# Patent

## Title
Antibody screening methods

## Abstract

Provided are methods and compositions for the production of novel antibodies that bind specifically to a target antigen. These methods and compositions are particularly useful for producing antibodies having the antigen binding specificity of a reference antibody but with improved properties (e.g., binding affinity, immunogenicity, and thermodynamic stability) relative to the reference antibody.

## Background
RELATED APPLICATIONS
This application claims priority to U.S. provisional applications 61/453,106 filed on Mar. 15, 2011, and 61/566,778 filed on Dec. 5, 2011, which are hereby incorporated by reference in their entireties.


BACKGROUND
Monoclonal antibodies are hugely important as research tools, diagnostics and therapeutics. This is, in large part, due to the fact that monoclonal antibodies can be selected to bind with high specificity and affinity to almost any structural epitope.
Classical methods of immunizing animals to obtain antibodies are slow and cumbersome and, as a result, many in vitro selection techniques have been now developed. Examples of the techniques include nucleic acid display, phage display, retroviral display, and cell surface display (e.g., yeast, mammalian, and bacterial cells). In spite of these technological developments, it is still relatively difficult to obtain antibodies that possess the desired kinetic properties, selectivity, biophysical properties, and immunogenicity necessary for therapeutic use.
Accordingly, there is a need in the art for improved methods for the selection of antibodies against a desired target.
SUMMARY OF THE INVENTION
The invention provides methods and compositions for the production of novel antibodies that bind specifically to a target antigen. The invention is particularly useful for producing novel antibodies having the antigen binding specificity of a reference antibody but with improved properties (e.g., binding affinity, immunogenicity, and thermodynamic stability) relative to the reference antibody. In particular, the methods disclosed herein make it possible to rapidly generate an entirely novel antibody molecule starting only from a CDR3 of known antigen-binding specificity.
The disclosed methods also allow for the rapid identification of novel pairs of VH and VL domains having a high intrinsic thermostability. Prior art methods for selecting VH/VL binding pairs generally involve the enforced covalent linkage of VH and VL domains (e.g., as Fab or scFv fragments) and selection of VH/VL pairs based solely upon binding affinity of the linked VH and VL domains to a target antigen, without any being paid attention to the strength of non-covalent interaction between VH and VL domains. In contrast, the methods disclosed herein select stable VH/VL pairs based upon the strength of the non-covalent interaction between unpaired VH and VL domains (in addition to the binding affinity for a target antigen). As a result, the novel methods disclosed herein yield VH/VL pairs with greater intrinsic thermostability than those obtained using prior art methods.
Accordingly, in one aspect the invention provides a method for producing a V domain that binds specifically to a target antigen. The method generally comprises: (a) providing a library of chimeric, unpaired VH or VL domains wherein diversity lies in the FR1-FR3 regions of each domain, and wherein each member of the library comprises the CDR3 region sequence from a reference antibody that binds specifically to the antigen; (b) contacting the library with the antigen; and (c) selecting from the library at least one chimeric, unpaired VH or VL domain that binds specifically to the antigen, thereby producing a V domain that binds specifically to the antigen.
In certain embodiments, the method further comprises introducing additional amino acid sequence diversity into the library of step (a). In one embodiment, additional amino acid sequence diversity is introduced by random mutagenesis.
In certain embodiments, the method further comprises the step of (d) introducing additional amino acid sequence diversity into the VH or VL domain(s) selected in step (c).
In certain embodiments, the CDR3 region sequence is from a rodent, lagomorph, avian, camelid, shark, or human antibody.
In certain embodiments, each member of the library comprises an identical CDR3 region sequence.
In certain embodiments, the FR4 region sequences of said domains are human sequences.
In certain embodiments, the FR1-FR3 region sequences of the VH and VL domains are human sequences.
In certain embodiments, each member of the library comprises FR1-FR3 sequences encoded by a single human antibody VH or VL gene.
In certain embodiments, the library is a nucleic acid display library e.g., a dsDNA display library.
In another aspect, the invention provides library of chimeric, unpaired VH or VL domains wherein diversity lies in the FR1-FR3 regions of said domains, and wherein each member of the library comprises the CDR3 region sequence from the VH or VL domain of a reference antibody.
In certain embodiments, the CDR3 region sequence is from a rodent, lagomorph, avian, camelid, shark, or human antibody.
In certain embodiments, each member of the library comprises an identical CDR3 region sequence.
In certain embodiments, the FR4 region sequences of said domains are human sequences.
In certain embodiments, the FR1-FR3 region sequences of the VH and VL domains are human sequences.
In certain embodiments, each member of the library comprises FR1-FR3 sequences encoded by a single human antibody VH or VL gene.
In certain embodiments, the library is a nucleic acid display library e.g., a dsDNA display library.
In another aspect, the invention provides a method for selecting a stable VH/VL pair. The method generally comprises: (a) providing a VH domain that binds specifically to an antigen; (b) contacting the VH domain with a library of VL domains such that a library of VH/VL pairs is formed; (c) contacting the library of VH/VL pairs with the antigen; and (d) selecting from the library of VH/VL pairs at least one VH/VL pair that binds specifically to the antigen, thereby selecting a stable VH/VL pair.
In certain embodiments, the method further comprises the step of introducing additional amino acid sequence diversity into library of VL domains of step (b). In one embodiment, the additional amino acid sequence diversity is introduced by random mutagenesis.
In certain embodiments, the library of VL domains of step (b) comprises human VL domains.
In certain embodiments, the library of VL domains or VH/VL pairs is a nucleic acid display library, e.g., a dsDNA display library.
In certain embodiments, the complementary VH domain of step (a) is produced by the methods disclosed herein.
In another aspect, the invention provides a method for selecting a bispecific, stable VH/VL pair. The method generally comprises: (a) providing a VH domain that binds specifically to a first antigen; (b) contacting the VH domain with a library of VL domains such that a library of VH/VL pairs is formed; (c) contacting the library of VH/VL pairs with a second antigen; (d) selecting from the library of VH/VL pairs at least one VH/VL pair that binds specifically to the second antigen; and (e) contacting the VH/VL pair(s) selected in step (d) with the first antigen; and (f) selecting at least one VH/VL pair that binds specifically to the first antigen, thereby selecting a bispecific, stable VH/VL pair.
In certain embodiments, the method further comprises the step of introducing additional amino acid sequence diversity into library of VL domains of step (b). In one embodiment, the additional amino acid sequence diversity is introduced by random mutagenesis.
In certain embodiments, the library of VL domains of step (b) comprises human VL domains.
In certain embodiments, the library of VL domains or VH/VL pairs is a nucleic acid display library, e.g., a dsDNA display library.
In certain embodiments, the complementary VH domain of step (a) is produced by the methods disclosed herein.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a schematic representation of exemplary CDR3/framework shuffling methods as disclosed herein.
FIG. 2 is a schematic representation of the construction of exemplary VH nucleic acid display libraries for use in the disclosed methods.
FIG. 3 is a schematic representation of exemplary nucleic acid display methods for use in the disclosed methods. The letter “b” represents biotin and the circles represent a tetrameric biotin binding molecule.
FIG. 4 depicts the results of in vitro binding assays measuring the binding to human or mouse PDGFRb of the XB1511VH domain, an unselected XB1511 CDR3/framework shuffled DNA display library (R0), and an XB1511 CDR3/framework shuffled DNA display library pool after four rounds of selection (R4).
FIG. 5 depicts the results of surface Plasmon resonance binding studies measuring the binding kinetics of XB1511 and the framework shuffled derivatives XB2202 and XB2708 to human PDGFRb.
FIG. 6 depicts the results of surface plasmon resonance binding assays measuring the binding kinetics of XB2202 to human (A) and mouse (B) PDGFRβ.
FIG. 7 depicts the results of surface plasmon resonance binding assays measuring the binding kinetics of XB2708 to human (A) and mouse (B) PDGFRβ.
FIG. 8 is a schematic representation of the construction of exemplary VL nucleic acid display libraries for use in the disclosed methods.
FIG. 9 is a schematic representation of exemplary methods for identification of stable VH/VL pairs.
FIG. 10 depicts the results of ELISA assays measuring the binding to human PDGFRb of XB1511/VL scFv comprising VL isolated from the second round screening pool of a VH/VL pairing DNA display screen.
FIG. 11 depicts the results of ELISA assays measuring the binding to human PDGFRb of XB1511/VL scFv comprising VL isolated from the third round screening pool of a VH/VL pairing DNA display screen.
FIG. 12 depicts the results of ELISA assays measuring the binding to human PDGFRb of XB2202/VL scFv comprising VL isolated from the second round screening pool of a VH/VL pairing DNA display screen.
FIG. 13 depicts the results of ELISA assays measuring the binding to human PDGFRb of unpaired VL from the XB1511/VL scFv set forth in FIG. 9.
FIG. 14 depicts the results of solution binding affinity studies measuring the binding to human PDGFRb of 35S Met labeled XB1511 VH domain and XB1511-containing scFV obtained from VH/VL pairing DNA display screens.
FIG. 15 depicts the results of solution binding affinity studies measuring the binding to human PDGFRb of 35S Met labeled XB2202 VH domain and XB2202-containing scFV obtained from VH/VL pairing DNA display screens.
FIG. 16 depicts the results of label-free migration assays measuring the ability of an XB1511-containing IgG1 to inhibit the migration of human foreskin fibroblasts.
FIG. 17 depicts the results of ELISA assays measuring the binding to human PDGFRb of XB2202 VH and XB2202/A4 scFv after incubation at various temperatures.



