# Patent

## Title
Anti-IL-23 heterodimer specific antibodies

## Abstract

The present disclosure provides an isolated or recombinant IL-23-binding protein comprising an antigen binding domain of an antibody, wherein the antigen binding domain specifically binds to IL-23 but does not significantly bind to an IL-12p40 subunit and does not significantly bind to an IL-23p19 subunit when they are not components of IL-23. The present disclosure also provides uses of the IL-23-binding protein.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is the U.S. National Phase of International Application No. PCT/AU2011/000923, filed on Jul. 20, 2011, and claims priority to U.S. Provisional Application No. 61/384,945 filed on Sep. 21, 2010, and Australian Patent Application No. 2010903234 filed on Jul. 20, 2010, the contents of each of these applications are incorporated herein by reference in their entirety and for all purposes.


REFERENCE TO A SEQUENCE LISTING
This application includes a Sequence Listing submitted electronically as a text file named 510922_ST25.txt, created on Jan. 4, 2013 with a size of 128,000 bytes. The Sequence Listing is incorporated by reference herein.
FIELD
The present disclosure relates to proteins that specifically bind to interleukin (IL)-23 and uses thereof.
BACKGROUND
Interleukin (IL)-23 was discovered by searching sequence databases with a computationally derived profil of members of the interleukin-6 helical cytokine family. This search led to the discovery of a novel cytokine subunit which was named IL-23p19 (p19) which was homologous to the IL-12p35 subunit. This IL-12p35 subunit dimerizes with IL-12p40 subunit to form IL-12. Expression of p19 with IL-12p40 led to the secretion of a heterodimeric protein which was called IL-23.
The p40 subunit of IL-23 has three domains labeled D1, D2 and D3. Each domain is a β-sheet structure with the D2 domain containing the C177 interchain disulphide bond. There is also an N-linked glycosylation site on D2.
The p19 subunit resembles IL-12p35 in that it contains a four helix bundle. However, a truncated helical length and a ‘tilt’ and ‘roll’ in IL23p19 relative to IL-12p35 results in an altered footprint. IL-23p19 also differs in the manner in which it interacts with IL-12p40 when compared to IL-12p35.
The specific effects of IL-23 on its target cell types are mediated by the IL-23R complex, which comprises IL-12β1 and IL-23R. IL-12β1 binding to IL-23 is mediated via the IL-12p40 subunit.
IL-23p19 of IL-23 is responsible for binding to IL-23R thereby conferring IL-23 selectivity on the IL-23R complex.
IL-23 is secreted by activated human macrophages as well as dendritic cells. IL-23 predominantly acts on memory T-cells and has been postulated to promote autoimmune disease through the regulation of IL-17A and IL-17F as demonstrated in the ability of murine splenocytes to secrete IL-17 in response to IL-23. In humans the IL-23/IL-17 pathway is present, and IL-23 has been shown to be a good inducer of IL-21, IL-22, IFN-γ, and TNF-α along with IL-17, all of which are pro-inflammatory cytokines. In vitro IL-6 and TGF-β1 promote the development of naïve T-cells to the TH17 T-cell pathway. These cells are further driven in an autocrine manner via secretion of IL-21. IL-23 and/or IL-1β are thought to maintain cells in this TH17 response.
Since both IL-12 and IL-23 contain a common subunit, it has been difficult to attribute disease states solely to overproduction of one interleukin or the other. However research indicates that IL-23 dysregulation has been implicated in psoriasis, Crohn's disease and multiple sclerosis, among other autoimmune diseases.
Given that IL-23 is involved in various pathological conditions, antagonists specific for this cytokine are desirable. However, specifically targeting this cytokine has proven difficult since both of the subunits of IL-23 are shared with other dimeric cytokines. For example, the IL-12p40 subunit is also a component of IL-12 and IL-23p19 is also a component of heterodimeric cytokines such as zcyto33f2 as described in U.S. Pat. No. 7,196,172.
SUMMARY
The present inventors have produced a protein that specifically binds to IL-23 but not to either of its component parts (IL-12p40 or IL-23p19) when not part of IL-23, e.g., IL-12p40 or IL-23p19 in isolation or when part of another cytokine (e.g., IL-12, both of which comprise IL-12p40; or zcyto33f2, which comprises IL-23p19). Such a protein is unlikely to cause the undesired effects of inhibiting the activity of cytokines that share the IL-12p40 or IL-23p19 subunit, and thus unlikely to have “off-target” effects in therapy. Moreover, such proteins provide the basis for specific tests to detect IL-23, e.g., in diagnosis/prognosis.
The present disclosure provides an isolated or recombinant IL-23-binding protein comprising an antigen-binding domain of an antibody, wherein the antigen-binding domain specifically binds to IL-23 but does not significantly bind to an IL-12p40 subunit and does not significantly bind to an IL-23p19 subunit when they are not components of IL-23.
The skilled artisan will understand from the foregoing, that the inclusion of the antigen-binding domain in the IL-23-binding protein means that the protein also specifically binds to IL-23 but does not significantly bind to an IL-12p40 subunit and does not significantly bind to an IL-23p19 subunit when they are not components of IL-23.
In one example, the antigen binding domain specifically binds to the heterodimeric interface of IL-23.
The present disclosure additionally or alternatively provides an isolated or recombinant IL-23-binding protein comprising an antigen binding domain of an antibody, wherein the antigen binding domain specifically binds to the heterodimeric interface of IL-23 but does not significantly bind to an IL-12p40 subunit and an IL-23p19 subunit when they are not components of IL-23.
The present disclosure additionally or alternatively provides an isolated or recombinant IL-23-binding protein comprising an antigen binding domain of an antibody, wherein the antigen binding domain:

    (i) specifically binds to IL-23 but does not significantly bind to an IL-12p40 subunit and does not significantly bind to an IL-23p19 subunit when they are not components of IL-23;
    (ii) binds to IL-23 in which hydrogens therein have been exchanged with deuterium; and
    (iii) upon binding to IL-23 in which hydrogens therein have been exchanged with deuterium reduces exchange of the deuterium to hydrogen in a region comprising residues 112-144 of SEQ ID NO: 2.


In one example, the reduction in exchange is statistically significant.
In one example, the reduction in exchange is calculated by determining the percentage change in deuterium content of regions of IL-23 before and after exchange and identifying regions having a change greater than 2 or 2.5 or 3 standard deviations greater than the average change for regions having the lowest percentage change (e.g., 50% of the regions tested with the lowest percentage change).
In one example, the antigen binding domain reduces exchange in a region comprising residues 91-144 of SEQ ID NO: 2 or a region comprising comprising residues 91-109 and 112-144 of SEQ ID NO: 2.
In one example, the antigen binding domain additionally reduces exchange in a region comprising residues 135-153 of SEQ ID NO: 1. In accordance with this example, the present disclosure additionally or alternatively provides an isolated or recombinant IL-23-binding protein comprising an antigen binding domain of an antibody, wherein the antigen binding domain:

    (i) specifically binds to IL-23 but does not significantly bind to an IL-12p40 subunit and does not significantly bind to an IL-23p19 subunit when they are not components of IL-23;
    (ii) binds to IL-23 in which hydrogens therein have been exchanged with deuterium; and
    (iii) upon binding to IL-23 in which hydrogens therein have been exchanged with deuterium reduces exchange of the deuterium to hydrogen in a region of the IL-12p40 subunit and in a region of the IL-23p19 subunit.


In one example, the IL-23-binding protein binds specifically to IL-23 but does not significantly bind to an isolated IL-12p40 subunit and does not significantly bind to an isolated IL-23p19 subunit.
In one example, the isolated IL-12p40 subunit comprises an additional sequence, e.g., FLAG tag or a Fc region of an antibody. For example, an IL-12p40 subunit comprises a sequence set forth in SEQ ID NO: 1 fused to a FLAG tag comprising a sequence set forth in SEQ ID NO: 17 or fused to a Fc region of an antibody, the Fc region comprising a sequence set forth in SEQ ID NO: 16.
In one example, the isolated IL-23p19 subunit comprises an additional sequence, e.g., a FLAG tag or a Fc region of an antibody. For example, an IL-23p19 subunit comprises a sequence set forth in SEQ ID NO: 2 fused to a FLAG tag comprising a sequence set forth in SEQ ID NO: 17 or fused to a Fc region of an antibody, the Fc region comprising a sequence set forth in SEQ ID NO: 16.
In one example, the IL-23-binding protein binds specifically to IL-23, wherein IL-12p40 and IL-23p19 subunits of IL-23 comprise an additional sequence, e.g., a FLAG tag or a Fc region of an antibody as described above.
In one example, an IL-23-binding protein of the present disclosure reduces binding of IL-23 to IL-23 receptor (IL-23R) with an IC50 of 1 nM or less, such as 750 pM or less, for example 500 pM or less. In one example, the IC50 of the IL-23-binding protein is 400 pM or less.
In one example, an IL-23-binding protein of the present disclosure reduces binding of IL-23 to IL-23R with an IC50 of between 100 nM and 1 nM, such as between 150 pM and 750 pM, for example between 150 pM and 500 pM. In one example, the IC50 of the IL-23-binding protein is between 160 pM and 400 pM.
In one example, an IL-23-binding protein of the present disclosure reduces binding of IL-23 to IL-23R with an EC50 of 1 nM or less, for example, 750 pM or less, for example, 500 pM or less, such as 400 pM or less. In one example, the EC50 is about 300 pM or less. For example, the EC50 is about 260 pM.
Methods for determining binding of IL-23 to IL-23R will be apparent to the skilled artisan. For example, in one method isolated or recombinant IL-23R or a cell expressing IL-23R is immobilized. Labeled IL-23 is then contacted to the immobilized receptor or cell in the presence or absence of a test protein, which is suspect of reducing binding of IL-23 to IL-23R and the amount of bound label detected. A reduction in the amount of bound label in the presence of the IL-23-binding protein when compared to the absence of the protein indicates that the protein reduces or prevents binding of IL-23 to IL-23R. By testing multiple concentrations of the IL-23-binding protein an IC50 and/or an EC50 is determined.
In another example, an IL-23-binding protein of the disclosure reduces IL-23-induced IL-17 secretion by splenocytes. In one method, cultured splenocytes (such as mouse splenocytes) are contacted with IL-23 in the presence or absence of the IL-23-binding protein. Following sufficient time for IL-17 secretion to occur, IL-17 levels are detected, e.g., using an enzyme linked immunosorbent assay (ELISA). A lower level of the cytokine in the presence of the protein compared to in the absence of the protein indicates that the protein neutralizes IL-23 activity. By testing multiple concentrations of the protein an IC50 and/or EC50 is determined.
In one example, the IC50 is 1 μM or less, for example, 800 μM or less, for example, 750 μM or less, such as 500 μM or less.
In one example, the IC50 is about 1 nM or less, for example, 800 pM or less. For example, the IC50 is 700 pM or less. In one example, the IC50 is between about 1 pM and 800 pM, for example, between about 100 pM and 700 pM, for example, between about 120 pM and 680 pM.
In one example, the EC50 is 1 μM or less, for example, 800 μM or less, for example, 750 μM or less, such as 500 μM or less.
In one example, the EC50 is 1 nM or less, for example, 500 pM or less, such as 400 pM or less. In one example, the EC50 is about 300 pM or less. For example, the EC50 is about 290 pM.
In one example, the IL-23-binding protein is capable of specifically binding to IL-23 and competitively inhibiting the binding of an antibody to IL-23, wherein the antibody comprises any one of the following:

    (i) a VH comprising a sequence set forth in SEQ ID NO: 7 and a VL comprising a sequence set forth in SEQ ID NO: 12; or
    (ii) a VH comprising a sequence set forth in SEQ ID NO: 49 and a VL comprising a sequence set forth in SEQ ID NO: 50.


Methods for determining competitive inhibition of binding of an antibody to IL-23 are described herein and are to be taken to apply mutatis mutandis to this example of the disclosure.
For example, the IL-23-binding protein binds to an epitope that is the same as or overlaps with the epitope bound by an antibody comprising any one of the following:

    (i) a VH comprising a sequence set forth in SEQ ID NO: 7 and a VL comprising a sequence set forth in SEQ ID NO: 12; or
    (ii) a VH comprising a sequence set forth in SEQ ID NO: 49 and a VL comprising a sequence set forth in SEQ ID NO: 50.


In one example, the antigen binding domain of an IL-23-binding protein of the disclosure specifically binds to the IL-23p19 subunit of IL-23 when a component of IL-23. For example, the antigen binding domain specifically binds to the IL-23p19 subunit of IL-23 when a component of IL-23 in a region comprising amino acids 112-144 of SEQ ID NO: 2.
In one example, the antigen binding domain of an IL-23-binding protein of the disclosure specifically binds to both the IL-12p40 subunit and the IL-23p19 subunit when components of IL-23. For example, the antigen binding domain binds to regions of the IL-12p40 subunit and the IL-23p19 subunit comprising atoms within about 50 Angstroms of one another, such as 40 Angstroms of one another, for example, 30 Angstroms of one another. In one example, atoms within the regions are within about 25 Angstroms of one another. For example, the antigen binding domain binds to the IL-23p19 subunit in a region comprising amino acids 112-144 of SEQ ID NO: 2 and to the IL-12p40 subunit in a region comprising amino acids 135-153 of SEQ ID NO: 1.
In one example, an IL-23-binding protein of the disclosure binds to IL-23 with a dissociation constant (kd) of at least about 1×10−2, such as, at least about 9×10−3, for example, at least about 8×10−3, for example, at least about 7×10−3.
In one example, an IL-23-binding protein of the disclosure binds to IL-23 with an association constant (ka) of at least about 1×104, such as, at least about 5×104, for example, at least about 1×105.
In one example, an IL-23-binding protein of the disclosure binds to IL-23 with an equilibrium constant (KD) of at least about 1×10−7, for example, 5×10−8, such as, at least about 1×10−8. In one example, an IL-23-binding protein of the disclosure binds to IL-23 with an equlibbrium constant (KD) of between about 1×10−7 and about 1×10−9, for example, between about 1×10−7 and about 1×10−9.
The present disclosure additionally or alternatively provides an isolated or recombinant IL-23-binding protein comprising an antigen binding domain of an antibody, which comprises an amino acid sequence set forth in any one of SEQ ID NOs: 21 to 50 or a sequence having at least about 80% identity thereto or an amino acid sequence encoded by a nucleic acid comprising a sequence set forth in any one of SEQ ID NOs: 57 to 77 or a sequence having at least about 80% identity thereto or a nucleic acid that hybridizes thereto under moderate to high stringency conditions.
The present disclosure also provides an isolated or recombinant protein IL-23-binding protein comprising an antigen binding domain of an antibody, which comprises an amino acid sequence set forth in any one of SEQ ID NOs: 26 to 29, 49, 50 or amino acids 1-120 of any one of SEQ ID NOs: 20 or 30 to 33, or amino acids 1-113 of SEQ ID NO: 45 or 46 or a sequence having at least about 80% identity thereto or an amino acid sequence encoded by a nucleic acid comprising a sequence set forth in any one of SEQ ID NOs: 6, 11, 57 to 60, 72, 73, 76 or 77 or a sequence having at least about 80% identity thereto or a nucleic acid that hybridizes under moderate to high stringency conditions.
In one example, the antigen binding domain of an IL-23-binding protein of the disclosure comprises a complementarity determining region (CDR) 3 of a variable region comprising a sequence set forth in any one of SEQ ID NOs: 7, 12, 26, 27, 28, 29, 49 or 50. Exemplary numbering schemes for determining CDRs are known in the art and any of those systems can be used to determine a CDR of an IL-23-binding protein of the present disclosure.
In one example, an IL-23-binding protein of the disclosure comprises a CDR3 defined according to the Kabat numbering system and comprising a sequence set forth in SEQ ID NO: 10, SEQ ID NO: 15, SEQ ID NO: 53 or SEQ ID NO: 56.
In one example, an IL-23-binding protein of the disclosure comprises a CDR3 defined according to the enhanced Chothia numbering system and comprising a sequence labeled as “CDR3” and shown in bold text in any one of FIG. 7A to 7F.
In some examples of the disclosure, the antigen binding domain is an antibody variable region comprising three CDRs of a variable region comprising an amino acid sequence set forth in any one of SEQ ID NOs: 26, 27, 28, 29, 49 or 50.
For example, the antigen binding domain is a VH comprising three CDRs of an amino acid sequence set forth in any one of SEQ ID NOs: 26, 27, 28, 29 or 49. In one example, the VH comprises three CDRs of a variable region comprising a sequence set forth in SEQ ID NO: 7. In one example, the VH comprises three CDRs of a variable region comprising a sequence set forth in SEQ ID NO: 33. In one example, the VH comprises three CDRs of a variable region comprising a sequence set forth in SEQ ID NO: 49. In one example, the CDRs are defined according to the Kabat numbering system. For example, the IL-23-binding protein comprises a VH including CDRs as follows:

    (i) a CDR1 comprising an amino acid sequence set forth in SEQ ID NO: 8 or 51 (or a sequence labeled as CDR1 and that is underlined in FIG. 7A, 7B or 7E);
    (ii) a CDR2 comprising an amino acid sequence set forth in any one of SEQ ID NOs: 9, 22, 24 or 52 (or a sequence labeled as CDR2 and that is underlined in FIG. 7A, 7B or 7E) optionally, wherein any one or more of the five C-terminal amino acids of the CDR2 amino acid sequence are substituted with any other naturally-occurring amino acid; and
    (iii) a CDR3 comprising an amino acid sequence set forth in SEQ ID NO: 10 or 53 (or a sequence labeled as CDR3 and that is underlined in FIG. 7A, 7B or 7E).


In a further example, the CDRs are defined according to the enhanced Chothia numbering system. For example, the VH includes CDRs as follows:

    (i) a CDR1 comprising an amino acid sequence labeled as CDR1 and shown in bold text in FIG. 7A, 7B or 7E) or comprising an amino acid sequence set forth in SEQ ID NO: 23 or 25;
    (ii) a CDR2 comprising an amino acid sequence labeled as CDR2 and shown in bold text in FIG. 7A, 7B or 7E); and
    (iii) a CDR3 comprising an amino acid sequence labeled as CDR3 and shown in bold text in FIG. 7A, 7B or 7E).


In another example, the antigen binding domain is a VL comprising three CDRs of an amino acid sequence set forth in any one of SEQ ID NOs: 27, 29 or 50. In one example, the VL comprises three CDRs of a variable region comprising a sequence set forth in SEQ ID NO: 12. In one example, the VL comprises three CDRs of a variable region comprising a sequence set forth in SEQ ID NO: 50.
In one example, the CDRs are defined according to the Kabat numbering system. For example, the IL-23-binding protein comprises a VL including CDRs as follows:

    (i) a CDR1 comprising an amino acid sequence set forth in SEQ ID NO: 13 or 54 (or a sequence labeled as CDR1 and that is underlined in FIG. 7C, 7D or 7F);
    (ii) a CDR2 comprising an amino acid sequence set forth SEQ ID NO: 14 or 55 (or a sequence labeled as CDR2 and that is underlined in FIG. 7C, 7D or 7F); and
    (iii) a CDR3 comprising an amino acid sequence set forth in SEQ ID NO: 15 or 56 (or a sequence labeled as CDR3 and that is underlined in FIG. 7C, 7D or 7F).


In a further example, the CDRs are defined according to the enhanced Chothia numbering system. For example, the VL includes CDRs as follows:

    (i) a CDR1 comprising an amino acid sequence labeled as CDR1 and shown in bold text in FIG. 7C, 7D or 7F).
    (ii) a CDR2 comprising an amino acid sequence labeled as CDR2 and shown in bold text in FIG. 7B); and
    (iii) a CDR3 comprising an amino acid sequence labeled as CDR3 and shown in bold text in FIG. 7B).


In one example, the antigen binding domain comprises a VH and a VL, each comprising three CDRs, e.g., as described above.
In one example, the antigen binding domain comprises six CDRs of one of the following pairs of variable regions:

    (i) a heavy chain variable region (VH) comprising a sequence set forth in SEQ ID NO: 26 and a light chain variable region (VL) comprising a sequence set forth in SEQ ID NO: 27;
    (ii) a VH comprising a sequence set forth in SEQ ID NO: 28 and a VL comprising a sequence set forth in SEQ ID NO: 29; or
    (iii) a VH comprising a sequence set forth in SEQ ID NO: 49 and a VL comprising a sequence set forth in SEQ ID NO: 50.


For example, the antigen binding domain comprises:

    (i) a heavy chain CDR1 comprising a sequence set forth in any one of SEQ ID NOs: 8 or 51 (or a sequence labeled as CDR1 and that is underlined in FIG. 7A, 7B or 7E);
    (ii) a heavy chain CDR2 comprising a sequence set forth in any one of SEQ ID NOs: 9, 22 or 52 (or a sequence labeled as CDR2 and that is underlined in FIG. 7A, 7B or 7E) optionally, wherein any one or more of the five C-terminal amino acids of the CDR2 amino acid sequence are substituted with any other naturally-occurring amino acid;
    (iii) a heavy chain CDR3 comprising a sequence set forth in any one of SEQ ID NOs: 10 or 53 (or a sequence labeled as CDR3 and that is underlined in FIG. 7A, 7B or 7E);
    (iv) a light chain CDR1 comprising a sequence set forth in any one of SEQ ID NOs: 13 or 54 (or a sequence labeled as CDR1 and that is underlined in FIG. 7C, 7D or 7F);
    (v) a light chain CDR2 comprising a sequence set forth in any one of SEQ ID NOs: 14 or 55 (or a sequence labeled as CDR2 and that is underlined in FIG. 7C, 7D or 7F); and
    (vi) and a light chain CDR3 comprising a sequence set forth in any one of SEQ ID NOs: 15 or 56 (or a sequence labeled as CDR3 and that is underlined in FIG. 7C, 7D or 7F).


