WO2014120916A1 - Anticorps à domaines pegylés monovalents pour la liaison à cd28 et leurs méthodes d'utilisation - Google Patents

Anticorps à domaines pegylés monovalents pour la liaison à cd28 et leurs méthodes d'utilisation Download PDF

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WO2014120916A1
WO2014120916A1 PCT/US2014/013842 US2014013842W WO2014120916A1 WO 2014120916 A1 WO2014120916 A1 WO 2014120916A1 US 2014013842 W US2014013842 W US 2014013842W WO 2014120916 A1 WO2014120916 A1 WO 2014120916A1
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seq
antibody
domain
peg
binding
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Suzanne J. Suchard
James K. TAMURA
Steven Grant
Christopher Plummer
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Domantis Ltd
Bristol Myers Squibb Co
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Domantis Ltd
Bristol Myers Squibb Co
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • C07K16/2818—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily against CD28 or CD152
    • 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
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/34—Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/40—Immunoglobulins specific features characterized by post-translational modification
    • 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
    • C07K2317/567—Framework region [FR]
    • 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
    • C07K2317/569—Single domain, e.g. dAb, sdAb, VHH, VNAR or nanobody®
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

  • PEGylated domain antibodies that bind CD28 and prevent the binding of CD28 to CD80 and/or CD86, wherein the PEGylated dAbs have increased in vivo half- life, increased protease resistance, increased solubility and stability, and decreased immunogenicity compared to non-PEGylated dAbs.
  • T cell co-stimulatory signals that generate T cell responses to antigen (Jenkins and Johnson (1993) Curr. Opin. Immunol. 5: 361 - 367). Co-stimulatory signals determine the magnitude of a T cell response to antigen and whether this response activates or inactivates subsequent responses to antigen (Mueller et al. (1989) Annu. Rev. Immunol. 7: 445- 480). T cell activation in the absence of co- stimulation results in an aborted or anergic T cell response (Schwartz, R. H. (1992) Cell 71 : 1065-1068).
  • T cell surface receptor CD28 B7-related molecules on antigen presenting cells
  • B7-1 and B7-2 B7-1 and B7-2, or CD80 and CD86, respectively
  • CD80 and CD86 B7-1 and B7-2
  • CD86 co-stimulatory molecules
  • the interaction of CD28 with B7-1 (CD80) and B7-2 (CD86) co-stimulatory molecules provides a major signaling pathway for augmenting and sustaining T cell responses (Freedman et al. (1987) J. Immunol. 137: 3260-3267; Freeman et al. (1989) J. Immunol. 143: 2714-2722; Freeman et al.
  • CD28 is constitutively expressed on the surface of T cells, virtually all human CD4+ T cells, to a lesser extent on human CD8 + T cells, some natural killer cells and all murine T cells.
  • CD28 is a type I transmembrane glycoprotein and is a member of the Immunoglobulin family by virtue of its single Ig variable-like extracellular domain which has a MYPPPY (SEQ ID NO: 639) motif required for binding CD80 and CD86 (Peach et al. 1994, J. Exp. Med. 180: 2049-2058).
  • CD28 has a cysteine residue located after the Ig variable-like domain, which is involved in its homodimerization.
  • the protein sequence of CD28 and a nucleic acid encoding a human CD28 are disclosed, for example, in Harper et al. J. Immunol. (1991) 147: 1037-44.
  • the sequence of a human mRNA encoding CD28 also is disclosed in NCBI Accession No. NM_006139, last updated April 19, 2009, for example.
  • the complete protein sequence of a human CD28 also is disclosed in NCBI Accession No. NP_006130, last updated April 19, 2009, for example.
  • CD28 transmits a signal that synergizes with the T cell receptor (TCR) signal to promote the activation of na ' ive T cells (Lanzavecchia et al. (1999) Cell 96: 1-4).
  • CD28 signaling regulates the threshold for T cell activation and significantly reduces the number of TCR engagements needed for effective T cell activation (Viola et al. (1996) Science 273 : 104-6).
  • CD28 co-stimulation results in enhanced T cell proliferation, production of multiple cytokines and cytokine receptors, increased expression of proteins involved in cell cycle progression, sustaining T cell survival, and sustained CD40Ligand (CD40L) expression on T cells (Sharpe et al. Fundamental Immunology, W.E. Paul Ed. Fifth Edition, Page 396).
  • CD28 signals have a critical role in regulating CD4 and CD8 T cell
  • CD28 also optimizes the responses of previously activated T cells, promoting IL-2 production and T cell survival.
  • 1L-4 production by na ' ive T cells is highly dependent on B7-1/B7-2 co-stimulation. Interruption of the CD28/B7 pathway during activation of na ' ive T cells impairs T cell proliferation and differentiation, while interruption of the CD28/B7 pathway in previously activated T cells diminishes T cell expansion but not effector cytokine production (Sharpe et al. Fundamental Immunology, W.E. Paul Ed. Fifth Edition, pages 393-404).
  • T helper cell-dependent antibody responses use the B7-CD28 pathway to provide co-stimulatory signals essential for cognate T cell/B cell interactions required for Immunoglobulin class switching and germinal center formation.
  • CD28 knock-out mice potentially reactive B cells accumulate within lymphoid follicles after antigenic stimulation, but are not able to proliferate or undergo somatic mutation, (Ferguson et al. (1996) J. Immunol, 156: 4576-4581 ).
  • B7- 1 and B7-2 are also ligands for a second, higher affinity receptor, CTLA4 (CD 152), which is present on the surface of activated T cells.
  • CTLA4 CD 152
  • B7- 1/B7-2 co-stimulation of inhibitory signals occurs when B7- 1 /B7-2 bind CTLA-4 (Brunei et al. ( 1987) Nature 328: 267-270, Linsley et al. (1991 ) J. Exp. Med. MA: 561-569).
  • the outcome of an immune response involves a balance between CD28 mediated T cell activation and CTLA-4 mediated T cell inhibition.
  • Inhibition of CD28 mediated T cell activation could inhibit undesired T cell responses occurring during autoimmunity, transplant rejection, or allergic responses.
  • inhibiting CD28 mediated T cell activation could delay graft rejection, prevent acute allograft rejection, induce donor specific tolerance, and prevent development and interrupt the progression of chronic allograft rejection, as well as prevent graft versus host disease (GVH), i.e., when transplanted T cells mount a vigorous immune response against host tissue alloantigens (Salama et al. (2001 ) J Clin. Invest. 108: 943-48).
  • GVH graft versus host disease
  • CD28 mediated T cell activation dampen the immune response through negating activation signaling through CD28, it should not impact the interaction of CD86 and CD80 to CTLA-4, thereby preserving CTLA-4 mediated inhibition of the T cell response.
  • inhibiting CD28 mediated T cell activation could be used to prevent induction of autoimmunity and moderate the progression and/or severity of established autoimmune diseases, including models of collagen induced arthritis, autoimmune thyroiditis, autoimmune uveitis, myasthenia gravis and lupus (Saloman et al. (2001 ) Ann. Rev. Immunol. 19: 225-252).
  • the present disclosure provide domain antibody polypeptides that are linked to polymer molecules that provide increased stability and half-life.
  • polymer molecules e.g., polyethylene glycol (PEG)
  • PEG polyethylene glycol
  • PEG modification of proteins has been shown to alter the in vivo circulating half-life, antigenicity, solubility, and resistance to proteolysis of the protein (Abuchowski et al., J. Biol. Chem.
  • PEGylated domain antibodies that monovalently bind CD28 that have increased in vivo half-life, increased protease resistance, increased solubility and stability, and decreased immunogenicity compared to non-PEGylated dAbs.
  • CD28/B7 (CD80 and CD86) interaction and pathways present important targets for the development of therapeutic approaches for the treatment of diseases and disorders that involve inappropriate cellular responses, such as transplant rejection, autoimmunity, and/or excessive antibody responses.
  • Domain antibodies that are monovalent for binding of CD28 can inhibit CD28 activity, dampening an immune response, while avoiding potential undesirable effects that can occur with antibodies capable of divalent or multivalent binding of CD28. Domain antibodies can also be applied to any of a number of uses for which standard divalent antibodies are also used, e.g., in vivo imaging and diagnosis.
  • domain antibodies described herein are PEGylated domain antibodies that bind CD28 and prevent or inhibit the binding of CD28 to CD80, CD86 and/or other ligands and inhibit CD28 signaling by CD80 and/or CD86 in receptor binding assays. Domain antibodies described herein also do not block the interaction of CD80 and CD86 to CTLA4. In an embodiment, domain antibodies described herein do not cross-react with CTLA4, and thus do not bind the common motif on CTLA4 and CD28 that binds CD80/86.
  • An isolated antibody polypeptide comprising a variable domain having a binding specificity to CD28 and at least 90% sequence identity to the amino acid sequence of dAb l h-239-891 (D70C), wherein the antibody polypeptide binds the amino acid sequence MYPPPY of CD28, and the antibody polypeptide comprises a polyethylene glycol (PEG) polymer.
  • D70C dAb l h-239-891
  • an antibody polypeptide comprising a variable domain having a binding specificity to CD28 and at least 90% sequence identity to the amino acid sequence of dAb l h-239-891 (D70C), wherein the antibody polypeptide binds the amino acid sequence MYPPPY of CD28, and the antibody polypeptide comprises a polyethylene glycol (PEG) polymer, wherein the PEG is linked via a cysteine residue.
  • D70C dAb l h-239-891
  • an antibody polypeptide comprising a variable domain having a binding specificity to CD28 and at least 90% sequence identity to the amino acid sequence of dAb l h-239-891 (D70C), wherein the antibody polypeptide binds the amino acid sequence MYPPPY of CD28, and the antibody polypeptide comprises a polyethylene glycol (PEG) polymer, wherein the PEG is linked via the Q3C, S9C, R18C, G41 C, K42C, K45C, S60C, D70C, T74C, Q79C, or K103C cysteine residue.
  • PEG polyethylene glycol
  • an antibody polypeptide comprising a variable domain having a binding specificity to CD28 and at least 90% sequence identity to the amino acid sequence of dAb l h-239-891 (D70C), wherein the antibody polypeptide binds the amino acid sequence MYPPPY of CD28, and the antibody polypeptide comprises a polyethylene glycol (PEG) polymer, wherein the PEG is linked via a cysteine residue, wherein the PEG is about 25 kDa to about 45 kDa.
  • PEG polyethylene glycol
  • An antibody polypeptide comprising a variable domain having a binding specificity to CD28 and at least 90% sequence identity to the amino acid sequence of dAb l h-239-891 (D70C), wherein the antibody polypeptide binds the amino acid sequence MYPPPY of CD28, and the antibody polypeptide comprises a polyethylene glycol (PEG) polymer, wherein the PEG is linked via a cysteine residue, and wherein the PEG is linear. Further provided is the antibody polypeptide, wherein the PEG is branched.
  • an antibody polypeptide comprising a variable domain having a binding specificity to CD28, wherein the antibody polypeptide binds the amino acid sequence MYPPPY of CD28, and the antibody polypeptide comprises a polyethylene glycol (PEG) polymer, wherein the amino acid sequence of the variable domain differs from the amino acid sequence of l h-239-891 (D70C) by up to 5 amino acids.
  • PEG polyethylene glycol
  • an antibody polypeptide comprising a variable domain having a binding specificity to CD28, wherein the antibody polypeptide binds the amino acid sequence MYPPPY of CD28, and the antibody polypeptide comprises a polyethylene glycol (PEG) polymer, wherein the amino acid sequence of the variable domain differs from the amino acid sequence of l h-239-891(D70C) by up to 2 amino acids. Also provided is the antibody polypeptide, wherein the amino acid sequence of the variable domain differs from the amino acid sequence of lh-239-891 (D70C) by up to 1 amino acid.
  • PEG polyethylene glycol
  • variable domain comprises the amino acid sequence of l h-239-891 (D70C), and wherein a PEG polymer is linked to the D70C cysteine residue.
  • variable domain comprises the amino acid sequence of lh-239-891(D70C), wherein a PEG polymer is linked to the D70C cysteine residue, and wherein the PEG is linear and is about 30 kDa.
  • variable domain comprises the amino acid sequence of lh-239-891(D70C), wherein a PEG polymer is linked to the D70C cysteine residue, and wherein the PEG is branched and is about 40 kDa.
  • vaector comprising any of the provided isolated nucleic acids.
  • a domain antibody which has an amino acid sequence at least 85% identical, e.g., at least 90% identical, at least 95% identical, and up to and including 96%, 97%, 98%, or 99% identical, to an amino acid sequence encoded by a nucleic acid molecule having a sequence selected from the group consisting of SEQ ID NOS: 1-57, which domain antibody specifically and monovalently binds CD28.
  • the domain antibody can comprise an amino acid sequence selected from the group consisting of SEQ ID NOs:58-398 and 640,and SEQ ID NOs:532-635, and in an exemplary embodiment, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO.-66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:272, SEQ ID N0.273, SEQ ID NO:274, SEQ ID NO:275, SEQ ID NO:276, SEQ ID NO:534, SEQ ID NO:535, SEQ ID NO:536, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:543, SEQ ID NO:545, SEQ ID NO:547, SEQ ID NO:548, SEQ ID NO:550, SEQ ID NO:55
  • the domain antibody can have an amino acid sequence at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:272, SEQ ID NO:273, SEQ ID NO:274, SEQ ID NO:275, SEQ ID NO:276, SEQ ID NO:534, SEQ ID NO:535, SEQ ID NO:536, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:543, SEQ ID NO:545, SEQ ID NO:547, SEQ ID NO:548, SEQ ID NO:550, SEQ ID
  • a domain antibody differs from the selected amino acid sequence at no more than 25 amino acid positions and has a sequence that is at least 80% identical to the selected sequence. In one embodiment, the domain antibody differs from the selected amino acid sequence at 25 or fewer amino acid positions, 20 or fewer amino acid positions, 15 or fewer amino acid positions, 10 or fewer amino acid positions, 5 or fewer amino acid positions, 2 or fewer amino acid positions, or as few as one amino acid position. In a further embodiment, the domain antibody is at least 80% identical to the selected sequence, for example, at least 70%> identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90%> identical, at least 95% identical, and up to and including 96%, 97%, 98%, or 99% identical.
  • a CD28 antagonist can have a CDRl sequence that is at least 50% identical to the CDRl sequence of the amino acid sequence selected from the group consisting of SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61 , SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:272, SEQ ID NO:273, SEQ ID NO:274, SEQ ID NO:275, SEQ ID NO:276, SEQ ID NO:534, SEQ ID NO:535, SEQ ID NO:536, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:543, SEQ ID NO:545, SEQ ID NO:547, SEQ ID NO:548, SEQ ID NO:550, SEQ ID NO:55 1 , SEQ ID NO:553, SEQ
  • the CDR1 can differ from the selected amino acid sequence at all CDR1 amino acid positions, 5 or fewer amino acid positions, 4 or fewer amino acid positions, 3 or fewer amino acid positions, 2 or fewer amino acid positions, or as few as one amino acid position.
  • the CDR1 can be at least 50% identical to the selected sequence, for example, at least 60% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, and up to and including 96%, 97%, 98%, or 99% identical.
  • a CD28 antagonist can have a CDR2 sequence that is at least 50% identical to the CDR2 sequence of the amino acid sequence selected from the group consisting of SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:272, SEQ ID NO:273, SEQ ID NO:274, SEQ ID NO:275, SEQ ID NO:276, SEQ ID NO:534, SEQ ID NO:535, SEQ ID NO:536, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:543, SEQ ID NO:545, SEQ ID NO:547, SEQ ID NO:548, SEQ ID NO:550, SEQ ID NO:551 , SEQ ID NO:553, SEQ ID
  • the CDR2 can differ from the selected amino acid sequence at all CDR2 amino acid positions, 5 or fewer amino acid positions, 4 or fewer amino acid positions, 3 or fewer amino acid positions, 2 or fewer amino acid positions, or as few as one amino acid position.
  • the CDR2 can be at least 50% identical to the selected sequence, for example, at least 60% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, and up to and including 96%, 97%, 98%, or 99% identical.
  • a CD28 antagonist can have a CDR3 sequence that is at least 50% identical to the CDR2 sequence of the amino acid sequence selected from the group consisting of SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61 , SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:272, SEQ ID NO:273, SEQ ID NO:274, SEQ ID NO:275, SEQ ID NO:276, SEQ ID NO:534, SEQ ID NO:535, SEQ ID NO:536, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:543, SEQ ID NO:545, SEQ ID NO:547, SEQ ID NO:548, SEQ ID NO:550, SEQ ID NO:551 , SEQ ID NO:553, SEQ
  • the CDR3 can differ from the selected amino acid sequence at all CDR3 amino acid positions, 5 or fewer amino acid positions, 4 or fewer amino acid positions, 3 or fewer amino acid positions, 2 or fewer amino acid positions, or as few as one amino acid position.
  • the CDR2 can be at least 50% identical to the selected sequence, for example, at least 60% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, and up to and including 96%, 97%, 98%, or 99% identical.
  • a dAb can comprise a CDR1 sequence at least 50 % identical to one of the CDR1 sequences selected from the group consisting of SEQ ID NO:484, SEQ ID NO:487, SEQ ID NO:490, SEQ ID NO:493, SEQ ID NO:496, SEQ ID NO:499, SEQ ID NO:502, SEQ ID NO:505, SEQ ID NO:508, SEQ ID NO:51 1, SEQ ID NO:514, SEQ ID NO:517, SEQ ID NO:520, SEQ ID NO:523, SEQ ID NO:526, SEQ ID NO:529 and SEQ ID NO:636; a CDR2 sequence at least 50 % identical to one of the CDR2 sequences selected from the group consisting of SEQ ID NO:485, SEQ ID NO:488, SEQ ID NO:491, SEQ ID
  • a dAb can comprise a CDR1 sequence selected from the group consisting of SEQ ID NO:484, SEQ ID NO:487, SEQ ID NO:490, SEQ ID NO:493, SEQ ID NO:496, SEQ ID NO:499, SEQ ID NO:502, SEQ ID NO:505, SEQ ID NO:508, SEQ ID NO:51 1 , SEQ ID NO:514, SEQ ID NO:517, SEQ ID NO:520, SEQ ID NO:523, SEQ ID NO:526, SEQ ID NO:529 and SEQ ID NO:636; a CDR2 sequence selected from the group consisting of SEQ ID NO:485, SEQ ID NO:488, SEQ ID NO:491 , SEQ ID NO:494, SEQ ID NO:497, SEQ ID NO:500, SEQ ID NO:503, SEQ ID NO:506, SEQ ID NO:509, SEQ ID NO:512, SEQ ID NO:515, SEQ ID O:518, SEQ ID NO:521
  • a dAb can comprise the amino acid sequence selected from the group consisting of SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:272, SEQ ID NO:273, SEQ ID NO:274, SEQ ID NO:275, SEQ ID NO:276, SEQ ID NO:472, SEQ ID NO:473, SEQ ID NO:474, SEQ ID NO:475, SEQ ID NO:476, SEQ ID NO:477, SEQ ID NO:478, SEQ ID NO:479, SEQ ID NO:480, SEQ ID NO:481, SEQ ID NO:482, SEQ ID NO:483, SEQ ID NO:534, SEQ ID NO:535, SEQ ID NO:536, SEQ ID NO:537, SEQ ID NO:539, SEQ
  • a dAb comprises an amino acid sequence that differs from that of SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61 , SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:68, SEQ ID NO:272, SEQ ID NO:273, SEQ ID NO:274, SEQ ID NO:275, SEQ ID NO:276, SEQ ID NO:534, SEQ ID NO:535, SEQ ID NO:536, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:543, SEQ ID NO:545, SEQ ID NO:547, SEQ ID NO:548, SEQ ID NO:550, SEQ ID NO:551, SEQ ID NO:553, SEQ ID NO:562, SEQ ID NO:567, SEQ ID NO:570
  • compositions comprising a therapeutically- active amount of any of the provided antibody polypeptides and a pharmaceutically acceptable carrier. Also provided is a pharmaceutical composition further comprising an immunosuppressive, immunomodulatory, and/or anti-inflammatory agent.
