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Antimicrobial Agents and Chemotherapy, May 2003, p. 1503-1508, Vol. 47, No. 5
0066-4804/03/$08.00+0 DOI: 10.1128/AAC.47.5.1503-1508.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Elliott Gorfain,
Linguang Cao, Jimmy H. Williams, and Fang Fang*
Perlan Therapeutics, San Diego, California
Received 7 October 2002/ Returned for modification 20 December 2002/ Accepted 11 February 2003
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For over a decade, science has tried to improve on nature by using multivalency to increase the avidities of antibodies. The majority of these proteins were engineered by fusing the antigen-binding scFv fragment of an antibody with a polymerization domain, such as streptavidin (10), the yeast protein GCN4 leucine zipper domain (7, 18), or the tetramerization domain of p53 (18). Fab fragments of antibodies, however, generally exhibit significantly higher binding affinities than their corresponding scFv fragments. Because of the greater complexity of assembling multichain proteins, little work has been done on making trimeric and tetrameric Fab molecules. Our method involves the generation of tripartite proteins consisting of a humanized Fab, a linker sequence derived from the human immunoglobulin D (IgD) hinge (13), and a multimerization domain derived from either of the human transcription factors, ATF
(15) or CREBPa (12). These molecules are produced and assembled in Escherichia coli at high levels. They are purified in soluble homogeneous form by a simple purification procedure. This method is suitable for broad application in making multivalent molecules.
To verify that this approach could be applied to a therapeutic target, we multimerized a humanized Fab based on MAb 1A6. Because the binding of bivalent MAb 1A6 was not strong enough to block HRV infection completely, we applied the premise that multivalency could enhance avidity by lowering koff (4, 9). We designed trivalent and tetravalent antibodies with the goal of improving efficacy via increased avidity. The multivalent humanized proteins possess a dramatically improved ability to protect cells in culture from HRV infection.
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t0 transcriptional terminator (20). The vector includes a mechanism for generating a variety of multimeric Fab molecules through insertion of polymerization domain sequences between a unique SacI site just before the stop codon in the CH domain and a unique EcoRI site just after the stop codon. The expression vector pTexK was derived from pBR322 and contains the isopropyl-ß-D-thiogalactopyranoside (IPTG)-inducible tac promoter and a kanamycin resistance gene.
The gene segment encoding the light chain was synthesized by PCR with two overlapping templates, the VL fragment derived from two versions of humanized scFv MAb 1A6 (HscB for Fab19 and HscE for Fab48 [11]) and the CL fragment derived from the human
1 light-chain constant region (14). The PCR product was cloned into the pCR 2.1 TOPO cloning vector (Invitrogen). The inserts of correct clones were sequenced in their entirety. A similar approach was used to synthesize the heavy chain and the terminator as an XbaI-HindIII fragment, with the CH1 domain derived from human IgG1 (5). The expression plasmid for Fab was made by ligating the SpeI-XbaI light-chain fragment and the XbaI-HindIII heavy-chain fragment into SpeI-HindIII-digested pTexK to generate pTexK-Fab.
To produce multimeric Fab proteins, DNA cassettes were synthesized by PCR with overlapping oligonucleotides as templates. The amino acid sequences encoded by these domains are listed in Table 1. DNAs encoding each of the hinge and multimerization domains were ligated into the appropriate Fab vector as SacI-EcoRI fragments.
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TABLE 1. Amino acid sequences
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Size-exclusion chromatography was performed on a Superdex 200 column (Amersham/Pharmacia) equilibrated with TBS at a flow rate of 0.4 ml/min. The column was calibrated with standard proteins (carbonic anhydrase, 29 kDa; albumin, 60 kDa; alcohol dehydrogenase, 150 kDa; ß-amylase, 200 kDa; blue dextran). The purified Fab and multivalent Fab proteins were analyzed at similar concentrations and resolved under the same running conditions.
