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WO2004108078A2 - Anticorps conçus de maniere rationnelle - Google Patents

Anticorps conçus de maniere rationnelle Download PDF

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Publication number
WO2004108078A2
WO2004108078A2 PCT/US2004/016574 US2004016574W WO2004108078A2 WO 2004108078 A2 WO2004108078 A2 WO 2004108078A2 US 2004016574 W US2004016574 W US 2004016574W WO 2004108078 A2 WO2004108078 A2 WO 2004108078A2
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WIPO (PCT)
Prior art keywords
fragment
peptide
immunoglobulin molecule
antibody
cells
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PCT/US2004/016574
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English (en)
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WO2004108078A3 (fr
Inventor
Katherine S. Bowdish
Shana Frederickson
Mark Renshaw
Cecilia Orencia
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Alexion Pharmaceuticals Inc.
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Publication of WO2004108078A2 publication Critical patent/WO2004108078A2/fr
Publication of WO2004108078A3 publication Critical patent/WO2004108078A3/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/12—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria
    • C07K16/1267—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria from Gram-positive bacteria
    • C07K16/1282—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from bacteria from Gram-positive bacteria from Clostridium (G)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/55—Fab or Fab'
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C07K2317/565—Complementarity determining region [CDR]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2318/00—Antibody mimetics or scaffolds
    • C07K2318/10—Immunoglobulin or domain(s) thereof as scaffolds for inserted non-Ig peptide sequences, e.g. for vaccination purposes

Definitions

  • the present invention relates to antibody molecules and biologically active peptides as diagnostic and therapeutic reagents.
  • Antibodies are produced by B lymphocytes and defend against infection. Antibodies are produced in millions of forms, each with a different amino acid sequence. Antibody molecules are composed of two identical light chains and two identical heavy chains. When digested by the enzyme papain, two identical Fab fragments are produced along with one Fc fragment. When digested with the enzyme pepsin one F(ab') 2 fragment is produced. Light and heavy chains consist of constant and variable regions. Within the variable regions are hypervariable regions (aka complementarity determining regions (CDRs)) which form the antigen binding site. The remaining parts of the variable regions are referred to as framework regions.
  • CDRs complementarity determining regions
  • Important biological functions such as receptor binding, activation and enzymatic activity, are often attributable to discrete regions of larger protein molecules, comprising a limited number of amino acid residues.
  • Peptides displaying binding, activation or enzymatic activity have also been discovered by screening libraries of peptides generated by the random linking of amino acid residues. These peptides may not correspond to a linear arrangement of amino acids in a larger protein molecule exhibiting similar biological activity and are referred to as discontinuous peptide epitopes or mimotopes.
  • Certain peptide mimetics have been described and cloned. See, e.g., U.S. Pat. No. 6,083,913 (thrombopoietin (TPO) mimetic), U.S. Pat.
  • Immunoglobulins or fragments thereof have a peptide of interest inserted into a complementarity determining region (CDR) of an antibody molecule.
  • the antibody molecule serves as a scaffold for presentation of the peptide and confers upon the peptide enhanced stability.
  • the peptide optionally replaces all the amino acids of a CDR region, or may be added to an existing CDR, whereby the original antigen specificity is disrupted, wherein the CDR region is defined by either of the two accepted schemes (See, Kabat et al., Sequences of Proteins of Immunologies Interest, 5 th ed (1991), NIH Publication 91-3242 and Chothia et al. J.Mol.
  • an immunoglobulin molecule or fragment has amino acids residues corresponding to one complementarity determining region (CDR) replaced with amino acid residues comprising a biologically active hemopoietic or thrombopoietic peptide.
  • amino acid residues corresponding to at least two complementarity determining regions (CDRs) are each replaced by amino acid residues comprising such a biologically active peptide.
  • one or more complementarity determining regions can be replaced with a peptide; for example, CDR3 of a heavy chain, CDR3 of a light chain, CDR3 of both a heavy and light chain, CDR2 and CDR3 of a heavy chain, or CDR2 and CDR3 of a light chain.
  • CDR3 of a heavy chain CDR3 of a light chain
  • CDR3 of both a heavy and light chain CDR2 and CDR3 of a heavy chain
  • CDR2 and CDR3 of a heavy chain CDR2 and CDR3 of a light chain.
  • Other combinations of replaced CDR regions are possible, including the replacement of CDR1.
  • replacement of a CDR one could add the peptide to a native CDR without actual replacement of amino acid residues while still disrupting the original antigen specificity.
  • a biologically active peptide is provided with enhanced activity by adding a proline to its carboxy terminus to form a proline-extended biologically active peptide which is used to replace or add to at least a portion of at least one CDR region in an immunoglobulin molecule or fragment thereof.
  • an immunoglobulin molecule or fragment thereof which has either a TPO mimetic peptide or EPO mimetic peptide as a replacement for at least one native CDR region.
  • the TPO mimetic peptide or EPO mimetic peptides may optionally be proline-extended as described herein.
  • the immunoglobulin molecule or fragment thereof is an Fab, a ScFv, a heavy chain variable region, a light chain or a full IgG molecule.
  • the immunoglobulin molecule or fragment thereof can also have a dimerization domain, so as to enable immunoglobulin molecules which have only one CDR replaced with a peptide to dimerize and thus activate receptors that require dimerization for activation.
  • the biologically active peptide can be a linear peptide epitope or a discontinuous peptide epitope.
  • the biologically active peptide when substituted for a CDR region, can have in addition to proline, one, two or more additional flanking amino acid residues proximate to the amino and/or the carboxyl termini of the peptide, which are positioned between the peptide and immunoglobulin framework region residues (i.e., at what was the junction between a CDR and the adjoining framework).
  • the flanking amino acid residues are not typically present in the active peptide. If preferred flanking amino acid residues are already known, the flanking amino acid residues are encoded by codons which designate those specific amino acid residues.
  • flanking amino acid residues may determine the presentation of the peptide in the immunoglobulin molecule or fragment thereof and thus may influence the binding and/or biological activity exhibited by the peptide.
  • This random collection of flanking amino acids allows for the selection of the best context to display the peptide sequence within the antibody framework that results in specific binding to the target molecule and the exhibition of optimal biological activity. Screening of libraries of immunoglobulins having a common peptide but different flanking amino acid residues can be carried out using binding, growth and activation assays known by those skilled in the art and as described herein.
  • the peptide replacing the amino acid residues comprising a CDR can be any peptide which specifically binds a target molecule and whose utility could be altered by incorporation in an antibody framework.
  • the peptide could also exhibit a specific activity (e.g., agonist, antagonist, enzymatic, etc.).
  • the peptide is an agonist or an antagonist for a cell surface receptor.
  • the cell surface receptor can be for a cytokine, a growth factor, or a growth inhibitor.
  • replacement of at least a portion of a CDR with a peptide provides an antibody that acts as an agonist.
  • the peptide used to replace at least a portion of a CDR may itself have agonist properties.
  • the peptide (although specifically binding to a receptor) may not exhibit agonist activity. Rather, agonist activity might be exhibited only when the peptide is substituted for at least a portion of a CDR and is thus present in the engineered antibody.
  • the presence or absence of proline flanking the peptide is not critical, but can, in some instances, be preferred.
  • an agonist antibody comprising an antibody framework engineered to contain at least one biologically active peptide inserted at, or in place of at least a portion of, one or more CDRs.
  • the biologically active peptide may or may not exhibit agonist activity prior to insertion into the antibody framework.
  • the antibody framework is engineered to contain two peptides capable of dimerizing with each other.
  • the present disclosure provides for an immunoglobulin molecule or fragment thereof comprising a region where amino acid residues corresponding to at least a portion of a complementary determining region (CDR) are replaced with a biologically active peptide, whereby the immunoglobulin molecule or fragment thereof exhibits agonist activity.
  • the biologically active peptide may or may not exhibit agonist activity prior to insertion into the antibody framework.
  • the immunoglobulin molecule or fragment thereof exhibits c-mpl agonist activity.
  • the present disclosure provides for an immunoglobulin molecule or fragment thereof comprising a biologically active peptide inserted at a complementary determining region (CDR), whereby the immunoglobulin molecule or fragment thereof exhibits agonist activity.
  • CDR complementary determining region
  • the present disclosure provides for an immunoglobulin molecule or fragment thereof comprising a region where amino acid residues corresponding to at least a portion of a complementary determining region (CDR) are replaced with a biologically active peptide, whereby the immunoglobulin molecule or fragment thereof exhibits c-mpl agonist activity.
  • CDR complementary determining region
  • the peptide replacing the amino acids of a CDR is an agonist TPO mimetic peptide.
  • One such agonist peptide has at least the sequence IEGPTLRQWLAARA (SEQ. ID. NO. 1).
  • Other sequences are possible for TPO agonist mimetic peptides, which can be found using binding, growth and activation assays known by those skilled in the art and as described herein.
  • Agonist TPO mimetic peptides when positioned in CDR regions can have one or more additional amino acid residues at the amino and/or carboxyl termini of the peptide which become covalently bonded to immunoglobulin framework residues.
  • TPO mimetic peptide has an additional proline residue added to the carboxyl terminus; IEGPTLRQWLAARAP (SEQ. ID. NO: 2).
  • Other immunoglobulin molecules or fragments thereof have a CDR region replaced by the TPO mimetic peptides comprising the amino acid sequence of SEQ. ID. NOs: 25, 27, 29, 31, 33, 35, 37, 39, 41 , 43, 45, 47, and 49 (see Fig. 5).
  • EPO mimetic peptide Another biologically active peptide that can replace the amino acid residues of a CDR is an agonist EPO mimetic peptide.
  • EPO agonist peptide has as its amino acid sequence DYHCRMGPLTWVCKPLGG (SEQ. ID. NO: 3).
  • Other amino acid sequences are possible for EPO agonist mimetic peptides, which can be found using binding, growth and activation assays known by those skilled in the art and as described herein.
  • Agonist EPO mimetic peptides when located in CDR regions can also have one or more additional amino acid residues at the amino and/or carboxyl termini of the peptide which become covalently bonded to immunoglobulin residues.
  • immunoglobulin molecules IgG or fragments (e.g., Fab, scFv, heavy or light chains) that have a CDR region replaced with a TPO or EPO mimetic peptide.
  • the TPO peptide can include at least the sequence IEGPTLRQWLAARA (SEQ. ID. NO:1) and may further optionally have an additional proline at the immediate downstream position.
  • the EPO mimetic encompasses at least the sequence DYHCRMGPLTWVCKPLGG (SEQ. ID. NO: 3). Likewise, it may optionally have an additional proline at the immediate downstream position.
  • any immunoglobulin molecule (antibody) or fragment thereof could potentially provide the framework and have a CDR replaced with a peptide according to the present disclosure.
  • the antibody is of human origin or humanized, such as an anti-tetanus toxoid immunoglobulin.
  • one or more amino acid residues in other regions of the immununoglobulin, other CDR region(s) and/or framework regions can be altered to modify the binding, activity and/or expression displayed by the peptide in the context of the immunoglobulin molecule.
  • recombinant antibodies and/or fragments thereof can be subjected to randomization methods known in the art to introduce mutations at one or more points in the sequence to alter the biological activity of the antibodies. After generation of such mutants using randomization methods such as those described herein, the resulting recombinants may be assayed for activity using binding, growth, expression and activation assays.
  • nucleic acid molecules encoding immunoglobulin molecules or fragments thereof which have the amino acids of one or more CDR regions replaced by a biologically active peptide.
  • These nucleic acid molecules can be present in an expression vector, which can be introduced (transfected) into a recombinant host cell for expression of these molecules.
  • methods of producing an immunoglobulin molecule or fragment thereof containing a biologically active peptide comprising culturing a recombinant host cell under conditions such that the nucleic acid contained within the cell is expressed.
  • compositions comprising an immunoglobulin molecule or fragment thereof which has amino acid residues corresponding to a CDR replaced with amino acid residues comprising a TPO or EPO mimetic peptide and a pharmaceutically acceptable carrier.
  • EPO mimetic peptides with additional flanking residues which are suitable for replacement of CDRs.
  • nucleic acid molecules encoding these peptides are also provided.
  • the methods encompass inserting a nucleic acid molecule encoding a biologically active peptide in place of at least a CDR region of a nucleic acid molecule encoding an immunoglobulin heavy or light chain or adding the molecule to the native CDR sequence and then expressing the nucleic acid molecule encoding the immunoglobulin heavy or light chain variable domain along with its complementary variable region domain, such that the two domains associate.
  • the methods encompass inserting a nucleic acid molecule encoding a biologically active peptide in place of at least a portion of a CDR region of a nucleic acid molecule encoding an immunoglobulin heavy or light chain or adding the molecule to the native CDR sequence; and expressing the nucleic acid molecule encoding the immunoglobulin heavy or light chain variable domain along with its complementarity variable region domain, such that the two chains associate.
  • this disclosure provides a method for producing in a polypeptide a binding site capable of binding a preselected agent, the method including the steps of introducing a nucleotide sequence that codes for an amino acid residue sequence defining said binding site into a CDR region of a nucleic acid comprising an immunoglobulin heavy or light chain gene by amplifying the CDR region of the immunoglobulin gene, the introduced nucleotide sequence having the formula - X a -Y-X b wherein X is the same or different at each occurrence and represents a randomizing trinucleotide, the sum of a and b is 4 or less and Y is a nucleotide sequence that encodes a minimum recognition domain of said binding site.
  • amplification is achieved using overlap PCR, however, any known amplification technique could be employed, such as, for example, the methods disclosed in W094/18221 , the disclosure of which is incorporated herein by reference.
  • this disclosure provides methods for creation of a library of monoclonal antibodies that can be screened for a desired activity.
  • These methods of making a library include the steps of inserting a nucleic acid molecule encoding a biologically active peptide into, or in place of at least a portion of, one or more CDR regions of a nucleic acid molecule encoding an immunoglobulin heavy or light chain, providing up to a pair of randomizing trinucleotides on either side of the inserted nucleic acid molecule, and expressing a library of monoclonal antibodies.
