Construction and characterization of a single-chain catalytic antibody

From Bioorganic Models to Cells

I endeavor to share how various choices-some deliberate, some unconscious-and the unmistakable influence of many others shaped my scientific pursuits. I am fascinated by how two long-term, major streams of my research, DNA replication and purine biosynthesis, have merged with unexpected interconnections. If I have imparted to many of the talented individuals who have passed through my lab a degree of my passion for uncloaking the mysteries hidden in scientific research and an understanding of the honesty and rigor it demands and its impact on the world community, then my mentorship has been successful.

Molecular engineering strategies and methods for the expression and purification of IgG1-based bispecific bivalent antibodies

In recent years, bispecific antibodies (BisAbs) have emerged as novel pharmaceutical candidates owing to their ability to engage two disease mediators simultaneously, thus providing a possible alternative therapeutic approach in complex diseases such as cancer and inflammation. Here we provide an overview of the molecular design, recombinant expression in mammalian cells and purification of BisAbs based on full-length IgG-scFv formats. Practical considerations and strategies to optimize transient expression and purification are also discussed.

Catalytic antibodies and their applications in biotechnology: state of the art

Catalytic antibodies are immunoglobulins endowed with enzymatic properties. Discovered in the second part of the 1980s, the enthusiasm they initially aroused was counterbalanced by the difficulty of their production and their low catalytic rates. Nevertheless, improvements in expression systems and engineering technologies, combined with various studies suggesting that catalytic antibodies play a role in the immune system, have opened the way to new applications for these proteins. Herein we review catalytic antibodies from a biotechnological point of view, focusing our study on the different production methods, expression systems and their potential clinical applications dedicated to these proteins.

Combining genetic and biochemical approaches to identify functional molecular contact points

Protein-protein interactions are required for many viral and cellular functions and are potential targets for novel therapies. Here we detail a series of genetic and biochemical techniques used in combination to find an essential molecular contact point on the duck hepatitis B virus polymerase. These techniques include differential immunoprecipitation, mutagenesis and peptide competition. The strength of these techniques is their ability to identify contact points on intact proteins or protein complexes employing functional assays. This approach can be used to aid identification of putative binding sites on proteins and protein complexes which are resistant to characterization by other methods.

Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9

Direct hydroxide attack on the scissile carbonyl of the substrate has been suggested as a likely mechanism for esterase antibodies elicited by phosphonate haptens, which mimic the transition states for the alkaline hydrolysis of esters.1 The unique amidase activity of esterase antibody 43C9 has been attributed to nucleophilic attack by an active-site histidine residue.2 Yet, the active site of 43C9 is strikingly similar to those of other esterase antibodies, particularly 17E8. We have carried out quantum mechanical calculations, molecular dynamics simulations, and free energy calculations to assess the mechanism involving direct hydroxide attack for 43C9. Results support this mechanism and suggest that the mechanism is plausible for other antiphosphonate antibodies that catalyze the hydrolysis of (p-nitro)phenyl esters.

Structural basis for amide hydrolysis catalyzed by the 43C9 antibody

Among catalytic antibodies, the well-characterized antibody 43C9 is unique in its ability to catalyze the difficult, but desirable, reaction of selective amide hydrolysis. The crystallographic structures that we present here for the single-chain variable fragment of the 43C9 antibody, both with and without the bound product p -nitrophenol, strongly support and extend the structural and mechanistic information previously provided by a three-dimensional computational model, together with extensive biochemical, kinetics, and mutagenesis results. The structures reveal an unexpected extended beta-sheet conformation of the third complementarity determining region of the heavy chain, which may be coupled to the novel indole ring orientation of the adjacent Trp H103. This unusual conformation creates an antigen-binding site that is significantly deeper than predicted in the computational model, with a hydrophobic pocket that encloses the p -nitrophenol product. Despite these differences, the previously proposed roles for Arg L96 in transition-state stabilization and for His L91 as the nucleophile that forms a covalent acyl-antibody intermediate are fully supported by the crystallographic structures. His L91 is now centered at the bottom of the antigen-binding site with the imidazole ring poised for nucleophilic attack. His L91, Arg L96, and the bound p -nitrophenol are linked into a hydrogen-bonding network by two well-ordered water molecules. These water molecules may mimic the positions of the phosphonamidate oxygen atoms of the antigen, which in turn mimic the transition state of the reaction. This network also contains His H35, suggesting that this residue may also stabilize the transition-states. A possible proton-transfer pathway from His L91 through two tyrosine residues may assist nucleophilic attack. Although transition-state stabilization is commonly observed in esterolytic antibodies, nucleophilic attack appears to be unique to 43C9 and accounts for the unusually high catalytic activity of this antibody.