Hydrodynamic characterization of anti-ICAM-1 proteins. Analytical ultracentrifugation and light scattering were performed by Alliance Protein Labs (Camarillo, Calif.) with purified proteins. All experiments were conducted in TBS at a concentration of test protein of approximately 0.5 mg/ml. Sedimentation velocity analysis was performed in a Beckman Optima XL-A analytical ultracentrifuge; data were analyzed with the programs SEDFIT (21) and SVEDBERG (16). Dynamic light-scattering data were collected with a Protein Solutions DynaPro MS/X instrument with 12-µl quartz cells and analyzed with the manufacturer's software. Samples were filtered through a Whatman Anotop 0.02-µm-pore-size filter prior to light-scattering analysis.
Surface plasmon resonance analysis. koffs were determined by surface plasmon resonance for the Fab19 monomer, dimeric CFY199, and tetrameric CFY196 by Research Consulting Services, BIAcore, Inc., Piscataway, N.J. Analysis was done on a BIAcore TM 3000 instrument (Biosensor, Piscataway, N.J.) at 25°C. The response data were generated from a four-channel CM5 chip onto which soluble ICAM-1 (Bender MedSystems, Vienna, Austria) was immobilized at 50 and 1,650 response units. Proteins were injected onto the chip at 100 nM in a running buffer consisting of 10 mM HEPES (pH 7.4), 150 mM NaCl, 3 mM EDTA, and 0.005% surfactant P20. The data were fit with BIAcore software to generate the rate constant and the half-life for the dissociation of each protein from ICAM-1 (see Table 3).
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TABLE 3. Dissociation kinetics of proteins
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Competitive ELISA. To prepare a tracer molecule that could compete with anti-ICAM-1 tetramers, we produced a horseradish peroxidase (HRP)-labeled protein. A cysteine was introduced into a tetrameric anti-ICAM-1 antibody by adding the sequence TGC to the carboxy terminus of CFY196 to generate a new tetrameric molecule, 196TGC. HRP was conjugated to 196TGC with the EZ-link Maleimide Activated Horseradish Peroxidase labeling kit (Pierce) to produce 196TGC-HRP.
To begin the enzyme-linked immunosorbent assay (ELISA), a 96-well enzyme immunoassay plate (Corning) was coated with 100 µl of soluble ICAM-1 (1 µg/ml in 0.1 M NaHCO3; Bender MedSystems) per well. After the plate was washed with TBST (50 mM Tris [pH 8.0], 150 mM NaCl, 0.05% Tween 20), it was blocked with 3% nonfat milk in TBST at 37°C for 1 h. After the samples were washed with TBST, anti-ICAM-1 Fab samples (monomer or multimer) serially diluted in 1% nonfat milk-TBST solution were added and the mixture was incubated at room temperature for 1 h. The plate was incubated at room temperature for 2 h, and then the wells were thoroughly washed with TBST. Bound HRP activity was measured with 100 µl of 3,3',5,5'-tetramethylbenzidine substrate solution (Kirkegaard & Perry Laboratories) per well. After 15 min, the color development was stopped by the addition of 100 µl of 0.12 N HCl per well and the absorbance was measured at 450 nm with a plate reader (ICN).
The percent inhibition of tracer antibody (196TGC-HRP) binding was calculated as 100 x [(A0 - As)/A0], where A0 is the OD450 of the reference well without samples (196TGC-HRP only) and As is the OD450 of the sample wells. The relative binding affinities of the anti-ICAM-1 antibodies were represented by the protein concentration that reduces tracer antibody binding by 50% (IC50).
Cell protection assays. To measure protection against viral infection, the level of cell death due to HRV infection after pretreatment with various concentrations of our proteins was compared to that for uninfected cells. In a standard assay, 105 HeLa cells were plated on the day before an assay in each well of a 48-well dish. Triplicate wells of cells were then incubated for 1 h at 37°C with protein preparations in a volume of 100 µl of cell medium at the indicated concentrations. This mixture was removed, and virus at a multiplicity of infection of 1 was added in 100 µl of cell medium. No additional anti-ICAM-1 proteins were added in this viral inoculum or later in the experiment. The dishes were incubated for 2 h at 33°C. The monolayers in the wells were then washed once with medium to remove unbound material and incubated with fresh medium. The infection was then allowed to proceed for 48 h at 33°C. The remaining viable cells were stained with 0.5% crystal violet in 20% methanol, washed extensively with water, extracted with methanol, and quantified by measuring the absorption at 570 nm. Under these conditions, the virus-infected, unprotected HeLa cells were all lysed by visual inspection; therefore, the absorbance of the triplicate virus samples represented the background crystal violet staining of the cell debris. The percent protection was calculated as 100 x [(absorbance of sample - absorbance of virus only)/(absorbance of uninfected samples - absorbance of virus only)].
