# Patent

## Title
Pharmaceutical composition comprising a bispecific antibody for EpCAM

## Abstract

The present invention provides a pharmaceutical composition comprising a bispecific single chain antibody construct. Said bispecific single chain antibody construct is characterized to comprise or consist of at least two domains, whereby one of said at least two domains specifically binds to human EpCAM and comprises at least one CDR-H3 region comprising the amino acid sequence NXID antigen and a second domain binds to human CD3 antigen. The invention further provides a process for the production of the pharmaceutical composition of the invention, a method for the prevention, treatment or amelioration of a tumorous disease and the use of the disclosed bispecific single chain antibody construct and corresponding means in the prevention, treatment or amelioration of a tumorous disease.

## Background
This application is a Continuation of U.S. patent application Ser. No. 10/554,851, filed Apr. 3, 2006, which is a National Stage application of PCT/EP2004/005687, filed May 26, 2004, which claims priority from European patent applications EP 03 01 2134.7, filed May 31, 2003, and EP 03 01 2133.9, filed May 31, 2003. The entire contents of each of the aforementioned applications are incorporated herein by reference.


The invention relates to a pharmaceutical composition comprising a bispecific single chain antibody construct. Said bispecific single chain antibody construct is characterized to comprise or consist of at least two domains, whereby one of said at least two domains specifically binds to human EpCAM antigen and comprises at least one CDR-H3 region comprising the amino acid sequence NXD and a second domain binds to human CD3 antigen. The invention further provides a process for the production of the pharmaceutical composition of the invention, a method for the prevention, treatment or amelioration of a tumorous disease and the use of the disclosed bispecific single chain antibody construct and corresponding means in the prevention, treatment or amelioration of a tumorous disease.
A variety of documents is cited throughout this specification. The disclosure content of said documents is herewith incorporated by reference.
Epithelial cell adhesion molecule (EpCAM, also called 17-1A antigen, KSA, EGP40, GA733-2, ks1-4 or esa) is a 40-kDa membrane-integrated glycoprotein of 314 amino acids with specific expression in certain epithelia and on many human carcinomas (reviewed in Baizar, J. Mol. Med. 1999, 77, 699-712). EpCAM was discovered and subsequently cloned through its recognition by the murine monoclonal antibody 17-1A/edrecolomab (Goettlinger, Int J Cancer. 1986; 38, 47-53 and Simon, Proc. Natl. Acad. Sci. USA. 1990; 87, 2755-2759). Monoclonal antibody 17-1A was generated by immunization of mice with human colon carcinoma cells (Koprowski, Somatic Cell Genet. 1979, 5, 957-971).
The EGF-like repeats of EpCAM were shown to mediate lateral and reciprocal interactions in homophilic cell adhesion (Balzar, Mol. Cell. Biol. 2001, 21, 2570-2580) and, for that reason, is predominantly located between epithelial cells (Litvinov, J Cell Biol. 1997, 139, 1337-1348, Balzar, J Mol Med. 1999, 77, 699-712 and Trebak, J Biol Chem. 2001, 276, 2299-2309). EpCAM serves to adhere epithelial cells in an oriented and highly ordered fashion (Litvinov, J Cell Biol. 1997, 139, 1337-1348). Data from experiments with transgenic mice and rats expressing human EpCAM on their epithelia suggest that EpCAM on normal tissue may however not be accessible to systemically administered antibody (McLaughlin, Cancer Immunol. Immunother., 1999, 48, 303-311). Upon malignant transformation of epithelial cells the rapidly growing tumor cells are abandoning the high cellular order of epithelia. Consequently, the surface distribution of EpCAM becomes less restricted and the molecule better exposed on tumor cells. Due to their epithelial cell origin, tumor cells from most carcinomas still express EpCAM on their surface.
In vivo, expression of EpCAM is related to increased epithelial proliferation and negatively correlates with cell differentiation (for review see Balzar, 1999, J. Mol. Med. 77, 699-712). Expression of EpCAM, as detected by immunohistochemistry using anti-EpCAM monoclonal antibodies, is essentially seen with all major carcinomas (reviewed in Balzar, J Mol Med. 1999, 77, 699-712). Best EpCAM expression was observed with non-small cell lung cancer (De Bree, Nucl Med Commun. 1994, 15, 613-27) and prostate cancer (Zhang, Clin Cancer Res. 1998, 4, 295-302) where 100% of tumor patient samples showed positive EpCAM staining. In these studies, EpCAM is also reported to homogeneously stained tumor tissues indicating that the antigen is expressed on a large proportion of cells of a′ given tumor. Because of its widespread expression, EpCAM is referred to as a “pan-carcinoma” antigen.
EpCAM has been shown in various studies to be beneficial in diagnosis and therapy of various carcinomas. Furthermore, in many cases, tumor cells were observed to express EpCAM to a much higher degree than their parental epithelium or less aggressive forms of said cancers. For example, EpCAM expression was shown to be significantly higher on neoplastic tissue and in adenocarcinoma than on normal prostate epithelium (n=76; p<0.0001), suggesting that increased EpCAM expression represents an early event in the development of prostate cancer (Poczatek, J Urol., 1999, 162, 1462-1644). In addition, in the majority of both squamous and adenocarcinomas of the cervix a strong EpCAM expression correlates with an increased proliferation and the disappearance of markers for terminal differentiation (Litvinov, Am. J. Pathol. 1996, 148, 865-75). One example is breast cancer where overexpression of EpCAM on tumor cells is a predictor of survival (Gastl, Lancet. 2000, 356, 1981-1982). Furthermore, EpCAM has been described as a marker for the detection of disseminated tumor cells in patients suffering from squamous cell carcinoma of the head, neck and lung (Chaubal, Anticancer Res 1999, 19, 2237-2242, Piyathilake, Hum Pathol. 2000, 31, 482-487). Normal squamous epithelium, as found in epidermis, oral cavity, epiglottis, pharynx, larynx and esophagus did not significantly express. EpCAM (Quak, Hybridoma, 1990, 9, 377-387).
In addition to the above-mentioned carcinomas, EpCAM has been shown to be expressed on the majority of primary, metastatic, and disseminated NSCLC (non small cell lung cancer cells) (Passlick, Int J Cancer, 2000, 87, 548-552), on gastric and gastro-oesophageal junction adenocarcinomas (Martin, J Clin Pathol 1999, 52, 701-4) and in cell lines derived from colorectal, pancreatic carcinomas and breast carcinomas (Szala, Proc Natl Acad Sci USA 1990, 87, 3542-6, Packeisen, Hybridoma, 1999, 18, 37-40).
Clinical trials have shown that the use of antibodies directed against 17-1A (EpCAM) for treatment of patients with surgically completely resected colorectal carcinoma leads to a significant benefit concerning the overall survival and the frequency of distant metastasis (Riethmüller, Lancet, 1994, 343, 1177-1183). Murine monoclonal antibody against EpCAM was found to reduce the 5-year mortality (Riethmüller, Lancet, 1994, 343, 1177-1183) and also the 7-year mortality (Riethmüller, Proceedings of the American Society of Clinical Oncology, 1996, 15, 444) of patients with minimal residual disease. Example of murine monoclonal antibody recognizing EpCAM is Edrecolomab (Panorex) (Koprowski, Somatic Cell Genet. 1979, 5, 957-971 and Herlyn, Cancer Res., 1980, 40, 717-721). However, the first administration of Panorex during adjuvant immunotherapy of colon cancer led to the development and exacerbation of Wegener's granulomatosis suggesting that mAb 17-1A should be applied cautiously in a patient with autoimmune disease (Franz, Onkologie, 2000, 23, 472-474). The limitations of Panorex are the rapid formation of human anti-mouse antibodies (HAMA), the limited ability to interact by its murine IgG2a Fc-portion with human immune effector mechanisms and the short half-life in circulation (Frodin, Cancer Res., 1990, 50, 4866-4871). Furthermore, the murine antibody caused immediate-type allergic reactions and anaphylaxis upon repeated injection in patients (Riethmüller, Lancet. 1994, 343, 1177-1183, Riethmüller, J Clin Oncol., 1998, 16, 1788-1794 and Mellstedt, Annals New York Academy of Sciences. 2000, 910, 254-261).
Humanized anti-EpCAM antibody called 3622W94 resulted in pancreatitis and increased serum levels of amylase, as being indicative for damage of pancreas epithelium, which were a dose-limiting toxicity of this high-affinity anti-EpCAM monoclonal antibody (LoBuglio, Proceedings of the American Society of Clinical Oncology (Abstract). 1997, 1562 and Khor, Proceedings of the American Society of Clinical Oncology (Abstract), 1997, 847).
Bispecific antibodies comprising a region directed against EpCAM and a region directed against CD3 have also been described. The authors of Möller & Reisfeld 1991 Cancer Immunol. Immunother. 33:210-216 describe the construction of two different bispecific antibodies by fusing a hybridoma producing monoclonal antibody against EpCAM with either of the two hybridomas OKT3 and 9.3. Furthermore, Kroesen, Cancer Research, 1995, 55:4409-4415 describe a quadroma bispecific monoclonal antibodies against CD3 (BIS-1) and EpCAM.
Other examples of bispecific antibodies against EpCAM comprise the bispecific antibody, BiUII, (anti-CD3 (rat IgG2b) x anti-EpCAM (mouse IgG2a)) a complete Ig molecule which also binds and activates Fc-receptor positive accessory cells (like monocytes/macrophages, NK cells and dendritic cells) through its Fc-region (Zeidler, J. Immunol., 1999, 163:1247-1252) and an anti-EpCAMxanti-CD3 bispecific antibody in the arrangement VL17-1A-VH17-1A-VHanti-CD3-VLanti-CD3 (Mack, Proc. Natl. Acad. Sci., 1995, 92:7021-7025).
In addition, other formats of antibody constructs comprising EpCAM have been described; e.g. a bispecific diabody having the structure VH anti-CD3-VL anti-EpCAM-VH-anti-EpCAM-VLanti-CD3 (Helfrich, Int. J. Cancer, 1998, 76:232-239) and a trispecific antibody having two different tumour antigen specificities (two antigen binding regions which bind two different antigens on a tumour cell) and which may have a further specificity for an antigen localized on an effector cell (DE 195 31 348).
There exist various descriptions in the prior art of using phage display technology to identify antibodies or fragments thereof, which specifically bind to the human EpCAM antigen (De Kruif JMB, 1995, 248:97-105, WO 99/25818). However, it has been extremely difficult to identify antibodies against EpCAM, which show cytotoxic activity sufficient for therapeutic applications in a bispecific format.
It is therefore an aim of the present invention to provide a bispecific single chain molecule with a binding domain specific for EpCAM with strong cytotoxic activity mediated by target specific activation of T cells.
Thus, the technical problem underlying the present invention was to provide means and methods for the generation of well tolerated and convenient medicaments for the treatment and or amelioration of tumorous diseases.
The solution to said technical problem is achieved by providing the embodiments characterized in the claims.
Accordingly, the present invention relates to a composition, preferably a pharmaceutical composition, comprising a bispecific single chain antibody construct, whereby said construct comprises or consists of at least two binding domains, whereby one of said domains binds to human EpCAM antigen and a second domain binds to human CD3 antigen, wherein said binding domain specific for EpCAM comprises at least one CDR-H3 region comprising the amino acid sequence NXD preferably in position 102 to 104 of SEQ ID NOs: 80, 88 and 96, or preferably in position 106 to 108 of SEQ ID NOs: 84 and 92, wherein X is an aromatic amino acid.
Preferably or alternatively, the present invention relates to a composition, preferably a pharmaceutical composition, comprising a bispecific single chain antibody construct, whereby said construct comprises or consists of at least two domains, whereby one of said at least two domains specifically binds to human EpCAM antigen and a second domain binds to human CD3 antigen, wherein said binding domain specific for EpCAM comprises at least one CDR-H3 region of least 9 amino acid residues and wherein said binding domain specific for EpCAM has a KD value of more than 5×10−9 M.
In accordance with this invention, the term “pharmaceutical composition” relates to a composition for administration to a patient, preferably a human patient. In a preferred embodiment, the pharmaceutical composition comprises a composition for parenteral, transdermal, intraluminal, intra-arterial, intrathecal or intravenous administration or for direct injection into the tumor. It is in particular envisaged that said pharmaceutical composition is administered to a patient via infusion or injection. Administration of the suitable compositions may be effected by different ways, e.g., by intravenous, subcutaneous, intraperitoneal, intramuscular, topical or intradermal administration. The pharmaceutical composition of the present invention may further comprise a pharmaceutically acceptable carrier. Examples of suitable pharmaceutical carriers are well known in the art and include phosphate buffered saline solutions, water, emulsions, such as oil/water emulsions, various types of wetting agents, sterile solutions, etc. Compositions comprising such carriers can be formulated by well known conventional methods. These pharmaceutical compositions can be administered to the subject at a suitable dose. The dosage regimen will be determined by the attending physician and clinical factors. As is well known in the medical arts, dosages for any one patient depends upon many factors, including the patient's size, body surface area, age, the particular compound to be administered, sex, time and route of administration, general health, and other drugs being administered concurrently. A preferred dosage for administration might be in the range of 0.24 μg to 48 mg, preferably 0.24 μg to 24 mg, more preferably 0.24 μg to 2.4 mg, even more preferably 0.24 μg to 1.2 mg and most preferably 0.24 μg to 240 μg units per kilogram of body weight per day. Particularly preferred dosages are recited herein below. Progress can be monitored by periodic assessment. Dosages will vary but a preferred dosage for intravenous administration of DNA is from approximately 106 to 1012 copies of the DNA molecule. The compositions of the invention may be administered locally or systematically. Administration will generally be parenteral, e.g., intravenous; DNA may also be administered directly to the target site, e.g., by biolistic delivery to an internal or external target site or by catheter to a site in an artery. In an preferred embodiment, the pharmaceutical composition is administered subcutaneously and in an even more preferred embodiment intravenously. Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishes, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like. In addition, the pharmaceutical composition of the present invention might comprise proteinaceous carriers, like, e.g., serum albumine or immunoglobuline, preferably of human origin. It is envisaged that the pharmaceutical composition of the invention might comprise, in addition to the proteinaceous bispecific single chain antibody constructs or nucleic acid molecules or vectors encoding the same (as described in this invention), further biologically active agents, depending on the intended use of the pharmaceutical composition. Such agents might be drugs acting on the gastro-intestinal system, drugs acting as cytostatica, drugs preventing hyperurikemia, agents such as T-cell co-stimulatory molecules or cytokines, drugs inhibiting immune reactions (e.g. corticosteroids) and/or drugs acting on the circulatory system, e.g. on the blood pressure, known in the art.
Possible indications for administration of the composition(s) of the invention are tumorous diseases especially epithelial cancers/carcinomas such as breast cancer, colon cancer, prostate cancer, head and neck cancer, skin cancer, cancers of the genito-urinary tract, e.g. ovarial cancer, endometrial cancer, cervix cancer and kidney cancer, lung cancer, gastric cancer, cancer of the small intestine, liver cancer, pancreas cancer, gall bladder cancer, cancers of the bile duct, esophagus cancer, cancer of the salivatory glands and cancer of the thyroid gland. The administration of the composition(s) of the invention is especially indicated for minimal residual disease preferably early solid tumor, advanced solid tumor or metastatic solid tumor, which is characterized by the local and non-local reoccurrence of the tumor caused by the survival of single cells.
The invention further envisages the co-administration protocols with other compounds, e.g. bispecific antibody constructs, targeted toxins or other compounds, which act via T cells. The clinical regimen for co-administration of the inventive compound(s) may encompass co-administration at the same time, before or after the administration of the other component.
A possible approach to demonstrate the efficacy/activity of the inventive constructs is an in vivo model like mouse. Suitable models may be transgenic and chimeric mouse models. Mouse models expressing human CD3 and human EpCAM, a chimeric mouse model expressing murine CD3 and into which tumour cells expressing human EpCAM can be transfected and chimeric mouse models comprising nude mice into which human tumours expressing EpCAM can be transplanted or tumour cells expressing human EpCAM can be injected and, additionally, human PBMCs are injected. The term “bispecific single chain antibody construct” relates to a construct comprising two antibody derived binding domains. One of said binding domains consists of variable regions (or parts thereof) of an antibody, antibody fragment or derivative thereof, capable of specifically binding to/interacting with human EpCAM antigen (target molecule 1). The second binding domain consists of variable regions (or parts thereof) of an antibody, antibody fragment or derivative thereof, capable of specifically binding to/interacting with human CD3 antigen (target molecule 2). As will be detailed below, a part of a variable region may be at least one CDR (“Complementary determining region”), most preferably at least the CDR3 region. Said two domains/regions in the single chain antibody construct are preferably covalently connected to one another as a single chain. This connection can be effected either directly (domain 1 [specific for the CD3 antigen]-domain 2 [specific for the EpCAM antigen] or domain 1 [specific for the EpCAM antigen]-domain 2 [specific for the CD3 antigen]) or through an additional polypeptide linker sequence (domain1-linker sequence-domain2). In the event that a linker is used, this linker is preferably of a length and sequence sufficient to ensure that each of the first and second domains can, independently from one another, retain their differential binding specificities. Most preferably and as documented in the appended examples, the “bispecific single chain antibody construct” to be employed in the pharmaceutical composition of the invention is a bispecific single chain Fv (scFv). Bispecific single chain molecules are known in the art and are described in WO 99/54440, Mack, J. Immunol. (1997), 158, 3965-3970, Mack, PNAS, (1995), 92, 7021-7025, Kufer, Cancer Immunol. Immunother., (1997), 45, 193-197, Löffler, Blood, (2000), 95, 6, 2098-2103 and Brühl, J. Immunol., (2001), 166, 2420-2426. A particularly preferred molecular format of the invention provides a polypeptide construct wherein the antibody-derived region comprises one VH and one VL region. The intramolecular orientation of the VH-domain and the VL-domain, which are linked to each other by a linker-domain, in the scFv format is not decisive for the recited bispecific single chain constructs. Thus, scFvs with both possible arrangements (VH-domain-linker domain-VL-domain; VL-domain-linker domain-VH-domain) are particular embodiments of the recited bispecific single chain construct.
