Method employing bispecific protein complex

Abstract

The present invention is directed to a method of controlling and directing cells, for example to stimulate an immune response, inhibit an immune response, direct tissue regeneration or prevent tissue damage for therapeutic activity through the use of heterodimerically-tethered bispecific protein complex of formula A-X:Y-B. Component A may present X on the surface of a cell, may bind a protein (including a marker) expressed on the surface of an effector cell, or A-X is expressed on the surface of an effector cell, whilst B is specific to an epitope on target cell or tissue of interest. X:Y is a heterodimeric-tether which is formed by a binding interaction between X and Y, which together with A and B assists and effects the controlling and directing of the selected cells.

Claims

1. A method of identifying a bispecific protein complex that destroys a target cell or modulates a function of a target cell, comprising (a) generating fusion proteins of formula A-X and B-Y and heterodimerically-tethered bispecific protein complexes of formula A-X:Y-B; (b) contacting a population of cells comprising an effector cell and a target cell with: i. a combination of the fusion proteins A-X and B-Y in an uncomplexed form, or ii. A-X:Y-B in a heterodimerically-tethered bispecific protein complex form; and (c) monitoring the population of cells for destruction of the target cell or modulation of the function of the target cell, thereby identifying the bispecific protein complex that destroys the target cell or modulates the function of the target cell, wherein X:Y is a heterodimeric-tether; : is a binding interaction between X and Y; A is a first protein component of the bispecific protein complex selected from an antibody or binding fragment thereof, and a protein, wherein A specifically binds a protein expressed on the surface of an effector cell; B is a second protein component of the bispecific protein complex selected from an antibody or binding fragment or an antigen, wherein B specifically binds a target cell; X is a scFv and Y is a peptide GCN4 or a fragment thereof (SEQ ID NO: 1 or amino acids 1-38 of SEQ ID NO: 1 or SEQ ID NO: 76 to 98), or X is a peptide GCN4 or a fragment thereof (SEQ ID NO: 1 or amino acids 1-38 of SEQ ID NO: 1 or SEQ ID NO: 76 to 98) and Y is a scFv; and wherein X or Y is specific to the peptide GCN4 or a fragment thereof (SEQ ID NO: 1 or amino acids 1-38 of SEQ ID NO: 1 or SEQ ID NO: 76 to 98), and wherein the scFv is 52SR4 (SEQ ID NO: 3 or amino acids 1-243 of SEQ ID NO: 3 or SEQ ID NO.99-100).

2. The method according to claim 1, wherein X or Y is an antigen with no corresponding mammalian sequence.

3. The method according to claim 1, wherein a binding affinity between X and Y is 5 nM, 900, 800, 700, 600, 500, 400 or 300 pM.

4. The method according to claim 1 where the bispecific protein complex comprises no more than two scFv and/or at least one Fab or Fab fragment.

5. The method according to claim 1, i. wherein the effector cell is a cell capable of a cellular response, wherein the cellular response is phagocytosis, cytotoxicity, generating an antibody, release of a soluble molecule, or a combination thereof; and/or ii. wherein A is independently selected from the group consisting of a full length antibody, a Fab fragment, a Fab fragment, a sdAb, a scFv, and an antigen.

6. The method according to claim 1, wherein the effector cell is selected from the group consisting of a B cell, T cell, an NK cell, monocyte, macrophage, dendritic cell, mast cell, neutrophil, eosinophil and basophil.

7. The method according to claim 6, wherein the effector cell is a B cell, wherein the B cell comprises a marker that is in a constant region of an antibody light chain or a constant region of an antibody heavy chain, expressed as part of an immunoglobulin on the surface of the cell.

8. The method according to claim 1, wherein B is a full length antibody, a Fab fragment, a Fab fragment, a sdAb, or a scFv.

9. The method according to claim 1, wherein the effector cell transgresses the blood brain barrier (BBB), wherein B binds a central nervous system expressed target.

10. The method according to claim 1, wherein B binds a cell surface marker on the target cell, wherein the cell surface marker is: i. a tumor antigen selected from erbB-2, CEA, NCAM, GD2, CD33, CD44, CD70, EpCAM, CD19, CD20, KDR, and Tag-72; or ii. a HER receptor; or iii. a B cell marker or T cell marker.

11. The method according to claim 1, wherein: i. X is fused to the N-terminal or C-terminal of A; or ii. X and/or Y is fused to the C-terminal of the heavy chain of an antibody or an antigen binding fragment thereof; or iii. Y is fused to the C-terminal of B.

12. The method of claim 1, wherein A is an antibody, an antigen binding fragment thereof or an antigen, wherein B is an antibody or an antigen binding fragment or a protein ligand.

13. The method of claim 6, wherein the protein expressed on the surface of the effector cell is CD45, CD2, CD3, CD4, CD5, CD7, CD8, CD11b, CD11c, CD13, CD14, CD15, CD16, CD19, CD20, CD23, CD25, CD27, CD33, CD38, CD56, CD57, CD64, CD80, CD83, CD86, CD123, CD127, CD137, CD138, CD196, CD209, HLA-DR, Lin- 1 to -3, or a combination thereof.

14. The method of claim 6, wherein the effector cell is a B cell comprising a marker, and the B cell marker is selected from the group consisting of CD19, CD20, CD21, CD22, CD23, CD24, CD27, CD35, CD38, CD40, CD45, CD43, CD81, CD138, CXCR4, BCMA and IL-6R.

15. The method of claim 6, wherein the effector cell is a T cell comprising a marker and the T cell marker is selected from the group consisting of CD2, CD3, CD4, CD5, CD6, CD7, CD8, CD25, CD127 CD196 (CCR6), CD197 (CCR7), CD62L, CD69 and CD45.

16. The method of claim 5, wherein the cellular response is release of an immunoglobulin, a cytokine, a chemokine, or a combination thereof.

Description

DESCRIPTION OF DRAWINGS

(1) FIG. 1 shows an A-X fusion protein expressed on the surface of a cell (wherein A is a surface protein which is not connected to an intra-cellular signalling domain and X is a scFv) and B is a Fab specific to an epitope on the surface of a target cell or tissue and Y is a peptide specific to X. Alternative formats for B-Y are also provided.

(2) FIG. 2 shows an A-X fusion protein expressed on the surface of a cell (wherein A is a surface protein which is connected to an intra-cellular signalling domain [also referred to herein as a chimeric receptor] and X is a scFv) and B is a Fab specific to an epitope on the surface of a target cell or tissue and Y is a peptide specific to X. Alternative formats for B-Y are also provided.

(3) FIG. 3 shows A-X wherein in A is a Fab or Fab specific to an antigen expressed on the surface of the cell (an effector cell) and X is a single chain Fv specific to Y. B is a Fab specific to an epitope on the surface of a target cell or tissue and Y is a peptide specific to X. Alternative formats for B-Y are also shown.

(4) FIG. 4 shows an A-X fusion protein expressed on the surface of a cell (wherein A is a surface protein which is connected to an intra-cellular signalling domain [also referred to herein as a chimeric receptor] and X is a scFv) and B is a Fab specific to surface antigen on the target cell and Y is a peptide. Alternatively B is a full length antibody comprising two Y peptides.

(5) FIG. 5 shows A-X wherein in A is a Fab or Fab specific to an antigen expressed on the surface of the cell (an effector cell) and X is a scFv) and B is a Fab specific to surface antigen on the target cell and Y is a peptide. Alternatively B is a full length antibody comprising two Y peptides.

DETAILED DESCRIPTION

(6) Bispecific protein complex as used herein refers to a molecule comprising two proteins (A and B referred to herein as bispecific components also referred to herein as the first protein component and second protein component, respectively of the bispecific) which are retained together by a heterodimeric-tether. In one embodiment one or both of the proteins have a binding domain, for example one or both of the proteins are antibodies or fragments thereof (in particular a Fab or Fab fragment, such complexes are also referred to as Fab-Kd-Fab). Fusion proteins as employed herein comprise a protein component A or B fused to a binding partner X or Y (as appropriate). In one embodiment the fusion protein is a translational protein expressed by recombinant techniques from a genetic construct, for example expressed in a host from a DNA construct. In the context of the present disclosure one of the key characteristics of a fusion protein is that it can be expressed as a single protein/unit from a cell (of course in the case of fusion proteins comprising a Fab/Fab fragment there will be two chains but this will be considered a single protein for the purpose of the present specification with one chain, typically the heavy chain fused at its C-terminus to X or Y as appropriate, optionally via a linker as described herein below).