DETAILED DESCRIPTION
The invention provides methods and compositions for the production of novel antibodies that bind specifically to a target antigen. The invention is particularly useful for producing antibodies having the antigen binding specificity of a reference antibody but with improved properties (e.g., binding affinity, immunogenicity, and thermodynamic stability) relative to the reference antibody.
I. DEFINITIONS
As used herein, the terms “VH domain” and “VL domain” refer to single antibody variable heavy and light domains, respectively, comprising FR (Framework Regions) 1, 2, 3 and 4 and CDR (Complementary Determinant Regions) 1, 2 and 3 (see e.g., Kabat et al. (1991) Sequences of Proteins of Immunological Interest. (NIH Publication No. 91-3242, Bethesda). The CDR boundaries can be defined using any art recognized numbering system.
As used herein, the term “V domain” refers to a single polypeptide comprising a VH domain or VL domain that is devoid of constant region sequences that facilitate the covalent pairing of said VH domain or VL domain with a complementary VL domain or VH domain, respectively.
As used herein, the term “FR1-FR3” refers to the region of a VH encompassing FR1, CDR2, FR2, CDR2 and CDR3, but excluding the CDR3 and FR4 regions.
As used herein, the term “chimeric” refers to an antibody variable domain comprising amino acid sequences from two or more different antibody variable domain, e.g., a variable domain with CDR3 sequences from a reference antibody and FR1-FR3 sequences from one or more different antibodies.
As used herein, the term “unpaired” refers to VH or VL that are not linked (either covalently or non-covalently) to a complementary VL or VH domain, respectively.
As used herein, the term “complementary VL or VH domain” refers to a VL or VH domain that associates with a VH or VL domain, respectively, to form a VH/VL pair.
As used herein, the term “VH/VL pair” refers to a non-covalent dimer of a single VH and a single VL domain, wherein the VL and VH domains are associated through the natural VH/VL dimer interface in a similar manner to that observed in a complete, tetrameric immunoglobulin molecule, and the dimer can bind specifically to at least one target antigen. A “stable VH/VL pair” is a VH/VL pair that does not exhibit significant dissociation of the substituent VH and VL domains under physiological conditions.
As used herein, the term “bispecific” refers to a VH/VL pair, wherein the VH and the VL domains bind to different antigens.
As used herein, the term “nucleic acid display library” refers to any art recognized in vitro cell-free phenotype-genotype linked display, including, without limitation those set forth in, for example, U.S. Pat. Nos. 7,195,880; 6,951,725; 7,078,197; 7,022,479; 6,518,018; 7,125,669; 6,846,655; 6,281,344; 6,207,446; 6,214,553; 6,258,558; 6,261,804; 6,429,300; 6,489,116; 6,436,665; 6,537,749; 6,602,685; 6,623,926; 6,416,950; 6,660,473; 6,312,927; 5,922,545; and 6,348,315, and in WO2010/011944, which are all hereby incorporated by reference in their entirety.
As used herein, the term “specifically binds to” refers to the ability of a binding molecule (e.g., a VH or VL domain) to bind to an antigen with an affinity of at least about 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M, 1×10−11 M, 1×10−12 M, or more, and/or bind to a target with an affinity that is at least two-fold greater than its affinity for a nonspecific antigen.
As used herein, the term “antigen” refers to the binding site or epitope recognized by a binding molecule (e.g., a VH or VL domain).
As used herein, the term “reference antibody” refers to any antibody that binds specifically to an antigen of interest.
As used herein, the term “antibody” refers to IgG, IgM, IgA, IgD or IgE or an antigen-binding fragment thereof (e.g. VH and/or VL), whether derived from any species naturally producing an antibody, or created by recombinant DNA technology.
II. METHODS FOR CDR3/FRAMEWORK SHUFFLING OF ANTIBODY VARIABLE DOMAINS
In one aspect, the invention provides a method for producing a V domain that binds specifically to a target antigen. This method allows for the rapid generation of an entirely novel antibody molecule starting only from a CDR3 of known antigen-binding specificity. The method generally comprises the steps of: (a) providing a library of chimeric, unpaired VH or VL domains wherein diversity lies in the FR1-FR3 regions of each domain, and wherein each member of the library comprises a CDR3 region sequence that binds specifically to the antigen; (b) contacting the library with the antigen; and (c) selecting from the library at least one chimeric, unpaired VH or VL domain that binds specifically to the antigen.
The CDR3 region sequence can be artificial, naturally derived, or a combination thereof. Naturally derived CDR3 region sequences can be from any organism that produces an antibody including, but not limited to, rodent, lagomorph, avian, camelid, shark, or human.
The CDR3 sequence can be from an antibody heavy chain or a light chain. However, the skilled worker will appreciate that the CDR3 must match the V-domain context into which it is placed e.g., a heavy chain CDR3 should be used in a VH domain library and a light chain CDR3 should be used in a VL domain library.
In certain embodiments, the library contains a single species of CDR3 sequence. In a particular embodiment, the CDR3 sequence is from a single reference antibody that binds to the target antigen. In other embodiments, the library contains multiple species of CDR3 sequence. In a particular embodiment, the multiple species of CDR3 sequence are variants of a single CDR3 sequence from a single reference antibody. Such variants can be produced by alteration (e.g. substitution, addition, deletion and/or modification) of at least one amino acid in the CDR3 sequence from the reference antibody. Alterations can be generated randomly (e.g., by random mutagenesis) or in a site-directed fashion using any art recognized means.
In general, the library comprises a diversity plurality of diverse FR1-FR3 region amino acid sequences. The plurality of FR1-FR3 region amino acid sequences can be from any source including, without limitation, naturally-occurring variable regions (e.g, from the antibody VH or VL gene repertoire of an animal), artificial antibody variable regions, or a combination thereof. In certain embodiments, each member of the library comprises FR1-FR3 sequences encoded by a single antibody VH or VL gene (e.g., a human VH or VL gene). In other embodiments, the FR1-FR3 region sequences are human sequences. In a particular embodiment, the FR1-FR3 region sequences are naturally-occurring human antibody variable region sequences from the B-cells of healthy donors.
In certain embodiments, the V domain further comprises an FR4 region. The FR4 region can be from the reference antibody or from another source. Suitable sources include, without limitation, naturally occurring human antibody variable regions, artificial antibody variable regions, or a combination thereof.
The V-domain library can be generated using any art recognized methods including, without limitation, ab initio nucleic acid synthesis and DNA or RNA polymerase-mediated assembly. In a preferred embodiment, the library is assembled by PCR using overlapping oligonucleotides. Suitable oligos for assembling a VH domain library include those set forth in SEQ ID No: 4-21. Suitable oligos for assembling a VL domain library include those set forth in SEQ ID No: 70-102.
The chimeric, unpaired VH or VL domain(s), selected using the methods of invention, can be paired with a complementary VL or VH, respectively, to generate a VH/VL pair using the methods disclosed herein.
III. METHODS FOR IDENTIFICATION OF STABLE VH/VL PAIRS
In another aspect, the invention provides a method for selecting stable VH/VL pairs. This method selects stable VH/VL binding pairs based upon the strength of the non-covalent interaction between unpaired VH and VL domains and allows for the rapid identification of novel pairs of VH and VL domains having a high intrinsic thermostability. The method generally comprises the steps of: (a) providing a VH domain that binds specifically to an antigen; (b) contacting the VH domain with a library of VL domains such that a library of VH/VL pairs is formed; (c) contacting the library of VH/VL pairs with the antigen; and (d) selecting from the library of VH/VL pairs at least one VH/VL pair that binds specifically to the antigen.
The VH domain that is used to screen for stable VH/VL pairs can be from any source (artificial, naturally derived, or a combination thereof). In certain embodiments, the VH domain is a from a reference antibody. In other embodiments, the VH domain is a chimeric VH domain selected using the CDR3/Framework methods disclosed herein.
The library of VL domains that is used to screen for stable VH/VL pairs can be from any source (artificial, naturally derived, or a combination thereof). In certain embodiments, the library of VL domains is a human VL domain library. In a particular embodiment, the human VL domain library comprises naturally-occurring human antibody VL region sequences from the B-cells of healthy donors. The VL domain libraries disclosed herein are particularly suitable for use in these methods.
Although it is preferred to screen a library of VL domains using a VH domain as the bait, the skilled worker will appreciate that it is entirely within the scope of the invention to perform the converse screen i.e., to screen a library of VH domains using a VL domain as the bait. This method general comprises that steps of: (a) providing a VL domain that binds specifically to an antigen; (b) contacting the VL domain with a library of VH domains such that a library of VH/VL pairs is formed; (c) contacting the library of VH/VL pairs with the antigen; and (d) selecting from the library of VH/VL pairs at least one VH/VL pair that binds specifically to the antigen, thereby selecting a stable VH/VL pair.
In another aspect, the invention provides, a method for selecting a stable VH/VL pair, wherein the method generally comprises: (a) providing a first nucleic acid display library of VH domains, wherein members of the library comprise a VH domain linked to its cognate nucleic acid coding sequence; (b) providing a second nucleic acid display library of VL domains, wherein members of the library comprise a VL domain linked to its cognate nucleic acid coding sequence; (c) contacting the first nucleic acid display library with the second nucleic acid display library such that a library of VH/VL pairs is formed; (d) contacting the library of VH/VL pairs with an antigen; and (e) selecting from the library of VH/VL pairs at least one VH/VL pair that binds specifically to the antigen, and, (f) ligating together the nucleic acid coding sequences of the VH and VL domains in the VH/VL pairs selected in step (e). This method is particularly advantageous in that it allows for the simultaneous screening of VH and VL domain libraries and the precise determination of the sequences of the VH and VL domains in each selected, stable VH/VL pair.
The nucleic acid coding sequences in each selected VH/VL pair can be ligated together using any appropriate art recognized means (e.g., chemical and/or enzymatic). RNA can be ligated with, for example, RNA ligase. DNA can be ligated, with, for example, DNA ligase. Ligation of the VH and VL domain nucleic acid coding sequences can be facilitated by the use of, for example, nucleic acid linkers, adaptors and/or restriction enzyme digestion. In certain embodiments, the nucleic acid coding sequences of the VH and VL domain in each selected VH/VL pair are ligated together to form a single, continuous nucleic acid sequence (linear or circular), and the VH and VL domain sequences present in the continuous nucleic acid sequence are determined. Nucleic acid sequence determination can achieved by any art-recognized means, including without limitation, single molecule DNA sequencing.
The above methods for identification of stable VH/VL pairs are particularly suitable for use in combination with the CDR3/framework shuffling methods disclosed herein. This combination of methods allows selection of a novel, stable VH/VL pair specific for a target antigen using only an antigen-specific CDR3 sequence as a starting point.
The methods of the invention are particularly useful for screening for stable VH/VL pairs. However, one skilled in the art will appreciate that the invention can be used more broadly to screen for any stable protein dimer, wherein at least one monomer of the dimer binds to a ligand. Suitable protein dimers include, without limitation, immunoglobulin superfamily members (e.g., T-cell receptors), hormones, cytokines, transcription factors, and the like.
IV. METHODS OF PRODUCING BISPECIFIC ANTIBODIES
In another aspect, the invention provides a method for selecting a bispecific, stable VH/VL pair, (e.g., a VH/VL pair in which the VH and VL domains bind to two different antigens). The method generally comprises the steps of: (a) providing a VH domain that binds specifically to a first antigen; (b) contacting the VH domain with a library of VL domains such that a library of VH/VL pairs is formed; (c) contacting the library of VH/VL pairs with a second antigen; (d) selecting from the library of VH/VL pairs at least one VH/VL pair that binds specifically to the second antigen; and (e) contacting the VH/VL pair(s) selected in step (d) with the first antigen; and (f) selecting at least one VH/VL pair that binds specifically to the first antigen.
In one embodiment, the first and second antigens are different epitopes present in a single molecule. In another embodiment, the first and second antigens are epitopes present in two separate molecules.
In certain embodiments, it is desirable to select for a promiscuous light chain that can bind to at least two different VH domains (with different antigen specificities) but that cannot, itself, specifically bind to an antigen (e.g., has a low affinity for all antigens). Such light chains are particularly useful in that they can be used in the assembly of full-length, bispecific, heterotetrameric antibodies. These bispecific antibodies generally comprising a first heavy chain with a first antigen specificity, a second heavy chain with second antigen specificity, and two molecules of the selected promiscuous light, wherein each heavy chain is paired with a different promiscuous light chain molecule.
V. LIBRARY SCREENING METHODS
The skilled worker will appreciate that any type of VH or VL domain expression library can be employed in the methods of the invention. Suitable expression libraries include, without limitation, nucleic acid display, phage display, retroviral display, and cell surface display libraries (e.g., yeast, mammalian, and bacterial cells). In certain embodiments, the library is a nucleic acid display library. In a preferred embodiment, the nucleic acid display library is a DNA-display library constructed as exemplified herein or in WO2010/011944, which is hereby incorporated by reference in its entirety.
Methods for screening expression libraries are well known in the art. See, for example, Antibody Engineering: Methods and Protocols. Methods in Molecular Biology Volume 248, (B. K. C. Lo, Ed) Humana Press, 2004 (ISBN: 1-58829-092-1), which is hereby incorporated by reference in its entirety. Suitable methods of screening nucleic acid display libraries, include, without limitation those set forth in U.S. Pat. Nos. 7,195,880; 6,951,725; 7,078,197; 7,022,479; 6,518,018; 7,125,669; 6,846,655; 6,281,344; 6,207,446; 6,214,553; 6,258,558; 6,261,804; 6,429,300; 6,489,116; 6,436,665; 6,537,749; 6,602,685; 6,623,926; 6,416,950; 6,660,473; 6,312,927; 5,922,545; and 6,348,315, and in WO2010/011944, which are all hereby incorporated by reference in their entirety. In a preferred embodiment, the screening of nucleic acid-display libraries is performed as exemplified herein or in WO2010/011944.
The methods of the invention are particularly well suited to generating VH or VL domains, and/or VH/VL pairs that bind to a target antigen with high affinity. To enhance affinity for the antigen, multiple rounds of library screening can be performed, with additional amino acid sequence diversity being introduced at each screening round, if desired. If desired, the stringency of the method can be enhanced by altering the assay conditions to reduce the affinity of the VH or VL domains for the antigen, for example, by altering the pH and/or salt concentration of the antigen binding reaction. Such methods selectively enrich for VH or VL domains with the highest affinity and stability.
The methods of the invention also allow for selection of VH or VL domains, and/or VH/VL pairs having a different antigen specificity to that of a starting reference antibody. For example, the HCDR3 from an antibody that only binds to human PDGFRb can be used to select for a VH domain, and/or VH/VL pair that binds to both human and mouse PDGFRb. Such a selection is exemplified in Example 2 herein.
In certain embodiments, additional amino acid sequence diversity is introduced into the VH or VL domain library, or the VH or VL domain(s) selected from the library. Amino acid sequence diversity can be introduced by any art-recognized means. In certain embodiments, amino acid sequence diversity is introduced by alteration of the nucleic acid sequence(s) encoding the VH or VL domain library, or the VH or VL domain. In certain embodiments amino acid sequence diversity is introduced by random mutagenesis. Such random mutagenesis can be achieved, for example, by low-fidelity PCR amplification of the nucleic acid sequence(s) encoding the VH or VL domain library, or the VH or VL domain.
VI. ANTIBODY FORMATS
The VH and/or VL domains employed in the methods of the invention can be used in isolation or fused to additional amino acids (e.g., epitope tags) and/or domains. In certain embodiments, at least one VH domain in a library is fused to at least one CH1 domain, CH2 domain, CH3 domain or a combination thereof. In a particular embodiment, at least one VH domain in a library is fused to at least one heavy chain constant region comprising at least one CH1 domain, CH2 domain and CH3 domain. In certain embodiments, at least one VL domain in a library is fused to at least one light chain constant region.
VH or VL domains, and/or VH/VL pairs selected using the methods of the invention can be incorporated into another antibody format including, without limitation, scFv, Fab, and/or complete tetrameric antibody.
VII. EXAMPLES
The present invention is further illustrated by the following examples which should not be construed as further limiting. The contents of Sequence Listing, figures and all references, patents and published patent applications cited throughout this application are expressly incorporated herein by reference.
Example 1. Isolation of VH Domains that Bind Specifically to Human PDGFRb
VH domains that bind specifically to human PDGFRb were selected using DNA display as set forth in WO2010/011944, which is hereby incorporated by reference in its entirety. Specifically, a naïve, human VH domain DNA display library containing derived from 10 bone marrow donors was subject to six rounds of selection against human PDGFRb. The selected binders were cloned and sequenced. From this screen VH domain clones A4, B4 and G2 were selected, the amino acid sequences of which are set forth in Table 1.