  • a pair of randomizing trinucleotides is provided on both sides of the inserted nucleic acid molecules.
  • the library of monoclonal antibodies thus produced can then be screened for a desired activity.
  • antibodies and fragments thereof have different amino acids flanking the peptide at the amino and the carboxyl termini where the peptide becomes bound to the antibody scaffold. This, results in a population of antibody molecules or fragments thereof that may differ in the presentation of the peptide. The population is screened for those antibodies that exhibit the biological activity of the peptide.
  • the amino acid immediately adjacent the peptide is a proline.
  • the activity of the biologically active peptide is to activate a target molecule, this may require dimerization of two target molecules (e.g. receptors in the hematopoietic superfamilies).
  • two peptides must be positioned to each bind a target molecule such that the two bound target molecules can then properly associate. This can be accomplished by having two peptides present on the same antibody or fragment thereof or by causing two antibody molecules each containing one peptide to bind together.
  • a single peptide can be inserted into or substituted for at least a portion of a CDR and then expressed as an immunoglobulin or a F(ab') 2 fragment.
  • two peptides can be inserted into or substituted for at least a portion of one or more CDRs and expresses as any antibody or antibody fragment.
  • the screening of antibodies or fragments thereof can be accomplished by panning with cells that have surface molecules to which the peptide specifically binds. Solid phase binding using purified target molecules or fragments thereof can also be used. Binding can also be carried out in solution using labeled target molecules. In addition, antibodies or fragments thereof can be screened by the use of biological assays for agonist or antagonist activity of the peptide.
  • CDR complementarity determining region
  • the biologically active peptide is a TPO mimetic or an EPO mimetic.
  • the antibodies of the library are displayed on phage.
  • methods of stimulating proliferation, differentiation or growth of cells which include contacting the cells with an effective amount of an immunoglobulin molecule or fragment thereof having one or more CDRs replaced with a biologically active peptide which binds to a receptor on the cells surface.
  • the biologically active peptide is a TPO mimetic or an EPO mimetic.
  • a method of stimulating proliferation, differentiation or growth of megakaryocytes by contacting megakaryocytes with an effective amount of an immunoglobulin molecule or fragment thereof having one or more CDRs replaced with a TPO mimetic peptide. Also provided is a method of increasing platelet production, which involves contacting megakaryocytes with an effective amount of an immunoglobulin molecule or fragment thereof having one or more CDR regions replaced with a TPO mimetic peptide.
  • the immunoglobulin molecule and the megagakarocytes can also be contacted in vitro and the resultant cells can be introduced into the patient.
  • an antibody or fragment thereof having at least one TPO mimetic peptide incorporated therein can be administered to a subject who intends to donate platelets, thus increasing the capacity of a donor to generate platelets to provide a more robust source of such platelets.
  • Also provided herein is a method of stimulating proliferation, differentiation or growth of hematopoietic cells, comprising contacting the cells with an effective amount of an immunoglobulin molecule or fragment thereof having one or more CDRs replaced with a EPO mimetic peptide.
  • Also embodied herein is a method of activating a homodimeric receptor protein, by contacting the receptor with an immunoglobulin molecule or fragment thereof having a CDR region replaced with a biologically active peptide that specifically binds the receptor and which has been dimerized.
  • the receptor is a thrombopoietin receptor.
  • Figure 1 is a diagrammatic representation of the vector pRL4.
  • Figures 2A and B show the sequence of the human tetanus toxoid antibody framework, light and heavy chains, respectively.
  • Figure 3 is a diagram depicting the grafting of the TPO mimetic peptide AF12505 into the heavy chain CDR3 region of the tetanus toxoid framework antibody.
  • XX represents flanking random amino acids.
  • Figure 4 is a diagram of the construction of a peptide cloned into the heavy chain CDR3 region.
  • Figure 5 represents the amino acid, and nucleotide sequences of clones that encode TPO mimetic peptide AF1205 with different random flanking residues.
  • Figure 6A-C depicts the nucleic acid sequence of plasmid pRL8 (SEQ. ID. NO: 60).
  • pRL8 is a modified version of pRL4 (pRL4 is also known as pComb 3X).
  • the pRL4 was modified between the Spe I and neighboring Sfi I restriction sites (shown by underlining) to include a flexible linker (murine kappa hinge region) followed by a Jun leucine zipper dimerization domain.
  • Figure 7 is a schematic depiction of a portion of the plasmid pRL8.
  • Figure 8 depicts the nucleic acid sequence of a portion of plasmid pRL8 (SEQ. ID. NO: 52) along with amino acid sequences corresponding to certain delineated nucleic acid sequences (SEQ. ID. NO: 53).
  • Figure 9 is a chart showing sequences of certain TPO positive clones herein.
  • Figure 10 is a bar graph showing activity of certain Fab clones containing 2 TPO mimetic peptides.
  • Figure 11 is a bar graph showing activity of certain Fab clones containing 2 or 3 TPO mimetic peptides.
  • Figure 12 graphically depicts the activity of Clone 59 as reflected by induction of luciferase activity.
  • Figure 13A depicts the amino acid sequence and nucleic acid sequence of the 5G1.1-TPO heavy chain (SEQ. ID. NOS: 67 and 68, respectively).
  • Figure 13B depicts the amino acid sequence and nucleic acid sequence of the 5G1.1 light chain (SEQ. ID. NOS: 69 and 70, respectively).
  • Figure 14 is a bar graph showing FACS analysis of cMpl receptor binding of purified 5G1.1+ TPO mimetic peptide compared to parental 5G1.1 antibody.
  • Figure 15 is a bar graph showing comparative activity of 5G1.1 antibody containing the TPO mimetic peptide in connection with cells transfected with a control vector containing no cMpl-R and cells transfected with a vector containing cMpl-R.
  • Figure 16 shows the sequence of clone 429/Xb4 (SEQ. ID. NO: 116)
  • Figure 17 is a flow chart showing the initial steps for making vector pRL5- Kappa. ⁇
  • Figure 18 is a flow chart showing additional steps for making vector pRL5- Kappa.
  • Figure 19 is a map of vector pRL5.
  • Figure 20 is a schematic of vector pRL5-Kappa.
  • Figure 21 A-l show the nucleic acid sequence of vector pRL5-Kappa.
  • Figures 22 and 23 show the human germline sequences with the highest homology to the TT-TPO starting antibody.
  • Figures 24 and 25 show the nucleic acid and amino acid sequences of the pAXB116Fab' heavy and light chain variable regions, respectively.
  • Figure 26 shows the nucleic acid sequences of the primers used to generate the pAXB116 heavy chain.
  • Figure 27 shows the nucleic acid sequences of the primers used to generate the pAXB116 light chain.
  • Figure 28 schematically shows the construction scheme for the plNG-pAXB116 vector.
  • Figure 29 shows the amino acid sequences for the heavy and light chain of clone 116.
  • Figure 30 shows the result of SDS-PAGE of pAXB116.
  • Figure 31 shows the proliferative effect of TPO and pAXB116 on CD34+ cord blood cells.
  • Figure 32 shows the activity of clone 116.
  • Figure 33 shows the sequences of heavy chain clones in accordance with an alternative embodiment of the present disclosure.
  • Figure 34 shows the relative activity of various H2/H3-(X4b) clones in 6cm luciferase assays.
  • Figure 35 shows the effect of the addition of 3 original TT amino acids on the placement of the TPO peptide in the HC-CDR2.
  • Figures 36A-E show the nucleic acid sequence (SEQ. ID NO. 141) of clone pRL5-116F and the amino acid sequences of the 116 light chain (SEQ. ID NO. 142) and the 116 heavy chain (SEQ. ID NO. 143).
  • Figure 37 shows the relative activity of 116 mutants in 6cm luciferase assays.
  • Figure 38 shows the amino acid sequences of various 116 variant clones.
  • immunoglobulin refers to an entire immunoglobulin molecule or molecules that contain immunologically active portions of whole immunoglobulin molecules and includes Fab, F(ab9)2, scFv, Fv, heavy chain variable regions and light chain variable regions.
  • immunoglobulin and antibody are used interchangeably herein. Any peptide that exhibits a useful property is suitable for insertion in an antibody framework. Peptide activities and uses include, but are not limited to, binding a receptor, binding a membrane bound surface molecule, binding a ligand, binding an enzyme or structural protein, activating or inhibiting a receptor, targeted drug delivery, or any enzymatic activity.
  • biological activity includes any activity associated with a molecule having activity in a biological system, including, but not limited to, the stimulatory or inhibitory activity triggered by protein-protein interactions as well as the kinetics surrounding such interactions including the stability of a protein-porotein complex. Enhancing or increasing “biological activity” herein is meant to include an increase in overall activity or an increase in any component of overall activity.
  • a peptide may exhibit one biological activity (such as, e.g., simply binding to a target) before insertion into the antibody framework, and a different or enhanced biological activity (such as, e.g., agonist activity) after insertion into the antibody framework.
  • one biological activity such as, e.g., simply binding to a target
  • a different or enhanced biological activity such as, e.g., agonist activity
  • EPO and TPO mimetic peptides which could benefit from display in the context of an immunoglobulin have been identified and are known to those who practice the art, e.g., EPO and TPO mimetic peptides.
  • Other examples include peptides that bind to receptors which are activated by ligand-induced homo-dimerization including active fragments displaying G-CSF activity, GHR activity and prolactin activity as described in Whitty and Borysenko, Chem Biol, (1999) Apr 6(4):R107-18; other examples of suitable peptides include a nerve growth factor mimetic from the CD loop as described in Zaccaro et al., Med. Chem.
  • N-terminal peptide of vMIP-ll as an antagonist of CXCR4 for HIV therapy as described in Luo et al., Biochemistry (2000) 39(44):13545-50; antagonist peptide ligand (AFLARAA) of the thrombin receptor for antithrombotic therapy as described in Pakala et al., Thromb. Res. (2000) 100(1): 89-96; peptide CGRP receptor antagonist CGRP (8-37) for attenuating tolerance to narcotics as described in Powell et al., Br. J. Pharmacol.
  • a random peptide epitope library is generated so that peptides are present on the surface of a bacteriophage particle. These collections, or libraries, of peptides can then be surveyed for those able to bind to a specific immobilized target protein.
  • Peptide mimetics used in accordance with this description are generally less than or equal to the number of amino acid residues that make up a CDR region, although they could be longer.
  • Any antibody can serve as a scaffold sequence, however typically human antibodies are chosen as human therapeutics is one of the ultimate objectives. Human or humanized antibodies are less likely to cause an adverse immune response in a human patient.
  • the major criteria in selecting an antibody to serve as a framework for insertion of a peptide, is that the replacement of one or more CDRs of the antibody with the peptide must change the antigen specificity.
  • the antibody can be a complete antibody or an Fab, scFv or F(ab') 2 fragment or portion thereof.
  • a library of antibodies can have one or more heavy and/or light chain CDRs replaced with a desired peptide.
  • the resulting library can then be screened to identify antibodies having a desired activity. It should be understood that randomization with in the substituted peptide can also be provided to generate an antibody library.
  • a useful antibody is the anti-tetanus toxoid (TT) Fab, as it is human and because modification of the HCDR3 is sufficient to change the antigen specificity of the antibody (Barbas et al., J. Am. Chem. Soc, 116, 1994, pages 2161-2162 and Barbas et al., Proc. Natl. Acad. Sci. USA, 92, 1995, pages 2529-2533).
  • TT anti-tetanus toxoid
  • Examples of methods which can be utilized to graft a desired peptide having biological activity in place of a CDR region include, but are not limited to, PCR overlap, restriction enzyme site cloning, site specific mutagenesis and completely synthetic means.
  • Site specific mutagenesis can be accomplished in several ways. One is based on dut/ung Kunkel mutagenesis (Kunkel, T.A., Proc. Natl. Acad. Sci. (1985) vol. 82, pp. 488-92). The Muta-Gene in Vitro Mutagenesis kit is available from BioRad based on this methodology (cat. # 170-3581 or 170-3580).
  • PCR amplification based mutagenesis approaches are also commercially available such as Stratagene's QuickChange Site-Directed Mutagenesis Kit and the ExSite PCR-based Site-Directed Mutagenesis Kit.
  • Another non-PCR method is available from Promega as the GeneEditor in vitro Site-Directed Mutagenesis System.
  • Completely synthetic means are also well-known and described, e.g., in Deng, et al., Methods Mol. Biol.
  • flanking sequences may be added to the carboxyl and/or amino terminal ends of the biologically active peptide. Flanking sequences can be useful to reduce structural constraints on the grafted peptide to allow it to more easily adopt a conformation necessary for biological activity.
  • a flanking region including a proline is covalently attached to the carboxy terminus of the biologically active peptide to create a proline extended biologically active peptide.
  • a flanking region can be generated by randomizing two amino acid positions on each side of the peptide graft in order to determine the best sequence.
  • a library having members with multiple varied sequences can be generated.
  • the resulting constructs are then tested for biological activity as described below by, e.g., panning techniques.
  • Recombinant proteins can be generated that have random amino acids at specific positions. This can be accomplished by modifying the encoding DNA.
  • a preferable deoxyribonucleotid ⁇ "doping strategy" is (NNK) X in order to cover all 20 amino acids and to minimize the number of encoded stop codons.
  • N may be A, C, G, or T (nominally equimolar)
  • K is G or T (nominally equimolar)
  • x is typically up to about 5, 6, 7, or 8 or more, thereby producing libraries of mono-, di-, tri-, quadra-, penta-, hexa-, hepta-, and octa- peptides or more.
  • the third position may also be G or C, designated "S”.
  • NNK or NNS (i) code for all the amino acids, (ii) code for only one stop codon, and (iii) reduce the range of codon bias from 6:1 to 3:1.
  • Other alternatives include, but are not limited to:
  • the third nucleotide position in the codon can be custom engineered using any of the known degenerate mixtures.