(7) The function of the heterodimeric tether X:Y is to retain the proteins A and B in proximity to each other so that function of A and B or the cells appended thereto can be effected.

(8) The term heterodimeric-tether as used herein refers to a tether comprising two different binding partners X and Y which form an interaction: (such as a binding) between each other which has an overall affinity that is sufficient to retain the two binding partners together. In one embodiment X and/or Y are unsuitable for forming homodimers.

(9) Heterodimerically-tethered and heterodimeric-tether are used interchangeably herein.

(10) In one embodiment unsuitable for forming homodimers as employed herein refers to formation of the heterodimers of X-Y are more preferable, for example more stable, such as thermodynamically stable, once formed than homodimers. In one embodiment the binding interaction between X and Y is monovalent.

(11) The term protein ligand as used herein means a binding partner (such as a ligand, a cytokine, a chemokine) of a cell surface protein (such as a transmembrane bound receptor).

(12) A component of a cell surface protein or a complex thereof as used herein means a defined region of a cell surface protein and include, but is not limited to, a transmembrane region, an intracellular signalling region and the like.

(13) In one embodiment the X-Y interaction is more favourable than the X-X or Y-Y interaction. This reduces the formation of homodimers X-X or Y-Y when the fusion proteins A-X and B-Yare mixed. Typically greater than 75% heterodimer is formed following 1:1 molar ratio mixing.

(14) If desired, a purification step (in particular a one-step purification), such as column chromatography may be employed, for example to purify the fusion protein units and/or bispecific protein complexes according to the present disclosure.

(15) In one embodiment a purification step is provided after expression of each fusion protein, although typically aggregate levels are low. Thus in one embodiment prior to in vitro mixing, the fusion protein(s) is/are provided in substantially pure form. Substantially pure form as employed herein refers to wherein the fusion protein is 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% monomer.

(16) In one embodiment no purification of the fusion protein or proteins is performed.

(17) In one embodiment each fusion protein unit is expressed in a different expression experiment/run.

(18) In one embodiment no purification of the fusion protein or proteins is performed before mixing to generate a bispecific protein complex. In one embodiment no purification of the fusion protein or proteins is performed before and/or after mixing.

(19) In one embodiment no purification is required after the bispecific protein complex formation.

(20) In one embodiment after mixing, and generally without further purification, at least 50% of the composition is the desired bispecific protein complex, for example at least 60, 65, 70, 75, 80% of the composition is the required bispecific protein complex.

(21) In one embodiment the ratio of A-X to B-Y employed in the in vitro mixing step is 1:1, in particular a 1:1 molar ratio.

(22) The present disclosure also extends to a method of preparing a bispecific complex according to the present disclosure comprising admixing a fusion protein A-X and B-Y, for example in a 1:1 molar ratio.

(23) In one embodiment the mixing occurs in vitro.

(24) In one embodiment mixing occurs in a cell, for example a host cell expressing said fusion proteins.

(25) In one embodiment, the mixing occurs in vivo, i.e. the fusion proteins A-X and B-Y interact with each other within a subject's body to form the heterodimeric-tether and in consequence, the bispecific protein complex.

(26) This is advantageous because one component, for example A-X may be administered or introduced and it is not activated until the further component B-Y is added and forms the heterodimeric-tether.

(27) In one embodiment, X and Y are completely specific for each other and do not bind to any other peptides/proteins in a cell or within a subject's body. This can be achieved for example by ensuring that X and Y are not naturally present in the target cell or in the target subject's body. This can be achieved, for example by selecting X or Y to be from a species or entity which is different to the subject (e.g. a yeast protein) and ensuring the other variable is specific to it. Advantageously, this prevents the binding of the fusion proteins A-X and/or B-Y to an undesired target, thereby generating unwanted off-target effects.

(28) Generally at least one of X or Y will be an antigen, such as a peptide. In the present disclosure the antigen, such as a peptide employed in X or Y has been chosen to be non-mammalian. That is not from a mammalian protein, such as not similar to or identical to a mammalian protein. In one embodiment a peptide or antigen employed in an X or Y is 90% identical or similar or less (such as 85, 80, 75, 70, 65, 60% or less) to a mammalian sequence over the same length. As discussed above this helps to ensure that the X:Y are specific for each other when employed in vivo and reduces the risk of off-target effects to patients.

(29) In one embodiment one (or at least one) of the binding partners is incapable of forming a homodimer, for example an amino acid sequence of the binding partner is mutated to eliminate or minimise the formation of homodimers.

(30) In one embodiment both of the binding partners are incapable of forming a homodimer.

(31) Incapable of forming homodimers or aggregates as employed herein, refers to a low or zero propensity to form homodimers or aggregate. Low as employed herein refers to 5% or less, such as 4, 3, 2, 1, 0.5% or less aggregate, for example after mixing or expression or purification.

(32) Small amounts of aggregate in the fusion proteins or residual in the heterodimerically-tethered bispecific protein complex may be acceptable in pharmaceutical compositions of the heterodimerically-tethered bispecific protein complex of the disclosure.

(33) In one embodiment: is a binding interaction based on attractive forces, for example Van der Waals forces, such as hydrogen bonding and electrostatic interactions, in particular, based on antibody specificity for an antigen (such as a peptide).

(34) In one embodiment conjugation/coupling chemistry is not employed to prepare the bispecific protein complexes of the present disclosure.

(35) Form the complex as employed herein refers to an interaction, including a binding interaction or a chemical reaction, which is sufficiently specific and strong when the fusion protein components A-X and B-Y are brought into contact under appropriate conditions that the complex is assembled and the fusion proteins are retained together.

(36) Retained together as employed herein refers to the holding of the components (the fusion proteins) in the proximity of each other, such that after X:Y binding the complex can be handled as if it were one molecule, and in many instances behaves and acts like a single molecule. In one embodiment the retention renders the complex suitable for use in the method disclosed herein, i.e. suitable for use in at least one functional screen.

(37) Specificity as employed herein refers to where, for example the partners in the interaction e.g. X:Y or A and antigen or B and antigen only recognise each other or have significantly higher affinity for each other in comparison to non-partners, for example at least 2, 3, 4, 5, 6, 7, 8, 9, 10 times higher affinity, than for example a background level of binding to an unrelated non partner protein.

(38) Specificity in relation to X and Y as employed herein refers to where the binding partners X and Y in the interaction only recognise each other or have significantly higher affinity for each other in comparison to non-partners, for example at least 2, 3, 4, 5, 6, 7, 8, 9, 10 times higher affinity.

(39) In one embodiment the binding interaction is reversible. In one embodiment the binding interaction is essentially irreversible.

(40) Essentially irreversible as employed herein refers to a slow off rate (dissociation constant) of the antibody or binding fragment.

(41) In one embodiment, the binding interaction between X and Y has a low dissociation constant. Examples of a low dissociation constant include 1-910.sup.2 s.sup.1 or less, for example 1-910.sup.3 s.sup.1, 1-910.sup.4 s.sup.1, 1-910.sup.5 s.sup.1, 1-910.sup.6 s.sup.1 or 1-910.sup.7 s.sup.1. Particularly suitable dissociation constants include 210.sup.4 s.sup.1 or less, for example 110.sup.5 s.sup.1, 110.sup.6 s.sup.1 or 110.sup.7 s.sup.1.

(42) Whilst not wishing to be bound by theory it is thought that the low dissociation constant (also referred to as off rate) allows the molecules to be sufficiently stable to render the bispecific protein complex useful, in treatment.

(43) In another embodiment, the affinity of X and Y for each other is 5 nM or stronger, for example 900 pM or stronger, such as 800, 700, 600, 500, 400 or 300 pM.