TABLE 1







Amino acid sequences of exemplary PDGFRb-binding VH domains.









Clone

SEQ ID


name
VH Amino Acid Sequence
NO.





A4
QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQG
1


XB1511
LEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRS




EDTAVYYCAIHGGDRSYWGQGTLVTVSS



 


B4
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYAISWVRQAPGQG
2



LEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRS




EDTAVYYCAIHGGDRSYWGQGTLVTVSS



 


G2
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYAISWVRQAPGQG
3



LEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRS




KDTAVYYCAIHGGDRSYWGQGTLVTVSS









Example 2. HCDR3 Shuffling
A. VH Library Construction
To screen for VH domains with improved binding characteristics, the HCDR3 sequence of clone A4 (designated XB1511) was shuffled into a naïve human VH library, which was further selected for binding to human and mouse PDGFRb. Specifically, the DNA sequence coding for the HCDR3 of clone A4 (SEQ ID NO: 1) was synthesized and assembled into a library comprising framework regions 1-3 of naïve human VH domains amplified from bone marrow B cells and PBMCs using framework specific oligonucleotides. Human VH framework regions 1-3 were amplified using 5′ VH family-specific and 3′ generic FR3 reverse primers to create separate libraries of VH family framework regions. The VH family framework libraries and the XB1511 HCDR3 were shuffled by further PCR amplification using 5′ T7TMV and 3′ XB1511 FR3CDR3FR4 oligos. This also added a T7TMV promoter sequence at the 5′ end for in vitro transcription/translation. A C-terminal Cμ3 sequence and a FLAG tag (for purification after translation) were also added by PCR using FR4 Cu3 Reverse and Y109 primers, respectively, together with the 5′ T7TMV primer. The nucleic acid sequences of the oligonucleotides used for preparation of the HCDR3-shuffled VH library are set forth in Table 2. A schematic representation of the general concept of CDR3/framework shuffling is set forth is FIG. 1, and a schematic representation of the VH library construction is set forth in FIG. 2.







TABLE 2







Oligonucleotides for constructing HCDR3 shuffled VH libraries











SEQ ID


Oligo
Sequence
NO.





FR3 Reverse
CGCACAGTAATACACGGC
 4.


 


VH1a
CAATTACTATTTACAATTACAATGCAGGTKCAGCTGGTGCAGTCTG
 5.


 


VH1b
CAATTACTATTTACAATTACAATGCAGGTCCAGCTTGTGCAGTCTG
 6.


 


VH1c
CAATTACTATTTACAATTACAATGSAGGTCCAGCTGGTACAGTCTG
 7.


 


VH1d
CAATTACTATTTACAATTACAATGCARATGCAGCTGGTGCAGTCTG
 8.


 


VH2
CAATTACTATTTACAATTACAATGCAGRTCACCTTGAAGGAGTCTG
 9.


 


VH3a
CAATTACTATTTACAATTACAATGGARGTGCAGCTGGTGGAGTCTG
10.


 


VH3b
CAATTACTATTTACAATTACAATGCAGGTGCAGCTGGTGGAGTCTG
11.


 


VH3c
CAATTACTATTTACAATTACAATGGAGGTGCAGCTGTTGGAGTCTG
12.


 


VH4a
CAATTACTATTTACAATTACAATGCAGSTGCAGCTGCAGGAG
13.


 


VH4b
CAATTACTATTTACAATTACAATGCAGGTGCAGCTACAGCAGTGG
14.


 


VH5
CAATTACTATTTACAATTACAATGGARGTGCAGCTGGTGCAGTCTG
15.


 


VH6
CAATTACTATTTACAATTACAATGCAGGTACAGCTGCAGCAGTCAG
16.


 


VH7
CAATTACTATTTACAATTACAATGCAGGTGCAGCTGGTGCAATCTG
17.


 


T7TMVUTR
TAATACGACTCACTATAGGGACAATTACTATTTACAATTACA
18.


 


XB1511
TGAGGAGACGGTGACCAGGGTTCCCTGGCCCCAGTAGCTCCTGTCG
19.


FR3CDR3FR4
CCCCCATGTKTCGCACAGTAATACACGGC



Reverse




 


FR4 Cu3
GGAGACGAGGGGGAAAAGGGTTGAGGAGACGGTGACCAG
20.


Reverse




 


Y109
TTTTTTTTTTTTTTTTTTTTAAATAGCGGATGCTAAGGACGACTTG
21.



TCGTCGTCGTCCTTGTAGTCGGAGACGAGGGGGAAAAGGGT









B. Library Screening

The HCDR3 shuffled VH domain library was then transcribed into an mRNA library and subjected to selection with dsDNA display technology as set forth in WO2010/011944. A schematic representation of the screening method is set forth in FIG. 3. The selection was carried out with human and mouse PDGFRb at alternate round for 4 rounds. Kinetic controlled on and off rate selection was applied at successive rounds to increase the stringency of the selection to improve the affinity. Specifically, selection was performed as follows: Round 1 (R1) with 10 nM of immobilized human PDGFRb; R2 with immobilized 100 nM mouse PDGFRb; R3 with 10 nM soluble human PDGFRb and competed with 200 nM immobilized human PDGFRb for 24 hours and 120 hours; and R4 with 10 nM mouse PDGFRb. The R4 binding pool was subcloned for DNA sequencing. Analysis of the sequences of the R4 binding pool showed that the HCDR3 of XB1511 was present in a variety of different framework contexts. No wild type parental sequence was obtained from the set of sequences analyzed. The amino acid sequences of the selected VH domains are set forth in Table 3.