The state of antibody catalysis

One of the fascinations of catalytic antibodies is the possibility of harnessing the mechanisms available to enzymes for chemical transformation and applying them to the broad realm of chemistry encountered in organic synthesis. Recently, the catalytic repertoire of antibodies has been extended to include mechanistically more complex bimolecular reactions and the immunological response to the hapten can be more thoroughly examined as a result of the advent of new screening technology using bacterial phages or auxotrophic cell lines.

Mimicry between receptors and antibodies. Identification of snake toxin determinants recognized by the acetylcholine receptor and an acetylcholine receptor-mimicking monoclonal antibody

In several instances, a monoclonal antibody raised against a receptor ligand has been claimed to mimic the ligand receptor. Thus, a specific monoclonal antibody (Malpha2-3) raised against a short-chain toxin from snake was proposed to mimic the nicotinic acetylcholine receptor (AChR) (). Further confirming this mimicry, we show that (i) like AChR, Malpha2-3 elicits anti-AChR antibodies, which in turn elicit anti-toxin antibodies; and (ii) the region 106-122 of the alpha-chain of AChR shares 66% primary structure identity with complementarity-determining regions of Malpha2-3. Also, a mutational analysis of erabutoxin a reveals that the epitope recognized by Malpha2-3 consists of 10 residues, distributed within the three toxin loops. Eight of these residues also belong to the 10-residue epitope recognized by AChR, a result that offers an explanation as to the functional similarities between the receptor and the antibody. Strikingly, however, most of the residues common to the two epitopes contribute differentially to the energetic formation of the antibody-toxin and the receptor-toxin complexes. Together, the data suggest that the mimicry between AChR and Malpha2-3 is partial only.

Characterization of an anti-CD44 single-chain FV antibody that stimulates natural killer cell activity and induces TNF alpha release

We report the functional characterization of a single-chain Fv (scFv) constructed from an anti-CD44 mAb (S5) that abrogates marrow rejection in a mismatched canine donor transplant model. The variable light chain (VL) and variable heavy chain (VH) domains of the parent anti-CD44 antibody were cloned and exact match PCR primers designed that spliced the mature variable domains together through a 15 amino acid [Gly4Ser]3 linker-encoding sequence. This gene was put under the control of a T7 promoter and expressed in Escherichia coli in insoluble inclusion bodies. The scFv was refolded in a cystine/cysteine redox buffer and purified to homogeneity using anion exchange chromatography. The concentration-dependent binding isotherm of the S5 scFv was determined using both direct binding and competitive inhibition flow cytometry assays. S5 scFv effectively blocked FITC-conjugated MAb S5 binding to canine peripheral blood mononuclear cells (PBMC), possessing a mean EC50 (15 nM) equivalent to Fab' fragments of parental S5 (14.7 nM) and approximately two-fold higher than Mab S5 (6 nM). It also binds directly to canine PBMC and possesses a mean EC50 similar to that of the Fab' fragments (1.01 nM vs 1.03 nM). The recombinant S5 scFv also retains the potent biological activity of the parent Mab, stimulating the activation of natural killer (NK) cell activity and the release of tumor necrosis factor alpha (TNF alpha) in canine PBMC. Like the parent antibody, scFv crossreacted with human CD44 as examined by direct binding to human PBMC in the flow cytometry assay as well as direct binding to human CD44 immunoglobulin fusion protein in an enzyme-linked immunosorbent assay (ELISA). It was also able to induce TNF alpha release in human PBMC. These results support previous work suggesting that monovalent binding is sufficient to generate the in vitro biological activity of S5 (1). The scFv S5 antibody will thus serve as a useful model for elucidating the mechanism of antibody abrogated marrow rejection and may serve as a human therapeutic agent.

Cloning, expression, and purification of an anti-desipramine single chain antibody in NS/O myeloma cells

Drug-specific monoclonal antibodies and their antigen-binding Fab fragments reverse acute desipramine toxicity in a rat experimental model by inducing a redistribution of drug from cardiac tissue into serum and extracellular fluid. In order to investigate the use of smaller recombinant antibody fragments such as single chain Fv (sFv) as an antidote, an efficient murine NS/O myeloma expression system was developed. The variable light (VL) and variable heavy (VH) domains of a murine anti-desipramine monoclonal antibody were cloned and sequenced. A 270 amino acid VH-(Gly4Ser)3-VL sFv was prepared by overlapping polymerase chain reaction (PCR) amplification of VH with heavy chain leader peptide, VL, and the linker. This construct was subcloned into a mammalian expression vector which utilizes the SR alpha promoter, a hybrid promoter consisting of the SV40 early promoter with portions of the human T-cell leukemia virus type I long terminal repeat and also containing the Escherichia cloi xanthine-guanine phosphoribosyltransferase gene for selection. NS/O myeloma cells were transfected by electroporation. Stable recombinant NS/O clones were screened for expression of sFv using reverse transcriptase-PCR to detect mRNA and an enzyme-linked immunosorbent assay (ELISA) to detect sFv. Secreted sFv from clones capable of growth to a cell density of 2-4 x 10(6) viable cells/mL was purified in a single step using a desipramine affinity column resulting in 12-39 mg/L of purified sFv. Affinity-purified sFv had comparable desipramine binding activity to Fab when evaluated by competitive ELISA.