The antibody construct may also comprise additional domains, e.g. for the isolation and/or preparation of recombinantly produced constructs.
A corresponding format for a bispecific single chain antibody construct is described in the appended example 1.
The term “single-chain” as used in accordance with the present invention means that said first and second domain of the bispecific single chain construct are covalently linked, preferably in the form of a co-linear amino acid sequence encodable by a single nucleic acid molecule.
The term “binding to/interacting with” as used in the context with the present invention defines a binding/interaction of at least two “antigen-interaction-sites” with each other. The term “antigen-interaction-site” defines, in accordance with the present invention, a motif of a polypeptide which shows the capacity of specific interaction with a specific antigen or a specific group of antigens. Said binding/interaction is also understood to define a “specific recognition”. The term “specifically recognizing” means in accordance with this invention that the antibody molecule is capable of specifically interacting with and/or binding to at least two amino acids of each of the human target molecule as defined herein. Said term relates to the specificity of the antibody molecule, i.e. to its ability to discriminate between the specific regions of the human target molecule as defined herein. The specific interaction of the antigen-interaction-site with its specific antigen may result in an initiation of a signal, e.g. due to the induction of a change of the conformation of the antigen, an oligomerization of the antigen, etc. Further, said binding may be exemplified by the specificity of a “key-lock-principle”. Thus, specific motifs in the amino acid sequence of the antigen-interaction-site and the antigen bind to each other as a result of their primary, secondary or tertiary structure as well as the result of secondary modifications of said structure. The specific interaction of the antigen-interaction-site with its specific antigen may result as well in a simple binding of said site to the antigen.
The term “specific interaction” as used in accordance with the present invention means that the bispecific single chain construct does not or essentially does not cross-react with (poly)peptides of similar structures. Cross-reactivity of a panel of bispecific single chain construct under investigation may be tested, for example, by assessing binding of said panel of bispecific single chain construct under conventional conditions (see, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1988 and Using Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1999) to the (poly)peptide of interest as well as to a number of more or less (structurally and/or functionally) closely related (poly)peptides. Only those antibodies that bind to the (poly)peptide/protein of interest but do not or do not essentially bind to any of the other (poly)peptides are considered specific for the (poly)peptide/protein of interest. Examples for the specific interaction of an antigen-interaction-site with a specific antigen comprise the specificity of a ligand for its receptor. Said definition particularly comprises the interaction of ligands which induce a signal upon binding to its specific receptor. Examples for corresponding ligands comprise cytokines which interact/bind with/to its specific cytokine-receptors. Also particularly comprised by said definition is the binding of an antigen-interaction-site to antigens like antigens of the selectin family, integrins and of the family of growth factors like EGF. An other example for said interaction, which is also particularly comprised by said definition, is the interaction of an antigenic determinant (epitope) with the antigenic binding site of an antibody.
The term “binding to/interacting with” may also relate to a conformational epitope, a structural epitope or a discontinuous epitope consisting of two regions of the human target molecules or parts thereof. In context of this invention, a conformational epitope is defined by two or more discrete amino acid sequences separated in the primary sequence which come together on the surface of the molecule when the polypeptide folds to the native protein (Sela, (1969) Science 166, 1365 and Layer, (1990) Cell 61, 553-6).
The term “discontinuous epitope” means in context of the invention non-linear epitopes that are assembled from residues from distant portions of the polypeptide chain. These residues come together on the surface of the molecule when the polypeptide chain folds into a three-dimensional structure to constitute a conformational/structural epitope.
The constructs of the present invention are also envisaged to specifically bind to/interact with a conformational/structural epitope(s) composed of and/or comprising the two regions of the human CD3 complex described herein or parts thereof as disclosed herein below.
Accordingly, specificity can be determined experimentally by methods known in the art and methods as disclosed and described herein. Such methods comprise, but are not limited to Western blots, ELISA-, RIA-, ECL-, IRMA-, EIA-tests and peptide scans.
The term “antibody fragment or derivative thereof” relates to single chain antibodies, or fragments thereof, synthetic antibodies, antibody fragments, such as Fab, a F(ab2)′, Fv or scFv fragments etc., or a chemically modified derivative of any of these. Antibodies to be employed in accordance with the invention or their corresponding immunoglobulin chain(s) can be further modified using conventional techniques known in the art, for example, by using amino acid deletion(s), insertion(s), substitution(s), addition(s), and/or recombination(s) and/or any other modification(s) (e.g. posttranslational and chemical modifications, such as glycosylation and phosphorylation) known in the art either alone or in combination. Methods for introducing such modifications in the DNA sequence underlying the amino acid sequence of an immunoglobulin chain are well known to the person skilled in the art; see, e.g., Sambrook (1989), loc. cit.
The term “(poly)peptide” as used herein describes a group of molecules which comprise the group of peptides, as well as the group of polypeptides. The group of peptides is consisting of molecules with up to 30 amino acids, the group of polypeptides is consisting of molecules with more than 30 amino acids.
The term “antibody fragment or derivative thereof” particularly relates to (poly)peptide constructs comprising at least one CDR.
Fragments or derivatives of the recited antibody molecules define (poly)peptides which are parts of the above antibody molecules and/or which are modified by chemical/biochemical or molecular biological methods. Corresponding methods are known in the art and described inter alia in laboratory manuals (see Sambrook et al.; Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press, 2nd edition 1989 and 3rd edition 2001; Gerhardt et al.; Methods for General and Molecular Bacteriology; ASM Press, 1994; Lefkovits; Immunology Methods Manual: The Comprehensive Sourcebook of Techniques; Academic Press, 1997; Golemis; Protein-Protein Interactions: A Molecular Cloning Manual; Cold Spring Harbor Laboratory Press, 2002).
Bispecific antibodies that specifically recognize the EpCAM antigen and the CD3 antigen are described in the prior art, e.g., in Mack (Proc. Natl. Acad. Sci., 1995, 92:7021-7025).
As mentioned above, the said variable domains comprised in the herein described bispecific single chain constructs are connected by additional linker sequences. The term “peptide linker” defines in accordance with the present invention an amino acid sequence by which the amino acid sequences of the first domain and the second domain of the defined construct are linked with each other. An essential technical feature of such peptide linker is that said peptide linker does not comprise any polymerization activity. A particularly preferred peptide linker is characterized by the amino acid sequence Gly-Gly-Gly-Gly-Ser, i.e. (Gly)4Ser, or polymers thereof, i.e. ((Gly)4Ser)x. The characteristics of said peptide linker, which comprise the absence of the promotion of secondary structures are known in the art and described e.g. in Dall'Acqua et al. (Biochem. (1998) 37, 9266-9273), Cheadle et al. (Mol Immunol (1992) 29, 21-30) and Raag and Whitlow (FASEB (1995) 9(1), 73-80). Also particularly preferred are peptide linkers which comprise less amino acid residues. An envisaged peptide linker with less than 5 amino acids can comprise 4, 3, 2 or one amino acids. A particularly preferred “single” amino acid in context of said “peptide linker” is Gly. Accordingly, said peptide linker may consist of the single amino acid Gly. Furthermore, peptide linkers which also do not promote any secondary structures are preferred. The linkage of said domains to each other can be provided by, e.g. genetic engineering, as described in the examples. Methods for preparing fused and operatively linked bispecific single chain constructs and expressing them in mammalian cells or bacteria are well-known in the art (e.g. WO 99/54440, Ausubel, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y. 1989 and 1994 or Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2001).
The bispecific single chain antibody constructs described herein above and below may be humanized or deimmunized antibody constructs. Methods for the humanization and/or deimmunization of (poly))peptides and, in particular, antibody constructs are known to the person skilled in the art.
Here it was surprisingly found that domains with specificity for the EpCAM antigen, comprising at least one CDR-H3 region comprising the amino acid sequence NXD (asparagine-X-aspartic acid) preferably in position 102 to 104 of SEQ ID NOs: 80, 88 and 96, or in position 106 to 108 of SEQ ID NOs: 84 and 92, wherein X is an aromatic amino acid are particularly useful in the specific format of a bispecific single chain antibody construct. These bispecific single chain antibody constructs are particularly useful as pharmaceutical compositions since these constructs are advantageous over constructs which do not comprise said amino acids.
Furthermore, it was surprisingly found that domains with specificity for the EpCAM antigen, comprising at least one CDR-H3 region of at least 9 amino acid residues and having a KD value of more than 5×10−9 M are particularly useful in the specific format of a bispecific single chain antibody construct. These bispecific single chain antibody construct are particularly useful as pharmaceutical compositions since these constructs are advantageous over constructs of less than 9 amino acid residues and wherein said binding domain specific for EpCAM has a KD value of less than 5×10−9 M.
The prior art constructs are characterized by less advantageous EC50 values and/or less efficient or complete purifications as shown in the appended examples. It was in particular surprising that the domain of the single chain constructs with specificity for the CD3 antigen to be employed in accordance with the invention are highly bioactive in N- as well as C-terminal position, wherein in particular arrangements in VH(anti-CD3)-VL(anti-CD3) are preferred. The constructs to be employed in the pharmaceutical composition of the invention are characterized by advantageous production and purification properties as well as by their high bioactivity, i.e. their desired cytotoxic activity. In particular, when the cytotoxic activity of the constructs of the invention were compared with cytotoxic activity of conventional M79xanti-CD3 and HD70xanti-CD3 constructs, the constructs of the invention showed clearly higher bioactivity (FIG. 11B). The corresponding high bioactivity is reflected by low to very low EC50 values as determined in cytotoxicity tests. The lower the EC50 value of the molecule is, the higher cytotoxicity, i.e. the effectivity in the cell lysis, of the construct is higher. On the other hand, the higher the EC50 value, the less effective the molecule is in inducing cell lysis. The term “EC50” corresponds, in context of this invention, to EC50 values as determined according to the methods known in the art and as illustrated in the appended examples: A standard dose-response curve is defined by four parameters: the baseline response (Bottom), the maximum response (Top), the slope, and the drug concentration that provokes a response halfway between baseline and maximum (EC50). EC50 is defined as the concentration of a drug or molecule that provokes a response half way between the baseline (Bottom) and maximum response (Top). A lower KD value of the constructs of the invention depicts higher binding affinity. E.g. a low KD of 10−9 M shows high binding affinity of the binding construct. On the other hand a high KD value of e.g. 10−6 M relates to lower binding affinity of the binding domain of the construct.
The percentage of cell lysis (i.e. cytotoxic activity) may be determined by, inter alia, release assays disclosed herein above, for example, 51Cr release assays, LDH-release assays and the like. Most preferably, in context of this invention fluorochrome release assays is employed as illustrated in the appended examples. Here, strong cytotoxic activity against EpCAM-positive cells (see CHO-EpCAM cells in appended example 3) of the bispecific single chain constructs described herein relates to a molecule comprising EC50 values preferably ≦500 pg/ml, more preferably ≦400 pg/ml, even more preferably ≦300 pg/ml, even more preferably ≦250 pg/ml, most preferably ≦200 pg/ml, ≦100 pg/ml, 50 pg/ml.
The bispecific constructs comprised in the pharmaceutical compositions of the present invention show a surprisingly high cytotoxic activity (preferably in the range of about 10 pg/ml to 170 pg/ml) compared to the prior art M79xanti-CD3 construct (VL17-1A-VH17-1A-VHCD3-VLCD3; 8628 pg/ml). A skilled person is aware that EC50 values may vary depending to the bioactivity assay. Factors affecting EC50 value may comprise type of effector cells, activity of effector cells, type of target cells, E:T ratio, incubation time, incubation temperature and other external circumstances. Different EC50 values of same constructs in different experiments may be compared with the EC50 values of controls. A construct having high cytotoxic activity according to the invention has at least 2.5 time lower EC50 value than the control (at least 2.5 times higher cytotoxicity than the control), preferably at least three times lower EC50 value and more preferably at least five times lower EC50 value.
Furthermore, the constructs of the invention bind EpCAM with a surprisingly high affinity measured by surface plasmon resonance)(BIAcore°. The prior art EpCAM and CD3 binding construct M79xanti-CD3 has a KD of 4×10−6 M and the constructs of the invention a KD of 2.3×10−7-2.5×10−7 M.
Preferably, the X in said NXD motif is W (tryptophan) or Y (tyrosine).
It is further envisaged that the pharmaceutical composition of the invention comprises a bispecific single chain antibody construct, wherein the CDR-H3 of the EpCAM specific domain comprises at least 9 amino acid residues, preferably at least 14 amino acids. Preferably the CDR-H3 comprises less than 18 amino acids, more preferably less than 15 amino acids. Thus, preferably the CDR-H3 comprises 9 to 17 amino acids, more preferably 9 to 15 amino acids and most preferably 10 or 14 amino acids.
Bispecific single chain antibody construct comprising a corresponding EpCAM specific domain have been surprisingly found to be advantagous in the format of the above described construct over other EpCAM specific domain known in the art. Such effect is demonstrated in appended examples 3, 4 and 5. The prior art EpCAM binding antibody M79 comprises eight amino acids in its CDR-H3 region and does not comprise the sequence NXD (FIG. 11A).
The pharmaceutical composition according to the invention may also comprise constructs, wherein said binding domain specific for EpCAM has a KD value of more than 5×10−9 M.
The pharmaceutical composition may additionally be characterized by the feature that said binding domain specific for the CD3 antigen has a KD value of more than 10−7 M.
The KD value is a physical value defining the tendency of a complex to dissociate. For the binding equilibrium A+BAB, the dissociation constant is given as the ratio of the two kinetic rate constants koff and kon: [A][B] (kon)/[AB] (koff). The smaller the dissociation constant the tighter A and B bind to each other. In biological systems a good, specific binder has a dissociation constant in the range of 10−9-10−7 M. KD can be measured with a number of methods known to the person skilled in the art, e.g. surface plasmon resonance (SPR, e.g. with BIAcore®), analytical ultracentrifugation, isothermal titration calorimetry, fluorescence anisotropy, fluorescence spectroscopy or by radiolabeled ligand binding assays.
The KDs of the constructs of the invention have been measured using the surface plasmon resonance (SPR) spectroscopy. The ligand is injected over the immobilized antigen chip surface and the change in optical density on the chip surface upon binding is measured. The change in optical density, monitored by a change in reflection angle, correlates directly to the amount of ligand binding to the chip surface—the biophysical phenomenon used is called surface plasmon resonance.
One of the interaction partners has to be immobilized on the surface of the sensor chip of the apparatus based on surface plasmon resonance (e.g. BIAcore®). The kinetics of association and dissociation of ligand with the immobilized antigen on the chip surface are observed in real time. The binding curves are fitted for kinetic rate constants kon and koff, resulting in an apparent equilibrium dissociation constant (KD).
It is particularly preferred, that said binding domain specific for EpCAM has a KD value in a range between 1×10−7 and 5×10−9 M and said binding domain specific for CD3 has a KD value in a range between 1×10−6 and 5×10−9 M.
In a particularly preferred embodiment, the pharmaceutical composition may additionally be characterized by the feature that said binding domain specific for the CD3 antigen has a KD value of >(more than) 1×10−7 M.
The constructs of the invention have the advantage that they may be used a number of times for killing tumour cells since the EpCAM binding part has an affinity with a KD value of more than 5×10−9 M. If the affinity of a bispecific construct for binding an EpCAM-expressing tumour cell is too high, the construct binds one EpCAM expressing tumour cell and remains on its surface even when it has been killed and cannot continue to another tumour cell to be killed. A further advantage of the construct of the invention is that the binding domain specific for EpCAM binds with a high affinity (corresponds to lower KD value), thus leading the circulating T-cells to the tumour cells marked with the bispecific construct. Therefore, the KD of the binding domain specific for EpCAM of the bispecific construct is preferably in the range of 10−7-5×10−9 M and the KD of the binding domain specific for CD3 is preferably in the range of 10−6-5×10−9 M. In a preferred embodiment, the KD value of the EpCAM binding domain is lower than the KD value of the CD3 binding domain corresponding to a higher affinity of the EpCAM binding domain compared to the CD3 binding domain.
Further it is envisaged that the pharmaceutical composition of the invention comprises a bispecific single chain antibody construct, wherein the CDR-H3 of the EpCAM specific domain comprises at least 9 amino acids, preferably at least 14 amino acids. Preferably the CDR-H3 comprises less than 18 amino acids, more preferably less than 15 amino acids. Thus, preferably the CDR-H3 comprises 9 to 17 amino acids, more preferably 9 to 15 amino acids and most preferably 10 or 14 amino acids.
In a preferred embodiment of the pharmaceutical composition of the invention the VH chain of the domain specific for human EpCAM antigen is selected from the group consisting of:

    (a) an amino acid sequence as shown in any of SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 88, SEQ ID NO: 92 and SEQ ID NO:96;
    (b) an amino acid sequence encoded by a nucleic acid sequence as shown in SEQ ID NO: 79, SEQ ID NO: 83, SEQ ID NO: 87, SEQ ID NO: 91 and SEQ ID NO: 95;
    (c) an amino acid sequence encoded by a nucleic acid sequence hybridizing with the complementary strand of a nucleic acid sequence as defined in (b) under stringent hybridization conditions;
    (d) an amino acid sequence encoded by a nucleic acid sequence which is degenerate as a result of the genetic code to a nucleotide sequence of any one of (b) and (c).


The term “hybridizing” as used herein refers to polynucleotides/nucleic acid sequences which are capable of hybridizing to the polynucleotides encoding bispecific single chain constructs as defined herein or parts thereof. Therefore, said polynucleotides may be useful as probes in Northern or Southern Blot analysis of RNA or DNA preparations, respectively, or can be used as oligonucleotide primers in PCR analysis dependent on their respective size. Preferably, said hybridizing polynucleotides comprise at least 10, more preferably at least 15 nucleotides in length while a hybridizing polynucleotide of the present invention to be used as a probe preferably comprises at least 100, more preferably at least 200, or most preferably at least 500 nucleotides in length.
It is well known in the art how to perform hybridization experiments with nucleic acid molecules, i.e. the person skilled in the art knows what hybridization conditions s/he has to use in accordance with the present invention. Such hybridization conditions are referred to in standard text books such as Molecular Cloning A Laboratory Manual, Cold Spring Harbor Laboratory (2001) N.Y. Preferred in accordance with the present inventions are polynucleotides which are capable of hybridizing to the polynucleotides of the invention or parts thereof, under stringent hybridization conditions.
“Stringent hybridization conditions” refer, e.g. to an overnight incubation at 42° C. in a solution comprising 50% formamide, 5×SSC (750 mM NaCl, 75 mM sodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1×SSC at about 65° C. Also contemplated are nucleic acid molecules that hybridize to the polynucleotides of the invention at lower stringency hybridization conditions. Changes in the stringency of hybridization and signal detection are primarily accomplished through the manipulation of formamide concentration (lower percentages of formamide result in lowered stringency); salt conditions, or temperature. For example, lower stringency conditions include an overnight incubation at 37° C. in a solution comprising 6×SSPE (20×SSPE=3M NaCl; 0.2M NaH2PO4; 0.02M EDTA, pH 7.4), 0.5% SDS, 30% formamide, 100 μg/ml salmon sperm blocking DNA; followed by washes at 50° C. with 1×SSPE, 0.1% SDS. In addition, to achieve even lower stringency, washes performed following stringent hybridization can be done at higher salt concentrations (e.g. 5×SSC). It is of note that variations in the above conditions may be accomplished through the inclusion and/or substitution of alternate blocking reagents used to suppress background in hybridization experiments. Typical blocking reagents include Denhardt's reagent, BLOTTO, heparin, denatured salmon sperm DNA, and commercially available proprietary formulations. The inclusion of specific blocking reagents may require modification of the hybridization conditions described above, due to problems with compatibility.
The recited nucleic acid molecules may be, e.g., DNA, cDNA, RNA or synthetically produced DNA or RNA or a recombinantly produced chimeric nucleic acid molecule comprising any of those polynucleotides either alone or in combination.
Preferably said pharmaceutical composition of the invention may comprise a bispecific single chain construct, wherein the VL chain domains specific for human EpCAM antigen is selected from the group consisting of:

    (a) an amino acid sequence as shown in any of SEQ ID NO: 82, SEQ ID NO: 86, SEQ ID NO: 90, SEQ ID NO: 94 and SEQ ID NO: 98;
    (b) an amino acid sequence encoded by a nucleic acid sequence as shown in SEQ ID NO: 81, SEQ ID NO: 85, SEQ ID NO: 89, SEQ ID NO: 93 and SEQ ID NO: 97;
    (c) an amino acid sequence encoded by a nucleic acid sequence hybridizing with the complementary strand of a nucleic acid sequence as defined in (b) under stringent hybridization conditions;
    (d) an amino acid sequence encoded by a nucleic acid sequence which is degenerate as a result of the genetic code to a nucleotide sequence of any one of (b) and (c).