TABLE 3







Amino acid sequences of exemplary PDGFRb-binding VH domains selected


from HCDR3 shuffled VH libraries.









Clone

SEQ ID


name
VH Amino Acid Sequence
NO.






XB1511 framework shuffled and selected with 2 rounds




on human and 2 rounds on mouse PDGFRb targets



XB2202
QVQLVQSGAEVKKPGSSVRVSCKASGGTFSRHAISWVRQAPGQG
22.



LEWIGGILPILKTPNYAQRFQGRVTINADESTSTVYMEMSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


C4.
QMQLVQSGAEVKKPGSSVRVSCKASGGTFSRHAISWVRQAPGQG
23.



LEWIGGILPILKTPNYAQRFQGRVTINADESTSTVYMEMSGLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


B12.
QMQLVQSGAEVKKPGSSVRVSCKASGGTFSRHAISWVRQAPGQG
24.



LEWIGGILPILKTPNYAQRFQGRVTINADESTSTVYMEMSSLRS




ENTAVYYCATHGGDRSYWGQGTLVTVSS



 


D07.
QMQLVQSGAEVKKPGSSVRVSCKASGGTFSRHAISWVRQAPGQG
25.



LEWIGGILPILKTPNYAQRFQGRVTINADESTSTVYMEMSSLRS




DDTAVYYCATHGGDRSYWGQGTLVTVSS



 


C05.
QMQLVQSGAEVKKPGSSVRVSCKASGGTFSRHAISWVRQAPGQG
26.



LEWIGGVLPILKTPNYAQRFQGRVTINADESTSTVYMELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


E05.
QVQLVQSGPKVKKPGSSVRVSCKASGGTFSRHAISWVRQAPGQG
27.



LEWIGGILPILKTPNYAQRFQGRVTINADESTSTVYMEMSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


E2.
QMQLVQSGAEVKKPGASVKISCKTSGYTFTDYYIQWVRQAPGQG
28.



LEWVGWINPNSGNTGYAQKFQGRVTMTRDTSISTAYMELSSLRS




EDTAVYYCATHGGDYSYWGQGTLVTVSS



 


A3.
QVQLVQSGAEVKKPGASVRVSCKASGYTFSDYYIQWVRQAPGQG
29.



LEWMGWINPNSGGTYFAQKFQGRVTMTRDTSISTAYMELSSLTS




DDTAVYYCATHGGDRGYWGQGTLVTVSS



 


C3.
QMQLVQSGAEVKKPGASVKVSCKASGYTFTDYYIQWVRQAPGQG
30.



LEWIGGILPILKTPNYAQRFQGRVTINADESTSTVYMEMSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


F10.
QMQLVQSGAEVKKPGASVKVSCKASGYTFTDYYIQWVRQAPGQG
31.



LEWMGWINPDSGGTYFAQKFQGRVAMTRDTSINTAYMELSSLRS




DDTAVYYCATHGGDRSYWGQGTLVTVSS



 


C12.
QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYYIQWVRQAPGEG
32.



LEWMGWMNPDSGGTIYAQKFQGRVTMTRDTSISTAYMELSRLRP




DDTAVYYCATHGGDRSYWGQGTLVTVSS



 


H2.
QMQLVQSGAEVKNPGASVKVSCKASGYPFSAYYIQWVRQAPGQG
33.



LEWMGWLNPNSGDTHSAQKFQGRVTMTRDTSISTAYMELSGLTS




DDTAVYYCATHGGDRSYWGQGTLVTVSS



 


F11.
QMQLVQSGAEVKNPGASVKVSCKASGYPFSAYYIQWVRQAPGQG
34.



LEWMGWLNPNSGDTHSAQKFQGRVTMTRDTSISTAYMELSGPTS




DDTAVYYCATHGGDRSYWGQGTLVTVSS



 


B1.
QMQLVQSGAEVRKPGASVKVSCKASGYSFSDYYIHWVRQAPGQG
35.



LEWIGWINPNNGNTTYAQKFQGRVTMIRDTSISTAYMELSELRS




DDTAVYYCATHGGDRSYWGQGTLVTVSS



 


E11.
QVQLVQSGAEVEKPGASVKVSCKASGYTFTDYYIHWVRQAPGQG
36.



LEWMRGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


H1.
EVQLLESGAEVKQPGASVKVSCKTSGYTFTDYHLHWVRQAPGQG
37.



LEWMGWINPNSGGTNSAPKFQGRVTMTRDTSISTAYMELSGLTS




DDTAVYYCATHGGDRSYWGQGTLVTVSS



 


E6.
QMQLVQSGAEVKRPGASVKVPCKASGYTFTDYYLHWVRQAPGQG
38.



LKWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


A1.
QVQLVQSGPEVKKPGTSVKVSCKASGFTFTSSAVQWVRQARGQR
39.



LEWIGWIVVGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


H7.
QVQLVQSGPEVKKPGTSVKVSCKASGFTFTSSAMQWVRQARGQR
40.



LEWIGWIVVGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


G04.
QVQLVQSGAEVKKPGASVKVSCKASGFTFTSYAISWVRQARGQR
41.



LEWIGWIVVGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


B2.
QVQLVQSGAEVKKPGASVKVSCKASGYSFTNYQVQWVRQAPGQG
42.



LEWLGVINTGVGSTNYAQKFQGRVTMTRDTATSTVYMELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


A7.
QVQLVQSGAEVKKPGASVKVSCKASGYSFTNYPVQWVRQAPGQG
43.



LEWLGVINTGVGSTNYAQKFQGRVTMTRDTATSIVYMELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


H3.
QVQLVQSGAEVKKPGASVKVSCRASGYTFTNSFMQWVRQVPGQR
44.



LEWVGLSNPSGDYTVYAPKFQGRVTMTTDTATSTFYMELFSLRS




DDTAVYYCATHGGDRSYWGQGTLVTVSS



 


B4.
QVQLVQSGAEVKKPGASVKVSCRASGYTFTNSFMQWVRQVPGQR
45.



LEWVGLSNPSGDYTVYAPKLQGRVTMTTDTATGTFYMELFSLRS




DDTAVYYCATHGGDRSYWGQGTLVTVSS



 


H05.
EVQLVQSGGGVVQPGGSLRLSCAASGFTFRSYGMHWVRQAPGKG
46.



LEWVAFILFDGNNKYYADSVKGRFTISSDNSKNTLYLQMNSLRA




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


D06.
QVQLVQSGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKG
47.



LEWVAVISYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRA




EDTAVYYCAKHGGDRSYWGQGTLVTVSS



 


F3.
QVQLVQSGAEVKKPGASVKVSCKASGYTFISHGMSWVRQAPGQG
48.



LEWMGWISADNGNTNYAQKFQERVTITRDMSTSTAYMELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


A12.
QVQLVQSGAEVKKPGASVKVSCKASGYTFISHGMSWVRQAPGQG
49.



LEWMGWISADNGNTKYAQKFQDRVTLTTDTSTSTAYLELRSLRS




DDTAVYYCATHGGDRSYWGQGTLVTVSS



 


G3.
QVQLVQSGAEVKKPGASVKVSCKVSGYTLTELSMHWVRQAPGKG
50.



LEWMGGFDPEDGETIYAQKFQGRVTMTRDTSISTAYMELSRLRS




DDTAVYYCATHGGDRSYWGQGTLVTVSS



 


F05.
QVQLVQSGAEVKRPGASVKVSCKASGYTLTELSMHWVRQAPGKG
51.



LEWMGGFDPEDGETIYAQKFQGRVTMTEDTSTDTAYMELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


H12.
QVQLVQSGAEVKKPGASVKVSCKASGYTFTDNYVHWVRQAPGQG
52.



LEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


G12.
QVQLVQSGAEVKKPGSSVKVSCKASGGAFNAYPISWVRQAPGQG
53.



LEWMGGIIPVSGTPNYAQKFQGRVTITADKSTYTAYMELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


C06.
QMQLVQSGAEVKKPGASVKVSCMASGYTFTGHYIHWVRQAPGQG
54.



LEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYTELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


C11.
QVQLVQSGAAVKKPGASVKVSRKASGYTFTNDYIHWVRQAPGQG
55.



LEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


F08.
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSSYIHWVRQAPGQG
56.



LEWMGGIIPIFGTANYAQKFQGRVTITADKSTSTAYMELSSLRS




EDTAMYYCATHGGDRSYWGQGTLVTVSS



 


E9.
QVQLVESGAEVRKPGESLQISCKASGYRFTNYWIGWVRQMPGKG
57.



LEWMGITYPADSTTVYSPSFQGQVTISADKSISTVFLQWSSLRS




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


E11.
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYWMHWVRQAPGKG
58.



LVWVSRINNDGSSTSYADSVKGRFTISRDTAKNTLYLQMNSLRA




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


H11.
QVQLLESGAEVKNPGASVKVSCKASGYPFSAYYIQWVRQAPGQG
59.



LEWMGWLNPNSGDTHSAQKFQGRVTMTRDTSISTAYMELSGLTS




DDTAVYYCATHGGDRSYWGQGTLVTVSS



 


C08.
EVQLLESEGGLVQPGGSLRLSCTASGFSFNAFWMHWVRQAPGKG
60.



LEWVSRISIDGTTTTYADSVQGRFTISRDNARNTLYLQMNSLRA




EDAAVYYCATHGGDRSYWSQGTLVTVSS



 



XB1511 framework shuffled and selected with human




PDGFRb and off rate selection



XB2708
QVQLVQSGGGVVQPGGSLRLSCAASGFTSRSYGMHWVRQAPGKG
61.



LEWVAFILFDGNNKYYADSVKGRFTISSDNSKNTLYLQMNSLRA




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


D03.
QVQLVQSGGGLVQPGGSLRLSCVASGFTFGNDWMHWVRQAPGKG
62.



LVWVSRINADGTSTAYAESVKGRFTVSRDNAKNTLYLQMNGLRA




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


A10.
QVQLVQSGGGLVQPGRSLRLSCAASGFTFDDYAMNWVRQAPGKG
63.



LEWVSLIYSDGSTYYADSVKGRFTISRDNSKKTLYLQMNNLRVE




DTAVYYCATHGGDRSYWGQGTLVTVSS



 


C09.
QVQLVQSGGALVQPGGSLRLSCAASGFTLSNNAMSWVRQAPGKR
64.



LEWVSAIDGSGGTTYYAGSVKGRFTISSDNSKNTVFLQMNSLRA




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


A06.
QVQLVQSGGGLVQPGGSLRLSCAASGFTFSGHWMHWVRQVPGKG
65.