  • the immune disease is an autoimmune disease or a graft-related disease.
  • the pharmaceutical composition is administered in combination with an immunosuppressive,
  • FIG. 1 depicts the sequence of l h-239-891 domain antibody and points to the specific residues that were mutated to cysteine (Cys), where the dAb was subsequently formatted by attaching a PEG polymer to the Cys, one at a time.
  • FIG. 2 shows the model of V k domain antibody (right side).
  • the residues Val-15, Pro-40, Gly-41 , Ser-56, Gly-57, Ser-60, Pro-80, Glu-81 , Gin- 100, Lys-107, and Arg-108 have been identified as solvent-accessible and pointing away from the CDRs. Thus, they were considered to be attractive candidates for residue mutation to cysteine and attachment of a PEG polymer.
  • the model of dV k domain antibody was also used to identify alternative amino-acid positions for BMS lh-239-891 (left) that would also be good candidates for a mutation to Cys and attachment of a PEG polymer, because each particular residue points into the aqueous medium (as opposed to being in the core of the folded molecule) and away from the CDRs.
  • residues include, for example, Q3, S9, R18, G41, K42, K45, S60, D70, T74, Q79, and K103.
  • the present disclosure provides domain antibodies to antagonize CD28 activity.
  • the domain antibodies may be linked to polymers to improve pharmacokinetic properties, such as stability and half-life.
  • polymers e.g., polyethylene glycol; PEG
  • PEG polyethylene glycol
  • PEG modification of proteins has been shown to alter the in vivo circulating half-life, antigenicity, solubility, and resistance to proteolysis of the protein (Abuchowski et al. (1977) J. Biol. Chem. , 252: 3578; Nucci et al. ⁇ 99 ⁇ ) Adv. Drug Delivery Reviews 6: 133; Francis et al., Pharmaceutical Biotechnology Vol. 3 (Borchardt, R. T. ed.); and
  • the term "human” when applied to a domain antibody or to an immunoglobulin variable domain means that the polypeptide has a sequence derived from a human immunoglobulin.
  • a sequence is "derived from” a human immunoglobulin coding sequence when the sequence is either: a) isolated from a human individual or from cells or a cell line from a human individual; b) isolated from a library of cloned human antibody gene sequences (or a library of human antibody V domain sequences); or c) when a cloned human antibody gene sequence (or a cloned human V region sequence (including, e.g., a germline V gene segment)) was used to generate one or more diversified sequences that were then selected for binding to a desired target antigen.
  • a human domain antibody has at least 70% identical, at least 75% identical, at least 80% identical, at least 85% amino acid identity (including, for example, 87%, 90%, 93%, 95%, 97%, 99%, or higher identity) to a naturally-occurring human immunoglobulin variable domain sequence, e.g., a naturally-occurring human immunoglobulin variable domain sequence disclosed in Kabat ("Sequences of Proteins of Immunological Interest", US Department of Health and Human Services 1991).
  • domain refers to a folded protein structure which retains its tertiary structure independently of the rest of the protein. Generally, domains are responsible for discrete functional properties of proteins, and in many cases may be added, removed, or transferred to other proteins without loss of function of the remainder of the protein and/or of the domain.
  • domain antibody is meant a folded polypeptide domain that comprises a sequence of a single immunoglobulin variable domain (V L or V H ) and that specifically and monovalently binds an antigen (e.g., CD28).
  • a “domain antibody” therefore includes complete antibody variable domains as well as modified variable domains, for example in which one or more loops have been replaced by sequences that are not characteristic of antibody variable domains, or antibody variable domains that have been truncated or comprise N- or C-terminal extensions, as well as folded fragments of variable domains which retain a dissociation constant of 500 nM or less (e.g., 450 nM or less, 400 nM or less, 350 nM or less, 300 nM or less, 250 nM or less, 200 nM or less, 150 nM or less, 100 nM or less) and the target antigen specificity of the full-length domain.
  • 500 nM or less e.g., 450 nM or less, 400 n
  • immunoglobulin variable and constant domains referred to herein.
  • a “dAb” is used interchangeably with “domain antibody” herein.
  • a domain antibody refers to a mammalian immunoglobulin polypeptide, including human, but also includes rodent (for example, as disclosed in
  • VHH - HH molecules are about 1 OX smaller than IgG molecules, and as single polypeptides, they are very stable, resisting extreme pH and temperature conditions.
  • Camelid antibodies are described in, for example, U.S. Pat. Nos. 5,759,808;
  • Humanized camelid VHH polypeptides are taught, for example in WO04/041 862, the teachings of which are incorporated herein in their entirety. It will be understood by one of skill in the art that naturally occurring camelid antibody single variable domain polypeptides may be modified according to the teachings of WO04/041862 (e.g., amino acid substitutions at positions 45 and 103) to generate humanized camelid VHH polypeptides. Also included herein are antibody single variable domain polypeptides which are nurse shark VHH- Nurse Shark VHH dAbs are described, for example, in Greenberg et al. (1995) Nature 374: 168-173 and U.S.
  • sequence characteristic of immunoglobulin variable domains refers to an amino acid sequence that is identical, over 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, or even 50 or more contiguous amino acids, to a sequence comprised by an immunoglobulin variable domain sequence.
  • sequence identity at the amino acid level can be about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher.
  • sequence identity can be about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher.
  • substantial identity exists when the nucleic acid segments will hybridize under selective
  • hybridization conditions e.g., very high stringency hybridization conditions
  • the nucleic acids may be present in whole cells, in a cell lysate, or in a partially purified or substantially pure form.
  • identity refers to the degree with which two nucleotide or amino acid sequences structurally resemble each other.
  • sequence “similarity” is a measure of the degree to which amino acid sequences share similar amino acid residues at corresponding positions in an alignment of the sequences. Amino acids are similar to each other where their side chains are similar. Specifically,
  • Similarity encompasses amino acids that are conservative substitutes for each other.
  • a “conservative” substitution is any substitution that has a positive score in the blosum62 substitution matrix (Hentikoff and Hentikoff (1992) Proc. Natl. Acad. Sci. USA 89:
  • sequence A is n% similar to sequence B
  • sequence B is meant that n% of the positions of an optimal global alignment between sequences A and B consists of identical amino acids or conservative substitutions.
  • two sequences are “similar” to each other, or share a "percent identity”, when aligned using either the Needleman- Wunsch algorithm or the "BLAST 2 sequences” algorithm described by Tatusova & Madden (1999) FEMS Microbiol Lett. 174: 247-250.
  • the Blosum 62 matrix is the default matrix.
  • Optimal global alignments can be performed using the following parameters in the Needleman- Wunsch alignment algorithm:
  • Substitution matrix blosum62.
  • Substitution matrix 10 for matches, 0 for mismatches.
  • Gap extension penalty 0.05
  • Typical conservative substitutions are exchanges among Met, Val, Leu, and lie; among Ser and Thr; among the residues Asp, Glu, and Asn; among the residues Gin, Lys, and Arg; or aromatic residues Phe and Tyr.
  • epitope refers to a unit of structure conventionally bound by an immunoglobulin V H /VL pair. Epitopes define the minimum binding site for an antibody, and thus represent the target of specificity of an antibody. In the case of a domain antibody, an epitope represents the unit of structure bound by a domain antibody in isolation. That is, the binding site is provided by one, single immunoglobulin variable domain. Epitopes can be linear or conformational, and can be as small as three amino acids. As used herein, the term “extended release”, or the equivalent terms “controlled release” or “slow release”, refer to drug formulations that release active drug, such as a polypeptide drug, over a period of time following administration to an individual.
  • Extended release of polypeptide drugs which can occur over a range of desired times, e.g., minutes, hours, days, weeks, or longer, depending upon the drug formulation, is in contrast to standard formulations in which substantially the entire dosage unit is available for immediate absorption or immediate distribution via the bloodstream.
  • Extended release formulations may result in a level of circulating drug from a single administration that is sustained, for example, for 8 hours or more, 12 hours or more, 24 hours or more, 36 hours or more, 48 hours or more, 60 hours or more, 72 hours or more 84 hours or more, 96 hours or more, or even, for example, for 1 week or 2 weeks or more, for example, 1 month or more.
  • CD28 activity is an activity involving or resulting from the binding of CD80, CD86 and/or another ligand to CD28, and includes, but is not limited to, activation of CD28-mediated cell signaling.
  • CD28 activity also includes the induction of T cell proliferation and the induction of cytokine secretion, e.g., interleukin 2 (IL-2), by T cells.
  • IL-2 interleukin 2
  • the term “does not substantially agonize” means that a given agent, e.g., a domain antibody, does not substantially activate one or more of the CD28 activities as the term “activate” is defined herein.
  • an agent that "does not substantially agonize” means that the agent does not activate more than 20% of the activity which is activated by CD80 and/or CD86 binding to CD28, and in an aspect, the agent does not activate more than about 10%, 8%, 5%, 3%, or 2% or less, including zero activation, of the activity which is activated by CD80 and/or CD86 binding to CD28.
  • a domain antibody set forth herein that does not substantially agonize CD28 activity does not agonize CD28 activity more than 5% of the activity obtained upon agonism of CD28 activity by anti-CD28 mAb 9.3 (Gibson, et al. (1996) JBC, 271 : 7079-7083) under otherwise identical assay conditions.
  • the terms “inhibit,” “inhibits” and “inhibited” refer to a decrease in a given measurable activity (e.g., binding activity) by at least 10% relative to a reference. Where inhibition is desired, such inhibition is at least about 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or more, up to and including 100%, i.e., complete inhibition or absence of the given activity. Inhibition of CD28 binding to CD80 or CD86 can be measured as described in the working examples herein. As used herein, the term
  • substantially inhibits refers to a decrease in a given measurable activity (e.g., the binding of CD28 to CD80 or CD86) by at least 50% relative to a reference.
  • substantially inhibits refers to a decrease in a given measurable activity of at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, and up to and including 100% relative to a reference.
  • inhibits the binding with reference to the binding of a domain antibody binding to CD28, or CD80 binding to CD28, or CD86 binding to CD28, refers to a decrease in binding by at least 10% relative to a reference.
  • “Inhibits the binding” refers to a decrease in binding of at least about 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or more, up to and including 100%.
  • isolated means that the compound is removed from at least one component with which the compound is naturally associated with in nature.
  • the terms “activate,” “activates” and “activated” refer to an increase in a given measurable activity by at least 5% relative to a reference, for example, at least 10%, 25%, 50%, 75%, or even 100%, or more.
  • CD28 antagonist refers to an agent that inhibits at least one activity mediated by CD28, by inhibiting the binding of CD80 and/or CD86 to CD28.
  • a CD28 activity is "antagonized” if the activity is reduced by at least 10%, and in an exemplary embodiment, at least about 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%,
  • a CD28 antagonist as the term is used herein comprises a domain antibody that binds monovalently to CD28.
  • a CD28 antagonist as set forth herein is an agent that inhibits some or all CD28 activity, while at the same time, the agent does not substantially agonize CD28 activity in combination with T cell receptor signaling.
  • CD28 agonist refers to an agent that activates at least one activity mediated by CD28, either alone or when combined with another co-stimulus, relative to a reference. An activity is “agonized” if the activity is increased by at least about 10%, e.g., 50%, in the presence, relative to the absence of an agonist.
  • CTLA4 activity includes, but is not limited to, inhibition of T cell function.
  • T cell function include, among others, T cell receptor mediated signaling, T cell proliferation, and induction of cytokine secretion.
  • immune disease refers to any disease which is associated with the development of an immune reaction in an individual, including a cellular and/or a humeral immune reaction.
  • immune diseases include, but are not limited to, inflammation, allergy, autoimmune diseases, and graft-related diseases.
  • autoimmune disease refers to disease conditions and states wherein the immune response of an individual is directed against the individual's own constituents, resulting in an undesirable and often debilitating condition.
  • autoimmune disease is intended to further include autoimmune conditions, syndromes, and the like.
  • Autoimmune diseases include, but are not limited to, Addison's disease, allergy, allergic rhinitis, ankylosing spondylitis, asthma, atherosclerosis, autoimmune diseases of the ear, autoimmune diseases of the eye, autoimmune atrophic gastritis, autoimmune hepatitis, autoimmune hemolytic anemia, autoimmune parotitis, autoimmune uveitis, celiac disease, primary biliary cirrhosis, benign lymphocytic angiitis, COPD, colitis, coronary heart disease, Crohn's disease, diabetes (Type 1), depression, diabetes, including Type 1 and/or Type 2 diabetes, epididymitis,
  • glomerulonephritis Goodpasture's syndrome, Graves' disease, Guillain-Barre syndrome, Hashimoto's disease, hemolytic anemia, idiopathic thrombocytopenic purpura, inflammatory bowel disease (IBD), immune response to recombinant drug products, e.g., factor VII in hemophilia, juvenile idiopathic arthritis, systemic lupus erythematosus, lupus nephritis, male infertility, mixed connective tissue disease, multiple sclerosis, myasthenia gravis, oncology, osteoarthritis, pain, primary myxedema, pemphigus, pernicious anemia, polymyositis, psoriasis, psoriatic arthritis, reactive arthritis, rheumatic fever, rheumatoid arthritis, sarcoidosis, scleroderma, Sjogren's syndrome,
  • IBD inflammatory bowel disease
  • Autoimmune diseases include, but are not limited to, conditions in which the tissue affected is the primary target, and in some cases, the secondary target.
  • Such conditions include, but are not limited to, AIDS, atopic allergy, bronchial asthma, eczema, leprosy, schizophrenia, inherited depression, transplantation of tissues and organs, chronic fatigue syndrome, Alzheimer's disease, Parkinson's disease, myocardial infarction, stroke, autism, epilepsy, Arthus's phenomenon, anaphylaxis, and alcohol and drug addiction.
  • antibody polypeptide refers to a polypeptide which either is an antibody or is a part of an antibody, modified or unmodified, which retains the ability to specifically bind antigen.
  • antibody polypeptide includes an antigen-binding heavy chain, light chain, heavy chain-light chain dimer, Fab fragment, F(ab')2 fragment, dAb, or an Fv fragment, including a single chain Fv (scFv).
  • scFv single chain Fv
  • the term "monovalent” means that a given domain antibody can bind only a single molecule of its target.
  • Naturally-occurring antibodies are generally divalent, in that they have two functional antigen-binding loops, each comprising a VH and a VL domain. Where steric hindrance is not an issue, a divalent antibody can bind two separate molecules of the same antigen. In contrast, a "monovalent" antibody has the capacity to bind only one such antigen molecule.
  • a divalent can bind two separate molecules of the same antigen.
  • “monovalent” antibody can also comprise more than one antigen binding site, e.g., two antigen binding sites, but the binding sites must be for different antigens, such that the antibody can only bind one molecule of CD28 at a time.
  • the antigen-binding domain of a monovalent antibody can comprise a V H and a V L domain, but in an aspect, comprises only a single immunoglobulin variable domain, i.e., a V H or a V L domain, that has the capacity to bind CD28 without the need for a corresponding V L or VH domain, respectively.
  • a monovalent antibody lacks the capacity to cross link molecules of a single antigen.
  • standard platelet aggregation assay means the assay described in the section herein below, entitled “Platelet Aggregation Assay.”
  • immunoglobulin variable regions as defined by Kabat et al. (Kabat et al. (1991 ) Sequences of Immunological Interest, 5 ed. U.S. Dept. Health & Human Services, Washington, D.C.), which is incorporated herein by reference.
  • linked refers to the attachment of a polymer moiety, such as PEG to an amino acid residue of a domain antibody. Attachment of a PEG polymer to an amino acid residue of a domain antibody, e.g., a domain antibody, is referred to as
  • PEGylation and may be achieved using several PEG attachment moieties including, but not limited to N-hydroxylsuccinimide (NHS) active ester, succinimidyl propionate (SPA), maleimide (MAL), vinyl sulfone (VS), or thiol.
  • a PEG polymer, or other polymer can be linked to a domain antibody at either a predetermined position, or may be randomly linked to the domain antibody molecule.
  • the PEG polymer may be linked to a domain antibody at a predetermined position.
  • a PEG polymer may be linked to any residue in a domain antibody, however, it is preferable that the polymer is linked to either a lysine or cysteine that is either naturally occurring in the domain antibody or that has been engineered into the domain antibody, for example, by mutagenesis of a naturally occurring residue in the domain antibody to either a cysteine or lysine.
  • PEG-linkage can also be mediated through a peptide linker attached to a domain antibody. That is, the PEG moiety can be attached to a peptide linker fused to a domain antibody, where the linker provides the site, e.g., a free cysteine or lysine, for PEG attachment.
  • linked can also refer to the association of two or more domain antibodies, e.g., dAb monomers, to form a dimer, trimer, tetramer, or other multimer.
  • Domain antibody monomers can be linked to form a multimer by several methods known in the art, including, but not limited to, expression of the domain antibody monomers as a fusion protein, linkage of two or more monomers via a peptide linker between monomers, or by chemically joining monomers after translation, either to each other directly, or through a linker by disulfide bonds, or by linkage to a di-, tri- or multivalent linking moiety (e.g., a multi-arm PEG).
  • dAb multimers are specifically contemplated herein, e.g., in the context of dual- or multi-specific domain antibody constructs, it is emphasized that for any given domain antibody construct, the construct should only be able to bind one molecule of CD28, i.e., the constructs should have only one CD28-binding element, and should not cross link CD28.
  • polymer refers to a macromolecule made up of repeating monomeric units, and can refer to a synthetic or naturally occurring polymer such as an optionally substituted straight or branched chain polyalkylene, polyalkenylene, or polyoxyalkylene polymer or a branched or unbranched polysaccharide.
  • PEG polyethylene glycol
  • PEG polymer refers to polyethylene glycol, and more specifically can refer to a derivatized form of PEG, including, but not limited to N- hydroxylsuccinimide (NHS) active esters of PEG such as succinimidyl propionate, benzotriazole active esters, PEG derivatized with maleimide, vinyl sulfones, or thiol groups.
  • NHS N- hydroxylsuccinimide
  • PEG formulations can include PEG-O-CH2CH2CH2-CO2-NHS; PEG-O-CH2-NHS; PEG-O-CH 2 CH 2 -CO 2 -NHS; PEG- S-CH2CH2-CO-NHS ; PEG-
  • PEG polymers set forth herein may be linear molecules, or may be branched wherein multiple PEG moieties are present in a single polymer. Some representative PEG conformations include, but are not limited to the following:
  • a "sulfhydryl-selective reagent” is a reagent which is useful for the attachment of a PEG polymer to a thiol-containing amino acid. Thiol groups on the amino acid residue cysteine are particularly useful for interaction with a sulfhydryl- selective reagent. Sulfhydryl-selective reagents which are useful for such attachment include, but are not limited to maleimide, vinyl sulfone, and thiol. The use of sulfhydryl- selective reagents for coupling to cysteine residues is known in the art and may be adapted as needed (see, e.g., Zalipsky (1995) Bioconjug. Chem. 6: 150; Greenwald et al. (2000) Crit. Rev. Ther. Drug Carrier Syst. 17: 101 ; Herman et al. (1994) Macromol. Chem. Phys. 195: 203).
  • PEG or another agent e.g., HSA
  • a domain antibody as described herein in an exemplary embodiment, will not impair the ability of the polypeptide to specifically bind CD28. That is, the PEG-linked domain antibody will retain its binding activity relative to a non-PEG-linked counterpart.
  • "retains activity” refers to a level of activity of a PEG-linked domain antibody which is at least 10% of the level of activity of a non-PEG-linked domain antibody, including at least about 20%, 30%, 40%, 50%, 60%, 70%, 80%, and up to 90%, including up to about 95%, 98%, and up to 100% of the activity of a non-PEG-linked domain antibody comprising the same antigen-binding domain or domains. More specifically, the activity of a PEG- linked domain antibody compared to a non-PEG linked domain antibody should be determined on an antibody polypeptide molar basis; that is equivalent numbers of moles of each of the PEG-linked and non-PEG-linked domain antibody should be used in each trial. In determining whether a particular PEG-linked domain antibody "retains activity", the activity of a PEG-linked domain antibody may be compared with the activity of the same domain antibody in the absence of PEG.