Exemplary IL-23-binding proteins of the disclosure comprise an antigen binding domain comprising a VH comprising an amino acid sequence set forth in any one of SEQ ID NOs: 26, 28 or 49. For example, the VH comprises an amino acid sequence set forth in any one of SEQ ID NO: 7, SEQ ID NO: 49 or amino acids 1-120 of any one of SEQ ID NOs: 30 to 44, or a sequence having at least about 80% identity to any one of the foregoing. In one example, the VH comprises an amino acid sequence set forth in any one of SEQ ID NO: 7, SEQ ID NO: 49 or amino acids 1-120 of any one of SEQ ID NOs: 30 to 33.
In another example, the VH comprises an amino acid sequence encoded by a nucleic acid comprising a sequence set forth in any one of SEQ ID NOs: 6, 19, 57 to 71, 76 or a sequence at least about 80% identical thereto or a nucleic acid that hybridizes thereto under moderate to high hybridization conditions. In one example, the VH comprises an amino acid sequence encoded by a nucleic acid comprising a sequence set forth in any one of SEQ ID NOs: 6, 19, 57 to 60, 76 or a sequence at least about 80% identical thereto or a nucleic acid that hybridizes thereto under moderate to high hybridization conditions.
In one example, the VH comprises a sequence set forth in SEQ ID NO: 28. In one example, the VH comprises a sequence set forth in amino acids 1-120 of SEQ ID NO: 30. In one example, the VH comprises a sequence set forth in amino acids 1-120 of SEQ ID NO: 31. In one example, the VH comprises a sequence set forth in amino acids 1-120 of SEQ ID NO: 32. In one example, the VH comprises a sequence set forth in amino acids 1-120 of SEQ ID NO: 33.
In one example, the VH comprises a sequence set forth in SEQ ID NO: 49.
In one example, the VH comprises a sequence set forth in SEQ ID NO: 7 or a humanized, deimmunized or synhumanized form thereof.
Exemplary IL-23-binding proteins of the disclosure comprise an antigen binding domain comprising a VL comprising an amino acid sequence set forth in any one of SEQ ID NOs: 27, 29 or 50. For example, the VL comprises an amino acid sequence set for in any one of SEQ ID NO: 12, SEQ ID NO: 50 or amino acids 1-113 of any one of SEQ ID NOs: 45 to 48 or a sequence having at least about 80% identity to any one of the foregoing. For example, the VL comprises an amino acid sequence set for in any one of SEQ ID NO: 12, SEQ ID NO: 50 or amino acids 1-113 of SEQ ID NO: 45 or 46 or a sequence having at least about 80% identity to any one of the foregoing.
In another example, the VL comprises an amino acid sequence encoded by a nucleic acid comprising a sequence set forth in any one of SEQ ID NO: 11, 18, 72 to 75 or 77 or a sequence at least about 80% identical thereto or a nucleic acid that hybridizes thereto under moderate to high hybridization conditions. For example, the VL comprises an amino acid sequence encoded by a nucleic acid comprising a sequence set forth in any one of SEQ ID NO: 11, 18, 72, 73 or 77 or a sequence at least about 80% identical thereto or a nucleic acid that hybridizes thereto under moderate to high hybridization conditions.
In one example, the VL comprises a sequence set forth in SEQ ID NO: 29. For example, the VL comprises a sequence set forth in SEQ ID NO: 45. For example, the VL comprises a sequence set forth in SEQ ID NO: 46.
In one example, the VL comprises a sequence set forth in SEQ ID NO: 50.
In one example, the VL comprises a sequence set forth in SEQ ID NO: 11 or a humanized, deimmunized or synhumanized form thereof.
Exemplary IL-23-binding proteins comprise a VH and a VL, wherein the V14 and VL bind to form a Fv comprising the antigen binding domain.
Exemplary IL-23-binding proteins comprise:

    (i) a VH comprising CDRs 1, 2 and 3 of a variable region comprising a sequence set forth in SEQ ID NO: 26 and a VL comprising CDRs 1, 2 and 3 of a variable region comprising a sequence set forth in SEQ ID NO: 27;
    (ii) a VH comprising CDRs 1, 2 and 3 of a variable region comprising a sequence set forth in SEQ ID NO: 28 and a VL comprising CDRs 1, 2 and 3 of a variable region comprising a sequence set forth in SEQ ID NO: 29; or
    (iii) a VH comprising CDRs 1, 2 and 3 of a variable region comprising a sequence set forth in SEQ ID NO: 49 and a VL comprising CDRs 1, 2 and 3 of a variable region comprising a sequence set forth in SEQ ID NO: 50.


CDRs in these sequences defined according to the Kabat numbering system or the enhanced Chothia numbering system are described herein and are to be taken to apply mutatis mutandis to the present example of the disclosure.
In one exemplary form of the disclosure an IL-23-binding protein comprises:

    (i) a VH comprising a CDR1 having a sequence set forth in SEQ ID NO: 8, a CDR2 having a sequence set forth in SEQ ID NO: 9 or 22 and a CDR3 having a sequence set forth in SEQ ID NO: 10; and
    (ii) a VL comprising a CDR1 having a sequence set forth in SEQ ID NO: 13, a CDR2 having a sequence set forth in SEQ ID NO: 14 and a CDR3 having a sequence set forth in SEQ ID NO 15.


In another exemplary form of the disclosure an IL-23-binding protein comprises:

    (i) a VH comprising a CDR1 having a sequence set forth in SEQ ID NO: 51, a CDR2 having a sequence set forth in SEQ ID NO: 52 and a CDR3 having a sequence set forth in SEQ ID NO: 53; and
    (ii) a VL comprising a CDR1 having a sequence set forth in SEQ ID NO: 54, a CDR2 having a sequence set forth in SEQ ID NO: 55 and a CDR3 having a sequence set forth in SEQ ID NO 56.


In some IL-23-binding proteins the VH and the VL are in a single polypeptide chain. Exemplary forms of such IL-23-binding proteins include:

    (i) a single chain Fv fragment (scFv);
    (ii) a dimeric scFv (di-scFv); or
    (iii) at least one of (i) and/or (ii) linked to a constant region, a Fc or a heavy chain constant domain (CH) 2 and/or CH3.


Other exemplary IL-23-binding proteins comprise the VL and VH in separate polypeptide chains. Exemplary forms of such IL-23-binding proteins include:

    (i) a diabody;
    (ii) a triabody;
    (iii) a tetrabody;
    (iv) a Fab;
    (v) a F(ab′)2;
    (vi) a Fv; or
    (iv) one of (i) to (iii) linked to a constant region, a Fc or a heavy chain constant domain (CH) 2 and/or CH3.


An example of an IL-23-binding protein of the disclosure is an antibody.
Some exemplary IL-23-binding proteins of the disclosure are chimeric, de-immunized, humanized, primatized, synhumanized or human.
In one example, the present disclosure provides an antibody comprising an antigen binding domain, wherein the antigen binding domain specifically binds to IL-23 but does not significantly bind to an IL-12p40 subunit and does not significantly bind to an IL-23p19 subunit when they are not components of IL-23, the antigen binding domain comprising a VH comprising a sequence set forth in SEQ ID NO: 26, 28 or 49 and/or a VL comprising a sequence set forth in any one of SEQ ID NOs: 27, 29 or 50. For example, the antibody comprises:

    (i) a VH comprising a sequence set forth in any one of SEQ ID NO: 7, SEQ ID NO: 49 or amino acids 1-120 of any one of SEQ ID NOs: 30 to 44 or a sequence having at least about 80% identity to any one of the foregoing; and/or
    (ii) a VL comprising an amino acid sequence set for in any one of SEQ ID NO: 12, SEQ ID NO: 50 or amino acids 1-113 of any one of SEQ ID NOs: 45 to 48. or a sequence having at least about 80% identity to any one of the foregoing.


In one example, the present disclosure provides an antibody comprising an antigen binding domain, wherein the antigen binding domain specifically binds to IL-23 but does not significantly bind to an IL-12p40 subunit and does not significantly bind to an IL-23p19 subunit when they are not components of IL-23, the antigen binding domain comprising:

    (i) a VH comprising a sequence set forth in SEQ ID NO: 26 and a VL comprising a sequence set forth in SEQ ID NO: 27;
    (ii) a VH comprising a sequence set forth in SEQ ID NO: 28 and a VL comprising a sequence set forth in SEQ ID NO: 29; or
    (iii) a VH comprising a sequence set forth in SEQ ID NO: 49 and a VL comprising a sequence set forth in SEQ ID NO: 50.


In one example, the present disclosure provides a humanized antibody comprising an antigen binding domain, wherein the antigen binding domain specifically binds to IL-23 but does not significantly bind to an IL-12p40 subunit and does not significantly bind to an IL-23p19 subunit when they are not components of IL-23, the antigen binding domain comprising a VH comprising a sequence set forth in SEQ ID NO: 28 and a VL comprising a sequence set forth in SEQ ID NO: 29.
In one example, the antigen binding domain of the humanized antibody comprises:

    (i) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 30 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 45;
    (ii) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 31 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 45;
    (iii) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 32 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 46;
    (iv) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 33 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 46;
    (v) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 34 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 46;
    (vi) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 35 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 47;
    (vii) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 33 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 48;
    (viii) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 34 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 48;
    (ix) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 32 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 48;
    (x) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 36 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 45;
    (xi) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 37 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 47;
    (xii) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 38 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 46;
    (xiii) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 39 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 46;
    (xiv) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 40 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 45;
    (xv) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 41 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 46;
    (xvi) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 42 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 46;
    (xvii) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 43 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 47;
    (xviii) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 38 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 48;
    (xix) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 39 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 48;
    (xx) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 44 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 47;
    (xxi) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 41 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 48; or
    (xxii) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 42 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 48.


In one example, the present disclosure provides a humanized antibody comprising an antigen binding domain, wherein the antigen binding domain specifically binds to IL-23 but does not significantly bind to an IL-12p40 subunit and does not significantly bind to an IL-23p19 subunit when they are not components of IL-23, the antigen binding domain comprising:

    (i) a Vii comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 30 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 45;
    (ii) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 31 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 45;
    (iii) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 32 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 46; or
    (iv) a VH comprising a sequence set forth in amino acids 1-120 of SEQ ID NO: 33 and a VL comprising a sequence set forth in amino acids 1-113 of SEQ ID NO: 46.


The present disclosure also provides a human antibody comprising an antigen binding domain of an antibody, wherein the antigen binding domain specifically binds to IL-23 but does not significantly bind to an IL-12p40 subunit and does not significantly bind to an IL-23p19 subunit when they are not components of IL-23, the antibody antigen binding domain comprising a heavy chain variable region (VH) comprising a sequence set forth in SEQ ID NO: 49 and a light chain variable region (VL) comprising a sequence set forth in SEQ ID NO: 50.
An exemplary form of an IL-23-binding protein of the disclosure is a chimeric antibody comprising a VH comprising a sequence set forth in SEQ ID NO: 7 linked to a constant region comprising a sequence set forth in SEQ ID NO: 3 or 16 and a VL comprising a sequence set forth in SEQ ID NO: 12 linked to a constant region comprising a sequence set forth in SEQ ID NO: 4. In one example, the chimeric antibody comprises a heavy chain comprising a sequence set forth in SEQ ID NO: 20 and a light chain comprising a sequence set forth in SEQ ID NO: 21.
The present disclosure additionally provides a monoclonal antibody comprising an antigen binding domain, wherein the antigen binding domain specifically binds to IL-23 but does not significantly bind to an IL-12p40 subunit and does not significantly bind to an IL-23p19 subunit when they are not components of IL-23, the antibody antigen binding domain comprising a VH comprising a sequence set forth in SEQ ID NO: 7 and a VL comprising a sequence set forth in SEQ ID NO: 12 or a chimeric, de-immunized, synhumanized or humanized form of the monoclonal antibody.
In one example, an IL-23-binding protein of the disclosure comprises a human or non-human primate heavy chain immunoglobulin constant region selected from a group consisting of IgG1, IgG2, IgG3, IgG4, IgM, IgD, IgE and IgA. An exemplary heavy chain immunoglobulin constant region is an IgG constant region, e.g., an IgG1 constant region. In one example, a constant region comprises a sequence set forth in SEQ ID NO: 3 or 16.
In another example, an IL-23-binding protein of the disclosure comprises a human or non-human primate light chain immunoglobulin constant region selected from a group consisting of kappa or lambda. In one example a kappa light chain constant region comprises a sequence set forth in SEQ ID NO: 4. In one example a lambda light chain constant region comprises a sequence set forth in SEQ ID NO:83.
In one example, the IL-23-binding protein neutralizes IL-23 activity.
In an example, the IL-23-binding protein is conjugated to a compound selected from the group consisting of a radioisotope, a detectable label, a therapeutic compound, a colloid, a toxin, a nucleic acid, a peptide, a protein, a compound that increases the half life of the protein in a subject and mixtures thereof.
The present disclosure also provides a nucleic acid encoding the IL-23-binding protein of the present disclosure. In this regard, the disclosure is not limited to the specific exemplified nucleic acids described herein, but also encompasses any nucleic acid that encodes an IL-23-binding protein of the disclosure as a result of degeneracy of the genetic code. For example, the nucleic acid may be codon optimized for expression in a particular cell type.
In one example, the nucleic acid comprises a sequence set forth in any one of SEQ ID NOs: 6, 11, 18, 19 or 57 to 77 or a sequence having at least about 80% identity thereto or a sequence that hybridizes thereto under moderate or high stringency conditions. In one example, the nucleic acid comprises a sequence set forth in any one of SEQ ID NOs: 6, 11, 18, 19, 57 to 60, 72, 73, 76 or 77 or a sequence having at least about 80% identity thereto or a sequence that hybridizes thereto under moderate or high stringency conditions.
In one example, such a nucleic acid is included in an expression construct in which the nucleic acid is operably linked to a promoter. Such an expression construct can be in a vector, e.g., a plasmid.
In examples of the disclosure directed to single polypeptide IL-23-binding proteins, the expression construct may comprise a promoter linked to a nucleic acid encoding that polypeptide chain.
In examples directed to multiple polypeptides that form an IL-23-binding protein, an expression construct of the disclosure comprises a nucleic acid encoding one of the polypeptides (e.g., comprising a VH) operably linked to a promoter and a nucleic acid encoding another of the polypeptides (e.g., comprising a VL) operably linked to a promoter.
In another example, the expression construct is a bicistronic expression construct, e.g., comprising the following operably linked components in 5′ to 3′ order:

    (i) a promoter
    (ii) a nucleic acid encoding a first polypeptide;
    (iii) an internal ribosome entry site; and
    (iv) a nucleic acid encoding a second polypeptide.


For example, the first polypeptide comprises a VH and the second polypeptide comprises a VL, or the first polypeptide comprises a VL and the second polypeptide comprises a VH.
The present disclosure also contemplates separate expression constructs one of which encodes a first polypeptide (e.g., comprising a VH) and another of which encodes a second polypeptide (e.g., comprising a VL). For example, the present disclosure also provides a composition comprising:

    (i) a first expression construct comprising a nucleic acid encoding a polypeptide (e.g., comprising a VH operably linked to a promoter); and
    (ii) a second expression construct comprising a nucleic acid encoding a polypeptide (e.g., comprising a VL operably linked to a promoter), wherein the first and second polypeptides associate to form an IL-23-binding protein of the present disclosure.


The present disclosure also provides an isolated cell expressing an IL-23-binding protein of the disclosure or a recombinant cell genetically-modified to express an IL-23-binding protein of the disclosure.
In one example, the cell comprises the expression construct of the disclosure or:

    (i) a first expression construct comprising a nucleic acid encoding a polypeptide (e.g., comprising a VH) operably linked to a promoter; and
    (ii) a second expression construct comprising a nucleic acid encoding a polypeptide (e.g., comprising a VL) operably linked to a promoter, wherein the first and second polypeptides associate to form an IL-23-binding protein of the present disclosure.


Examples of cells of the present disclosure include bacterial cells, yeast cells, insect cells or mammalian cells.
The present disclosure additionally provides methods for producing an IL-23-binding protein of the disclosure. For example, such a method involves maintaining the expression construct(s) of the disclosure under conditions sufficient for the IL-23-binding protein to be produced.
In one example, a method for producing an IL-23-binding protein of the disclosure comprises culturing the cell of the disclosure under conditions sufficient for the IL-23-binding protein to be produced and, optionally, secreted.
In one example, the method for producing an IL-23-binding protein of the disclosure additionally comprises isolating the IL-23-binding protein.
The present disclosure also provides a composition comprising an IL-23-binding protein of the disclosure and a suitable carrier or diluent. In one example, the carrier or diluent is pharmaceutically acceptable.
The present disclosure additionally provides a method for treating or preventing symptoms of an IL-23-mediated condition in a cell, tissue, organ or subject, the method comprising administering an IL-23-binding protein of the disclosure or nucleic acid encoding same or cell expressing same or a composition of the disclosure to the cell, tissue, organ or subject.
The present disclosure also provides for use of an IL-23-binding protein of the disclosure or a composition of the disclosure in medicine.
The present disclosure additionally or alternatively provides for use of an IL-23-binding protein of the disclosure in the manufacture of a medicament for the treatment of n IL-23-mediated condition.
In one example, the condition is a TH17 cell-mediated condition. In one example, the condition is an inflammatory condition or an autoimmune condition.
For example, the condition is psoriasis, Crohn's disease or multiple sclerosis. In one exemplary form, the condition is psoriasis.
The present disclosure also provides an IL-23-binding protein, antibody, composition of the disclosure for use in the treatment of psoriasis or Crohn's disease or multiple sclerosis.
The present disclosure additionally provides a method for detecting IL-23 in a sample, the method comprising contacting a sample with an IL-23-binding protein of the disclosure such that an antigen-protein complex forms and detecting the complex, wherein detecting the complex is indicative of IL-23 in the sample.
In one example, the method comprises contacting a sample with an IL-23-binding protein of the present disclosure, which is immobilized on a solid or semi-solid substrate such that a protein-antigen complex forms and detecting the complex. In some examples, detecting the complex comprises contacting the complex with a second protein comprising an antigen binding domain of an antibody that binds to IL-23 and/or IL-23p19 and/or IL-12p40 at a distinct site from an IL-23-binding protein of the disclosure and detecting the second protein.
For example, the second protein is labeled with a detectable label. Alternatively, a further labeled protein is used that binds to the second protein.
In another example, the method comprises

    (i) contacting a sample with a protein comprising an antigen binding domain of an antibody that binds to IL-23 and/or IL-23p19 and/or IL-12p40 at a distinct site from an IL-23-binding protein of the disclosure, which is immobilized on a solid or semi-solid substrate such that a protein-antigen complex forms; and
    (ii) detecting the complex by contacting the complex with an IL-23-binding protein of the disclosure and detecting the IL-23-binding protein of the disclosure.


For example, the IL-23-binding protein of the disclosure is labeled with a detectable label. Alternatively, a further labeled protein is used that binds to the IL-23-binding protein of the disclosure.
The present disclosure also provides a method for diagnosing or prognosing a condition in a subject, the method comprising performing a method of the disclosure to detect IL-23 in a sample from the subject, wherein detection of IL-23 in the sample is indicative of the condition.
In one example, the method comprises determining the level of IL-23 in the sample, wherein an increased or decreased level of IL-23 in the sample compared to a control sample is indicative of the condition.
Exemplary conditions are described herein and are to be taken to apply mutatis mutandis to the present example of the disclosure.
The ability to specifically bind to IL-23 also permits imaging applications, e.g., to diagnose or prognose conditions. Accordingly, present disclosure additionally provides a method for localizing and/or detecting IL-23 in a subject, the method comprising detecting in vivo the IL-23-binding protein or antibody of the disclosure bound to IL-23, if present, wherein the IL-23-binding protein or antibody is conjugated to a detectable label. In one example, the method additionally comprises administering the IL-23-binding protein or antibody to the subject.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 comprises a series of graphical representations showing the specificity of chimeric antibody E11E7Chimera for IL-23. Panel A shows reactivity of E11E7Chimera for human IL-23. Panel B shows reactivity of E11E7Chimera for human IL-23p19-Fc fusion protein. Panel C shows reactivity of E11E7Chimera for human IL-12p40-Fc fusion protein. Panel D shows reactivity of E11E7Chimera for mouse IL-23.
FIG. 2 is a diagrammatic representation showing the position of regions of IL-23 protected by binding of E11E7 during hydrogen/deuterium exchange experiments. Black atoms represent amino acids on IL-23p19 that demonstrated high % deuterium difference across overlapping peptides. Gray atoms represent amino acids on IL-12p40 that demonstrated high % deuterium difference across overlapping peptides. The value (25.867 is the distance in Angstroms between some atoms of the regions in IL-23p19 and IL-12p40)
FIG. 3 is a graphical representation showing inhibition of binding of IL-23 to IL-23 receptor (IL-23R) by E11E7Chimera or an anti-IL-12-p40 antibody, as indicated.
FIG. 4 is a graphical representation showing E11E7 or E11E7Chimera-mediated neutralization of IL-23-induced IL-17 secretion by mouse splenocytes. Values are expressed as percentage inhibition compared to IL-23-induced IL-17 secretion by mouse splenocytes in the absence of antibody.
FIG. 5A is a graphical representation showing clinical score over time in an IL-23-mediated mouse model of psoriasis in animals treated with E11 E7Chimera, an anti-IL-23p19 antibody or an isotype control antibody (as indicated).
FIG. 5B is a graphical representation showing epidermal thickness in an IL-23-mediated mouse model of psoriasis in animals treated with E11 E7Chimera, an anti-IL-23p19 antibody or an isotype control antibody (as indicated).
FIGS. 6A and 6B are graphical representations showing binding of E11 E7Chimera and humanized forms of E11E7 to IL-23 as determined using ELISA.
FIGS. 7A to 7F are diagrammatic representations showing sequences and/or alignments of sequences of variable regions of antibodies. FIG. 7A shows an alignment of VH regions of E11E7 and humanized forms thereof. FIG. 7B shows alignments of VH regions of selected humanized forms of E11E7. FIG. 7C shows an alignment of VL regions of E11E7 and humanized forms thereof. FIG. 7D shows alignments of VL regions of selected humanized forms of E11E7. FIG. 7E shows the amino acid sequence of the VH of human antibody ST883/885. FIG. 7F shows the amino acid sequence of the VL of human antibody ST883/885. The symbols beneath the alignments are: “*”, meaning the residues in the alignment are identical; “:” meaning that the residues in the alignment are strongly conserved (strongly conserved groups, STA; NEQK; NHQK; NDEQ; QHRK; MILV; MILF; HY; FYW), and “.” meaning the residues are weakly conserved (weakly conserved groups, CSA; ATV; SAG; STNK; STPA; SGND; SNDEQK; NDEQHK; NEQHRK; FVLIM; HFY). A consensus sequence is also shown in which is “X” indicates a site of variation. Beneath the “X” is indicated all amino acids that occur at that site in the analyzed sequences. Boxed regions contain CDRs (as indicated) as defined by the Kabat numbering system and the enhanced Chothia numbering system. CDRs defined by the Kabat numbering system are underlined. CDRs defined by the enhanced Chothia numbering system are shown in bold.
FIG. 8 includes a series of graphical representations showing binding of humanized forms of E11E7 to IL-23 but not significantly binding to IL-12p40 or IL-23p19. Blank refers to assay conditions in which the coating antigen is omitted.
FIG. 9 is a graphical representations showing binding of fully human antibody ST883/885IgG to IL-23 but not significantly binding to IL-12p40 or IL-23p19. Blank refers to assay conditions in which the coating antigen is omitted.
FIGS. 10A and 10B are graphical representations showing detection of recombinant IL-23 using E11E7 as a capture antibody as performed via ELISA (A) and the detection of native IL-23, by E11E7, produced by the cell line THP-1 when stimulated with Pokeweed Mitogen (PWM) and lipopolysaccharide (LPS), as measured by ELISA (B).
FIG. 11 is a diagrammatic representation showing methods for producing anti-IL-23 antibodies by immunizing animals.
FIG. 12 is a diagrammatic representation showing methods for producing anti-IL-23 antibodies by phage display.