LVWVSHISNDGSITRYADSVKGRFTVARDNAKNTMYLQMNSLRA




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


C05.
QVQLVQSGGGLVKPGGSLRLSCAASGFIFSSNWMHWVRQVPGKG
66.



LEWVSRIKTDGSSTSYADSVKGRFTISRDNAKNTLYLQMNSLRA




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


H01.
QVQLVQSGGGLVQPGGSLRLSCAASGFTLSSDWMHWVRQAPGKG
67.



LVWVSRISSDGSTTAYADSVRGRFTISRDNAKNTLYLQMNSLRA




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


G04.
QVQLVQSGGGLVQPGGSLRLSCAASGFTLSSDWMHWVRQAPGKG
68.



LVWVSRISSDGSTTAYADSVRGRFTISRDNTKNTLYLQMNSLRA




EDTAVYYCATHGGDRSYWGQGTLVTVSS



 


G07.
QVQLVQSGGGLVQPGGSLRLSCAASGFTFSSDWMHWVRQAPGEG
69.



LVWVSRISSDGSSTAYADSVKGRFTISRDNAKNTVSLQMNSLRA




EDTAVYYCATHGGDRSYWGQGTLVTVSS









C. Binding Specificity of Selected HCDR3 Shuffled VH Domains

The R4 binding pool selected above was assessed for binding to both human and mouse PDGFRb using a 35S Met-labelled in vitro translated library. Specifically, binding of the pool to epoxy beads, 100 nM of human IgG, human PDGFRb and mouse PDGFRb were assessed. As shown in FIG. 4, the parental XB1511 VH domain showed specific binding to human PDGFRb, and undetectable binding to mouse PDGFRb. The framework shuffled pre-selected library showed weak binding to human PDGFRb. However, in contrast, the R4 framework shuffled library showed significant binding to both human and mouse PDGFRb.
D. Binding Affinity of Selected HCDR3 Shuffled VH Domains
The R4 framework shuffled human and mouse PDGFRb enriched VH domain pool was cloned into E. coli expression vectors, produced and purified. The binding kinetics of the VH domains to human and mouse PDFGR was determined using surface Plasmon resonance on a Biacore T100. Briefly, human and mouse PDGFR-hIgG1-Fc chimeric fusion protein were separately immobilized using a Series CMS sensorchip (CMS) coupled to anti-hIgG1 Fc monoclonal antibody. For each cycle, the PDGFR fusion protein was first captured, followed by the injection of VH for 115 seconds at a flow rate of 100 uL/min (association). Immediately following the association phase is a dissociation phase of 600 seconds. The surface was regenerated at each cycle with a single injection 3M MgCl2 (10 uL/min, 60 seconds). Multiple concentrations of VH were injected (0.55 nM-40 nM) and the resulting sensorgram were analyzed with T100 Evaluation software. The binding kinetics was determined using 1:1 binding curve fitting. The binding kinetics of VH domain clones XB2202 and XB2708 to human and mouse PDGFRb are shown in FIGS. 4, 5 and 6. These results show that XB2202 and XB2708 have a 50-150 fold affinity improvement compared to parental XB1511. Specifically, XB2202 and XB2708 have Kds of 249 pM and 93 pM, respectively and off rates (Koff) of 1.86×10−3 and 9.267×10−4, respectively. Both XB2202 and XB2708 bound to human and mouse PDGFRb. It is of particular note that, although they shared the same HCDR3, XB2202 was derived from a VH1 family germline sequence and XB2708 was derived from VH3 family germline sequence.
Example 3. Identification of Stable VL/VH Pairs
A. Construction of VL DNA Libraries
Human VL libraries (Vkappa and Vlamda) were constructed from B cells of young healthy donors (Allcells) by RT-PCR. To ensure the diversity of the library, 300 million mononuclear cells from bone marrow of each donor and total of 10 donors and 100 million of peripheral blood mononuclear cells from each donor and total of 10 donors were obtained for naive VH and VL library construction. A schematic of the library generation method is set forth in FIG. 8.
Oligonucleotide primers for cDNA synthesis and subsequent PCR amplification of the Vkappa and Vlamda sequences were design as set forth in Table 4. Specifically, multiple sense primers were designed from the Vκ and Vλ FR1 regions of each family with an upstream UTR sequence. The anti-sense primers for κ and λ gene amplification were designed from the constant regions nested to Cκ1 (Cκ2) or Jλ with the same Cκ2 downstream (JλCκ2). The Vκ and Vλ libraries carry the same C-terminal sequence for PCR amplification during the selection cycles.
mRNA was prepared with individual donors using a FastTrack mRNA preparation kit (Invitrogen) following the protocol provided by the kit. First strand cDNA was synthesized from the isolated mRNA using primers specific for the light chain kappa and lambda constant regions (Cκ1 and Cλ1).
PCR amplification of the Vkappa and Vlamda sequences was performed with Cκ2 and Vκ family specific or JλCκ2 mix and Vλ family specific oligos using cDNA synthesized from mRNA prepared from the various source of B cells as template. The PCR was performed with individual families and individual donors for 18-20 cycles. After gel purification, Vκ and Vλ libraries from different sources were pooled to generate Vκ and Vλ libraries.







TABLE 4







Oligonucleotides for constructing human Vλ and Vκ DNA display libraries











SEQ ID


Oligo
Sequence
NO.












Ck1
CAACTGCTCATCAGATGGCGG
70.


 


Cl1
CAGTGTGGCCTTGTTGGCTTG
71.


 


Ck2
AGATGGTGCAGCCACAGTTCG
72.


 


Jl1-3Ck2
AGATGGTGCAGCCACAGTTCGTAGACGGTSASCTTGGTCCC
73.


 


Jl7Ck2
AGATGGTGCAGCCACAGTTCGGAGACGGTCAGCTGGGTGCC
74.


 


T7TMVUTR
TAATACGACTCACTATAGGGACAATTACTATTTACAATTACA
75.


 


Vλ oligos




UTRVk1a
CAATTACTATTTACAATTACAATGRACATCCAGATGACCCAG
76.


 


UTRVk1b
CAATTACTATTTACAATTACAATGGMCATCCAGTTGACCCAG
77.


 


UTRVk1c
CAATTACTATTTACAATTACAATGGCCATCCRGATGACCCAG
78.


 


UTRVk1d
CAATTACTATTTACAATTACAATGGTCATCTGGATGACCCAG
79.


 


UTRVk2a
CAATTACTATTTACAATTACAATGGATATTGTGATGACCCAG
80.


 


UTRVk2b
CAATTACTATTTACAATTACAATGGATRTTGTGATGACTCAG
81.


 


UTRVk3a
CAATTACTATTTACAATTACAATGGAAATTGTGTTGACRCAG
82.


 


UTRVk3b
CAATTACTATTTACAATTACAATGGAAATAGTGATGACGCAG
83.


 


UTRVk3c
CAATTACTATTTACAATTACAATGGAAATTGTAATGACACAG
84.


 


UTRVk4a
CAATTACTATTTACAATTACAATGGACATCGTGATGACCCAG
85.


 


UTRVk5a
CAATTACTATTTACAATTACAATGGAAACGACACTCACGCAG
86.


 


UTRVk6a
CAATTACTATTTACAATTACAATGGAAATTGTGCTGACTCAG
87.


 


UTRVk6b
CAATTACTATTTACAATTACAATGGATGTTGTGATGACACAG
88.


 


Vλ oligos




UTRVL1a
CAATTACTATTTACAATTACAATGCAGTCTGTGCTGACKCAG
89.


 


UTRVL1b
CAATTACTATTTACAATTACAATGCAGTCTGTGYTGACGCAG
90.


 


UTRVL2
CAATTACTATTTACAATTACAATGCAGTCTGCCCTGACTCAG
91.


 


UTRVL3a
CAATTACTATTTACAATTACAATGTCCTATGWGCTGACTCAG
92.


 


UTRVL3b
CAATTACTATTTACAATTACAATGTCCTATGAGCTGACACAG
93.


 


UTRVL3c
CAATTACTATTTACAATTACAATGTCTTCTGAGCTGACTCAG
94.


 


UTRVL3d
CAATTACTATTTACAATTACAATGTCCTATGAGCTGATGCAG
95.


 


UTRVL4
CAATTACTATTTACAATTACAATGCAGCYTGTGCTGACTCAA
96.


 


UTRVL5
CAATTACTATTTACAATTACAATGCAGSCTGTGCTGACTCAG
97.


 


UTRVL6
CAATTACTATTTACAATTACAATGAATTTTATGCTGACTCAG
98.


 


UTRVL7
CAATTACTATTTACAATTACAATGCAGRCTGTGGTGACTCAG
99.


 


UTRVL8
CAATTACTATTTACAATTACAATGCAGACTGTGGTGACCCAG
100.


 


UTRVL4/9
CAATTACTATTTACAATTACAATGCWGCCTGTGCTGACTCAG
101.


 


UTRVL10
CAATTACTATTTACAATTACAATGCAGGCAGGGCTGACTCAG
102.





R = A/G, Y = C/T, K = G/T, M = A/C, S= G/C, W = A/T






B. Generation of VL Fusion Libraries by dsDNA Display

Vk and VL DNA libraries generated using the methods set forth in this Example were transcribed into mRNA libraries using the T7 Megascript kit (Invitrogen, Cat#AM1334). The mRNA was purified with RNeasy MinElute Cleanup Kit (Qiagen, Cat#74204) following protocol provided by the kit. A total of 600 pmol of RNA (300 pmol of Vk and Vl libraries) was ligated and assembled with dsDNA display linkers and components as described in WO2010/011944. The assembled VL library was subjected to in vitro translation system to create a fusion library in which each VL domain (phenotype) is stably fused to its coding sequence (genotype). 35S Met was incorporated in the translation process to radiolabel the fusions. The library was then purified with oligo dT cellulose, converted into a dsDNA display library using the standard molecular biology techniques of reverse transcription, RNaseH digestion, 2nd strand DNA synthesis, followed by flag tag purification. A schematic of this process is set forth in FIG. 3.
C. Identification of VL Pairs for XB1511, and XB2202 VH Domains
As a proof of concept, PDGFRb VH binding domain XB1511 was translated as free protein (with incorporation of 35S Met in the translation reaction) and affinity purified through a c-terminal flag tag. The XB1511 and a purified VL fusion library (prepared as above) were then mixed at an equal molar ratio and incubated at 25 C overnight to allow for in vitro association of VH and VL fusion domains through their hydrophobic patch. The mixture was then contacted with PDGFRb target pre-immobilized on Epoxy450 beads or in solution and captured by protein A beads, Complexes that bound to the immobilized PDGFRb target were washed and eluted with 0.1N KOH. PCR was performed with VL specific primer sets to recover the VLs that bound to the PDGFRb target, both as VH-VL pairs and as unpaired VL domains. The VL pairing was performed for 3 rounds, with low stringency (100 nM PDGFRb) for the first 2 rounds and higher stringency (10 nM PDGFRb) for the third round. PDGFRb VH binding domain XB2202 was also paired with VL library similarly for 2 rounds. For each round of XB2202 VL pairing and selection, the stringency was increased by kinetic controlled on and off rate strategy to identify VLs that can pair with VH stably and enhance the VH binding. A schematic of this process is set forth in FIG. 9.
VL pools identified above were then cloned into Blunt Zero TOPO vector (Invitrogen) and VL-encoding DNA sequences were amplified from the resultant bacterial colonies by PCR using M13 forward and reverse primers. The individual amplified VL-encoding DNA sequences were then sequenced. The sequence data obtained from VL pools showed that a diverse repertoire of VLs was enriched through the process. Multiple families and frameworks were present in the pool. Several VLs were present as replicates or families. Distinct VL families could be identified and several VLs were present more than once. Exemplary VL sequences identified using the methods of the invention that pair with the PDGFRb-binding VH domains XB1511 and XB2202 are set forth in Table 4 herein.