Production of engineered IgM-binding single-chain antibodies in Escherichia coli

Two single-chain antibodies were engineered and tested as novel binding proteins with specificity for immunoglobulin M. Genes for the two single-chain Fv proteins were assembled from the variable light chain cDNA and variable heavy chain cDNA of monoclonal antibodies DA4.4 and Bet 2, which specifically bind human IgM and mouse IgM, respectively. Both single-chain Fv proteins were designed with a 14-amino acid linker which bridged the variable light chain and variable heavy chain domains. The two proteins were expressed in Escherichia coli, purified and assayed for IgM-binding activity. Both proteins demonstrate a binding specificity for their corresponding IgM which is similar to the monoclonal antibodies from which they were derived. These small IgM-binding proteins may have applications in the investigation of the immune response and in the detection and purification of monoclonal antibodies, cell-associated antibodies, and IgM from serum.

Selection of catalytic antibodies for a biosynthetic reaction from a combinatorial cDNA library by complementation of an auxotrophic Escherichia coli: antibodies for orotate decarboxylation

Antibodies capable of decarboxylating orotate were sought by immunization with a hapten designed to elicit antibodies with combining sites that resemble the orotate-binding and catalytic portion of the active site of the enzyme orotidine 5'-monophosphate (OMP) decarboxylase (orotidine-5'-monophosphate carboxy-lyase, EC 4.1.1.23). Active recombinant antibody fragments (Fabs) were selected from a combinatorial cDNA library by complementation of a pyrF strain of Escherichia coli and growth of the library-expressing cells on pyrimidine-free medium. In this biological screen, a sufficiently active antibody from the library would decarboxylate orotate to produce uracil, a pyrimidine source for the auxotroph, and would provide the cells with a growth advantage compared to cells without an active antibody. Six recombinant Fabs yielded identifiable colonies in a screen of 16,000 transformants. To enhance its stability and expression level, one of the six positive fragments was converted into single-chain form. In this form, the antibody fragment conferred a definite growth advantage to the auxotroph that was eliminated when the hapten was included in the medium. The purified single-chain antibody displayed orotate decarboxylase activity in vitro, as determined by a 14CO2 displacement assay. The specific activity of the antibody is approximately 10(-7) times that of naturally occurring OMP decarboxylase, but this antibody-catalyzed rate is estimated to be 10(8) times the background rate. The results offer the potential to use these methods to obtain catalytic antibodies for other biosynthetic reactions as well as to assess the effectiveness of the hapten transition state or active site analog in eliciting antibody catalysts.

Dissection of an antibody-catalyzed reaction

Antibody 43C9 accelerates the hydrolysis of a p-nitroanilide by a factor of 2.5 x 10(5) over the background rate in addition to catalyzing the hydrolysis of a series of aromatic esters. Since this represents one of the largest rate accelerations achieved with an antibody, we have undertaken a series of studies aimed at uncovering the catalytic mechanism of 43C9. The immunogen, a phosphonamidate, was designed to mimic the geometric and electronic characteristics of the tetrahedral intermediate that forms upon nucleophilic attack by hydroxide on the amide substrate. Further studies, however, revealed that the catalytic mechanism is more complex and involves the fortuitous formation of a covalent acyl-antibody intermediate as a consequence of complementary side chain residues at the antibody-binding site. Several lines of evidence indicate that the catalytic mechanism involves two key residues: His-L91, which acts as a nucleophile to form the acyl-antibody intermediate, and Arg-L96, which stabilizes the anionic tetrahedral moieties. Support for this mechanism derives from the results of site-directed mutagenesis experiments and solvent deuterium isotope effects as well as direct detection of the acyl-antibody by electrospray mass spectrometry. Despite its partial recapitulation of the course of action of enzymic counterparts, the reactivity of 43C9, like other antibodies, is apparently limited by its affinity for the inducing immunogen. To go beyond this level, one must introduce additional catalytic functionality, particularly general acid-base catalysis, through either improvements in transition-state analog design or site-specific mutagenesis.