  • the group NNK, NNN, NNY, NNR, NNS cover the most commonly used doping strategies and the ones used herein.
  • the collection of engineered antibodies that are created during this process can be surveyed for those that exhibit properties of the peptide as, e.g., phage displayed antibodies, essentially as has been described in Barbas, C.F., III, Kang, A.S., Lerner R.A., and Benkovic, S.J., Assembly of combinatorial antibody libraries on phage surfaces: the gene III site, Proc. Natl. Acad. Sci. USA, 88, 1991 , pages 7978-7982 incorporated herein by reference.
  • This technology allows recombinant antibodies (as complete antibodies, Fab F(ab') 2 , or scFv) to be expressed on the surface of a filamentous bacteriophage. That same phage will have within it the genes encoding that specific antibody.
  • any other known method of introducing randomization into a sequence may be utilized herein.
  • error prone PCR can introduce random mutations into nucleic acid sequences (See, e.g., Hawkins et al., J. Mol. Biol, (1992) 226(3): 889-96). Briefly, PCR is run under conditions which compr mise the fidelity of replication, thus introducing random mutations in sequences as those skilled in the art would accomplish. After generation of such random mutants, they can be placed into phage display formats, panned and thus evaluated for activity.
  • Single chain libraries can be utilized in accordance with the present disclosure because an entire binding domain is contained on one polypeptide.
  • the light chain variable region is separated from heavy chain variable region by a linker region.
  • the use of short linkers ( ⁇ 11 amino acids) favors a dimeric complex where VH of one ScFv associates with VL of another ScFv molecule and visa versa, these molecules are termed diabodies (Kortt, A.A., Malky, R.L., Caldwell, J.B., Gruen, L.C., Ivanci, N., Lawrence, M.G. et al. Eur. J. Biochem. 221 51-157, 1994).
  • pRL4 which is also known as pComb 3X (see Fig. 1). This vector enables display of chimeric expression products on the surface of packaged phagemid particles.
  • pRL4 is a modified version of pComb3H (Barbas, CF. Ill and Burton, D.R. 1994. Monoclonal Antibodies from Combinatorial Libraries. Cold Spring Harbor Laboratory Course Manual, Cold Spring Harbor, N.Y.; Burton, D.R.; Barbas, CF. III. Advances in Immunology 57:191 -280, 1994; Lang, I.M., Chuang, T.L., Barbas, CF. 3 rd , Schleef, R.R. J. Biol. Chem.
  • pRL4 allows for dimerization of scFv antigen binding domains on the phage surface and in soluble form as detailed below.
  • a supE bacterial host such as ER2537 (F' Sup E, New England Biolabs, Beverly, MA)
  • the amber mutation is suppressed approximately fifty percent of the time..
  • Diabodies are expected to fold such that the VH of one scFv will pair with the V[_ of a second scFv-plll resulting in divalent antibody fragments.
  • a non-sup E host such as TOP10F' (InVitrogen, Carlsbad, CA)
  • the amber stop codon is recognized yielding soluble scFv diabodies.
  • the single chain antibody fragments are cloned downstream of the E. coli lacZ promoter, ribosome binding site, and omp A leader sequence. These elements allow induction of expression by IPTG, and the secretion out of the cell via the omp A leader sequence when expressed in the suppressor strain ER2537.
  • the single chain fragments are fused in frame with filamentous phage gene III (gill) sequences (amino acids 230-406).
  • the gill protein product, pill is a minor coat protein necessary for infectivity.
  • the scFv-gene HI fusion proteins are inserted into the membrane. Upon superinfection with helper phage, ⁇ these fragments are exported out of the cell on the surface of phage as pill-antibody fragments.
  • Other possible proteins to be used for fusion on the surface of phagemids include filamentous coat protein pVIII and other coat proteins.
  • Fab fragment libraries that maintain the native antigen recognition site, are useful to ensure that affinity is maintained.
  • the light and heavy chains are cloned as a single Sfil fragment.
  • the light chain fragments are cloned downstream of the E. coli lacZ promoter, ribosome binding site, and omp A leader sequence. These elements allow induction of expression by IPTG, and secretion out of the cell via the omp A leader sequence.
  • the light chain fragments are followed by a stop codon, a second ribosome binding site, the E. coli pel B leader sequence and heavy chain.
  • Hybrid heavy chain genes are fused in frame with filamentous phage gene III (gill) sequences (amino acids 230-406). An amber stop codon is present at the fusion junction.
  • a single polycistronic message is transcribed and translated as two polypeptides, a light chain and a heavy chain-gene III fusion protein.
  • the polypeptides are transported to the bacterial periplasmic space as directed by the leader sequences.
  • the heavy chain-pill fusion proteins are inserted into the membrane, and the light and heavy chains are associated covalently through disulfide bonds, forming the antigen binding sites.
  • the human constant region CH1 and C sequences include the cysteines that form the disulfide bond between heavy and light chains.
  • Fab-cplll fusion Upon superinfection with helper phage, these fragments are exported out of the cell on the surface of phage as Fab-cplll fusion.
  • a non-sup host such as TOP10F (Invitrogen, Carlsbad, CA)
  • the amber stop codon is recognized yielding soluble Fab fragments.
  • Important features of the pRL4 phage display system used include a purification His 6 tag, an HA epitope tag following the heavy chain, as well as a suppressible amber stop codon which is located between the heavy chain and the phage gene III.
  • the HA tag is recognized by HA.11 antibody (Babco, Berkeley, CA) and 12CA5 antibody (Roche Molecular Biochemical, Indianapolis, Ind.).
  • the His6 tag allows affinity purification of antibody fragments by Nickel-chelate chromatograph ⁇
  • amber stop allows for quick conversion from a fusion Fab-cplll product (for incorporation on the phage coat) when the stop is suppressed, to the soluble Fab which is made in a non-suppressor bacterial host.
  • Selection involves isolating from the library the best candidates that specifically bind to the peptides target molecule and display biological activity.
  • the phage expressing antibody fragments on their surface can be produced and concentrated so that all members of a library can be allowed to bind to the target molecule.
  • the target molecule can be immobilized on a microtiter dish, on whole cells, the membranes of whole cells, or present in solution. Non-specific Ab-phage are washed away, and bound phage particles are released from the antigen, often by the use of low pH.
  • the recovered Ab-phage are infectious and so can be amplified in a bacterial host. Typically, multiple rounds of this sort of selection are performed. Individual antibody fragment clones can then be analyzed as soluble Fabs or scFvs for identification of those that specifically recognize the target molecule.
  • initial libraries are electroporated into host cells, such as ER2537.
  • Library cultures are grown to log phase and superinfected with helper phage, such as VCSM13, a commercially available helper phage (Stratagene, La Jolla, CA). Superinfection provides the remaining phage components needed for packaging plasmids into phagemid particles. Alternatively, phage display without the use of helper phage may be utilized.
  • phagemids in the culture supernate are precipitated with polyethylene glycol (PEG). PEG precipitated phage are used in panning (solid phase cell surface, intemalization and membrane), FACS sorting, or magnetic sorting to purify specific binding antibodies from non specific binders.
  • PEG polyethylene glycol
  • a typical panning protocol is as follows:
  • Block phage particles with PBS + 1%BSA or 10% FBS + 4% milk powder + NaN 3 (except when internalized antibodies are assayed).
  • Specific antibody-phage bound to cells can be eluted by low pH, for example with 76 mM citric acid ph 2.5 in PBS for 5 to 10 minutes at room temperature.
  • antibody-phage can be used to infect ER2537 bacteria and amplify during overnight growth for the next round of panning. Generally, 3-4 rounds of panning are performed on each library. Phage ELISAs using commercially available secondary antibody (sheep anti-M13 antibody-HRP) or soluble antibody ELISAs using a commercially available HA. 11 antibody (Babco, Berkeley, CA) that recognizes the HA tag incorporated into each antibody from PRL4 sequences, can be performed following each round of panning to allow estimation of the enrichment of binding antibodies over non-binders.
  • the antibody-phage can be picked as single colonies from agar plates, grown as monoclonal antibody-phage and screened by ELISA for identification of specific binders. FACS analysis may also be utilized. Specifically the antibody-phage are infected into ToplOF' bacteria and plated for single colonies. Single colonies are picked form agar plates, grown and induced with IPTG. Soluble antibody is screened by ELISA for identification of specific binders. Screening can be done against live cells, against intact, mildly fixed target cells, or recombinant protein(s).
  • bioassays for functional screens of agonist antibodies can be carried out. Dimerization is often a prerequisite for activation of many receptors and thus bioassays focus on agonist antibodies that stimulate receptors via promotion of dimerization.
  • single chain multivalency is approached in linker design.
  • Fab fragment multivalency can be approached in a number of ways. A number of recent reports in the literature have shown success in dimeric antibody fragment formation which is applicable to phage display (DeKruif, J., and Logtenberg, T. 1996. J. Biol. Chem. 271 :7630-7634, Pack, P., and Pluckthun, A. 1992.
  • Divalent Fabs can be created in at least two ways. In one approach dimerization is achieved by addition of a dimerization domain to pRL4, forming pRL8 (See Figs. 6A-C, 7 and 8). There are a number of dimerization domains (lexA, Zn fingers, fos, jun etc.) that can be utilized in these vectors to obtain multivalency of Fab fragments. Dimerization domains are selected from, but not limited to, the following: jun (DeKruif, J. and Logtenberg, T. J. Biol. Chem.
  • Gin invertase from the bacteriophage Mu (Spaeny-Dekking, L., Schaji, E., Franken, K., van de Putte, P., Goosen, N. J. Bacteriol. 34:1779-1786, 1995), E. coli NTRC protein dimerization domain (Klose, K.E., North, A.K., Stedman, K.M., Kustu, S. J. Mol. Biol. 241:233-245, 1994), and HSV-1 ICP4 dimerization domain (GaJlinari, P., Wiebauer, K., Nardi, M.C, Jiricny, J. J. Virol.
  • dimerization can be achieved in cells through the use of full IgG vectors, or dimerization domains such as CH3 dimerization domains. Those of ordinary skill in the art are familiar with these and other dimerization domains and their use to dimerize proteins.
  • Chemical dimerization may be also achieved using a variety of chemical crosslinking reagents.
  • SMCC Succinimidyl trans-4 (maleimidylmethyl) cyclohexane-1 -carboxylate
  • This reagent will modify primary amino groups in the antibody. After incubating the antibody with the SMCC at room temperature, the reaction is run over a PD-10 column.
  • This maleimide derivitized Fab can be added to either a second Fab or a separate batch of the same Fab that has been treated with TCEP [(Tris (2- carboxyethyl) phosphine, hydrochloride): Molecular Probes Cat #T-2556] to reduce the thiol groups to SH. The reduction reaction is carried out in the dark for 15 minutes. The conjugation of the maleimide Fab and the thiol reduced Fab occurs at a 1 :1 ratio. Dimers are isolated by passing the reaction over a sephadex 200 gel filtration column. Other chemical linkers known to those skilled in the art may be used for dimerization.
  • Fab'2 involves cloning the human IgG hinge region, and optionally part of the CH2, as part of the Fd which includes additional cysteines and is described, e.g., in Better, et al., PNAS USA (1993) 90(2): 457-61, incorporated herein by reference.
  • the additional thiol groups on the Fd hinge can interact and cause two Fab' molecules to dimerize, creating a Fab'2.
  • Fab'2 can be purified directly from the bacterial cells. Additionally, undimerized Fab' from the bacteria can be isolated and chemically converted to Fab'2.
  • variable regions of the antibody can be cloned as a single chain wherein the variable light (VL) is connected to the variable heavy (VH) by a linker region. If that linker region is short (for example 5-7 amino acids), the folding of the scFv will favor association of two scFvs where the VL of one scFv paris with the VH of the second scFv. In this manner, two antigen binding sites are presented on the diabody.
  • Antibody constructs which contain two binding sites may be generated using any of these methods in order to test agonist activity and/or be used as the final therapeutic product.
  • the library of panned molecules are restricted with Sac I and Spe I and cloned into pRL8.
  • Subcloning to pRL8 vector individually or en masse following FACS sorting or panning allows expression of dimeric soluble binding Fabs for analysis in bioassays.
  • the antibody fragments are transported to the periplasmic space and form dimers there. The advantage of this approach is that it permits panning of monomeric Fab fragments, favoring high affinity Fabs.
  • pRL4 has the hemagglutinin decapeptide tag recognized by the commercially available HA. 11 antibody (Babco, Berkeley, CA). Fabs identified in FACS sorting or panning to be tested in bioassay are preincubated with HA. 11 which will promote dimerization, prior to addition to bioassays.
  • binding scFv's or Fabs are identified by panning or another selection method, the individual clones, each expressing a unique dimerized antibody fragment on the phage surface are tested for proliferation, differentiation, activation or survival effects on target cells. In addition, soluble dimerized antibody are examined in bioassays.
  • Transcriptional based assays Transiently co-transfect full length cMpl receptor with c-Fos promoter luciferase reporter construct. 24 hour post transfection starve the cells in 0.5% FCS for 24 hours. Stimulate the cells, harvest after 6 hours and take luciferase readings (see also Example 1 , Biological Assays section).
  • TF-1 cell Human erythroleukemia cell line proliferation. TF-1 cells express both full length and a truncated form of the Epo-R. (J.Cell Physiol., 1989, Vol 140, pages 323-334).
  • the EPO receptor couples directly to JAK2 kinase to induce tyrosine phosphorylation.
  • Epo induces cFos in TF-1 cells. c-Fos transcriptional activation. (Witthuhn et al., Cell, (1993), Vol. 74, pages 227-236).
  • bioassays can be used in high-throughput screening. Those of ordinary skill in the art are familiar with these and other suitable bioassays.