(44) Affinity is a value calculated from the on and off rate of the entity. The term affinity as used herein refers to the strength of the sum total of non-covalent interactions between a single binding site of a molecule (e.g. an antibody) and its binding partner (e.g. a peptide).

(45) The affinity of a molecule for its binding partner can generally be represented by the dissociation constant (KD). Cell surface marker is a moiety, for example a protein expressed on the surface of the cell that be employed alone or in combination with other surface marker to identify and/or isolate the cell. The marker may be associated with the lineage of the cell or activation status of the cell, a molecule expressed by the cell or the like.

(46) In one embodiment the cell surface marker is a tumor antigen, such as erbB-2, CEA, NCAM, GD2, CD33, CD44, CD70, EpCAM, CD19, CD20, KDR, Tag-72, In another embodiment the cell surface marker is a protein such as a membrane protein which effects transfer through the blood-brain barrier (e.g. a transporter) of proteins, cells and other molecules from the blood to the brain.

(47) In another embodiment the cell surface marker is on cells that are able to transgress the blood brain barrier.

(48) Transmembrane domain or region is employed interchangeably herein to refer to a protein which spans the cell membrane thereby bridging the intra-cellular domain and the extracellular domain. See for example WO2004/039840 and WO2007/060406 both incorporated herein by reference.

(49) A transmembrane region generally serves to anchor A-X to the cell membrane (thus the extracellular ligand-binding region is membrane-bound) and includes any protein (or nucleic acid encoding such a protein). Such a region can be derived from a wide variety of sources such as all or part of the alpha, beta, or zeta chain of the T cell receptor (TCR), CD28, CD4, CD5, CD8, CD3, CD16, CD22, CD23, CD45, CD80, CD86, CD64, CD9, CD37, CD122, CD137 or CD154, a cytokine receptor such as an interleukin receptor, TNF-R, a tyrosine kinase receptor or interferon receptor, or a colony stimulating factor receptor. Alternatively, the transmembrane region may be synthetic. Suitable synthetic transmembrane regions will comprise predominantly hydrophobic amino acids such as leucine and valine.

(50) When A comprises a transmembrane region, a spacer region may optionally be included at the N terminal of the transmembrane region. Furthermore, an intracellular signalling region may optionally be included at the C terminal of that transmembrane region.

(51) Spacer domain as employed herein refers to a polypeptide region separating the transmembrane region of A from X and may like in the case of artificial T cell receptors (Cytotherapy 2003 5 (3) 211-226) be necessary for optimal effector cell function. Examples of spacer regions are domains derived from naturally expressed cell surface molecules such as immunoglobulin, CD28, CD4, CD8, MHC. Combinations of region from these molecules may also be combined. Specific examples include the hinge, CH2 and CH3 region of human IgG1 or the hinge region of human IgG1 combined with an extracellular domain of human CD28 as described (J. Immunol 1998 161 2791-2797).

(52) An intracellular signalling region includes any protein (or nucleic acid encoding such a protein) that can participate in the generation of a signal that results in direct or indirect production of an intracellular messenger system. Particular intracellular messenger systems include one or more kinase pathways such as a tyrosine kinase pathway, a MAP kinase pathway, or protein kinase C pathway; a G-protein or phospholipase-mediated pathway; a calcium-mediated pathway; a cAMP- or cGMP-mediated pathway; or one or more pathways involving synthesis of one or more cytokines such as an interleukin, e.g. IL-2, or transcription factors such as NFB, NFAT or AP-1. The intracellular signalling regions are most preferably selected such that they act cooperatively.

(53) Intracellular signalling regions may be derived from one or more naturally-occurring protein signalling sequences. Suitable examples include without limitation sequences derived from the TCR such as part of the zeta, eta or epsilon chain. and include the first (TCR1), second (TCR2) and third (TCR3) immunoreceptor tyrosine-based activation motifs (ITAMs) of the TCR zeta chain, FcR such as FcRIII or FcRI, FcR such as FcRI; CD3; CD3; CD3; and CD5, CD22, CD79a, CD79b, or CD66d. Particularly preferred ITAMs include those derived from TCR1, TCR2, TCR3 and FcRI; CD4; CD8; and the gamma chain of a Fc receptor.

(54) Signalling regions can be derived from activating or inhibitory immune check point receptors or ligands (Nat Rev Drug Discovery. 2015. 14. 561-584) including: CD40, CD40L, TL1A, TBFRSF25, GITR, GITR, CD137, CD137L, CD134, CD134L, CD70, CD27, HHLA2, TMIGD2, ICOSL, ICOS, CD80, CD86, CD28, LAG3, CTLA-4, PD1, PDL1, PDL2, VISTA, BTNL2, B7-H3, B7-H4, CD48, CD244, BTLA, CD160, LIGHT, HVEM, Butryophilin or siglec family members.

(55) Chimeric receptor as employed herein as employed herein refers an engineered receptor which grafts two sequences from different origins onto a cell, in particular an effector cell. The bispecific protein complexes may be tethered to a solid substrate surface, for example attached to a bead, or they may be suspended in a liquid (e.g. a solution or media) form, for example within a well or within a droplet.

(56) In one embodiment, at least one of the first binding partner, X, and the second binding partner, Y, of the binding pair are independently selected from a peptide and a protein; for example the first binding partner or second binding partner is a peptide.

(57) Suitable peptides include the group comprising GCN4, Fos/Jun (human and murine Fos have a Uniprot number P01100 and P01101 respectively and human and murine jun have a Uniprot number 05412 and 05627 respectively), HA-tag which correspond to amino acids 98 to 106 of human influenza hemagglutinin, polyhistidine (His), c-myc and FLAG. Other peptides are also contemplated as suitable for use in the present disclosure and particularly suitable peptides are affinity tags for protein purification because such peptides have a tendency to bind with high affinity to their respective binding partners.

(58) In one embodiment the peptide is not E5B9.

(59) The term peptide as used herein refers to a short polymer of amino acids linked by peptide bonds, wherein the peptide contains in the range of 2 to 100 amino acids, for example 5 to 99, such as 6 to 98, 7 to 97, 8 to 96 or 5 to 25. In one embodiment a peptide employed in the present disclosure is an amino acid sequence of 50 amino acid residues or less, for example 40, 30, 20, 10 or less. Polypeptide and protein are employed interchangeably herein. In one embodiment, the protein is an antibody or an antibody fragment.

(60) The term antibody as used herein refers to an immunoglobulin molecule capable of specific binding to a target antigen, such as a carbohydrate, polynucleotide, lipid, polypeptide, peptide etc., via at least one antigen recognition site (also referred to as a binding site herein), located in the variable region of the immunoglobulin molecule.

(61) As used herein antibody molecule includes antibodies and binding fragments thereof.

(62) Antibody fragments as employed herein refer to antibody binding fragments including but not limited to Fab, modified Fab, Fab, modified Fab, F(ab)2, Fv, single domain antibodies, scFv, bi, tri or tetra-valent antibodies, Bis-scFv, diabodies, triabodies, tetrabodies and epitope-binding fragments of any of the above (see for example Holliger and Hudson, 2005, Nature Biotech. 23(9):1126-1136; Adair and Lawson, 2005, Drug Design ReviewsOnline 2(3), 209-217). The methods for creating and manufacturing these antibody fragments are well known in the art (see for example Verma et al., 1998, Journal of Immunological Methods, 216:165-181). Other antibody fragments for use in the present disclosure include the Fab and Fab fragments described in International patent applications WO05/003169, WO05/003170 and WO05/003171. Multi-valent antibodies may comprise multiple specificities e.g. bispecific or may be monospecific (see for example WO92/22853, WO05/113605, WO2009/040562 and WO2010/035012).

(63) A binding fragment as employed herein refers to a fragment capable of binding a target peptide or antigen with sufficient affinity to characterise the fragment as specific for the peptide or antigen.