In a preferred embodiment of the pharmaceutical composition of this invention, the VH and VL regions of said human CD3 specific domain are derived from an CD3 specific antibody selected from the group consisting of X35-3, VIT3, BMA030 (BW264/56), CLB-T3/3, CRIS7, YTH12.5, F111-409, CLB-T3.4.2, TR-66, WT32, SPv-T3b, 11D8, XIII-141, XIII-46, XIII-87, 12F6, T3/RW2-8C8, T3/RW2-4B6, OKT3D, M-T301, SMC2, WT31 and F101.01. These CD3-specific antibodies are well known in the art and, inter alia, described in Tunnacliffe (1989), Int. Immunol. 1, 546-550. In a more preferred embodiment, said VH and VL regions of said CD3 specific domain are derived from OKT-3 (as defined and described above). Even more preferred. (and as illustrated in the appended examples) said VH and VL regions are or are derived from an antibody/antibody derivative with specificity for the CD3 molecule described by Traunecker (1991), EMBO J. 10, 3655-3659. In accordance with this invention, said VH and VL regions are derived from antibodies/antibody derivatives and the like which are capable of specifically recognizing the human CD3-ε chain in the context of other TCR subunits, e.g. in mouse cells transgenic for human CD3-ε chain. These transgenic mouse cells express human CD3-ε chain in a native or near native conformation. Accordingly, the VH and VL regions derived from an CD3-ε chain specific antibody is most preferred in accordance with this invention and said (parental) antibodies should be capable of specifically binding epitopes reflecting the native or near native structure or a conformational epitope of human CD3 presented in context of the TCR complex. Such antibodies have been classified by Tunnacliffe (1989) as “group II” antibodies. Further classifications in Tunnacliffe (1989) comprise the definition of “group I” and “group III” antibodies directed against CD3. “Group I” antibodies, like UCHT1, recognize CD3-ε chain expressed as recombinant protein and as part of the TCR on the cell surface. Therefore, “group I” antibodies are highly specific for CD3-ε chain. In contrast, the herein preferred “group II antibodies” recognize CD3-ε chain only in the native TCR complex in association with other TCR subunits. Without being bound by theory, it is speculated in context of this invention that in “group II” antibodies, the TCR context is required for recognition of CD3-ε chain. CD3-γ chain and δ chain, being associated with ε chain, are also involved in binding of “group II antibodies”. All three subunits express immunoreceptor-tyrosine activation motifs (ITAMs) which can be tyrosine phosphorylated by protein tyrosine-based kinases. For this reason group II antibodies induce T cell signaling via CD3-ε chain, γ chain and δ chain, leading to a stronger signal compared to group I antibodies selectively inducing T cell signaling via CD3-ε chain. Yet, since for therapeutic applications induction of a strong T cell signaling is desired, the VH (anti-CD3)/VL (anti-CD3)-regions (or parts thereof) to be employed in the bispecific single chain constructs comprised in the inventive pharmaceutical composition, are preferably derived from antibodies directed against human CD3 and classified in “group II” by Tunnacliffe (1989), loc.cit.
In one embodiment the present invention relates to a pharmaceutical composition wherein said bispecific single chain antibody construct comprises an amino acid sequence selected from the group of:

    (a) an amino acid sequence as shown in any of SEQ ID NOs: 2, 4, 8, 10, 12, 14, 16, 18, 20, 30, 36, 39, 42, 44, 46, 48, 50, 52, 54, 56, 58 and 60;
    (b) an amino acid sequence encoded by a nucleic acid sequence as shown in any of SEQ ID NOs: 1, 3, 7, 9, 11, 13, 15, 17, 19, 29, 35, 38, 41, 43, 45, 47, 49, 51, 53, 55, 57 and 59;
    (c) an amino acid sequence encoded by a nucleic acid sequence hybridizing with the complementary strand of a nucleic acid sequence as defined in (b) under stringent hybridization conditions;
    (d) an amino acid sequence encoded by a nucleic acid sequence which is degenerate as a result of the genetic code to a nucleotide sequence of any one of (b) and (c).


The present invention also provides for a pharmaceutical composition comprising a nucleic acid sequence encoding a bispecific single chain antibody construct as defined above.
Said nucleic acid molecule may be a natural nucleic acid molecule as well as a recombinant nucleic acid molecule. The nucleic acid molecule may, therefore, be of natural origin, synthetic or semi-synthetic. It may comprise DNA, RNA as well as PNA (peptide nucleic acid) and it may be a hybrid thereof.
Thus, the present invention relates to a pharmaceutical composition comprising a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of:

    (a) a nucleotide sequence encoding the mature form of a protein comprising the amino acid sequence of the bispecific single chain antibody constructs defined herein, preferably as given in SEQ ID Nos: 2, 4, 8, 10, 12, 14, 16, 18, 20, 30, 36, 39, 42, 44, 46, 48, 50, 52, 54, 56, 58 and 60;
    (b) a nucleotide sequence comprising or consisting of the DNA sequence as given in SEQ ID Nos: 1, 3, 7, 9, 11, 13, 15, 17, 19, 29, 35, 38, 41, 43, 45, 47, 49, 51, 53, 55, 57 and 59;
    (c) a nucleotide sequence hybridizing with the complementary strand of a nucleotide sequence as defined in (b) under stringent hybridization conditions;
    (d) a nucleotide sequence encoding a protein derived from the protein encoded by a nucleotide sequence of (a) or (b) by way of substitution, deletion and/or addition of one or several amino acids of the amino acid sequence encoded by the nucleotide sequence of (a) or (b);
    (e) a nucleotide sequence encoding a protein having an amino acid sequence at least 60% identical to the amino acid sequence encoded by the nucleotide sequence of (a) or (b);
    (f) a nucleotide sequence which is degenerate as a result of the genetic code to a nucleotide sequence of any one of (a) to (e);