  • Several non-radioactive assays have been developed in which either DNA synthesis or enzyme activity can be analyzed. For example, an MTT cell proliferation assay (Promega Corporation, Madison, Wl) that is based on an assay described by Mosmann (Mossman, T. 1983. J. Immunol. Methods 65:55-57 incorporated herein by reference) can be used. This protocol is fast and easy.
  • MTT (3-[4,5- dimethylthiazol-2-yl]-2,5-diphenyl-tetrazoIium bromide), a tetrazolium salt
  • MTT a tetrazolium salt
  • the dehydrogenase content, and therefore the amount of colored product produced is proportional to cell number.
  • the colored product is detectable in an ELISA plate reader at 570nm.
  • Assays are performed in triplicate, en masse in 96 well microtiter plates. Briefly, target cells are plated in 100 ⁇ l aliquots in culture medium in 96-well plates. Following addition of various concentrations of antibodies, cells are incubated for 48- 72 hours at 37°C and 5% C0 2 in a fully humidified atmosphere. MTT is added to each well, and proliferation monitored via ELISA plate reader.
  • bacterial cells containing phagemids expressing antibodies are grown overnight at 37°C in 96 well deep well plates in 1 ml of a media that is a mixture of mammalian cell media and bacterial media (in the case of TF-1 cells: RPMI 2.7/SB 0.3/Carb 100ug/ml).
  • TF-1 cells are a human bone marrow erythroleukemia cell line that responds to multiple cytokines (Kitamura, T., Tange, T., Terasawa, T., Chiba, S., Kuwaki, T., Miyagawa, K., Piao, Y.F., Miyazono, K., Urabe, A., Takaku, F., Cell Physiol.
  • cytokines Kitamura, T., Tange, T., Terasawa, T., Chiba, S., Kuwaki, T., Miyagawa, K., Piao, Y.F., Miyazono, K., Urabe, A., Takaku, F., Cell Physiol.
  • MTS proliferation assay kit (catalogue number G5421) can be purchased from Promega, Inc. (Madison, Wl). Plates are kept at 37 C0 2 incubator and read at OD 90 at 1 hour, 4 hours, 8 hours with microplate reader.
  • cytokines The activities of cytokines are often synergistic. Synergy could be manifested through the binding of ligands to two different receptors which then sends the correct signal, or via a priming effect whereby interaction of ligand/receptor primes the cell to respond to a second cytokine. Furthermore, cytokines that act early in lineage development are more often synergistic than cytokines that act at later stages in a developmental pathway. Therefore, suboptimal concentrations of growth factors can be used in these bioassays to examine synergism. Conditions for suboptimal concentrations are determined for each assay.
  • Bone marrow stromal cells can also be added in bioassays to provide other necessary factors that may play a role in a synergistic response.
  • cell proliferation can be examined by monitoring DNA synthesis.
  • a non-radioactive, colorimetric assay that examines 5-bromo-2'-deoxy-uridine (BrdU) incorporation (Roche Molecular Biochemicals, Indianapolis, IN) can be performed in microtiter plate format. Here, cells are cultured in 96-well plates and incubated with BrdU and sub-optimal concentrations of cytokines. The amount of BrdU is determined after labeling with a peroxidase labeled anti-BrdU antibody. Final results are analyzed by ELISA plate reader at 405nm.
  • a radioactive mitogenesis assay that measures the rate of DNA synthesis as an indication of proliferation can also be used.
  • changes in rate of incorporation of [ 3 H]- thymidine in target cells is examined.
  • these assays permit concurrent and rapid screening of many antibody fragments. They have been widely used as a convenient method of assessing the stimulatory and inhibitory effects on the growth of many different cells. Cells are cultured in suspension until they reach exponential growth rate. Cells are then washed free of the medium in which they were cultured, and replated in fresh medium.
  • Cells are aliquoted into 96 well plates in a total volume of 100 ul at a concentration of about 1 -2 x 10 5 cells/ml. Dilutions of phage supernatant, soluble dimerized Fab or ScFv antibodies are added and cells are incubated for 18-48 hours in a gassed C0 2 incubator at a temp of 37°C Following incubation, [ 3 H]thymidine (937kBq) is added to each well and incubated for a further 4 hours. The cells are then removed from the incubator and counted directly in a bench top microplate scintillation counter such as Packard Top Count NXT Instrument (Packard, Meriden, CT).
  • a bench top microplate scintillation counter such as Packard Top Count NXT Instrument (Packard, Meriden, CT).
  • cells can be serially transferred to GF/C filters on a Millipore cell harvester (Millipore, Bedford, MA) or similar apparatus. Radioactivity associated with acid-insoluble material retained on the filter is then determined. Dilutions of commercially available growth factors are applied to positive control wells. Negative controls would include supernatants from cells carrying non-insert containing plasmids or irrelevant antibodies treated similarly.. The relative growth promoting activities of the standard and the diluents of the phage supernatants under test are compared to quantify the growth promoting activity in the sample.
  • Activation can be tested for by assaying second messengers or by transcriptional readout assays.
  • Survival can be assayed, for example, by monitoring apoptosis using assays such as tunnel assays or by other methods known to those who practice the art.
  • cAMP calcium concentration
  • DAG diacylglycerol
  • IP3 inositol 1 ,4,5-triphosphate
  • Measurement of spikes in intracellular calcium concentration, intracellular pH and membrane potential in high throughput screening assays can be performed using instruments such as the FLIPR Fluormetric Imaging Plate Reader System (Molecular Devices, Sunnyvale, CA). A number of fluorescent probes are available for examination of second messenger concentrations (Molecular Probes, Eugene OR).
  • Measurement of concentrations of second messengers can also be done on the single cell level (DeBernardi, M.A. and Brooker, G. Proc. Natl. Acad. Sci USA 93:4577-4582, 1996).
  • assays that examine other signaling events such as phosphorylation, apoptosis or levels of RNA or protein of specific genes would be useful.
  • cytokines have been shown to activate the enzyme PI 3-K (reviewed in Silvennoinen, O., Ihle, J.N. Signaling by the Hematopoietic Cytokine Receptors, R.G. Landes company, Austin, TX 1996).
  • tyrosine kinases have been shown to be central mediators for cytokine receptor signaling (Ihle, J.N., Witthuhn, B.A., Jo, F. W. Annu. Rev. Immunol. 13:369-398, 1995).
  • tyrosine kinases e.g., members of the Src family
  • RNA or proteins e.g., c-Jun and c-Fos are rapidly and transiently upregulated upon cytokine stimulation, while c-Myc induction is slower.
  • a growth factor ' or growth factor mimetic agonist or inhibitory antibody
  • a myc read-out assay cells such as IL-3 dependent FDCP-mix cell line is starved of IL-3 growth factor for 8 hours, followed by exposure to growth factor mimetics, or native growth factors for 2 hours at 37°C
  • the cells are harvested, RNA is isolated, and reverse transcriptase- polymerase chain reactions (RT-PCR) are performed with primers specific for the myc gene.
  • the RT-PCR reactions are electrophoresed in horizontal agarose gels for quantitation of PCR product. In this case expression of a single gene is being monitored.
  • agonist antibodies could be identified under conditions of high probe sensitivity and a dynamic range. In this way, up to 10,000 or more could be analyzed for changes in expression. Desired genes that could be monitored could include c- myc, c-jun, NF- ⁇ B, among others. These genes are downstream of various signal transduction pathways and their expression should change upon a mitogenic response.
  • CHIP Affymetrix, Santa Clara, CA
  • oligonucleotides from desired test genes can be printed out onto glass surface.
  • Target cells are exposed to test agonist antibodies.
  • RNA is isolated from the cells exposed to test agonist antibodies, copied to cDNA, and in vitro transcribed in the presence of biotin.
  • Hybridization of in vitro transcribed, biotinylated mRNA is used as probe in the arrays. Chips are then scanned to determine genes that show increases in transcription upon exposure to test agonist antibodies. In another version of CHIP technology (Incyte, Palo Alto, CA), the amount of DNA is not normalized on the glass, therefore, one would set up a competitive hybridization.
  • RNA is isolated from the cells before and after exposure to agonist.
  • cDNA is made from each sample whereby one cDNA reaction has one label incorporated, for example, Cy-3, and the other cDNA population has a different label incorporated, for example Cy-5. Signals are detected and compared on a dual laser scan to collect images.
  • Visual assays can also be used such as traditional methylcellulose colony forming assays (Stem Cell Technologies, Vancouver BC, Canada). In these assays, colony growth, and morphological changes are scored via light microscope. Visual examination for proliferation or differentiation effects in semi-solid agar cultures or methylcellulose can be performed using the appropriate cell line. Williams Hematology 5 (eds. E. Beutler, M.A. Lichtman, B.S. Coller L T.J. Kipps), McGraw-Hill, Inc., pp L22- L26, 1995). Addition of methylcellulose allows clonal progeny of a single progenitor cell to stay together and facilitates the recognition and enumeration of distinct colonies.
  • a basic methylcellulose medium such as Iscove's MDM, BSA, (-mercaptoethanol, L-glutamine) except colony- stimulating factor supplements and test antibodies (phage supernatants, soluble antibodies) are added to see if they can substitute for growth factors.
  • Cells in methylcellulose culture are incubated for 10-12 days following the addition of antibodies in a 37°C humidified atmosphere of 5% C0 2 in air. After 10-12 days of incubation, colonies are counted using an inverted microscope. After another 8-10 days, colonies are counted again. Comparisons are made between media containing antibodies and controls with and without growth factors.
  • colonies can be picked from methylcellulose and individual cells examined cytologically by staining with Wright's stain (see Atlas of Hematological Cytology, F.G.J. Hayhoe and R.J. Flemans, Wiley-lnterScience 1970).
  • the receptor-binding affinities of antibody fragments can be calculated (Lfas & Johnson, 1990) from association and dissociation rate constants measured using a BIACORE surface plasmon resonance system (Pharmacia Biosensor).
  • a biosensor chip is activated for covalent coupling of gD-mpl receptor using N-ethyl-N"'-(3- dimethylaminopropyl)-carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) according to the supplier's (Pharmacia Biosensor) instructions.
  • gD-mpl is buffer- exchanged into 10 mM sodium acetate buffer (pH 4.5) and diluted to approximately 30 ⁇ g/mL.
  • Equilibrium dissociation constants, K d s, from SPR measurements are calculated as kotf/kon- Standard deviations, s on for kon and s 0 ff for o ff, are typically obtained from measurements with > 4 protein concentrations (k o n) or with > 7 protein concentrations (ko f f).
  • Dissociation data are fit to a simple AB->A+B model to obtain koff +/- s.d. (standard deviation of measurements).
  • Pseudo-first order rate constant (ks) are calculated for each association curve, and plotted as a function of protein concentration to obtain kon +/- s.e. (standard error of fit).
  • the coding regions for both the light and heavy chains, or fragments thereof can be separately cloned out of a bacterial vector and into mammalian vector(s).
  • a single vector system such as pDR1 or its derivatives, can be used to clone both light and heavy chain cassettes into the same plasmid.
  • dual expression vectors where heavy and light chains are produced by separate plasmids can be used.
  • Mammalian signal sequences need to be either already present in the final vector(s) or appended to the 5' end of the light and heavy chain DNA inserts. This can be accomplished by initial transfer of the chains into a shuttle vector(s) containing the proper mammalian leader sequences.
  • the light chain and heavy chain regions, or fragments thereof are introduced into final vector(s) where the remaining constant regions for lgG1 are provided either with or without introns.
  • primer design for PCR amplifying the light and heavy chain variable regions out of pRL4 may need to include exon splice donor sites in order to get proper splicing and production ⁇ of the antibodies in mammalian cells.
  • the production of antibody heavy and light chains can be driven by promoters that work in mammalian cells such as, but not limited to, CMV, SV40, or IgG promoters.
  • the vector(s) will contain a selectable marker for growth in bacteria (such as, but not limited to, ampicillin, chloramphenicol, kanamycin, or zeocin resistance).
  • selectable markers for mammalian cells such as, but not limited to, DHFR, GS, gpt, Neomyocin, or hygromyocin resistance
  • IgG vector(s) may also be present in the IgG vector(s), or could be provided on a separate plasmid by co-transfection.
  • antibodies made in accordance with the disclosure herein provide increased half-life (duration of action) to the activity of small peptides or peptide mimetics such as the TPO mimetic described herein.
  • the serum half-life of an antibody can itself be prolonged by making derivatives that are pegylated. See, e.g., Lee, et al., Bioconjug. Chem (1999) 10(6): 973-81 , incorporated herein by reference.
  • Another advantage, e.g., of the TPO mimetic antibody described herein is that normal TPO treatment may result in generation of TPO neutralizing antibodies in patients which interfere with the activity of a patient's naturally occurring TPO.
  • the present TPO mimetic antibody substantially reduces the likelihood that a detrimental immune response will be produced toward native TPO because it has a different amino acid sequence.
  • Detectable markers include radioactive and non-radioactive labels and are well-known to those with skill in the art. Common non-radioactive labels include detectable enzymes such as horseradish peroxidase, alkaline phosphatase and fluorescent molecules. Fluorescent molecules absorb light at one wavelength and emit it at another, thus allowing visualization with, e.g., a fluorescent microscope. Spectrophotometers, fluorescence microscopes, fluorescent plate readers and flow sorters are well-known and are often used to detect specific molecules which have been made fluorescent by coupling them covalently to a fluorescent dye.
  • Fluorochromes such as green flurorescent protein, red shifted mutants of green fluorescent protein, amino coumarin acetic acid (AMCA), fluorescein isothiocyanate (FITC), tetramethylchodamine isothiocyanate (TRITC), Texas Red, Cy3.0 and Cy ⁇ .O are examples of useful labels.
  • the molecules can be used in cell isolation strategies such as fluorescence- activated cell sorting (FACS) if fluorescent markers are used, In fluorescence-activated cell sorting, cells tagged with fluorescent molecules are sorted electronically on a flow cytometer such as a Becton-Dickinson (San Jose, California) FACS IV cytometer or equivalent instrument.
  • the fluorescent molecules are antibodies that recognize specific cell surface antigens.