(64) The term Fab fragment as used herein refers to an antibody fragment comprising a light chain fragment comprising a VL (variable light) domain and a constant domain of a light chain (CL), and a VH (variable heavy) domain and a first constant domain (CH1) of a heavy chain. In one example the heavy chain sequences of the Fab fragment terminates at the interchain cysteine of CH1. In one embodiment the Fab fragment employed in a fusion protein of the present disclosure, such as A-X and/or B-Y is monovalent.

(65) A Fab fragment as employed herein refers to a Fab fragment further comprising all or part of a hinge region. In one embodiment the Fab fragment employed in a fusion protein of the present disclosure, such as A-X and/or B-Y is monovalent.

(66) The term single-chain Fv or abbreviated as scFv, as used herein refers to an antibody fragment that comprises VH and VL antibody domains linked (for example by a peptide linker) to form a single polypeptide chain. The constant regions of the heavy and light chain are omitted in this format. Single-chain Fv as employed herein includes disulfide stabilised versions thereof wherein in addition to the peptide linker a disulfide bond is present between the variable regions.

(67) Disulfide stabilised scFv may eliminate the propensity of some variable regions to dynamically breath, which relates to variable regions separating and coming together again. The term single domain antibody as used herein refers to an antibody fragment consisting of a single monomeric variable antibody domain. Examples of single domain antibodies include VH or VL or VHH.

(68) In one embodiment the antibody binding fragment and/or the bispecific antibody complex does not comprise an Fc region. Does not comprise an Fc region as employed herein refers to the lower constant domains, such as CH2, CH3 and CH4 which are absent. However, constant domains such as CH1, CKappa/CLambda may be present.

(69) In one embodiment, the antibody heavy chain comprises a CH1 domain and the antibody light chain comprises a CL domain, either kappa or lambda.

(70) In one embodiment, the antibody heavy chain comprises a CH1 domain, a CH2 domain and a CH.sub.3 domain and the antibody light chain comprises a CL domain, either kappa or lambda.

(71) In one embodiment, the first protein, A, and/or second protein, B, of the bispecific protein complex is an antibody or antibody fragment. Such a bispecific protein complex may be referred to as a bispecific antibody complex.

(72) Bispecific protein complex comprise a protein capable of binding the cell surface and protein capable of binding a soluble molecule secrete from the cell, tethered together by X and Y.

(73) In one embodiment the bispecific protein complex is an bispecific antibody complex.

(74) In one embodiment Bispecific antibody complex as employed herein refers to a bispecific protein complex comprising at least two antibody binding sites wherein the component antibodies, fragments or both are complexed together by a heterodimeric-tether.

(75) Complexed (or in complex with) as employed herein generally refers to where A-X and B-Y are tethered together by the interaction X:Y.

(76) Uncomplexed as employed herein refers to where A-X and B-Y are separate molecules.

(77) In one embodiment each antibody or fragment employed in the bispecific antibody complex of the disclosure comprises one binding site i.e. each binding site is monovalent for each target antigen.

(78) Antigen as employed herein as employed herein refers to a molecule which under appropriate conditions stimulates the body to raise antibodies to it.

(79) The full length antibody or antibody fragment employed in the fusion proteins (A-X or B-Y) may be monospecific, monovalent, multivalent or bispecific.

(80) In one embodiment, the antibody or antibody fragment employed in the first fusion protein (A-X) is a monospecific antibody or antibody fragment, in particular a monovalent Fab, Fab, scFv, Fv, VHH or similar.

(81) In one embodiment, the antibody or antibody fragment employed in the second fusion protein (B-Y) is a monospecific antibody or antibody fragment, in particular a monovalent Fab, Fab, scFv or similar.

(82) Monospecific as employed herein refers to the ability to bind only one target antigen.

(83) Monovalent as employed herein refers to the antibody or antibody fragment having a single binding site and therefore only binding the target antigen only once.

(84) In one embodiment, the antibody or antibody fragment employed in the first fusion protein (A-X) is multivalent, that is has two or more binding domains.

(85) In one embodiment, the antibody or antibody fragment employed in the second fusion protein (B-Y) is multivalent, that is has two or more binding domains.

(86) In one embodiment, the antibody or antibody fragment employed in the first fusion protein (A-X) is monovalent and the antibody or antibody fragment employed in the second fusion protein (B-X) is monovalent.

(87) In one embodiment, the antibody or antibody fragment employed in the first fusion protein (A-X) is monovalent and the antibody or antibody fragment employed in the second fusion protein (B-Y) is multivalent.

(88) In one embodiment, the antibody or antibody fragment employed in the first fusion protein (A-X) is multivalent and the antibody or antibody fragment employed in the second fusion protein (B-Y) is monovalent.

(89) In one embodiment, the antibody or antibody fragment employed in the first fusion protein (A-X) is multivalent and the antibody or antibody fragment employed in the second fusion protein (B-Y) is multivalent.

(90) In one embodiment A-X or B-Y is not a fusion protein comprising two scFvs one specific to the antigen CD33 and one specific to the antigen CD3 or alternatively a bispecific complex format specific to these two antigens.

(91) In one embodiment the A-X or B-Y is not a fusion protein comprising a scFv (or alternatively another antibody format) specific to CD3 linked to a peptide E5B9.

(92) A binding domain or site as employed herein is the part of the antibody that contacts the antigen/epitope and participates in a binding interaction therewith. In one embodiment the binding domain contains at least one variable domain or a derivative thereof, for example a pair of variable domains or derivatives thereof, such as a cognate pair of variable domains or a derivative thereof.

(93) In one embodiment the binding domain comprises 3 CDRs, in particular where the binding domain is a domain antibody such as a VH, VL or VHH. In one embodiment the binding domain comprises two variable domains and 6 CDRs and a framework and together these elements contribute to the specificity of the binding interaction of the antibody or binding fragment with the antigen/epitope.

(94) A cognate pair as employed herein refers to a heavy and light chain pair isolated from a host as a pre-formed couple. This definition does not include variable domains isolated from a library, wherein the original pairings from a host is not retained. Cognate pairs may be advantageous because they are often affinity matured in the host and therefore may have high affinity for the antigen to which they are specific.

(95) A derivative of a naturally occurring domain as employed herein is intended to refer to where one, two, three, four or five amino acids in a naturally occurring sequence have been replaced or deleted, for example to optimize the properties of the domain such as by eliminating undesirable properties but wherein the characterizing feature(s) of the domain is/are retained. Examples of modifications are those to remove glycosylation sites, or solvent exposed lysines. These modifications can be achieved by replacing the relevant amino acid residues with a conservative amino acid substitution.

(96) In one embodiment, the bispecific antibody complexes of the present disclosure or antibody/fragment components thereof are processed to provide improved affinity for a target antigen or antigens. Such variants can be obtained by a number of affinity maturation protocols including mutating the CDRs (Yang et al., J. Mol. Biol., 254, 392-403, 1995), chain shuffling (Marks et al., Bio/Technology, 10, 779-783, 1992), use of mutator strains of E. coli (Low et al., J. Mol. Biol., 250, 359-368, 1996), DNA shuffling (Patten et al., Curr. Opin. Biotechnol., 8, 724-733, 1997), phage display (Thompson et al., J. Mol. Biol., 256, 77-88, 1996) and sexual PCR (Crameri et al., Nature, 391, 288-291, 1998). Vaughan et al. (supra) discusses these methods of affinity maturation.

(97) In one embodiment, the first antibody or antibody fragment (A) is specific to a first antigen and the second antibody or antibody fragment (B) is specific to a second antigen, and generally the first and second antigens are different. Advantageously, the bispecfic antibody complex may be specific for two different antigens. This presents the possibility of the antibody complex binding to two different antigens, each located on a different entity, thereby bringing the two entities into close physical proximity with each other.

(98) In one embodiment, the first antibody/fragment (A), second antibody/fragment (B) or both the first and second antibody/fragment of the bispecific antibody complex of the present disclosure may be a Fab.

(99) In one embodiment, the first antibody/fragment (A), second antibody/fragment (B) or both the first and second antibody/fragment of the bispecific antibody complex of the present disclosure may be a Fab.