DETAILED DESCRIPTION
General
Throughout this specification, unless specifically stated otherwise or the context requires otherwise, reference to a single step, composition of matter, group of steps or group of compositions of matter shall be taken to encompass one and a plurality (i.e. one or more) of those steps, compositions of matter, groups of steps or groups of compositions of matter. Thus, as used herein, the singular forms “a”, “an” and “the” include plural aspects unless the context clearly dictates otherwise. For example, reference to “a” includes a single as well as two or more; reference to “an” includes a single as well as two or more; reference to “the” includes a single as well as two or more and so forth. Each example of the disclosure is to be applied mutatis mutandis to each and every other embodiment unless specifically stated otherwise.
Each example of the disclosure is to be applied mutatis mutandis to a protein comprising a an antigen binding domain of an antibody, the antigen binding domain comprising a VH comprising a sequence set forth in SEQ ID NO: 49 and a VL comprising a sequence set forth in SEQ ID NO: 50.
Each example of the disclosure is to be applied mutatis mutandis to a protein comprising a an antigen binding domain of an antibody, the antigen binding domain comprising a VH comprising a sequence set forth in SEQ ID NO: 7 and a VL comprising a sequence set forth in SEQ ID NO: 12 or a humanized form thereof, e.g., comprising a VH and a VL of an antibody described in any one of rows 2-23 of Table 1.
Each example of the disclosure is to be applied mutatis mutandis to a protein comprising a an antigen binding domain of an antibody, the antigen binding domain comprising a VH and a VL of an antibody described in any one of rows 2, 3, 6 or 7 of Table 1.
Those skilled in the art will appreciate that the disclosure herein is susceptible to variations and modifications other than those specifically described. It is to be understood that the disclosure encompasses all such variations and modifications. The disclosure also includes all of the steps, features, compositions and compounds referred to or indicated in this specification, individually or collectively, and any and all combinations or any two or more of said steps or features.
The present disclosure is not to be limited in scope by the specific embodiments described herein, which are intended for the purpose of exemplification only. Functionally-equivalent products, compositions and methods are clearly within the scope of the disclosure.
The compositions of matter and methods described herein are produced or performed without undue experimentation using, unless otherwise indicated, conventional techniques of molecular biology, microbiology, virology, recombinant DNA technology, peptide synthesis in solution, solid phase peptide synthesis, and immunology. Such procedures are described, for example, in Sambrook, Fritsch & Maniatis, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, New York, Second Edition (1989), whole of Vols I, II, and III; Benny K. C. Lo, Antibody Engineering: Methods and Protocols, (2004) Humana Press, Vol. 248; DNA Cloning: A Practical Approach, Vols. I and II (D. N. Glover, ed., 1985), IRL Press, Oxford, whole of text; Oligonucleotide Synthesis: A Practical Approach (M. J. Gait, ed, 1984) IRL Press, Oxford, whole of text, and particularly the papers therein by Gait, pp 1-22; Atkinson et al, pp 35-81; Sproat et al, pp 83-115; and Wu et al, pp 135-151; 4. Nucleic Acid Hybridization: A Practical Approach (B. D. Hames & S. J. Higgins, eds., 1985) IRL Press, Oxford, whole of text; Immobilized Cells and Enzymes: A Practical Approach (1986) IRL Press, Oxford, whole of text; Perbal, B., A Practical Guide to Molecular Cloning (1984); Methods In Enzymology (S. Colowick and N. Kaplan, eds., Academic Press, Inc.), whole of series; J F Ramalho Ortigao, “The Chemistry of Peptide Synthesis” In: Knowledge database of Access to Virtual Laboratory website (Interactiva, Germany); Sakakibara, D., Teichman, J., Lien, E. Land Fenichel, R. L. (1976). Biochem. Biophys. Res. Commun. 73 336-342; Merrifield, R. B. (1963). J. Am. Chem. Soc. 85, 2149-2154; Barany, G. and Merrifield, R. B. (1979) in The Peptides (Gross, E. and Meienhofer, J. eds.), vol. 2, pp. 1-284, Academic Press, New York. 12. Wünsch, E., ed. (1974) Synthese von Peptiden in Houben-Weyls Metoden der Organischen Chemie (Müler, E., ed.), vol. 15, 4th edn., Parts 1 and 2, Thieme, Stuttgart; Bodanszky, M. (1984) Principles of Peptide Synthesis, Springer-Verlag, Heidelberg; Bodanszky, M. & Bodanszky, A. (1984) The Practice of Peptide Synthesis, Springer-Verlag, Heidelberg; Bodanszky, M. (1985) Int. J. Peptide Protein Res. 25, 449-474; Handbook of Experimental Immunology, Vols. I-IV (D. M. Weir and C. C. Blackwell, eds., 1986, Blackwell Scientific Publications); and Animal Cell Culture: Practical Approach, Third Edition (John R. W. Masters, ed., 2000), ISBN 0199637970, whole of text.
The term “and/or”, e.g., “X and/or Y” shall be understood to mean either “X and Y” or “X or Y” and shall be taken to provide explicit support for both meanings or for either meaning.
As used herein, the term “between” in the context of a range between two values or a residue in a protein or polypeptide between two residues shall be read in an inclusive manner, i.e., as including any values/residues located between the two recited values/residues and the two recited values/residues. For example, the term “between 1 and 10” shall be understood to include 1, 2, 3, 4, 5, 6, 7, 8, 9 and 10.
In the context of the present specification refers to “any one of [or any one or more of] SEQ ID NOs: XX to YY” will be understood to provide literal support for a statement or claim defining any one (or one or more) of the sequences falling between (as defined herein) the recited SEQ ID NOs.
Throughout this specification the word “comprise”, or variations such as “comprises” or “comprising”, will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps.
Key to Sequence Listing


    SEQ ID NO: 1 is an amino acid sequence of a human IL-12p40 subunit.
    SEQ ID NO: 2 is an amino acid sequence of a human IL23p19 subunit.
    SEQ ID NO: 3 is an amino acid sequence of a human IgG1 heavy chain constant region.
    SEQ ID NO: 4 is an amino acid sequence of a human light chain kappa constant region.
    SEQ ID NO: 5 is a nucleotide sequence encoding a fusion protein comprising an IL-12p40 subunit and an IL-23p19 subunit separated by a flexible linker.
    SEQ ID NO: 6 is a nucleotide sequence encoding a VH of antibody E11E7.
    SEQ ID NO: 7 is an amino acid sequence of a VH of antibody E11E7.
    SEQ ID NO: 8 is an amino acid sequence of a CDR1 of a VH of antibody E11E7 (according to the Kabat numbering system).
    SEQ ID NO: 9 is an amino acid sequence of a CDR2 of a VH of antibody E11E7 (according to the Kabat numbering system).
    SEQ ID NO: 10 is an amino acid sequence of a CDR3 of a VH of antibody E11E7 (according to the Kabat numbering system).
    SEQ ID NO: 11 is a nucleotide sequence encoding a VL of antibody E11E7.
    SEQ ID NO: 12 is an amino acid sequence of a VL of antibody E11E7. SEQ ID NO: 13 is an amino acid sequence of a CDR1 of a VL of antibody E11E7 (according to the Kabat numbering system).
    SEQ ID NO: 14 is an amino acid sequence of a CDR2 of a VL of antibody E11E7 (according to the Kabat numbering system).
    SEQ ID NO: 15 is an amino acid sequence of a CDR3 of a VL of antibody E11 E7 (according to the Kabat numbering system).
    SEQ ID NO: 16 is an amino acid sequence of a human heavy chain constant region.
    SEQ ID NO: 17 is an amino acid sequence of a FLAG tag.
    SEQ ID NO: 18 is a nucleotide sequence encoding a VL of the E11E7 chimeric antibody.
    SEQ ID NO: 19 is a nucleotide sequence encoding a VH of the E11E7 chimeric antibody.
    SEQ ID NO: 20 is an amino acid sequence of a heavy chain of a chimeric antibody comprising E11E7 VH and human constant region (designated E11E7Chimera).
    SEQ ID NO: 21 is an amino acid sequence of a light chain of a chimeric antibody comprising E11E7 VL and human constant region (designated E11E7Chimera).
    SEQ ID NO: 22 is an amino acid sequence of an alternative CDR2 of a VH of an antibody that binds to IL-23 as described herein.
    SEQ ID NO: 23 is an amino acid sequence of a consensus sequence of a CDR1 of a VH of an anti-IL-23 antibody (according to the enhanced Chothia numbering system).
    SEQ ID NO: 24 is an amino acid sequence of a consensus sequence of a CDR2 of a VH of an anti-IL-23 antibody (according to the Kabat numbering system).
    SEQ ID NO: 25 is an amino acid sequence of a consensus sequence of a CDR1 of a VH of a humanized anti-IL-23 antibody (according to the enhanced Chothia numbering system).
    SEQ ID NO: 26 is an amino acid sequence of a consensus sequence of a VH of an anti-IL-23 antibody.
    SEQ ID NO: 27 is an amino acid sequence of a consensus sequence of a VL of an anti-IL-23 antibody.
    SEQ ID NO: 28 is an amino acid sequence of a consensus sequence of a VH of a humanized anti-IL-23 antibody.
    SEQ ID NO: 29 is an amino acid sequence of a consensus sequence of a VL of a humanized anti-IL-23 antibody.
    SEQ ID NO: 30 is an amino acid sequence of humanized antibody heavy chain number 20.
    SEQ ID NO: 31 is an amino acid sequence of humanized antibody heavy chain number 21.
    SEQ ID NO: 32 is an amino acid sequence of humanized antibody heavy chain number 6.
    SEQ ID NO: 33 is an amino acid sequence of humanized antibody heavy chain number 8.
    SEQ ID NO: 34 is an amino acid sequence of humanized antibody heavy chain number 9.
    SEQ ID NO: 35 is an amino acid sequence of humanized antibody heavy chain number 16.
    SEQ ID NO: 36 is an amino acid sequence of humanized antibody heavy chain number 1.
    SEQ ID NO: 37 is an amino acid sequence of humanized antibody heavy chain number 13.
    SEQ ID NO: 38 is an amino acid sequence of humanized antibody heavy chain number 7.
    SEQ ID NO: 39 is an amino acid sequence of humanized antibody heavy chain number 11.
    SEQ ID NO: 40 is an amino acid sequence of humanized antibody heavy chain number 18.
    SEQ ID NO: 41 is an amino acid sequence of humanized antibody heavy chain number 5.
    SEQ ID NO: 42 is an amino acid sequence of humanized antibody heavy chain number 10.
    SEQ ID NO: 43 is an amino acid sequence of humanized antibody heavy chain number 14.
    SEQ ID NO: 44 is an amino acid sequence of humanized antibody heavy chain number 15.
    SEQ ID NO: 45 is an amino acid sequence of humanized antibody light chain number 4.
    SEQ ID NO: 46 is an amino acid sequence of humanized antibody light chain number 22.
    SEQ ID NO: 47 is an amino acid sequence of humanized antibody light chain number 12.
    SEQ ID NO: 48 is an amino acid sequence of humanized antibody light chain number 23.
    SEQ ID NO: 49 is an amino acid sequence of VH of human antibody number ST883/885.
    SEQ ID NO: 50 is an amino acid sequence of VL of human antibody number ST883/885.
    SEQ ID NO: 51 is an amino acid sequence of a CDR1 of a VH of human antibody number ST883/885.
    SEQ ID NO: 52 is an amino acid sequence of a CDR2 of a VH of human antibody number ST883/885.
    SEQ ID NO: 53 is an amino acid sequence of a CDR3 of a VH of human antibody number ST883/885.
    SEQ ID NO: 54 is an amino acid sequence of a CDR1 of a VL of human antibody number ST883/885.
    SEQ ID NO: 55 is an amino acid sequence of a CDR2 of a VL of human antibody number ST883/885.
    SEQ ID NO: 56 is an amino acid sequence of a CDR3 of a VL of human antibody number ST883/885.
    SEQ ID NO: 57 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 20.
    SEQ ID NO: 58 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 21.
    SEQ ID NO: 59 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 6.
    SEQ ID NO: 60 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 8.
    SEQ ID NO: 61 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 9.
    SEQ ID NO: 62 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 16.
    SEQ ID NO: 63 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 1.
    SEQ ID NO: 64 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 13.
    SEQ ID NO: 65 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 7.
    SEQ ID NO: 66 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 11.
    SEQ ID NO: 67 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 18.
    SEQ ID NO: 68 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 5.
    SEQ ID NO: 69 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 10.
    SEQ ID NO: 70 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 14.
    SEQ ID NO: 71 is a nucleotide sequence encoding a VH of humanized antibody heavy chain number 15.
    SEQ ID NO: 72 is a nucleotide sequence encoding a VL of humanized antibody light chain number 4.
    SEQ ID NO: 73 is a nucleotide sequence encoding a VL of humanized antibody light chain number 22.
    SEQ ID NO: 74 is a nucleotide sequence encoding a VL of humanized antibody light chain number 12.
    SEQ ID NO: 75 is a nucleotide sequence encoding a VL of humanized antibody light chain number 23.
    SEQ ID NO: 76 is a nucleotide sequence encoding VH of human antibody number ST883/885.
    SEQ ID NO: 77 is a nucleotide sequence encoding VL of human antibody number ST883/885.
    SEQ ID NO: 78 is an amino acid sequence of a fusion protein comprising the following
    linked components: IL-12p40-linker-IL-23p19.
    SEQ ID NO: 79 is an amino acid sequence of a HIS tag.
    SEQ ID NO: 80 is an amino acid sequence of an AviHIS tag.
    SEQ ID NO: 81 is an amino acid sequence of a leader sequence of a heavy chain of an antibody.
    SEQ ID NO: 82 is an amino acid sequence of a leader sequence of a light chain of an antibody.
    SEQ ID NO: 83 is an amino acid sequence of a human light chain lambda constant region