Antigen recognition and targeted delivery by the single-chain Fv

The single-chain Fv (sFv) has proven attractive for immuno-targeting, both alone and as a targeting element within sFv fusion proteins. This chapter summarizes the features of sFv proteins that have sparked this interest, starting with the conservation of Fv architecture that makes general sFv design practical. The length and composition of linkers used to bridge V domains are discussed based on the sFv literature; special emphasis is given to the (Gly4Ser)3 15-residue linker that has proven of broad utility for constructing Fv regions of antibodies and other members of the immunoglobulin superfamily. The refolding properties of sFv proteins are summarized and examples given from our laboratory. Spontaneous refolding from the fully reduced and denatured state, typified by 26-10 sFv, is contrasted with disulfide-restricted refolding, exemplified by MOPC 315 and R11D10 sFv proteins, which recover antigen binding only if their disulfides have been oxidized prior to removal of denaturant. The medical value of sFv proteins hinges on their reliability in antigen recognition and rapidity in targeted delivery. Detailed analysis of specificity and affinity of antigen binding by the 26-10 antidigoxin sFv has demonstrated very high fidelity to the binding properties of the parent 26-10 sFv. These results gave confidence to the pursuit of more complex biomedical applications of these proteins, which is indicated by our work with the R11D10 sFv for the imaging of myocardial infarctions. Diagnostic imaging and therapeutic immunotargeting by sFv present significant opportunities, particularly as a result of their pharmacokinetic properties. Intravenously administered sFv offers much faster clearance than conventional Fab fragments or intact immunoglobulin with minimal background binding.

Medical applications of single-chain antibodies

A single-chain antibody or single-chain Fv (sFv) incorporates the complete antibody binding site in a single polypeptide chain of minimal size, with an approximate molecular weight of 26,000. In antibodies, the antigen combining site is part of the Fv region, which is composed of the VH and VL variable domains on separate heavy and light chains. Efforts over nearly two decades have indicated that Fv fragments can only rarely be prepared from IgG and IgA antibodies by proteolytic dissection. Beginning in 1988, single-chain analogues of Fv fragments and their fusion proteins have been reliably generated by antibody engineering methods. The first step involves obtaining the genes encoding VH and VL domains with desired binding properties; these V genes may be isolated from a specific hybridoma cell line, selected from a combinatorial V-gene library, or made by V gene synthesis. The single-chain Fv is formed by connecting the component V genes with an oligonucleotide that encodes an appropriately designed linker peptide, such as (Gly4-Ser)3. The linker bridges the C-terminus of the first V region and N-terminus of the second, ordered as either VH-linker-VL or VL-linker-VH. In principle, the sFv binding site can faithfully replicate both the affinity and specificity of its parent antibody combining site, as demonstrated in our model studies with the 26-10 anti-digoxin sFv. Furthermore, the sFv remains stable at low concentrations that promote VH and VL dissociation from the Fv heterodimer, resulting in loss of Fv binding. Intravenously administered sFv proteins exhibit accelerated biodistribution and exceptionally fast clearance compared to IgG or Fab. These pharmacokinetic properties allow rapid imaging by sFv, which therefore may be labeled with a short-lived isotope such as Tc-99m. Expression of a single gene product from fused sFv and effector genes facilitates immunotargeting of the effector protein, as shown for single-chain Fv toxin fusion proteins.

Antibody engineering using Escherichia coli as host

The expression of immunoglobulin fragments with antigen binding activities in E. coli is now routinely possible. Using such expression systems, Fv, Fab, and scFv fragments and single VH domains can be produced as secreted proteins in yields of the order of milligrams per liter. Moreover, expression systems are being rapidly developed for the production of antibody scFv or Fab fragments by repertoire cloning followed by selection. Diverse repertoires of genes encoding VH and VL domains can be isolated by the PCR and cloned for expression using these systems, which allow the selection of recombinants that produce fragments with the desired antigen binding specificities. This technology is rapidly evolving and, coupled with the development of systems for the random mutagenesis and selection of higher-affinity antibody fragments, could, in the longer term, provide an alternative rapid route to hybridoma technology.

Sequential 1H and 15N NMR assignments and secondary structure of a recombinant anti-digoxin antibody VL domain

A uniformly 15N-labeled recombinant light-chain variable (VL) domain from the anti-digoxin antibody 26-10 has been investigated by heteronuclear two-dimensional (2D) and three-dimensional (3D) NMR spectroscopy. Complementary homonuclear 2D NMR studies of the unlabeled VL domain were also performed. Sequence-specific assignments for 97% of the main-chain and 70% of the side-chain proton resonances have been obtained. Patterns of nuclear Overhauser effects observed in 2D NOESY, 3D NOESY-HSQC, and 3D NOESY-TOCSY-HSQC spectra afford a detailed characterization of the VL domain secondary structure in solution. The observed secondary structure--a nine-stranded antiparallel beta-barrel--corresponds to that observed crystallographically for VL domains involved in quaternary associations. The locations of slowly exchanging amide protons have been discerned from a 2D TOCSY spectrum recorded after dissolving the protein in 2H2O. Strands B, C, E, and F are found to be particularly stable. The possible consequences of these results for domain-domain interactions are discussed.