(100) In one embodiment, the first antibody/fragment (A), second antibody/fragment (B) or both the first and second antibody/fragment of the bispecific antibody complex of the present disclosure may be a scFv.

(101) In one embodiment, the first (A) or second (B) antibody/fragment or both the first and second antibody/fragment of the bispecific antibody complex of the present disclosure is/are a VHH. For convenience bispecific protein complexes of the present disclosure are referred to herein as A-X:Y-B. A and B and X and Y are nominal labels referred to for assisting the explanation of the present technology.

(102) Attached as employed herein refers to connected or joined directly or indirectly via a linker, such as a peptide linker examples of which are discussed below. Directly connected includes fused together (for example a peptide bond) or conjugated chemically.

(103) Binding partner as employed herein refers to one component part of a binding pair.

(104) In one embodiment, the affinity of the binding partners is high, 5 nM or stronger, such as 900, 800, 700, 600, 500, 400, 300 pM or stronger.

(105) Binding pair as employed herein refers to two binding partners which specifically bind to each other. Examples of a binding pair include a peptide and an antibody or binding fragment specific thereto, or an enzyme and ligand, or an enzyme and an inhibitor of that enzyme.

(106) In one embodiment, the first binding partner (X) is selected from the group comprising: a full length antibody, a Fab, a Fab, Fv, dsFv, a scFv and a sdAb, wherein examples of a sdAb include VH or VL or V.sub.HH.

(107) When X is an antibody or binding fragment thereof then Y is a protein or peptide, in particular a peptide.

(108) In one embodiment, the second partner (Y) is selected from the group comprising: a full length antibody, a Fab, a Fab, Fv, dsFv, a scFv and a sdAb, wherein examples of a sdAb include VH or VL or VHH.

(109) When Y is an antibody or binding fragment thereof then X is a protein or peptide, in particular a peptide.

(110) In one embodiment, where A is an antibody or fragment thereof the first binding partner (X) is attached to the C-terminal of the heavy or light chain of the first antibody or antibody fragment, for example, the first binding partner (X) is attached to the C-terminal of the heavy chain of the first antibody or antibody fragment (A).

(111) In another embodiment, where B is an antibody or fragment thereof the second binding partner (Y) is attached to the C-terminal of the heavy or light chain of the second antibody or antibody fragment, for example the second binding partner (Y) is attached to the C-terminal of the heavy chain of the second antibody or antibody fragment (B).

(112) In one embodiment X is attached to the C-terminal of the heavy chain of the antibody or fragment (protein A) and Y is attached to the C-terminal of the heavy chain of the antibody or fragment (protein B).

(113) In one embodiment X is attached via a linker (such as ASGGGG SEQ ID NO: 71 or ASGGGGSG SEQ ID NO: 72) or any other suitable linker known in the art or described herein below, to the C-terminal of the heavy chain of the antibody or fragment (protein A) and Y is attached via a linker (such as ASGGGG SEQ ID NO: 71 or ASGGGGSG SEQ ID NO: 72) to the C-terminal of the heavy chain of the antibody or fragment (protein B).

(114) Examples of a suitable binding pair (X or Y) may include GCN4 (SEQ ID NOs: 1 or 76-98 or lacking the HIS tag, amino acids 1-38 of SEQ ID NOs: 1 or 76-98) or a variant thereof and 52SR4 (SEQ ID NOs: 3, 99 or 100 or lacking the HIS tag amino acids 1 to 243 of SEQ ID NO:3) or a variant thereof, which is a scFv specific for GCN4.

(115) In a one embodiment, the first binding partner (nominally X) is GCN4 (for example as shown in SEQ ID NOs: 1, 76-98) or a fragment or variant thereof (for example without the His tag) and the second binding partner (nominally Y) is a scFv or sdAb specific for GCN4 (for example as shown in SEQ ID NOs: 3, 99 or 100) or a variant thereof.

(116) In one embodiment, the first binding partner (nominally X) is a sFv or sdAb specific for GCN4 (for example as shown in SEQ ID NO: 3) or a variant thereof and the second binding partner (nominally Y) is GCN4 (for example as shown in SEQ ID NO: 1) or a fragment or variant thereof.

(117) GCN4 variants include an amino acid sequence with at least 80%, 85%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98%, or 99% identity to SEQ ID NO: 1. GCN4 variants also include an amino acid having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% to a sequence encoded by a nucleotide sequence SEQ ID NO: 2.

(118) A suitable scFv specific to GCN4 is 52SR4 (SEQ ID NOs: 3, 99 or 100 or amino acids 1-243 of SEQ ID NO: 3) or a variant thereof. Variants of 52SR4 include an amino acid sequence with at least 80%, or 85%, or 90%, or 95%, or 98%, or 99% identity to SEQ ID NO: 3. 52SR4 variants also include an amino acid sequence having at least at least 80%, or 85%, or 90%, or 95%, or 98%, or 99% to a sequence encoded by a nucleotide sequence SEQ ID NO: 4.

(119) The present inventors have found that the single chain antibody 52SR4 and peptide GCN4, are a binding pair suitable for use in the bispecific protein complexes of the present disclosure.

(120) Alternatively, any suitable antibody/fragment and antigen (such as a peptide) may be employed as X and Y. Preferably such an X and Y pair result in greater than 75% heterodimer when A-X and Y-B are combined in a 1:1 molar ratio.

(121) In one embodiment, the first binding partner (X) and the second binding partner (Y) are a protein.

(122) In one embodiment, the first binding partner (X) is an enzyme or an active fragment thereof and the second binding partner (Y) is a ligand or vice versa.

(123) In one embodiment, the first binding partner (X) is an enzyme or an active fragment thereof and the second binding partner (Y) is an inhibitor of that enzyme or vice versa.

(124) Active fragment as employed herein refers to an amino acid fragment, which is less than the whole amino acid sequence for the entity and retains essentially the same biological activity or a relevant biological activity, for example greater than 50% activity such as 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%.

(125) In another embodiment, the first binding partner X is glutathione (GSH) and the second binding partner Y is glutathione-S-transferase (GST) or vice versa.

(126) In another embodiment, X is Fos and Y is Jun or vice versa.

(127) In another embodiment, X is His and Y is anti-His or vice versa.

(128) In another embodiment, the binding pair is clamodulin binding peptide and Y is calmodulin or vice versa.

(129) In another embodiment, X is maltose-binding protein and Y is an anti-maltose binding protein or fragment thereof or vice versa.

(130) Other enzyme-ligand combinations are also contemplated for use in binding partners. Also suitable are affinity tags known in the art for protein purification because these have a tendency to bind with high affinity to their respective binding partners.

(131) Identity, as used herein, indicates that at any particular position in the aligned sequences, the amino acid residue is identical between the sequences. Similarity, as used herein, indicates that, at any particular position in the aligned sequences, the amino acid residue is of a similar type between the sequences. For example, leucine may be substituted for isoleucine or valine. Other amino acids which can often be substituted for one another include but are not limited to: phenylalanine, tyrosine and tryptophan (amino acids having aromatic side chains); lysine, arginine and histidine (amino acids having basic side chains); aspartate and glutamate (amino acids having acidic side chains); asparagine and glutamine (amino acids having amide side chains); and cysteine and methionine (amino acids having sulphur-containing side chains).

(132) Degrees of identity and similarity can be readily calculated (Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York, 1988; Biocomputing. Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part 1, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987, Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991, the BLAST software available from NCBI (Altschul, S. F. et al., 1990, J. Mol. Biol. 215:403-410; Gish, W. & States, D. J. 1993, Nature Genet. 3:266-272. Madden, T. L. et al., 1996, Meth. Enzymol. 266:131-141; Altschul, S. F. et al., 1997, Nucleic Acids Res. 25:3389-3402; Zhang, J. & Madden, T. L. 1997, Genome Res. 7:649-656,).

(133) In one embodiment, the first or second binding partner (X or Y) is a protein or peptide.

(134) In one embodiment, the first and second fusion proteins comprise one or more peptide linkers. The linkers may be incorporated at various locations in the fusion proteins. For example, a linker may be introduced between a binding partner and the protein attached thereto.