Selected Definitions



The term “isolated protein” or “isolated polypeptide” is a protein or polypeptide that by virtue of its origin or source of derivation is not associated with naturally-associated components that accompany it in its native state or is substantially free of other proteins from the same species. A protein may be rendered substantially free of naturally associated components by isolation, using protein purification techniques known in the art. The term “recovering” as used herein, refers to the process of rendering a chemical species, such as a polypeptide, substantially free of naturally associated components by isolation, e.g., using protein purification techniques known in the art. In one example, an isolated protein is substantially purified. By “substantially purified” is meant the protein is substantially free of contaminating agents, e.g., at least about 70% or 75% or 80% or 85% or 90% or 95% or 96% or 97% or 98% or 99% free of contaminating agents.
The term “recombinant” shall be understood to mean the product of artificial genetic recombination. Accordingly, in the context of a recombinant protein comprising an antibody antigen binding domain, this term does not encompass an antibody naturally-occurring within a subject's body that is the product of natural recombination that occurs during B cell maturation. However, if such an antibody is isolated, it is to be considered an isolated protein comprising an antibody variable region. Similarly, if a nucleic acid encoding the protein is isolated and expressed using recombinant means, the resulting protein is a recombinant protein comprising an antibody antigen binding domain A recombinant protein also encompasses a protein expressed by artificial recombinant means when it is within a cell, tissue or subject, e.g., in which it is expressed.
The term “IL-23-binding protein” shall be taken to include a single polypeptide chain (i.e., a series of contiguous amino acids linked by peptide bonds), or a series of polypeptide chains covalently or non-covalently linked to one another (i.e., a polypeptide complex) capable of binding to IL-23 in the manner described and/or claimed herein. For example, the series of polypeptide chains can be covalently linked using a suitable chemical or a disulphide bond. Examples of non-covalent bonds include hydrogen bonds, ionic bonds, Van der Waals forces, and hydrophobic interactions.
The term “polypeptide chain” from the foregoing paragraph will be understood to mean a series of contiguous amino acids linked by peptide bonds.
As used herein, the term “antigen binding domain” shall be taken to mean a region of an antibody that is capable of specifically binding to an antigen, i.e., a VH or a VL or a Fv. The antigen binding domain need not be in the context of an entire antibody, e.g., it can be in isolation (e.g., a domain antibody) or in another form, e.g., as described herein, such as a scFv.
For the purposes for the present disclosure, the term “antibody” includes a protein capable of specifically binding to one or a few closely related antigens (e.g., IL-23) by virtue of an antigen binding site contained within a Fv. This term includes four chain antibodies (e.g., two light chains and two heavy chains), recombinant or modified antibodies (e.g., chimeric antibodies, humanized antibodies, human antibodies, CDR-grafted antibodies, primatized antibodies, de-immunized antibodies, synhumanized antibodies, half antibodies, bispecific antibodies). An antibody generally comprises constant domains, which can be arranged into a constant region or constant fragment or fragment crystallisable (Fc). Exemplary forms of antibodies comprise a four-chain structure as their basic unit. Full-length antibodies comprise two heavy chains ( ̃50-70 kD) covalently linked and two light chains ( ̃23 kDa each). A light chain generally comprises a variable region (if present) and a constant domain and in mammals is either a κ light chain or a λ. light chain. A heavy chain generally comprises a variable region and one or two constant domain(s) linked by a hinge region to additional constant domain(s). Heavy chains of mammals are of one of the following types α, δ, ε, γ, or μ. Each light chain is also covalently linked to one of the heavy chains. For example, the two heavy chains and the heavy and light chains are held together by inter-chain disulfide bonds and by non-covalent interactions. The number of inter-chain disulfide bonds can vary among different types of antibodies. Each chain has an N-terminal variable region (VH or VL wherein each are  ̃110 amino acids in length) and one or more constant domains at the C-terminus. The constant domain of the light chain (CL which is  ̃110 amino acids in length) is aligned with and disulfide bonded to the first constant domain of the heavy chain (CH1 which is 330-440 amino acids in length). The light chain variable region is aligned with the variable region of the heavy chain. The antibody heavy chain can comprise 2 or more additional CH domains (such as, CH2, CH3 and the like) and can comprise a hinge region between the CH1 and CH2 constant domains. Antibodies can be of any type (e.g., IgG, IgE, IgM, IgD, IgA, and IgY), class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass. In one example, the antibody is a murine (mouse or rat) antibody or a primate (such as, human) antibody. In one example, the antibody is humanized, synhumanized, chimeric, CDR-grafted or deimmunized.
As used herein, “variable region” refers to the portions of the light and/or heavy chains of an antibody as defined herein that is capable of specifically binding to an antigen and, includes amino acid sequences of complementarity determining regions (CDRs); i.e., CDR1, CDR2, and CDR3, and framework regions (FRs). For example, the variable region comprises three or four FRs (e.g., FR1, FR2, FR3 and optionally FR4) together with three CDRs. In the case of a protein derived from an IgNAR, the protein may lack a CDR2. VH refers to the variable region of the heavy chain. VL refers to the variable region of the light chain
As used herein, the term “complementarity determining regions” (syn. CDRs; i.e., CDR1, CDR2, and CDR3) refers to the amino acid residues of an antibody variable region the presence of which are major contributors to specific antigen binding. Each variable region typically has three CDR regions identified as CDR1, CDR2 and CDR3. In one example, the amino acid positions assigned to CDRs and FRs are defined according to Kabat Sequences of Proteins of Immunological Interest, National Institutes of Health, Bethesda, Md., 1987 and 1991 (also referred to herein as “the Kabat numbering system”. In another example, the amino acid positions assigned to CDRs and FRs are defined according to the Enhanced Chothia Numbering Scheme (http://www.bioinfo.org.uk/mdex.html). According to the numbering system of Kabat, VH FRs and CDRs are positioned as follows: residues 1-30 (FR1), 31-35 (CDR1), 36-49 (FR2), 50-65 (CDR2), 66-94 (FR3), 95-102 (CDR3) and 103-113 (FR4). According to the numbering system of Kabat, VL FRs and CDRs are positioned as follows: residues 1-23 (FR1), 24-34 (CDR1), 35-49 (FR2), 50-56 (CDR2), 57-88 (FR3), 89-97 (CDR3) and 98-107 (FR4). The present disclosure is not limited to FRs and CDRs as defined by the Kabat numbering system, but includes all numbering systems, including the canonical numbering system or of Chothia and Lesk J. Mol. Biol. 196:901-917, 1987; Chothia et al. Nature 342, 877-883, 1989; and/or Al-Lazikani et al., J Mol Biol 273, 927-948, 1997; the numbering system of Honnegher and Plükthun J. Mol. Biol., 309: 657-670, 2001; or the IMGT system discussed in Giudicelli et al., Nucleic Acids Res., 25: 206-211 1997. In one example, the CDRs are defined according to the Kabat numbering system. Optionally, heavy chain CDR2 according to the Kabat numbering system does not comprise the five C-terminal amino acids listed herein or any one or more of those amino acids are substituted with another naturally-occurring amino acid. In an additional, or alternative, option, light chain CDR1 does not comprise the four N-terminal amino acids listed herein or any one or more of those amino acids are substituted with another naturally-occurring amino acid. In this regard, Padlan et al., FASEB J., 9: 133-139, 1995 established that the five C-terminal amino acids of heavy chain CDR2 and/or the four N-terminal amino acids of light chain CDR1 are not generally involved in antigen binding.
“Framework regions” (FRs) are those variable region residues other than the CDR residues.
As used herein, the term “Fv” shall be taken to mean any protein, whether comprised of multiple polypeptides or a single polypeptide, in which a VL and a VH associate and form a complex having an antigen binding site, i.e., capable of specifically binding to an antigen. The VH and the VL which form the antigen binding site can be in a single polypeptide chain or in different polypeptide chains. Furthermore an Fv of the disclosure (as well as any protein of the disclosure) may have multiple antigen binding sites which may or may not bind the same antigen. This term shall be understood to encompass fragments directly derived from an antibody as well as recombinant forms of such proteins. In some examples, the VH is not linked to the heavy chain constant domain CH1 and/or the VL is not linked to a light chain constant domain CL. Exemplary Fv containing polypeptides or proteins include a Fab fragment, a Fab′ fragment, a F(ab′) fragment, a scFv, a diabody, a triabody, a tetrabody or higher order complex, or any of the foregoing linked to a constant region or domain thereof, e.g., CH2 or CH3 domain, e.g., a minibody. An “Fab fragment” consists of a monovalent antigen-binding fragment of an immunoglobulin, and can be produced by digestion of a whole antibody with the enzyme papain, to yield a fragment consisting of an intact light chain and a portion of a heavy chain or can be produced using recombinant means. A “Fab′ fragment” of an antibody can be obtained by treating a whole antibody with pepsin, followed by reduction, to yield a molecule consisting of an intact light chain and a portion of a heavy chain comprising a VH and a single constant domain. Two Fab′ fragments are obtained per antibody treated in this manner. A Fab′ fragment can also be produced by recombinant means. An “F(ab′)2 fragment” of an antibody consists of a dimer of two Fab′ fragments held together by two disulfide bonds, and is obtained by treating a whole antibody molecule with the enzyme pepsin, without subsequent reduction. An “Fab2” fragment is a recombinant fragment comprising two Fab fragments linked using, for example a leucine zipper or a CH3 domain. A “single chain Fv” or “scFv” is a recombinant molecule containing the variable region fragment (Fv) of an antibody in which the variable region of the light chain and the variable region of the heavy chain are covalently linked by a suitable, flexible polypeptide linker. A detailed discussion of exemplary Fv containing proteins falling within the scope of this term is provided herein below.
As used herein, the term “specifically binds” or “binds specifically” shall be taken to mean that an IL-23-binding protein of the disclosure reacts or associates more frequently, more rapidly, with greater duration and/or with greater affinity with a particular antigen or antigens or cell expressing same than it does with alternative antigens or cells. For example, a protein that “specifically binds” to an antigen binds that antigen with greater affinity, avidity, more readily, and/or with greater duration than it binds to other antigens. It is also understood by reading this definition that, for example, a protein that specifically binds to a first antigen may or may not specifically bind to a second antigen. As such, “specific binding” does not necessarily require exclusive binding or non-detectable binding of another antigen, this is meant by the term “selective binding”. In one example, “specific binding” an IL-23-binding protein of the disclosure to an antigen, means that the protein binds to the antigen with an affinity constant of 100 nM or less, such as 50 nM or less, for example 20 nM or less, such as, 1 nM or less.
As used herein, the term “does not significantly bind” shall be taken to mean that an IL-23-binding protein of the disclosure displays 10 fold, or 20 fold or 50 fold or 60 fold or 70 fold or 80 fold or 90 fold or 100 fold, less binding to the IL-23p19 subunit and to the IL-12p40 subunit when they are not components of IL-23 than it does to IL-23, when tested under the same conditions. In some examples, an IL-23-binding protein of the disclosure has an equilibrium constant (KD) for the IL-23p19 subunit and for the IL-12p40 subunit when they are not components of IL-23 of 1×10−6 or less and, for example, the protein has a KD for IL-23 of at least about 1×10−8, such as 5×10−9. This decreased level of binding may be measured by ELISA or biosensor analysis (e.g., Biacore). In one example, an IL-23-binding protein of the disclosure does not detectably bind to IL-23p19 or IL-12p40 when they are not components of IL-23, e.g., as measured by ELISA or Biacore or Western Blot or FACS. In this regard, “does not detectably bind” shall be understood to mean that the level of binding is not significantly greater than background, e.g., as determined using an isotype control antibody.
The term “the IL-12p40 subunit and IL-23p19 subunit when they are not components of IL-23” encompasses the IL-23p19 subunit or the IL-12p40 subunit in isolation or when they are complexed with another polypeptide (i.e., the IL-12p40 subunit may be complexed with a polypeptide other than IL-23p19, such as IL-12p35).
The term “IL-23” as used herein includes a heterodimeric human cytokine belonging to a family of five such heterodimeric cytokines including IL-12 and IL-27 (Trinchieri, Pflanz et al. 2003 Immunity 19 641-4). The term includes a heterodimeric protein comprising the subunits IL-23p19 and IL-12p40 which are linked together, e.g., with a disulfide bridge. The term IL-23 is intended to include recombinant IL-23 (rIL-23), which can be prepared by standard recombinant expression methods. In some examples, the disclosure encompasses human IL-23 (abbreviated herein as hIL-23, or IL-23), including recombinant forms thereof (i.e., rhIL-23). The term “IL- 12/23” as used herein, refers to IL-12 and IL-23 collectively.
The term “IL-12p40”, identical to “IL-23p40”, and also referred to simply as “p40” and “p40 subunit” or “IL-12p40 subunit”, as used herein, includes the 40 kDa subunit of the cytokine IL-12 and the 40 kDa subunit of the cytokine IL-23 (e.g., of human IL-12 and/or IL-23). For the purposes of nomenclature and not limitation an amino acid sequence of an IL-12p40 subunit is set forth in SEQ ID NO: 1. In one example, an IL-12p40 subunit as discussed herein comprises a sequence set forth in SEQ ID NO: 1.
The term “isolated IL-12p40 subunit” shall betaken to mean the IL-12p40 subunit as defined above in a form in which it does not form a component of a heterodimer, e.g., with another interleukin protein. This term does not mean that the “isolated IL-12p40 subunit” contains no other protein or polypeptide sequences. For example, the IL-12p40 subunit can be fused to another polypeptide, e.g., a FLAG tag or a Fc region of an antibody. This term also is not limited to the IL-12p40 subunit in monomeric form (however this is one example of the “isolated IL-12p40 subunit” encompassed by the definition), since if it is fused to a Fc region of an antibody it may form homodimers.
The term “IL-23p19”, also referred to simply as “p19” or “p19 subunit”, as used herein, includes the 19 kDa subunit of the cytokine IL-23 (e.g., of human IL-23). For the purposes of nomenclature and not limitation an amino acid sequence of an IL-23p19 subunit is set forth in SEQ ID NO: 2. In one example, an IL-23p19 subunit as discussed herein comprises a sequence set forth in SEQ ID NO: 2.
The term “isolated IL-23p19 subunit” shall betaken to mean the IL-23p19 subunit as defined above in a form in which it does not form a component of a heterodimer, e.g., with another interleukin protein. This term does not mean that the “isolated IL-23p19 subunit” contains no other protein or polypeptide sequences. For example, the IL-23p19 subunit can be fused to another polypeptide, e.g., a FLAG tag or a Fc region of an antibody. This term also is not limited to the IL-23p19 subunit in monomeric form (however this is one example of the “isolated IL-23p19 subunit” encompassed by the definition), since if it is fused to a Fc region of an antibody it may form homodimers.
As used herein, the term “heterodimer” shall be understood to mean a protein complex comprising two different cytokine subunits, e.g. IL-23p19 and IL-12p40 forms an IL-23 heterodimer; and IL-12p40 and IL-12p35 form an IL-12 heterodimer. As used herein, the term “monomeric” shall be taken to mean that a subunit of IL-12 is not in direct contact with another cytokine subunit.
“Biological activity” as used herein, refers to one or more biological properties of IL-23. Biological properties of IL-23 include but are not limited to binding IL-12Rβ1 on a cell and/or IL-23R on a cell, inducing IFN-γ production following binding to a cell, inducing IL-17 production following binding to a cell, inducing IL-21 production following binding to a cell, inducing IL-22 production following binding to a cell, inducing TH17 cell differentiation and activating the antigen-presenting functions of dendritic cells, and selectively inducing proliferation of memory T cells.
As used herein, the term “heterodimeric interface” shall be taken to mean a region of IL-23 surrounding sites at which IL-12p40 and IL-23p19 contact one another and/or are linked to one another and/or are sufficiently close to permit binding of a protein such that it binds to IL-23 while not significantly binding to an IL-12p40 subunit and/or an IL-23p19 subunit when they are not components of IL-23. In this regard, this term does not limit to only those residues in IL-12p40 and IL-23p19 that actually contact one another. Rather, the residues need only be within the region of the proteins involved in heterodimerization (e.g., as depicted in FIG. 2) and exposed as to permit protein binding and to permit specific binding to IL-23 heterodimer In one example, the “heterodimeric interface” is an epitope that is produced by dimerization of the protein, e.g., comprises amino acids of IL-12p40 and IL-23p19.
As used herein, the term “epitope” (syn. “antigenic determinant”) shall be understood to mean a region of IL-23 to which a protein comprising an antigen binding domain of an antibody binds. This term is not necessarily limited to the specific residues or structure to which the protein makes contact. For example, this term in intended to encompass a region which includes amino acids contacted by the protein and/or 10 or more or 5-10 or 2-5 or 1-3 amino acids outside of this region. In some examples, the epitope is a linear series of amino acids produced upon dimerization of IL-12p40 and IL-23p19. However, an epitope can also comprise a series of discontinuous amino acids that are positioned close to one another (e.g., within about 50 Angstroms of one another, such as 40 Angstroms of one another, for example, 30 Angstroms of one another, such as within about 25 Angstroms of one another) when IL-23 is folded, i.e., a “conformational epitope”. The skilled artisan will also be aware that the term “epitope” is not limited to peptides or polypeptides. For example, the term “epitope” includes chemically active surface groupings of molecules such as sugar side chains, phosphoryl side chains, or sulfonyl side chains, and, in certain embodiments, may have specific three dimensional structural characteristics, and/or specific charge characteristics. An epitope or peptide or polypeptide comprising same can be administered to an animal to generate antibodies against the epitope.
The term “competitively inhibits” shall be understood to mean that an IL-23-binding protein of the disclosure reduces or prevents binding of an antibody comprising a heavy chain variable region comprising a sequence set forth in SEQ ID NO: 7 and a light chain variable region comprising a sequence set forth in SEQ ID NO: 12 to IL-23. It will be apparent from the foregoing that the protein need not completely inhibit binding of the antibody, rather it need only reduce binding by a statistically significant amount, for example, by at least about 10% or 20% or 30% or 40% or 50% or 60% or 70% or 80% or 90% or 95%. Methods for determining competitive inhibition of binding are known in the art and/or described herein. For example, the antibody is exposed to IL-23 either in the presence or absence of the protein. If less antibody binds in the presence of the protein than in the absence of the protein, the protein is considered to competitively inhibit binding of the antibody. For example, the protein and antibody are exposed to IL-23 substantially simultaneously. In one example, the competitive inhibition of binding is caused by the antigen binding domain of the protein on IL-23 overlapping with the antigen binding domain of the antibody.
“Overlapping” in the context of two epitopes shall be taken to mean that two epitopes share a sufficient number of amino acid residues to permit a protein that binds to one epitope to competitively inhibit the binding of a protein that binds to the other epitope. For example, the present disclosure encompasses a protein that binds to an epitope sharing a sufficient number of residues to prevent binding of an antibody comprising a heavy chain variable region comprising a sequence set forth in SEQ ID NO: 7 and a light chain variable region comprising a sequence set forth in SEQ ID NO: 12 to its epitope.
A “moderate stringency” is defined herein as being a hybridization and/or washing carried out in 2×SSC buffer, 0.1% (w/v) SDS at a temperature in the range 45° C. to 65° C., or equivalent conditions. A “high stringency” is defined herein as being a hybridization and/or wash carried out in 0.1×SSC buffer, 0.1% (w/v) SDS, or lower salt concentration, and at a temperature of at least 65° C., or equivalent conditions. Reference herein to a particular level of stringency encompasses equivalent conditions using wash/hybridization solutions other than SSC known to those skilled in the art. For example, methods for calculating the temperature at which the strands of a double stranded nucleic acid will dissociate (also known as melting temperature, or Tm) are known in the art. A temperature that is similar to (e.g., within 5° C. or within 10° C.) or equal to the Tm of a nucleic acid is considered to be high stringency. Medium stringency is to be considered to be within 10° C. to 20° C. or 10° C. to 15° C. of the calculated Tm of the nucleic acid.
As used herein, a “condition” is a disruption of or interference with normal function, and is not to be limited to any specific condition, and will include diseases or disorders.
As used herein, the terms “preventing”, “prevent” or “prevention” include administering a therapeutically effective amount of an IL-23-binding protein of the disclosure sufficient to stop or hinder the development of at least one symptom of a specified disease or condition.
As used herein, the terms “treating”, “treat” or “treatment” include administering a therapeutically effective amount of a protein described herein sufficient to reduce or eliminate at least one symptom of a specified disease or condition.
As used herein, the term “subject” shall be taken to mean any animal, such as, a mammal. In one example, the mammal is a human or non-human primate. For example, the mammal is a human.
Reference herein to a “sample” should be understood as a reference to any sample derived from a subject such as, but not limited to, a body fluid (e.g., blood or synovial fluid or cerebrospinal fluid), cellular material (e.g. tissue aspirate), tissue biopsy specimens or surgical specimens. The “sample” includes extracts and/or derivatives and/or fractions of said sample, e.g., serum, plasma, peripheral blood mononuclear cells (PBMC), or a buffy coat fraction.
As used herein, the term “diagnosis”, and variants thereof such as, but not limited to, “diagnose”, “diagnosed” or “diagnosing” includes any primary diagnosis of a clinical state or diagnosis of recurrent disease.
“Prognosis”, “prognosing” and variants thereof as used herein refer to the likely outcome or course of a disease, including the chance of recovery or recurrence or the outcome of treatment.
Proteins Comprising Antibody Variable Regions
Antibodies
Immunization-Based Methods
To generate antibodies, IL-23 or a modified form thereof (e.g., a fusion protein comprising IL12p40 subunit fused to IL-23p19 subunit) or nucleic acid encoding same, optionally formulated with any suitable or desired carrier, adjuvant, or pharmaceutically acceptable carrier, is conveniently administered to a subject (such as, a non-human subject, such as, a mouse, a rat, a chicken etc.) in the form of an injectable composition. Injection may be intranasal, intramuscular, sub-cutaneous, intravenous, intradermal, intraperitoneal, or by other known route. Optionally, the IL-23 or DNA encoding same is administered numerous times. Means for preparing and characterizing antibodies are known in the art. (See, e.g., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988).
The production of polyclonal antibodies may be monitored by sampling blood of the immunized animal at various points following immunization. A second, booster injection, may be given, if required to achieve a desired antibody titer. The process of boosting and titering is repeated until a suitable titer is achieved. When a desired level of immunogenicity is obtained, the immunized animal is bled and the serum isolated and stored, and/or the animal is used to generate monoclonal antibodies (Mabs).
Monoclonal antibodies are exemplary antibodies contemplated by the present disclosure. Generally, such a method involves, immunizing a subject (e.g., a rodent, e.g., mouse or rat) with IL-23 or nucleic acid encoding same under conditions sufficient to stimulate antibody producing cells. In some examples, a mouse genetically-engineered to express human immunoglobulin proteins and not express murine immunoglobulin proteins, is immunized to produce an antibody (e.g., as described in PCT/US2007/008231 and/or Lonberg et al., Nature 368 (1994): 856-859). Following immunization, antibody producing somatic cells (e.g., B lymphocytes) are fused with immortal cells, e.g., immortal myeloma cells. Various methods for producing such fused cells (hybridomas) are known in the art and described, for example, in Kohler and Milstein, Nature 256, 495-497, 1975. The hybridoma cells can then be cultured under conditions sufficient for antibody production.
The present disclosure contemplates other methods for producing antibodies, e.g., ABL-MYC technology (as described, for example in Largaespada et al, Curr. Top. Microbiol. Immunol, 166, 91-96. 1990).
Library-Based Methods
The present disclosure also encompasses screening of libraries of antibodies or proteins comprising variable regions thereof to identify an IL-23-binding protein of the disclosure.
Examples of this disclosure include naïve libraries (from unchallenged subjects), immunized libraries (from subjects immunized with an antigen) or synthetic libraries. Nucleic acid encoding antibodies or regions thereof (e.g., variable regions) are cloned by conventional techniques (e.g., as disclosed in Sambrook and Russell, eds, Molecular Cloning: A Laboratory Manual, 3rd Ed, vols. 1-3, Cold Spring Harbor Laboratory Press, 2001) and used to encode and display proteins using a method known in the art. Other techniques for producing libraries of proteins are described in, for example in U.S. Pat. No. 6,300,064 (e.g., a HuCAL library of Morphosys AG); U.S. Pat. Nos. 5,885,793; 6,204,023; 6,291,158; or 6,248,516.
The IL-23-binding proteins according to the disclosure may be soluble secreted proteins or may be presented as a fusion protein on the surface of a cell, or particle (e.g., a phage or other virus, a ribosome or a spore). Various display library formats are known in the art. For example, the library is an in vitro display library (e.g., a ribosome display library, a covalent display library or a mRNA display library, e.g., as described in U.S. Pat. No. 7,270,969). In yet another example, the display library is a phage display library wherein proteins comprising antigen binding domains of antibodies are expressed on phage, e.g., as described in U.S. Pat. Nos. 6,300,064; 5,885,793; 6,204,023; 6,291,158; or 6,248,516. Other phage display methods are known in the art and are contemplated by the present disclosure. Similarly, methods of cell display are contemplated by the disclosure, e.g., bacterial display libraries, e.g., as described in U.S. Pat. No. 5,516,637; yeast display libraries, e.g., as described in U.S. Pat. No. 6,423,538 or a mammalian display library.
Methods for screening display libraries are known in the art. In one example, a display library of the present disclosure is screened using affinity purification, e.g., as described in Scopes (In: Protein purification: principles and practice, Third Edition, Springer Verlag, 1994). Methods of affinity purification typically involve contacting proteins comprising antigen binding domains displayed by the library with a target antigen (e.g., IL-23) and, following washing, eluting those domains that remain bound to the antigen.
Any variable regions or scFvs identified by screening are readily modified into a complete antibody, if desired. Exemplary methods for modifying or reformatting variable regions or scFvs into a complete antibody are described, for example, in Jones et al., J Immunol Methods. 354:85-90, 2010; or Jostock et al., J Immunol Methods, 289: 65-80, 2004. Alternatively, or additionally, standard cloning methods are used, e.g., as described in Ausubel et al (In: Current Protocols in Molecular Biology. Wiley Interscience, ISBN 047 150338, 1987), and/or (Sambrook et al (In: Molecular Cloning: Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, New York, Third Edition 2001).
Selection of Proteins that Specifically Bind to IL-23
Suitable methods for selecting a protein comprising an antibody binding domain that specifically binds to IL-23 are available to those skilled in the art.
For example, a screen may be conducted to identify proteins capable of binding to IL-23 of the disclosure. Any proteins that bind to IL-23 are then screened to identify those that are incapable of binding to IL-23p19 or IL-12p40 when not components of IL-23 (e.g., in isolation or part of another cytokine, e.g., IL-12). Of course, the order of these screens can also be reversed.
An example of this type of screen is depicted in FIG. 11 and/or exemplified herein. Following repeated administration of recombinant IL-23 or genetic immunization of a vector expressing IL-23 to mice, a fusion of murine splenocytes with myeloma cells is performed resulting in hybridoma cells. Antibodies secreted by these hybridoma cells are then screened in a first round against native IL-23. Positive hybridomas are then tested in the second round against FLAG-tagged IL-23, IL-23p19 and IL-12p40. Antibodies that are positive for IL-23-binding but not IL-23p19 and IL-12p40 are heterodimeric specific antibodies.
In the case of displayed proteins, panning can be used to subtract those proteins that do not bind specifically to IL-23. For example, phage displaying proteins that bind to IL-23 are then exposed to IL-23p19 or IL-12p40 when not components of the IL-23 (e.g., in isolation or part of another cytokine) thereby removing binding proteins that bind discreetly to IL-12p40 or IL-23p19, i.e., cross-reactive proteins.
An example of this type of method is depicted in FIG. 12 and/or exemplified herein. In this example, phage are first screened (or panned) for binding to IL-23, with unbound phage removed and bound phage retained. The bound phage are then tested for binding to IL-12p40 and IL-23p19 subunits with bound phage removed and unbound phage retained. After several rounds of panning an antibody fragment having the requisite specificity for IL-23 is obtained.
Another method involves identifying an epitope formed or exposed upon dimerization of IL-23p19 and IL-12p40 that is not present or exposed when those polypeptides are not dimerized and using a peptide or polypeptide comprising said epitope as an antigen to produce proteins of the disclosure.
Deimmunized, Chimeric, Humanized, Synhumanized, Primatized and Human Proteins
The IL-23-binding proteins of the present disclosure may be may be a humanized protein.
The term “humanized protein” shall be understood to refer to a protein comprising a human-like variable region including CDRs from an antibody from a non-human species (e.g., mouse or rat or non-human primate) grafted onto or inserted into FRs from a human antibody (this type of antibody is also referred to a “CDR-grafted antibody”). As exemplified herein, humanized proteins also include proteins in which one or more residues of the human protein are modified by one or more amino acid substitutions and/or one or more FR residues of the human protein are replaced by corresponding non-human residues. Humanized proteins may also comprise residues which are found in neither the human antibody or in the non-human antibody. Any additional regions of the protein (e.g., Fc region) are generally human. Humanization can be performed using a method known in the art, e.g., U.S. Pat. Nos. 5,225,539, 6,054,297, 7,566,771 or 5,585,089. The term “humanized protein” also encompasses a super-humanized protein, e.g., as described in U.S. Pat. No. 7,732,578.
In one example, the present disclosure provides a humanized antibody comprising:

    (i) a heavy chain comprising a sequence set forth in SEQ ID NO: 30 and a light chain comprising a sequence set forth in SEQ ID NO: 45;
    (ii) a heavy chain comprising a sequence set forth in SEQ ID NO: 31 and a light chain comprising a sequence set forth in SEQ ID NO: 45;
    (iii) a heavy chain comprising a sequence set forth in SEQ ID NO: 32 and a light chain comprising a sequence set forth in SEQ ID NO: 46;
    (iv) a heavy chain comprising a sequence set forth in SEQ ID NO: 33 and a light chain comprising a sequence set forth in SEQ ID NO: 46;
    (v) a heavy chain comprising a sequence set forth in SEQ ID NO: 34 and a light chain comprising a sequence set forth in SEQ ID NO: 46;
    (vi) a heavy chain comprising a sequence set forth in SEQ ID NO: 35 and a light chain comprising a sequence set forth in SEQ ID NO: 47;
    (vii) a heavy chain comprising a sequence set forth in SEQ ID NO: 33 and a light chain comprising a sequence set forth in SEQ ID NO: 48;
    (viii) a heavy chain comprising a sequence set forth in SEQ ID NO: 34 and a light chain comprising a sequence set forth in SEQ ID NO: 48;
    (ix) a heavy chain comprising a sequence set forth in SEQ ID NO: 32 and a light chain comprising a sequence set forth in SEQ ID NO: 48;
    (x) a heavy chain comprising a sequence set forth in SEQ ID NO: 36 and a light chain comprising a sequence set forth in SEQ ID NO: 45;
    (xi) a heavy chain comprising a sequence set forth in SEQ ID NO: 37 and a light chain comprising a sequence set forth in SEQ ID NO: 47;
    (xii) a heavy chain comprising a sequence set forth in SEQ ID NO: 38 and a light chain comprising a sequence set forth in SEQ ID NO: 46;
    (xiii) a heavy chain comprising a sequence set forth in SEQ ID NO: 39 and a light chain comprising a sequence set forth in SEQ ID NO: 46;
    (xiv) a heavy chain comprising a sequence set forth in SEQ ID NO: 40 and a light chain comprising a sequence set forth in SEQ ID NO: 45;
    (xv) a heavy chain comprising a sequence set forth in SEQ ID NO: 41 and a light chain comprising a sequence set forth in SEQ ID NO: 46;
    (xvi) a heavy chain comprising a sequence set forth in SEQ ID NO: 42 and a light chain comprising a sequence set forth in SEQ ID NO: 46;
    (xvii) a heavy chain comprising a sequence set forth in SEQ ID NO: 43 and a light chain comprising a sequence set forth in SEQ ID NO: 47;
    (xviii) a heavy chain comprising a sequence set forth in SEQ ID NO: 38 and a light chain comprising a sequence set forth in SEQ ID NO: 48;
    (xix) a heavy chain comprising a sequence set forth in SEQ ID NO: 39 and a light chain comprising a sequence set forth in SEQ ID NO: 48;
    (xx) a heavy chain comprising a sequence set forth in SEQ ID NO: 44 and a light chain comprising a sequence set forth in SEQ ID NO: 47;
    (xxi) a heavy chain comprising a sequence set forth in SEQ ID NO: 41 and a light chain comprising a sequence set forth in SEQ ID NO: 48; or
    (xxii) a heavy chain comprising a sequence set forth in SEQ ID NO: 42 and a light chain comprising a sequence set forth in SEQ ID NO: 48.
    (i) a heavy chain comprising a sequence set forth in SEQ ID NO: 30 and a light chain comprising a sequence set forth in SEQ ID NO: 45;
    (ii) a heavy chain comprising a sequence set forth in SEQ ID NO: 31 and a light chain comprising a sequence set forth in SEQ ID NO: 45;
    (iii) a heavy chain comprising a sequence set forth in SEQ ID NO: 32 and a light chain comprising a sequence set forth in SEQ ID NO: 46; or
    (iv) a heavy chain comprising a sequence set forth in SEQ ID NO: 33 and a light chain comprising a sequence set forth in SEQ ID NO: 46.