  • the term "in vivo half-life” refers to the time taken for the serum concentration of a ligand (e.g., a domain antibody) to reduce by about 50%, in vivo, for example due to degradation of the ligand and/or clearance or sequestration of the ligand by natural mechanisms.
  • a ligand e.g., a domain antibody
  • the domain antibodies described herein can be stabilized in vivo and their half-life increased by binding to molecules, such as PEG, which resist degradation and/or clearance or sequestration.
  • the half-life of a domain antibody is increased if its functional activity persists, in vivo, for a longer period than a similar antibody polypeptide which is not linked to a PEG polymer.
  • the half-life of a PEGylated domain antibody is increased by at least about 10%, 20%, 30%, 40%, 50%, or more relative to a non-PEGylated domain antibody. Increases in the range of 2X, 3X, 4X, 5X, 10X, 20X, 30X, 40X, 50X, or more of the half-life are possible. Alternatively, or in addition, increases in the range of up to 30X, 40X, 50X, 60X, 70X, 80X, 90X, 100X, or 1 50X of the half-life are possible.
  • a PEG-linked domain antibody has a half-life of between 0.25 and 170 hours, including between 1 and 100 hours, further including between 30 and 100 hours, and still further including between 50 and 100 hours, and up to 170, 180, 190, and 200 hours or more.
  • hydrodynamic size refers to the apparent size of a molecule
  • hydrodynamic size of a protein depends on both mass and shape (conformation), such that two proteins having the same molecular mass may have differing hydrodynamic sizes based on the overall conformation of the protein. Hydrodynamic size is measured, for example, by size exclusion chromatography.
  • the hydrodynamic size of a PEG-linked antibody polypeptide can be in the range of about 24 kD to 500 kD; 30 to 500 kD; 40 to 500 kD; 50 to 500 kD; 100 to 500 kD; 150 to 500 kD; 200 to 500 kD; 250 to 500 kD; 300 to 500 kD; 350 to 500 kD; 400 to 500 kD, and 450 to 500 kD.
  • the hydrodynamic size of a PEGylated domain antibody is about 30 to 40 kD; 70 to 80 kD, or 200 to 300 kD.
  • the domain antibody should have a hydrodynamic size of between about 50 and 100 kD.
  • the domain antibody preparation should have a hydrodynamic size of greater than about 200 kD.
  • IC5 0 refers to the concentration of an inhibitor necessary to inhibit a given activity by about 50%.
  • IC 50 is determined by assaying a given activity, e.g., binding of CD28 to CD80 or CD86, in the presence of varying amounts of the inhibitor (e.g., domain antibody), and plotting the inhibitor concentration versus the activity being targeted. Binding of CD28 to CD80 or CD86 is measured herein by the method described the working examples. Alternatively, surface plasmon resonance (SPR) can be used.
  • SPR surface plasmon resonance
  • EC 50 refers to the concentration of compound or domain antibody that provokes a response in a subject, wherein the response is halfway between the baseline and the maximum response.
  • the baseline and maximum responses of a subject, with respect to a compound or domain antibody, can be determined by any technique known in the art.
  • fused to a domain antibody generally means that a polypeptide is fused to a given antibody through use of recombinant DNA techniques, though fusion may occur chemically at the protein level.
  • an antibody “fused to” another polypeptide e.g., to another antibody of different binding specificity, does not exist in nature and is generated through recombinant means.
  • fused to a domain antibody also encompasses the linkage of a polypeptide to a given domain antibody through, for example, disulfide or other chemical linkages, where the fused polypeptide is not naturally found fused to the domain antibody.
  • Fc domain refers to the constant region antibody sequences comprising CH2 and CH3 constant domains as delimited according to Kabat et al., supra.
  • the Fc portion of the heavy chain polypeptide has the ability to self-associate, a function which facilitates the formation of divalent antibodies.
  • the term "lacks an Fc domain” means that a given domain antibody lacks at least the portion of an
  • immunoglobulin Fc domain (as such domains are defined according to Kabat et al., 1991 , Sequences of Immunological Interest, 5 th ed. U.S. Dept. Health & Human Services, Washington, D.C.) sufficient to mediate the dimerization of Fc-containing domain antibodies. Dimerization of Fc-containing domain antibodies is measured, for example, by chromatographic methods or by surface plasmon resonance. A domain antibody lacking an Fc domain avoids Fc-platelet interactions and therefore avoids induction of platelet aggregation.
  • symptom of disease refers to a decrease of a symptom by at least 10% based on a clinically measurable parameter, or by at least one point on a clinically-accepted scale of disease or symptom severity.
  • symptom(s) of systemic lupus erythematosus refers to any of the clinically relevant symptoms of SLE known to those of skill in the art.
  • Non-limiting examples include the accumulation of IgG autoantibodies (e.g., against nuclear antigens such as chromatin, snRNPs (especially Ul, Sm, Ro/SSA and La/SSB), phospholipids and cell surface molecules), hemolytic anemia,
  • nuclear antigens such as chromatin, snRNPs (especially Ul, Sm, Ro/SSA and La/SSB), phospholipids and cell surface molecules), hemolytic anemia,
  • a reduction in such a symptom is a reduction by at least 10% in a clinically measurable parameter, or by at least one point on a clinically-accepted scale of disease severity.
  • the phrase "specifically binds" refers to the binding of an antigen by a domain antibody with a dissociation constant (3 ⁇ 4) of 1 ⁇ or lower as measured by surface plasmon resonance analysis using, for example, a BIAcore 1 M surface plasmon resonance system and BIAcoreTM kinetic evaluation software (e.g., version 2.1 ).
  • the affinity or 3 ⁇ 4 for a specific binding interaction in an aspect, is about 500 nM or lower, and in another aspect, about 300 nM or lower.
  • a "generic ligand” is a ligand that binds a substantial proportion of functional members in a given repertoire, e.g., in a phage display library.
  • the same generic ligand can bind many members of the repertoire regardless of their target ligand specificities.
  • the presence of a functional generic ligand binding site indicates that the repertoire member is expressed and folded correctly.
  • binding of the generic ligand to its binding site provides a method for preselecting functional polypeptides from a repertoire of polypeptides.
  • Generic ligands include, for example, Protein A, Protein G and Protein L.
  • universal framework refers to a single antibody framework sequence corresponding to the regions of an antibody conserved in sequence as defined by Kabat (Kabat et al. ( 1991 ) Sequences of Immunological Interest, 5 th ed. U.S. Dept. Health & Human Services, Washington, D.C.) or corresponding to the human germline immunoglobulin repertoire or structure as defined by Chothia and Lesk, (1987) J. Mol. Biol. 196: 910-917.
  • CTLA-4 a/k/a/ CD 152; a high affinity CD80/CD86 receptor on T cells CRS cytokine release syndrome
  • PEGylated domain antibodies are provided that are monovalent for binding to CD28. While not wishing to be bound by any particular theory, it is believed that monovalency for CD28 binding removes the possibility for cross-linking cell surface receptors that occurs with prior art antibodies. Thus, in one aspect, the domain antibodies disclosed herein not only inhibit or antagonize the binding of CD80 or CD86 to CD28, they do not substantially agonize CD28 activity.
  • the antibodies monovalent for CD28 binding are human domain antibodies.
  • Human domain antibodies can be administered to human patients while largely avoiding the anti-antibody immune response often provoked by the administration of antibodies from other species, e.g., mouse. While murine antibodies can be
  • human antibodies as disclosed herein are produced without the need for laborious and time-consuming genetic manipulation of a murine antibody sequence.
  • the heavy and light polypeptide chains of antibodies comprise variable (V) regions that directly participate in antigen interactions, and constant (C) regions that provide structural support and function in non-antigen-specific interactions with immune effectors.
  • the antigen binding domain of a conventional antibody is comprised of two separate domains: a heavy chain variable domain (V H ) and a light chain variable domain (VL, which can be either V K or V ⁇ ).
  • the antigen binding site itself is formed by six polypeptide loops: three from the VH domain (H I , H2 and H3) and three from the VL domain (LI , L2 and L3).
  • C regions include the light chain C regions (referred to as C L regions) and the heavy chain C regions (referred to as CH I , CH2 and C3 ⁇ 43 regions).
  • a naturally-occurring antibody generally comprises two antigen binding domains and is therefore divalent.
  • Fab fragments VL-CL/C H 1 -VH
  • Fab' fragment a Fab with the heavy chain hinge region
  • F(ab') 2 fragment a dimer of Fab' fragments joined by the heavy chain hinge region
  • Recombinant methods have been used to generate such fragments and to generate even smaller antigen-binding fragments, e.g., those referred to as “single chain Fv” (variable fragment) or “scFv,” consisting of V L and VH joined by a peptide linker (VL-linker-V H ).
  • Fab fragments, Fab' fragments and scFv fragments are monovalent for antigen binding, as they each comprise only one antigen binding domain comprising one V H V L dimer.
  • a domain antibody binds antigen independently of other V domains; however, a domain antibody can be present in a homo- or heteromultimer with other VH or VL domains where the other domains are not required for antigen binding by the dAb, i.e., where the dAb binds antigen independently of the additional VH or V L domains.
  • the preparation of domain antibodies is described and exemplified herein below.
  • Antibody single variable domains for example, VHH
  • VHH are the smallest antigen- binding antibody unit known.
  • human antibodies are especially advantageous, primarily because they are not as likely to provoke an immune response when administered to a patient.
  • Comparisons of camelid V H H with the V H domains of human antibodies reveals several key differences in the framework regions of the camelid VHH domain corresponding to the V H /V L interface of the human V H domains. Mutation of these residues of human V H 3 to more closely resemble the VHH sequence (specifically Gly 44 ⁇ Glu, Leu 45 ⁇ Arg and Trp 47 ⁇ Gly) has been performed to produce
  • Domain antibodies can be generated in several different ways.
  • the nucleic acid sequence encoding heavy and light chains of an antibody known to bind CD28 can be manipulated to generate a number of different domain antibodies that are monovalent for CD28 binding.
  • monovalent antigen-binding polypeptide constructs such as Fab fragments, scFv, dAbs, or even bispecific antibodies (i.e., antibodies that comprise two different antigen-binding moieties and can therefore bind two separate antigens, and in an aspect, simultaneously) that are monovalent for CD28.
  • One means of generating domain antibodies specific for CD28 is to amplify and express the V H and V L regions of the heavy chain and light chain gene sequences isolated, for example, from a hybridoma (e.g., a mouse hybridoma) that expresses domain antibody.
  • a hybridoma e.g., a mouse hybridoma
  • the boundaries of VH and VL domains are set out by Kabat et al. (Kabat et al. ( 1991 ) Sequences of Immunological Interest, 5 th ed. U.S. Dept. Health & Human Services, Washington, D.C.).
  • VH and VL domains of heavy and light chain genes The information regarding the boundaries of the VH and VL domains of heavy and light chain genes is used to design PCR primers that amplify the V domain from a heavy or light chain coding sequence encoding an antibody known to bind CD28.
  • the amplified V domains are inserted into a suitable expression vector, e.g., pHEN- 1 (Hoogenboom et al. ( 1991 ) Nucleic Acids Res. 19: 4133-4137) and expressed, e.g., as a fusion of the V H and VL in a scFv or other suitable monovalent format.
  • the resulting polypeptide is then screened for high affinity monovalent binding to CD28.
  • screening for binding is performed as known in the art or as described herein below.
  • library screening methods can be used to identify monovalent CD28-specific binding proteins.
  • Phage display technology provides an approach for the selection of domain antibodies which bind a desired target from among large, diverse repertoires of domain antibodies.
  • These phage-antibody libraries can be grouped into two categories: natural libraries which use rearranged V genes harvested from human B cells (Marks et al. (1991) J Mol. Biol., 222: 581 ; Vaughan et al.
  • Methods involving genetic display packages are well-suited for the selection of monovalent CD28-specific antibody constructs because they generally express only monovalent fragments, rather than whole, divalent antibodies, on the display packages.
  • Methods for the preparation of phage display libraries displaying various antibody fragments are described in the preceding references. Such methods are also described, for example, in U.S. Patent No. 6,696,245, which is incorporated herein by reference.
  • the methods described in the '245 patent generally involve the randomization of selected regions of immunoglobulin gene coding regions, in particular VH and V L coding regions, while leaving other regions non-randomized (see below).
  • the '245 patent also describes the generation of scFv constructs comprising individually randomized VH and VL domains.
  • Analysis of the structures and sequences of antibodies has shown that five of the six antigen binding loops (H I , H2, LI , L2, L3) possess a limited number of main-chain conformations or canonical structures (Chothia and Lesk (1987) J. Mol. Biol. 196: 901 ; Chothia et al. (1989) Nature 342: 877).
  • the main-chain conformations are determined by (i) the length of the antigen binding loop, and (ii) particular residues, or types of residue, at certain key positions in the antigen binding loop and the antibody framework.
  • H3 region is much more diverse in terms of sequence, length and structure (due to the use of D segments), it also forms a limited number of main-chain conformations for short loop lengths which depend on the length and the presence of particular residues, or types of residue, at key positions in the loop and the antibody framework (Martin et al. ( 1996) J. Mol. Biol. 263 : 800; Shirai et al. (1996) FEBS Letters 399: 1.
  • a domain antibody comprises the amino acid sequence of a given human germ line V region gene segment, e.g., VH germline gene segment DP-47, or V K germline gene segment DPK9.
  • variable region polypeptides can be used for the production of scFvs or Fabs, e.g., a scFv or Fab comprising (i) an antibody heavy chain variable domain (VH), or antigen binding fragment thereof, which comprises the amino acid sequence of germline V H segment DP-47 and (ii) an antibody light chain variable domain (VL), or antigen binding fragment thereof, which comprises the amino acid sequence of germline V K segment DPK9.
  • VH antibody heavy chain variable domain
  • VL antibody light chain variable domain
  • variable region polypeptides can also be expressed as domain antibodies and screened for high affinity binding to CD28.
  • the repertoire can be cloned into or generated in a vector suitable for phage display, e.g., a lambda or filamentous bacteriophage display vector and is then screened for binding to a given target antigen, e.g., CD28.
  • a domain antibody is a folded polypeptide domain which comprises sequences characteristic of immunoglobulin variable domains and which specifically binds an antigen (e.g., dissociation constant of 500 nM or less), and which binds antigen as a single variable domain; that is, there is one binding site provided by a domain antibody without any complementary variable domain.
  • an antigen e.g., dissociation constant of 500 nM or less
  • a domain antibody therefore includes complete antibody variable domains as well as modified variable domains, for example in which one or more loops have been replaced by sequences which are not characteristic of antibody variable domains or antibody variable domains which have been truncated or comprise N- or C-terminal extensions, as well as folded fragments of variable domains which retain a dissociation constant of about 500 nM less (e.g., about 450 nM or less, about 400 nM or less, about 350 nM or less, about 300 nM or less, about 250 nM or less, about 200 nM or less, about 150 nM or less, about 100 nM or less) and the target antigen specificity of the full-length domain.
  • nM less e.g., about 450 nM or less, about 400 nM or less, about 350 nM or less, about 300 nM or less, about 250 nM or less, about 200 nM or less, about 150 nM or less, about 100 nM or less
  • an antibody single variable domain useful in the compositions and methods set forth herein is selected from the group of VH and VL, including Vk apP a and V] am bda-
  • the domain antibodies of use herein are "human" as that term is defined herein.
  • two or more non-complementary epitope binding domains are linked so that they are in a closed conformation as herein defined.
  • they may be further attached to a skeleton which may, as an alternative, or on addition to a linker described herein, facilitate the formation and/or maintenance of the closed conformation of the epitope binding sites with respect to one another.
  • domain antibodies disclosed herein may be constructed using scaffold or skeleton frameworks as discussed herein.
  • Ligand skeletons may be based on immunoglobulin molecules or may be non- immunoglobulin in origin as set forth elsewhere herein.
  • Immunoglobulin skeletons as herein defined may include any one or more of those selected from the following: an immunoglobulin molecule comprising at least (i) the CL (kappa or lambda subclass) domain of an antibody; or (ii) the CHI domain of an antibody heavy chain; an immunoglobulin molecule comprising the CHI and CH2 domains of an antibody heavy chain; an immunoglobulin molecule comprising the CH I, CH2 and CH3 domains of an antibody heavy chain; or any of the subset (ii) in conjunction with the CL (kappa or lambda subclass) domain of an antibody.
  • a hinge region domain may also be included.
  • Such combinations of domains may, for example, mimic natural antibodies, such as IgG or IgM, or fragments thereof, such as Fv, scFv, Fab, or F(ab') 2 molecules. Those skilled in the art will be aware that this list is not intended to be exhaustive.
  • Each epitope binding domain comprises a protein scaffold and one or more CDRs which are involved in the specific interaction of the domain with one or more epitopes.
  • an epitope binding domain disclosed herein comprises three CDRs.
  • Suitable protein scaffolds in addition to those based on immunoglobulin domains, may also be based on protein scaffolds or skeletons other than immunoglobulin domains.
  • natural bacterial receptors such as SpA have been used as scaffolds for the grafting of CDRs to generate ligands which bind specifically to one or more epitopes. Details of this procedure are described in US 5,83 1 ,012.
  • Other suitable scaffolds include those based on fibronectin and affibodies (Affibody, Bromma, Sweden). Details of suitable procedures are described in WO 98/58965.
  • Other suitable scaffolds include lipocallin and CTLA4, as described in van den Beuken et al , (2001 ) J Mol.
  • Biol.3 ⁇ Q: 591 -601 and scaffolds such as those described in WO 00/69907 (Medical Research Council), which are based for example on the ring structure of bacterial GroEL or other chaperone polypeptides.
  • Other non-immunoglobulin based scaffolds which may be used include those based on the LDL receptor class A, EGF domain monomers and multimers, and scaffolds available from Biorexis (King of Prussia, PA) or Avidia (Mountain View, CA).
  • Other non-immunoglobulin scaffolds which may be used are described, for example, in WO 05/040229, WO 04/04401 1 , and US 2005/0089932.
  • the members of the immunoglobulin superfamily all share a similar fold for their polypeptide chain.
  • antibodies are highly diverse in terms of their primary sequence
  • comparison of sequences and crystallographic structures has revealed that, contrary to expectation, five of the six antigen binding loops of antibodies (H I , H2, LI , L2, L3) adopt a limited number of main-chain conformations, or canonical structures (Chothia and Lesk ( 1987) J. Mol. Biol, 196: 901 ; Chothia et al. (1989) Nature, 342: 877).
  • H3 region is much more diverse in terms of sequence, length, and structure (due to the use of D segments), it also forms a limited number of main-chain conformations for short loop lengths which depend on the length and the presence of particular residues, or types of residues, at key positions in the loop and the antibody framework (Martin et al. (1996) J. Mol. Biol , 263 : 800; Shirai et al. (1996) FEBS Letters, 399: 1 ).
  • the ligands disclosed herein can be selected and/or assembled from libraries of domains, such as libraries of VH domains and/or libraries of Vi. domains. Moreover, the ligands disclosed herein may themselves be provided in the form of libraries.
  • libraries of ligands and/or domains are designed in which certain loop lengths and key residues have been chosen to ensure that the main-chain conformation of the members is known.
  • these are real conformations of immunoglobulin superfamily molecules found in nature, to minimize the chances that they are non-functional, as discussed above.
  • Germline V gene segments serve as one exemplary basic framework for constructing antibody or T cell receptor libraries; other sequences are also of use. Variations may occur at a low frequency, such that a small number of functional members may possess an altered main-chain conformation, which does not affect its function.