(135) In one embodiment, the linker is a peptide linker.

(136) The term peptide linker as used herein refers to a peptide with an amino acid sequence. A range of suitable peptide linkers will be known to the person of skill in the art.

(137) In one embodiment, the binding partners of the bispecific protein complexes are joined to their respective proteins via peptide linkers.

(138) In one embodiment the fusion proteins are a translational fusion, that is a fusion protein expressed in a host cell comprising a genetic construct from which the fusion protein is expressed.

(139) In one embodiment the fusion protein is prepared by fusing the heavy chain or light chain of A to X and/or the heavy chain or light chain of B to Y optionally via a peptide linker.

(140) In one embodiment, the peptide linker is 50 amino acids in length or less, for example 20 amino acids or less.

(141) Generally it will be more efficient to express the fusion protein recombinantly and therefore a direct peptide bond or a peptide linker that can be expressed by a host cell may be advantageous.

(142) In one embodiment, the linker is selected from a sequence shown in sequence 5 to 75 or PPP (Tables 5, 6 and 7)

(143) TABLE-US-00004 TABLE5 SEQIDNO: SEQUENCE 5 DKTHTCAA 6 DKTHTCPPCPA 7 DKTHTCPPCPATCPPCPA 8 DKTHTCPPCPATCPPCPATCPPCPA 9 DKTHTCPPCPAGKPTLYNSLVMSDTAGTCY 10 DKTHTCPPCPAGKPTHVNVSVVMAEVDGTCY 11 DKTHTCCVECPPCPA 12 DKTHTCPRCPEPKSCDTPPPCPRCPA 13 DKTHTCPSCPA

(144) TABLE-US-00005 TABLE6 SEQ IDNO: SEQUENCE 14 SGGGGSE 15 DKTHTS 16 (S)GGGGS 17 (S)GGGGSGGGGS 18 (S)GGGGSGGGGSGGGGS 19 (S)GGGGSGGGGSGGGGSGGGGS 20 (S)GGGGSGGGGSGGGGSGGGGSGGGGS 21 AAAGSG-GASAS 22 AAAGSG-XGGGS-GASAS 23 AAAGSG-XGGGSXGGGS-GASAS 24 AAAGSG-XGGGSXGGGSXGGGS-GASAS 25 AAAGSG-XGGGSXGGGSXGGGSXGGGS-GASAS 26 AAAGSG-XS-GASAS 27 PGGNRGTTTTRRPATTTGSSPGPTQSHY 28 ATTTGSSPGPT 29 ATTTGS 30 AAAAAAAAAAAAA 31 EPSGPISTINSPPSKESHKSP 32 GTVAAPSVFIFPPSD 33 GGGGIAPSMVGGGGS 34 GGGGKVEGAGGGGGS 35 GGGGSMKSHDGGGGS 36 GGGGNLITIVGGGGS 37 GGGGVVPSLPGGGGS 38 GGEKSIPGGGGS 39 RPLSYRPPFPFGFPSVRP 40 YPRSIYIRRRHPSPSLTT 41 TPSHLSHILPSFGLPTFN 42 RPVSPFTFPRLSNSWLPA 43 SPAAHFPRSIPRPGPIRT 44 APGPSAPSHRSLPSRAFG 45 PRNSIHFLHPLLVAPLGA 46 MPSLSGVLQVRYLSPPDL 47 SPQYPSPLTLTLPPHPSL 48 NPSLNPPSYLHRAPSRIS 49 LPWRTSLLPSLPLRRRP 50 PPLFAKGPVGLLSRSFPP 51 VPPAPVVSLRSAHARPPY 52 LRPTPPRVRSYTCCPTP- 53 PNVAHVLPLLTVPWDNLR 54 CNPLLPLCARSPAVRTFP

(145) (S) is optional in sequences 17 to 20. Another linker may be peptide sequence GS.

(146) Examples of rigid linkers include the peptide sequences GAPAPAAPAPA (SEQ ID NO: 69), PPPP (SEQ ID NO: 70) and PPP.

(147) TABLE-US-00006 TABLE7 SEQIDNO: SEQUENCE 55 DLCLRDWGCLW 56 DICLPRWGCLW 57 MEDICLPRWGCLWGD 58 QRLMEDICLPRWGCLWEDDE 59 QGLIGDICLPRWGCLWGRSV 60 QGLIGDICLPRWGCLWGRSVK 61 EDICLPRWGCLWEDD 62 RLMEDICLPRWGCLWEDD 63 MEDICLPRWGCLWEDD 64 MEDICLPRWGCLWED 65 RLMEDICLARWGCLWEDD 66 EVRSFCTRWPAEKSCKPLRG 67 RAPESFVCYWETICFERSEQ 68 EMCYFPGICWM

(148) In one aspect, there is provided a method of producing a bispecific protein complex of the present disclosure, comprising the steps of: (a) producing a first fusion protein (A-X), comprising a first protein (A), attached to a first binding partner (X) of a binding pair; (b) producing a second fusion protein (B-Y), comprising a second protein (B), attached to a second binding partner (Y) of a binding pair; and (c) mixing the first (A-X) and second fusion proteins (B-Y) prepared in step a) and b) together.

(149) Typically the mixing of A-X and B-Y in step (c) is in a 1:1 molar ratio.

(150) In one embodiment each fusion proteins employed in the complexes of the present disclosure are produced by expression in a host cell or host cells in an expression experiment.

(151) In one aspect, there is provided a method of preparing a bispecific protein complex of the present disclosure, comprising the steps of: (a) expressing a first fusion protein (A-X), comprising a first protein (A), attached to a first binding partner (X) of a binding pair; (b) expressing a second fusion protein (B-Y), comprising a second protein (B), attached to a second binding partner (Y) of a binding pair;
wherein fusion protein A-X and B-Y are expressed from the same host cell or distinct host cells.

(152) Distinct host cells as employed herein refers to individual cells, including cells of the same type (even same clonal type).

(153) In one embodiment the expression is transient expression. The use of transient expression is highly advantageous when combined with the ability to generate bispecific complexes without recourse to purification. This results in a rapid method to generate bispecific protein complexes as transient transfection is much simpler and less resource intensive than stable transfection.

(154) In one embodiment the expression is stable expression i.e. wherein the DNA encoding the fusion protein in question is stably integrated into the host cell genome.

(155) In one embodiment the fusion proteins of the present disclosure are mixed in an aqueous environment, for example one fusion protein may be bound to a solid surface such as a bead or a plate and the other fusion protein can be introduced thereto in an aqueous solution/suspension. The solid phase allows excess components and reagents to be washed away readily. In one embodiment neither fusion is attached a solid phase and are simply mixed in a liquid/solution/medium. Thus in one embodiment A-X and B-Y are mixed as free proteins in an aqueous media.

(156) Advantageously, the method of the present disclosure can be employed to prepare complexes formed between heterogenous pairs (i.e. between the first fusion protein [A-X] and second fusion protein [B-Y]) wherein interactions between homogenous pairs (i.e. between two first fusion proteins [A-X] or two second fusion proteins [B-Y]) are minimised. Thus the present method allows large numbers of bispecific protein complexes to be prepared, with minimal or no contamination with homodimeric complexes. An advantage of the constructs and method of the present disclosure is that the ratio of A-X to B-Y is controlled by the properties of the A-X and B-Y and in particular a molar ratio of 1:1 can be achieved. This element of control is a significant improvement over the certain prior art methods.

(157) If present constant region domains of a bispecific antibody complex or antibody molecule of the present disclosure, if present, may be selected having regard to the proposed function of the complex or antibody molecule, and in particular the effector functions which may be required. For example, the constant region domains may be human IgA, IgD, IgE, IgG or IgM domains. In particular, human IgG constant region domains may be used, especially of the IgG1 and IgG3 isotypes when the antibody molecule is intended for therapeutic uses and antibody effector functions are required. Alternatively, IgG2 and IgG4 isotypes may be used when the antibody molecule is intended for therapeutic purposes and antibody effector functions are not required. It will be appreciated that sequence variants of these constant region domains may also be used. For example IgG4 molecules in which the serine at position 241 has been changed to proline as described in Angal et al., 1993, Molecular Immunology, 1993, 30:105-108 may be used. Accordingly, in the embodiment where the antibody is an IgG4 antibody, the antibody may include the mutation S241P.