Viral protection assays were performed in a similar manner with BEAS-2B cells, except these cells do not lyse upon rhinoviral infection. The progression of infection was measured by determining the titers of the progeny virus released into the medium. The BEAS-2B human respiratory epithelial cells were pretreated with 100 µl of 1 µg of monomeric Fab19 (21 nM), trimeric CFY195 (5.8 nM), tetrameric CFY196 (4.3 nM), or anti-ICAM-1 MAb 84H10 (6.7 nM; MAb 1379; Chemicon) per ml. These solutions were then removed, and the monolayers were infected with HRV serotype 15 at a multiplicity of infection of 30. After 2 h of viral attachment, the cells were washed with epithelial cell medium to remove any unbound virus and incubated in fresh medium at 33°C. After 48 h, the titer of the progeny virus released into the cell medium was measured by using HeLa cells as a target. The titers of virus from protected cells were compared and expressed as a percentage of the titers obtained from unprotected cells.
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and CREBPa. Changes of the residues in the a and d positions of the heptad repeats [(abcdefg)n] resulted in dimers, trimers, and tetramers in a context-dependent manner (Table 1). These compact domains were attached to the Fab at the Fd carboxy terminus by linkers derived from the long, flexible human IgD hinge sequence. After translation, the light and composite heavy chains are secreted into the periplasmic space, where the complete assembly of multimeric Fab occurs.
Tetrameric, trimeric, dimeric, and monomeric Fab proteins were produced in E. coli and purified to a yield of 1 to 10 mg of homogeneous protein per liter of shaker flask culture. The tetrameric molecules have four flexible Fab arms available for binding. Cross-linking studies with a zero-length cross-linker revealed that the tetramers formed from ATF
coiled-coil domains are parallel in orientation (data not shown). A theoretical model of one of these tetrameric chimeric proteins, CFY484, is depicted in Fig. 1.
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FIG. 1. Illustration of our conception of the tetrameric Fab anti-ICAM-1 molecule. A homology model of Fab19 was attached to a modeled representation of a hinge and multimerization domain to form a tetravalent Fab protein. Molecular models were constructed by using the programs Swiss Model and Swiss PDB Viewer (6). Each polypeptide chain is represented by a different color.
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Characterization of oligomeric status.
The oligomeric status of each fusion protein was characterized by size-exclusion chromatography, analytical ultracentrifugation, and dynamic light scattering. By gel filtration analysis with Superdex 200, monomeric Fab19 has a retention time of 24.83 min. Under the same chromatography conditions, the retention time of CFY199 is 18.35 min, that of CFY195 is 17.04 min, and that of CFY196 is 16.03 min. The mobility of standards in the same column suggests that Fab19 is a monomer, CFY199 is a dimer, and CFY195 and CFY196 are higher-order multimers. Sedimentation velocity experiments further characterize these multimers. Data from the analytical ultracentrifugation (22) as well as dynamic light scattering (28) experiments are summarized in Table 2. These analyses confirmed the results obtained by size-exclusion chromatography. They also demonstrated that CFY199 is a dimer, that CFY193B and CFY195 are trimers, and that CFY196 and CFY484 are tetramers. Therefore, CREB-IL is a dimerization domain, ATF
-LL and ATF
-II are trimerization domains, and ATF
-LI is a tetramerization domain.
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TABLE 2. Physical characteristics of purified multimeric proteins
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While the surface with a high level of substitution exhibited a convolution of the effects of multivalency and mass action, the advantage of multivalent binding is apparent. If one compares the dissociation from the surfaces with low and high levels of substitution, the rate of dissociation of monomeric Fab19 is slowed 1.3-fold, dimeric CFY199 dissociates 3-fold more slowly, and tetrameric CFY196 dissociates 30-fold more slowly. These data demonstrate that multivalency has provided the characteristic that we sought: a tetravalent protein with a greatly diminished koff.