  • Canonical structure theory is also of use to assess the number of different main- chain conformations encoded by ligands, to predict the main-chain conformation based on ligand sequences and to choose residues for diversification which do not affect the canonical structure. It is known that, in the human V K domain, the LI loop can adopt one of four canonical structures, the L2 loop has a single canonical structure and that 90% of human V K domains adopt one of four or five canonical structures for the L3 loop (Tomlinson et al. ( 1995) supra); thus, in the V K domain alone, different canonical structures can combine to create a range of different main-chain conformations.
  • the domain encodes a different range of canonical structures for the L I , L2, and L3 loops, and that V K and W % domains can pair with any VH domain which can encode several canonical structures for the H I and H2 loops
  • the number of canonical structure combinations observed for these five loops is very large. This implies that the generation of diversity in the main-chain conformation may be essential for the production of a wide range of binding specificities.
  • by constructing an antibody library based on a single known main-chain conformation it has been found, contrary to expectation, that diversity in the main-chain conformation is not required to generate sufficient diversity to target substantially all antigens. Even more surprisingly, the single main-chain conformation need not be a consensus structure. A single naturally occurring conformation can be used as the basis for an entire library.
  • the ligands disclosed herein possess a single known main-chain conformation.
  • the single main-chain conformation that is chosen is in an aspect, commonplace among molecules of the immunoglobulin superfamily type in question. A conformation is commonplace when a significant number of naturally occurring molecules are observed to adopt it. Accordingly, in one aspect disclosed herein, the natural occurrence of the different main-chain conformations for each binding loop of an immunoglobulin domain are considered separately and then a naturally occurring variable domain is chosen which possesses the desired combination of main-chain conformations for the different loops. If none is available, the nearest equivalent may be chosen. It is preferable that the desired combination of main-chain conformations for the different loops is created by selecting germline gene segments which encode the desired main- chain conformations. It is more preferable, that the selected germline gene segments are frequently expressed in nature, and most preferable that they are the most frequently expressed of all natural germline gene segments.
  • the incidence of the different main-chain conformations for each of the antigen binding loops may be considered separately.
  • H I , H2, LI , L2, and L3 a given conformation that is adopted by between 20% and 100% of the antigen binding loops of naturally occurring molecules is chosen. Typically, its observed incidence is above 35% (i.e. between 35% and 1 00%) and, ideally, above 50% or even above 65%. Since the vast majority of H3 loops do not have canonical structures, it is preferable to select a main-chain conformation which is commonplace among those loops which do display canonical structures. For each of the loops, the conformation which is observed most often in the natural repertoire is therefore selected.
  • the natural occurrence of combinations of main-chain conformations is used as the basis for choosing the single main-chain conformation.
  • the natural occurrence of canonical structure combinations for any two, three, four, five, or for all six of the antigen binding loops can be determined.
  • the chosen conformation is commonplace in naturally occurring antibodies and most preferable that it observed most frequently in the natural repertoire.
  • human antibodies for example, when natural combinations of the five antigen binding loops, HI , H2, LI , L2, and L3, are considered, the most frequent combination of canonical structures is determined and then combined with the most popular
  • Domain antibodies are prepared in a number of ways. For each of these approaches, well-known methods of preparing (e.g., amplifying, mutating, etc.) and manipulating nucleic acid sequences are applicable.
  • One means of preparing a domain antibody is to amplify and express the VH or VL region of a heavy chain or light chain gene for a cloned antibody known to bind the desired antigen. That is, the V H or V L domain of a known domain antibody coding region can be amplified and expressed as a single domain (or as a fusion of a single domain) and evaluated for binding to CD28.
  • the boundaries of VH and VL domains are set out by Kabat et al. (Kabat et al. ( 1991 ) Sequences of Immunological Interest, 5 th ed. U.S. Dept. Health & Human Services, Washington, D.C.).
  • VH and VL domains of heavy and light chain genes The information regarding the boundaries of the VH and VL domains of heavy and light chain genes is used to design PCR primers that amplify the V domain from a cloned heavy or light chain coding sequence encoding an antibody known to bind CD28.
  • the amplified V domain is inserted into a suitable expression vector, e.g., pHEN-1 (Hoogenboom et al. (1991) Nucleic Acids Res. 19: 4133-4137) and expressed, either alone or as a fusion with another polypeptide sequence.
  • pHEN-1 Hoogenboom et al. (1991) Nucleic Acids Res. 19: 4133-4137
  • the V H gene is produced by the recombination of three gene segments, V H , D and J H .
  • V H three gene segments
  • D and J H three gene segments
  • there are approximately 51 functional VH segments (Cook and Tomlinson (1995) Immunol Today 16: 237), 25 functional D segments (Corbett et al. (1997) J. Mol. Biol. 268: 69) and 6 functional 3 ⁇ 4 segments (Ravetch et al. (1981) Cell 27: 583), depending on the haplotype.
  • the VH segment encodes the region of the polypeptide chain which forms the first and second antigen binding loops of the V H domain (H I and H2), while the VH, D and JH segments combine to form the third antigen binding loop of the V H domain (H3).
  • the v L gene is produced by the recombination of only two gene segments, VL and JL- In humans, there are approximately 40 functional V K segments (Sellable and Zachau ( 1993) Biol. Chem. Hoppe-Seyler 314: 1001 ), 31 functional ⁇ segments (Williams et al. ( 1996) J. Mol. Biol. 264: 220; Kawasaki et al. (1997) Genome Res. 7: 250), 5 functional J K segments (Hieter et al. (1982) J. Biol. Chem. 257: 15 16) and 4 functional i ⁇ segments (Vasicek and Leder ( 1990) J. Exp. Med. 172: 609), depending on the haplotype.
  • V L segment encodes the region of the polypeptide chain which forms the first and second antigen binding loops of the VL domain (LI and L2), while the VL and JL segments combine to form the third antigen binding loop of the V L domain (L3).
  • Antibodies selected from this primary repertoire are believed to be sufficiently diverse to bind almost all antigens with at least moderate affinity.
  • High affinity antibodies are produced in vivo by "affinity maturation" of the rearranged genes, in which point mutations are generated and selected by the immune system on the basis of improved binding.
  • a repertoire of VR or VL domains in an aspect, human VH or V L domains, is screened by, for example, phage display, panning against the desired antigen.
  • Methods for the construction of bacteriophage display libraries and lambda phage expression libraries are well known in the art, and taught, for example, by: McCafferty et al. ( 1990) Nature 348: 552; Kang et al. ( 1991 ) Proc. Natl. Acad. Sci. U.S.A ., 88: 4363 ; Clackson et al. (1991 ) Nature 352: 624; Lowman et al. (1991 ) Biochemistry 30: 10832; Burton et al.
  • the repertoire of VH or VL domains can be a naturally-occurring repertoire of immunoglobulin sequences or a synthetic repertoire.
  • a naturally-occurring repertoire is one prepared, for example, from immunoglobulin-expressing cells harvested from one or more individuals. Such repertoires can be "na ' ive,” i.e., prepared, for example, from human fetal or newborn immunoglobulin-expressing cells, or rearranged, i.e., prepared from, for example, adult human B cells.
  • Natural repertoires are described, for example, by Marks et al. (1991 ) J Mol. Biol. 222: 581 and Vaughan et al. (1996) Nature Biotech. 14: 309. If desired, clones identified from a natural repertoire, or any repertoire, for that matter, that bind the target antigen are then subjected to mutagenesis and further screening in order to produce and select variants with improved binding characteristics.
  • Synthetic repertoires of domain antibodies are prepared by artificially introducing diversity into a cloned V domain. Synthetic repertoires are described, for example, by Hoogenboom & Winter (1992) J. Mol. Biol. 227: 381 ; Barbas et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89: 4457; Nissim et al. (1994) EMBO J. 13 : 692; Griffiths et al. (1994) EMBO J. 13 : 3245; DeKriuf et al. (1995) J Mol. Biol. 248: 97; and WO 99/20749.
  • VH domain repertoires are prepared in VH or VK backgrounds, based on artificially diversified germline VH or VK sequences.
  • the VH domain repertoire can be based on cloned germline VH gene segments V3-23/DP47 (Tomlinson et al. (1992) J Mol. Biol. 227: 776) and JH4b.
  • the V K domain repertoire can be based, for example, on germline V K gene segments 02/012/DPK9 (Cox et al. (1994) Eur. J. Immunol. 24: 827) and J K 1. Diversity is introduced into these or other gene segments by, for example, PCR mutagenesis.
  • DVT codon (A/G/T) (A/G/C)T )
  • DVC codon (A/G/T)(A/G/C)C)
  • DVY codon ((A/G/T)(A/G/C)(C/T).
  • the DVT codon encodes 22% serine and 1 1 % tyrosine, asparagine, glycine, alanine, aspartate, threonine and cysteine, which most closely mimics the distribution of amino acid residues for the antigen binding sites of natural human antibodies.
  • Repertoires are made using PCR primers having the selected degenerate codon or codons at each site to be diversified. PCR mutagenesis is well known in the art.
  • diversity is introduced into the sequence of human germline VH gene segments V3-23/DP47 (Tomlinson et al. (1992) J. Mol. Biol. 227: 7768) and JH4b using the NNK codon at sites H30, H3 1 , H33, H35, H50, H52, H52a, H53, H55, H56, H58, H95, H97, and H98, corresponding to diversity in CDRs 1 , 2 and 3, with the numbering as used in U.S. Patent No. 6,696,245.
  • diversity is also introduced into the sequence of human germline VH gene segments V3-23/DP47 and JH4b, for example, using the NNK codon at sites H30, H3 1 , H33 , H35, H50, H52, H52a, H53, H55, H56, H58, H95, H97, H98, H99, H 100, Hl OOa, and Hl OOb, corresponding to diversity in CDRs 1 , 2 and 3, with the numbering as used in U.S. Patent No. 6,696,245.
  • diversity is introduced into the sequence of human germline V K gene segments 02/012/DPK9 and J K 1 , for example, using the NNK codon at sites L30, L3 1 , L32, L34, L50, L53, L91 , L92, L93, L94, and L96, corresponding to diversity in CDRs 1 , 2 and 3,with the numbering as used in U.S. Patent No. 6,696,245.
  • nucleic acid molecules and vector constructs required for the compositions and methods set forth herein are available in the art and are constructed and manipulated as set forth in standard laboratory manuals, such as Sambrook et al. (1989), Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, USA and subsequent editions.
  • vector refers to a discrete element that is used to introduce heterologous DNA into cells for the expression and/or replication thereof. Methods by which to select or construct and, subsequently, use such vectors are well known to one of skill in the art. Numerous vectors are publicly available, including bacterial plasm ids, bacteriophage, artificial chromosomes and episomal vectors. Such vectors may be used for simple cloning and mutagenesis; alternatively, as is typical of vectors in which repertoire (or pre-repertoire) members herein are carried, a gene expression vector is employed. A vector of use set forth herein is selected to
  • each vector contains various functional components, which generally include a cloning (or "polylinker") site, an origin of replication and at least one selectable marker gene. If a given vector is an expression vector, it additionally possesses one or more of the following: enhancer element, promoter, transcription termination and signal sequences, each positioned in the vicinity of the cloning site, such that they are operatively linked to the gene encoding a polypeptide repertoire member as set forth herein.
  • Both cloning and expression vectors generally contain nucleic acid sequences that enable the vector to replicate in one or more selected host cells.
  • this sequence is one that enables the vector to replicate independently of the host chromosomal DNA and includes origins of replication or autonomously replicating sequences.
  • origins of replication or autonomously replicating sequences are well known for a variety of bacteria, yeast and viruses.
  • the origin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria, the 2 micron plasmid origin is suitable for yeast, and various viral origins (e.g. SV 40, adenovirus) are useful for cloning vectors in mammalian cells.
  • the origin of replication is not needed for mammalian expression vectors unless these are used in mammalian cells able to replicate high levels of DNA, such as COS cells.
  • a cloning or expression vector also contains a selection gene also referred to as selectable marker.
  • This gene encodes a protein necessary for the survival or growth of transformed host cells grown in a selective culture medium. Host cells not transformed with the vector containing the selection gene will therefore not survive in the culture medium.
  • Typical selection genes encode proteins that confer resistance to antibiotics and other toxins, e.g. ampicillin, neomycin, methotrexate or tetracycline, complement auxotrophic deficiencies, or supply critical nutrients not available in the growth media. Because the replication of vectors herein is most conveniently performed in E. coli, an E.
  • co/z ' -selectable marker for example, the ⁇ - lactamase gene that confers resistance to the antibiotic ampicillin
  • co/z ' -selectable marker for example, the ⁇ - lactamase gene that confers resistance to the antibiotic ampicillin
  • E. coli plasmids such as pBR322 or a pUC plasmid such as pUCl 8 or pUC19.
  • other plasmid microorganism combinations can also be reasonably substituted.
  • Expression vectors usually contain a promoter that is recognized by the host organism and is operably linked to the coding sequence of interest. Such a promoter may be inducible or constitutive.
  • operably linked refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner.
  • a control sequence "operably linked" to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences.
  • Promoters suitable for use with prokaiyotic hosts include, for example, the ⁇ - lactamase and lactose promoter systems, alkaline phosphatase, the tryptophan (trp) promoter system and hybrid promoters such as the tac promoter. Promoters for use in bacterial systems will also generally contain a Shine-Dalgarno sequence operably linked to the coding sequence.
  • vectors may be expression vectors that enable the expression of a nucleotide sequence corresponding to a polypeptide library member. Thus, selection is performed by separate propagation and expression of a single clone expressing the polypeptide library member or by use of any selection display system. As described above, one selection display system uses bacteriophage display. Thus, phage or phagemid vectors can be used. Vectors may be phagemid vectors, which have an E. coli origin of replication (for double stranded replication) and also a phage origin of replication (for production of single-stranded DNA).
  • the vector contains a ⁇ - lactamase or other selectable marker gene to confer selectivity on the phagemid, and a lac promoter upstream of a expression cassette that consists (N to C terminal) of a pelB leader sequence (which directs the expressed polypeptide to the periplasmic space), a multiple cloning site (for cloning the nucleotide version of the library member), optionally, one or more peptide tags (for detection), optionally, one or more TAG stop codons and the phage protein pill.
  • the vector encodes, rather than the pelB leader sequence, a eukaryotic GAS 1 leader sequence which serves to direct the secretion of the fusion polypeptide to the periplasmic space in E. coli or to the medium in eukaryotic cell systems.
  • a eukaryotic GAS 1 leader sequence which serves to direct the secretion of the fusion polypeptide to the periplasmic space in E. coli or to the medium in eukaryotic cell systems.
  • the vector is able to replicate as a plasmid with no expression, produce large quantities of the polypeptide library member only, or produce phage, some of which contain at least one copy of the polypeptide-plll fusion on their surface.
  • An example of a vector is the pHEN l phagemid vector (Hoogenboom et al.
  • vectors as set forth herein employs conventional ligation techniques. Isolated vectors or DNA fragments are cleaved, tailored, and re-ligated in the form desired to generate the required vector. If desired, sequence analysis to confirm that the correct sequences are present in the constructed vector is performed using standard methods. Suitable methods for constructing expression vectors, preparing in vitro transcripts, introducing DNA into host cells, and performing analyses for assessing expression and function are known to those skilled in the art. The presence of a gene sequence in a sample is detected, or its amplification and/or expression quantified by conventional methods, such as Southern or Northern analysis, Western blotting, dot blotting of DNA, RNA or protein, in situ hybridization, immunocytochemistry or sequence analysis of nucleic acid or protein molecules. Those skilled in the art will readily envisage how these methods may be modified, if desired. 3.3. Screening Domain Antibodies for Antigen Binding
  • phage Following expression of a repertoire of domain antibodies on the surface of phage, selection is performed by contacting the phage repertoire with immobilized target antigen, washing to remove unbound phage, and propagation of the bound phage, the whole process frequently referred to as "panning". This process is applicable to the screening of domain antibodies as well as other antibody fragments that can be expressed on a display library, e.g., scFv, Fab, etc.
  • phage are pre-selected for the expression of properly folded member variants by panning against an immobilized generic Hgand (e.g., protein A or protein L) that is only bound by folded members.
  • an immobilized generic Hgand e.g., protein A or protein L
  • Screening is commonly performed using purified antigen immobilized on a solid support, for example, plastic tubes or wells, or on a chromatography matrix, for example SepharoseTM (Pharmacia). Screening or selection can also be performed on complex antigens, such as the surface of cells (Marks et al. (1993) BioTechnology 1 1 : 1 145; de Kruif et al. (1995) Proc. Natl. Acad. Sci. U.S.A. 92: 3938). Another alternative involves selection by binding biotinylated antigen in solution, followed by capture on streptavidin- coated beads.
  • panning is performed by immobilizing antigen (generic or specific) on tubes or wells in a plate, e.g., Nunc MAXISORPTM immunotube 8 well strips. Wells are coated with 150 ⁇ of antigen (100 ⁇ g/ml in PBS) and incubated overnight. The wells are then washed 3 times with PBS and blocked with 400 ⁇ PBS-2% skim milk (2%
  • coli host cells e.g., TG I
  • TG I coli host cells
  • Infected cells are spun down, resuspended in fresh medium and plated in top agarose.
  • Phage plaques are eluted or picked into fresh cultures of host cells to propagate for analysis or for further rounds of selection.
  • One or more rounds of plaque purification are performed if necessary to ensure pure populations of selected phage.
  • Other screening approaches are described by Harrison et al. (1996) supra.
  • variable domain fusion proteins are easily produced in soluble form by infecting non-suppressor strains of bacteria, e.g., HB215 1 that permit the secretion of soluble gene III fusion protein.
  • non-suppressor strains of bacteria e.g., HB215 1 that permit the secretion of soluble gene III fusion protein.
  • the fusion polypeptide can be secreted by eukaryotic (e.g., yeast or mammalian) or prokaryotic (e.g., E. coli) cells.
  • the V domain sequence can be sub-cloned into an appropriate expression vector to produce soluble protein according to methods known in the art.
  • Domain antibodies secreted into the periplasmic space or into the medium of bacteria are harvested and purified according to known methods (Harrison et al. (1996) supra). Skerra & Pluckthun ( 1988) Science 240: 1038 and Breitling et al. ( 1991 ) Gene 104: 147 describe the harvest of domain antibodies from the periplasm, and Better et al. (1988) Science 240: 1041 describes harvest from the culture supernatant.
  • purification can also be achieved by binding to generic ligands, such as protein A or Protein L.
  • the variable domains can be expressed with a peptide tag, e.g., the Myc, HA or 6X-His tags (SEQ ID NO: 644), which facilitate purification by affinity chromatography.
  • domain antibodies are concentrated by any of several methods well known in the art, including, for example, ultrafiltration, diafiltration and tangential flow filtration.
  • the process of ultrafiltration uses semi-permeable membranes and pressure to separate molecular species on the basis of size and shape.
  • the pressure is provided by gas pressure or by centrifugation.
  • Commercial ultrafiltration products are widely available, e.g., from Millipore (Bedford, MA; examples include the Centricon 1 M and MicroconTM concentrators) and Vivascience (Hannover, Germany; examples include the Vivaspin concentrators).
  • a molecular weight cutoff smaller than the target polypeptide usually 1 /3 to 1 /6 the molecular weight of the target polypeptide, although differences of as little as 10 kD can be used successfully
  • the polypeptide is retained when solvent and smaller solutes pass through the membrane.
  • a molecular weight cutoff of about 5 kD is useful for concentration of domain antibodies described herein.
  • Diafiltration which uses ultrafiltration membranes with a "washing" process, is used where it is desired to remove or exchange the salt or buffer in a polypeptide preparation.
  • the polypeptide is concentrated by the passage of solvent and small solutes through the membrane, and remaining salts or buffer are removed by dilution of the retained polypeptide with a new buffer or salt solution or water, as desired, accompanied by continued ultrafiltration.
  • new buffer is added at the same rate that filtrate passes through the membrane.
  • a diafiltration volume is the volume of polypeptide solution prior to the start of diafiltration - using continuous diafiltration, greater than 99.5% of a fully permeable solute can be removed by washing through six diafiltration volumes with the new buffer.
