureus cells in a mixed cell population with ~100% efficiency and specificity. We ascribe the excellent performance of our nanoconjugate to its single-domain antibody component and recommend it as a general purpose recognition element.

Multivalent anchoring and oriented display of single-domain antibodies on cellulose

Antibody engineering has allowed for the rapid generation of binding agents against virtually any antigen of interest, predominantly for therapeutic applications. Considerably less attention has been given to the development of diagnostic reagents and biosensors using engineered antibodies. Recently, we produced a novel pentavalent bispecific antibody (i.e., decabody) by pentamerizing two single-domain antibodies (sdAbs) through the verotoxin B subunit (VTB) and found both fusion partners to be functional. Using a similar approach, we have engineered a bispecific pentameric fusion protein consisting of five sdAbs and five cellulose-binding modules (CBMs) linked via VTB. To find an optimal design format, we constructed six bispecific pentamers consisting of three different CBMs, fused to the Staphylococcus aureus-specific human sdAb HVHP428, in both orientations. One bispecific pentamer, containing an N-terminal CBM9 and C-terminal HVHP428, was soluble, non-aggregating, and did not degrade upon storage at 4 °C for over six months. This molecule was dually functional as it bound to cellulose-based filters as well as S. aureus cells. When impregnated in cellulose filters, the bispecific pentamer recognized S. aureus cells in a flow-through detection assay. The ability of pentamerized CBMs to bind cellulose may form the basis of an immobilization platform for multivalent display of high-avidity binding reagents on cellulosic filters for sensing of pathogens, biomarkers and environmental pollutants.

Selection of non-aggregating VH binders from synthetic VH phage-display libraries

The particular interest in VH antibody fragments stems from the fact that they can rival their "naturally occurring" single-domain antibody (sdAb) counterparts (camelid VHHs and shark VNARs) with regard to such desirable characteristics as stability, solubility, expression, and ability to penetrate cryptic epitopes and outperform them in terms of less immunogenicity, a much valued property in human immunotherapy applications. However, human VHs are typically prone to aggregation. Various approaches for developing non-aggregating human VHs with binding specificities have relied on a combination of recombinant DNA technology and phage-display technology. VH gene libraries are constructed synthetically by randomizing the CDRs of a single VH scaffold fused to a gene encoding a phage coat protein. Recombinant phage expressing the resulting VH libraries in fusion with the pIII protein is propagated in Escherichia coli. Monoclonal phage displaying VHs with specificities for target antigens are isolated from the libraries by a process called panning. The exertion of stability pressure in addition to binding pressure during panning ensures that the isolated VH binders are also non-aggregating. The genes encoding the desired VHs selected from the libraries are packaged within the phage particles, linking genotype and phenotype, hence making possible the identification of the selected VHs through identifying its physically linked genotype. Here, we describe the application of recombinant DNA and phage-display technologies for the construction of a phage-displayed human VH library, the panning of the library against a protein, and the expression, purification, and characterization of non-aggregating VHs isolated by panning.

Comprehensive analysis of the factors contributing to the stability and solubility of autonomous human VH domains

We report a comprehensive analysis of sequence features that allow for the production of autonomous human heavy chain variable (V(H)) domains that are stable and soluble in the absence of a light chain partner. Using combinatorial phage-displayed libraries and conventional biophysical methods, we analyzed the entire former light chain interface and the third complementarity determining region (CDR3). Unlike the monomeric variable domains of camelid heavy chain antibodies (V(H)H domains), in which autonomous behavior depends on interactions between the hydrophobic former light chain interface and CDR3, we find that the stability of many in vitro evolved V(H) domains is essentially independent of the CDR3 sequence and instead derives from mutations that increase the hydrophilicity of the former light chain interface by replacing exposed hydrophobic residues with structurally compatible hydrophilic substitutions. The engineered domains can be expressed recombinantly at high yield, are predominantly monomeric at high concentrations, unfold reversibly, and are even more thermostable than typical camelid V(H)H domains. Many of the stabilizing mutations are rare in natural V(H) and V(H)H domains and thus could not be predicted by studying natural sequences and structures. The results demonstrate that autonomous V(H) domains with structural properties beyond the scope of natural frameworks can be derived by using non-natural mutations, which differ from those found in camelid V(H)H domains. These findings should enable the development of libraries of synthetic V(H) domains with CDR3 diversities unconstrained by structural demands.

Design of synthetic antibody libraries

Antibody libraries came into existence 15 years ago when the accumulating sequence data of immunoglobulin genes and the advent of polymerase chain reaction technology made it possible to clone antibody gene repertoires. Since then, virtually hundreds of antibody libraries have been constructed, employing limitless maneuvers from the antibody engineering molecular bag of tricks towards the crucial parameters that determine library quality, library size, diversity and robustness. Phage and additional display and screening technologies were applied to pan out desired binding specificities from antibody libraries. Several biotech companies established themselves as key operators in the multibillion-dollar field of recombinant antibody technology. Out of nineteen FDA-approved therapeutic antibodies, one was isolated from an antibody library and many more are in various stages of clinical evaluation. This review highlights key milestones in the short history of antibody libraries and attempts to predict the future impact of antibody libraries on drug discovery.

Synthesis and characterization of CN-modified protein analogues as potential vibrational contrast agents

A recombinant VH single-domain antibody recognizing staphylococcal protein A was functionalized on reactive lysine residues with N-hydroxysuccimidyl-activated 4-cyanobenzoate. Surface plasmon resonance analysis of antibody-antigen binding revealed that modified and unmodified antibodies bound protein A with similar affinities. Raman imaging of the modified antibodies indicated that the benzonitrile group provides vibrational contrast enhancement in a region of the electromagnetic spectrum that is transparent to cellular materials. Thus, the modified single-domain antibody may be amenable to detecting protein A from samples of the human pathogen Staphylococcus aureus using vibronic detection schemes such as Raman and coherent anti-Stokes Raman scattering. The generality of this labeling strategy should make it applicable to modifying an array of proteins with varied structure and function.

The assembly of single domain antibodies into bispecific decavalent molecules

Bispecific antibodies present unique opportunities in terms of new applications for engineered antibodies. However, designing ideal bispecific antibodies remains a challenge. Here we describe a novel bispecific antibody model in which five single domain antibodies (sdAbs) are fused via a linker sequence to the N-terminus of the verotoxin B (VTB) subunit, a pentamerization domain, and five sdAbs are fused via a linker sequence to the VTB C-terminus. Fifteen such decavalent bispecific molecules, termed decabodies, were constructed and characterized for the purpose of identifying an optimal decabody design. One of the fifteen molecules existed in a non-aggregated decavalent form. In conjunction with the isolation of sdAbs with the desired specificities from non-immune phage display libraries, the decabody strategy provides a means of generating high avidity bispecific antibody reagents, with good physical properties, relatively quickly.

Survey of the year 2005 commercial optical biosensor literature

We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.