TABLE 4







Light chain variable domain (VL) amino acid sequences of exemplary


anti-PDGFRβ antibodies.









Clone

SEQ ID


name
VL Amino Acid Sequence
NO.






PR2 VL sequences from XB1511 pairing



B10.
QSVLTQSPDLQSVTPREKLTITCRASQTIGSTLHWYQQKPGQSPR
103



LVIKYAYQSVSGVPSRFSGSGSGTEFTLTINGLEAEDAATYYCHQ




SSSLPWTFGQGTKLTVL



 


H10.
QSVLTQSPDFQSVSPKDKVTITCRASQSIGSSLHWYQQKPGQSPK
104



LLIKYSSQSFSGVPSRFSGSASGTEFTLTITGLEAEDAATYYCHQ




SSSLPHTFGQGTKVTVL



 


F10.
QSVLTQSPEFQSVTPKEKVTITCRASQSIGSGLHWYQQKPHQSPK
105



LLIRYASQSMSGVPSRFSGSGSGTDFTLTISRLEVEDAAMYYCHQ




SSSLPWTFGQGTKVTVL



 


B12.
QSVLTQSPDFQSVTPKQNVTFTCRASQSIGIKLHWYQQKPDQSPK
106



VLIKYASQPFSGVPSRFSGRGSGTDFTLTINSLEAEDAATYYCHQ




TSSLPLTFGGGTKVTVL



 


B11.
QSVLTQSPGTLSLSPGERATLSCRASQSVSSNYLAWYQQKPGQAP
107



RLLIYGASSRASGIPVRVSGSGSGTDFTLTISRLEPEDFAVYYCQ




QYGSSPWTFGQGTKLTVL



 


E7.
QSVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAP
108



RLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQ




QYGSSPQTFGQGTKLTVL



 


E8.
QSVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAP
109



RLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQ




QYGSSPPYTFGQGTKLTVL



 


H8.
QSVLTQSPGTLSLSPGERATLSCRASQSVSSNYLAWYLQKPGQAP
110



RLLISGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQ




QYAGSPFTFGPGTKLTVL



 


H12.
QSVLTQSPGTLSLSPGERATLSCRASQSVRSSYVAWYQQKPGQAP
111



RLLISGASRRATGIPDRFTGSGSGTDFTLTISRLEPEDFAVYHCQ




QFGSSPWTFGQGTKLTVL



 


F8.
QSVLTQPPSASGTPGQRVTISCSGGRSNIGGNAVNWYQQKPGQAP
112



RLLIHVASRRVTGIPDRFSGSGSGTDFTLTISRLEPEDFAIYYCQ




QYGSSPLTFGGGTKLTVL



 


D11.
QSVLTQSPGTLSLSPGERATLSCRASQNITSNFFAWYQQKPGQAP
113



RLLIYGASSRATGIPDRISGSGSGTDFTLTISRLEPEDFALYYCQ




QYGASPRTFGQGTQLTVL



 


G8.
QSVLTQSPGTLSLSPGDRATLSCRASQSLSGTYLAWYQQKPGQAP
114



RLLIYDASNRAAGIPKRFSGSGSRTDFTLTISRVDPADSAVYYCQ




QYGSALLTFGGGTKVTVL



 


H9.
QSVLTQSPGTLSLSPGESATLSCRASEDIYNNYLAWYQHKRGQPP
115



RLLIFRASTRATGIPTRFSGSGSGRDFVLTINRLEPEDFAVYYCQ




QYGNSWTFGQGTKLTVL



 


H11.
QSVLTQSPDFQSVTPKEKVTITCRASQSIGSSLHWYQQKPDQSPK
116



LLITFASQSFSGVPSRFSGSGSGTDFTLTINSLEAEDAATYYCHQ




SRNLPFTFGPGTKLTVL



 


G12.
QSVLTQSPDFQSVTPKEEVTITCRASESIGTALHWYQQKPDQSPK
117



LLIKYSSQSISGVPSRFVGRGSETEFTLTINSLEAENAATYYCHQ




SRSFPLTFGQGTQLTVL



 


E11.
QSVLTQSPGTLSLSPGERATLSCRTSQILHSQYLAWYQQKRGQAP
118



RLLIFRASTRATGIPERFSGSGSGRDFVLTISRLEPEDSAVYYCQ




QYETSWTFGQGTKVTVL



 


F12.
QSVLTQDPVVSVALGQTVRITCQGDTLRTCYASWYQQRPRQAPIL
119



VIYGENNRPSGIPARFSGSSSGSTASLTITGAQAEDEGDYYCHCR




DGLNHLVFGGGTKVTVL



 


C8.
QSVLTQPPSVSAAPGQKVTISCSGSTSNIGKNFVSWYQHLPGTAP
120



KLLIYDNYQRFSGIPDRFSGFKSGTSATLSITGLQTADEADYYCG




TWDSSLSVVIFGGGTKLTVL



 


A8.
QAGLTQSPDFQSVTPKERVTITCRASRYIGSNLHWYQQKPDQPPK
121



LLIKLASQSFSGVPPRFSGGGSGTDFTLTINGLEAEDAATYYCHQ




TGSFPYTFGQGTKLTVL



 


B8.
QAVLTQEPSLTVSPGGTVTLTCGSSTGAVTSGHSPFWFQQRPGQA
122



PRTLIYDTSNKQSWTPARFSGSLLGGKAALTLSGAQPEDEAEYYC




LLSYSGPRVVFGGGTKVTVL



 


F7.
QAVVTQSPDSLAVSLGERATISCKSSXSLLYRSNNKNYLAWYQQK
123



PGQPPRLLISWASTRESGVPDRFSGSGSGTDFTLTVSRLRAEDAA




VYYCQQSYRTPFSFGPGTKVTVL



 


B7.
SYVLTQPLSVSVALGQTARISCGGANIANKNVHWYQLQPGQAPVL
124



VIYRDSNRPSGIPERFSGSNSGNTATLTITRAQARDEADYYCQVW




DSSSVIIGGGTKVTVL



 


G9.
SYVLTQDPAVSVALGQTVRITCQGDSLRTYYASWYRQKPGQAPVL
125



VFYGKDNRPSGIPDRFSGSSSGNTASLTITGAQAEDEADYYCKSR




DSSAMRWVFGGGTKLTVL



 


A9.
NFMLTQEPSLTVSPGGTVTLTCGSSTGAVTSGHYPYWFQQKPGQV
126



PRTFIYDTHNRHSWTPVRFSGSLFGGKAALTLSGAQPEDEAEYYC




LLYFNPTRVFGGGTKLTV



 


A11.
NFMLTQPPSASASLGASVTLTCTLSSGYSNYKVDWYQQRPGKGPR
127



FVMRVGTGGIVGSKGDGIPDRFSVLGSGLNRYLTIKNIQEEDESD




YHCGADHGRVFGGGTKLTVL



 


E12.
QPVLTQPPSVSVAPGKTARITCGGNNIGSKSVHWYHLRPGQAPVL
128



VIYFDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVW




HSGVIFGGGTKLTVL



 


H7.
QPVLTQSLDFQSVTPKEKVTITCRASQNIGNSLHWYQQKPNQSPK
129



VLIKYASQSFSGVPSRFSGSGFGTDFTLTINSLEPEDAATYYCHQ




SRSSHTFGQGTKLTVL



 


A10.
EIVLTQSPGNLSLSPGERATLSCTRCTGNIASHFVQWYQQRPGSS
130



PTTVIFGNNQRPSGVSDRFSGSIDSSSNSASLTISRLKTEDEADY




YCQSFDVYSHEVVFGGGTKLTVL



 


C11.
QTVVTQTPVSLSVTPGQPASISCKSSQSLLNSDDGKTYLYWYLQR
131



PGQPPHLLIYEVSKRFSGVPDRFSGSGSGTDFTLR SRVEAEDVG




VFYCMQSTHFPFTFGPGTKVTVL



 


D10.
NIQMTQSPVSLSASLGDTVSITCQASHDISNYLNWYQQKPGKAPK
132



LLIYDASHLEAGVPSRFRGSGSGTDFTLTINRLEPEDFAVYYCQQ




YDSPPWTFGQGTKLTVL



 


D12.
DVVLTQSPGTMSLSPGERATLSCRASQSVSRTYLAWHQQKPGQAP
133



RLLIYGASSRAAGIPDRFSGSGSGTDFTLSISRLEPEDFAVYYCQ




QHDTSQWTFGQGTKLTVL



 


C7.
DIVMTQTPLSLSVTPGQPASISCKSSQSLLHSDGKTHLFWYLQRP
134



GQSPQLLIYEVSGRFSGVSERFSGSGSGTDFTLKISRVEAEDVGV




YYCMQGLHIPHTFGQGTKVEIK



 


D7.
DIVMTQSPLSLPVTLGQPASISCRSSHSLVHSDGNIYLNWYHQRP
135



GQSPRRLIYSVSKRDSGVPDRFSGSGSRTDFTLKISRVEAEDVGV




YFCMQSTHQWTFGQGTKVEIK



 


C9.
VIWMTQSPSTVSASVGDRVTITCRASQSISSWLAWYQQKPGKAPN
136



LLIYEASRLESGIPSRFSGSGSGTEFTLTXSSLQPDDFATYYCQQ




YDSYSRTFGQGTKVAIK



 