  • the antibodies are conjugated to fluorescent markers such as fluorescein isothiocyanate (FITC) or Phycoerythrin (PE).
  • Magnetic sorting is also possible.
  • the antibody is linked directly or indirectly to magnetic microbeads.
  • Cells are precoated with antibodies that recognize cell surface molecules, e.g., receptors involved in proliferation, differentiation, activation or survival.
  • the antibodies are attached to magnetic beads conjugated with a secondary immunoglobulin that binds to the primary antibody displaying the peptide, such as to the HA molecular tag engineered into each antibody.
  • the cells are then removed with a magnet.
  • Magnetic sorting can be positive selection where cells of interest are bound by the antibody and hence the magnet, or negative selection where undesired cells are isolated onto the magnet.
  • radiolabeled antibodies can be used for diagnostic purposes.
  • Antibodies and fragments thereof disclosed herein are useful for the amplification of a variety of clinically relevant cell types.
  • Treatment can be in vivo or ex vivo.
  • agonist antibodies are useful to treat patients suffering from a deficiency in a cell population caused by disease, disorder or treatment related to for example suppression of hematopoiesis where less than the normal number of cells of a given lineage or lineages are present in a patient.
  • the following represent only some examples of the conditions that can be treated with the antibodies containing biologically active peptides disclosed herein, those who practice the art would be able to identify other diseases and conditions that would benefit from such treatment.
  • HIV-infected patients, patients undergoing chemotherapy, bone marrow transplant patients, stem cell transplant patients, and patients suffering from myeloproliferative disorders show subnormal levels of specific hematopoietic lineages.
  • Thrombocytopenia can be a result of chemotherapy, bone marrow transplantation or chronic disease such as idiopathic thrombocytopenia (ITP) which all result in low platelet levels.
  • ITP idiopathic thrombocytopenia
  • the present TPO mimetic antibodies can be used to treat such patients.
  • the molecules encompassed by the claimed invention can also be used for ex vivo proliferation and differentiation of cells. This is useful for gene therapy purposes, for example for traditional viral vector approaches, and for autologous bone marrow transplants.
  • certain antibodies in accordance with the present disclosure can be radiolabeled for radioimmunotherapy or conjugated to toxins to deliver such toxins to specific cell types and result in the killing of those cells.
  • a biologically active c-mpl agonist antibody capable of stimulating proliferation, differentiation and maturation of hematopoietic cells may be used in a sterile pharmaceutical preparation or formulation to stimulate megakaryocytopoietic or thrombopoietic activity in patients suffering from thrombocytopenia due to impaired production, sequestration, or increased destruction of platelets.
  • Thrombocytopenia- ass ⁇ ciated bone marrow hypoplasia may be effectively treated with the disclosed antibodies as well as disorders such as disseminated intravascular coagulation (DIC), immune thrombocytopenia (including HIV-induced ITP and non HIV-induced ITP), chronic idiopathic thrombocytopenia, congenital thrombocytopenia, myelodysplasia, and thrombotic thrombocytopenia.
  • DIC disseminated intravascular coagulation
  • immune thrombocytopenia including HIV-induced ITP and non HIV-induced ITP
  • chronic idiopathic thrombocytopenia congenital thrombocytopenia
  • myelodysplasia myelodysplasia
  • thrombotic thrombocytopenia e.g., thrombotic thrombocytopenia.
  • TPO thrombopoietin
  • TPO thrombopoietin
  • An example of an assay useful for determining activity of TPO mimetics is the rebound thrombocytosis assay which involves administering to mice a single injection of goat anti-mouse platelet serum to induce acute thrombocytopenia (day 0). On days 5 and 6 mice are injected with test samples. On day 8 platelet counts are determined ( 35 S incorporation into platelets).
  • EPO mimetic antibodies herein stimulate hematopoiesis in a manner similar to naturally occurring EPO. Such therapy is useful in treating conditions where red blood cell production is compromised such as in chronic renal failure.
  • the biological activity of EPO mimetic antibodies may be determined using in vitro or in vivo assays.
  • EPO mimetic antibodies can be evaluated for the extent of erythropoiesis or receptor binding. Tests to determine biological activity are well-known to those of skill in the art. For example, the biological activity of erythropoietin can be measured as described in, e.g., U.S. Pat. No. 5,614,184 and U.S. Pat. No. 5,580,853 herein incorporated by reference.
  • the route of antibody administration is in accord with known methods, e.g., injection or infusion by intravenous, intraperitoneal, intracerebral, intramuscular, subcutaneous, intraocular, infraarterial, intrathecal, inhalation or intralesional routes, topical or by sustained release systems as noted below.
  • the antibody is preferably administered continuously by infusion or by bolus injection.
  • the antibodies of the invention may be prepared in a mixture with a pharmaceutically acceptable carrier. Techniques for formulation and administration of the compounds of the instant application may be found in "Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, PA, latest edition.
  • This therapeutic composition can be administered intravenously or through the nose or lung, preferably as a liquid or powder aerosol (lyophilized).
  • the composition may also be administered parenterally or subcutaneously as desired.
  • the therapeutic composition should be sterile, pyrogen-free and in a parenterally acceptable solution having due regard for pH, isotonicity, and stability. These conditions are known to those skilled in the art.
  • dosage formulations of the compounds of the present invention are prepared for storage or administration by mixing the compound having the desired degree of purity with physiologically acceptable carriers, excipients, or stabilizers.
  • physiologically acceptable carriers excipients, or stabilizers.
  • Such materials are non-toxic to the recipients at the dosages and concentrations employed, and may include buffers such as TRIS HCl, phosphate, citrate, acetate and other organic acid salts; antioxidants such as ascorbic acid; low molecular weight (less than about ten residues) peptides such as polyarginine, proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidinone; amino acids such as glycine, glutamic acid, aspartic acid, or arginine; monosaccharides, disaccharides, and other carbohydrates including cellulose or its derivatives, glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as manni
  • the antibody formulation When used for in vivo administration, the antibody formulation must be sterile and can be formulated according to conventional pharmaceutical practice. This is readily accomplished by filtration through sterile filtration membranes, prior to or following lyophilization and reconstitution. The antibody ordinarily will be stored in lyophilized form or in solution. Other vehicles such as naturally occurring vegetable oil like sesame, peanut, or cottonseed oil or a synthetic fatty vehicle like ethyl oleate or the like may be desired. Buffers, preservatives, antioxidants and the like can be incorporated according to accepted pharmaceutical practice.
  • compositions suitable for use include compositions wherein one or more rationally designed antibodies are contained in an amount effective to achieve their intended purpose. More specifically, a therapeutically effective amount means an amount of antibody effective to prevent, alleviate or ameliorate symptoms of disease or prolong the survival of the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein. Therapeutically effective dosages may be determined by using in vitro and in vivo methods.
  • an effective amount of antibody to be employed therapeutically will depend, for example, upon the therapeutic objectives, the route of administration, and the condition of the patient.
  • the attending physician takes into consideration various factors known to modify the action of drugs including severity and type of disease, body weight, sex, diet, time and route of administration, other medications and other relevant clinical factors. Accordingly, it will be necessary for the therapist to titer the dosage and modify the route of administration as required to obtain the optimal therapeutic effect.
  • the clinician will administer antibody until a dosage is reached that achieves the desired effect. The progress of this therapy is easily monitored by conventional assays.
  • the therapeutically effective dose can be estimated initially from cell culture assays.
  • a dose can be formulated in animal models to achieve a circulating concentration range that includes the EC 50 as determined in cell culture (e.g., the concentration of the test molecule which promotes or inhibits cellular proliferation or differentiation). Such information can be used to more accurately determine useful doses in humans.
  • Toxicity and therapeutic efficacy of the antibody molecules described herein can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD 50 (the dose lethal to 50% of the population) and the ED 50 (the dose therapeutically effective in 50% of the population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio between LD 5 o and ED 50 .
  • Molecules which exhibit high therapeutic indices are preferred.
  • the data obtained from these cell culture assays and animal studies can be used in formulating a range of dosage for use in human.
  • the dosage of such molecules lies preferably within a range of circulating concentrations that include the ED 50 with little or no toxicity.
  • the dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
  • the exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. (See e.g., Fingl et al, 1975, in "The Pharmacological Basis of Therapeutics", Ch. 1 p.1).
  • Dosage amount and interval may be adjusted individually to provide plasma levels of the antibody which are sufficient to promote or inhibit cellular proliferation or differentiation or minimal effective concentration (MEC).
  • MEC minimal effective concentration
  • the MEC will vary for each antibody, but can be estimated from in vitro data using described assays. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. However, HPLC assays or bioassays can be used to determine plasma concentrations.
  • Dosage intervals can also be determined using MEC value.
  • Antibody molecules should be administered using a regimen which maintains plasma levels above the MEC for 10-90% of the time, preferably between 30-90% and most preferably between 50-90%.
  • the effective local concentration of the antibody may not be related to plasma concentration.
  • a typical daily dosage might range from about 1 ⁇ /kg to up to 10OOmg/kg or more, depending on the factors mentioned above.
  • the clinician will administer the molecule until a dosage is reached that achieves the desired effect. The progress of this therapy is easily monitored by conventional assays.
  • from about 0.001 mg/kg to abut 1000 mg/kg, more preferably about 0.01 mg to 100 mg/kg, more preferably about 0.010 to 20 mg/kg of the agonist antibody might be an initial candidate dosage for administration to the patient, whether, for example, by one or more separate administrations, or by continuous infusion.
  • the treatment is repeated until a desired suppression of disease symptoms occurs or the desired improvement in the patient's condition is achieved.
  • other dosage regimes may also be useful.
  • the present antibodies can also be used in diagnostic assays, e.g., for detecting expression of certain proteins in specific cells, tissues, or serum.
  • diagnostic assay techniques known in the art may be used, such as competitive binding assays, direct or indirect sandwich assays and immunoprecipitation assays conducted in either heterogeneous or homogeneous phases (Zola, Monoclonal Antibodies: A Manual of Techniques, CRC Press, Inc. (1987) pp. 147-158).
  • the antibodies used in the diagnostic assays can be labeled with a detectable moiety.
  • the detectable moiety should be capable of producing, either directly or indirectly, a detectable signal.
  • the detectable moiety may be a radioisotope, such as 3 H, 14 C, 32 P, 35 S, or 125 l, a fluorescent or chemiluminescent compound, such as fluorescein isothiocyanate, rhodamine, or luciferin, or an enzyme, such as alkaline phosphatase, beta-galactosidase or horseradish peroxidase.
  • a radioisotope such as 3 H, 14 C, 32 P, 35 S, or 125 l
  • a fluorescent or chemiluminescent compound such as fluorescein isothiocyanate, rhodamine, or luciferin
  • an enzyme such as alkaline phosphatase, beta-galactosidase or horseradish peroxidase.
  • Any method known in the art for conjugating the antibody to the detectable moiety may be employed, including those methods described by Hunter et al., Nature, 144:945 (1962); David
  • the present antibodies also are useful for the affinity purification of proteins from recombinant cell culture or natural sources.
  • the antibodies are immobilized on a suitable support, such a Sephadex resin or filter paper, using methods well known in the art.
  • the immobilized antibody then is contacted with a sample containing the protein to be purified, and thereafter the support is washed with a suitable solvent that will remove substantially all the material in the sample except the protein, which is bound to the immobilized antibody. Finally, the support is washed with another suitable solvent that will release the protein from the antibody.
  • TPO mimetic-peptide IEGPTLRQWLAARA SEQ. ID. NO: 1 was grafted into the anti-tetanus toxoid (TT) Fab heavy chain CDR3 (HCDR3), replacing the entire HCDR3 sequence GDTIFGVTMGYYAMDV (SEQ. ID. NO: 4).
  • Figure 2A shows the sequence for the human tetanus toxoid antibody employed. Two grafting approaches were taken. In the first approach the agonist peptide was inserted into the H-CDR3 region with two glycines flanking each side. This was to reduce structural constraints on the grafted peptide so that it could more easily adopt the needed conformation.
  • Figure 4 outlines the library construction process. Briefly, the anti-tetanus toxoid Fab was amplified as two fragments. Fragment A was amplified using a forward primer (N-Omp: 5' TAT CGC GAT TGC AGT GGC ACT GGC 3') (SEQ. ID. NO: 5) that annealed to the Omp A leader for the light chain in combination with a backward primer (TPOCDR3-B: 5' GC CAG CCA TTG CCG CAG CGT CGG CCC TTC AAT YNN YNN TCT CGC ACA ATA ATA TAT GGC 3') (SEQ. ID. NO: 6) that annealed at the end of the heavy chain framework region (FR) 3.
  • N-Omp 5' TAT CGC GAT TGC AGT GGC ACT GGC 3'
  • TPOCDR3-B 5' GC CAG CCA TTG CCG CAG CGT CGG CCC TTC AAT YNN
  • the reverse primer contained a tail encoding the new CDR3.
  • Fragment B was generated using a forward primer (TPOCDR3-F: 5' CCG ACG CTG CGG CAA TGG CTG GCG GCG CGC GCG NNY NNY TGG GGC CAA GGG ACC ACC GT 3')(SEQ. ID. NO:7) that annealed at the FR4 and the reverse primer Seq-G3Rev (5' TCA AAA TCA CCG GAA CCA GAG C 3') (SEQ. ID. NO: 8) which annealed in the gene III region of the plasmid, downstream of the heavy chain stop signal.
  • the TPOCDR3-F primer also had a tail of bases that encoded the new CDR3 region.
  • TAQ DNA Polymerase (Perkin Elmer) was used in the following PCR program: 94° 30 seconds, then 30 cycles of 94° for 15 sec, 55° for 15 seconds, and 72° for 90 seconds, followed by an extension period at 72° for 10 minutes, and a hold at 4°. After the fragments were generated by PCR and gel purified, they were combined for an overlap extension PCR. The new CDR3 primer encoded regions were complementary and provided 23 bases of overlap. Primers N- Omp and SeqG3Rev were used in the overlap PCR protocol to generate the full Fab DNA product.