The term “mature form of the protein” defines in context with the present invention a protein translated from its corresponding mRNA and optional subsequently modified.
The term “hybridizing” has been defined in the context of the present invention herein above.
It is evident to the person skilled in the art that regulatory sequences may be added to the nucleic acid molecule comprised in the pharmaceutical composition of the invention. For example, promoters, transcriptional enhancers and/or sequences which allow for induced expression of the polynucleotide of the invention may be employed. A suitable inducible system is for example tetracycline-regulated gene expression as described, e.g., by Gossen and Bujard (Proc. Natl. Acad. Sci. USA 89 (1992), 5547-5551) and Gossen et al. (Trends Biotech. 12 (1994), 58-62), or a dexamethasone-inducible gene expression system as described, e.g. by Crook (1989) EMBO J. 8, 513-519.
Furthermore, it is envisaged for further purposes that nucleic acid molecules may contain, for example, thioester bonds and/or nucleotide analogues. Said modifications may be useful for the stabilization of the nucleic acid molecule against endo- and/or exonucleases in the cell. Said nucleic acid molecules may be transcribed by an appropriate vector containing a chimeric gene which allows for the transcription of said nucleic acid molecule in the cell. In this respect, it is also to be understood that such polynucleotide can be used for “gene targeting” or “gene therapeutic” approaches. In another embodiment said nucleic acid molecules are labeled. Methods for the detection of nucleic acids are well known in the art, e.g., Southern and Northern blotting, PCR or primer extension. This embodiment may be useful for screening methods for verifying successful introduction of the nucleic acid molecules described above during gene therapy approaches.
Said nucleic acid molecule(s) may be a recombinantly produced chimeric nucleic acid molecule comprising any of the aforementioned nucleic acid molecules either alone or in combination. Preferably, the nucleic acid molecule is part of a vector.
The present invention therefore also relates to a pharmaceutical composition comprising a vector comprising the nucleic acid molecule described in the present invention.
Many suitable vectors are known to those skilled in molecular biology, the choice of which would depend on the function desired and include plasmids, cosmids, viruses, bacteriophages and other vectors used conventionally in genetic engineering. Methods which are well known to those skilled in the art can be used to construct various plasmids and vectors; see, for example, the techniques described in Sambrook et al. (loc cit.) and Ausubel, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y. (1989), (1994). Alternatively, the polynucleotides and vectors of the invention can be reconstituted into liposomes for delivery to target cells. As discussed in further details below, a cloning vector was used to isolate individual sequences of DNA. Relevant sequences can be transferred into expression vectors where expression of a particular polypeptide is required. Typical cloning vectors include pBluescript SK, pGEM, pUC9, pBR322 and pGBT9. Typical expression vectors include pTRE, pCAL-n-EK, pESP-1, pOP13CAT.
Preferably said vector comprises a nucleic acid sequence which is a regulatory sequence operably linked to said nucleic acid sequence encoding a bispecific single chain antibody constructs defined herein.
Such regulatory sequences (control elements) are known to the artisan and may include a promoter, a splice cassette, translation initiation codon, translation and insertion site for introducing an insert into the vector. Preferably, said nucleic acid molecule is operatively linked to said expression control sequences allowing expression in eukaryotic or prokaryotic cells.
It is envisaged that said vector is an expression vector comprising the nucleic acid molecule encoding a bispecific single chain antibody constructs defined herein.
The term “regulatory sequence” refers to DNA sequences which are necessary to effect the expression of coding sequences to which they are ligated. The nature of such control sequences differs depending upon the host organism. In prokaryotes, control sequences generally include promoters, ribosomal binding sites, and terminators. In eukaryotes generally control sequences include promoters, terminators and, in some instances, enhancers, transactivators or transcription factors. The term “control sequence” is intended to include, at a minimum, all components the presence of which are necessary for expression, and may also include additional advantageous components.
The term “operably linked” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. A control sequence “operably linked” to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences. In case the control sequence is a promoter, it is obvious for a skilled person that double-stranded nucleic acid is preferably used.
Thus, the recited vector is preferably an expression vector. An “expression vector” is a construct that can be used to transform a selected host and provides for expression of a coding sequence in the selected host. Expression vectors can for instance be cloning vectors, binary vectors or integrating vectors. Expression comprises transcription of the nucleic acid molecule preferably into a translatable mRNA. Regulatory elements ensuring expression in prokaryotes and/or eukaryotic cells are well known to those skilled in the art. In the case of eukaryotic cells they comprise normally promoters ensuring initiation of transcription and optionally poly-A signals ensuring termination of transcription and stabilization of the transcript. Possible regulatory elements permitting expression in prokaryotic host cells comprise, e.g., the PL, lac, trp or tac promoter in E. coli, and examples of regulatory elements permitting expression in eukaryotic host cells are the AOX1 or GAL1 promoter in yeast or the CMV-, SV40-, RSV-promoter (Rous sarcoma virus), CMV-enhancer, SV40-enhancer or a globin intron in mammalian and other animal cells.
Beside elements which are responsible for the initiation of transcription such regulatory elements may also comprise transcription termination signals, such as the SV40-poly-A site or the tk-poly-A site, downstream of the polynucleotide. Furthermore, depending on the expression system used leader sequences capable of directing the polypeptide to a cellular compartment or secreting it into the medium may be added to the coding sequence of the recited nucleic acid sequence and are well known in the art; see also, e.g., the appended examples. The leader sequence(s) is (are) assembled in appropriate phase with translation, initiation and termination sequences, and preferably, a leader sequence capable of directing secretion of translated protein, or a portion thereof, into the periplasmic space or extracellular medium. Optionally, the heterologous sequence can encode a fusion protein including an N-terminal identification peptide imparting desired characteristics, e.g., stabilization or simplified purification of expressed recombinant product; see supra. In this context, suitable expression vectors are known in the art such as Okayama-Berg cDNA expression vector pcDV1 (Pharmacia), pEF-Neo, pCDM8, pRc/CMV, pcDNA1, pcDNA3 (In-vitrogene), pEF-DHFR and pEF-ADA, (Raum et al. Cancer Immunol Immunother (2001) 50(3), 141-150) or pSPORT1 (GIBCO BRL).
Preferably, the expression control sequences will be eukaryotic promoter systems in vectors capable of transforming of transfecting eukaryotic host cells, but control sequences for prokaryotic hosts may also be used. Once the vector has been incorporated into the appropriate host, the host is maintained under conditions suitable for high level expression of the nucleotide sequences, and as desired, the collection and purification of the polypeptide of the invention may follow; see, e.g., the appended examples.
An alternative expression system which could be used to express a cell cycle interacting protein is an insect system. In one such system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia larvae. The coding sequence of a recited nucleic acid molecule may be cloned into a nonessential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of said coding sequence will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein coat. The recombinant viruses are then used to infect S. frugiperda cells or Trichoplusia larvae in which the protein of the invention is expressed (Smith, J. Virol. 46 (1983), 584; Engelhard, Proc. Nat. Acad. Sci. USA 91 (1994), 3224-3227).
Additional regulatory elements may include transcriptional as well as translational enhancers. Advantageously, the above-described vectors of the invention comprises a selectable and/or scorable marker.
Selectable marker genes useful for the selection of transformed cells and, e.g., plant tissue and plants are well known to those skilled in the art and comprise, for example, antimetabolite resistance as the basis of selection for dhfr, which confers resistance to methotrexate (Reiss, Plant Physiol. (Life Sci. Adv.) 13 (1994), 143-149); npt, which confers resistance to the aminoglycosides neomycin, kanamycin and paromycin (Herrera-Estrella, EMBO J. 2 (1983), 987-995) and hygro, which confers resistance to hygromycin (Marsh, Gene 32 (1984), 481-485). Additional selectable genes have been described, namely trpB, which allows cells to utilize indole in place of tryptophan; hisD, which allows cells to utilize histinol in place of histidine (Hartman, Proc. Natl. Acad. Sci. USA 85 (1988), 8047); mannose-6-phosphate isomerase which allows cells to utilize mannose (WO 94/20627) and ODC (ornithine decarboxylase) which confers resistance to the ornithine decarboxylase inhibitor, 2-(difluoromethyl)-DL-ornithine, DFMO (McConlogue, 1987, In: Current Communications in Molecular Biology, Cold Spring Harbor Laboratory ed.) or deaminase from Aspergillus terreus which confers resistance to Blasticidin S (Tamura, Biosci. Biotechnol. Biochem. 59 (1995), 2336-2338).
Useful scorable markers are also known to those skilled in the art and are commercially available. Advantageously, said marker is a gene encoding luciferase (Giacomin, P I. Sci. 116 (1996), 59-72; Scikantha, J. Bact. 178 (1996), 121), green fluorescent protein (Gerdes, FEBS Lett. 389 (1996), 44-47) or β-glucuronidase (Jefferson, EMBO J. 6 (1987), 3901-3907). This embodiment is particularly useful for simple and rapid screening of cells, tissues and organisms containing a recited vector.
As described above, the recited nucleic acid molecule can be used alone or as part of a vector to express the encoded polypeptide in cells, for, e.g., gene therapy. The nucleic acid molecules or vectors containing the DNA sequence(s) encoding any one of the above described bispecific single chain antibody constructs is introduced into the cells which in turn produce the polypeptide of interest. Gene therapy, which is based on introducing therapeutic genes into cells by ex-vivo or in-vivo techniques is one of the most important applications of gene transfer. Suitable vectors, methods or gene-delivery systems for in-vitro or in-vivo gene therapy are described in the literature and are known to the person skilled in the art; see, e.g., Giordano, Nature Medicine 2 (1996), 534-539; Schaper, Circ. Res. 79 (1996), 911-919; Anderson, Science 256 (1992), 808-813; Verma, Nature 389 (1994), 239; Isner, Lancet 348 (1996), 370-374; Muhlhauser, Circ. Res. 77 (1995), 1077-1086; Onodera, Blood 91 (1998), 30-36; Verma, Gene Ther. 5 (1998), 692-699; Nabel, Ann. N.Y. Acad. Sci. 811 (1997), 289-292; Verzeletti, Hum. Gene Ther. 9 (1998), 2243-51; Wang, Nature Medicine 2 (1996), 714-716; WO 94/29469; WO 97/00957, U.S. Pat. No. 5,580,859; U.S. Pat. No. 5,589,466; or Schaper, Current Opinion in Biotechnology 7 (1996), 635-640. The recited nucleic acid molecules and vectors may be designed for direct introduction or for introduction via liposomes, or viral vectors (e.g., adenoviral, retroviral) into the cell. Preferably, said cell is a germ line cell, embryonic cell, or egg cell or derived therefrom, most preferably said cell is a stem cell. An example for an embryonic stem cell can be, inter alia, a stem cell as described in, Nagy, Proc. Natl. Acad. Sci. USA 90 (1993), 8424-8428.
In accordance with the above, the present invention relates to methods to derive vectors, particularly plasmids, cosmids, viruses and bacteriophages used conventionally in genetic engineering that comprise a nucleic acid molecule encoding the polypeptide sequence of a bispecific single chain antibody constructs defined herein. Preferably, said vector is an expression vector and/or a gene transfer or targeting vector. Expression vectors derived from viruses such as retroviruses, vaccinia virus, adeno-associated virus, herpes viruses, or bovine papilloma virus, may be used for delivery of the recited polynucleotides or vector into targeted cell populations. Methods which are well known to those skilled in the art can be used to construct recombinant vectors; see, for example, the techniques described in Sambrook et al. (loc cit.), Ausubel (1989, loc cit.) or other standard text books. Alternatively, the recited nucleic acid molecules and vectors can be reconstituted into liposomes for delivery to target cells. The vectors containing the nucleic acid molecules of the invention can be transferred into the host cell by well-known methods, which vary depending on the type of cellular host. For example, calcium chloride transfection is commonly utilized for prokaryotic cells, whereas calcium phosphate treatment or electroporation may be used for other cellular hosts; see Sambrook, supra.
The recited vector may be the pEF-DHFR, pEF-ADA or pEF-neo.
The vectors pEF-DHFR and pEF-ADA have been described in the art, e.g. in Mack et al. (PNAS (1995) 92, 7021-7025) and Ram et al. (Cancer Immunol Immunother (2001) 50(3), 141-150).
It is further envisaged that the pharmaceutical composition of the invention comprises a host transformed or transfected with a vector defined herein above.
Said host may be produced by introducing said at least one of the above described vector or at least one of the above described nucleic acid molecules into the host. The presence of said at least one vector or at least one nucleic acid molecule in the host may mediate the expression of a gene encoding the above described bespecific single chan antibody constructs.
The described nucleic acid molecule or vector which is introduced in the host may either integrate into the genome of the host or it may be maintained extrachromosomally.
The host can be any prokaryote or eukaryotic cell.
The term “prokaryote” is meant to include all bacteria which can be transformed or transfected with a DNA or RNA molecules for the expression of a protein of the invention. Prokaryotic hosts may include gram negative as well as gram positive bacteria such as, for example, E. coli, S. typhimurium, Serratia marcescens and Bacillus subtilis. The term “eukaryotic” is meant to include yeast, higher plant, insect and preferably mammalian cells. Depending upon the host employed in a recombinant production procedure, the protein encoded by the polynucleotide of the present invention may be glycosylated or may be non-glycosylated. Especially preferred is the use of a plasmid or a virus containing the coding sequence of the polypeptide of the invention and genetically fused thereto an N-terminal FLAG-tag and/or C-terminal His-tag. Preferably, the length of said FLAG-tag is about 4 to 8 amino acids, most preferably 8 amino acids. An above described polynucleotide can be used to transform or transfect the host using any of the techniques commonly known to those of ordinary skill in the art. Furthermore, methods for preparing fused, operably linked genes and expressing them in, e.g., mammalian cells and bacteria are well-known in the art (Sambrook, loc cit.).
Preferably, said the host is a bacteria, an insect, fungal, plant or animal cell.
It is particularly envisaged that the recited host may be a mammalian cell, more preferably a human cell or human cell line.
Particularly preferred host cells comprise CHO cells, COS cells, myeloma cell lines like SP2/0 or NS/0.
The pharmaceutical composition of the invention may also comprise a proteinaceous compound capable of providing an activation signal for immune effector cells useful for cell proliferation or cell stimulation.
The proteinaceous compound is not understood as an additional domain of the above defined bispecific single chain antibody construct, but at least one additional component of the pharmaceutical composition of the invention.
In the light of the present invention, said “proteinaceous compounds” providing an activation signal for immune effector cells” may be, e.g. a further activation signal for T cells (e.g. a further costimulatory molecule: molecules of the B7-family, Ox40 L, 4.1 BBL), or a further cytokine: interleukin (e.g. IL-2), or an NKG-2D engaging compound. Preferred formats of proteinaceous compounds comprise additional bispecific antibodies and fragments or derivatives thereof, e.g. bispecific scFv. Proteinaceous compounds can comprise, but are not limited to scFv fragments specific for the T cell receptor or superantigens. Superantigens directly bind to certain subfamilies of T cell receptor variable regions in an MHC-independent manner thus mediating the primary T cell activation signal. The proteinaceous compound may also provide an activation signal for immune effector cell which is a non-T cell. Examples for immune effector cells which are non-T cells comprise, inter alia, NK cells.
An additional technical feature of the pharmaceutical composition of the invention is that said pharmaceutical composition is thermostable at ≧37° C.
An alternative embodiment of the invention relates to a process for the production of a pharmaceutical composition of the invention, said process comprising culturing a host defined herein above under conditions allowing the expression of the construct and recovering the produced bispecific single chain antibody construct from the culture.
The transformed hosts can be grown in fermentors and cultured according to techniques known in the art to achieve optimal cell growth. The polypeptide of the invention can then be isolated from the growth medium, cellular lysates, or cellular membrane fractions. The isolation and purification of the, e.g., microbially expressed polypeptides of the invention may be by any conventional means such as, for example, preparative chromatographic separations and immunological separations such as those involving the use of monoclonal or polyclonal antibodies directed, e.g., against a tag of the polypeptide of the invention or as described in the appended examples.
The conditions for the culturing of a host which allow the expression are known in the art and discussed herein above. The same holds true for procedures for the purification/recovery of said constructs.
A further alternative embodiment of the invention relates to the use of a bispecific single chain antibody construct as defined above, a nucleic acid sequence as defined above, a vector as defined above, a host as defined above and/or produced by a process as defined above for the preparation of a pharmaceutical composition for the prevention, treatment or amelioration of a tumorous disease.
In particular, the pharmaceutical composition of the present invention may be particularly useful in preventing, ameliorating and/or treating cancer.
Preferably said tumorous disease is epithelial cancer or a minimal residual cancer.
It is envisaged by the present invention that the above defined bispecific single chain antibody construct, nucleic acid molecules and vectors are administered either alone or in any combination using standard vectors and/or gene delivery systems, and optionally together with a pharmaceutically acceptable carrier or excipient. Subsequent to administration, said nucleic acid molecules or vectors may be stably integrated into the genome of the subject.
On the other hand, viral vectors may be used which are specific for certain cells or tissues and persist in said cells. Suitable pharmaceutical carriers and excipients are well known in the art. The pharmaceutical compositions prepared according to the invention can be used for the prevention or treatment or delaying the above identified diseases.
Furthermore, it is possible to use a pharmaceutical composition of the invention which comprises described nucleic acid molecules or vectors in gene therapy. Suitable gene delivery systems may include liposomes, receptor-mediated delivery systems, naked DNA, and viral vectors such as herpes viruses, retroviruses, adenoviruses, and adeno-associated viruses, among others. Delivery of nucleic acids to a specific site in the body for gene therapy may also be accomplished using a biolistic delivery system, such as that described by Williams (Proc. Natl. Acad. Sci. USA 88 (1991), 2726-2729). Further methods for the delivery of nucleic acids comprise particle-mediated gene transfer as, e.g., described in Verma, Gene Ther. 15 (1998), 692-699.
Furthermore the invention relates to a method for the prevention, treatment or amelioration of a tumorous disease comprising the step of administering to a subject in the need thereof an effective amount a bispecific single chain antibody construct as defined above, a nucleic acid sequence as defined above, a vector as defined as defined above, a host as defined above and/or produced in by a process as defined above.
Preferably said subject is a human.
The method for the prevention, treatment or amelioration of the invention may comprise the co-administration of an above defined proteinaceous compound capable of an activation signal for immune effector cells to the subject. The co-administration may be a simultaneous co-administration or a non-simultaneous co-administration.
It is particularly preferred for the use and the method of the invention that said tumorous disease is epithelial cancer, preferably adenocarcinomas, or a minimal residual cancer, preferably early solid tumor, advanced solid tumor or metastatic solid tumor.
Finally, the present invention relates to a kit comprising a bispecific single chain antibody construct as defined above, a nucleic acid sequence as defined above, a vector as defined above and/or a host as defined above. It is also envisaged that the kit of this invention comprises a pharmaceutical composition as described herein above, either alone or in combination with further medicaments to be administered to a patient in need of medical treatment or intervention.