  • the process can be performed in a discontinuous manner, wherein the sample is repeatedly diluted and then filtered back to its original volume to remove or exchange salt or buffer and ultimately concentrate the polypeptide.
  • Equipment for diafiltration and detailed methodologies for its use are available, for example, from Pall Life Sciences (Ann Arbor, MI) and Sartorius
  • Tangential flow filtration also known as “cross-flow filtration,” also uses ultrafiltration membrane. Fluid containing the target polypeptide is pumped tangentially along the surface of the membrane. The pressure causes a portion of the fluid to pass through the membrane while the target polypeptide is retained above the filter. In contrast to standard ultrafiltration, however, the retained molecules do not accumulate on the surface of the membrane, but are carried along by the tangential flow. The solution that does not pass through the filter (containing the target polypeptide) can be repeatedly circulated across the membrane to achieve the desired degree of concentration.
  • Protein concentration is measured in a number of ways that are well known in the art. These include, for example, amino acid analysis, absorbance at 280 nm, the
  • the SDS-PAGE method uses gel electrophoresis and Coomassie Blue staining in comparison to known concentration standards, e.g., known amounts of a domain antibody. Quantitation can be done by eye or by densitometry.
  • Domain antibodies described herein retain solubility at high concentration (e.g., at least 4.8 mg (-400 ⁇ ) in aqueous solution (e.g., PBS), and in an aspect, at least about 5 mg/ml (-417 ⁇ ), 10 mg/ml (-833 ⁇ ), 20 mg/ml (-1.7 mM), 25 mg/ml (-2.1 mM), 30 mg/ml (-2.5 mM), 35 mg/ml (-2.9 mM), 40 mg/ml (-3.3 mM), 45 mg/ml (-3.75 mM), 50 mg/ml (-4.2 mM), 55 mg/ml (-4.6 mM), 60 mg/ml (-5.0 mM), 65 mg/ml (-5.4 mM), 70 mg/ml (-5.8 mM), 75 mg/ml (-6.3 mM), 100 mg/ml (-8.33 mM), 150 mg/ml (-12.5 mM), 200 mg/ml (-16.7
  • domain antibodies A full length conventional four chain antibody, e.g., IgG is about 150 kD in size.
  • domain antibodies which have a general structure comprising 4 framework (FW) regions and 3 CDRs, have a size of approximately 12 kD, or less than 1/ 10 the size of a conventional antibody.
  • domain antibodies are approximately half the size of a scFv molecule ( ⁇ 26 kD), and approximately one-fifth the size of a Fab molecule ( ⁇ 60 kD).
  • the size of a domain antibody-containing structure disclosed herein may be 100 kD or less, including structures of, for example, about 90 kD or less, 80 kD or less, 70 kD or less, 60 kD or less, 50 kD or less, 40 kD or less, 30 kD or less, 20 kD or less, down to and including about 12 kD, or a domain antibody in isolation.
  • solubility of a domain antibody is primarily determined by the interactions of the amino acid side chains with the surrounding solvent. Hydrophobic side chains tend to be localized internally as a polypeptide folds, away from the solvent- interacting surfaces of the polypeptide. Conversely, hydrophilic residues tend to be localized at the solvent- interacting surfaces of a polypeptide. Generally, polypeptides having a primary sequence that permits the molecule to fold to expose more hydrophilic residues to the aqueous environment are more soluble than one that folds to expose fewer hydrophilic residues to the surface. Thus, the arrangement and number of hydrophobic and hydrophilic residues is an important determinant of solubility.
  • polypeptide solubility can be maintained or enhanced by the addition of glycerol (e.g., -10% v/v) to the solution.
  • glycerol e.g., -10% v/v
  • Amino acid residue 103 of VH is also implicated in solubility, with mutation from Trp to Arg tending to confer increased V H solubility.
  • domain antibodies are based on the DP47 germline VH gene segment or the DPK9 germline V K gene segment.
  • these germline gene segments are capable, particularly when diversified at selected structural locations described herein, of producing specific binding domain antibodies that are highly soluble.
  • the four framework regions which are, in an aspect, not diversified, can contribute to the high solubility of the resulting proteins. It is expected that a domain antibody that shares a percent sequence identity with one having a known high solubility will also tend to be highly soluble.
  • one means of prediction or recognition that a given domain antibody would have the high solubility recited herein, one can compare the sequence of a domain antibody to one or more domain antibodies having known solubility.
  • domain antibody when a domain antibody is identified that has high binding affinity but unknown solubility, comparison of its amino acid sequence with that of one or more (in an aspect, more) domain antibodies known to have high solubility (e.g., a dAb sequence disclosed herein) can permit prediction of its solubility. While it is not an absolute predictor, where there is a high degree of similarity to a known highly soluble sequence, e.g., 90-95% or greater similarity, and particularly where there is a high degree of similarity with respect to hydrophilic amino acid residues, or residues likely to be exposed at the solvent interface, it is more likely that a newly identified binding polypeptide will have solubility similar to that of the known highly soluble sequence.
  • Molecular modeling software can also be used to predict the solubility of a polypeptide sequence relative to that of a polypeptide of known solubility. For example, the substitution or addition of a hydrophobic residue at the solvent-exposed surface, relative to a molecule of known solubility that has a less hydrophobic or even hydrophilic residue exposed in that position is expected to decrease the relative solubility of the polypeptide. Similarly, the substitution or addition of a more hydrophilic residue at such a location is expected to increase the relative solubility.
  • the domain antibody inhibits binding of CD28 to CD80 with an IC50 in the range of 1 pM to 1 .5 ⁇ , inclusive; IC50 for inhibition of CD28 binding to CD80.
  • the IC 50 can be in the range of 1 pM to 1 ⁇ , 1 pM to 900 nM, 1 pM to 800 nM, 1 pM to 700 nM, 1 pM to 600 nM, 1 pM to 500 nM, 1 pM to 400 nM, 1 pM to 300 nM, 1 pM to 200 nM, 1 pM to 100 nM, 1 pM to 50 nM, 1 pM to 10 nM, 1 pM to 1 nM, 1 pM to 500 pM, 1 pM to 100 pM, 1 pM to 50 pM, 1 pM to 10 pM, or 1 pM to 5 pM.
  • Further acceptable ranges include, for example, 50 pM to 1 ⁇ , 100 pM to 500 nM, 125 pM to 250 nM, 150 pM to 200 nM, 150 pM to 100 nM, and 200 pM to 50 nM.
  • the domain antibody inhibits binding of CD28 to CD86 with an IC 5 o in the range of 1 pM to 1.5 ⁇ , inclusive; IC 50 for inhibition of CD28 binding to CD86.
  • the IC 50 can be in the range of 1 pM to 1 ⁇ , 1 pM to 900 nM, 1 pM to 800 nM, 1 pM to 700 nM, 1 pM to 600 nM, 1 pM to 500 nM, 1 pM to 400 nM, 1 pM to 300 nM, 1 pM to 200 nM, 1 pM to 100 nM, 1 pM to 50 nM, 1 pM to 10 nM, 1 pM to 1 nM, 1 pM to 500 pM, 1 pM to 100 pM, 1 pM to 50 pM, 1 pM to 10 pM, or 1 pM to 5 pM.
  • Further acceptable ranges include, for example, 50 pM to 1 ⁇ , 100 pM to 500 nM, 1 25 pM to 250 nM, 1 50 pM to 200 nM, 150 pM to 100 nM, and 200 pM to 50 nM.
  • the antigen-binding affinity of a domain antibody can be conveniently measured by Surface Plasmon Resonance (SPR) using the BIAcore system (Pharmacia Biosensor, Piscataway, N.J.).
  • SPR Surface Plasmon Resonance
  • antigen is coupled to the BIAcore chip at known concentrations, and variable domain polypeptides are introduced. Specific binding between the variable domain polypeptide and the immobilized antigen results in increased protein concentration on the chip matrix and a change in the SPR signal.
  • Changes in SPR signal are recorded as resonance units (RU) and displayed with respect to time along the Y axis of a sensorgram.
  • Baseline signal is taken with solvent alone
  • BlAcore kinetic evaluation software (e.g., version 2.1 ) is used.
  • SPR can be used to monitor antagonism of CD28 binding to CD80 or CD86 by a domain antibody preparation by measuring the displacement or inhibition of binding of CD28 to CD80 or CD86 caused the monovalent antibody preparation.
  • SPR can also be used to monitor the dimerization, or in an aspect, the lack of dimerization, occurring via Fc region in antibody preparations as described herein.
  • High affinity is dependent upon the complementarity between a surface of the antigen and the CDRs of the antibody or antibody fragment. Complementarity is determined by the type and strength of the molecular interactions possible between portions of the target and the CDR, for example, the potential ionic interactions, van der Waals attractions, hydrogen bonding or other interactions that can occur. CDR3 tends to contribute more to antigen binding interactions than CDRs 1 and 2, probably due to its generally larger size, which provides more opportunity for favorable surface interactions. (See, e.g., Padlan et al. (1994) Mol. Immunol. 31 : 169-217; Chothia & Lesk (1987) /. Mol. Biol. 196: 904-917; and Chothia et al. (1985) J. Mol. Biol. 186: 651-663.) High affinity indicates domain antibody/antigen pairings that have a high degree of complementarity, which is directly related to the structures of the variable domain and the target.
  • a domain antibody is linked to another domain antibody to form a heterodimer in which each individual domain antibody is capable of binding a different cognate antigen.
  • Fusing domain antibodies as heterodimers, wherein each monomer binds a different target antigen, can produce a dual-specific ligand capable, for example, of bridging the respective target antigens.
  • dual specific ligands may be used to target cytokines and other molecules which cooperate synergistically in therapeutic situations in the body of an organism.
  • Domain antibodies set forth herein include CD28-binding domain antibody clones, and clones with substantial sequence similarity or percent identity to them that also bind target antigen with high affinity.
  • substantially sequence similarity or identity is at least 70% similarity or identity.
  • An additional measure of identity or similarity is the ability to hybridize under highly stringent hybridization conditions.
  • a first sequence encoding a domain antibody is substantially similar to a second coding sequence if the first sequence hybridizes to the second sequence (or its complement) under highly stringent hybridization conditions (such as those described by Sambrook et al., Molecular Cloning, Laboratory Manuel, Cold Spring, Harbor Laboratory press, New York).
  • Highly stringent hybridization conditions refer to hybridization in 6X SSC at about 45°C, followed by one or more washes in 0.2X SSC, 0.1% SDS at 65°C.
  • Very highly stringent hybridization conditions refer to hybridization in 0.5M sodium phosphate, 7% SDS at 65°C, followed by one or more washes at 0.2X SSC, 1% SDS at 65°C.
  • Exemplary domain antibodies include:
  • lh-239-880 (SEQ ID NO:265) lh-239-881 (SEQ ID NO:266) lh-239-882 (SEQ ID NO:267) lh-239-883 (SEQ ID NO:268)
  • Exemplary domain antibodies may include one or more of the following CDRs:
  • a domain antibody as described herein binds to CD28 yet does not substantially agonize CD28 signaling. Activation of the CD28 pathway manifests a number of different outcomes that can be measured in order to assess the effect of a given domain antibody on the activity of the pathway. However, for the assessment of the antagonist or agonist function of domain antibodies described herein, at least one of the following CD28 assays can be used.
  • activation of T cells is measured.
  • human CD3 positive T cells are stimulated with anti-CD3 plus transfected CHO cells expressing either CD80 or CD86. This results in proliferation of the T cells and is CD28 dependent as domain antibodies block the proliferation response.
  • induction of T cell proliferation and induction of cytokine secretion is measured.
  • the assay comprises stimulation of human CD3 positive T cells with anti-CD28 mAb 9.3 (Gibson, et al. (1996) J. Biol. Chem. , 271 : 7079-7083). This results in up-regulation of T cell receptor-mediated signaling and secretion of cytokines and is CD28-dependent, as mAb 9.3 blocks the proliferation response.
  • cytokines that may be measured include, but are not limited to, GM-CSF, IL-2, IL-3, IL- 4, IL-5, IL-6, IL-10, IL- 12 IL- 13, IL- 15, IL- 17, IL-21 , IL-22, IL-24, TGFp, TNF-a, TNF- ⁇ , IFN- ⁇ , lFN- ⁇ , IFN- ⁇ .
  • cytokines may be detected and/or measured according to the disclosure set forth herein.
  • an assay for CD28 activity may also include the assessment of CTLA4 activity.
  • a domain antibody according to the present disclosure does not inhibit the CTLA-4-mediated inhibition of T cell function, including inhibition of T cell receptor mediated signaling, inhibition of T cell proliferation, and inhibition of cytokine secretion.
  • domain antibodies set forth herein can possess multiple functions and activities, and therefore, may be assayed by multiple distinct assays.
  • domain antibodies have multiple defining characteristics (e.g., CD28 binding affinity, CDR domain identity, and amino acid sequence, among others), and therefore, each distinct domain antibody can be characterized in multiple ways and through multiple parameters.
  • characterization of each such domain antibody can therefore provide unique identifying characteristics for the domain antibody.
  • PEGylated domain antibodies which have increased half-life and in an aspect, also resistance to degradation without a loss in activity (e.g., binding affinity) relative to non-PEGylated domain antibodies.
  • domain antibodies according to this aspect can be coupled, using methods known in the art to polymer molecules (in an aspect, PEG) useful for achieving the increased half-life and degradation resistance properties encompassed herein.
  • Polymer moieties which can be utilized can be synthetic or naturally occurring and include, but are not limited to straight or branched chain polyalkylene, polyalkenylene or polyoxyalkylene polymers, or a branched or unbranched polysaccharide such as a homo- or heteropolysaccharide.
  • Examples of synthetic polymers which may be used include straight or branched chain poly(ethylene glycol) (PEG), poly(propylene glycol), or poly(vinyl alcohol) and derivatives or substituted forms thereof.
  • Useful substituted polymers include substituted PEG, including methoxy(polyethylene glycol).
  • Naturally occurring polymer moieties which may be used herein in addition to or in place of PEG include lactose, amylose, dextran, or glycogen, as well as derivatives thereof which would be recognized by one of skill in the art.
  • Derivatized forms of polymer molecules as set forth herein include, for example, derivatives which have additional moieties or reactive groups present therein to permit interaction with amino acid residues of the domain antibodies described herein.
  • Such derivatives include N-hydroxylsuccinimide (NHS) active esters, succinimidyl propionate polymers, and sulfhydryl-selective reactive agents such as maleimide, vinyl sulfone, and thiol.
  • NHS N-hydroxylsuccinimide
  • succinimidyl propionate polymers succinimidyl propionate polymers
  • sulfhydryl-selective reactive agents such as maleimide, vinyl sulfone, and thiol.
  • Derivatized polymers include, but are not limited to PEG polymers having the formulae: PEG-O-CH2CH2CH2-CO2-NHS; PEG- 0-CH 2 -NHS; PEG-0-CH 2 CH 2 -C0 2 -NHS; PEG-S-CH 2 CH 2 -CO-NHS; PEG-0 2 CNH- CH(R)-C0 2 -NHS; PEG-NHCO-CH 2 CH 2 -CO-NHS; and PEG-0-CH 2 -C0 2 -NHS; where R is (CH2)4)NHCC>2(mPEG).
  • PEG polymers useful as set forth herein may be linear molecules, or may be branched wherein multiple PEG moieties are present in a single polymer.
  • Useful PEG derivatives include, but are not limited to, mPEG-MAL, mPEG2- MAL, mPEG-(MAL) 2 , multi-arm PEG, mPEG-SPA, mPEG2-NHS, and mPEG2- (MAL) 2 , illustrated below:
  • the reactive group (e.g., MAL, NHS, SPA, VS, or Thiol) may be attached directly to the PEG polymer or may be attached to PEG via a linker molecule.
  • the size of polymers useful as set forth herein can be in the range of between about 500 Da to 60 kD, for example, between about 1000 Da and 60 kD, 10 kD and 60 kD, 20 kD and 60 kD, 30 kD and 40 kD, 40 kD and 60 kD, and up to between 50 kD and 60 kD.
  • the polymers used herein, particularly PEG can be straight chain polymers or can possess a branched conformation. Depending on the combination of molecular weight and conformation, the polymer molecules useful as set forth herein, when attached to a domain antibody, will yield a molecule having an average hydrodynamic size of between about 24 and 500 kD.
  • the hydrodynamic size of a polymer molecule used herein refers to the apparent size of a molecule (e.g., a protein molecule) based on the diffusion of the molecule through an aqueous solution.
  • the diffusion, or motion of a protein through solution can be processed to derive an apparent size of the protein, where the size is given by the Stokes radius or hydrodynamic radius of the protein particle.
  • the "hydrodynamic size" of a protein depends on both mass and shape (conformation), such that two proteins having the same molecular mass may have differing hydrodynamic sizes based on the overall conformation of the protein.
  • the hydrodynamic size of a PEG- linked domain antibody can be in the range of about 24 kD to 500 kD; 30 to 500 kD; 40 to 500 kD; 50 to 500 kD; 100 to 500 kD; 150 to 500 kD; 200 to 500 kD; 250 to 500 kD; 300 to 500 kD; 350 to 500 kD; 400 to 500 kD, and 450 to 500 kD.
  • the hydrodynamic size of a PEGylated domain antibody as described herein is about 30 to 40 kD; 70 to 80 kD or 200 to 300 kD.
  • the size of a polymer molecule attached to a domain antibody may thus be varied depending upon the desired application. For example, where the PEGylated domain antibody is intended to leave the circulation and enter into peripheral tissues, it is desirable to keep the size of the attached polymer low to facilitate extravazation from the blood stream. Alternatively, where it is desired to have the PEGylated domain antibody remain in the circulation for a longer period of time, a higher molecular weight polymer can be used (e.g., a 30, 40, or 60 kD polymer).
  • the polymer (PEG) molecules useful as set forth herein can be attached to domain antibodies using methods that are well known in the art.
  • the first step in the attachment of PEG or other polymer moieties to a domain antibody is the substitution of the hydroxyl end-groups of the PEG polymer by electrophile-containing functional groups.
  • PEG polymers are attached to either cysteine or lysine residues present in the domain antibody.
  • the cysteine and lysine residues can be naturally occurring, or can be engineered into the domain antibody molecule.
  • cysteine residues can be recombinantly engineered at the C-terminus of domain antibodies, or residues at specific solvent accessible locations in the domain antibody can be substituted with cysteine or lysine.
  • a PEG moiety is attached to a cysteine residue which is present in the hinge region at the C-terminus of a domain antibody.
  • a PEG moiety or other polymer is attached to a cysteine or lysine residue which is either naturally occurring at or engineered into the N-terminus of a domain antibody as set forth herein.
  • a PEG moiety or other polymer is attached to a domain antibody as set forth herein at a cysteine or lysine residue (either naturally occurring or engineered) which is at least 2 residues away from (e.g., internal to) the C- and/or N-terminus of the domain antibody.
  • the PEG polymer(s) is attached to one or more cysteine or lysine residues present in a framework region (FWs) and one or more heterologous CDRs of a domain antibody.
  • CDRs and framework regions e.g., CDR1 -CDR3 and FW1-FW4 are those regions of domain antibody as defined in the Kabat database of Sequences of Proteins of Immunological Interest (Kabat et al. (1991 ) Sequences of Immunological Interest, 5 th ed. U.S. Dept. Health & Human Services, Washington, D.C.).
  • a PEG polymer is linked to a cysteine or lysine residue in the VH
  • Cysteine and/or lysine residues of DP47 which may be linked to PEG disclosed herein include the cysteine at positions 22, or 96 and the lysine at positions 43, 65, 76, or 98 of SEQ ID NO:641.
  • Cysteine and/or lysine residues of DPK9 which may be linked to PEG disclosed herein include the cysteine residues at positions 23, or 88 and the lysine residues at positions 39, 42, 45, 103, or 107 of SEQ ID NO:643.
  • the DPK9 sequence of SEQ ID NO:643 is 95 amino acids in length; however, it is understood in the art that residues 103 and 107 are provided by the sequence encoded by the J gene segment, when fused to the DPK9 sequence.