  • Taq DNA Polymerase (Perkin Elmer) was used in the following PCR program: 94° 30", then 20 cycles of 94° 30", 56° 30", and 72° 3'15", then an extension period of 72° for 15' followed by a 4° hold.
  • an Sfi 1 digest was performed at 50° for 5 hours. Inserts were ligated into Sfi 1 digested pRL4 vector overnight. Ligation products were ethanol precipitated, resuspended in H 2 0, and then electroporated into competent ER2537 bacteria (suppressor strain, New England Biolabs). Following one hour of shaking in 5 mis SOC, an equal volume of SB was added.
  • Carbenicillin was added to 20ug/ml and the culture shaken for one hour at 37°, followed by one hour at 37° in 50ug/ml carbenicillin.
  • the library culture was transferred into a flask containing 100 mis fresh SB, 50 ug/ml Carbenicillin, and 10 12 VCS M13 helper phage. After two hours at 37°, kanamycin was added to select for those bacteria that had been infected with helper phage. The following day, the overnight cultures were spun down and the phage in the supemate were precipitated on ice using 4% PEG/0.5 M NaCl. After spinning down the phage, the pellet was resuspended in 1 %BSA/PBS, filtered and dialyzed against PBS. Library phage were stored at 4°.
  • Fabs containing the non-rand ⁇ mly linked peptide was performed as described above by substituting primers TPOCDR3-B and TPOCDR3-F with alternate specific primers.
  • primers used were TPOCDR3g-B (5' GC CAG CCA TTG CCG CAG CGT CGG CCC TTC AAT NGG NGG TCT CGC ACA ATA ATA TAT GGC 3') (SEQ. ID.
  • TPOCDR3g-F 5' CCG ACG CTG CGG CAA TGG CTG GCG GCG CGC GCG GGN GGN TGG GGC CAA GGG ACC ACC GT 3')(SEQ. ID. NO: 10).
  • GG-(IEGPTLRQWLAARA)-GG SEQ. ID. NO: 29
  • primers used were TPO-CDR3-ggB (5' GC CAG CCA TTG CCG CAG CGT CGG CCC TTC AAT NCC NCC TCT CGC ACA ATA ATA TAT GGC 3')(SEQ. ID.
  • TPOCDR3g-F (5' CCG ACG CTG CGG CAA TGG CTG GCG GCG CGC GCG GGN GGN TGG GGC CAA GGG ACC ACC GT 3') (SEQ. ID. NO: 12).
  • platelets In order to select for the optimal peptide display, panning was performed on human platelets. Because platelets express approximately 1800 TPO receptors per cell on their surface (cMpl receptors), they represented a good cell target. In addition, platelets are readily available from a local Blood Bank. To 1 ml of concentrated indated human platelets from the Blood Bank, 50 uls of freshly prepared Fab-phage were added in a 15ml conical tube with 0.1% NaN 3 . The tube was mixed at room temperature for 1 -2 hours. Typically, 10 mis of 50% human serum (taken off the remaining platelets) + 50% ⁇ IMDM/10% FBS/0.1% azide/2mM EDTA ⁇ was added to the phage/cells.
  • Platelets were pelleted at 5500xg for 5 minutes at room temperature. Supernatant was drained and the pellet was left resting under -500 uls of the wash for 20 minutes. The platelets were very gently resuspended and then 10mls of 25% human serum (taken off the remaining platelets) +75% ⁇ IMDM/10% FBS/0.1% azide/2mM EDTA ⁇ was added to the phage/cells. The centrifugation, pellet rest, and resuspension of the platelets was repeated. In panning rounds 3 and 4, a third wash was performed. The washed phage/cells were transferred to an eppindorf tube and spun at 5200xg.
  • Phage were eluted from the platelets 10 minutes at room temperature using acid elution buffer (0.1 M HCl, 1mg/ml BSA, and glycine to pH 2.2). Platelets were pelleted at max speed and the eluted phage transferred to a 50 ml conical tube, neutralized with 2M Tris Base. Phage were then allowed to infect fresh ER2537 bacteria for 15 minutes at room temperature and amplified overnight as described above. Four rounds of platelet panning were performed.
  • acid elution buffer 0.1 M HCl, 1mg/ml BSA, and glycine to pH 2.2.
  • Phage were then allowed to infect fresh ER2537 bacteria for 15 minutes at room temperature and amplified overnight as described above. Four rounds of platelet panning were performed.
  • Pelleted cells were resuspended in 50 uls of 1:10 diluted (in PBS / 1% BSA / 0.1% NaN 3 ) 2° anti-HA antibody [Rat IgG anti-HA High Affinity clone 3F10 (Roche Molecular Biochem icals)] was added. After 30 minutes at room temperature, the cells were washed with 1 ml FACS buffer as above. Following centrifugation, cells were resuspended in 100 uls of 1:160 diluted (in PBS /1% BSA /0.1% NaN 3 ) 3° anti-Rat IgG-FITC antibody (Sigma) and incubated 20 minutes at room temperature in the dark.
  • CMK cells a Megakaryocytic cell line (from German Collection of Microorganisms and Cell Cultures) which also expresses the cMpl receptor.
  • Fab clones that bound CMK cells were then analyzed to verify that the platelet and CMK cell binding was occurring via the cMpl receptor.
  • 293 EBNA cells were transfected with or without the cMpl-R, which had been cloned from Tf-1 cells by RT-PCR. 1 X 10 6 transfected cells were incubated with bacterial supernate from each Fab clone (pre-blocked as described above) for 20-30 minutes at room temperature.
  • Anti-TT Fab does not bind to control vector or cMpl-R transfected 293 cells. However, Fab clone X1c shows a shift from 3% binding of control (non-cMpl receptor) transfected cells to 95% binding of cells expressing the cMpl-R.
  • Clones were tested for agonist activity using a transcriptional based assay measuring luciferase activity driven by the c-Fos promoter. Dimerization of the cMpl receptor activates Jak which stimulates the MAP kinase pathway. Thus activation can be measured by assaying luciferase production and activity stimulated by MAP kinase via the cFos promoter. Since dimerization of the cMpl receptor is required for activation, either full IgG or dimerized Fab fragments capable of dimerizing the receptor, could be used to stimulate cMpl receptor activity. Fabs produced in bacteria were dimerized via the HA tag utilizing the 12CA5 anti-HA antibody.
  • Fab containing bacterial supernatants (2mls) mixed with 12CA5 were applied to NIH3T3 cells which had been co-transfected with either a control vector or the cMpl receptor and the Fos promoter/luciferase reporter construct. Co-transfections of 3T3 cells were performed by plating NIH 3T3 cells at 3 x 10 5 cells per 6 cm dish and then transfecting the following day.
  • NIH 3T3 cells were transfected using the Effectine lipofection reagent (Qiagen), transfecting each plate with 0.1 ug pEGFP (a tracer to measure transfection efficiency), 0.2 ug of the Fos promoter/luciferase construct and 0.7 ug of either the empty control vector or the plasmid expressing the cMpl receptor.
  • 3T3 cells were placed in 0.5% serum 24 hours post transfection and incubated for an additional 24 hours in this low serum media to reduce the background activation of the Fos promoter. Antibody supernatants were then applied to these cells for 6 hours. Cells were harvested and luciferase assays performed using 50 ug of cell lysate.
  • Activation of cMpl receptor can be tested in a similar manner using full IgGs (converted from Fab as described herein) produced by transient or stable transfection of mammalian cells rather than bacterially produced Fabs dimerized by anti-HA 12CA5.
  • Experimentally transient transfection can be performed essentially as described here. For transfections 2 x 10 6 cells (such as 293 EBNA) would be plated in 6cm dishes for each test sample.
  • each plate would be transfected with 2.5 ug of total DNA (2 ug total of the light chain and heavy chain plasmid(s), 0.25 ug of pAdVAntage (Promega, Madison, Wisconsin), and 0.25 ug of pEGFP) using the Effectine reagent (Qiagen).
  • the 293 cells would be placed in 0.5% serum 24 hours post transfection and incubated for an additional 24 hours in this low serum media to obtain full IgG. Residual growth factors are negligible in this media in stimulating receptors as seen in controls experiments. After 24 hours supernatants would be collected and spun for 5 minutes at 3000rpm to remove any residual cells.
  • 3mls of the conditioned 293 cell supernatants would be applied to NIH3T3 cells as described above.
  • Another approach to linking two agonistic peptides together in an antibody framework is to insert the agonist peptide in more than one position within a single Fab fragment.
  • additional libraries containing TPO mimetic sequences grafted into a human antibody framework were constructed. Following selection of peptides properly presented in the context of CDR1, CDR2 or CDR3 of the light chain, or CDR2 of the heavy chain, the binding sequences were combined into a single Fab molecule, for example as listed in Table 1 below, and analyzed for enhanced activity.
  • the first round of PCR was performed using the program: 94° 30", then 30 cycles of 94° 15", 56° 30", and 72° 2', followed by elongation for 10' at 72° and a 4° hold.
  • Overlap PCR was performed for 10 cycles without primers using the program listed above to allow the full DNA template to be generated by the polymerases. Primers were then added to the PCR reaction tubes for 20 cycles of the same program for amplification.
  • the fragment A was created using the forward primer lead VH ( 5' GCT GCC CAA CCA GCC ATG GCC 3')(SEQ. ID. NO: 13), which annealed at the pel B leader signal located in front of the heavy chain, and the reverse primer HR2 CMPL ANTI (5 1 AGC CAG CCA CTG GCG CAG GGT TGG GCC TTC GAT MNN MNN TCC CAT CCA CTC AAG CCC TTG 3')(SEQ. ID. NO: 51) that annealed at the end of the heavy chain FR2.
  • the reverse primer contained a tail encoding the new CDR2.
  • Fragment B was created using forward primer HR2 cMpl CODE (5' CCA ACC CTG CGC CAG TGG CTG GCT GCT CGC GCT NNK NNK AGA GTC ACC ATT ACC GCG GAC 3')(SEQ. ID. NO: 14) which annealed at FR3 of the heavy chain and reverse primer N-dp (5' AGC GTA GTC CGG AAC GTC GTA CGG 3')(SEQ. ID. NO: 15) which annealed in the HA epitope tag region of the plasmid, downstream of the heavy chain constant region.
  • the HR2 cMpl CODE primer also had a tail of bases that encoded the new CDR2 region.
  • the new CDR2 primer encoded regions were complementary and provided 24 bases of overlap.
  • Primers leadVH and N-dp were used in the overlap PCR protocol to generate the full heavy chain DNA product.
  • a Xho I / Spe I digest was performed at 37° for 3 hours. Inserts were gel purified and then ligated into Xho I / Spe I digested pRL4 vector containing the anti-TT light chain. Ligation products were precipitated and electroporated into ER2537 bacteria as described above for the generation of the Fab-phage library.
  • the light chain CDR3 library was similarly made using primers for Fragment A of forward primer N-omp and reverse primer LR3 cMpl ANTI
  • Both LR3 cMpl primers contain a tail of nucleotides encoding the new CDR3 peptide library, which provides the 24 basepair overlap region for the fusion PCR of Fragment A and Fragment B.
  • a Sac I / Xba I digest was performed at 37° for 3 hours. The light chain fragments were then ligated into Sac I / Xba I digested pRL4 containing the anti-TT heavy chain overnight at room temperature. Ligation products were precipitated and electroporated into ER2537 bacteria as described above for the generation of the Fab- phage library.
  • the construction of the light chain CDR2 library was carried out as described above for the light chain CDR3 library with the exception that specific primers LR2 cMpl ANTI (5' AGC CAG CCA CTG GCG CAG GGT TGG GCC TTC GAT MNN MNN ATA GAT GAG GAG.CCT GGG AGC 3')(SEQ. ID. NO: 19) which annealed at the end of light chain FR2 and primer LR2 cMpl CODE (5' CCA ACC CTG CGC CAG TGG CTG GCT GCT CGC GCT NNK NNK GGC ATC CCA GAC AGG TTC AGT 3')(SEQ. ID.
  • the libraries were separately subjected to another panning experiment using cMpl receptor transfected 293 cells instead of platelets during the panning.
  • the 293 cells were observed to reproducibly transfect at a high efficiency and express very high levels of the functional cMpl-receptor on their surface. Thus these cells represented a good cell target for use in panning.
  • different groups of plates of 293 cells were separately and sequentially transfected four days in a row. Each group of plates was then sequentially used for the four separate rounds of panning. Each round of harvesting of the cells and panning occurred two days after transfection.
  • cells were removed from the plates using cell disassociation buffer, spun down at 1500 rpm for 5 minutes and resuspended in IMDM supplemented with 10% FCS, 0.1% sodium azide and 5mM EDTA at a concentration of 1 x 10 6 cell per ml (3x10 6 for LC-CDR1).
  • 3 x 10 11 phage from each library were separately applied to 2 ml of cells (6x10 6 for LC-CDR1 and 2 x 10 6 cells for all others) and rotated in a 15 ml conical tube for two hours at room temperature. Cells were washed twice using 10 mis of the IMDM/10% FCS/0.1% sodium azide/5mM EDTA buffer.
  • Phage were eluted in acid and amplified as previously described in Example 1.
  • round two 4 x 10 6 cells (6x10 6 for LC-CDR1 ) were used in 2 ml of buffer and 3 x 10 11 phage from the amplified round one eluted phage was combined with 3 x 10 11 phage from the un-panned library and added to the cells. Washing, elution and amplification proceeded similar to round one.
  • round three 4 x 10 6 cells (6x10 6 for LC-CDR1) were used in 2 ml of buffer and 3 x 10 11 phage from the amplified round two eluted phage were used. Cells were washed three times prior to elution.
  • Combinations where one of the TPO mimetic peptides is in the light chain and the other is in the heavy chain are made using simple cloning techniques using the pooled plasmid DNAs, and the unique restriction sites flanking the heavy (Xho l-Spel) and light chains (Sac l-Xba I).