The Figures show:
FIG. 1:
DNA and amino acid sequence of the anti-CD3-anti-EpCAM constructs A) anti-CD3 VHVL stL x 3-1 VHVL (SEQ ID NO.:11,12), B) anti-CD3 VHVL aL x 4-7 VHVL (SEQ ID NO.:1,2), C) anti-CD3 VHVL aL Ser x 4-7 VHVL (SEQ ID NO.:7, 8), D) anti-CD3 VHVL stL x 4-7 VHVL (SEQ ID NO.:13,14), E) anti-CD3 VHVL stL x 4-7 VLVH (SEQ ID NO.:15,16), F) anti-CD3 VHVL aL x 5-10 VHVL (SEQ ID NO.:3,4), G) anti-CD3 VHVL aL Ser x 5-10 VHVL (SEQ ID NO.:9, 10), H) anti-CD3 VHVL stL x 5-10 VHVL (SEQ ID NO.:17,18), I) anti-CD3 VHVL stL x 5-10 VLVH (SEQ ID NO.:19,20), J) anti-CD3 VHVL aL x 3-1 VHVL (SEQ ID NO.:45, 46), K) anti-CD3 VHVL aL Ser x 3-1 VHVL (SEQ ID NO.:47,48), L) anti-CD3 VHVL aL x 3-5 VHVL (SEQ ID NO.:49,50), M) anti-CD3 VHVL aL Ser x 3-5 VHVL (SEQ ID NO.:51,52), N) anti-CD3 VHVL stL x 3-5 VHVL (SEQ ID NO.:53,54), O) anti-CD3 VHVL aL x 4-1 VHVL (SEQ ID NO.:55,56), P) anti-CD3 VHVL aL Ser x 4-1 VHVL (SEQ ID NO.:57,58) and Q) anti-CD3 VHVL stL x 4-1 VHVL (SEQ ID NO.:59,60).
FIG. 2:
FACS analysis of the constructs A) anti-CD3 VHVL stL x 5-10 VHVL (SEQ ID NO.:18), B) anti-CD3 VHVL stL x 4-7 VHVL (SEQ ID NO.:14), C) anti-CD3 VHVL aL x 5-10 VHVL (SEQ ID NO.:4), D) anti-CD3 VHVL aL x 4-7 VHVL (SEQ ID NO.:2), E) anti-CD3 VHVL aL Ser x 5-10 VHVL (SEQ ID NO.:10), F) anti-CD3 VHVL aL Ser x 4-7 VHVL (SEQ ID NO.:8), G) anti-CD3 VHVL stL x 3-1 VHVL (SEQ ID NO.:12), H) anti-CD3 VHVL stL x 5-10 VLVH (SEQ ID NO.:20) and I) anti-CD3 VHVL stL x 4-7 VLVH (SEQ ID NO.:16) in CD3 positive Jurkat and EpCAM-positive Kato III cells. A shift to the right shows binding. In Jurkat and KatoIII cells the dotted line indicates the shift of the negative control (only secondary antibody), dashed line shows the binding of an anti-EpCAM-anti-CD3 control antibody and the bold line shows the bispecific construct of interest.
FIG. 3:
DNA and amino acid sequence of the anti-EpCAM-anti-CD3-constructs A) 4-7 VLVHx anti-CD3 VHVL (SEQ ID NO.:41,42), B) 3-5 VLVHx anti-CD3 VHVL (SEQ ID NO.:29,30), C) 3-1 VLVHx anti-CD3 VHVL (SEQ ID NO.:35,36), D) 4-1 VLVHx anti-CD3 VHVL (SEQ ID NO.:38,39) and E) 5-10 VLVHx anti-CD3 VHVL (SEQ ID NO.:43,44).
FIG. 4: FACS analysis of the constructs A) 4-7 VLVHx anti-CD3 VHVL (SEQ ID NO.:42), B) 3-5 VLVHx anti-CD3 VHVL (SEQ ID NO.:30), C) 3-1 VLVHx anti-CD3 VHVL (SEQ ID NO.:36), D) 4-1 VLVHx anti-CD3 VHVL (SEQ ID NO.:39) and E) 5-10 VLVHx anti-CD3 VHVL (SEQ ID NO.: 44) constructs in CD3 positive Jurkat and EpCAM-positive Kato III cells. A shift to the right shows binding.
FIG. 5:
A representative elution pattern of an EpCAM bispecific antibody containing protein fractions from a Zn-Chelating Fractogel® column at 280 nm. High adsorption at 280 nm from 50-450 ml retention time was due to non-bound protein in the column flow through. The arrow at the peak at 530.09 ml indicates the EpCAM bispecific construct containing protein fraction that was used or further purification.
FIG. 6:
A representative protein elution pattern from a Sephadex® S200 gelfiltration column at 280 nm. The protein peak at 82.66 ml containing bispecific antibodies against CD3 and EpCAM corresponds to a molecular weight of ca. 52 kD. Fractions were collected from 40-140 ml retention time.
FIG. 7
A) Cation exchange chromatogram of 3-1 x anti-CD3 (SEQ ID NO.:36) shows the overall charge isoforms of the protein. Cation exchange chromatography was performed on a MiniS® (Amersham) column. After washing with 20 mM MES buffer pH 5.5, the protein was eluted with a gradient of elution buffer containing 1 M NaCl: 0-30% in 60 column volumes. The bispecific construct was eluted at 23.58 ml. Unspecific protein was eluted with 1 M NaCl starting at 50 ml.
B) Cation exchange chromatogram of 5-10 x anti-CD3 (SEQ ID NO.:44) shows the overall charge isoforms of the protein. Cation exchange chromatography was performed as in FIG. 7A. The bispecific construct was eluted at a shoulder at 35.77 ml. Unspecific protein was eluted with 1 M NaCl starting at 50 ml.
FIG. 8:
A) Representative SDS-PAGE analysis of EpCAM bispecific single chain antibody protein fractions. Lane M: Molecular weight marker Lane 1: cell culture supernatant; lane 2: IMAC flow through; lane 3: IMAC wash; lane 4: IMAC eluate; lane 5: purified antibody against EpCAM and CD3 obtained from gel filtration.
B) Representative Western blot analysis of purified EpCAM bispecific single chain antibody protein fractions Lane 1: cell culture supernatant; lane 2: IMAC flow through; lane 3: IMAC wash; lane 4: IMAC eluate; lane 5: purified antibody against EpCAM and CD3 obtained from gel filtration.
FIG. 9:
Cytotoxicity assay of C-terminal EpCAM binders anti-CD3×3-1 (SEQ ID NO.:46), anti-CD3 x-5-10 (SEQ ID NO.:4), and anti-CD3×4-7 (SEQ ID NO.:2). CB15 T cell clone and CHO-EpCAM cells were used in an E:T ratio of 5:1. CHO-EpCAM cells were stained with PKH26 dye and the cells were counted after bispecific single chain antibody incubation with FACS analysis.
FIG. 10:
Cytotoxicity assay of N-terminal EpCAM binders 3-1xanti-CD3 (SEQ ID NO.:36), and 5-10xanti-CD3 (SEQ ID NO.:44). CB15 T cell clone and CHO-EpCAM cells were used in an E:T ration of 5:1. CHO-EpCAM cells were stained with PKH26 dye and the cells were counted after bispecific single chain antibody incubation with FACS analysis.
FIG. 11:
A) Sequence alignment of the CDR3 of the VH chains of EpCAM 3-1 (SEQ ID NO.: 80), EpCAM 4-1 (SEQ ID NO.: 88), EpCAM 5-10 (SEQ ID NO.: 96), EpCAM 3-5 (SEQ ID NO.: 84), EpCAM 4-7 (SEQ ID NO.:92), compared with CDR3 of the VH chain of EpCAM M79, HD70 and 3B10. The NXD motif is depicted as bold.
B) Comparison of the cytotoxic activity of 3-1xanti-CD3 (SEQ ID NO.: 36), 5-10xanti-CD3 (SEQ ID NO.:44), anti-CD3×4-7 (SEQ ID NO.:2) and anti-CD3×5-10 (SEQ ID NO.:18) with M79Xanti-CD3 and HD70xanti-CD3 controls. PBMC cells and Kato III cells were used in a E:T ratio of 10:1. KatoIII cells were stained with propidium iodide and the cells were counted after bispecific single chain antibody incubation with FACS analysis.



The invention will now be described by reference to the following biological examples which are merely illustrative and are not to be construed as a limitation of scope of the present invention.
EXAMPLE 1
Cloning and Expression of the EpCAM Constructs
A number of constructs comprising anti-CD3 and anti-EpCAM in various structures) and domain arrangements were generated. Anti-EpCAM VH and VL variable domains of the antibodies 3-1 are shown in SEQ ID NO.:79, 80, 81, 82, 3-5 in SEQ ID NO.:83, 84, 85, 86, 4-1 in SEQ ID NO.:87, 88, 89, 90, 4-7 SEQ ID NO.:91, 92, 93, 94 and 5-10 in SEQ ID NO.:95, 96, 97, 98. The constructs are summarized in Table 1.







TABLE 1







anti-CD3-anti-EpCAM and anti-EpCAM-anti-CD3 constructs










SEQ ID NO.:

Domain
Distinctive


Construct No.
Construct
arrangement
feature










anti-CD3xanti-EpCAM constructs










SEQ ID NO.: 1, 2
anti-CD3x4-7
VH-VLXVH-VL



SEQ ID NO.: 3, 4
anti-CD3x5-
VH-VLXVH-VL



10


SEQ ID NO.: 45, 46
anti-CD3x3-1
VH-VLXVH-VL


SEQ ID NO.: 49, 50
anti-CD3x3-5
VH-VLXVH-VL


SEQ ID NO.: 55, 56
anti-CD3x4-1
VH-VLXVH-VL


SEQ ID NO.: 7, 8
anti-CD3x
VH-VLXVH-VL
Cys-Ser



4-7Cys-Ser

mutation


SEQ ID NO.: 9, 10
anti-CD3x
VH-VLXVH-VL
Cys-Ser



5-10Cys-Ser

mutation


SEQ ID NO.: 47, 48
anti-CD3x3-1
VH-VLXVH-VL
Cys-Ser





mutation


SEQ ID NO.: 51, 52
anti-CD3x3-5
VH-VLXVH-VL
Cys-Ser





mutation


SEQ ID NO.: 57, 58
anti-CD3x4-1
VH-VLXVH-VL
Cys-Ser





mutation


SEQ ID NO.: 11, 12
anti-CD3x3-1
VH-VLXVH-VL
(G4S)3 -linker


SEQ ID NO.: 13, 14
anti-CD3x4-7
VH-VLXVH-VL
(G4S)3 -linker


SEQ ID NO.: 15, 16
anti-CD3x4-7
VH-VLXVL-VH
(G4S)3 -linker


SEQ ID NO.: 17, 18
anti-CD3x5-
VH-VLXVH-VL
(G4S)3 -linker


1
10


SEQ ID NO.: 19, 20
anti-CD3x5-
VH-VLXVL-VH
(G4S)3 -linker



10


SEQ ID NO.: 53, 54
anti-CD3x3-5
VH-VLXVH-VL
(G4S)3 -linker


SEQ ID NO.: 59,
anti-CD3x4-1
VH-VLXVH-VL
(G4S)3 -linker


60







anti-EpCAM- anti-CD3 constructs










SEQ ID NO.: 29, 30
3-5xanti-CD3
VL-VHxVH-VL



SEQ ID NO.: 35, 36
3-1xanti-CD3
VL-VHxVH-VL


SEQ ID NO.: 38, 39
4-1xanti-CD3
VL-VHxVH-VL


SEQ ID NO.: 41, 42
4-7xanti-CD3
VL-VHxVH-VL


SEQ ID NO.: 43, 44
5-10xanti-
VL-VHxVH-VL



CD3









1.1 Cloning of C-Terminal EpCAM-Binders

1.1.1 Preparation of Anti-CD3 PCR Products

a) Anti-CD3 Constructs with Original 18 Amino Acid Linker (SEQ ID NOs.:1, 2, 3 and 4)