  • specific cysteine or lysine residues may be linked to PEG in the VH canonical framework region DP38, or DP45.
  • solvent accessible sites in the domain antibody which are not naturally occurring cysteine or lysine residues may be mutated to a cysteine or lysine for attachment of a PEG polymer.
  • Solvent accessible residues in any given domain antibody can be determined using methods known in the art such as analysis of the crystal structure of the domain antibody.
  • V H dAb HEL4 (SEQ ID NO:399; a domain antibody that binds hen egg lysozyme)
  • the residues Gin- 13, Pro- 14, Gly- 15, Pro-41 , Gly-42, Lys-43, Asp-62, Lys-65, Arg-87, Ala- 88, Glu-89, Gin- 1 12, Leu- 1 15, Thr- 1 17, Ser- 1 19, and Ser-120 have been identified as being solvent accessible, and disclosed herein would be attractive candidates for mutation to cysteine or lysine residues for the attachment of a PEG polymer.
  • the model of the V k domain antibody (FIG.
  • a PEG polymer is linked to multiple solvent accessible cysteine or lysine residues, or to solvent accessible residues which have been mutated to a cysteine or lysine residue.
  • only one solvent accessible residue is linked to PEG, either where the particular domain antibody only possesses one solvent accessible cysteine or lysine (or residue modified to a cysteine or lysine) or where a particular solvent accessible residue is selected from among several such residues for PEGylation.
  • V k model antibody Primary amino acid sequence of V k model antibody:
  • PEG attachment schemes disclosed herein are provided by the company Nektar (SanCarlos, CA).
  • Nektar SanCarlos, CA
  • active esters of PEG polymers which have been derivatized with N-hydroxylsuccinimide, such as succinimidyl propionate may be used.
  • PEG polymers which have been derivatized with sulfhydryl-selective reagents such as maleimide, vinyl sulfone, or thiols may be used.
  • PEG derivatives which may be used as disclosed herein to generate PEGylated antibodies can be found in the Nektar Catalog (available on the world wide web at nektar.com).
  • PEG derivatives disclosed herein include, but are not limited to PEG- succinimidyl succinate, urethane linked PEG, PEG phenylcarbonate, PEG succinimidyl carbonate, PEG-carboxymethyl azide, dimethylmaleic anhydride PEG, PEG
  • a domain antibody composition comprises a domain antibody and PEG polymer wherein the ratio of PEG polymer to domain antibody is a molar ratio of at least 0.25: 1. In a further embodiment, the molar ratio of PEG polymer to domain antibody is 0.33 : 1 or greater. In a still further embodiment the molar ratio of PEG polymer to domain antibody is 0.5: 1 or greater.
  • ligands disclosed herein or libraries for use herein can be constructed by varying the binding site of the molecule in order to generate a repertoire with structural and/or functional diversity. This means that variants are generated such that they possess sufficient diversity in their structure and/or in their function so that they are capable of providing a range of activities.
  • the desired diversity is typically generated by varying the selected molecule at one or more positions.
  • the positions to be changed can be chosen at random or are in an aspect, selected.
  • the variation can then be achieved either by randomization, during which the resident amino acid is replaced by any amino acid or analogue thereof, natural or synthetic, producing a very large number of variants or by replacing the resident amino acid with one or more of a defined subset of amino acids, producing a more limited number of variants.
  • Various methods have been reported for introducing such diversity. Error-prone PCR (Hawkins et al. (1992) J. Mol. Biol, 226: 889), chemical mutagenesis (Deng et al. (1994) J. Biol.
  • loop randomization has the potential to create approximately more than 10 15 structures for H3 alone and a similarly large number of variants for the other five loops, it is not feasible using current transformation technology or even by using cell free systems to produce a library representing all possible combinations.
  • 6 x 10 10 different antibodies which is only a fraction of the potential diversity for a library of this design, were generated (Griffiths et al. ⁇ 99 ) supra).
  • the binding site for the target is most often the antigen binding site.
  • libraries of or for the assembly of antibody ligands in which only those residues in the antigen binding site are varied.
  • CDRl Determining Region
  • antibody diversity is the result of two processes: somatic recombination of germline V, D, and J gene segments to create a naive primary repertoire (so called germline and junctional diversity) and somatic hypermutation of the resulting rearranged V genes.
  • somatic hypermutation spreads diversity to regions at the periphery of the antigen binding site that are highly conserved in the primary repertoire (see Tomlinson et al. (1996) J. Mol. Biol , 256: 813).
  • This complementarity has probably evolved as an efficient strategy for searching sequence space and, although apparently unique to antibodies, it can easily be applied to other polypeptide repertoires.
  • the residues which are varied are a subset of those that form the binding site for the target. Different (including overlapping) subsets of residues in the target binding site are diversified at different stages during selection, if desired.
  • an initial 'naive' repertoire is created where some, but not all, of the residues in the antigen binding site are diversified.
  • the term "naive” refers to antibody molecules that have no predetermined target. These molecules resemble those which are encoded by the immunoglobulin genes of an individual who has not undergone immune diversification, as is the case with fetal and newborn individuals, whose immune systems have not yet been challenged by a wide variety of antigenic stimuli.
  • This repertoire is then selected against a range of antigens or epitopes. If required, further diversity can then be introduced outside the region diversified in the initial repertoire. This matured repertoire can be selected for modified function, specificity or affinity.
  • naive repertoires of binding domains for the construction of ligands or a na ' ive library of ligands, in which some or all of the residues in the antigen binding site are varied.
  • the "primary" library mimics the natural primary repertoire, with diversity restricted to residues at the centre of the antigen binding site that are diverse in the germline V gene segments (germline diversity) or diversified during the recombination process (junctional diversity).
  • residues which are diversified include, but are not limited to, H50, H52, H52a, H53, H55, H56, H58, H95, H96, H97, H98, L50, L53, L91 , L92, L93, L94, and L96.
  • diversity is restricted to residues that are diversified during the recombination process (junctional diversity) or are highly somatically mutated).
  • residues which are diversified include, but are not limited to: H31 , H33, H35, H95, H96, H97, H98, L30, L31 , L32, L34, and L96.
  • a feature of side-chain diversity in the antigen binding site of human antibodies is a pronounced bias which favours certain amino acid residues. If the amino acid composition of the ten most diverse positions in each of the V H , V K , and Vj, regions are summed, more than 76% of the side-chain diversity comes from only seven different residues, these being, serine (24%), tyrosine (14%), asparagine (1 1 %), glycine (9%), alanine (7%), aspartate (6%), and threonine (6%).
  • This bias towards hydrophilic residues and small residues which can provide main-chain flexibility probably reflects the evolution of surfaces which are predisposed to binding a wide range of antigens or epitopes and may help to explain the required promiscuity of antibodies in the primary repertoire.
  • the distribution of amino acids at the positions to be varied mimics that seen in the antigen binding site of antibodies.
  • Such bias in the substitution of amino acids that permits selection of certain polypeptides (not just domain antibodies) against a range of target antigens is easily applied to any polypeptide repertoire.
  • There are various methods for biasing the amino acid distribution at the position to be varied including the use of trinucleotide mutagenesis, see WO 97/08320), of which one advantageous method, due to ease of synthesis, is the use of conventional degenerate codons.
  • (AGT)(AGC)T, (AGT)(AGC)C, and (AGT)(AGC)(CT) are those closest to the desired amino acid profile: they encode 22% serine and 1 1% tyrosine, asparagine, glycine, alanine, aspartate, threonine, and cysteine, and in an aspect, these codons are used in the construction of a library.
  • dual-specific ligands comprising domain antibodies which each have respective specificities; that is, the first and the second epitopes bound by the dual-specific ligand are, in an aspect, different or are two copies of the same epitopes, the epitopes being bound by a respective variable domain.
  • a "dual-specific ligand” refers to a ligand comprising a first domain antibody and a second domain antibody as herein defined, wherein the variable regions are capable of binding to two different antigens or two epitopes on the same antigen which are not normally bound by a monospecific immunoglobulin.
  • a "dual-specific ligand” refers to a ligand comprising a domain antibody and an immunoglobulin variable domain as herein defined, wherein the variable regions are capable of binding to two different antigens or two epitopes on the same antigen which are not normally bound by a monospecific immunoglobulin.
  • the two epitopes may be on the same hapten, but are not the same epitope or sufficiently adjacent to be bound by a
  • Dual specific ligands disclosed herein are composed of variable domains which have different specificities, and do not contain mutually complementary variable domain pairs which have the same specificity.
  • Dual-specific ligands may be, or be part of, polypeptides, proteins, or nucleic acids, which may be naturally occurring or synthetic.
  • the dual- or multispecific ligand may comprise a first domain capable of binding a target molecule, and a second domain capable of binding a molecule or group which extends the half-life of the ligand.
  • the molecule or group may be a bulky agent, such as HSA or a cell matrix protein.
  • the phrase "molecule or group which extends the half-life of a ligand" refers to a molecule or chemical group which, when bound by a dual-specific ligand as described herein increases the in vivo half-life of such dual specific ligand when administered to an animal, relative to a ligand that does not bind that molecule or group.
  • the closed conformation multispecific ligand may be capable of binding the target molecule only on displacement of the half-life enhancing molecule or group.
  • a closed conformation multispecific ligand is maintained in circulation in the bloodstream of a subject by a bulky molecule such as HSA.
  • HSA bulky molecule
  • variable domains are derived from an antibody directed against the first and/or second antigen or epitope.
  • variable domains are derived from a repertoire of single variable antibody domains.
  • the repertoire is a repertoire that is not created in an animal or a synthetic repertoire.
  • the single variable domains are not isolated (at least in part) by animal immunization. Thus, the single domains can be isolated from a na ' ive library.
  • a multi-specific l igand comprising a first epitope binding domain having a first epitope binding specificity and a non- complementary second epitope binding domain having a second epitope binding specificity.
  • the first and second binding specificities may be the same or different.
  • a closed conformation multi-specific ligand comprising a first epitope binding domain having a first epitope binding specificity and a non-complementary second epitope binding domain having a second epitope binding specificity wherein the first and second binding specificities are capable of competing for epitope binding such that the closed conformation multi-specific ligand cannot bind both epitopes simultaneously.
  • Ligands according to any aspect as disclosed herein, as well as domain antibody monomers useful in constructing such ligands may advantageously dissociate from their cognate target(s) with a K d of about 300 nM to l p M or 5 pM (ie, 3 x 10 ⁇ 7 to 5 x 10 ",2 M), in an aspect, about 50 nM to20 pM, or 5 nM to 200 pM or 1 nM to 100 pM, 1 x 10 "7 M or less, 1 x 10 "8 M or less, 1 x 10 "9 M or less, 1 x 10 "i0 M or less, 1 x 10 "u M or less; and/or a K 0 ff rate constant of about 5 x 10 "1 to 1 x 10 "7 S “1 , in an aspect, about ] x 10 "2 to 1 x 10 "6 S “1 , or 5 x 10 "3 to 1 x 10 "5 S “1 , or 5 10 "
  • a domain antibody monomer is provided (or dual specific ligand comprising such a domain antibody) that binds to serum albumin (SA) with a Ka of 1 nM to 500 ⁇ (i.e., 1 x 10 "9 M to 5 x 10 ⁇ 4 M), in an aspect, 100 nM to 10 ⁇ .
  • SA serum albumin
  • the affinity (e.g. K ⁇ j and/or K 0ff as measured by surface plasmon resonance, e.g. using BiaCore) of the second dAb for its target is from 1 to 100,000 times (in an aspect, 100 to 100,000, in a further aspect, 1000 to 100000, or
  • the affinity of the first domain antibody for SA 10000 to 100000 times ( 10000 to 100000 times) the affinity of the first domain antibody for SA.
  • the first domain antibody binds SA with an affinity of approximately 10 ⁇
  • the second domain antibody binds its target with an affinity of about 100 pM.
  • the serum albumin is human serum albumin (HSA).
  • the first domain antibody (or a domain antibody monomer) binds SA (eg, HSA) with a K d of approximately about 50 nM, in an aspect, about 70 nM, and in another aspect, about 100, 150, or 200 nM.
  • SA eg, HSA
  • dimers, trimers and polymers of the aforementioned domain antibody monomers are also provided.
  • Ligands disclosed herein can be linked to an antibody Fc region, comprising one or both of C H 2 and (3 ⁇ 43 domains, and optionally a hinge region.
  • vectors encoding ligands linked as a single nucleotide sequence to an Fc region may be used to prepare such polypeptides.
  • ligands disclosed herein may be free of an Fc domain.
  • nucleic acid molecules encoding at least a dual- or multispecific ligand as herein defined.
  • the ligand is a closed conformation ligand. In another embodiment, it is an open conformation ligand.
  • the multispecific ligand may be encoded on a single nucleic acid molecule; alternatively, each epitope binding domain may be encoded by a separate nucleic acid molecule.
  • the domains may be expressed as a fusion polypeptide, or may be separately expressed and subsequently linked together, for example using chemical linking agents. Ligands expressed from separate nucleic acids will be linked together by appropriate means.
  • the nucleic acid may further encode a signal sequence for export of the polypeptides from a host cell upon expression and may be fused with a surface component of a filamentous bacteriophage particle (or other component of a selection display system) upon expression.
  • Leader sequences which may be used in bacterial expression and/or phage or phagemid display, include pelB, stll, ompA, phoA, bla, ompT and pelA.
  • the second configuration as disclosed herein includes a vector comprising nucleic acid.
  • a host cell transfected with a vector may be configured to produce, for example on the surface of a bacteriophage particle, epitope binding domains for selection. This allows selection of displayed domains and thus selection of "multispecific ligands" using the method as disclosed herein.
  • an antibody is herein defined as an antibody or fragment (Fab, Fv, disulfide linked Fv, scFv, diabody) which comprises at least one heavy and a light chain variable domain, at least two heavy chain variable domains or at least two light chain variable domains. It may be at least partly derived from any species naturally producing an antibody, or created by recombinant DNA technology; whether isolated from serum, B-cells, hybridomas, transfectomas, yeast or bacteria).
  • the dual-specific ligand comprises at least one single heavy chain variable domain of an antibody and one single light chain variable domain of an antibody, or two single heavy or light chain variable domains.
  • the ligand may comprise a VH/V l pair, a pair of VH domains or a pair of VL domains.
  • the first and the second variable domains of such a ligand may be on the same polypeptide chain. Alternatively they may be on separate polypeptide chains. In the case that they are on the same polypeptide chain they may be linked by a linker, which may be a peptide sequence, as described above.
  • the first and second variable domains may be covalently or non-covalently associated.
  • the covalent bonds may be disulphide bonds.
  • variable domains are selected from V-gene repertoires selected for instance using phage display technology as herein described, then these variable domains comprise a universal framework region, such that is they may be recognized by a specific generic ligand as herein defined.
  • the use of universal frameworks, generic ligands, and the like is described in WO 99/20749.
  • V-gene repertoires are used variation in polypeptide sequence is, in an aspect, located within the structural loops of the variable domains.
  • the polypeptide sequences of either variable domain may be altered by DNA shuffling or by mutation in order to enhance the interaction of each variable domain with its complementary pair.
  • DNA shuffling is known in the art and taught, for example, by Stemmer (1994) Nature 370: 389-391 and U.S. Patent No. 6,297,053, both of which are incorporated herein by reference.
  • Other methods of mutagenesis are well known to those of skill in the art.
  • the 'dual-specific ligand' is a single chain Fv fragment. In an alternative embodiment, the 'dual-specific ligand' consists of a Fab format.
  • a further aspect disclosed herein provides nucleic acid encoding at least a 'dual- specific ligand' as herein defined.
  • both antigens or epitopes may bind simultaneously to the same antibody molecule. Alternatively, they may compete for binding to the same antibody molecule.
  • both variable domains of a dual specific ligand are able to independently bind their target epitopes. Where the domains compete, the one variable domain is capable of binding its target, but not at the same time as the other variable domain binds its cognate target; or the first variable domain is capable of binding its target, but not at the same time as the second variable domain binds its cognate target.
  • variable regions may be derived from antibodies directed against target antigens or epitopes. Alternatively they may be derived from a repertoire of single antibody domains such as those expressed on the surface of filamentous bacteriophage. Selection may be performed as described below.
  • nucleic acid molecules and vector constructs required for the performance as disclosed herein may be constructed and manipulated as set forth in standard laboratory manuals, such as Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, USA.
  • nucleic acids useful as disclosed herein is typically carried out in recombinant vectors.
  • a further aspect disclosed herein provides a vector comprising nucleic acid encoding at least a 'dual-specific ligand' as herein defined.
  • vector refers to a discrete element that is used to introduce heterologous DNA into cells for the expression and/or replication thereof.
  • Methods by which to select or construct and, subsequently, use such vectors are well known to one of ordinary skill in the art. Numerous vectors are publicly available, including bacterial plasmids, bacteriophage, artificial chromosomes, and episomal vectors. Such vectors may be used for simple cloning and mutagenesis; alternatively gene expression vector is employed.
  • a vector of use as disclosed herein may be selected to accommodate a polypeptide coding sequence of a desired size, typically from 0.25 kilobase (kb) to 40 kb or more in length.
  • a suitable host cell is transformed with the vector after in vitro cloning manipulations.
  • Each vector contains various functional components, which generally include a cloning (or "polylinker") site, an origin of replication, and at least one selectable marker gene. If given vector is an expression vector, it additionally possesses one or more of the following: enhancer element, promoter, transcription termination, and signal sequences, each positioned in the vicinity of the cloning site, such that they are operatively linked to the gene encoding a ligand as disclosed herein.
  • Both cloning and expression vectors generally contain nucleic acid sequences that enable the vector to replicate in one or more selected host cells.
  • this sequence is one that enables the vector to replicate independently of the host chromosomal DNA and includes origins of replication or autonomously replicating sequences.
  • origins of replication or autonomously replicating sequences are well known for a variety of bacteria, yeast, and viruses.
  • the origin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria, the 2 micron plasmid origin is suitable for yeast, and various viral origins (e.g. SV 40, adenovirus) are useful for cloning vectors in mammalian cells.
  • the origin of replication is not needed for mammalian expression vectors unless these are used in mammalian cells able to replicate high levels of DNA, such as COS cells.
  • a cloning or expression vector may contain a selection gene also referred to as selectable marker.
  • This gene encodes a protein necessary for the survival or growth of transformed host cells grown in a selective culture medium. Host cells not transformed with the vector containing the selection gene will therefore not survive in the culture medium.
  • Typical selection genes encode proteins that confer resistance to antibiotics and other toxins, e.g. ampicillin, neomycin, methotrexate or tetracycline, complement auxotrophic deficiencies, or supply critical nutrients not available in the growth media.
  • Domains useful as disclosed herein, once selected using methods exemplified above, may be combined by a variety of methods known in the art, including covalent and non-covalent methods.
  • Methods include the use of polypeptide linkers, as described, for example, in connection with scFv molecules (Bird et al, (1988) Science 242: 423-426). Discussion of suitable linkers is provided in Bird et al, Science 242: 423-426; Hudson el al , (1999) J. Immunol. Methods 231 : 177- 189; Hudson et al, Proc. Nat 7 Acad. Sci. USA 85 : 5879- 5883. Linkers are in an aspect, flexible, allowing the two single domains to interact.
  • the linkers used in diabodies, which are less flexible, may also be employed (Holliger et al , (1993) PNAS (USA) 90: 6444-6448).
  • the linker employed is not an immunoglobulin hinge region.
  • Variable domains may be combined using methods other than linkers. For example, the use of disulphide bridges, provided through naturally-occurring or engineered cysteine residues, may be exploited to stabilize V H "VH > VL"VL or H-VL dimers (Reiter et al , (1994) Protein Eng. 7: 697-704) or by remodeling the interface between the variable domains to improve the "fit" and thus the stability of interaction (Ridgeway et al, (1996) Protein Eng. 7: 617-621 ; Zhu et al, (1997) Protein Science 6: 781-788).