  • the plasmid DNA for the H-CDR3 peptide grafted heavy chains were combined and digested by Xho I and Spe I.
  • the purified heavy chain inserts were ligated into the Xho l/Spe I digested plasmid containing the L-CDR2 grafts.
  • the resulting library contained heavy chains with CDR3 peptide grafts and light chains with CDR2 peptide grafts. It should be understood that individual clones could also be combined rather that using pools of clones for the pairing of two peptide containing CDRs. For example, a single heavy chain clone with a CDR3 peptide graft was paired with several individual light chain CDR1 clones to create Fabs with multiple copies of TPO mimetic peptides.
  • Combinations where two TPO mimetic peptides were combined within a given heavy chain was performed using overlap PCR to generate the fragment for cloning.
  • Two overlapping primers which bind between CDR2 and CDR3, and flanking primers, such as “N omp" and “lead B” primers from the light chain and "Lead VH” and “Ndp” primers for the heavy chain were used.
  • the first PCR was performed using lead VH (a primer that anneals in the vector at the heavy chain pelB leader signal) and a reverse primer annealing at FR3 using the H-CDR2 pooled plasmid DNA as the template.
  • the sequence of that primer was 5' CCA TGT AGG CTG TGC CCG TGG ATT 3' (SEQ. ID. NO: 63).
  • the pooled plasmids containing the H-CDR3 grafts underwent PCR with a forward primer annealing in FR3 (which is complementary to the above FR3- reverse primer) and N-dp (which anneals in the vector at an epitope tag sequence).
  • the sequence of that primer was 5' CCA CGG GCA CAG CCT ACA TGG AGC 3' (SEQ. ID. NO: 64).
  • the first PCR products were purified then combined in an overlap PCR reaction, where fusion of the two fragments occurred through the complementary FR2 sequences.
  • the negative controls can include uninduced cells, cells treated with an irrelevant Fab (anti-tetanus toxoid), cells treated with a Fab clone that only weakly binds cMpl receptor, and X4b and/or X1c Fabs which do bind the cMpl receptor but only have a single binding domain and so can not activate the receptor.
  • the positive control was the addition of TPO. All remaining samples were from the newly formed combination libraries. As can be observed, several clones have significant activity as Fabs. This indicates that incorporation of multiple TPO mimetic peptides into a single Fab molecule is able to bind two receptors and cause receptor activation.
  • Fab 59 the agonistic activity obtained can be as high as native TPO activity.
  • Clone 59 containing two TPO mimetic peptides (HC CDR3 sample x4c and C CDR2 sample 19 as identified in Fig. 9) and a His6 tag was partially purified from a bacterial periplasmic prep by FPLC using nickel column chromatography. The activity of this Fab was measured and found to be approximately equivalent to that of TPO (see Figure 12), as estimated by cMpl-R specific induction of luciferase activity in direct comparison to known concentrations of TPO. A quantitative western blot was performed in order to determine the Fab 59 antibody concentrations.
  • the TPO mimetic peptide graft in Fab clone X4b has been transplanted into the heavy chain CDR3 of another antibody framework, 5G1.1. Construction of 5G1.1 is described in U.S. Appln. Ser. No. 08/487,283, incorporated herein by reference. The sequence was cloned into 5G1.1 in such a fashion as to replace the native CDR3 with 5' ttg cca ATT GAA GGG CCG ACG CTG CGG CAA TGG CTG GCG GCG CGC GCG cct gtt 3' (SEQ. ID. NO: 65).
  • the peptide graft translated into amino acids is Leu Pro He Glu Gly Pro Thr Leu Arg Gin Trp Leu Ala Ala Arg Ala Pro Val (SEQ. ID. NO: 66).
  • the 5G1+peptide was produced as a whole IgG antibody (See Figures 13A and 13B).
  • binding Fabs X1c and X4b showed strong staining as did the 5G1.1 +peptide. None of those clones demonstrated binding to the non-receptor expressing cells indicating that the cell staining is occurring through specific recognition of the cMpl receptor. The parental 5G1.1 without the TPO mimetic peptide did not show staini g to any of the cells tested.
  • the ability of the 5G1.1+ peptide whole IgG to activate the cMpl receptor using the luciferase reporter assay has been determined (see Figure 15).
  • the results herein indicate that the configuration of a whole IgG causes steric limitations in its ability to productively bring the two cMpl receptors together for activation.
  • activation by the 5G1.1 containing the peptide was observed only when the cMpl-R was expressed on the cell surface.
  • EPO mimetic-peptide DYHCRMGPLTWVCKPLGG (SEQ. ID. NO: 3) (designated EMP2 in Wrighton et al. 1996) was grafted separately into the anti-tetanus toxoid Fab heavy and light chain CDR3 region creating two antibody libraries as XXDYHXRMGPLTWVXKPLGGXX (SEQ. ID. NO: 71). Randomized positions were generated using an NNK doping strategy. As with the TPO mimetic peptide, two amino acids flanking the EPO mimetic peptide were randomized in order to select for the optimum presentation of the peptide.
  • cysteine residues which formed a disulfide bridge in the original cyclic peptide, were randomized. This was done not only because the CDRs already form loop structures and so the disulfide bridge was not necessary to constrain the peptide, but also because the cysteines might in fact disrupt the normal disulfide bonds of the antibody.
  • the CDR 3 of the anti-TT antibody heavy chain was completely replaced by the EPO peptide library graft.
  • the generation of the library was essentially as described for the TPO heavy chain CDR2 library.
  • Two alternate primers were used for the HCDR3 library: the reverse primer HR3 EPO ANTI (5' CAC CCA GGT CAG TGG GCC CAT GCG MNN ATG ATA GTC MNN MNN TCT CGC ACA ATA ATA TAT GGC 3')(SEQ. ID.
  • the light chain CDR3 EPO peptide library was constructed essentially as described above for the light chain CDR3 TPO peptide library using reverse primer LR3 EPO ANTI (5' CAC CCA GGT CAG TGG GCC CAT GCG MNN ATG ATA GTC MNN MNN ACA GTA GTA CAC TGC AAA ATC 3') (SEQ.
  • EXAMPLE 6 A library was generated by the insertion of a TPO mimetic peptide and previously selected flanking amino acids (NP-IEGPTLRQWLAARA-RG) (SEQ. ID. NO: 61) into a collection of human kappa gene fragments, in this case the CDR2 of the light chain. Stocks of human kappa light chains from multiple human peripheral blood lymphocyte (PBL) donors had been previously generated and cloned into pBluescript II SK+. Those constructs served as the source of antibody gene fragments.
  • PBL peripheral blood lymphocyte
  • RNA from human PBLs was isolated using TRI Reagent (Molecular Research Center, Cincinnati, OH) followed by mRNA purification with Oligotex mRNA purification System (QIAGEN, Valencia, CA) according to kit instructions.
  • First strand cDNA was made using Superscript RTase II cDNA Synthesis Kit (Life Technologies, Rockville, Maryland) with a modified oligo dT primer.
  • the sequence of the primer was 5' TAGGATGCGGCCGCACAGGTC(T 20 ) 3' (SEQ. ID. NO: 62). Samples were cleaned up over a PCR purification Kit spin column (QIAGEN, Valencia, CA) according to kit directions.
  • Light chain products were amplified using the reverse "Not I” primer and forward primers which annealed at the framework 1 (FR1 ) position of Kappa chains on the 1 st strand cDNA.
  • the "Not I” primer had sequence which was identical to the 5' end of the modified oligo dT primer (5' TAGGATGCGGCCGCACAGGTC 3')(SEQ. ID. NO: 72).
  • the set of Kappa FR1 primers used were:
  • XVB Vk2b CACGCGCACAACACGTCTAGAGATRTTGTGATGACTCAG (SEQ. ID. NO: 78)
  • XVB Vk3a CACGCGCACAACACGTCTAGAGAAATTGTGTTGACRCAG (SEQ. ID. NO: 79)
  • a typical amplification reaction contained 2 ⁇ ls cDNA reaction, dNTPs, "Not I" reverse primer, one of the XVB forward primers, Opti-prime buffer #5 (Stratagene, La Jolla, CA), and Expand High Fidelity polymerase mixture (Roche Molecular Biochemicals, Indianapolis, IN ). Samples were heated to 94°C for 2 minutes, then carried through 10 cycles of 94°C for 15 seconds, 56°C for 30 seconds, and 72°C for 1 minute, followed by 20 cycles of 94°C for 15 seconds, 56°C for 30 seconds, and 72°C for (1 minute + 5 seconds/cycle). The cycles were followed by an extended incubation at 72°C (7 minutes) prior to 4°C hold.
  • TPO light chain framework library For construction of the TPO light chain framework library, equal amounts of four different kappa light chain libraries from four different patients were used as the starting template for the PCR reactions (25ng total per reaction). The TPO mimetic peptide and selected flanking amino acids were incorporated into the light chains by overlap PCR. In the first round of PCR a set of reverse primers (VK ANTI primers) which bound to the kappa light chain FR2 were separately combined with the forward T7 seq-F primer (5'-ATTAATACGACTCACTATAGGG-3') (SEQ. ID. NO: 86) to synthesize the N terminal piece of the light chain and part of the TPO mimetic peptide within the LC CDR2 position.
  • VK ANTI primers reverse primers which bound to the kappa light chain FR2 were separately combined with the forward T7 seq-F primer (5'-ATTAATACGACTCACTATAGGG-3') (SEQ. ID. NO: 86) to synth
  • VK CODE primers which bound to FR3 were combined separately with the T3 reverse primer (5'- AATTAACCCTCACTAAAGGG-3') (SEQ. ID. NO: 87) to synthesize the rest of the TPO mimetic peptide within the LC CDR2 position and the C terminal half of the light chain by PCR. Separate reactions were performed for each pair of primer combinations in duplicate.
  • Fragments from the first rounds of PCR were gel purified. Those purified fragments were then combined, in an antibody family specific manner, in overlap PCR reactions to generate the full light chain. Reactions for each family were performed in triplicate using 40ng of both the N-terminal and C-terminal piece of the light chain in each reaction. The reactions were run for 10 cycles prior to the addition of the T3 and T7 Seq-F primers, followed by an additional 25 cycles after primer addition. The full length LC fusion PCR products were gel purified, digested with Sac I and Xba I, and then again gel purified. The light chain inserts were then ligated into an appropriate phage display vector, which had been similarly digested with Xba I and Sac I and gel purified.
  • the pRL5-kappa vector used had restriction sites which were compatible with the LC fragments and contained the remaining Kappa constant region from the native Sac I site to the C-terminal Cys.
  • the anti-tetanus toxoid heavy chain was inserted into the vector by Xho I and Spe I for Fab production.
  • the ligation mixture was transformed by electroporation into XL-1 Blue bacteria (Stratagene, La Jolla CA) and amplified.
  • the library was panned four rounds on 293 EBNA cells transfected with the cMpl-R in a manner similar to that previously described. Clones obtained during panning were screened for binding by FACs analysis on 293 EBNA cells transfected with or without the cMpl-R as previously described. A number of clones, which specifically bound the cMpl-R, were obtained. DNA fingerprinting of the resulting light chains by digestion with Bst N1 indicated that the clones could be divided into 5 different groups.
  • the level of activation using bacterial supernatants of one such clone 429/X4b was approximately 10-20 fold lower than that observed with TPO, as estimated by comparing activity to known concentrations of TPO and using quantitative western blots to determine the concentration of the antibody in the supernatant. Additional clones can be screened in a similar fashion on order to identify clones with greater activity.
  • Fabs or various other LC, HC or intrachain CDR combinations, could be used as a therapeutic product.
  • these clones could be converted to framework germline sequences (either with or without codon optimization) for use as a therapeutic agent so long as activity was maintained.
  • the Not I site in pAX131 was removed by digesting the vector with Not I, using Klenow polymerase to fill in the Not I overhangs, and then re-ligating the vector. See Figure 17. Further modification was made by digesting pAX 131 with EcoR I and Xba I. An insert that replaced the elements removed by such digestion was generated using overlapping oligonucleotides with the following changes: conversion of the Sac I site to a new Xba I site (single underline in primer sequences below), conversion of the original Xba I site to a Not I site (double underline in the primer sequences below), and ending the insert with a Spe I overhang which is compatible with the vector's Xba I digest generated overhang.
  • the human kappa constant region was PCR amplified from human cDNA using primers that introduced the upstream Xba I site and in the downstream position a TAA stop codon followed by a Not I site.
  • the primers used were CKXba I (5' GGA GTC TAG ATA ACT GTG GCT GCA CCA TCT GTC TTC 3') (SEQ. ID. NO: 109) and CKNotl (5' AGG AGC GGC CGC TTA ACA CTC TCC CCT GTT GAA GCT C 3') (SEQ. ID. NO: 110).
  • the suitability of a germline V gene to act as the acceptor V region in a humanization procedure will be influenced by the likelihood of successful retaining antigen binding activity. In general, using germline V gene as acceptor may not keep the affinity equal to rearranged one.
  • two TPO peptides “QLIEGPTLRQWLAARANS” (SEQ ID NO. 152) and “LPIEGPTLRQWLAARAPV” (SEQ ID NO. 39) were grafted into VH CDR2 and CDR3 respectively. These peptides provide the antigen binding activity of the pAXB116 antibody.
  • the candidate acceptor V region should be conserved in the most of individuals and exhibit no allotypic variation. It should also be represented functionally in rearranged V region genes, so that the human population will be tolerant of the encoded polypeptide product.
  • the highest homology of human germline sequences with TT-TPO antibody variable regions are shown in Figs. 22 and 23 .
  • Figs. 24 and 25 show the sequence of the pAXB116 Fab' Heavy and light chain variable regions, respectively.
  • the cDNA sequence with the best E. coli codon usage Henaut and Danchin: Analysis and Predictions from Escherichia coli sequences in: Escherichia coli and Salmonella, Vol. 2, Ch.