C12.
DVVMTQSPSSLSASVGDRVTITCRTSQGIRNYLSWYQQKPAKAPK
137



LLIHGASGLQSGVPSRFSGSGSGTNFTLTISSLQPEDFATYYCQQ




SFSMRTFGQGTKVEIK



 


D8.
EIVMTQSPGTLTLSPGEGATLSCRASQSVTSNYLAWYQQRPGASS
138



LQSGQAPRLLIYDASNRATGIPDRFSGSGFGTDFTLTISRLEPED




FAVYYCQQYVNSRTFGQGTKVEIK



 


D9.
EIVMTQSPVTLSVSPGERATLSCRASQSVSSKLAWYQQKPGQAPR
139



LLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAIYYCQQ




YNDFFTFGPGTKVDIK



 


G7.
EIVLTQTPLSSPVTLGQPASISCRSSESPVHSDGNIYLSWLHQRP
140



GQPPRLLLYKISNRMSGVPDRFSGSGAGTDFTLKISRVEAEDVGV




YYCMQATQFPSFGQGTKLEIK



 


G11.
EIVLTQSPGTLSLSPGEGATLSCRASQSVSSRNLAWYQQKPGQAP
141



RLLIYGGSIRASGTSTRFSGSGSGTDFTLTINRLEPEDFAVYYCQ




QYGDSVFTFGPGTKVDIK



 


F9.
NIQMTQSPSSLSASVGDRVNITCRASDNIGNYLNWYQHKPGKAPT
142



VLIYAASTLHYGVPSRFSGRGSGTDFTVTISSLQPEDSATYYCQQ




SYSTPRTFGQGTRVELK



 


E9.
AIQMTQSPSSLSASVGDRVTITCRASESISNYLNWYQQKPGKAPK
143



LLLSAASRLQSGVPSRFSGSGSGTDFTLTITSLQPEDLATYYCQE




SYSTLLYTFGQGTKLEIK



 



VL sequences from XB2202 VL pairing



B1.
SYELTQPPSVSVAPGKTASITCGGNNIGYDSVHWYQQKPGQAPVL
144



VVFDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVW




ESGSEHYVFGTGTQLTVL



 


E6.
LPVLTQPPSVSVAPGQTARISCGGNNIGATTVHWYQHRPGQAPVS
145



VIFYDNDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVW




ESTSDHPTFGGGTQLTVL



 


F3.
QSVLTQPPSVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVL
146



VIYYDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVW




DSSSDHWVFGGGTKLTVL



 


H4.
SYELTQSPSVSVPPGQTARITCGGNNIVSKGVHWYQQRPGQAPVL
147



VVYDDSDRPSGIPERFAGFNSGNTATLTISRVEAGDEADYYCQVW




DSSSGHRGVFGGGTKVTVL



 


H5.
SYELTQPPSVSMAPGKTARITCGGNNLGSKIVHWYQQKPGQAPVV
148



VIYSDRDRPSGVPERFSGSNSGNSATLTISGVEAGDEADYYCQVW




DSATDHVVFGGGTKLTVL



 


B5.
SYELTQPPSVSVAPGQTATITCAGNNIGGKSVQWYQQKPGQAPVV
149



VVYDDYGRPSGIPERVSGSNSGNTATLTLTRVEAGDEADYYCQVW




DSDRHHVVFGGGTKLTVL



 


G6.
QLVLTQPPSVSVSPGQTASITCSGDNLGHTNACWYQQNPGQSPVL
150



VIYQDTKRPSGIPERFSGSNSGNPATLTIXRVXAGDEANYYCQVW




DINDDYAVFGTGTXLTVL



 


C1.
QSVLTQSPGTLSLSPGERATLSCTASQSVSSTYLTWYQQKPGQAP
151



RLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQ




QYVSSPPMYTFGQL



 


F1.
DIQMTQSPSTLSASVGDRVTISCRASQNIDYDLAWYQXKPGKAPX
152



LLIYGASNLEGGVPSXFSGXGSGTEFTLTISSLQPDXSATYYCQQ




YVTYPLTFGQGTRLEIK



 


A3.
AIQMTQSPSSLSASVGDRVTMTCQASQVIDKYVNWYRQRPGKAPE
153



LLIYGASTLESGVPSRFSGSGSGTQFTFSITSVQPEDFATYICQQ




YDSVPLTFGPGTILDVKRTVA



 


B4.
DIQLTQSPSSLSASIGDRVTITCQASQDIFHYLNWFQQKPGKAPK
154



LLIYEASNLETGVPSRFSGSGSVTDFTFTISSLQPEDIATYYCQQ




YEDLPSFGGGTKVDIKRTVA



 


B6.
EIVLTQSPGTLSLSPGERATLSCRASQSFGSNYLAWYQHKPGQAP
155



RLLIFAASNRATGIPDRFTGSASGTDFTLTINRVEPEDLAVYYCQ




QYGSFPYSFGQGTKLEIK



 


F2.
NIQMTQSPSSLSASVGDRVTITCQASQFIHIYLNWYQQKLGKAPK
156



LLIYGASNLERGVPSRFSGRGSETDFTFTIDSLQPEDIATYFCQQ




YQNPPFTFGGGTKVEINGTVA



 


D3.
AIRMTQSPSSLSASIGDRISVTCRASQDVGIYVAWFQQKPGKPPR
157



SLIYAASYLQTAVPPKFRGSGSGTDFTLTISDLQPDDFATYYCQQ




YKTFPHTFGQGTKLDFKRTVA



 


G2.
VIWMTQSPSTLSASVGDRVTITCRASQDINTWLAWYQQKPGKAPK
158



LLMFKVSTLESGDFSRFSGSGSGTEFTLTVSSLQPDDSAIYYCQQ




YHSYPYTFGQGTRLEIK



 


A4.
DVVMTQSPSSLSASVGDRVTITCQASQDISNWLNWYQQKPGKAPK
159



LLIYEASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQ




YNNVLRTFGQGTKVEIK



 


G4.
EIVMTXSPATLSVSPGERVTLSCRVSQNVFSDLAWYQRKTGQSPR
160



LLIHGASTRATGIPTRFSGSGSGTEFTLTISSLXSDDFAVYYCQQ




YNKWPTFGQGTKVEIK



 


D5.
AIQLTQSPSSLSASVGDRVNITCRASDNIGNYLNWYQHKPGKAPT
161



VLIYAASTLHYGVPSRFSGRGSGTDFTVTISSLRSDDFAVYYCQQ




YYNWPPWTFGQGTTVDIKRTVA



 


A1.
EIVLTQSPATLSLSPGERATLSCRASQSVSSFLAWYQQKPGQAPR
162



LLIFEASTRATGISARFSGSGSGTDFTLTISTLEPEDFAVYYCQQ




RSNGVTFGQGTRLEIK



 


H2.
DIQMTQSPSTLSASVGDTVTITCRATESISIWLAWYQQEPGKAPN
163



LLVSQASSLKTGVPSRFSASGSGTEFTLTISSLHPDDFATYVCQH




YHTYPFTFGPGTKVDMKRTVA



 


E2.
EIVLTQSPDSXAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQK
164



PGQPPRLLIYWASTRESGVPDRFSGSGSGTDFTLTISRLQAEDVA




VYYCQQYYLTPTFTVTFGQGTKLEIK



 


F4.
DIQLTQSPSSVSASVGDRVTITCRASQDISSWLAWYQQKPGKAPK
165



FLIYRATNLQSGVPSRFSGSGSGTDFTLTISSLQPGDFATYYCQQ




TNTFPLTFGGGTKVEVKRTVA



 


C5.
DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNRNYLAWYQKK
166



PGQPPKLLFYWASTRESGVSDRFSGSGSGTDFTLTISSLQAEDVA




VYYCQQYHTTPYTFGQGTKLEIK



 


E5.
VIWMTQSPSSLSASVGDRVSITCRASQTFTSHLNWYQQKPGQPPK
167



LLIFAASNLQSGVPSRFSGSGSGTDFTLTINGLQATDFATYYCQQ




SFSSPWTFGQGTTVDVKGTVA



 


F6.
DIQMTQSPSSLSASVGDRVTITCRASQSVNVYLNWYQQKPGKAPK
168



LLIYSASTLQSGVPSRFTGSGSRTDFTLTINGLQPEDFATYYCQQ




SFTTLVTFGPGTRVDVTRTVA



 


G5.
DIQMTQSPSSLSASVGDRVTITCRASQDISSSLAWYQQKPGKAPK
169



PLIYDASTLQTGVPSRFSGRASGTDFTLTIDSLQPEDFATYCCQQ




FNSYPLSFGGGTKVELKRTVA



 


A5.
SYELTQPPSASASLGASVTLTCTVSSGYRSYEVDWFQQRPGKGPR
170



FVMRVGTGGIVGSRGDGIPDRFSVWGSGLNRYLTIEDIQEEDESD




YYCGADHGSGSNLVYVFGTGTKVTVL



 


D6.
QLVLTQPPSASASLGASVTLTCTLSSDYSSYNVDWYQQRPGMGPR
171



FLMRVGTGGIVGSRGDGIPDRFSVKGSGLNRYLTIKNIQEEDESD




YYCGADHGSGSDFVYVFGIGTKLTVL



 


E4.
QSVLTQPPSASGTPGQRVTISCSGSSTNIGSNAVNWYQQLPRTAP
172



KLLIYTNNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEANYYCA




AWDDSLNGPVFGGGTQLTVL



 


F5.
QSVLTQPPSASGTPGQTVIISCSGGGSNIGSNFGYWYQQFPGTAP
173



KLLIYTTDRRPSGVPDRFSGSKSGTTASLAISGLRSEDEADYYCA




AWDDRLSGPVFGGGTQLTVL



 


G1.
QTVVTQPPSVSGTPGQRVTISCSGSSSNIGSNSVDWYQQFPGSAP
174



KLLIYTTNQRPSGVPDRFSGSKSGTSASLAISGLRSEDEADYYCA




TWDDDLSNPKWVFGGGTKLTVL



 


E3.
DIVMTQSPLSLPVTPGEPASISCRSSQSLLHSNGYNFLDWYLQKP
175



GQSPQLLIYLGSNRASGVPDRFSGSGSGTDFTLKISRVEAEDVGI




YYCMQALQTSWTFGQGTKLEIK



 


A2.
DICRIRPLIRLTIGTITIYNYNGCCDDTVSTLPARHPWTAGLHLQ
176



SPRRLMYQVSTRDSGVPDRFSGSGSGTDFTLRISRVEAEDVGVYY




CMQGTHWPYTFGQGTKLEIRRTVA



 