  • variable domains of immunoglobulins and in particular antibody VH domains, may be employed as appropriate.
  • dual specific ligands can be in "closed” conformations in solution.
  • a “closed” configuration is that in which the two domains (for example VH and VL) are present in associated form, such as that of an associated VH-VL pair which forms an antibody binding site.
  • scFv may be in a closed conformation, depending on the arrangement of the linker used to link the VH and VL domains. If this is sufficiently flexible to allow the domains to associate, or rigidly holds them in the associated position, it is likely that the domains will adopt a closed conformation.
  • VH domain pairs and VL domain pairs may exist in a closed conformation. Generally, this will be a function of close association of the domains, such as by a rigid linker, in the ligand molecule. Ligands in a closed conformation will be unable to bind both the molecule which increases the half-life of the ligand and a second target molecule. Thus, the ligand will typically only bind the second target molecule on dissociation from the molecule which increases the half-life of the ligand. Moreover, the construction of VH/VH, V L /VL or VH VL dimers without linkers provides for competition between the domains.
  • Ligands as disclosed herein may moreover be in an open conformation. In such a conformation, the ligands will be able to simultaneously bind both the molecule which increases the half-life of the ligand and the second target molecule.
  • variable domains in an open configuration are (in the case of V H -V L pairs) held far enough apart for the domains not to interact and form an antibody binding site and not to compete for binding to their respective epitopes.
  • V H /V H or V L /V L dimers the domains are not forced together by rigid linkers. Naturally, such domain pairings will not compete for antigen binding or form an antibody binding site.
  • the open fonn of the dual specific ligand may thus exist in equilibrium with the closed form in solution, it is envisaged that the equilibrium will favor the closed form; moreover, the open form can be sequestered by target binding into a closed conformation.
  • certain dual specific ligands disclosed herein are present in an equilibrium between two (open and closed) conformations.
  • Dual specific ligands disclosed herein may be modified in order to favor an open or closed conformation. For example, stabilization of V H -V L interactions with disulphide bonds stabilizes the closed conformation.
  • linkers used to join the domains may be constructed such that the open from is favored; for example, the linkers may sterically hinder the association of the domains, such as by incorporation of large amino acid residues in opportune locations, or the designing of a suitable rigid structure which will keep the domains physically spaced apart. 6.2.3. Characterization of the Dual-Specific Ligand.
  • binding of the dual-specific ligand to its specific antigens or epitopes can be tested by methods which will be familiar to those skilled in the art and include ELISA. In one embodiment, binding is tested using monoclonal phage ELI SA.
  • Phage ELISA may be performed according to any suitable procedure: an exemplary protocol is set forth below.
  • phage produced at each round of selection can be screened for binding by ELISA to the selected antigen or epitope, to identify "polyclonal" phage antibodies. Phage from single infected bacterial colonies from these populations can then be screened by ELISA to identify "monoclonal” phage antibodies. It is also desirable to screen soluble antibody fragments for binding to antigen or epitope, and this can also be undertaken by ELISA using reagents, for example, against a C- or IM-terminal tag (see for example Winter et al. (1994) Ann. Rev. Immunology 12, 433-55 and references cited therein.
  • the diversity of the selected phage monoclonal antibodies may also be assessed by gel electrophoresis of PCR products (Marks et al. ( 1991) supra; Nissim et al. (1994) supra), probing (Tomlinson et al , ( 1992) J. Mol. Biol. 227, 776) or by sequencing of the vector DNA.
  • the PEGylated domain antibodies as described herein may confer a distinct advantage over non-PEGylated domain antibodies, in that the PEGylated antibody molecules will have a greatly prolonged in vivo half-life. It will be understood, in the context of the present disclosure, that a particular half-life of any composition may be either increased or decreased by the route of administration of the composition to a patient.
  • the increased half-life of the molecules described herein is conferred by the increased hydrodynamic size of the domain antibody resulting from the attachment of PEG polymer(s). More specifically, it is believed that two parameters play an important role in determining the serum half-life of PEGylated domain antibodies.
  • the first criterion is the nature and size of the PEG attachment, i.e., if the polymer used is simply a linear chain or a branched/forked chain, wherein the branched/forked chain gives rise to a longer half-life.
  • the second is the location of the PEG moiety or moieties on the domain antibody in the final format and how many "free" unmodified PEG arms the molecule has.
  • the resulting hydrodynamic size of the PEGylated domain antibody reflects the serum half-life of the molecule. Accordingly, the larger the hydrodynamic size of the PEGylated molecule, the greater the serum half-life.
  • a domain antibody as described herein is stabilized in vivo by fusion with a moiety, such as PEG, that increases the hydrodynamic size of the domain antibody.
  • a moiety such as PEG
  • the half-life of a PEGylated domain antibody as described herein is increased by about 10%, 20%, 30%, 40%, 50%, or more relative to a non-PEGylated dAb (wherein the domain antibody of the PEGylated domain antibody and non-PEGylated domain antibody are the same).
  • Increases in the range of 2x, 3x, 4x, 5x, 7x, l Ox, 20x, 30x, 40x, and up to 50x or more of the half-life are possible.
  • increases in the range of up to 30x, 40x, 50x, 60x, 70x, 80x, 90x, l OOx, or 150x of the half-life are possible.
  • Half lives (t1 ⁇ 2-a and ⁇ 1 ⁇ 2- ⁇ ) and AUC can be determined from a curve of serum concentration of ligand against time.
  • the WinNonlin analysis package (available from Pharsight Corp., Mountain View, CA 94040, USA) can be used, for example, to model the curve.
  • a first phase the alpha phase
  • a second phase (beta phase) is the terminal phase when the ligand has been distributed and the serum concentration is decreasing as the ligand is cleared from the patient.
  • the "ta half-life” is the half-life of the first phase and the " ⁇ half-life” is the half-life of the second phase.
  • a domain antibody-containing composition e.g., a domain antibody-effector group composition is contemplated having a ta half-life in the range of about 0.25 hours to 6 hours or more.
  • the lower end of the range is about 30 minutes, 45 minutes, 1 hour, 1.3 hours, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 10 hours, 1 1 hours, or 12 hours.
  • a domain antibody-containing composition will have a ta half-life in the range of up to and including 12 hours.
  • the upper end of the range is about 1 1, 10, 9, 8, 7, 6, or 5 hours.
  • An example of a suitable range is about 1.3 to 6 hours, 2 to 5 hours, or 3 to 4 hours.
  • a domain antibody-containing composition comprising a ligand has a tp half-life in the range of about 1 - 170 hours or more.
  • the lower end of the range is about 2.5 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 1 1 hours, or 12 hours.
  • a domain antibody-containing composition, e.g. a dAb-effector group composition has a tp half-life in the range of up to and including 21 days.
  • the upper end of the range is about 12 hours, 24 hours, 2 days, 3 days, 5 days, 10 days, 15 days, or 20 days.
  • a dAb containing composition disclosed herein will have a tp half-life in the range about 2-100 hours, 4-80 hours, and 10-40 hours. In a further embodiment, it will be in the range of about 12-48 hours. In a further embodiment still, it will be in the range of about 12-26 hours.
  • a domain antibody-containing composition comprising a ligand having a half-life in the range of 1 -170 hours or more. In one embodiment, the lower end of the range is about 1.3 hours, 2.5 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 1 1 hours, or 12 hours.
  • a domain antibody-containing composition e.g.
  • a dAb-effector group composition has a half-life in the range of up to and including 21 days. In one embodiment, the upper end of the range is about 12 hours, 24 hours, 2 days, 3 days, 5 days, 10 days, 15 days, or 20 days.
  • a domain antibody-containing composition comprising a ligand has an AUC value (area under the curve) in the range of 1 mg-min/ml or more.
  • the lower end of the range is about 5, 10, 15, 20, 30, 100, 200, or 300 mg min/ml.
  • a ligand or composition disclosed herein has an AUC in the range of up to about 600 mg min/ml.
  • the upper end of the range is about 500, 400, 300, 200, 150, 100, 75, or 50 mg-min/ml.
  • Exemplary ligands disclosed herein will have an AUC in the range selected from the group consisting of the following: about 15 to 150 mg min/ml, 15 to 100 mg-min/ml, 15 to 75 mg-min/ml, and 15 to 50 mg- .min/ml.
  • the ligands disclosed herein are capable of binding to one or more molecules which can increase the half-life of the ligand in vivo.
  • molecules are polypeptides which occur naturally in vivo and which resist degradation or removal by endogenous mechanisms which remove unwanted material from the organism.
  • the molecule which increases the half-life in the organism may be selected from the following:
  • Proteins from the extracellular matrix for example collagen, laminins, integrins, and fibronectin.
  • Collagens are the major proteins of the extracellular matrix.
  • about 15 types of collagen molecules are currently known, found in different parts of the body, e.g. type I collagen (accounting for 90% of body collagen) found in bone, skin, tendon, ligaments, cornea, internal organs, or type II collagen found in cartilage, invertebral disc, notochord, vitreous humour of the eye.
  • Plasma proteins such as fibrin, a-2
  • Plasminogen is the inactive precursor of the trypsin-like serine protease plasmin. It is normally found circulating through the blood stream. When plasminogen becomes activated and is converted to plasmin, it unfolds a potent enzymatic domain that dissolves the fibrinogen fibers that entangle the blood cells in a blood clot. This is called fibrinolysis.
  • Immune system proteins such as IgE, IgG, and IgM.
  • Transport proteins such as retinol binding protein, a- 1 microglobulin.
  • Defensins such as beta-defensin 1 , neutrophil defensins 1 , 2, and 3.
  • Proteins found at the blood brain barrier or in neural tissues such as melanocortin receptor, myelin, ascorbate transporter.
  • Transferrin receptor specific ligand-neuropharmaceutical agent fusion proteins see U.S. Patent No. 5,977,307; brain capillary endothelial cell receptor, transferrin, transferrin receptor, insulin, insulin-like growth factor 1 (IGF 1 ) receptor, insulin-like growth factor 2 (IGF 2) receptor, insulin receptor.
  • IGF 1 insulin-like growth factor 1
  • IGF 2 insulin-like growth factor 2
  • Proteins localised to the kidney such as polycystin, type IV collagen, organic anion transporter Kl , Heymann's antigen.
  • Proteins localised to the lung such as secretory component (binds IgA).
  • HSP 27 Proteins localised to the heart, for example HSP 27. This is associated with dilated cardiomyopathy.
  • Proteins localised to the skin for example keratin.
  • Bone specific proteins such as bone morphogenic proteins (BMPs), which are a subset of the transforming growth factor ⁇ superfamily that demonstrate osteogenic activity. Examples include BMP-2, -4, -5, -6, -7 (also referred to as osteogenic protein (OP-1 ) and -8 (OP-2).
  • BMP-2, -4, -5, -6, -7 also referred to as osteogenic protein (OP-1 ) and -8 (OP-2).
  • Tumour specific proteins including human trophoblast antigen, herceptin receptor, oestrogen receptor, cathepsins (e.g. cathepsin B) (found in liver and spleen).
  • Disease-specific proteins such as antigens expressed only on activated T cells: including LAG-3 (lymphocyte activation gene), osteoprotegerin ligand (OPGL) (see Nature 402, 304-309; 1999); OX40 (a member of the TNF receptor family, expressed on activated T cells and the only co-stimulatory T cell molecule known to be specifically up-regulated in human T cell leukemia virus type-I (HTLV-I)- producing cells.) (see J. Immunol.
  • metalloproteases associated with arthritis/cancers
  • metalloproteases including CG6512 Drosophila, human paraplegin, human FtsH, human AFG3L2, murine ftsH
  • angiogenic growth factors including acidic fibroblast growth factor (FGF-1), basic fibroblast growth factor (FGF-2), vascular endothelial growth factor / vascular permeability factor (VEGF/VPF), transforming growth factor-a (TGF a), tumor necrosis factor-alpha (TNF-a), angiogenin, interleukin-3 (1L-3), interleukin-8 (IL-8), platelet-derived endothelial growth factor (PD-ECGF), placental growth factor (P1GF), midkine platelet-derived growth factor-BB (PDGF), fractalkine.
  • FGF-1 acidic fibroblast growth factor
  • FGF-2 basic fibroblast growth factor
  • VEGF/VPF vascular endothelial growth factor / vascular permeability factor
  • HSPs Stress proteins
  • HSPs Stress proteins
  • a dual specific which binds to extracellular HSP can be localized to a disease site.
  • Proteins involved in Fc transport such as:
  • the Brambell receptor also known as FcRB.
  • FcRB The Brambell receptor
  • the functions include the transport of IgG from mother to child across the placenta and the protection of IgG from degradation thereby prolonging its serum half- life of IgG. It is thought that the receptor recycles IgG from endosome (see Holliger et al, (1997) Nat. Biotechnol. 15: 632-6).
  • Other proteins involved in Fc transport include the neonatal Fc receptor (FcRn) described in Gastinel et al. (1992) PNAS 89: 638; and Roopenian et al. (2003) ./. Immunol. 170: 3528.
  • Ligands disclosed herein may be designed to be specific for the above targets without requiring any increase in or increasing half-life in vivo.
  • ligands disclosed herein can be specific for targets selected from the foregoing which are tissue-specific, thereby enabling tissue-specific targeting of the dual specific ligand, or a domain antibody that binds a tissue-specific therapeutically relevant target, irrespective of any increase in half-life, although this may result.
  • targets selected from the foregoing which are tissue-specific, thereby enabling tissue-specific targeting of the dual specific ligand, or a domain antibody that binds a tissue-specific therapeutically relevant target, irrespective of any increase in half-life, although this may result.
  • the ligand or domain antibody targets kidney or liver, this may redirect the ligand or domain antibody to an alternative clearance pathway in vivo (for example, the ligand may be directed away from liver clearance to kidney clearance).
  • Polypeptides useful for increasing half-life include, but are not limited to those shown in Annex I.
  • PEGylated domain antibodies and domain antibody multimers described herein possess increased stability to the action of proteases. In the presence of pepsin many domain antibodies are totally degraded at pH 2 because the protein is unfolded under the acid conditions, thus making the protein more accessible to the protease enzyme.
  • PEGylated domain antibody molecules including domain antibody multimers, wherein it is believed that the PEG polymer provides protection of the polypeptide backbone due the physical coverage of the backbone by the PEG polymer, thereby preventing the protease from gaining access to the polypeptide backbone and cleaving it.
  • a PEGylated domain antibody having a higher hydrodynamic size (e.g., 200 to 500 kD) is generated as disclosed herein, because the larger hydrodynamic size will confirm a greater level of protection from protease degradation than a PEGylated domain antibody having a lower hydrodynamic size.
  • a PEG- or other polymer-linked antibody single variable domain monomer or multimer is degraded by no more than 10% when exposed to one or more of pepsin, trypsin, elastase, chymotrypsin, or carboxypeptidase, wherein if the protease is pepsin then exposure is carried out at pH 2.0 for 30 minutes, and if the protease is one or more of trypsin, elastase, chymotrypsin, or carboxypeptidase, then exposure is carried out at pH 8.0 for 30 minutes.
  • a PEG- or other polymer-linked domain antibody monomer or miiltimer is degraded by no more than 10% when exposed to pepsin at pH 2.0 for 30 minutes, in an aspect, no more than 5%, and in another aspect, not degraded at all.
  • a PEG- or other polymer- linked domain antibody miiltimer e.g., hetero- or homodimer, trimer, tetramer, octamer, etc.
  • a PEG- or other polymer- linked domain antibody miiltimer e.g., hetero- or homodimer, trimer, tetramer, octamer, etc.
  • a PEG- or other polymer-linked domain antibody monomer or multimer is degraded by no more than 10% when exposed to trypsin, elastase, chymotrypsin, or carboxypeptidase at pH 8.0 for 30 minutes, in an aspect, no more than 5%, and in a further aspect, not degraded at all.
  • a PEG- or other polymer-linked domain antibody multimer (e.g., hetero- or homodimer, trimer, tetramer, octamer, etc.) disclosed herein is degraded by less than 5%, and is, in an aspect, not degraded at all in the presence of trypsin, elastase, chymotrypsin, or carboxypeptidase at pH 8.0 for 30 minutes.
  • the relative ratios of protease : PEG-domain antibody may be altered as disclosed herein to achieve the desired level of degradation as described above.
  • the ratio of protease to PEG-domain antibody may be from about 1 :30, to about 10:40, to about 20:50, to about 30:50, about 40:50, about 50:50, about 50:40, about 50:30, about 50:20, about 50: 10, about 50: 1 , about 40: 1, and about 30: 1.
  • a method for decreasing the degradation of domain antibody comprising linking a domain antibody monomer or multimer to a PEG polymer according to any of the embodiments described herein.
  • the domain antibody is degraded by no more than 10%> in the presence of pepsin at pH 2.0 for 30 minutes.
  • a PEG-linked dAb multimer is degraded by no more than 5%, and in an aspect, not degraded at all in the presence of pepsin at pH 2.0 for 30 minutes.
  • the domain antibody is degraded by no more than 10% when exposed to trypsin, elastase, chymotrypsin, or carboxypeptidase at pH 8.0 for 30 minutes, in an aspect, no more than 5%, and in another aspect, not degraded at all.
  • Degradation of PEG-linked domain antibody monomers and multimers as set forth herein may be measured using methods which are well known to those of skill in the art. For example, following incubation of a PEG-linked domain antibody with pepsin at pH 2.0 for 30 minutes, or with trypsin, elastase, chymotrypsin, or carboxypeptidase at pH 8.0 for 30 minutes, the domain antibody samples may be analyzed by gel filtration, wherein degradation of the domain antibody monomer or multimer is evidenced by a gel band of a smaller molecular weight than an un-degraded (i.e., control domain antibody not treated with pepsin, trypsin, chymotrypsin, elastase, or carboxypeptidase) domain antibody.
  • un-degraded i.e., control domain antibody not treated with pepsin, trypsin, chymotrypsin, elastase, or carboxypeptidase
  • Molecular weight of the domain antibody bands on the gel may be determined by comparing the migration of the band with the migration of a molecular weight ladder. Other methods of measuring protein degradation are known in the art and may be adapted to evaluate the PEG-linked domain antibody monomers and multimers as disclosed herein.
  • Domain antibodies as described herein are useful for antagonizing the activity of
  • domain antibodies as described herein can be used to treat a patient having a condition, disease or disorder mediated in whole or in part by CD28 activity.
  • Domain antibodies as described herein are useful for the treatment or prevention of diseases or disorders in which inappropriate activation of a CD28 -mediated pathway is involved. Domain antibodies as described herein are also useful for the treatment, prevention, or alleviation of symptoms of diseases or disorders in which inappropriate activation of a CD28-mediated pathway is involved.
  • autoimmune diseases frequently involve inappropriate regulation or activity of CD28 pathways.
  • Administration of a domain antibody as described herein to an individual suffering from such a disease, including an autoimmune disease can reduce one or more symptoms of the disease.
  • diseases for which the domain antibodies described herein can be therapeutically useful include, but are not limited to, Addison's disease, allergy, ankylosing spondylitis, asthma, atherosclerosis, autoimmune diseases of the ear, autoimmune diseases of the eye, autoimmune atrophic gastritis, autoimmune hepatitis, autoimmune hymolytic anemia, autoimmune parotitis, primary biliary cirrhosis, benign lymphocytic aniitis, colitis, coronary heart disease, Crohn's disease, diabetes (Type I), diabetes, including Type 1 and/or Type 2 diabetes, epididymitis, glomerulonephritis, Goodpasture's syndrome, Graves' disease, Guillain- Barre syndrome, Hashimoto's disease,
  • Autoimmune- mediated conditions include, but are not limited to, conditions in which the tissue affected is the primary target, and in some cases, the secondary target.
  • Such conditions include, but are not limited to, AIDS, atopic allergy, bronchial asthma, eczema, leprosy, schizophrenia, inherited depression, transplantation of tissues and organs, chronic fatigue syndrome, Alzheimer's disease, Parkinson's disease, myocardial infarction, stroke, autism, epilepsy, Arthus's phenomenon, anaphylaxis, and alcohol and drug addiction.