In one example, a humanized protein comprises the regions between 27d and 34, 50 and 55, and 89 and 96 in a light chain sequence disclosed herein; and 31 and 35b, 50 and 58, and 95 and 101 in a heavy chain sequence disclosed herein (numbering according to the Kabat numbering system). In this regard, Padlan et al., FASEB 1, 9: 133-139, 1995 presents evidence that these regions are those most likely to bind or contact antigen.
The IL-23-binding proteins of the present disclosure may be human proteins. The term “human protein” as used herein refers to proteins having variable and, optionally, constant antibody regions derived from or corresponding to sequences found in humans, e.g. in the human germline or somatic cells. The “human” antibodies can include amino acid residues not encoded by human sequences, e.g. mutations introduced by random or site directed mutations in vitro (in particular mutations which involve conservative substitutions or mutations in a small number of residues of the protein, e.g. in 1, 2, 3, 4 or 5 of the residues of the protein. These “human antibodies” do not necessarily need to be generated as a result of an immune response of a human, rather, they can be generated using recombinant means (e.g., screening a phage display library) and/or by a transgenic animal (e.g., a mouse) comprising nucleic acid encoding human antibody constant and/or variable regions and/or using guided selection (e.g., as described in or U.S. Pat. No. 5,565,332). This term also encompasses affinity matured forms of such antibodies. A human protein will also be considered to include a protein comprising FRs from a human antibody or FRs comprising sequences from a consensus sequence of human FRs and in which one or more of the CDRs are random or semi-random, e.g., as described in U.S. Pat. Nos. 6,300,064 and/or 6,248,516.
The IL-23-binding proteins of the present disclosure may be synhumanized proteins. The term “synhumanized protein” refers to a protein prepared by a method described in WO2007/019620. A synhumanized IL-23-binding protein includes a variable region of an antibody, wherein the variable region comprises FRs from a New World primate antibody variable region and CDRs from a non-New World primate antibody variable region. For example, a synhumanized IL-23-binding protein includes a variable region of an antibody, wherein the variable region comprises FRs from a New World primate antibody variable region and CDRs from a mouse or rat antibody, e.g., E11E7 as described herein. In one example, the synhumanized IL-23-binding protein is an IL-23-binding antibody in which one or both of the variable regions are synhumanized.
The IL-23-binding proteins of the present disclosure may be primatized proteins. A “primatized protein” comprises variable region(s) from an antibody generated following immunization of a non-human primate, e.g., a cynomolgus macaque). Optionally, the variable regions of the non-human primate antibody are linked to human constant regions to produce a primatized antibody. Exemplary methods for producing primatized antibodies are described in U.S. Pat. No. 6,113,898.
In one example an IL-23-binding protein of the disclosure is a chimeric protein. The term “chimeric proteins” refers to proteins in which an antigen binding domain is from a particular species (e.g., murine, such as mouse or rat) or belonging to a particular antibody class or subclass, while the remainder of the protein is from a protein derived from another species (such as, for example, human or non-human primate) or belonging to another antibody class or subclass. In one example, a chimeric protein is a chimeric antibody comprising a VH and a VL from a non-human antibody (e.g., a murine antibody) and the remaining regions of the antibody are from a human antibody. The production of such chimeric proteins is known in the art, and may be achieved by standard means (as described, e.g., in U.S. Pat. Nos. 6,331,415; 5,807,715; 4,816,567 and 4,816,397).
The present disclosure also contemplates a deimmunized protein, e.g., as described in WO2000/34317 and WO2004/108158. De-immunized antibodies and proteins have one or more epitopes, e.g., B cell epitopes or T cell epitopes removed (i.e., mutated) to thereby reduce the likelihood that a subject will raise an immune response against the antibody or protein. For example, an IL-23-binding protein of the disclosure is analyzed to identify one or more B or T cell epitopes and one or more amino acid residues within the epitope is mutated to thereby reduce the immunogenicity of the IL-23-binding protein.
Other IL-23-Binding Proteins Comprising an Antigen Binding Domain
The present disclosure also contemplates other antigen binding domain-containing proteins, such as:

    (i) a single-domain antibody, which is a single polypeptide chain comprising all or a portion of the VH or a VL of an antibody (see, e.g., U.S. Pat. No. 6,248,516);
    (ii) diabodies, triabodies and tetrabodies, e.g., as described in U.S. Pat. No. 5,844,094 and/or US2008152586;
    (iii) scFvs, e.g., as described in U.S. Pat. No. 5,260,203;
    (iv) minibodies, e.g., as described in U.S. Pat. No. 5,837,821;
    (v) “key and hole” bispecific proteins as described in U.S. Pat. No. 5,731,168;
    (vi) heteroconjugate proteins, e.g., as described in U.S. Pat. No. 4,676,980;
    (vii) heteroconjugate proteins produced using a chemical cross-linker, e.g., as described in U.S. Pat. No. 4,676,980;
    (viii) Fab′-SH fragments, e.g., as described in Shalaby et al, J. Exp. Med., 175: 217-225, 1992; or
    (ix) Fab3 (e.g., as described in EP19930302894).

Constant Domain Fusions



The present disclosure encompasses a protein comprising an antigen binding domain of an antibody and a constant region (e.g., Fc) or a domain thereof, e.g., CH2 and/or CH3 domain. Suitable constant regions and/or domains will be apparent to the skilled artisan and/or the sequences of such polypeptides are readily available from publicly available databases, such as is available from the National Center for Biotechnology Information. Kabat et al also provide description of some suitable constant regions/domains In some examples, the constant region or portion thereof of the IL-23-binding protein is derived from a human antibody. The constant region or portion thereof may be derived from any antibody class, including IgM, IgG, IgD, IgA and IgE, and any antibody isotype, including IgG1, IgG2, IgG3 and IgG4. Exemplary sequences of constant regions are included in US20070148167.
Constant regions and/or domains thereof are useful for providing or modifying or enhancing biological activities such as, dimerization, extended serum half life (e.g., by binding to FcRn), antigen dependent cell cytotoxicity (ADCC), complement dependent cytotoxicity (CDC), and/or antigen dependent cell phagocytosis (ADCP).
The present disclosure also contemplates proteins comprising mutant constant regions or domains, e.g., as described in U.S. Pat. Nos. 7,217,797; 7,217,798; or US20090041770 (having increased half-life) or US2005037000 (increased ADCC).
For example, the IL-23-binding protein comprises one or more amino acid substitutions that increase the half-life of the protein. For example, the IL-23-binding protein comprises a constant region comprising one or more amino acid substitutions that increase the affinity of the constant region for the neonatal Fc region (FcRn). For example, the constant region has increased affinity for FcRn at lower pH, e.g., about pH 6.0, to facilitate Fc/FcRn binding in an endosome. In one example, the constant region has increased affinity for FcRn at about pH 6 compared to its affinity at about pH 7.4, which facilitates the re-release of Fc into blood following cellular recycling. These amino acid substitutions are useful for extending the half life of a protein, by reducing clearance from the blood.
Exemplary amino acid substitutions include T250Q and/or M428L or T252A, T254S and T266F or M252Y, S254T and T256E or H433K and N434F according to the EU numbering system. Additional or alternative amino acid substitutions are described, for example, in US20070135620 or U.S. Pat. No. 7,083,784.
Neutralizing proteins of the present disclosure can comprise an IgG4 constant region or a stabilized IgG4 constant region. The term “stabilized IgG4 constant region” will be understood to mean an IgG4 constant region that has been modified to reduce Fab arm exchange or the propensity to undergo Fab arm exchange or formation of a half-antibody or a propensity to form a half antibody. “Fab arm exchange” refers to a type of protein modification for human IgG4, in which an IgG4 heavy chain and attached light chain (half-molecule) is swapped for a heavy-light chain pair from another IgG4 molecule. Thus, IgG4 molecules may acquire two distinct Fab arms recognizing two distinct antigens (resulting in bispecific molecules). Fab arm exchange occurs naturally in vivo and can be induced in vitro by purified blood cells or reducing agents such as reduced glutathione. A “half antibody” forms when an IgG4 antibody dissociates to form two molecules each containing a single heavy chain and a single light chain.
In one example, a stabilized IgG4 constant region comprises a proline at position 241 of the hinge region according to the system of Kabat (Kabat et al., Sequences of Proteins of Immunological Interest Washington D.C. United States Department of Health and Human Services, 1987 and/or 1991). This position corresponds to position 228 of the hinge region according to the EU numbering system (Kabat et al., Sequences of Proteins of Immunological Interest Washington D.C. United States Department of Health and Human Services, 2001 and Edelman et al., Proc. Natl. Acad. USA, 63, 78-85, 1969). In human IgG4, this residue is generally a serine. Following substitution of the serine for proline, the IgG4 hinge region comprises a sequence CPPC. In this regard, the skilled person will be aware that the “hinge region” is a proline-rich portion of an antibody heavy chain constant region that links the Fc and Fab regions that confers mobility on the two Fab arms of an antibody. The hinge region includes cysteine residues which are involved in inter-heavy chain disulfide bonds. It is generally defined as stretching from Glu226 to Pro243 of human IgG1 according to the numbering system of Kabat. Hinge regions of other IgG isotypes may be aligned with the IgG1 sequence by placing the first and last cysteine residues forming inter-heavy chain disulphide (S—S) bonds in the same positions (see for example WO2010/080538).
Mutant Proteins
As discussed herein, the present disclosure provides a protein or nucleic acid having at least 80% identity to the sequence of the disclosure.
In one example, an IL-23-binding protein of the disclosure comprises a VH comprising a sequence at least about 80% or 85% or 90% or 95% or 97% or 98% or 99% identical to a sequence set forth in set forth in any one of SEQ ID NO: 7 or amino acids 1-120 of any one of SEQ ID NOs: 30 to 44, or SEQ ID NO: 49, wherein the protein is capable of specifically binding to IL-23 but not significantly binding to an IL-12p40 subunit and not significantly binding to an IL-23p19 subunit when they are not components of IL-23. Alternatively, or additionally, the protein comprises a CDR (e.g., three CDRs) at least about 80% or 85% or 90% or 95% or 97% or 98% or 99% identical to CDR(s) of a VH as described herein according to any example, and capable of specifically binding to IL-23 but not significantly binding to an IL-12p40 subunit and not significantly binding to an IL-23p19 subunit when they are not components of IL-23. Methods for determining binding of a protein to IL-23, IL-23p19 and IL-12p40 are described herein.
For example, the inventors have produced a series of VH regions having variation at about 30% of residues. Thus, a protein can comprise a VH comprising a sequence at least about 70% identical to a VH sequence disclosed herein. In one example, the sequence is at least 85% or 95% identical.
The inventors have also produced a series of humanized VH regions having variation at about 11% of residues. Thus, a protein can comprise a VH comprising a sequence at least about 89% identical to a VH sequence disclosed herein. In one example, the sequence is at least 90% or 95% identical.
The inventors have also identified residues in heavy chain CDR2 according to the Kabat numbering system that can be mutated while maintaining the specific binding to IL-23 without significantly binding to an IL-12p40 subunit and without significantly binding to an IL-23p19 subunit when they are not components of IL-23. For example, two of 16 residues can be mutated (12.5% of residues). Thus, a protein can comprise a CDR2 having at least about 87.5% identity to a heavy chain CDR2 sequence disclosed herein.
As discussed herein, it is also known in the art that the five C-terminal residues of heavy chain CDR2 can be mutated to conservative or non-conservative amino acid substitutions (31% of residues) (Padlan et al., FASEB J., 9: 133-139, 1995). Thus, a protein can comprise a CDR2 having at least about 69% identity to a heavy chain CDR2 sequence disclosed herein.
The inventors have also identified residues in heavy chain CDR1 according to the enhanced Chothia numbering system that can be mutated while maintaining the specific binding to IL-23 without significantly binding to an IL-12p40 subunit and without significantly binding to an IL-23p19 subunit when they are not components of IL-23. For example, two of seven residues can be mutated (28% or 43% of residues) or three of seven residues can be mutated (43% of residues). Thus, a protein can comprise a CDR2 having at least about 72% identity to a heavy chain CDR1 sequence disclosed herein.
In another example, a nucleic acid of the disclosure comprises a sequence at least about 80% or 85% or 90% or 95% or 97% or 98% or 99% identical to a sequence set forth in any one of SEQ ID NOs: 6, 19, 57 to 71 or 76. The present disclosure also encompasses nucleic acids encoding a protein comprising a sequence set forth in any one of SEQ ID NOs: SEQ ID NO: 7, 26, 28, or amino acids 1-120 of any one of SEQ ID NOs: 30 to 44, or SEQ ID NO: 49, which differs from a sequence exemplified herein as a result of degeneracy of the genetic code.
In one example, an IL-23-binding protein of the disclosure comprises a VL comprising a sequence at least about 80% or 85% or 90% or 95% or 97% or 98% or 99% identical to a sequence set forth in any one of SEQ ID NO: 12 or amino acids 1-113 of any one of SEQ ID NOs: 45 to 48 or SEQ ID NO: 50, wherein the protein is capable of specifically binding to IL-23 but not significantly binding to an IL-12p40 subunit and not significantly binding to an IL-23p19 subunit when they are not components of IL-23. Alternatively, or additionally, the protein comprises a CDR (e.g., three CDRs) at least out 80% or 85% or 90% or 95% or 97% or 98% or 99% identical to CDR(s) of a VL as described herein according to any example, and capable of specifically binding to IL-23 but not significantly binding to an IL-12p40 subunit and not significantly binding to an IL-23p19 subunit when they are not components of IL-23.
For example, the inventors have produced a series of VL regions having variation at about 32% of residues. Thus, a protein can comprise a VL comprising a sequence at least about 68% identical to a VL sequence disclosed herein. In one example, the sequence is at least 85% or 95% identical.
The inventors have also produced a series of humanized VL regions having variation at about 14% of residues. Thus, a protein can comprise a VH comprising a sequence at least about 86% identical to a VH sequence disclosed herein. In one example, the sequence is at least 90% or 95% identical.
In another example, a nucleic acid of the disclosure comprises a sequence at least about 80% or 85% or 90% or 95% or 97% or 98% or 99% identical to a sequence set forth in any one of SEQ ID NOs: 11, 18, 72 to 75 or 77. The present disclosure also encompasses nucleic acids encoding a protein comprising a sequence set forth in any one of SEQ ID NO: 12, 27, 29 or amino acids 1-113 of any one of SEQ ID NOs: 45 to 48 or SEQ ID NO: 50, which differs from a sequence exemplified herein as a result of degeneracy of the genetic code.
The % identity of a nucleic acid or polypeptide is determined by GAP (Needleman and Wunsch. Mol. Biol. 48, 443-453, 1970) analysis (GCG program) with a gap creation penalty=5, and a gap extension penalty=0.3. The query sequence is at least 50 residues in length, and the GAP analysis aligns the two sequences over a region of at least 50 residues. For example, the query sequence is at least 100 residues in length and the GAP analysis aligns the two sequences over a region of at least 100 residues. In one example, the two sequences are aligned over their entire length.
The present disclosure contemplates mutant forms of an IL-23-binding protein of the disclosure. For example, such a mutant protein comprises one or more conservative amino acid substitutions compared to a sequence set forth herein. In some examples, the IL-23-binding protein comprises 10 or fewer, e.g., 9 or 8 or 7 or 6 or 5 or 4 or 3 or 2 or 1 conservative amino acid substitutions. A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain and/or hydropathicity and/or hydrophilicity.
Families of amino acid residues having similar side chains have been defined in the art, including basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), β-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Hydropathic indices are described, for example in Kyte and Doolittle J. Mol. Biol., 157: 105-132, 1982 and hydrophylic indices are described in, e.g., U.S. Pat. No. 4,554,101.
The present disclosure also contemplates non-conservative amino acid changes. For example, of particular interest are substitutions of charged amino acids with another charged amino acid and with neutral or positively charged amino acids. In some examples, the protein comprises 10 or fewer, e.g., 9 or 8 or 7 or 6 or 5 or 4 or 3 or 2 or 1 non-conservative amino acid substitutions.
A mutant form of a protein described herein according to any example retains the ability to specifically bind to IL-23 while not significantly binding to an IL-12p40 subunit and/or an IL-23p19 subunit when they are not components of IL-23. Methods for determining specific binding to IL-23 are described herein. For example, a labeled protein is brought into contact with immobilized IL-23 or IL-12p40 subunit or IL-23p19 subunit.
Following washing, bound label is detected. The labeled protein is also brought into contact with immobilized IL-23p19 and/or IL-12p40 and, following washing, bound label is detected. Detection of label bound to IL-23 but not to IL-23p19 or IL-12p40 indicates that the mutant protein retains the ability to specifically bind to IL-23. An optional additional step in the foregoing methods comprises detecting label bound to the IL-23p19 subunit or and/IL-12p40 subunit. If label is detected bound to IL-23 but not significantly bound to IL-12p40 and/or IL-23p19, the protein is considered to specifically bind to IL-23 while not significantly binding to an IL-12p40 subunit and/or an IL-23p19 subunit when they are not components of IL-23.
In one example, the mutation(s) occur within a FR of an IL-23-binding protein of the disclosure. In another example, the mutation(s) occur within a CDR of an IL-23-binding protein of the disclosure.
Exemplary methods for producing mutant forms of protein include:

    
    
        mutagenesis of DNA (Thie et al., Methods Mol. Biol. 525:309-22, 2009) or RNA (Kopsidas et al., Immunol. Lett. 107(2):163-8, 2006; WO1999/058661);
        introducing a nucleic acid encoding the polypeptide into a mutator cell, e.g., XL-1Red, XL-mutS and XL-mutS-Kanr bacterial cells (Stratagene);
        DNA shuffling, e.g., as disclosed in Stemmer, Nature 370:389-91, 1994; and
        site directed mutagenesis, e.g., as described in Dieffenbach (ed) and Dveksler (ed) (In: PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratories, NY, 1995).
    
    


Exemplary methods for determining biological activity of the mutant proteins of the disclosure will be apparent to the skilled artisan and/or described herein. For example, methods for determining antigen binding, competitive inhibition of binding, affinity, association, dissociation and therapeutic efficacy are described herein.
In one example, a mutant protein is produced by or following affinity maturation.
Exemplary Proteins
Exemplary variable region containing proteins produced by the inventors and their encoding nucleic acids are described in Table 1.







TABLE 1







Sequences of proteins and encoding nucleic acids














Heavy 
Variable
Light
Variable




chain
heavy chain
chain
light chain




amino acid
nucleotide
amino acid
nucleotide



Antibody
SEQ ID
SEQ ID
SEQ ID
SEQ ID



Name
NO
NO
NO
NO















1
E11E7Chimera
20
6
21
11


2
 8-22
33
60
46
73


3
21-4 
31
58
45
72


4
 9-22
34
61
46
73


5
16-12
35
62
47
74


6
20-4 
30
57
45
72


7
 6-22
32
59
46
73


8
 8-23
33
60
48
75


9
 9-23
34
61
48
75


10
 6-23
32
59
48
75


11
1-4
36
63
45
72


12
13-12
37
64
47
74


13
 7-22
38
65
46
73


14
11-22
39
66
46
73


15
18-4
40
67
45
72


16
 5-22
41
67
46
73


17
10-22
42
69
46
73


18
14-12
43
70
47
74


19
 7-23
38
65
48
75


20
11-23
39
66
48
75


21
15-12
44
71
47
74


22
 5-23
41
68
48
75


23
10-23
42
69
48
75


24
ST883/885
 491
76
 501
77





1variable region sequence only.