D1.
DIVMTQTPLSLSVTPGQPAAISCKSSQSLVHRDGKTYLYWYLQKP
177



GHSPQLLVYEASSRFSGVPDRISGSASGTQFTLNISRVEAEDVGL




YYCMQSRNLPKTFGQGTKVEIK



 


C4.
SYELTQPTSLSASPGASASLTCTLSSGFNVVSYNIYWYQQKPGSP
178



PQYLLRYRSDSDRHQGSGVPSRFSGSKDASANAGILVISALQSDD




EADYYCMVWYSAWVFGGG



 


E1.
SYELTQPLSVSVALGQTATITCAGNNIGTYYVHWYQQRPGQAPVL
179



VMYRDTNRPSGISDRFSGSNSGDTATLTICGVQVGDEADYYCHVL




DSSTIVIFGGGTQLTVL



 


A6.
QSVLTQSPATLSVSPGERASLSCRASQSVSSNLAWYQQKPGQAPR
180



LLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAVYYCHQ




YNNWPLYTFGQGTKLTVL



 


H1.
QSVLTQDPAVPVALGQTVRITCQGDSLRTYYASWYQQKPGQAPLL
181



VIYGKNTRPSGIPVRFSGSSSGNTASLTITGAQAEDEADYYCNSR




DSSGYLLLFGTGTKLTVL



 


B2.
QAVLTQEPSLTVSPGGTVTLTCGSSTGAVTSGHYPYWFQQKPGQA
182



PRTLIYDASNKHSWTPARFSGSLLGGKAALTLSGAQPEDEAEYYC




LLSYSGAGVFGTGTKVTVL



 


C2.
DIQMTQSPSSLSASVGDRVAIACRPSQDIGTDLGWYQQKPGKAPK
183



LLIFDSSTLQSGVPSRFSGSLSGTDFILTITNLQPEDFATYYCLQ




DYSFPYTFGQGTKLQIKRTVA



 


G3.
SYVLTQPPSVSVSPGQTASITCSGDELKYKYTCWYHQKPGQSPVL
184



LIYQDTKRPSGIPERFSGSRSENTATLTISGTQAMDEADYYCQAW




DSSHAVFGRGTQLTVL



 


H3.
H3SYVLTQPPSVSVFPGQTARITCSGSTFPKLYSFWYQQKTGQAP
185



LLVIYKDTERPSGIPERFSGSTSGTTVTLIISGVQPEDDADYYCQ




SEDSRGPVFGGGTKVTVL



 


D4.
GVVMTQTPLSSLVTLGQPASISCRSSESVVHDDGNTYLSWLQQRP
186



GQPPRLLIYKISNRFSGVPDRFSGSGAGTDFTLKISRVEPEDVGV




YYCVQATHFPVTFGGGTRVEIK



 


C6.
QSALTQPASVSASPGQSVTISCTGTSDDVGRYDYVSWYQQHPGGA
187



PKLILYDVNRRPSGVSDRFSGSKSANKASLTISGLQADDEGDYYC




CSYTTGSTLYLFGTGTQLTVL









D. Evaluation of Identified VH and VL Pairs

To evaluate the characteristics of the identified VH-VL pairs, 10-12 scFVs from each pool were constructed and produced by either in vitro translation or by E. coli expression, followed by affinity purification.
A PDGFRb binding ELISA assay was performed to assess the binding of the scFv to immobilized PDGFRb and to determine the EC50. Specifically, 2 ug/mL of human PDGFRb and human Fc or IgG in PBS was immobilized on Maxisorp plates at 4° C. overnight. The plate was then washed and blocked with superblock. In vitro translated crude scFv lysate was diluted 1:3 in 1×PBST. 100 ul of the diluted scFv lysate was loaded into each well of Maxisorp plates and incubated for 1 hour at room temperature. scFv that bound to immobilized PDGFRb was detected by anti-flag antibody-HRP at 1:5000 dilution and a TMB substrate. The plate was read on a Molecular Device plate reader with end point assay at OD 450 nm. As shown in FIGS. 10, 11 and 12, in the ELISA binding assay, greater than 50% of the scFvs generated for XB1511 and XB2202 showed specific binding to hPDGFRb. In contrast, the unpaired VLs alone did not show binding to PDGFRb (see FIG. 13).
The affinity of several scFvs was determined by solution based equilibrium binding assay. Specifically, 120 pmol of scFv RNA was translated into free protein with 35S Met incorporated. The translated reaction mixture was 3-fold diluted in binding buffer containing 1×PBS with 0.025% triton, 1 mg/mL BSA and 0.1 mg/mL sssDNA. Human PDGFRb was diluted in the same binding buffer to final concentrations from 100 nM to 0 nM. The diluted scFv mixture was incubated with hPDGFRb in final volume of 100 ul on Kingfisher plates (Thermofisher Scientific, 97002084). Following incubation, 25 ul of protein A magnetic beads (Invitrogen) were used to capture the PDGFRb from solution. The captured PDGFRb was washed and eluted in kingfisher Reader (Thermofisher Scientific). The amount of scFv (labeled with 35S Met) bound to the magnetic bead-immobilized hPDGFRb was counted using a scintillation counter and the Kd was calculated with Graph Pad Prism 5. For the XB1511-derived scFv tested, 2 scFv showed an 8-10 fold higher KD, 1 showed 2.5 fold higher KD, and 4 showed a similar KD when compared to XB1511 VH alone (FIG. 14). Only 1 scFv showed a lower KD than XB1511 VH alone. As shown in FIG. 15, both of the XB2202-derived scFv tested showed approximately an 8-10 fold better KD when compared to XB2202 VH alone.
Example 4. Conversion of VH-VL Pairs to Heterotetrameric IgG and Demonstration of Biological Activity
XB1511 VH and D8 VL were expressed as heterotetrameric IgG in 293T cells. Cell culture supernatant was collected after 48 hours and 96 hours and the expressed IgG was purified with protein A agarose beads. The IgG was produced at 8 mg/L without any optimization. To evaluate the biological activity of the XB1511/D8 IgG, HFF-1 human foreskin fibroblasts were seeded in 384-well BIND biosensors and allowed to attach overnight in serum-free media. The fibroblast cells were then stimulated with 5 ng/mL or 10 ng/mL of PDGFBB ligand and allowed to migrate for 18 hours. BIND Scanner images were captured every 15 minutes and software analysis tools used to measure the track lengths of individual cell migration responses. Track length is represented by a “heat map” from blue (no migration) to red (maximal migration). As shown in FIG. 16, the XB1511/D8 IgG was able to completely block the PDGFBB-induced migration of human fibroblasts.
Example 5. scFv Thermostability
The thermostability of the XB2202 VH and scFv XB2202-A4 were determined. Specifically, 1 mg/mL of XB2202 and XB2202-A4 were incubated at 4 C, 37 C, 60 C and 70 C for 12 hours and PDGFRb binding ELISA was performed to test the binding activity of the protein after incubation. As shown in FIG. 17, XB2202 VH lost significant PDGFRb binding activity after incubation at 60 C and completely lost binding activity after incubation at 70 C. The Tm of XB2202 was measured to be approximately 62 C. In contrast, scFv XB2202-A4 was completely active after 12 hour incubation at 70 C, indicating that the Tm of scFv XB2202 was greater than 70 C.

## Claims

1. A method for producing a variable heavy (VH) domain that binds a target antigen, the method comprising:
(a) providing a library of chimeric, unpaired VH domains, the library comprising diversity in FR1-FR3 regions of the VH domains, and wherein each member of the library comprises a CDR3 region from the VH domain of a reference antibody that binds specifically to the target antigen;
(b) contacting the library with the target antigen; and
(c) selecting from the library at least one chimeric, unpaired VH domain that binds specifically to the target antigen, thereby producing a VH domain that binds specifically to the target antigen.

2. The method of claim 1, further comprising introducing amino acid sequence diversity into the library of step (a).

3. The method of claim 1, further comprising:
(d) introducing amino acid sequence diversity into the VH domain(s) selected in step (c).

4. The method of claim 2, wherein the amino acid sequence diversity is introduced by random mutagenesis.

5. The method of claim 1, further comprising combining the VH domain(s) selected in step (c) with a VL domain.

6. The method of claim 1, wherein the CDR3 region is from a rodent, lagomorph, avian, camelid, shark, or human antibody.

7. The method of claim 1, wherein each member of the library comprises an identical CDR3 region.

8. The method of claim 1, wherein each member of the library further comprises a human FR4 region.

9. The method of claim 1, wherein sequences of the FR1-FR3 regions of said VH domains are human sequences.

10. The method of claim 1, wherein each member of the library comprises FR1-FR3 regions individually encoded by a single human antibody VH gene.

11. The method of claim 1, wherein the library is a nucleic acid display library.

12. The method of claim 1, wherein the library is generated using the oligonucleotide sequence set forth in SEQ ID NO: 19, and at least one oligonucleotide having a sequence selected from the group consisting of SEQ ID NOs: 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, and 21.

13. The method of claim 5, wherein the VL domain is generated using at least one oligonucleotide having a sequence selected from the group consisting of SEQ ID NOs: 70, 71, 72, 73, 74, 75, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, and 102.

14. A method for producing an antibody comprising a stable variable heavy (VH) domain/variable light (VL) domain (VH/VL) pair, the method comprising:
(a) providing a library of chimeric, unpaired VH domains, the library comprising diversity in FR1-FR3 regions of the VH domains, and wherein each member of the library comprises a CDR3 region from the VH domain of a reference antibody that binds specifically to the target antigen;
(b) contacting the library with the target antigen;
(c) selecting from the library at least one chimeric, unpaired VH domain that binds specifically to the target antigen; and
(d) contacting the unpaired VH domain selected in step (c) with a VL domain, thereby producing an antibody with a stable VH/VL pair.

15. A method for producing an antibody comprising a stable variable heavy (VH) domain/variable light (VL) domain (VH/VL) pair, the method comprising:
(a) providing a library of chimeric, unpaired VH domains, the library comprising diversity in FR1-FR3 regions of the VH domains, and wherein each member of the library comprises a CDR3 region from the VH domain of a reference antibody that binds specifically to the target antigen;
(b) contacting the library with the target antigen;
(c) selecting from the library at least one chimeric, unpaired VH domain that binds specifically to the target antigen;
(d) contacting the at least one unpaired VH domain selected in step (c) with a library of unpaired VL domains such that a library of VH/VL pairs is formed;
(e) contacting the library of VH/VL pairs with the antigen; and
(f) selecting from the library of VH/VL pairs at least one VH/VL pair that binds specifically to the antigen, thereby producing an antibody comprising a stable VH/VL pair.