  • the domain antibodies described herein also can be therapeutically useful in graft-related diseases, such as graft versus host disease (GVHD), acute transplantation rejection, and chronic transplantation rejection.
  • graft-related diseases such as graft versus host disease (GVHD), acute transplantation rejection, and chronic transplantation rejection.
  • domain antibodies described herein are additionally useful in the way that generally any antibody preparation is useful, e.g., for in vivo imaging or diagnostic uses, in vitro diagnostic uses, etc.
  • domain antibodies e.g., with a fluorescent, colorimetric, enzymatic or radioactive label.
  • Methods of labeling domain antibodies are well known in the art.
  • the domain antibodies set forth herein can be incorporated into pharmaceutical compositions suitable for administration to a subject.
  • the pharmaceutical composition comprises a domain antibody and a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier includes any and all solvents, dispersion media, coatings, antibacterial, and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible.
  • pharmaceutically acceptable carrier excludes tissue culture medium comprising bovine or horse serum.
  • pharmaceutically acceptable carriers include one or more of water, saline, phosphate buffered saline, dextrose, glycerol, ethanol and the like, as well as combinations thereof.
  • isotonic agents for example, sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride in the composition.
  • Pharmaceutically acceptable substances include minor amounts of auxiliary substances such as wetting or emulsifying agents, preservatives or buffers, which enhance the shelf life or effectiveness of the domain antibody.
  • compositions as described herein may be in a variety of forms. These include, for example, liquid, semi-solid, and solid dosage forms, such as liquid solutions (e.g., injectable and infusible solutions), dispersions or suspensions, powders, liposomes, and suppositories.
  • liquid solutions e.g., injectable and infusible solutions
  • dispersions or suspensions e.g., dispersions or suspensions
  • powders e.g., liposomes, and suppositories.
  • Typical preferred compositions are in the form of injectable or infusible solutions, such as compositions similar to those used for passive
  • parenteral e.g., intravenous, subcutaneous, intraperitoneal, intramuscular.
  • compositions typically must be sterile and stable under the conditions of manufacture and storage.
  • the composition can be formulated as a solution, microemulsion, dispersion, liposome, or other ordered structure suitable to high drug concentration.
  • Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filter sterilization.
  • dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • sterile powders for the preparation of sterile injectable solutions methods of preparation include vacuum drying and freeze-drying that yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • the proper fluidity of a solution can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • domain antibodies described herein can be administered by a variety of methods known in the art, although for many therapeutic applications, the preferred route/mode of administration is intravenous injection or infusion.
  • the polypeptide can also be administered by intramuscular or subcutaneous injection.
  • the active compound may be prepared with a carrier that will protect the compound against rapid release, such as a controlled release formulation, including implants, and microencapsulated delivery systems.
  • a carrier that will protect the compound against rapid release, such as a controlled release formulation, including implants, and microencapsulated delivery systems.
  • Domain antibodies are well suited for formulation as extended release preparations due, in part, to their small size, the number of moles per dose can be significantly higher than the dosage of, e.g., full sized antibodies.
  • Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid.
  • Prolonged absorption of injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, monostearate salts and gelatin. Many methods for the preparation of such formulations are patented or generally known to those skilled in the art. See, e.g., Sustained and Controlled Release Drug Delivery
  • a domain antibody is co-formulated with and/or co-administered with one or more additional therapeutic agents.
  • a domain antibody can be co-formulated and/or co-administered with one or more additional antibodies that bind other targets (e.g., antibodies that bind other cytokines or that bind cell surface molecules), or, for example, one or more cytokines.
  • targets e.g., antibodies that bind other cytokines or that bind cell surface molecules
  • Such combination therapies may utilize lower dosages of the administered therapeutic agents, thus avoiding possible toxicities or complications associated with the various monotherapies.
  • compositions disclosed herein can include a "therapeutically effective amount” or a “prophylactically effective amount” of a domain antibody.
  • a “therapeutically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic result.
  • a therapeutically effective amount of the domain antibody can vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of domain antibody to elicit a desired response in the individual.
  • a therapeutically effective amount is also one in which any toxic or detrimental effects of the antibody or antibody portion are outweighed by the therapeutically beneficial effects.
  • a “prophylactically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result. Typically, because a prophylactic dose is used in subjects prior to or at an earlier stage of disease, the prophylactically effective amount will be less than the therapeutically effective amount.
  • Dosage regimens may be adjusted to provide the optimum desired response (e.g., a therapeutic or prophylactic response). For example, a single bolus may be
  • Dosage unit form refers to physically discrete units suited as unitary dosages for the mammalian subjects to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • a non-limiting range for a therapeutically or prophylactically effective amount of a domain antibody is 0.1-20 mg/kg, and in an aspect, 1-10 mg/kg. It is to be noted that dosage values can vary with the type and severity of the condition to be alleviated. It is to be further understood that for any particular subject, specific dosage regimens should be adjusted over time according to the individual need and the professional judgment of the administering clinician.
  • the efficacy of treatment with a domain antibody as described herein is judged by the skilled clinician on the basis of improvement in one or more symptoms or indicators of the disease state or disorder being treated.
  • An improvement of at least 10% (increase or decrease, depending upon the indicator being measured) in one or more clinical indicators is considered "effective treatment," although greater improvements are included, such as about 20%, 30%, 40%, 50%, 75%, 90%, or even 100%, or, depending upon the indicator being measured, more than 100% (e.g., two-fold, three-fold, ten-fold, etc., up to and including attainment of a disease-free state.
  • Indicators can be physical measurements, e.g., enzyme, cytokine, growth factor or metabolite levels, rate of cell growth or cell death, or the presence or amount of abnormal cells.
  • One can also measure, for example, differences in the amount of time between flare-ups of symptoms of the disease or disorder (e.g., for remitting/relapsing diseases, such as multiple sclerosis).
  • non-physical measurements such as a reported reduction in pain or discomfort or other indicator of disease status can be relied upon to gauge the effectiveness of treatment.
  • various clinically acceptable scales or indices can be used, for example, the Crohn's Disease Activity Index, or CDAI (Best et al.
  • Gastroenterology 70: 439 which combines both physical indicators, such as hematocrit and the number of liquid or very soft stools, among others, with patient-reported factors such as the severity of abdominal pain or cramping and general well-being, to assign a disease score.
  • the efficacy of treatment for psoriasis can be monitored using the Salford Psoriasis Index (SPI) or Psoriasis Area Severity Index (PASI).
  • SPI Salford Psoriasis Index
  • PASI Psoriasis Area Severity Index
  • the PASI is most commonly used method to assess psoriasis disease severity in clinical trials, although it can be exceedingly cumbersome for use in daily clinical practice.
  • the method involves the body being divided into four sections (Legs, which have 40% of a person's skin; the Body (trunk area: stomach, chest, back, etc.) with 30%; the Arms (20%); and the Head (10%)). Each of these areas is scored by itself, and then the four scores are combined into the final PASI. For each section, the percent of area of skin involved, is estimated and then transformed into a grade from 0 to 6:
  • the severity is estimated by four different parameters: Itching, Erythema (redness), Scaling and Thickness (psoriatic skin is thicker than normal skin). Severity parameters are measured on a scale of 0 to 4, from none to maximum.
  • the total PASI is calculated as a sum of PASIs for all four skin sections.
  • Computer-aided measurement of psoriatic lesion area was found to improve the power of the clinical trial, compared to the standard approach. The physician's estimations of the psoriatic lesion area tend to overestimate.
  • the modified PASI which involves computer aided area measurement as a continuous variable is named: Computer aided psoriasis continuous area and severity score cPcASl.
  • organ transplant rejection can also be monitored.
  • the survival rates of organ transplant patients (currently around 70-85% for 5 years for all transplanted organs) have improved as a result of advances in organ preservation and immunosuppressive treatments.
  • organ rejection especially the acute rejection that occurs in the first few weeks following surgery, as well as chronic graft rejection, is still one of the major causes of functional failure in organ transplantation.
  • Current diagnosis or confirmation of graft rejection following solid organ transplantation requires biopsy of the tissue in order to detect the infiltration of immune cells (e.g., T-cells, macrophages, etc.) into the graft and other pathological changes.
  • immune cells e.g., T-cells, macrophages, etc.
  • Tissue biopsy is not only invasive, but it is associated with increased health risk to the patent and is prone to sampling errors that can lead to false negative results.
  • Alternative non-invasive methods are being developed, such as magnetic resonance imaging (MRI) which can be used to monitor the accumulation of immune cells at the rejected organ (Ho et al., (2004) Curr. Pharm. Biotech., 5: 551-566).
  • MRI magnetic resonance imaging
  • prophylaxis performed using a composition as described herein is “effective” if the onset or severity of one or more symptoms is delayed or reduced by at least 10%, or abolished, relative to such symptoms in a similar individual (human or animal model) not treated with the composition.
  • the domain antibodies described herein bind human CD28, where one is to evaluate its effect in an animal model system
  • the polypeptide must cross-react with one or more antigens in the animal model system, in an aspect, at high affinity.
  • One of skill in the art can readily determine if this condition is satisfied for a given animal model system and a given domain antibody. If this condition is satisfied, the efficacy of the domain antibody can be examined by administering it to an animal model under conditions which mimic a disease state and monitoring one or more indicators of that disease state for at least a 10% improvement. 10.
  • Domain antibodies as described herein are useful for the treatment of autoimmune disorders in which CD28 signaling is inappropriately active. There are several animal models in which the therapeutic efficacy of a given domain antibody can be assessed, as discussed below.
  • IBD ulcerative colitis .
  • Several mouse models of mucosal inflammation that resemble IBD have provided insight into the mechanisms governing both normal and pathological mucosal immune function.
  • the injection into immunodeficient mice of a subset of CD4(+) T lymphocytes, the CD4(+)CD45RBhigh cells leads to inflammation of the intestine.
  • Pathogenesis is due in part to the secretion of proinflammatory cytokines.
  • the induction of colitis can be prevented by co-transfer of another CD4(+) subpopulation, the CD4(+)CD45RBlow T cells.
  • This population behaves analogously to the CD4(+)CD45RBhigh population in terms of the acquisition of activation markers and homing to the host intestine.
  • their lymphokine profile when activated is different, and anti-inflammatory cytokines secreted and/or induced by CD4(+)CD45RBlow T cells prevent colitis.
  • De Winter et al. provide a description of the adoptive transfer model and the factors that promote and prevent colitis pathogenesis.
  • RA Rheumatoid arthritis
  • TCR T cell receptor
  • All offspring develop a joint disease highly reminiscent of RA in man.
  • the trigger for the murine disorder is chance recognition of a NOD-derived major histocompatibility complex (MHC) class II molecule by the transgenic TCR; progression to arthritis involves CD4+ T, B, and probably myeloid cells.
  • MHC major histocompatibility complex
  • CIA collagen-induced arthritis
  • rodents rat and mouse
  • CII type II collagen
  • CIA Susceptibility to CIA in rodents is linked to the class II molecules of the major histocompatibility complex (MHC), and the immune response to CII is characterized by both the stimulation of collagen-specific T cells and the production of high titers of antibody specific for both the immunogen (heterologous CII) and the autoantigen (mouse CII).
  • MHC major histocompatibility complex
  • CII immunogen
  • human CII autoantigen
  • murine CIA is characterized by an intense synovitis that corresponds precisely with the clinical onset of arthritis. This experimental data is useful evaluating CIA because of the pathological similarities between CIA and RA.
  • T-cell-antigen-receptor-transgenic T cell for the study of T-cell activation in vivo provides a model for antigen-induced T-cell proliferation.
  • Pape et al., (1997) Immunol. Rev. 156: 67-78 discuss adoptive transfer of TCR-transgenic T cells uniformly expressing an identifiable TCR of known
  • peptide/MHC specificity can be used to monitor the in vivo behavior of antigen-specific T cells.
  • the system was used to demonstrate that naive T cells are initially activated within the T-cell zones of secondary lymphoid tissue to proliferate in a B7-dependent manner. If adjuvants or inflammatory cytokines are present during this period, enhanced numbers of T cells accumulate, migrate into B-cell-rich follicles, and acquire the capacity to produce IFN-gamma and help B cells produce IgG2a. If inflammation is absent, most of the initially activated antigen-specific T cells disappear without entering the follicles, and the survivors are poor producers of IL-2 and IFN-gamma.
  • WO2010/009391 which is herein incorporated by reference. Selections of dAbs were carried out with recombinant human CD28/Fc Chimera (R&D Systems, Abingdon, UK). The domain antibody library used for selections was based on a single human VH framework (V3-23 aka DP47, and JH4b) and a single human VL framework (012/02 aka DPK9, and JKI). The dAb genes were genetically linked to the fd phage gene III protein under the control of the GAS 1 leader sequence in the pDOM4 vector which contained all the fd genes necessary to generate infective phage particles.
  • the first round of phage selection was performed by premixing phage library (4 pools for the VH libraries [VH1 1- 13, VH14- 15, VH16- 17, VH18- 19] and a single pool for the VK library) with 2% MPBS (Phosphate Buffered Saline supplemented with 2% Marvel dried skim milk powder) and adding CD28-Fc (R&D Systems, UK) to a final concentration of 100 nM.
  • MPBS Phosphate Buffered Saline supplemented with 2% Marvel dried skim milk powder
  • CD28-Fc R&D Systems, UK
  • the mixture was incubated for at least 1 hour at room temperature with mixing end-over-end then the antigen-phage complexes captured using protein G Dynabeads (Dynal, Sweden) and washed 8 times with 1ml PBST (PBS supplemented with 0.1 % Tween 20) followed by a singe wash in 1 ml PBS.
  • the washed phage were eluted from the antigen/bead complex by incubating with 0.5 ml of 1 mg/ml trypsin Type XIII from Bovine Pancreas (Sigma Aldrich, UK) in PBS (supplemented with 5 niM Tris-HCl pH 7.4, 0.1 mM CaCl 2 ).
  • Eluted phage were used to infect E. coli and the output phage titres were determined to be between lxl 0 4 to lxl 0 5 titer units (t.u.)/ml, wherein t.u./ml is a measure of infective phage particles per ml.
  • a measure of t.u. is determined through the infection of E. coli with phage of a given dilution, followed by growth of infected E. coli on selective agar plates.
  • a second round of selection was performed using enriched phage recovered from the previous round of selection with a final concentration of 50nM CD28-Fc followed by capture using protein G beads as described above. Output titres were in the range lxl O 6 to lxl 0 9 t.u./ml.
  • a third round of selection using 10 iiM CD28-Fc followed by capture using protein G beads was performed. The eluted phage titres were in the range of 2x10 9 to 8xl 0 9 t.u./ml.
  • Monoclonal phage ELISAs were carried out following selection rounds 2 and 3. All washes were performed using 3 washes of 250 ⁇ PBST followed by 3 washes of 250 ⁇ PBS. Plates were coated overnight at 4°C with 1 mg/ml and 0.6 mg/ml CD28-Fc in PBS respectively. Plates were washed, then blocked with 2% MPBS for 1 hour at room temperature. The plates were washed and phage supe natants added to an equal volume of 2% MPBS and incubated for 1 hour at room temperature.
  • the plates were washed and bound phage detected with anti-M13-HRP conjugate (GE Healthcare, UK) diluted 1 :5000 in 2% MPBS and incubated for 1 hour at room temperature.
  • the plates were washed and the ELISA developed using SureBlue 1 -Component TMB Micro Well Peroxidase solution (KPL Inc, USA). Specific phage were identified by comparison with a plate coated with 1 mg/ml Fc (Sigma Aldrich, UK). After round 2, specific phages were mainly identified in library pools VH14-15, VH18-19 and VK, whereas by round 3, few specific phage remained. All round 2 pools were subcloned into pDOM5 and screened as soluble phage.
  • Binding dAbs were identified as follows. Ninety-six individual colonies
  • the plates were blocked for 1 hour at room temperature with 200 ⁇ of PBS containing 1 % Tween 20 and then washed.
  • the clarified dAb containing culture supernatant was added to the ELISA plate in the presence of either protein A for VH (Sigma, UK) or protein L for VK (Sigma, UK) to increase the ELISA signal strength by cross-linking the VH or VK dAbs respectively.
  • the plates were incubated for 1 hour at room temperature then washed.
  • Bound dAb was detected using a two step process, firstly 9E10 (anti-myc IgG, Sigma- Aldrich, UK) diluted 1 :2000 in PBST was added for 1 hour at room temp then washed, followed by anti-mouse Fc-HRP dilute 1 .2000 in PBST for 1 hour at room temperature. The plates were washed and the ELISA developed using SureBlue 1 -Component TMB Micro Well Peroxidase solution (KPL Inc, USA) and the color allowed to develop. The colorimetric reaction was stopped by the addition of an equal volume of 1 M HCL and the ELISA plate read at 450nm. CD28 specific clones were identified by comparison to a control plate coated with Fc alone.
  • the dAb amino acid sequences in the examples below do not necessarily correspond exactly to the dAb sequences disclosed in the Sequence Listing.
  • the dAb amino acid sequences may contain additional amino acid residues at the N-termninus of the protein, which are introduced to facilitate cloning into an expression vector.
  • the amino acid sequence of recombinatnly expressed dAbs may contain a Ser Thr sequence at the N-terminus. These additional N- terminal residues are not believed to affect the biological activity of the dAbs.
  • VK l h-239-891
  • VK l h-239-850
  • PKLLfYFTgRLQSGVPSR jGSGSG--TDFTLT
  • YYADSy KGR : sISRDNSKNTLYLQB StRAEDTAVYYCAEY
  • the dAb activity was tested in vitro as follows. Seven of the dAbs (DOM21-4, DOM21 -6, DOM21- 18, DOM21 -20, DOM21-22, DOM21 -27 and DOM21-28) were expressed and purified on a larger scale. Endotoxin depleted dAbs samples at a stock concentration of 100 ⁇ were used to determine whether the dAbs could inhibit the activity of CD28 in a cell based in vitro assay similar to that described by Boulougouris, J. Immunol. 1998, 161 (8): 3919-3924.
  • Proliferation assays were performed in triplicate in 96-well plates in a final volume of 200 ⁇ per well using RPMI 1640 medium containing 10% FCS and antibiotics.
  • Human CD4 positive T-cells (5 x 10 4 ) were cultured in the presence of 1 ⁇ g/ml anti-CD3 antibody (OKT3) plus transfected CHO cells expressing either CD80 or CD86 and dAb or control antibody at a range of concentrations. Assays were incubated at 37° C for between 18 hours to 72 hours in the presence of 1 ⁇ [ J H]-thymidine per well.

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Abstract

Cette invention concerne des anticorps à domaines PEGylés (dAb) qui se lient de manière monovalente à CD28 et empêchent ou inhibent la liaison de CD28 à CD80, CD86 et/ou autres ligands et inhibent la signalisation CD28 par CD80 et/ou CD86 dans des dosages de liaison au récepteur ainsi que des méthodes pour les utiliser. Les dAb PEGylés selon l'invention manifestent une demi-vie in vivo plus longue, une résistance accrue aux protéases, une solubilité et stabilité accrues, un ciblage tissulaire amélioré et une immunogénicité réduite comparés aux dAB non-PEGylés.
PCT/US2014/013842 2013-02-01 2014-01-30 Anticorps à domaines pegylés monovalents pour la liaison à cd28 et leurs méthodes d'utilisation Ceased WO2014120916A1 (fr)

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WO2016054218A1 (fr) * 2014-09-30 2016-04-07 Bristol-Myers Squibb Company Méthodes de traitement de lupus érythémateux systémique à l'aide d'un anticorps à domaine dirigé contre cd28
WO2023193817A1 (fr) * 2022-04-08 2023-10-12 Adagene Pte. Ltd. Anticorps anti-cd28 et leurs méthodes d'utilisation
WO2024151687A1 (fr) 2023-01-09 2024-07-18 Flagship Pioneering Innovations V, Inc. Commutateurs génétiques et leur utilisation dans le traitement du cancer

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