(158) It will also be understood by one skilled in the art that antibodies may undergo a variety of posttranslational modifications. The type and extent of these modifications often depends on the host cell line used to express the antibody as well as the culture conditions. Such modifications may include variations in glycosylation, methionine oxidation, diketopiperazine formation, aspartate isomerization and asparagine deamidation. A frequent modification is the loss of a carboxy-terminal basic residue (such as lysine or arginine) due to the action of carboxypeptidases (as described in Harris, R J. Journal of Chromatography 705:129-134, 1995). Accordingly, the C-terminal lysine of the antibody heavy chain may be absent.

(159) The present disclosure also provides a composition comprising one or more bispecific protein complexes as described above, wherein the composition predominantly comprises heterodimeric bispecific complexes according to the present disclosure, for example with minimal or no contamination with homodimeric complexes.

(160) In one embodiment, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 90%, or at least 95% of the fusion proteins in the composition are in a bispecific protein complex form.

(161) In one embodiment, at least 60% of the fusion proteins in the composition are in a bispecific protein complex form.

(162) In one embodiment the complexes formed require one purification step, for example column chromatography.

(163) In one embodiment the method further comprises at least one purification step, for example after expression of a fusion protein according to the present disclosure and before mixing the fusion proteins.

(164) In one aspect the present disclosure relates to a fusion protein, a heterodimerically-tethered bispecific protein complex, a composition comprising a fusion protein or said bispecific protein complex, a multiple, array, library as defined herein.

(165) In one embodiment, the bispecific protein complex is in solution or suspension.

(166) In one embodiment, the bispecific protein complexes are fixed on a solid substrate surface.

(167) In one embodiment, the multiplex is in the form of an array, for example in a microplate, such as a 96 or 384 well plate. Such arrays can be readily implemented in screening assays to identify bispecific protein complexes with desired functionality.

(168) In another embodiment, the bispecific protein complexes are conjugated to beads.

(169) A fusion protein as defined above is a component of the bispecific protein complex according to the present disclosure. In one aspect, the present disclosure relates to a fusion protein described herein.

(170) In one embodiment there is provided a fusion protein obtained or obtainable for a method of the present disclosure.

(171) In one embodiment there is provided an bispecific antibody complex obtained or obtainable from a method of the present disclosure

(172) The present disclosure also extends to a kit, for example comprising A-X and B-Y in a complexed or uncomplexed form, for use in the method of the present disclosure.

(173) In another embodiment, the kit further comprises instructions for use.

(174) In yet another embodiment, the kit further comprises one or more reagents for performing one or more functional assays.

(175) In a further aspect, there is provided a nucleotide sequence, for example a DNA sequence encoding a fusion protein and/or a bispecific protein complex as defined above.

(176) In one embodiment, there is provided a nucleotide sequence, for example a DNA sequence encoding a bispecific protein complex according to the present disclosure.

(177) In one embodiment there is provided a nucleotide sequence, for example a DNA sequence encoding a bispecific or multispecific antibody molecule according to the present disclosure.

(178) The disclosure herein also extends to a vector comprising a nucleotide sequence as defined above including a vector suitable for use in vivo, such as for expression of A-X in an effector cell, under the control of a suitable promoter.

(179) The term vector as used herein refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. An example of a vector is a plasmid, which is a circular double stranded DNA loop into which additional DNA segments may be ligated. Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) can be integrated into the genome of a host cell, where they are subsequently replicated along with the host genome. In the present specification, the terms plasmid and vector may be used interchangeably as a plasmid is the most commonly used form of vector.

(180) General methods by which the vectors may be constructed, transfection methods and culture methods are well known to those skilled in the art. In this respect, reference is made to Current Protocols in Molecular Biology, 1999, F. M. Ausubel (ed), Wiley Interscience, New York and the Maniatis Manual produced by Cold Spring Harbor Publishing.

(181) The term selectable marker as used herein refers to a protein whose expression allows one to identify cells that have been transformed or transfected with a vector containing the marker gene. A wide range of selection markers are known in the art. For example, typically the selectable marker gene confers resistance to drugs, such as G418, hygromycin or methotrexate, on a host cell into which the vector has been introduced. The selectable marker can also be a visually identifiable marker such as a fluorescent marker for example. Examples of fluorescent markers include rhodamine, FITC, TRITC, Alexa Fluors and various conjugates thereof.

(182) Also provided is a host cell comprising one or more cloning or expression vectors comprising one or more DNA sequences encoding an antibody of the present disclosure. Any suitable host cell/vector system may be used for expression of the DNA sequences encoding the antibody molecule of the present disclosure. Bacterial, for example E. coli, and other microbial systems may be used or eukaryotic, for example mammalian, host cell expression systems may also be used. Suitable mammalian host cells include CHO, myeloma or hybridoma cells.

(183) The present disclosure also provides a process for the production of a fusion protein according to the present disclosure comprising culturing a host cell containing a vector of the present disclosure under conditions suitable for leading to expression of protein from DNA encoding the molecule of the present disclosure, and isolating the molecule.

(184) The bispecific antibody complexes of the present disclosure may for example be conjugated to a fluorescent marker which facilitates the detection of bound antibody-antigen complexes. Such bispecific antibody complexes can be used for immunofluorescence microscopy.

(185) Alternatively, the bispecific antibody complexes may also be used for western blotting or ELISA.

(186) In one embodiment, there is provided a process for purifying an antibody (in particular an antibody or fragment according to the invention).

(187) In one embodiment, there is provided a process for purifying a fusion protein or bispecific protein complex according the present disclosure comprising the steps: performing anion exchange chromatography in non-binding mode such that the impurities are retained on the column and the antibody is maintained in the unbound fraction. The step may, for example be performed at a pH about 6-8.

(188) The process may further comprise an initial capture step employing cation exchange chromatography, performed for example at a pH of about 4 to 5.

(189) The process may further comprise of additional chromatography step(s) to ensure product and process related impurities are appropriately resolved from the product stream.

(190) The purification process may also comprise of one or more ultra-filtration steps, such as a concentration and diafiltration step.

(191) Purified form as used supra is intended to refer to at least 90% purity, such as 91, 92, 93, 94, 95, 96, 97, 98, 99% w/w or more pure.

(192) In the context of this specification comprising is to be interpreted as including.

(193) Aspects of the disclosure comprising certain elements are also intended to extend to alternative embodiments consisting or consisting essentially of the relevant elements.

(194) Positive embodiments employed herein may serve basis for the excluding certain aspects of the disclosure.

(195) Disclosures in the context of the method relating to the bispecific complexes apply equally to the complexes per se and vice versa.

REFERENCES

(196) 1. Ribosome display efficiently selects and evolves high-affinity antibodies in vitro from immune libraries. Hanes J, Jermutus L, Weber-Bornhauser S, Bosshard H R, Plckthun A. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 14130-14135 2. Directed in Vitro Evolution and Crystallographic Analysis of a Peptide-binding Single Chain Antibody Fragment (scFv) with Low Picomolar Affinity. Zhand C, Spinelli S, Luginbuhl B, Amstutz P, Cambillau C, Pluckthun A. (2004) J. Biol. Chem. 279, 18870-18877 3. Antigen recognition by conformational selection. Berger C, Weber-Bornhauser S, Eggenberger Y, Hanes J, Pluckthun A, Bosshard H. R. (1999) F.E.B.S. Letters 450, 149-153

EXAMPLES

Example 1: Directing Engrafted T Cells or NK Cells to Kill Cancer Cells

(197) (Illustrated in FIGS. 2 and 4)

(198) In this example A-X, is a fusion of X (a scFv (52SR4 having amino acid sequence such as that shown in SEQ ID NOs: 99 or 100) with binding specificity for Y (GCN4) with A comprising a spacer region, a transmembrane region and a signalling region capable of delivering an activating signal to T cells or NK cells. The components of A could be those commonly used in the chimeric antigen receptors used to direct T cells to cancer cells (Nat Revs Drug Discovery 2015: vol 14 p 499-509) and having amino acid sequence as shown in X-A SEQ ID NO: 109-116). B-Y is a fusion of B, an antibody or antibody fragment or derivative specific for the cancer antigen fused to Y (GCN4 peptide having an amino acid sequence as shown in SEQ ID NO: 76-98).