  • TPO peptides in heavy chain CDR2 and CDR3 of pAXB116 Fab' are indicated by double underlines and wavelines respectively.
  • pelB leader cDNA sequences are overlined .
  • pAXB116 Fab'-gVk denotes light chain variable region of human germline derived pAXB116 Fab'.
  • pAXB116 Fab'-gVh denotes heavy chain variable region of human germline derived pAXB116 Fab'. Assembly of pAXB116 construct pAXB116 was generated synthetically using PCR technology .
  • the pAXB116 variable heavy chain contained CDR2-TPO and CDR3-TPO was linked to the human lgG1 CH1+Hinge+ 2C9(hlgG1 CH2) (Better et al., Proc Natl Acad Sci U S A 1993 Jan 15;90(2):457-61) using three oligos (UDEC1709, UDEC1710 and UDEC1711 from Oligos Etc., Inc., see Fig. 26), the pAXB116 variable light chain was fused with human light chain constant region by three oligos ( UDEC1712, UDEC1713 and UDEC1714, see Fig. 27).
  • the PCR products were TA cloned into pCR2.1-TOPO vector (TOPO TA cloning Kits, Invitrogen) and sequenced (MWG Biotech Inc.) confirmed.
  • the pAXB116 heavy chain was digested with Ncol/Xbal and light chain by Ncol/Xhol. Fragments were gel isolated and separately cloned into plNG3302 vector (commercially available from XOMA Inc., Berkeley, California, USA) with pelB leader and opened with Ncol/Xbal and Ncol/Xhol.
  • the plNG-pAXB116 Fab was generated by grafting heavy chain EcoRI/Xbal fragment into upstream of plNG-pAXB116 light chain Bcll/Xbal sites.
  • Figure 28 schematically shows the construction scheme for the plNG-pAXB116 vector.
  • the amino acid sequence of the pAXB116 heavy chain is shown in Fig. 29 .
  • the amino acid sequence of the pAXB116 light chain is shown in Fig. 29.
  • E.coli strain E104 (derivative of E. coli W3110 (ATCC 27352)) was transformed with plNG-pAXB116 Fab construct and used for production of pAXB116 Fab' and (Fab')2.
  • L-arabinose from 20% W/V solution is added to a final concentration of 0.1%.
  • the bacterial culture was then incubated for up to 16 hours post-induction at 37°C Secreted products were detected directly in the cell-free culture supernatant.
  • CD34 + cord blood cells (Poeisis) were thawed, washed, resuspended in BIT9500 serum- substituted medium (StemCell Technologies, Inc.), and plated at 3.5 x 10 5 per well in a 96 well flat-bottom plate with increasing concentrations of either recombinant human TPO (R&D Systems), circle, or pAXB116, square. After four days of culture at 37°C in a 5% C0 2 incubator, 1 ⁇ Ci of 3 H thymidine (Perkin Elmer) was added to each well and cells were further incubated for 16 hours.
  • EXAMPLE 9 A third heavy chain CDR2 library was constructed replacing part of the tetanus toxoid (TT) heavy chain CDR2 with the TPO mimetic peptide flanked by two random amino acids on each side.
  • Computer modeling indicated that it might be beneficial to stability and folding of the heavy chain to retain four amino acids of the original TT HC CDR2. Specifically, the first three amino acids of the TT heavy chain CDR2 (GLY-ILE-PHE) and the last amino acid of the heavy chain CDR2 (GLY).
  • the final product would contain these original four amino acids with the TPO mimetic peptide and random flanking amino acids positioned between the first three original amino acids and last original amino acid: GIFXXIEGPTLRQWLAARAXXG (SEQ. ID NO. 119).
  • the clones of the rounds three and four pool from panning are used as the starting point for insertion of a second TPO mimetic peptide.
  • this library has been combined with the clone X4b containing a TPO mimetic peptide in the heavy chain CDR3 by sub-cloning, to create clones, which contain two TPO mimetic peptides (one in heavy chain CDR2 and one in heavy chain CDR3). These new clones are screened for TPO mimetic activity.
  • the second peptide may be placed in light chain CDR1 , CDR2 or CDR3, or heavy chain CDR1.
  • the goal of this example is to optimize the placement of the TPO peptide in the HC-CDR2.
  • the placement of the TPO peptide interrupts a ⁇ -strand (See Figure 35).
  • the addition of 3 original TT amino acids restores the ⁇ - strand.
  • the result is an increased expression of the Fab when only one TPO peptide is grafted in the CDR2 position.
  • Example 10 Conversion of 116 into pRL5 vector plNG-pAXB 116 DNA was used as a template to generate light and heavy chain fragments of 116 by PCR.
  • the PCR reactions introduced restriction site modifications to the 116 sequence thereby allowing cloning of the fragments into our phage display vector pRL5.
  • PCR recovery of the heavy chain constant region fragment was done in such a way as to remove a portion of the hinge region sequence.
  • the HC fragment of 116 was recovered as two pieces in order to restore an Apa I site near the juncture of the VH and CH1 domains.
  • PCR was performed using plNG-pAXB 116 as the template DNA with primers "116 VL-Fr1 for" (5' gac gcg cac aac acg GAG CTC GAA ATT GTG CTG ACC CAG AGC 3') (SEQ. ID NO. 135) and "116 CK rev” (5' aga cag tga gcg ccg TCT AGA a TTA GCA TTC GCC GCG GTT AAA G 3') (SEQ. ID NO.
  • the ligation reaction was electroporated into Top10F' cells (Invitrogen) and grown overnight in SB media at 37° with 50 ug/ml carbenicillin.
  • DNA of the intermediate vector pool pRL5-116 LC was prepared from the resulting bacterial pellet using the QIAGEN Plasmid Maxiprep Kit.
  • PCR was performed using plNG-pAXB 116 as the template DNA with primers "116 VH-CH1 for" (5' gac gcg cac aac acg GGC CCG AGC GTG TTT CCG CTG 3') (SEQ. ID NO. 137) and "116 VH-hinge rev” (5' aga cag tga gcg ccg ACT AGT TTT ATC GCA GCT TTT CGG TT 3') (SEQ. ID NO.
  • the ligation reaction was electroporated into TOP10F' cells, and plated on LB-carbenicillin plates. Bacterial colonies were picked the following day and grown overnight in SB media with 50 ug/ml carbenicillin at 37°. DNA was prepared using QIAprep Spin Miniprep Kit (QIAGEN). All clones were submitted for DNA sequence verification of the entire 116 light chain as well as the constant region fragment of 116 HC. Clone 4E was selected as having the proper sequences (intermediate vector pRL5-116 / 4E).
  • PCR was performed using plNG-pAXB 116 as the template DNA with primers "116 VH-Fr1 for" (5' gag ccg cac gag ccc CTC GAG CAG GTG CAG CTG GTG CAG AG 3') (SEQ. ID NO. 139) and "116 VH-CH1 rev” (5' gca aag tgt gag GG GCC CTT GGT GCT CGC GCT GCT 3') (SEQ. ID NO. 140) in a reaction using Amplitaq Gold (Applied Biosystems) and 10.0ng template vector per 50 ⁇ l PCR reaction to promote the accurate replication of the desired PCR fragment.
  • the PCR product was separated from unused primers and reaction components using QIAquick PCR Purification Kit (QIAGEN).
  • the PCR fragment was then digested with restriction enzymes Apa I at 25° and Xho I at 37° in sequential reactions. From there, the DNA fragment was run on an agarose gel and electro- eluted into dialysis tubing prior to ligation into pRL5-116 / 4E (Xho I / Apa I digested and gel purified) using T4 DNA Ligase (Invitrogen).
  • the ligation reaction was electroporated into TOP10F' cells (Invitrogen) and plated on LB-Carbenicillin.
  • the heavy and light chain sequences were treated as two separate entities. Each chain was then used as a query sequence to search the protein data bank for antibodies with similar primary structure using the program psi-blast. The structures of the top scoring sequences for both the light and heavy chain were combined to create a composite antibody Fab structure. The back bone of this composite structure was then used as a template on which the residues unique to TPO could be added and any amino acid insertions or deletions could be made using SwissModel. Once the necessary changes were made to convert the composite Fab structure to a model of TPO the entire TPO model was minimized against an energy score using conjugate gradient minimization techniques in SwissModel.
  • Overlap PCR was used to create the new randomized library as well as the single mutant with conversion of the two asparagines back to serines.
  • the fragment A was created using the vector specific forward primer Lead VH (SEQ. ID NO.13) as previously described (Example 2), and the reverse primer 116REV (5' AAA GGT GCC GCC GCT CGC TTT GCA 3') (SEQ. ID NO. 144) that annealed to framework 1 just upstream of the two serines.
  • Fragment B was created using the forward primer 116SSTOXX ( ⁇ ! GGC GGC ACC TTT NNK NNK TAT GCG ATT AGC TGG GTG CGC CAG 3') (SEQ.
  • the 116SSTOXX forward primer contained the two randomized positions (NNK) and contained a 12bp region complementary to the 116REV primer for overlap per extension. After the individual fragments were generated they were gel purified and were combined for overlap per extension using the Lead VH and NDP primers to generate a library of full heavy chain fragments of 116, as previously described (Example 2). These heavy chains were then digested with Xho 1 and Spe 1 as previously described (Example 2) and cloned back into the 116 pRL5 vector which was similarly digested.
  • the individual mutant converting the two germline serines back into their original asparagines was similarly constructed with the exception that the forward primer 116SSTONN 116SSTOXX (5' GGC GGC ACC TTT AAC AAC TAT GCG ATT AGC TGG GTG CGC CAG 3') (SEQ. ID NO. 146), was used instead of the 116SSTOXX primer.
  • NIH 3T3 cells were transiently transfected with the cMpl-R and a Fos promoter/luciferase reporter plasmid as described in Example 1. The following day cells were split into 96 well dishes at 10,000 cells per well. After 4-6 hrs, during which time cells attached and adhered to the plate, cells were then washed once with PBS and the media was changed to low serum (5%) media for and additional 24 hrs. Bacterial overnights of the test clones grown in 96 well plates were spun down at 2000 rpm.
  • clones from the randomized library were selected, which also had asparagines in both of these two positions, although different codons were used in these clones coding for asparagine.
  • clones containing proline and arginine, glycine and glutamate, and glutamine and aspartate were selected.
  • the clone names and amino acids respectively are 116-NN (asparagine-asparagine), 116-XX12 (proline-arginine), 116-10B12 (glycine-glutamate), and 116-13F2 (glutamine-aspartate) (See Figure 38).
  • clones can be cloned into an expression vector (such as, for example the XOMA plNG vector system) for purification of the Fab protein.
  • the purified antibodies can be compared to 116 purified in the same manner to accurately compare the specific activities of parental 116 to the selected mutant forms.

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Abstract

L'invention concerne des anticorps ou des fragments correspondants comprenant au moins deux régions CDR remplacées par des peptides biologiquement actifs ou fusionnées avec ceux-ci. Les compositions contenant ces anticorps ou des fragments correspondants sont utiles dans des applications thérapeutiques et diagnostiques.
PCT/US2004/016574 2003-06-02 2004-05-26 Anticorps conçus de maniere rationnelle WO2004108078A2 (fr)

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AU2003295623B2 (en) * 2000-12-05 2008-06-05 Alexion Pharmaceuticals, Inc. Rationally designed antibodies
US9718883B2 (en) 2003-09-10 2017-08-01 Amgen Fremont Inc. Antibodies to M-CSF
US10144768B2 (en) 2015-12-04 2018-12-04 Novartis Ag Antibody cytokine engrafted compositions and methods of use for immunoregulation
US11066469B2 (en) 2019-06-12 2021-07-20 Novartis Ag Natriuretic peptide receptor 1 antibodies and methods of use
US11932673B2 (en) 2017-07-12 2024-03-19 Maxion Therapeutics Limited Sodium channel inhibitors
US11930837B2 (en) 2017-05-24 2024-03-19 Novartis Ag Antibody-cytokine engrafted proteins and methods of use for immune related disorders
US12006354B2 (en) 2017-05-24 2024-06-11 Novartis Ag Antibody-IL2 engrafted proteins and methods of use in the treatment of cancer

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WO1996040750A1 (fr) * 1995-06-07 1996-12-19 Glaxo Group Limited Peptides et composes se fixant a un recepteur de thrombopoietine

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MANJUNATHA KINI R ET AL: 'A Novel Approach to the Design of Potent Bioactive Peptides by Incorporation of Proline Brackets: Antiplatelet Effects of Arg-Gly-Asp Peptides.' FEBS LETTERS. vol. 375, 1995, pages 15 - 17, XP002994872 *

Cited By (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2003295623B2 (en) * 2000-12-05 2008-06-05 Alexion Pharmaceuticals, Inc. Rationally designed antibodies
US9718883B2 (en) 2003-09-10 2017-08-01 Amgen Fremont Inc. Antibodies to M-CSF
US10280219B2 (en) 2003-09-10 2019-05-07 Amgen Fremont Inc. Antibodies to M-CSF
US10144768B2 (en) 2015-12-04 2018-12-04 Novartis Ag Antibody cytokine engrafted compositions and methods of use for immunoregulation
US11136366B2 (en) 2015-12-04 2021-10-05 Novartis Ag Methods of treating immune related disorders using antibody-cytokine engrafted compositions
US11930837B2 (en) 2017-05-24 2024-03-19 Novartis Ag Antibody-cytokine engrafted proteins and methods of use for immune related disorders
US12006354B2 (en) 2017-05-24 2024-06-11 Novartis Ag Antibody-IL2 engrafted proteins and methods of use in the treatment of cancer
US11932673B2 (en) 2017-07-12 2024-03-19 Maxion Therapeutics Limited Sodium channel inhibitors
US11066469B2 (en) 2019-06-12 2021-07-20 Novartis Ag Natriuretic peptide receptor 1 antibodies and methods of use

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