The N-terminal original anti-CD3 containing the 18 amino acid linker (SEQ ID NO.:70) was obtained by PCR using the CD19xCD3 construct (Löffler A et al., Blood 2000 95:2098-103) as template and the following primers (CD3 VH BsrGI: AGGTGTACACTCCGATATCAAACTGCAGCAG (SEQ ID NO.:5), CD3 VL BspEI: AATCCGGATTTCAGCTCCAGCTTGG (SEQ ID NO.:6)).
b) Anti-CD3 Constructs with Original 18 Amino Acid Linker and Cys to Ser Mutation in CDRH3 (SEQ ID Nos. 7,8, 9 and 10)
The N-terminal original anti-CD3 containing the 18 amino acid linker (Seq ID NO.:70) and the Cys to Ser mutation was obtained by PCR using a CD19xanti-CD3 (C→S mutation) construct as template and the primers CD3 VH BsrGI and CD3 VL BspEI (Seq ID Nos. 5 and 6). The CDRH3 sequence with the Cys-Ser mutation is shown in SEQ ID NO.:78.
c) Anti-CD3-Anti-EpCAM Constructs with (G4S)3 Linker (Seq ID Nos. 11, 12, 13, 14, 15, 16, 17, 18, 19 and 20)
The N-terminal anti-CD3 containing the 15 amino acid standard (G4S)3 linker, (SEQ ID NO.:99) was obtained by PCR using the CD19xCD3 (Löffler A et al., Blood 2000 95:2098-103) as template. The anti-CD3 VH region and the anti-CD3 VL region were separately amplified by the following primers (CD3 VH: CD3 VH BsrG1 AGGTGTACACTCCGATATCAAACTGCAGCAG (SEQ ID NO.:5), 3′′CD3 VH GS15 GGAGCCGCCGCCGCCAGAACCACCACCACCTGAGGAGACTGTGAGAGTGGTGCCTTG (SEQ ID NO.:21); CD3 VL: 5′′CD3 VL GS15 GGCGGCGGCGGCTCCGGTGGTGGTGGTTCTGACATTCAGCTGACCCAGTCTCC (SEQ ID NO.:22), CD3 VL BspEI AATCCGGATTTCAGCTCCAGCTTGG (SEQ ID NO.:6)). Overlapping complementary sequences introduced into the PCR products were used to form the coding sequence of a 15-amino acid (G4S)3 (single-letter amino acid code) (SEQ ID NO.:99) linker during the subsequent fusion PCR. This amplification step was performed with the primer pair CD3 VH BsrGI (SEQ ID NO.:5) and CD3 VL BspEI (SEQ ID NO.:6).
1.1.2 Cloning of the Anti-CD3xanti EpCAM Constructs in VHanti-CD3-VLanti-CD3 x VHanti-EpCAM-VLanti-EpCAM Orientation (SEQ ID NO.:1,2, SEQ ID NO.:3,4, SEQ ID NO.:7,8, SEQ ID NO.:9,10, SEQ ID NO.:11,12, SEQ ID NO.:13,14 and SEQ ID NO.:17,18)
The N-terminal original anti-CD3 containing the 18 amino acid linker (SEQ ID NO.:70) or the N-terminal original anti-CD3 containing the 15 amino acid standard (G4S)3 linker (SEQ ID NO.:99) was cleaved with the restriction enzymes BsrGI and BspEI and subsequently cloned into the bluescript KS vector (Stratagene, La Jolla, Calif.), containing the amino acid sequence of an eukaryotic secretory signal (leader peptide) as a EcoRI/BsrGI-Fragment. After cleavage of this construct with EcoRI and BspEI the resulting DNA fragment comprising the respective anti-CD3 scFv with the leader peptide was cloned into a EcoRI/BspEI cleaved plasmid containing the c-terminal EpCAM binders 3-1 (SEQ ID NO.:79-82), 4-7 (SEQ ID NO.:91-94), or 5-10 (SEQ ID NO.:95-98) in pEFDHFR. pEFDHFR was described in Mack et al. Proc. Natl. Acad. Sci. USA 92 (1995) 7021-7025).
1.1.3. Cloning of the Anti-CD3xanti EpCAM Constructs in VHanti-CD3-VLanti-CD3 x VLanti-EpCAM-VHanti-EpCAM Orientation (SEQ ID Nos.: 15, 16, 19 and 20)
The C-terminal anti-EpCAM antibody 4-7 (SEQ ID NO.:91-94) in VLVH orientation containing the 15 amino acid standard linker (SEQ ID NO.:99) was obtained by PCR. The 4-7 VH region and the 4-7 VL region were separately amplified by the following primers (4-7 VL: 4-7. VL BspEI FOR CTGAAATCCGGAGGTGGTGGATCCGAGCTCGTGATGACCCAGACTCC (SEQ ID NO.:100), 4-7 VL GS15 REV GGAGCCGCCGCCGCCAGAACCACCACCACCTTTGATCTCAAGCTTGGTCCCC (SEQ ID NO.:101); 4-7 VH: 4-7 VH GS15 FOR GGCGGCGGCGGCTCCGGTGGTGGTGGTTCTGAGGTGCAGCTGCTCGAGCAG (SEQ ID NO.:23), 4-7 VH SalI REV TTTTAAGTCGACCTAATGATGATGATGATGATGTGAGGAGACGGTGACCGTGG (SEQ ID NO.:24)). Overlapping complementary sequences introduced into the PCR products were used to form the coding sequence of a 15-amino acid (G4S)3 (single-letter amino acid code) linker (SEQ ID NO.:99) during the subsequent fusion PCR. This amplification step was performed with the primer pair 4-7 VL BspEI FOR and 4-7 VH SalI REV (SEQ ID NO.100, SEQ ID NO.:24).
The C-terminal anti-EpCAM antibody 5-10 (SEQ ID NO.:95-98) in VLVH orientation containing the 15 amino acid standard linker (SEQ ID NO.:99) was obtained by PCR. The 5-10 VH region and the 5-10 VL region were separately amplified by the following primers (5-10 VL: 5-10 VL BspEI FOR CTGAAATCCGGAGGTGGTGGATCCGAGCTCGTGATGACACAGTCTCCAT (SEQ ID NO.:25), 5-10 VL GS15 REV GGAGCCGCCGCCGCCAGAACCACCACCACCTTTGATCTCAAGCTTGGTCCCAG (SEQ ID NO.: 26); 5-10 VH: 5-10 VH GS15 FOR GGCGGCGGCGGCTCCGGTGGTGGTGGTTCTGAGGTGCAGCTGCTCGAGC (SEQ ID NO.:27), 5-10 VH SalI REV TTTTAAGTCGACCTAATGATGATGATGATGATGTGAGGAGACGGTGACCGTGG (SEQ ID NO.:28)). Overlapping complementary sequences introduced into the PCR products were used to form the coding sequence of a 15-amino acid (G4S)3 linker (SEQ ID NO.:99) during the subsequent fusion PCR. This amplification step was performed with the primer pair 5-10 VL BspEI FOR and 5-10 VH SalI REV (SEQ ID NO.:25, SEQ ID NO:28).
These PCR products (5-10 VLVH and 4-7 VLVH) were cleaved with BspEI and Sa/I and ligated in the BspEI/SalI cleaved anti-CD3 VHVL stLx5-10 VHVL (SEQ ID NO.:17,18) or anti-CD3 VHVL stL x 4-7 (SEQ ID NO.:13, 14) VHVL in pEFDHFR replacing the 5-10 VHVL DNA fragment.
1.1.4. Expression and Binding of the Anti-CD3-EpCAM Constructs
After confirmation of the sequence coding for the bispecific single chain by sequencing the plasmid was transfected into DHFR deficient CHO cells for eukaryotic expression. Eukaryotic protein expression in DHFR deficient CHO cells was performed as described in Kaufmann R. J. (1990) Methods Enzymol. 185, 537-566). The transfected cells were then expanded and 1 liter of supernatant produced. Expression and binding of the bispecific single chain molecules were confirmed by FACS analyses. For that purpose the EpCAM positive human gastric cancer cell line Kato III (obtained from American Type Culture Collection (ATCC) Manassas, Va. 20108 USA, ATCC number: HTB-103) was used. Binding of the anti-CD3 part was demonstrated on Jurkat cells (ATCC TIB 152).
Cells were cultured according to the recommendations of the supplier and ca. 200000 cells were incubated with 10 μg/ml of the construct in 50 μl PBS with 2% FCS. The binding of the construct was detected with an anti-His antibody (Penta-His Antibody, BSA free, obtained from Quiagen GmbH, Hilden, FRG) at 2 μg/ml in 50 μl PBS with 2% FCS. As a second step reagent a R-Phycoerythrin-conjugated affinity purified F(ab′)2 fragment, goat anti-mouse IgG, Fc-gamma fragment specific antibody, diluted 1:100 in 50 μl PBS with 2% FCS (obtained from Dianova, Hamburg, FRG) was used. The samples were measured on a FACSscan (BD biosciences, Heidelberg, FRG). All the constructs comprising anti-CD3 and anti-EpCAM showed stronger binding affinity to CD3 and to EpCAM than the prior art anti-EpCAM (M79)xanti-CD3 bispecific antibody (FIG. 2).
1.2 N-Terminal EpCAM Binders
1.2.1 Cloning of the Anti-EpCAMxanti-CD3 Constructs
Cloning of the Construct 3-5xanti-CD3 (SEQ ID NOs.29, 30):
The C-terminal 3-5 in VH-VL orientation was obtained by PCR for the construction of 3-5 xanti-CD3 (SEQ ID NO.:29) molecule. Fragments I and II were amplified by PCR using primer pairs me 81 (SEQ ID NO.:31)/me 90 (SEQ ID NO.:34) and me 83 (SEQ ID NO.:32)/me 84 (SEQ ID NO.:33), respectively. Hot Start PCR was done using the Expand High Fidelity System of Roche Diagnostics. 20 cycles (94° C./30 sec; 60° C./1 min; 72° C./1 min) were used for amplification followed by one cycle of 3 min at 72° C.
PCR fragments I and II were subjected to electrophoresis on a 1.5% agarose gel. Fragments were mixed (1 ng of each) and used as a template for the next PCR reaction performed with primer pair me 81 (SEQ ID NO.:31) and me 84 (SEQ ID NO:33) for amplification of fragment III. PCR was performed as described above. Fragment III was purified on an agarose gel and digested with BssHII and BspEI (Biolabs), purified and subsequently cloned into the corresponding sites of the pEF-dHFR-signal peptide (77/78)-anti-CD3 cloning vector, which facilitates cloning of anti-target variable regions in front of the anti-CD3 region. The vector has a unique BssHII site just after the signal peptide followed by BspEI site, linker (G4S) and anti-CD3 region. The cloned region was verified by restriction digests and by DNA-sequencing.
Sequences of the Primers Used:







Me 81:


(SEQ ID NO.: 31)


5′-GGA TGC GCG CGA GCT CGT GAT GAC CCA GAC TCCA


CTC TCC-3′


 


Me 83:


(SEQ ID NO.: 32)


5′-GGT TCT GGC GGC GGC GGC TCC GGT GGT GGT GGT


TCT GAG GTG CAG CTG CTC GA CAG TCT G-3′


 


Me 84:


(SEQ ID NO.: 33)


5′-GTG CTC CGG AGG AGA CGG TGA CCG TGG TCC CTT


GGC CCC AG-3′


 


Me 90:


(SEQ ID NO.: 34)


5′-CCG GAG CCG CCG CCG CCA GAA CCA CCA CCA CCT


TTG ATC TCA AGC TTG GTC CC-3′






Cloning of the Construct 3-1xanti-CD3 (SEQ ID NO.:35, 36),

The C-terminal 3-1 in VH-VL orientation was obtained by PCR for the construction of 3-1 xanti-CD3 (SEQ ID NO.:35) molecule. Fragments I and II were amplified by PCR using primer pairs me 91a (SEQ ID NO.:37)/me 90 (SEQ ID NO.:34) and me 83 (SEQ ID NO.:32)/me 84 (SEQ ID NO.:33), respectively. PCR was performed as above.
Agarose gel fragments comprising PCR fragments I and II were used as a template for the next PCR reaction performed with primer pair me 91a (SEQ ID NO.:37) and me 84 (SEQ ID NO.:33) for amplification of fragment III. PCR was performed as described above except, annealing was performed at 68° C. instead of at 60° C. Fragment III was purified on an agarose gel and digested with BsrGI and BspEI (Biolabs), purified and subsequently cloned into the corresponding sites of the pEF-dHFR-M79 X anti-CD3 cloning vector. The cloned region was verified by restriction digests and by DNA-sequencing.







Me 91a:


(SEQ ID NO.: 37)


5′-GGA TTG TAC A CTCC GA GCT CGT CAT GAC CCA GTC


 


TCC ATC TTA TCT TGC TGC-3′






Cloning of the Construct 4-1 xanti-CD3 (SEQ ID NO.:38, 39):

The C-terminal 4-1 in VH-VL orientation was obtained by PCR for the construction of 4-1 xanti-CD3 (SEQ ID NO.:38, 39) molecule. Fragments I and II were amplified by PCR using primer pairs me 92a (SEQ ID NO.:40)/me 90 (SEQ ID NO.:34) and me 83 (SEQ ID NO.:32)/me 84 (SEQ ID NO.:33), respectively. PCR was performed as above in annealing temperature of 60° C.
Agarose gel fragments comprising PCR fragments I and II were used as a template for the next PCR reaction performed with primer pair me 92a (SEQ ID NO.:40) and me 84 (SEQ ID NO.:33) for amplification of fragment III. PCR was performed as described above except, annealing was performed at 68° C. instead of at 60° C. Fragment III was purified on an agarose gel and digested with BsrGI and BspEI (Biolabs), purified and subsequently cloned into the corresponding sites of the pEF-dHFR-M79 X anti-CD3 is cloning vector. The cloned region was verified by restriction digests and by DNA-sequencing.