Methods for Producing Proteins

Recombinant Expression

As discussed herein, a nucleic acid encoding an IL-23-binding protein of the disclosure (and/or polypeptides included in such a protein) is introduced into an expression construct, such that it is operably linked to a promoter to thereby facilitate its expression. Methods for producing expression constructs, e.g., cloning into expression constructs/vectors are known in the art and/or described in Ausubel et al (In: Current Protocols in Molecular Biology. Wiley Interscience, ISBN 047 150338, 1987), and (Sambrook et al (In: Molecular Cloning: Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, New York, Third Edition 2001) and U.S. Pat. No. 7,270,969.
In one example, the IL-23-binding protein of the disclosure is expressed in a bacterial cell. Typical promoters suitable for expression in bacterial cells such as for example a bacterial cell selected from the group comprising E. coli, Staphylococcus sp, Corynebacterium sp., Salmonella sp., Bacillus sp., and Pseudomonas sp., include, but are not limited to a promoter such as lacz, Ipp, a temperature-sensitive (L or (R promoters, T7, T3, SP6 or semi-artificial promoters such as the IPTG-inducible tac promoter or lacUV5 promoter.
In another example, the IL-23-binding protein is expressed in a yeast cell. Typical promoters suitable for expression in yeast cells such as, Pichia pastoris, Saccharomyces cerevisiae and S. pombe, include, but are not limited to promoters from the following genes ADH1, GAL1, GAL4, CUP1, PHO5, nmt, RPR1, or TEF1.
In a further example, the IL-23-binding protein is expressed in an insect cell. Typical promoters suitable for expression in insect cells, or in insects, include, but are not limited to, the OPEI2 promoter, the insect actin promoter isolated from Bombyx muri, the Drosophila sp. dsh promoter (Marsh et al Hum. Mol. Genet. 9, 13-25, 2000).
An IL-23-binding protein of the disclosure can also be expressed in plant cells. Promoters for expressing peptides in plant cells are known in the art, and include, but are not limited to, the Hordeum vulgare amylase gene promoter, the cauliflower mosaic virus 35S promoter, the nopaline synthase (NOS) gene promoter, and the auxin inducible plant promoters P1 and P2.
In one example, an IL-23-binding protein of the disclosure is expressed in a mammalian cell or in a mammal. Typical promoters suitable for expression in a mammalian cell include, for example a promoter selected from the group consisting of, retroviral LTR elements, the SV40 early promoter, the SV40 late promoter, the CMV IE (cytomegalovirus immediate early) promoter, the EF1 (promoter (from human elongation factor 1), the EM7 promoter, the UbC promoter (from human ubiquitin C). Examples of useful mammalian host cell lines include monkey kidney CV1 line transformed by SV40 (COS-7); human embryonic kidney line (HEK-293 cells); baby hamster kidney cells (BHK); Chinese hamster ovary cells (CHO); African green monkey kidney cells (VERO-76); or myeloma cells (e.g., NS/0 cells). In one example, the cells are CHO cells.
Other elements of expression constructs/vectors are known in the art and include, for example, enhancers, transcriptional terminators, polyadenylation sequences, nucleic acids encoding selectable or detectable markers and origins of replication.
In one example, an expression construct is a bicistronic expression construct. By “bicistronic” is meant a single nucleic acid molecule that is capable of encoding two distinct polypeptides from different regions of the nucleic acid, for example, a single nucleic acid capable of encoding a VH containing polypeptide and a VL containing polypeptide as distinct polypeptides. Generally, the regions encoding each distinct polypeptide are separated by an internal ribosome entry site (IRES) and the region 5′ of the IRES does not comprise a transcription termination sequence. Exemplary IRESs are described, for example, in US20090247455.
Following production of a suitable expression construct, it is introduced into a suitable cell using any method known in the art. Exemplary methods include microinjection, transfection mediated by DEAE-dextran, transfection mediated by liposomes such as by using lipofectamine (Gibco, Md., USA) and/or cellfectin (Gibco, Md., USA), PEG-mediated DNA uptake, electroporation and microparticle bombardment such as by using DNA-coated tungsten or gold particles (Agracetus Inc., WI, USA) amongst others.
The cells used to produce the IL-23-binding protein of this disclosure are then cultured under conditions known in the art to produce an IL-23-binding protein of the disclosure.
Cell free expression systems are also contemplated by the present disclosure, e.g., the TNT T7 and TNT T3 systems (Promega), the pEXP1-DEST and pEXP2-DEST vectors (Invitrogen).
Protein Purification
Following production/expression, an IL-23-binding protein of the disclosure is purified using a method known in the art. Such purification generally provides the IL-23-binding protein of the disclosure substantially free of nonspecific protein, acids, lipids, carbohydrates, and the like. For example, the IL-23-binding protein will be in a preparation wherein more than about 90% (e.g. 95%, 98% or 99%) of the protein in the preparation is an IL-23-binding protein of the disclosure.
Standard methods of peptide purification are employed to obtain an isolated protein of the disclosure, including but not limited to various high-pressure (or performance) liquid chromatography (HPLC) and non-HPLC polypeptide isolation protocols, such as size exclusion chromatography, ion exchange chromatography, phase separation methods, electrophoretic separations, precipitation methods, salting in/out methods, immunochromatography, and/or other methods.
Alternatively, affinity purification is useful for isolating a fusion protein comprising a label. Methods for isolating a protein using affinity chromatography are known in the art and described, for example, in Scopes (In: Protein purification: principles and practice, Third Edition, Springer Verlag, 1994). For example, an antibody or compound that binds to the label (in the case of a polyhistidine tag this may be, for example, nickel-NTA) may be immobilized on a solid support. A sample comprising a protein is then contacted to the immobilized antibody or compound for a time and under conditions sufficient for binding to occur. Following washing to remove any unbound or non-specifically bound protein, the protein is eluted.
In the case of a protein comprising a Fc region of an antibody, protein A or protein G or modified fours thereof can be used for affinity purification. Protein A is useful for isolating purified proteins comprising a human γ1, γ2, or γ4 heavy chain Fc region. Protein G is recommended for all mouse Fc isotypes and for human γ3.
Conjugates
The present disclosure also provides an IL-23-binding protein of the disclosure conjugated to another compound, e.g., a conjugate (or immunoconjugate). The other compound can be directly or indirectly bound to the IL-23-binding protein (e.g., can comprise a linker in the case of indirect binding). The compound can be covalently or non-covalently linked to the IL-23-binding protein. Examples of compounds include, a radioisotope (e.g., iodine-131, yttrium-90 or indium-111), a detectable label (e.g., a fluorophore or a fluorescent nanocrystal), a therapeutic compound (e.g., a chemotherapeutic or an anti-inflammatory), a colloid (e.g., gold), a toxin (e.g., ricin or tetanus toxoid), a nucleic acid, a peptide (e.g., a serum albumin binding peptide), a protein (e.g., a protein comprising an antigen binding domain of an antibody or serum albumin), a compound that increases the half life of the protein in a subject (e.g., polyethylene glycol or other water soluble polymer having this activity) and mixtures thereof. Exemplary compounds that can be conjugated to an IL-23-binding protein of the disclosure and methods for such conjugation are known in the art and described, for example, in WO2010/059821.
Anti-Idiotype Antibodies
In addition to the IL-23-binding proteins of the disclosure that bind specifically to IL-23, the present disclosure also provides an anti-idiotypic (anti-Id) antibody specific for the protein of the disclosure. An anti-Id antibody is an antibody that recognizes unique determinants generally associated with the antigen-binding domain of an IL-23-binding protein of the disclosure. The anti-Id can be prepared by immunizing an animal with the protein of the disclosure or antigen binding domain thereof. The immunized animal will recognize and respond to the idiotypic determinants of the immunizing protein and produce an anti-Id antibody. The anti-Id antibody may also be used as an “immunogen” to induce an immune response in yet another animal, producing a so-called anti-anti-Id antibody.
Screening Assays
Proteins comprising antibody variable regions of the disclosure are readily screened for biological activity, e.g., as described below.
Binding Assays
One form of such an assay is an antigen binding assay, e.g., as described in Scopes (In: Protein purification: principles and practice, Third Edition, Springer Verlag, 1994). Such a method generally involves labeling the IL-23-binding protein and contacting it with immobilized antigen. Following washing to remove non-specific bound protein, the amount of label and, as a consequence, bound protein is detected. Of course, the IL-23-binding protein can be immobilized and the antigen labeled. Panning-type assays, e.g., as described or exemplified herein can also be used.
Neutralization Assays
An exemplary in vitro method for determining the effect (or neutralization activity) of an IL-23-binding protein of the disclosure is to contact IL-23 to a population of cells comprising immune cells upon which the IL-23 acts in the presence or absence of an IL-23-binding protein of the disclosure. Cell proliferation is then measured using a standard method, e.g., 13H thymidine incorporation or 5,6-carboxy fluorescein diacetate succinimidyl ester (CFSE) labeling and/or cytokine secretion. An increase or decrease in cell proliferation and/or cytokine secretion compared to a sample incubated in the absence of the protein indicates that the IL-23-binding protein modulates IL-23 activity. Such a method is exemplified herein.
Another method for determining the ability of an IL-23-binding protein of the disclosure to neutralize IL-23 activity is a receptor binding assay. In such a method, an IL-23 receptor or cell expressing same is immobilized. Labeled IL-23 (e.g., between 50 ng/ml and 150 ng/ml, such as 100 ng/ml) is then contacted to the immobilized receptor or cell in the presence or absence of a test protein and the amount of bound label detected. The IL-23-binding protein and the IL-23 can be contacted with one another prior to contacting the receptor or can be contacted to the receptor substantially simultaneously. A reduction in the amount of bound label in the presence of the IL-23-binding protein compared to in the absence of the protein indicates that the protein reduces or prevents binding of IL-23 to IL-23R.
By testing multiple concentrations of the IL-23-binding protein an IC50 is determined, i.e., a concentration of the protein that reduces the amount of IL-23 that binds to IL-23R. In one example, the IC50 is about 1 nM or less, such as 750 pM or less, for example, 500 pM or less. For example, the IC50 is 400 pM or less. In one example, the IC50 is between about 1 pM and 500 pM, for example, between about 50 pM and 450 pM. For example, the IC50 is between about 100 pM and 400 pM, for example, between about 150 pM and 400 pM.
Similarly, an EC50 can be determined, i.e., a concentration of the protein that achieves 50% of the maximum inhibition of binding of IL-23 to IL-23R achieved by the protein. In one example, the EC50 is 1 nM or less, for example, 750 pM or less, for example, 500 pM or less, such as 400 pM or less. In one example, the EC50 is about 300 pM or less. For example, the EC50 is about 260 pM.
Another method for determining the ability of an IL-23-binding protein of the disclosure to neutralize IL-23 activity is to contact splenocytes with IL-23 in the presence or absence of the IL-23-binding protein and to detect secretion of a cytokine, such as, IL-17. A lower level of the cytokine in the presence of the protein compared to in the absence of the protein indicates that the protein neutralizes IL-23 activity. By testing multiple concentrations of the protein an IC50 is determined, i.e., a concentration at which 50% of the maximum inhibition of cytokine secretion occurs.
By testing multiple concentrations of the IL-23-binding protein an IC50 is determined, i.e., a concentration of the protein that reduces the amount of cytokine (e.g., IL-17) secreted. In one example, the IC50 is about 1 nM or less, such as 900 pM or less, for example, 800 pM or less. For example, the IC50 is 700 pM or less. In one example, the IC50 is between about 1 pM and 800 pM, for example, between about 50 pM and 700 pM. For example, the IC50 is between about 100 pM and 700 pM, for example, between about 120 pM and 680 pM.
Similarly, an EC50 can be determined, i.e., a concentration of the protein that achieves 50% of the maximum inhibition of cytokine (e.g., IL-17) secretion achieved by the protein. In one example, the EC50 is 1 nM or less, for example, 500 pM or less, such as 400 pM or less. In one example, the EC50 is about 300 pM or less. For example, the EC50 is about 290 pM.
Cell Killing Assays
In another example, the ability of an IL-23-binding protein of the disclosure (e.g., linked to a toxic compound or a constant region) is assessed by determining their ability to induce death of a cell. In the case of a Fc linked protein it is desirable to perform such an assay in the presence of immune effector cells and/or complement (e.g., to facilitate ADCC/CDC).
In Vivo Therapeutic Efficacy Assays
In another example, the activity of an IL-23-binding protein of the disclosure is determined by administering the IL-23-binding protein to an animal model. For example, the IL-23-binding protein is administered to NOD mice to test its ability to suppress, prevent, treat or delay diabetes (e.g., as described in Tang et al., J. Exp. Med., 199: 1455-1465, 2004) and/or to a mouse model of GVHD (e.g., as described in Trenado et al., J. Clin. Invest., 112: 1688-1696, 2002) and/or to a mouse model of psoriasis (e.g., Wang et al., J Clin Invest. 118(7): 2629-2639, 2008) and/or to a model of rheumatoid arthritis e.g., a SKG strain of mouse (Sakaguchi et al., Nature, 426: 454-460, 1995), rat type II collagen arthritis model, mouse type II collagen arthritis model or antigen induced arthritis models in several species (Bendele J Musculoskel Neuron Interact; 1(4):377-385, 2001) and/or a model of multiple sclerosis (for example, experimental autoimmune encephalomyelitis (EAE) and/or inflammatory airway disease (for example, OVA challenge or cockroach antigen challenge).
In one example, the activity of an IL-23-binding protein of the disclosure is determined in an IL-23-induced animal model of psoriasis, e.g., as exemplified herein. For example, a non-human mammal (e.g., a mouse) is administered IL-23 subcutaneously such that a localized inflammatory response is induced. Proteins are tested for their ability to prevent or treat the inflammatory response by administering before or after administration of IL-23. Animals are then assessed for erythema and/or induration and/or skin samples are collected from each mouse and fixed for histological assessment.
Competitive Binding Assays
Assays for determining a protein that competitively inhibits binding of an antibody of the disclosure will be apparent to the skilled artisan. For example, the antibody of the disclosure is conjugated to a detectable label, e.g., a fluorescent label or a radioactive label. The labeled antibody and the test protein are then mixed and contacted with IL-23 or an epitope thereof. The level of labeled antibody is then determined and compared to the level determined when the labeled antibody is contacted with the IL-23 or epitope in the absence of the protein. If the level of labeled antibody is reduced in the presence of the test protein compared to the absence of the protein, the protein competitively inhibits binding of the antibody.
Optionally, the test protein is conjugated to a different label than the antibody. This permits detection of the level of binding of the test protein to the protein or epitope.
In another example, the test protein is permitted to bind to IL-23 or a region thereof prior to contacting the IL-23 with an antibody described herein. A reduction in the amount of bound antibody in the presence of the protein compared to in the absence of the protein indicates that the protein competitively inhibits binding of the antibody to IL-23. A reciprocal assay can also be performed using labeled protein and first allowing the antibody to bind to IL-23. In this case, a reduced amount of labeled protein bound to IL-23 in the presence of the antibody compared to in the absence of antibody indicates that the protein competitively inhibits binding of the antibody to IL-23.
Epitope Mapping Assays
In another example, the epitope bound by a protein described herein is mapped. Epitope mapping methods will be apparent to the skilled artisan. For example, a series of overlapping peptides spanning the IL-23 sequence or a region thereof comprising an epitope of interest, e.g., peptides comprising 10-15 amino acids are produced. The IL-23-binding protein is then contacted to each peptide or a combination thereof and the peptide(s) to which it binds determined. This permits determination of peptide(s) comprising the epitope to which the IL-23-binding protein binds. If multiple non-contiguous peptides are bound by the protein, the protein may bind a conformational epitope.
Alternatively, or in addition, amino acid residues within IL-23 are mutated, e.g., by alanine scanning mutagenesis, and mutations that reduce or prevent protein binding are determined. Any mutation that reduces or prevents binding of the IL-23-binding protein is likely to be within the epitope bound by the protein.
A further method involves binding IL-23 or a region thereof to an immobilized protein of the present disclosure and digesting the resulting complex with proteases. Peptide that remains bound to the immobilized protein are then isolated and analyzed, e.g., using mass spectrometry, to determine their sequence.
A further method involves converting hydrogens in IL-23 or a region thereof to deuterium atoms and binding the resulting protein to an immobilized protein of the present disclosure. The deuterium atoms are then converted back to hydrogen, the IL-23 or region thereof isolated, digested with enzymes and analyzed, e.g., using mass spectrometry to identify those regions comprising deuterium, which would have been protected from conversion to hydrogen by the binding of a protein described herein. A form of this method is exemplified herein.
Affinity Assays
Optionally, the dissociation constant (Kd) or association constant (Ka) or affinity constant (KD) of a protein for IL-23 or an epitope thereof is determined. These constants for a IL-23-binding protein is in one example measured by a radiolabeled or fluorescently-labeled IL-23-binding assay. This assay equilibrates the protein with a minimal concentration of labeled IL-23 in the presence of a titration series of unlabeled IL-23. Following washing to remove unbound IL-23, the amount of label is determined.
Affinity measurements can be determined by standard methodology for antibody reactions, for example, immunoassays, surface plasmon resonance (SPR) (Rich and Myszka Curr. Opin. Biotechnol 11: 54, 2000; Englebienne Analyst. 123: 1599, 1998), isothermal titration calorimetry (ITC) or other kinetic interaction assays known in the art.
In one example, the constants are measured by using surface plasmon resonance assays, e.g., using BIAcore surface plasmon resonance (BIAcore, Inc., Piscataway, N.J.) with immobilized IL-23 or a region thereof. Exemplary SPR methods are described in U.S. Pat. No. 7,229,619.
Half Life Assays
Some proteins encompassed by the present disclosure have an improved half-life, e.g., are modified to extend their half-life compared to proteins that are unmodified. Methods for determining a protein with an improved half-life will be apparent to the skilled person. For example, the ability of a protein to bind to a neonatal Fc receptor (FcRn) is assessed. In this regard, increased binding affinity for FcRn increased the serum half-life of the molecule (see for example, Kim et al., Eur J. Immunol., 24:2429, 1994).
The half-life of an IL-23-binding protein of the disclosure can also be measured by pharmacokinetic studies, e.g., according to the method described by Kim et al, Eur J of Immunol 24:542, 1994. According to this method radiolabeled protein is injected intravenously into mice and its plasma concentration is periodically measured as a function of time, for example at 3 minutes to 72 hours after the injection. The clearance curve thus obtained should be biphasic, that is, an alpha phase and beta phase. For the determination of the in vivo half-life of the protein, the clearance rate in beta-phase is calculated and compared with that of the wild type or unmodified protein.
Stability Assays
Stability of an IL-23-binding protein of the disclosure can be assessed by any of a variety of assays. For example, the protein is exposed to a condition, e.g., heat or acid or stored for a period of time (e.g., 1 month) at room temperature. Aggregation of the protein can then be assessed by determining turbidity (with an increase in turbidity following exposure to the condition indicating instability), size exclusion chromatography, non-reducing gel electrophoresis or a binding or neutralization study described herein.
Pharmaceutical Compositions
The IL-23-binding protein of the present disclosure or nucleic acid encoding same or cell expressing same (syn. active ingredient) is useful for parenteral, topical, oral, or local administration, aerosol administration, or transdermal administration, for prophylactic or for therapeutic treatment. In one example, the IL-23-binding protein of the present disclosure or nucleic acid encoding same or cell expressing same is for parenteral administration, such as intravenous or subcutaneous administration.
Formulation of a protein or nucleic acid encoding same or cell expressing same to be administered will vary according to the route of administration and formulation (e.g., solution, emulsion, capsule) selected. An appropriate pharmaceutical composition comprising protein or nucleic acid encoding same or cell expressing same to be administered can be prepared in a physiologically acceptable carrier. A mixture of proteins can also be used. For solutions or emulsions, suitable carriers include, for example, aqueous or alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles can include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's or fixed oils. A variety of appropriate aqueous carriers are known to the skilled artisan, including water, buffered water, buffered saline, polyols (e.g., glycerol, propylene glycol, liquid polyethylene glycol), dextrose solution and glycine. Intravenous vehicles can include various additives, preservatives, or fluid, nutrient or electrolyte replenishers (See, generally, Remington's Pharmaceutical Science, 16th Edition, Mack, Ed. 1980). The compositions can optionally contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents and toxicity adjusting agents, for example, sodium acetate, sodium chloride, potassium chloride, calcium chloride and sodium lactate. The IL-23-binding protein of this disclosure can be lyophilized for storage and reconstituted in a suitable carrier prior to use according to art-known lyophilization and reconstitution techniques.
The optimum concentration of the active ingredient(s) in the chosen medium can be determined empirically, according to procedures well known to the skilled artisan, and will depend on the ultimate pharmaceutical formulation desired.
The dosage ranges for the administration of the IL-23-binding protein of the disclosure are those large enough to produce the desired effect. For example, the composition comprises a therapeutically or prophylactically effective amount of the IL-23-binding protein or nucleic acid encoding same or cell expressing same.
As used herein, the term “effective amount” shall be taken to mean a sufficient quantity of the IL-23-binding protein, nucleic acid or cells to induce/increase or inhibit/reduce/prevent signaling of IL-23 in a subject. The skilled artisan will be aware that such an amount will vary depending on, for example, the protein, nucleic acid or cells and/or the particular subject and/or the type or severity of a condition being treated. Accordingly, this term is not to be construed to limit the disclosure to a specific quantity, e.g., weight or number of proteins, nucleic acids or cells.
As used herein, the term “therapeutically effective amount” shall be taken to mean a sufficient quantity of protein, nucleic acid or cells to reduce or inhibit one or more symptoms of a condition.
As used herein, the term “prophylactically effective amount” shall be taken to mean a sufficient quantity of protein, nucleic acid or cells to prevent or inhibit or delay the onset of one or more detectable symptoms of a condition.
The dosage should not be so large as to cause adverse side effects, such as hyper viscosity syndromes, pulmonary edema, congestive heart failure, and the like. Generally, the dosage will vary with the age, condition, sex and extent of the disease in the patient and can be determined by one of skill in the art. The dosage can be adjusted by the individual physician in the event of any complication. Dosage can vary from about 0.1 mg/kg to about 300 mg/kg, e.g., from about 0.2 mg/kg to about 200 mg/kg, such as, from about 0.5 mg/kg to about 20 mg/kg, in one or more dose administrations daily, for one or several days.
One or more proteins of the present disclosure can be administered to an individual by an appropriate route, either alone or in combination with (before, simultaneous with, or after) another drug or agent. For example, the IL-23-binding protein of the present disclosure can also be used in combination with proteins, e.g., a TNF antagonist, an anti-IL-12/23 antibody, an anti-inflammatory or a painkiller. The IL-23-binding protein of the present disclosure can be used as separately administered compositions given in conjunction with antibiotics and/or antimicrobial agents. It will be appreciated by those skilled in the art that the IL-23-binding proteins of the present disclosure may be introduced into a subject by administering an expression construct of the disclosure or a cell expressing an IL-23-binding protein of the disclosure. A variety of methods can be used for introducing a nucleic acid encoding the antibody into a target cell in vivo. For example, the naked nucleic acid may be injected at the target site, may be encapsulated into liposomes, or may be introduced by way of a viral vector.
Diagnostic Assays
The following assays can be performed with an IL-23-binding protein of the disclosure.
An immunoassay is an exemplary assay format for diagnosing a condition in a subject or detecting IL-23 in a sample. The present disclosure contemplates any form of immunoassay, including Western blotting, enzyme-linked immunosorbent assay (ELISA), fluorescence-linked immunosorbent assay (FLISA), competition assay, radioimmunoassay, lateral flow immunoassay, flow-through immunoassay, electrochemiluminescent assay, nephelometric-based assays, turbidometric-based assay, and fluorescence activated cell sorting (FACS)-based assays.
One form of a suitable immunoassay is, for example, an ELISA or FLISA.
In one form such an assay involves immobilizing an IL-23-binding protein of the disclosure onto a solid matrix, such as, for example a polystyrene or polycarbonate microwell or dipstick, a membrane, or a glass support (e.g. a glass slide). A test sample is then brought into direct contact with the IL-23-binding protein and any antigen in the sample is bound or captured. Following washing to remove any unbound protein in the sample, a protein that binds to IL-23 at a distinct epitope (e.g., binds to IL-23p19 or IL-12p40) is brought into direct contact with the captured antigen. This detector protein is generally labeled with a detectable reporter molecule, such as for example, an enzyme (e.g. horseradish peroxidase (HRP)), alkaline phosphatase (AP) or (3-galactosidase. Alternatively, a second labeled protein can be used that binds to the detector protein. Following washing to remove any unbound protein the detectable marker is detected by the addition of a substrate, such as for example hydrogen peroxide, TMB, or toluidine, or 5-bromo-4-chloro-3-indol-beta-D-galaotopyranoside (x-gal). Of course, the immobilized (capture) protein and the detector protein may be used in the opposite manner.
The level of the antigen in the sample is then determined using a standard curve that has been produced using known quantities of the marker or by comparison to a control sample.
In the case of FLISA, a fluorescent label is used to determine the level of a labeled protein in a sample rather than an enzyme.
The assays described above are readily modified to use chemiluminescence or electrochemiluminescence as the basis for detection.
As will be apparent to the skilled artisan, other detection methods based on an immunosorbent assay are useful in the performance of the present disclosure. For example, an immunosorbent method based on the description supra using a radiolabel for detection, or a gold label (e.g. colloidal gold) for detection, or a liposome, for example, encapsulating NAD+ for detection or an acridinium linked immunosorbent assay.
In some examples of the disclosure, the level of IL-23 is determined using a surface plasmon resonance detector (e.g., BIAcoreTM, GE Healthcare, Piscataway, N.J.), a flow through device, for example, as described in U.S. Pat. No. 7,205,159; a micro- or nano-immunoassay device (e.g., as described in US20030124619); a lateral flow devices (e.g., as described in US20040228761 or US20040265926); a fluorescence polarization immunoassay (FPIA e.g., as described in U.S. Pat. Nos. 4,593,089 or 4,751,190); or an immunoturbidimetric assay (e.g., as described in U.S. Pat. Nos. 5,571,728 or 6,248,597.
Imaging Methods
As will be apparent to the skilled artisan from the foregoing, the present disclosure also contemplates imaging methods using an IL-23-binding protein of the disclosure. For imaging, a protein is generally conjugated to a detectable label, which can be any molecule or agent that can emit a signal that is detectable by imaging. However, a secondary labeled compound that specifically binds to an IL-23-binding protein of the disclosure may also be used. Exemplary detectable labels include a protein, a radioisotope, a fluorophore, a visible light emitting fluorophore, infrared light emitting fluorophore, a metal, a ferromagnetic substance, an electromagnetic emitting substance a substance with a specific magnetic resonance (MR) spectroscopic signature, an X-ray absorbing or reflecting substance, or a sound altering substance.
The IL-23-binding protein of the disclosure (and, if used the labeled secondary compound) can be administered either systemically or locally to an organ, or tissue (or tumor, in the case of a cancer) to be imaged, prior to the imaging procedure. Generally, the IL-23-binding protein is administered in doses effective to achieve the desired optical image of a tumor, tissue, or organ. Such doses may vary widely, depending upon the particular protein employed, condition to be imaged, tissue, or organ subjected to the imaging procedure, the imaging equipment being used, and the like.
In some examples of the disclosure, the IL-23-binding protein is used as in vivo optical imaging agents of tissues and organs in various biomedical applications including, but not limited to, imaging of tumors, tomographic imaging of organs, monitoring of organ functions, coronary angiography, fluorescence endoscopy, laser guided surgery, photoacoustic and sonofluorescence methods, and the like.
Examples of imaging methods include magnetic resonance imaging (MRI), MR spectroscopy, radiography, computerized tomography (CT), ultrasound, planar gamma camera imaging, single-photon emission computed tomography (SPECT), positron emission tomography (PET), other nuclear medicine-based imaging, optical imaging using visible light, optical imaging using luciferase, optical imaging using a fluorophore, other optical imaging, imaging using near infrared light, or imaging using infrared light.
In some examples, an imaging agent is tested using an in vitro or in vivo assay prior to use in humans, e.g., using a model described herein.
Samples and Control Samples
As will be apparent to the skilled artisan, some of the examples described herein require some degree of quantification to determine the level of IL-23. Such quantification may be determined by the inclusion of a suitable control sample in an assay of the disclosure.
In one example, a suitable control sample is a sample that is derived from a healthy subject or a normal subject.
In the present context, the term “healthy subject” shall be taken to mean an individual who is known not to suffer from a condition associated with IL-23, e.g., an inflammatory condition.
The term “normal subject” shall be taken to mean an individual having a normal level of IL-23 in a sample compared to a population of individuals.
The present disclosure also contemplates the control sample as being a data set obtained from a normal and/or healthy subject or a population of normal and/or healthy subjects.
In one example, a method of the disclosure additionally comprises determining the level of IL-23 in a control sample, e.g., using a method described herein.
In one example, a sample from the subject and a control sample are assayed at approximately or substantially the same time.
In one example, the sample from the subject and the control sample are assayed using the same method of the disclosure as described herein in any one or more embodiments to allow for comparison of results.
Conditions
Exemplary conditions which may be treated/prevented/diagnosed/prognosed by performing a method of the disclosure include inflammatory conditions, GVHD, infection and cancer.
Exemplary inflammatory conditions include inflammatory bowel disease (IBD), systemic lupus erythematosus, rheumatoid arthritis, juvenile chronic arthritis, spondyloarthropathies, systemic sclerosis (scleroderma), idiopathic inflammatory myopathies (dermatomyositis, polymyositis), Sjogren's syndrome, systemic vaculitis, sarcoidosis, autoimmune hemolytic anemia (immune pancytopenia, paroxysmal nocturnal hemoglobinuria), autoimmune thrombocytopenia (idiopathic thrombocytopenic purpura, immune-mediated thrombocytopenia), thyroiditis (Grave's disease, Hashimoto's thyroiditis, juvenile lymphocytic thyroiditis, atrophic thyroiditis), diabetes mellitus, immune-mediated renal disease (glomerulonephritis, tiibulointerstitial nephritis), demyelinating diseases of the central and peripheral nervous systems such as multiple sclerosis, idiopathic polyneuropathy, hepatobiliary diseases such as infectious hepatitis (hepatitis A, B, C, D, E and other nonhepatotropic viruses), autoimmune chronic active hepatitis, primary biliary cirrhosis, granulomatous hepatitis, and sclerosing cholangitis, inflammatory and fibrotic lung diseases (e.g., cystic fibrosis), gluten-sensitive enteropathy, Whipple's disease, autoimmune or immune-mediated skin diseases including bullous skin diseases, erythema multiforme and contact dermatitis, psoriasis, allergic diseases of the lung such as eosinophilic pneumonia, idiopathic pulmonary fibrosis and hypersensitivity pneumonitis. For example, the inflammatory condition is inflammatory arthritis, e.g., RA or juvenile chronic arthritis.
In another example, the inflammatory condition is an inflammatory neurological condition, e.g., a myelin associated condition, e.g., multiple sclerosis.
In another example, the inflammatory condition is an inflammatory skin disease (e.g., an autoimmune or immune-mediated skin disease), e.g., a bullous skin diseases, erythema multiforme, contact dermatitis. Alternatively, the skin disease is psoriasis.
In another example, the inflammatory condition is an inflammatory mucosal condition, e.g., an inflammatory disease of the bowel (e.g., inflammatory bowel disease, Crohn's disease or ulcerative colitis), or an inflammatory disease of the lung (e.g., airway hyperreactivity or asthma).
In one example, a condition is a TH17 cell-mediated condition. As used herein, the term “TH17 cell-mediated condition” shall be taken to mean any condition characterized or caused by excessive numbers or activity of TH17 cells. The skilled artisan will be aware that a TH17 cell is a CD4+ T cell that expresses IL-17. Exemplary TH17 cell-mediated conditions include autoimmune/inflammatory conditions (e.g., psoriasis, inflammatory bowel disease, arthritis (e.g., rheumatoid arthritis), multiple sclerosis and inflammatory bowel disease (e.g., Crohn's disease)) and graft versus host disease.
In one example, a condition is psoriasis.
In another example, a condition is Crohn's disease.
In a further example, a condition in multiple sclerosis.
In one example, the multiple sclerosis is relapsing-remitting multiple sclerosis, and the IL-23-binding protein or antibody is administered while the condition is in remission to there by prevent a relapse.
Kits
The present disclosure additionally comprises a kit comprising one or more of the following:

    (i) an IL-23-binding protein of the disclosure or expression construct(s) encoding same;
    (ii) a cell of the disclosure; or
    (iii) a pharmaceutical composition of the disclosure.


In the case of a kit for detecting IL-23, the kit can additionally comprise a detection means, e.g., linked to an IL-23-binding protein of the disclosure.
In the case of a kit for therapeutic/prophylactic use, the kit can additionally comprise a pharmaceutically acceptable carrier or diluent.
Optionally a kit of the disclosure is packaged with instructions for use in a method described herein according to any embodiment.
The present disclosure is described further in the following non-limiting Examples.
General Methods
HEK293/pTT5 Expression System
For all transfections involving the HEK293E/pTT5 expression system, HEK293E cells were cultured in complete cell growth media (1 L of F17 medium (InvitrogenTM), 9 ml of Pluronic F68 (InvitrogenTM), 2 mM Glutamine containing 20% (w/v) Tryptone NI (OrganotechnieTM) with Geneticin (50 mg/ml, InvitrogenTM) at 50 μl/100 ml culture). Briefly, the day before transfection cells were harvested by centrifugation and resuspended in fresh media without Geneticin. The following day cells were transfected by dropwise addition of a transfection mixture comprising DNA and FuGENE (Roche) according to manufacturer's directions. Transfected cultures were incubated overnight at 37° C., 5% CO2 with gentle shaking (120 rpm) prior to the addition of Tryptone and Geneticin (12.5 mL and 250 uL per 500 mL of culture volume respectively). The following day 12.5 ml of Tryptone and 250 μl of Geneticin were added per 500 ml culture. The culture was incubated at 37° C., 5% CO2 and 120 rpm for seven days, then the supernatants were harvested and purified.
IL-23 Protein
Human IL-23 (comprising of IL-12p40 (SEQ ID NO: 1) covalently linked to IL-23p19 (SEQ ID NO: 2) was purchased (Ebiosciences or RnD Systems). Alternatively, IL-23, IL-12p40 and IL-23p19 were produced in the mammalian HEK293E/pTT5 expression system through transfection of DNA expression constructs as described previously. The following proteins were produced:







TABLE 2







List of IL-23 proteins used in these experiments.












Subunit A 
TAG A
Subunit B
TAG B


Name
(SEQ ID)
(SEQ ID)
(SEQ ID)
(SEQ ID)





IL-23Fc
p40
human Fc
p19
FLAG



(SEQ ID NO: 1)
(SEQ ID NO: 16)
(SEQ ID NO: 2)
(SEQ ID NO: 17)


IL-23His
p40-linker-p19
HIS
N/A
N/A



(SEQ ID NO:78)
(SEQ ID NO: 79)




IL-23AviHis
p40
None
p19
AviTag&HIS



(SEQ ID NO: 1)

(SEQ ID NO: 2)
(SEQ ID NO: 80)


IL-12p40Fc
p40
human Fc
N/A
N/A



(SEQ ID NO: 1)
(SEQ ID NO: 16)




IL-12p19Fc
p19
human Fc





(SEQ ID NO: 2)
(SEQ ID NO: 16)









Culture supernatants containing the secreted proteins were harvested by centrifugation at 2000×g for 10 mins to remove the cells. Proteins containing a HIS Tag were purified from the supernatant via the His8 affinity tag using a HisTrapTM HP column (GE Healthcare). Proteins containing a Fc region were purified using Protein A chromatography as described below for the purification of antibodies. Eluted proteins were buffer-exchanged into PBS using a concentrator (Amicon) or via desalting or via size-exclusion chromatography.
For phage display the AvitagTM sequence of the recombinant human IL-23AviHIS was biotinylated using the enzyme BirA. This resulted in specific biotinylation at a single amine containing amino acid in the AviTag sequence. Free biotin was removed from the protein preparation either by dialysis against PBS using a Slide-A-Lyzer dialysis cassette (Pierce) with a 3.5 kDa molecular weight cut-off or a desalting column (GE Healthcare).
Construction of Vectors Expressing Antibodies
Heavy chain variable region (VH) amino acid sequences were formatted in silico onto a human IgG1 constant region comprising CH1, hinge, CH2 and CH3 domains (see for example NCBI accession number P01857.1). Similarly, light chain variable region sequences were formatted in silico onto either a human kappa or lambda constant region (see for example NCBI accession numbers AAI10395 (kappa) and AAI07853 (lambda)) according to the isotype of the parental variable region. Amino acid sequences were subsequently back-translated into DNA sequences (GeneArt, Germany). The resulting genes were synthesized de novo by assembly of synthetic oligonucleotides (GeneArt, Germany). Heavy and light-chain genes were subsequently cloned into variants of the expression vector pTT5 (Durocher et al., Nucleic Acids Research 30, E9, 2002) containing either a heavy- or a light- chain leader sequence, respectively (SEQ ID NOs: 81 and 82, respectively).
Expression and Purification of Antibodies
Antibodies were produced through co-transfection of heavy- and light-chain containing pTT5 plasmids into the cell line HEK293E using the transfection reagent FuGENE (Roche) as described above. After seven days supernatants were harvested by centrifugation and adjusted to pH 7.4 prior to loading onto a HiTrapTM Protein A column (5 ml, GE Healthcare). The column was washed with 50 ml of 1×PBS (pH 7.4). Elution was performed using 0.1M citric acid pH 2.5. The eluted antibody was desalted using Zeba Desalting columns (Pierce) into 1×PBS (pH 7.4). The antibodies were analyzed using SDS-PAGE. The concentration of the antibody was determined using a BCA assay kit (Pierce) according to manufacturer's instrcutions.
Detecting Binding of Antibodies to IL-23 by ELISA
A NuncMaxisorp 96-well plate was coated with human IL-23 diluted to 1 μs/ml in carbonate coating buffer and overnight incubation at 4° C. The plate was washed (three times in 1×PBS-Tween20 (0.05%)) then blocked for an hour with 1% BSA in PBS at room temperature. Biotinylated antibody was prepared starting from 10 μg/ml and serial half log dilutions were performed then 100 μl was added to the plate and incubated for an hour. The plate was washed and Streptavidin-HRP at 1:2000 dilution was added to all wells and further incubated for an hour. The plate was washed and subsequently developed using TMB (Sigma). The color development reaction was stopped by addition of an equal volume of 1M HCl. Absorbance of the resulting reaction was determined using a plate-based spectrophotometer.
Surface Plasmon Resonance (SPR) Analysis of IL-23-binding Antibodies
Using a Biacore 3000, Protein A (Pierce) was immobilized on a CM5 chip using amine coupling chemistry to give 3000 Response Units (RU). Antibody was captured on the surface of the chip in flow cell 2 or 4 with a control surface in flow cell 1 or 3. Human IL-23 was then passed over both flow cells and the response units measured. The surface was then regenerated with 10 mM glycine pH 2.5. For a kinetic run this process was repeated with 5 dilutions of IL-23. Data was double referenced using an injection of running buffer before being fitted using a 1:1 Langmuir equation to determine ka, kd and KD.
Antibody Inhibition of IL-23-Induced IL-17 Production in Murine Splenocytes
Spleens were obtained from C57BL/6 mice and prepared by first homogenizing the spleens followed by lysis of the red blood cells using NH4Cl. The splenocytes were then washed in media (RPMI, 10% FBS, 2 mM L-Glutamine, 100U of Pen/Strep) by resuspension and centrifugation. The antibody was diluted in culture media sufficient to generate a titration curve across a 96-well plate. 100 ng/mL of human IL-23 (EBiosciences) was added to each well and incubated at 37° C. with 5% CO2 humidity for 1 hour. The cells were added to the wells giving a cell concentration of 5×106 cells/mL in a total volume of 200 μl/well. Cultures were incubated at 37° C. with 5% CO2 with humidity for 4 days. The supernatants were harvested at the end of incubation and a Duoset ELISA murine IL-17 kit (R&D Systems) was used to detect murine IL-17 produced.
EXAMPLE 1
Production of Monoclonal Antibodies That Specifically Bind IL-23
Hybridoma Generation
Monoclonal antibodies against heterodimeric IL-23 were generated by genetic immunization with corresponding conventional protein immunization of rats. For genetic immunization, the DNA sequence for human IL-23 (containing a GS linker to facilitate the expression of the molecule from one promoter; SEQ ID NO: 5) was cloned into a plasmid for genetic immunization using restriction enzyme technology. The resulting plasmids allow the secretion of soluble IL-23 tagged by a c-myc epitope at the N- or C-terminus. The c-myc epitope was utilized to confirm expression of the soluble IL-23.
Rats were then immunized six times with the plasmid using a Helios gene gun (Bio-Rad, Germany) according to a published procedure (Kilpatrick et al., Hybridoma 17: 569-576, 1998). One week after the last application of the immunization plasmid each rat is boosted by intradermal injection of recombinant human IL-23 protein (Ebiosciences).
Four days later, the rats were killed and their lymphocytes fused with myeloma cells using polyethylene glycol (HybriMaxTM; Sigma-Aldrich, Germany), seeded at 100,000 cells per well in 96- well microtiter plates and grown in DMEM medium supplemented with 10% fetal bovine serum and HAT additive for hybridoma selection ((Kilpatrick et al., 1998, supra)).
Screening of Hybridoma for Antibody Specificity
Full-length native IL-23 (Ebioscience) was coated onto a 96-well plate (Maxisorp, Nunc). Hybridoma supernatant from each hybridoma was added to the IL-23 coated wells and bound antibody detected using secondary antibodies specific for murine (rat) antibodies with a HRP conjugate facilitating a color reaction. Hybridomas which displayed positive binding for IL-23 were subcloned via limiting dilution, in which cells were diluted in culture media and deposited into fresh 96-well plates at a ratio of less than 1 cell/well. After the clones recovered additional ELISAs were performed on the hybridoma supernatant.
Anti-FLAG M2 antibody (Sigma-Aldrich) was coated onto ELISA plates overnight. These plates were then used to capture individually: FLAG-tagged IL-23p19, FLAG-tagged IL-12p40 and FLAG-tagged IL-23. Hybridoma supernatant from the clones was added and hybridomas that were positive for binding to IL-23 but not IL-12p40 or IL-23p19 were expanded.
Identification and Molecular Characterization of Rat Antibody E11E7 with IL-23 Heterodimer Specificity
Using the above method of immunization and screening one rat hybridoma out of approximately 83 hybridomas screened secreted an antibody that bound strongly to IL-23 but not significantly to IL-12p40 or IL-23p19. This antibody, termed E11E7 was sequenced by reverse transcriptase polymerase chain reaction using RNA isolated from E11E7-expressing hybridoma cells. Briefly, RNA was prepared using TRI reagent (Sigma) according to the manufacturer's protocol. cDNA synthesized from 100-200 ng RNA using the AccuScript® High Fidelity 1st Strand cDNA Synthesis Kit (Stratagene) was subsequently used as a template for PCR. Primers from the Novagen Mouse IgG Primer Set were used to amplify putative E11E7 heavy- and light-chain sequences from the cDNA using the polymerase UltraPfuII-HS essentially according to manufacturer's instructions (Stratagene). Thermocycling was performed using an Eppendorf Mastercycler and the following cycling parameters:

    (94° C. 2 min) 1 cycle; followed by;
    (94° C. 30 sec, 60° C. 30 sec, 72° C. 45 sec) 30 cycles; followed by
    (72° C. 5 min) 1 cycle


Following electrophoresis on an agarose gel (0.7-1.0%), PCR products were excised and cleaned using the Qiaquick gel extraction kit (Qiagen). A-tailing was performed through incubation of Taq-polymerase (InvitrogenTM) and dATP at 72° C. for 15 minutes. A-tailed PCR products were then ligated into pGEM-T Easy (Promega) and transformed into TOP10 competent cells (InvitrogenTM) according to manufacturer's instructions. PCR screening of transformants using vector-specific primers identified clones possessing a plasmid containing an insert of  ̃500 bp. Plasmid DNA was subsequently isolated from insert-containing clones using a QIAprep spin miniprep kit (QIAgen) and sequenced (AGRF, Brisbane). The nucleotide sequences for the variable heavy (SEQ ID NO: 6) and variable light chains (SEQ ID NO: 11) were then translated into primary amino acid sequence (SEQ ID NO: 7 for VH and SEQ ID NO: 12 for VL).
A rat-human chimeric antibody was generated through formatting the rat E11E7 heavy- and light-chain variable region amino acid sequences onto human constant regions. Genes were synthesized following back-translation and subsequently cloned into the expression vector pTT5 as described in the general methods. The nucleotide sequence of the VH comprises a sequence set forth in SEQ ID NO: 19. The nucleotide sequence of the VL comprises a sequence set forth in SEQ ID NO: 18. Amino acid sequences of these full length heavy- and light chains are given in SEQ ID NOs: 20 and 21, respectively.
E11E7Chimera was biotinylated (Pierce EZ-Link Sulfo-NHS) and screened for binding to IL-23Fc, IL-23p19Fc, IL-12p40Fc and murine IL-23 (Ebiosciences) using ELISA techniques described in the general methods. Biotinylated E11E7Chimera bound to IL-23 strongly and showed little to no binding to the individual subunits or to murine IL-23 (FIG. 1). This demonstrated that E11E7Chimera was specific for the human IL-23 complex but not the individual subunits.
Mapping of the Epitope of E11E7
Epitope mapping was performed on the E11E7Chimera to determine the location on IL-23 to which the antibody binds. Using hydrogen/deuterium exchange experiments (essentially as described in U.S. Pat. No. 06,797,482B2), critical regions on IL-23 involved in the binding to E11E7 were identified. Hydrogen was exchanged in solution for deuterium on IL-23. This deuterated IL-23 was then bound by a FAb fragment of E11E7Chimera in solution. The complex was exchanged back to hydrogen, except for the regions on IL-23 that were in contact with the antibody and therefore protected from exchange. The IL-23: Antibody complex was then digested and analyzed via mass spectroscopy to identify regions containing deuterium. The following results were obtained:







TABLE 3







Deuterium difference of IL-23 peptides before and 


after incubation with E11E7








IL-12p40
IL-23p19














%


%


Sequence
Sequence
Deuterium
Sequence
Sequence
Deuterium


Start
End
Difference
Start
End
Difference















3
9
 8%
17
23
13%


3
12
 7%
17
24
11%


12
23
 6%
26
37
17%


15
23
 4%
27
37
13%


26
54
 7%
40
68
18%


29
54
 9%
40
69
19%


29
80
 5%
71
80
 1%


57
80
 6%
72
81
 5%


62
80
 4%
81
88
 6%


83
90
 9%
83
88
 6%


85
90
 5%
91
105
17%


93
109
 6%
91
109
25%


112
121
 9%
112
115
13%


112
122
 5%
112
140
36%


124
125
 5%
112
144
32%


128
132
12%
115
140
36%


131
132
 8%
143
144
11%


135
150
12%
143
153
 5%


135
153
12%
145
153
 6%


156
170
 8%
155
170
 5%


158
170
 9%
160
170
12%


173
187
 5%





173
189
 2%





187
189
 1%





208
231
 7%





208
233
 8%





234
247
 8%





236
246
11%





249
251
 1%





250
251
 2%





253
274
 9%





254
274
 2%





277
296
 8%





278
296
 7%





299
306
 5%





302
306
 6%









The sequences used for this analysis corresponds to SEQ ID NO: 1 for the IL-12p40 subunit and SEQ ID NO: 2 for the IL-23p19 subunit. For each individual subunit the mean±standard deviation (S.D.) % deuterium difference was calculated across 50% of the peptides with the lowest deuterium content. A value greater then the mean+3 S.D. was considered significantly. The mean (50%)+3 S.D. % deuterium difference across the p40 subunit was 10.2%. The mean (50%)+3 S.D. % deuterium difference across the p19 subunit was 18.1%. Overlapping peptides sequences in which the % deuterium difference was greater then the mean (50%)±3 S.D. are highlighted in bold in Table 3. These data demonstrates that residues on IL-12p40 and IL-23p19 were protected from deuterium exchange upon binding of E11E7Chimera.
Peptides with the highest deuterium content (p40: 135-153; p19: 112-144) were mapped on a crystal structure of IL-23 (FIG. 2). The FAb arm of an antibody having a diameter  ̃50 Angstroms (as measured across the crystal structure 3HMX) could well bind across the 25 Angstrom span between atoms within the highlighted regions of p40 and p19.
E11E7Chimera Inhibits IL-23-binding to IL-23R
hIL23R-HIS was diluted to 1 μg/ml in carbonate coating buffer and added to each well of a 96 well plate and incubated at 4° C. overnight. The plate was then washed three times. The wells were then blocked by adding 200 μl of blocking buffer to each well and incubating the plate at 25° C. for 1 hour. E11E7Chimera or anti-p40 antibody was diluted in antibody diluent sufficient to generate a titration curve starting at 10 μg/ml. Biotinylated hIL-23 (E-bioscience) was diluted to 100 ng/ml final concentration in antibody diluent. hIL-23 was pre-incubated with the antibody in a deep well container for 2 hours. The plate was washed as previously described and wells subsequently incubated with the antibody/hIL-23 solution for 2 hours at 25° C. The plate was then washed as previously described and 100 μl of Streptavidin HRP (BD Phamingen) at 1:5000 in antibody diluent was used to detect bound biotinylated cytokine. After incubation at 25° C. for 1 hour the plate was washed again as previously described. 100 μl TMB substrate solution (Sigma-Aldrich) was added to each well and the color allowed to develop for 15 minutes. 100 μl of 1M HCl was added to stop the color development reaction and absorbance was determined at 450 nm (ref. 620 nm).
E11E7 was able to inhibit the binding of IL-23 to IL-23R when compared to the anti-p40 antibody which was unable to inhibit IL-23-binding to IL-23R at the highest concentration tested (FIG. 2).
E11E7 is a Potent Inhibitor and IL-23 Bioactivity In-Vitro
In SPR assays, the affinity of E11E7Chimera exceeded the sensitivity of the Biacore 3000 and has a KD less then 100 pM. E11E7 and its chimera, E11E7Chimera, were screened for their IL-23 neutralization ability using the murine splenocyte assay. Both antibodies displayed strong neutralization of human IL-23 induced murine IL-17 secretion (FIG. 4). These results demonstrate that an antibody that binds to the heterodimeric complex but not the individual subunits of IL-23 is a potent neutralizer of IL-23 bioactivity.
E11E7Chimera is Efficacious in the IL-23-Driven Murine Model of Psoriasis
Treatment of C57B1/6J mice with IL-23 intradermally to the back for 6 days induced a localized inflammatory response characterized by erythema and induration, with histological evidence of epidermal hyperplasia, parakeratosis, and localized inflammatory infiltrate. Antibodies were tested for their ability to decrease the inflammatory response at a single dose on the day before cytokine treatment commenced. One day before the start of cytokine injection they were given a single intraperitoneal injection of E11E7Chimera, a human p19 specific antibody (Antibody 7G10 from U.S. Pat. No. 7,807,160) or an isotype control antibody at a dose of 10 mg/kg. Mice were scored daily for erythema and induration in the test area. All treatments and observations were performed blinded. At the termination of the study, skin samples were collected from each mouse and fixed for histological processing and Haematoxylin and Eosin (H&E) staining by standard protocols.
Values for epidermal thickness were determined by printing off a paper copy of the lower power images of the sections of skin from each mouse. The skin section on each image was divided into four quadrants by the use of three vertical lines. The epidermal thickness was then measured at the point of intersection for the three lines used to delineate the quadrants, i.e. three thickness measurements per photograph. The actual distances in mm were then converted to microns using the scale on each image. In those instances where the measuring point intersected a region considered to be non-representative of epidermal thickness such as a hair follicle or sweat gland the location of the measuring point was adjusted to an adjacent section of skin. Measurements were done blinded by two independent observers.
Both groups that received E11E7Chimera and the Anti-p19 antibody had a reduced clinical score, from day 5 onwards, relative to an isotype control, demonstrating efficacy of the antibodies in this study (FIG. 5A). It was also observed that E11E7Chimera demonstrated improved efficacy over the Anti-p 19 antibody from day 6 onwards.
E11E7Chimera and anti-p19 antibodies demonstrated a statistically significant decrease in epidermal thickness relative to the isotype control (FIG. 5B). Treatment with E11E7Chimera led to significantly lower epidermal thickness score then treatment with anti-p19 antibodies. This correlates well with the clinical scoring demonstrating that E11E7Chimera is a potent inhibitor of IL-23, more potent that the anti-p19 antibody, when tested in this murine psoriasis model.
Humanization of Rat Antibody E11E7
Parallel strategies of SuperhumanisationTM (US 2003/0039649) and 3D modeling (Lo Methods Mol Biol 248: 135-159, 2004) were employed to select suitable human frameworks capable of supporting the CDRs of the rat E11E7 antibody.
Selection of Human Framework Acceptors Using 3D Modeling
Independent 3D models of the rat VH and VL were constructed using the database of crystal structures (Worldwide Protein Data Bank pdb), http://www.wwpdb.org) and software package Discovery Studio v3.0 (Accelrys®, USA). Briefly, the protein data bank database was interrogated by Basic Local Alignment Search Tool (BLAST) searches using either the rat heavy chain variable region or light chain variable region to identify antibodies of similar (>70% homology) polypeptide sequence with accompanying crystal structure information. These structures were subsequently used to build homology models based on the amino acid sequence homology shared by the rat variable regions and that of the identified crystal structures.
Rat VH and VL models were used to predict which framework region amino acids were likely to interact with amino acids in the CDRs and thus require preserving in the chosen human acceptors for optimal activity of the humanized antibodies. These models were also used to identify suitable human VH and VL acceptor frameworks from the protein data bank based on their framework structural homology with those of the rodent antibody. To ensure correct heavy- and light-chain pairing, VH and VL human acceptor frameworks of same antibody crystal structure were progressed through the humanization process. Human acceptor antibodies with better rodent-human heavy chain framework region structural homology were preferred over those with better rodent-human light chain framework homology. For the rat antibody E11E7 the selected human acceptor frameworks were pdb accession codes 3B2U, 3L5Y, 1U6A and 1QLR. Of the selected frameworks, 3L5Y and 1U6A were not progressed due to containing multiple amino acid residue changes verses the human germline sequences.
SuperhumanisationTM of Rat E11E7
Briefly, canonical structures were assigned to rat E11E7 heavy- and light-chains through inspection of their respective amino acid sequences. E11E7 was assigned the canonical structure 3-1-1/1-1 (VL/VH). Human germline sequences sharing the same canonical structure were used as acceptor frameworks for the grafting of donor CDRs.
Humanization Data Summary
As a result of the humanization processes 22 humanized antibodies were produced and tested for their ability to bind human IL-23 (Table 4). Briefly, 2 mL transfections of the 22 humanized antibodies were screened for antibody expression level and binding activity via SPR. Protein A was immobilized onto FC1 and FC2 (or alternatively FC3 and FC4) of a CM5 research grade sensor chip using amine coupling, giving approximately 3000 RU. FC1 was used as a blank throughout the experiments. The experiments were run in HBS-P buffer (SPR). Antibody-containing cell culture supernatants were diluted in 10× HBS-P buffer at a ratio of 9:1. The diluted antibody was injected over FC2 at a flow rate of 20 μl/min. IL-23 (HEK293E-derived) was passed over the surface of FC1 and FC2 at a concentrations of 5 μg/ml as a kinetic injection with 5 min dissociation time across both FC. Regeneration of the surface was performed using 10 mM Glycine, pH 1.5. The sensorgram data from FC2 were subtracted from FC1 and a buffer only control. Antibodies that captured at a level greater than 50RU and had an IL23 capture/antibody capture ratio greater than 0.1 were scaled-up and purified for further testing.
The Sequence IDs of the variable heavy and light chains for each antibody are given in the Table 4 along with kd (off-rates) of selected tested antibodies.







TABLE 4







Humanized E11E7 based antibodies













Heavy Chain 
Light Chain
SEQ ID



Antibody
SEQ ID NO
NO
kd (Vs)
















E11E7Chimera
20
21
5.98E−05



 8-22
33
46
1.17E−04



21-4 
31
45
1.91E−04



 9-22
34
46
1.98E−04



16-12
35
47
2.24E−04



20-4 
30
45
2.31E−04



 6-22
32
46
2.41E−04



 8-23
33
48
2.85E−04



 9-23
34
48
5.60E−04



 6-23
32
48
5.66E−04



1-4
36
45
6.16E−04



13-12
37
47
8.55E−04



 7-22
38
46
1.02E−03



11-22
39
46
1.21E−03



18-4 
40
45
1.33E−03



 5-22
41
46
1.98E−03



10-22
42
46
3.13E−03



14-12
43
47
3.49E−03



 7-23
38
48
3.91E−03



11-23
39
48
4.62E−03



15-12
44
47
6.00E−03



 5-23
41
48
6.39E−03



10-23
42
48
0.013










All tested humanized antibodies demonstrated binding to IL-23 via surface plasmon resonance (Table 4). Antibodies 1-4,6-22, 8-22, 20-4, 9-22 and 21-4 were tested for binding to IL-23 with ELISA (FIG. 6). All antibodies tested demonstrated binding to IL-23 similar to that of E11E7Chimera. These data confirm successful retention of binding activity in the humanized E11E7 antibodies.
Sequences of humanized antibodies and E 11E7 VD and VL are shown in FIG. 7. This figure also shows regions of conservation/identity and a consensus sequence.
Several antibodies were further tested for their ability to bind to IL-23 via Biacore (Table 5). Four out of the 5 of the humanized antibodies tested bound IL-23 with a picomolar range affinity (KD). The antibodies had a faster off-rate when compared to E11E7Chimera.







TABLE 5







Binding of E11E7Chimera and humanized 


antibodies to IL-23 as measured by SPR













kd (1/s)
KD (M)



Antibody
ka (1/Ms)
less then 
less then
Chi2














E11E7Chimera
5.42E+05
1.00E−05**
1.00E−10**
0.852


21-4 
5.21E+05
2.02E−04
3.88E−10
1.33


 8-22
4.68E+05
1.97E−04
4.21E−10
1.32


 6-22
4.65E+05
4.00E−04
8.60E−10
1.31


1-4
3.48E+05
7.33E−04
2.11E−09
1.65


20-4 
4.29E+05
2.02E−04
4.70E−10
1.25





**These values are below the limit of sensitivity of the Biacore 3000 which is kd = 1.00E−05 1/s and for KD is 1.00E−10M).






Specificity of the Humanized Antibodies for IL-23

Four antibodies were selected, based on the results presented in Table 5, to be further screened for their ability to bind selectively to IL-23. Antibodies 21-4,8-22, 6-22 and 20-4 all demonstrated specific binding to IL-23 and did not significantly bind to either IL-12p40 or IL-23p19 as demonstrated by ELISA (FIG. 8).
EXAMPLE 2
Production of Human Monoclonal Antibodies That Specifically Bind IL-23
Phage Display
A naive bacteriophage (phage) library (XOMA corporation, Berkeley) comprising a plurality of individual human FAb fragments was screened in an attempt to isolate antibodies that bind IL23 but do not significantly bind the individual subunits of IL23, p19 and p40.
Crosslinking Antigens to Dynal M450 Magnetic Epoxy Beads
One mL of Dynal M450 epoxy beads was washed once with 1 mL of 100 mM sodium phosphate pH8.0. The washed beads were resuspended in a further 0.5 mL of 100 mM sodium phosphate pH8.0 and 1.4 moles of the ligand to be coupled added; the final coupling volume being made up to 1 mL with 100 mM sodium phosphate pH8.0. The coupling reaction was allowed to proceed overnight (−16 hours) at room temperature with slow rotation. Beads were subsequently blocked by addition of 200 of 1M tris pH7.4 and slow rotation for 30 minutes at room temperature. Beads were washed 3× in PBS and re-suspended in 1 mL PBS.
Phage Library Biopanning
Following several unsuccessful phage display campaigns using different reagents and/or panning conditions, anti-IL-23 antibodies with the aforementioned specificity were isolated from the phage display library. The general protocol followed the method outlined by Marks et al. (Marks and Bradbury Methods Mol Biol 248: 161-176, 2004). Briefly, each phage display campaign involved three rounds of biopanning with independent screening of both kappa chain- and lambda chain containing libraries. For each round of biopanning phage particles taken from each library were blocked by mixing 1:1 with blocking buffer (5% skim milk in phosphate buffered saline pH 7.4) and incubating for 1 hr at room temperature. The blocked phage library was then pre-depleted where applicable for 1 hr at room temperature using antigens which were blocked as described for the library.
Library panning was conducted by mixing the blocked and pre-depleted library with the selection complexes (pre-blocked) in 1.5 mL microcentrifuge tubes and rotating for 1 hr at room temperature. Non-specifically bound phage were removed using a series of washes. Each wash involved pulling the bead complexes from the solution onto the tube wall using a magnetic rack, aspirating the supernatant and then re-suspending the beads in fresh wash buffer. This was repeated a number of times with either PBS wash buffer (PBS with 0.5% skim milk) or PBS-T wash buffer (PBS with 0.05% TWEEN-20 (Sigma-Aldrich) and 0.5% skim milk). Phage that remained bound after the washing process were eluted.
At the end of the first and second rounds of panning, the output phage were added to a 10 mL culture of exponentially growing TG1 E. coli (yeast-tryptone (YT) growth media) and allowed to infect the cells by incubating for 30 mins at 37° C. without shaking, then with shaking at 250 rpm for 30 mins. The phagemids encoding the phage display output were then rescued as phage particles following a standard protocol (Marks and Bradbury, 2004, supra). At the end of the third panning round TG1 cells were infected with output phage, but the cells were plated on solid YT growth media (supplemented with 2% glucose and 100 μg/mL carbenicillin) at a sufficient dilution to produce discrete E. coli colonies.
Expression of Fabs for Screening
Discrete E. coli colonies from the third round of biopanning the phage library were used to inoculate 1 mL aliquots of 2YT growth media (supplemented with 2% glucose and 100 μg/mL carbenicillin) in 96 well deep well plates. Plates were grown overnight at 30° C. shaking at 380 rpm (Innova 44R shaker, 1 inch orbit) to produce a masterplate. For Fab induction bacteria were diluted 1:100 in a further 96 well deep well plate containing fresh 2YT media (supplemented with 100 μg/mL carbenicillin) and grown at 37° C. 380 rpm until OD600 reached 0.5. A final concentration of 1.25 mM IPTG was added and plates were subsequently grown overnight (−16 hours) at 25° C. shaking as before.
Preparation of Soluble Fabs:
Bacterial pellets from induction plates were harvested by centrifugation at 2000 g for 10 minutes (room temperature). Spent media was discarded and pellets resuspended in 200 μl per well of lysozyme buffer composed of 160 μg/mL lysozyme, 10 μg/mL RNAse, 5 μg/mL DNAse and protease inhibitor cocktail (cOmplete, Roche). Plates were incubated at 21° C. 400 rpm for 30 minutes prior to the addition of a further 100 μl per well of lysozyme buffer and further incubation at 21° C. 400 rpm for 30 minutes. Plates were subsequently centrifuged at 3000 g for 15 minutes (room temperature) prior to usage of the Fab extracts in assays.
ELISA Screens for Fab Expression, and Binding to Antigens IL-23, IL-23p19-Fc and IL-12p40-Fc
A NuncMaxisorp 96-well plate was coated with untagged human IL-23 at 1 μg/ml in carbonate coating buffer and incubated overnight at 4° C. Further plates were coated as described for IL-23 using the antigens human p19-Fc, human p40-Fc and either anti-kappa or anti-lambda antibodies. Plates were washed then blocked for an hour with 1% BSA in PBS at room temperature. Plates were washed again prior to the addition of 50 μl per well of Fab extract and incubation for a further hour at room temperature. Plates were washed prior to the addition of 50 μl per well of 1:2000 diluted anti-v5-HRP antibody conjugate (InvitrogenTM) and incubated for a further hour at room temperature. Plates were washed, developed and read as described previously.
Results of Phage Display of Lead Fabs Showing IL-23-binding Specificity Following numerous screening approaches one Fab (named ST883/885) out of 768
Fabs screened from campaigns 4 and 5, bound IL-23 with little or no binding observed to IL-23p19-Fc or IL-12p40-Fc. Bacteria containing phagemids encoding ST883/885 Fabs with this specificity were regrown overnight in 5 mLs of LB broth (supplemented with 100 μg/ml ampicillin) and used to isolate plasmid DNA for sequencing. The variable heavy chain of ST883/885 is given as SEQ ID NO: 49 and the variable light chain as SEQ ID NO: 50.
The VH and VL of ST883/885 were PCR amplified and subcloned into their respective pTT5 heavy and light chain expression vectors. The full-length antibody termed ST883/885IgG was then expressed as a human IgG1 lambda isotype antibody in HEK293E cells as described above. Antibody was purified by Protein A chromatography (as described previously) following removal of the cells from the suspension by centrifugation. As shown in FIG. 9, the antibody was found to be specific for IL-23 with no significant binding to IL-12p40 and IL-23p19.
EXAMPLE 3
Detection of Endogenous IL-23 by an IL-23 specific antibody
IL-23 specific antibodies such as E11E7 are useful in the detection of IL-23 in biological samples.
To demonstrate the effectiveness of E11E7 to detect IL-23 a standard sandwich ELISA was developed. E11E7 at 2 ug/ml in PBS was coated onto a Maxisorp plate (Nunc) and incubated at 4° C. The following day, the plate was washed using PBS with 0.05% Tween-20 (PBS-T) and blocked in 10% feotal calf serum in PBS for 1 hr. rhIL23 was added at a maximum concentration of 3 ng/ml and serial dilutions performed across the plate. The plate was incubated for 1 hour then washed 3× with PBS-T. The complex was detected using biotinylated IL-23 detection Ab followed by 3×PBS-T washed and then Strepavidin HRP detection. Recombinant IL-23 was detected in a dose-titration using E11E7 as a capture antibody (FIG. 10A).
To determine whether E11E7 could be used to detect native IL-23, THP-1 cells were stimulated with 1 ug/mL of Pokeweed Mitogen (PWM) and different concentrations of Lipopolysaccharide (LPS) in culture for 24 hours. The supernatants were then collected and assayed in the above described ELISA format. E11E7 was able to detect native IL-23 at several concentrations of LPS that were tested (FIG. 10B).
EXAMPLE 4
Production of Further Antibodies and Antibody Fragments
4.1 Generation of Hybridoma Cell Lines
Monoclonal antibodies against heterodimeric IL-23 are generated by conventional protein immunization or using genetic immunization essentially as described in Example 1. This method is modified in some forms to immunize mice rather than rats.
Hybridoma screening and DNA sequencing are performed essentially as described in Example 1 and/or depicted in FIG. 11.
4.2 Isolation of Further IL-23 Heterodimer Antibodies from Display Libraries
For primary selections, libraries of phage displaying antibody fragments are panned against FLAG-tagged IL-23 protein and positive binding phage retained. Then depletion of phage positive for IL-23p19 subunit binding is performed using Anti-FLAG M2 coated beads (Sigma) and FLAG-tagged p19 in conjunction with depletion of phage positive for IL-12p40 subunit binding using Anti-FLAG M2 coated beads (Sigma) and FLAG-tagged IL-12p40. This will leave phage displaying antibody fragments that are specific for the heterodimeric interface of IL-23 (FIG. 11) (Henderikx et al, Selection of antibodies against biotinylated antigens. Antibody Phage Display: Methods and protocols, Ed. O'Brien and Atkin, Humana Press (2002)). Further affinity maturation of these antibody fragments is performed by screening against Anti-FLAG M2 coated beads (Sigma) and FLAG-tagged IL-23. Phage vectors from selection outputs are then isolated by plasmid preps (Qiagen) and antibody fragment inserts released by restriction digest. These inserts are ligated into a phage expression vector and used to transform E. coli strain HB2151 for soluble expression and screening of antibody fragments. Alternatively the antibody fragment inserts are sequenced and are expressed with a truncated human constant region.
EXAMPLE 5
Construction of Vectors Expressing Antibodies and Expression and Purification of Antibodies
Vectors expressing antibodies are produced essentially as described above. Antibodies are then expressed and purified essentially as described above.
EXAMPLE 6
Characterization of Purified Antibodies
Antibodies expressed and purified as described in Example 5 are characterized using an ELISA assay, a IL-23/IL-23R inhibition assay and an IL-17 release assay using mouse splenocytes essentially as described above.
EXAMPLE 7
Characterization of the Epitope for Heterodimer Specific Antibodies
Using point mutation technology an alanine is introduced into the protein sequence of IL-23 at each position in which a side chain is predicted to be in contact with solution based on the three dimensional X-ray crystal structures (3D85). Each IL-23 protein containing a single alanine point mutation is then expressed and purified using the methods described above for the expression and purification of IL-23. Using SPR technology the candidate antibody is immobilized on the surface of a Protein A chip and each IL-23 variant protein is passed over the surface and the binding kinetics measured. Protein variants that fail to bind or bind weakly to the immobilized antibody may contain a point mutation at the antibody's epitope on IL-23.
In a further experiment, each IL-23 variant is coated onto an ELISA plate. After blocking, the candidate antibody is then added along with a polyclonal antibody specific to IL-23. Both antibodies are then detected using their corresponding secondary antibodies. Situations in which the candidate antibody fails to bind to the IL-23 variant, but when the polyclonal antibody binds to the IL-23 variant, may indicate that the amino acid position of the alanine mutation on the IL-23 variant serves as an amino acid position that interacts with the candidate antibody.

## Claims

1. An isolated or recombinant antibody or antigen-binding fragment thereof that specifically binds to IL-23, comprising a heavy chain CDR1comprising the amino acid sequence of SEQ ID NO: 8, a heavy chain CDR2 comprising the amino acid sequence of SEQ ID NO: 9 or 22, a heavy chain CDR3 comprising the amino acid sequence of SEQ ID NO: 10, a light chain CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a light chain CDR2comprising the amino acid sequence of SEQ ID NO: 14, and a light chain CDR3 comprising the amino acid sequence of SEQ ID NO: 15.

2. The antibody or antigen-binding fragment thereof of claim 1, wherein the antibody or antigen-binding fragment thereof specifically binds to an IL-23heterodimeric complex, but does not specifically bind to an IL-12p40 subunit or an IL-23p19subunit individually.

3. The antibody or antigen-binding fragment thereof of claim 1, wherein the antibody or antigen-binding fragment thereof specifically binds to:
(a) the heterodimeric interface of IL-23;
(b) the IL-23p19 subunit of IL-23 when said subunit is a component of an IL-23 heterodimeric complex; or
(c) the IL-23p19 subunit of IL-23 in a region comprising amino acids 112-144 of SEQ ID NO:2 when said subunit is a component of an IL-23 heterodimeric complex.

4. The antibody or antigen-binding fragment thereof of claim 1, wherein the antibody or antigen-binding fragment thereof reduces binding of IL-23 to the IL-23receptor (IL-23R) with an IC50 of 1nM or less or an EC50 of 1nM or less.

5. The antibody or antigen-binding fragment thereof of claim 1, wherein the antibody or antigen-binding fragment thereof is chimeric, deimmunized, CDR-grafted, humanized, primatized or synhumanized.

6. The antibody or antigen-binding fragment thereof of claim 1, wherein the antibody or antigen-binding fragment thereof is a single chain Fv (scFv) or a dimeric scFv (di-scFv) that is optionally linked to an Fc, a heavy chain constant domain 2(CH2), or heavy chain constant domain 3(CH3).

7. The antibody or antigen-binding fragment thereof of claim 1, wherein the antibody or antigen-binding fragment thereof is an Fab, F(ab')2, Fv, or a diabody, triabody, or tetrabody that is optionally linked to an Fc, a heavy chain constant domain 2 (CH2), or heavy chain constant domain 3(CH3).

8. The antibody or antigen-binding fragment thereof of claim 7, wherein the antibody or antigen-binding fragment thereof is chimeric, de-immunized, humanized, primatized, or synhumanized.

9. The antibody or antigen-binding fragment thereof of claim 8, wherein the antibody or antigen-binding fragment thereof is a humanized antibody comprising:
(a) a VH comprising amino acids 1-120 of SEQ ID NO: 30 and a VL comprising amino acids 1-113 of SEQ ID NO: 45;
(b) a VH comprising amino acids 1-120 of SEQ ID NO: 31 and a VL comprising amino acids 1-113 of SEQ ID NO: 45;
(c) a VH comprising amino acids 1-120 of SEQ ID NO: 32 and a VL comprising amino acids 1-113 of SEQ ID NO: 46; or
(d) a VH comprising amino acids 1-120 of SEQ ID NO: 33 and a VL comprising amino acids 1-113 of SEQ ID NO: 46.

10. The antibody or antigen-binding fragment thereof of claim 8, wherein the antibody or antigen-binding fragment thereof is a chimeric antibody comprising a VH comprising the amino acid sequence of SEQ ID NO: 7 linked to a human heavy chain constant region and a VL comprising the amino acid sequence of SEQ ID NO: 12 linked to a human light chain constant region.

11. The antibody or antigen-binding fragment thereof of claim 8, wherein the antibody or antigen-binding fragment thereof is a monoclonal antibody comprising a VH comprising the amino acid sequence of SEQ ID NO: 7 and a VL comprising the amino acid sequence of SEQ ID NO: 12, or a chimeric, deimmunized, CDR-grafted, humanized or synhumanized form thereof.

12. The antibody or antigen-binding fragment thereof of claim 1, wherein the antibody or antigen-binding fragment thereof is conjugated to a compound.

13. A composition comprising the antibody or antigen-binding fragment thereof of claim 1 and a suitable carrier or diluent.

14. A recombinant nucleic acid encoding an antibody or antigen-binding fragment thereof that specifically binds to IL-23, and comprises a heavy chain CDR1comprising the amino acid sequence of SEQ ID NO: 8, a heavy chain CDR2 comprising the amino acid sequence of SEQ ID NO: 9 or 22, a heavy chain CDR3 comprising the amino acid sequence of SEQ ID NO: 10, a light chain CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a light chain CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a light chain CDR3comprising the amino acid sequence of SEQ ID NO: 15.

15. A recombinant cell comprising the nucleic acid of claim 14.

16. A method for treating an IL-23-mediated inflammatory condition in a subject, comprising administering to the subject an effective amount of an isolated or recombinant antibody or antigen-binding fragment thereof, that specifically binds to IL-23and comprises a heavy chain CDR1 comprising the amino acid sequence of SEQ ID NO: 8, a heavy chain CDR2 comprising the amino acid sequence of SEQ ID NO: 9 or 22, a heavy chain CDR3 comprising the amino acid sequence of SEQ ID NO: 10, a light chain CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a light chain CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a light chain CDR3comprising the amino acid sequence of SEQ ID NO: 15, thereby treating the IL-23-mediated inflammatory condition.