Functional characterization of effectiveness of multivalent Fab fusion proteins against ICAM-1. We compared the effectiveness of multimeric Fab19 using three methods: a competitive ELISA measuring ICAM-1 binding and two viral protection assays.
Because conventional ELISA cannot distinguish between the high-affinity anti-ICAM-1 multimers, we designed a two-step competition ELISA using high-affinity tetrameric 196TGC linked to HRP (196TGC-HRP) as a tracer. The anti-ICAM-1 proteins to be assessed were bound to immobilized ICAM-1, and then 196TGC-HRP was added and allowed to compete with the tested protein for ICAM-1 binding. Monomeric Fab19 inhibited only 25% tracer antibody (196TGC-HRP) binding at the highest concentration tested; however, the trimer (CFY195) and the tetramer (CFY196) gave much higher percent inhibitions, with IC50s equal to 0.54 and 0.069 µg/ml, respectively (Fig. 2).
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FIG. 2. Competitive ELISA results. The graph shows the percent inhibition of tracer antibody binding as a function of the amount of each protein added to wells coated with soluble human ICAM-1. Triangles, CFY196; squares, CFY195; diamonds, Fab19.
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FIG. 3. Protection of HeLa cells from HRV infection by proteins that are multimers of anti-ICAM-1 Fab19. Percent protection was calculated as indicated in Materials and Methods, with 100% protection being equivalent to the staining of uninfected cells and 0% protection being equivalent to the staining of infected untreated cells. Circles, MAb RR1; triangles, CFY193B; squares, CFY202; diamonds, CFY196. The points represent mean values from one experiment in which the samples were tested in triplicate. The error bars represent standard deviations.
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FIG. 4. Reduction of viral titer in protected respiratory epithelial cells. Viral titers from HRV serotype 15-infected BEAS-2B cells before infection and 48 h after infection are shown. Each percentage is the mean from two independent experiments measured from cells pretreated with the indicated proteins. The error bars represent the standard deviations. A value of 100% corresponds to the titer of virus produced from infected cells with no protective pretreatment.
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Application of this technology has enabled us to generate receptor blockers that prevent HRV infection in tissue culture at a concentration much lower than that which was previously attainable. We have demonstrated that the activities of our ICAM-1-binding proteins improve in proportion to their valency. In both tissue culture models presented here, we inhibited HRV infection most effectively with tetrameric CFY196. In these experiments, CFY196 was able to compete effectively with multivalent rhinovirus for ICAM-1 binding. The greatly diminished koff and high avidity of CFY196 suggest potential for in vivo therapeutic effectiveness.
The final tetrameric chimera is more than 200-fold more effective than the corresponding Fab at binding to ICAM-1 and preventing HRV infection. While the particular Fab used in this study is of moderate affinity, similar improvement is to be expected for any binding interaction in which the target presents multiple ligands in reasonable molecular proximity. Natural dimeric antibodies range in affinity (Kd) from about 10-7 M-1 to below 10-11 M-1. For the tightest natural antibodies, a 50- to 100-fold increase in affinity may be both hard to measure and functionally trivial. Nevertheless, increased avidity through multimerization provides an important engineering tool for increasing binding affinity that is completely separate and complementary to any affinity maturation process.
Our multimerization domains could be used as a cassette to improve a whole host of antibodies in development for therapeutic application. In addition, multimers may be used in any context in which greater binding efficiency is desired. Application of our method requires only the availability of a moiety that can be adapted for use as part of a chimeric protein. Furthermore, multimerization may be used in any context in which greater valency alone is desirable for improved function.
Contract service work was provided by John Philo (Alliance Protein Labs) and Research Consulting Services, BIAcore, Inc. This work was partially supported by NIH SBIR grant 1 R43 AI49624-01A1.
Present address: The Salk Institute, San Diego, Calif. ![]()
Present address: RNAture, Irvine, Calif. ![]()
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1 gene. Nucleic Acids Res. 10:4071-4079.
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