(199) The A-X fusion polynucleotide sequence is delivered to and protein expressed on T or NK cells for infusion into patients. A-X can be pre-complexed with B-Y before infusion or cells expressing A-X can be infused and B-Y delivered to the patient subsequently to form the A-X:Y-B complex in vivo.

(200) The time of delivery and half-life of B-Y can be tuned to reduce side effects of cell infusion & rapid target lysis. Targeting can be stopped by withdrawal of administration of B-Y.

(201) During the course of disease & treatment the specificity of B in B-Y can be changed. This could facilitate the re-direction of engrafted cells to a second tumour antigen in the case of tumour cell escape or target the engrafted cells for destruction to terminate treatment.

(202) This modular ability to deliver engrafted cell specificity has advantages over receptors utilising CD16 to capture of IgG specificities (Cancer Res 2013 74 (1) 93-103) as these could bind to autoantibodies in vivo and hence target engrafted T cells to self-antigens & tissues generating acute autoimmunity. The specificity of X for Y only expressed on the targeting moiety of choice would prevent this.

Example 2: Directing Engrafted T Regulatory Cells to a Selected Location to Prevent Autoimmunity

(203) (Illustrated in FIG. 1)

(204) In this example A-X, is a fusion of X (a scFv (52SR4 having amino acid sequence such as that shown in SEQ ID NOs: 99 or 100) with binding specificity for Y (GCN4 peptide having an amino acid sequence as shown in SEQ ID NO: 76-98) with A comprising a spacer region, a transmembrane region to facilitate cell surface expression of X. X-A having amino acid sequence such as that shown in SEQ ID NOs: 105-109. B-Y is a fusion of B, an antibody or antibody fragment or derivative specific for a tissue specific antigen fused to Y (GCN4).

(205) The A-X fusion polynucleotide sequence is delivered to and protein expressed on T regulatory cells for infusion into patients. A-X can be pre-complexed with B-Y before infusion or cells expressing A-X can be infused and B-Y delivered to the patient subsequently to form the A-X:Y-B complex in vivo.

(206) The time of delivery and half-life of B-Y can be tuned to reduce side effects of cell infusion & rapid target lysis. During the course of disease & treatment the specificity of B in B-Y can be changed. This could facilitate the re-direction of engrafted cells to a different site or target the engrafted cells for destruction to terminate treatment.

Example 3: Directing Haemopoetic Stem Cells to a Selected Location to Expand & Differentiate for Treatment of a Wide Range of Diseases

(207) (Illustrated in FIG. 1)

(208) In this example A-X, is a fusion of X (a scFv (52SR4 having amino acid sequence such as that shown in SEQ ID NOs: 99 or 100) with binding specificity for Y (GCN4 peptide having an amino acid sequence as shown in SEQ ID NO: 76-98) with A comprising a spacer region, a transmembrane region to facilitate cell surface expression of X. X-A having amino acid sequence such as that shown in SEQ ID NOs: 105-109. B-Y is a fusion of B, an antibody or antibody fragment or derivative specific for a tissue specific antigen fused to Y (GCN4).

(209) The A-X fusion polynucleotide sequence is delivered to and expressed on haemopoetic stem cells for infusion into patients. A-X can be pre-complexed with B-Y before infusion or cells expressing A-X can be infused and B-Y delivered to the patient subsequently to form the A-X:Y-B complex in vivo.

(210) The time of delivery and half-life of B-Y can be tuned to reduce side effects of cell infusion & rapid target lysis. During the course of disease & treatment the specificity of B in B-Y can be changed. This could facilitate the re-direction of engrafted cells to a different site or target the engrafted cells for destruction to terminate treatment.

Example 4: Directing T Cells or NK Cells In Vivo to Kill Cancer Cells

(211) (Illustrated in FIGS. 3 and 5)

(212) In this example A-X, is a fusion of X (a scFv (52SR4) with binding specificity for Y (GCN4) with A comprising an antibody or antibody fragment or derivative specific to T cells or NK cells. B-Y is a fusion of B, an antibody or antibody fragment or derivative specific for a tissue specific antigen fused to Y (GCN4).

(213) A-X can be pre-complexed with B-Y before delivery or B-Y can delivered to the patient subsequently to form the A-X:Y-B complex in vivo. This would allow pre-loading of either effector or target cells whichever proved clinically of most benefit.

(214) The time of delivery and half-life of either or both A-X and B-Y can be tuned to complement treatment.

Example 5: Directing T Regulatory Cells In Vivo to a Selected Location to Prevent Autoimmunity

(215) (Illustrated in FIGS. 3 and 5)

(216) In this example A-X, is a fusion of X (a scFv (52SR4) with binding specificity for Y (GCN4) with A comprising an antibody or antibody fragment or derivative specific to T regulatory cells. B-Y is a fusion of B, an antibody or antibody fragment or derivative specific for a tissue specific antigen fused to Y (GCN4).

(217) A-X can be pre-complexed with B-Y before delivery or B-Y can delivered to the patient subsequently to form the A-X:Y-B complex in vivo. This would allow pre-loading of either effector or target cells whichever proved clinically of most benefit.

(218) The time of delivery and half-life of either or both A-X and B-Y can be tuned to complement treatment.

Example 6: Directing Haemopoetic Stem Cells to a Selected Location to Expand & Differentiate for Treatment of a Wide Range of Diseases

(219) (Illustrated in FIGS. 3 and 5)

(220) In this example A-X, is a fusion of X (a scFv (52SR4) with binding specificity for Y (GCN4) with A comprising an antibody or antibody fragment or derivative specific to haemopoetic stem cells. B-Y is a fusion of B, an antibody or antibody fragment or derivative specific for a tissue specific antigen fused to Y (GCN4).

(221) A-X can be pre-complexed with B-Y before delivery or B-Y can delivered to the patient subsequently to form the A-X:Y-B complex in vivo. This would allow pre-loading of either effector or target cells whichever proved clinically of most benefit.

(222) The time of delivery and half-life of either or both A-X and B-Y can be tuned to complement treatment.

Example 7: The Use of the Complex of A-X:Y-B for Screening

(223) The formation of the complex of A-X:Y-B for screening can be used to generate large numbers of different B molecules in B-X and different A molecules in A-Y for screening the optimal combination of molecules in in vitro or in vivo assays mimicking the clinical scenarios of examples 1 to 6. This would facilitate selection of optimal A and B molecules in a bispecific format for cell direction and function in vivo.

Example 8: Utilising Cells that can Cross the Blood Brain Barrier to Direct Antibody Specificities to a Central Nervous System (CNS) Target for Treatment of Neurodegenerative and/or Neuroinflammatory Diseases

(224) (Illustrated in FIGS. 3 and 5)

(225) In this example A-X, is a fusion of X (a scFv (52SR4) with binding specificity for Y (GCN4) with A comprising an antibody or antibody fragment or derivative specific to effector cells that are able to transgress the blood brain barrier or A is a protein that facilitates expression of X on the surface of effector cells able to transgress the blood brain barrier. These effector cells act to carry a cargo of B-Y. B-Y is a fusion of B, an antibody or antibody fragment or derivative specific for a CNS expressed antigen fused to Y (GCN4). The binding of B to its target antigen in the CNS provides therapeutic benefit.

(226) A-X can be pre-complexed with B-Y before delivery or B-Y can delivered to the patient subsequently to form the A-X:Y-B complex in vivo. This would allow optimal loading of guidance cells for clinically benefit.

(227) The time of delivery and half-life of either or both A-X and B-Y can be tuned to complement treatment.