Me 92a:



(SEQ ID NO.: 40)



5′-GGA TTG TAC A CTCC GA GCT CGT GAT GAC ACA



 



GTCTCC ATC CTC C-3′






Cloning of the Construct 4-7xanti-CD3 (SEQ ID NO.:41,42)

The C-terminal 4-7 in VH-VL orientation was obtained by PCR for the construction of 4-7 xanti-CD3 (SEQ ID NO.:41, 42) molecule. Fragments I and II were amplified by PCR using primer pairs me 81 (SEQ ID NO.:31)/me 90 (SEQ ID NO.:34) and me 83 (SEQ ID NO.:32)/me 84 SEQ ID NO.:33), respectively. PCR was performed as above with an annealing temperature of 60° C.
Agarose gel fragments comprising PCR fragments I and II were used as a template for the next PCR reaction performed with primer pair me 81 (SEQ ID NO.:31) and me 84 (SEQ ID NO.:33) for amplification of fragment III. PCR was performed as described above. Fragment III was purified on an agarose gel and digested with BssHII and BspEI (Biolabs), purified and subsequently cloned into the corresponding sites of the pEF-dhfr-signal peptide (77/78)-anti-CD3 cloning vector. The cloned region was verified by restriction digests and by DNA-sequencing.
Cloning of the Construct 5-10xanti-CD3 (SEQ ID NO.:43, 44)
The C-terminal 5-10 in VH-VL orientation was obtained by PCR for the construction of 5-10xanti-CD3 (SEQ ID NO.:43, 44) molecule. Fragments I and II were amplified by PCR using primer pairs me 92a (SEQ ID NO.:40)/me 90 (SEQ ID NO.:34) and me 83 (SEQ ID NO.:32)/me 84 (SEQ ID NO.:33), respectively. PCR was performed as above with an annealing temperature of 60° C.
Agarose gel fragments comprising PCR fragments I and II were used as a template for PCR with primer pair me 92a (SEQ ID NO.:40) and me 84 (SEQ ID NO.:33) for amplification of fragment III. PCR was performed as described above except, annealing was performed at 68° C. instead of at 60° C. Fragment III was purified on an agarose gel and digested with BsrGI and BspEI (Biolabs), purified and subsequently cloned into the corresponding sites of the pEF-dhfr-M79 X anti-CD3 cloning vector. The cloned region was verified by restriction digests and by DNA-sequencing.
1.2.2 Expression of Anti-EpCAMxanti-CD3 Bispecific Molecules
CHO-cells lacking DHFR gene were maintained in alpha MEM medium (Life Technologies, cat. no: 32561) supplemented with 10% fetal Calf Serum (Life Technologies, heat inactivated at 65° C. for 30 minutes) and with HT (Hypoxanthin and Thymidine; Life Technologies, cat. no: 41065-012). The cells were transfected with pEF-dHFR-3-1xanti-CD3 (SEQ ID NO.:35, 36), pEF-dHFR-3-5xanti-CD3 (SEQ ID NO.:29, 30), pEF-dHFR-4-1xanti-CD3 (SEQ ID NO.:38, 39), pEF-dHFR-4-7xanti-CD3 (SEQ ID NO.:41, 42) and pEF-dHFR-5-10xanti-CD3 (SEQ ID NO.:43, 44) using Lipofectamine 2000 kit (Invitrogen; cat. no:11668-019) according to the instructions provided by the Manufacturer. After 48 hrs, the cells were subjected to selection by transferring the transfected cells into the selection medium (alpha MEM medium (cat. no:32561) containing heat inactivated 10% dialysed fetal Calf Serum (Life Technologies). After 2-3 weeks of selection, the cells were grown for 8 to 9 days (in 500 ml of selection medium) for production of bispecific molecules in 2 liter Tissue culture Roller Bottles (Falcon (cat. no: 353068; Becton Dickinson Labware). The tissue culture medium was centrifuged at 4° C. for 10 minutes at 300 g (1300 rpm) to remove the cells and cell debris. The supernatant containing the secreated bispecific molecules was stored at −20° C. until further analysis.
1.2.3 Binding Assays of Bispecific Anti EpCAMxanti CD3 Variants
In order to analyze the binding strength of the bispecific anti-EpCAMxanti-CD3 single chain constructs of the invention, the following binding assay was carried out.
250000 Jurkat cells (for CD3 binding) and Kato cells (for EpCAM binding) were independently incubated with crude supernatants (50 μl) containing bispecific construct for 45 min. at 4° C. Thereafter, the cells were washed twice in FACS buffer (phosphate-buffered saline containing 1% fetal calf serum (FCS) and 0.05% sodium azide) and incubated with mouse anti-His antibody (Dianova, DIA910) for 60 min. at 4° C. Washing steps were performed as above.
The cells were finally incubated either with goat anti-mouse-FITC-conjugated antibody (BD 550003) or with anti-mouse-PE conjugated antibody (IgG) (Sigma, P8547). After washing steps, 10,000 events were analysed using FACS Calibur (B&D). All the EpCAM constructs showed strong binding (FIG. 4).
EXAMPLE 2
Purification of the EpCAM Constructs
In order to purify the bispecific single chain constructs comprising anti-EpCAM and anti-CD3 the CHO-EpCAM cells were grown in roller bottles with HiClone® CHO modified DMEM medium (HiQ) for 7 days before harvest. The cells were removed by centrifugation and the supernatant containing the expressed protein was stored at −20° C.
Äkta FPLC System® (Pharmacia) and Unicorn Software® were used for chromatography. All chemicals were of research grade and purchased from Sigma (Deisenhofen) or Merck (Darmstadt).
IMAC was performed, using a Fractogel® column (Pharmacia) that was loaded with ZnCl2 according to the manufacturers protocol. The column was equilibrated with buffer A2 (20 mM NaPP pH 7.5, 0.4 M NaCl) and the cell culture supernatant (500 ml) was applied to the column (10 ml) with a flow rate of 3 ml/min. The column was washed with buffer A2 to remove unbound sample. Bound protein was eluted using a 2-step gradient of buffer B2 (20 mM NaPP pH 7.5, 0.4 M NaCl, 0.5 M Imidazol). In Step 1 20% buffer B2 in 10 column volumes was used and in Step 2 100% buffer B2 in 10 column volumes was used. Eluted protein fractions from the 100% step were pooled for further purification.
Gel filtration chromatography was performed on a Sephadex S200 HiPrep® column (Pharmacia) equilibrated with PBS (Gibco). Eluted protein samples (flow rate 1 ml/min) were subjected to SDS-Page and Western Blot for detection.
The column was previously calibrated for molecular weight determination (molecular weight marker kit, Sigma MW GF-200).
Protein concentrations were determined using protein assay dye (MicroBCA, Pierce) and IgG (Biorad) as standard protein. The yields of the protein are shown in Table 2. All constructs were producible.







TABLE 2







Yields of the single-chain bispecific constructs


comprising anti-EpCAM and anti-CD3











Yield




[μg purified protein per



Construct
liter culture]














4-1 x anti-CD3 (SEQ ID NO.: 39)
172.5



3-5 x anti-CD3 (SEQ ID NO.: 30)
265



4-7 x anti-CD3 (SEQ ID NO.: 42)
37



anti-CD3 x 4-7. (SEQ ID NO.: 2)
112.5



anti-CD3 Cys-Ser x 4-7 (SEQ ID
140



NO.: 8)



3-1 x anti-CD3 (SEQ ID NO.: 36)
265



5-10 x anti-CD3 (SEQ ID NO.: 44)
400



anti-CD3 x 5-10 (SEQ ID NO.: 4)
195










A further high resolution cation exchange chromatography was performed on a MiniS® column (Amersham), equilibrated with 20 mM MES buffer pH 5.5. The sample was diluted 1:3 with the same buffer before loading to the column. Bound protein was eluted with a gradient of equilibration buffer containing 1M NaCl: 0-30% in 60 column volumes. Remaining protein was eluted in 3 column volumes of 1M NaCl (FIG. 7).
The EpCAM bispecific single chain construct proteins were isolated in a two-step purification process including immobilized metal affinity chromatography (IMAC) (FIG. 5) and gel filtration (FIG. 6). The main product had a molecular weight of 52 kDa under native conditions as determined by gelfiltration in PBS.
Purified bispecific protein was analyzed in SDS PAGE under reducing conditions performed with precast 4-12% Bis Tris gels (Invitrogen). Sample preparation and application were according to the manufacturers protocol. The molecular weight was determined with MultiMark® protein standard (Invitrogen). The gel was stained with colloidal Coomassie (Invitrogen protocol). The purity of the isolated protein was shown to be >95% (FIG. 8A). Western Blot was performed with an Optitran BA-S83® membrane and the Invitrogen Blot Module according to the manufacturers protocol. The antibodies used were Penta H is (Qiagen) and Goat-anti-Mouse-Ig labeled with alkaline phosphatase (AP) (Sigma), the chromogenic substrate solution was BCIP/NBT liquid (Sigma). The EpCAM bispecific protein could be specifically detected by Western Blot (FIG. 8B). The main signal corresponds to the main band in the SDS PAGE at 52 kD corresponding to the purified bispecific molecule.
EXAMPLE 3
Cytotoxicity Assays of the Constructs Comprising Anti-CD3 and Anti-EpCAM
In order to test the bioactivity of the constructs comprising anti-EpCAM and anti-CD3 a FACS based cytotoxicity test was performed.
For the cytotoxicity test, CHO cells from the American Type Cell Culture Collection (ATCC, Manassas, USA) were transfected with epithelial cell adhesion molecule (EpCAM). A cell clone derived from this transfection, referred to as CHO-EpCAM cells, was used for the experiments. CHO-EpCAM (1.5×107) cells were washed free of serum two times with PBS and incubated with PKH26 dye (Sigma-Aldrich Co.) according to the manufacturers instructions. After staining cells were washed two times with RPMI/10% FCS.
Cells were counted and mixed with CB15 effector cells. The CD4-positive T cell clone CB15 was provided by Dr. Fickenscher, University of Erlangen/Nuernberg, Germany. Cells were cultured as recommended by the suppliers. The resulting cell suspension contained 400.000 target and 2×106 effector cells per ml. 50 μl of the mixture was used per well in a 96 well round bottom plate.
Antibodies were diluted in RPMI/10% FCS to the required concentration and 50 μl of this solution was added to the cell suspension. A standard reaction was incubated for 16 h at 37° C./5% CO2. Propidium iodide was added to a final concentration of 1 μg/ml. After 10 min of incubation at room temperature cells were analysed by FACS. PKH26 fluorescence was used for positive identification of target cells. Cytotoxicity was measured as ratio of PI positive over all target cells. Sigmoidal dose response curves typically had R2 values >0.97 as determined by Prism Software (GraphPad Software Inc., San Diego, USA) (FIGS. 9 and 10). EC50 values calculated by the analysis program were used for comparison of bioactivity. All the constructs of the invention show at least 50 times better cytotoxicity (maximum EC50-value 169 pg/ml) than the prior art construct M79xanti-CD3 (8628 pg/ml).
EXAMPLE 4
Determination of the Binding Affinity by BIAcoreTM 2000 of the Constructs Comprising Anti-EpCAM and Anti-CD3 to EpCAM
In order to show the superior binding affinity of the constructs of the invention, the KD values of the constructs and of the prior art anti-EpCAM construct (M79)xanti-CD3 were determined.
Kinetic binding experiments were performed using surface plasmon resonance on the BIAcoreTM 2000, Biacore AB (Uppsala, Sweden) with a flow rate of 5 μL/min and HBS-EP (0.01 M HEPES, pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.005% surfactant P20) as running buffer at 25° C. The extracellular domain of the EpCAM antigen (residues 17-265) was immobilized onto flow cells 2-4 on a CM5 sensor chip. The chip surface was activated injecting 80 μL of 0.1 M sodium-hydroxysuccinimid, 0.4 M N-ethyl-N′(3-dimethylaminepropyl)-carbodiimid (NHS/EDC). The antigen was coupled by manual injection of 60 μg/mL EpCAM in 0.01 M sodium-acetate, pH 4.7. Different densities of antigen were immobilized on flow cells 2-4 adjusting the amount of manual injection times. Flow cell 1 was left empty while flow cell 2 was coated with the highest density of EpCAM (4100 RU). Flow cell 3 was coated with 1⁄4 of the amount of antigen immobilized on flow cell 2 (974 RU) and flow cell 4 was coated with lowest density of Ep-CAM antigen (265 RU). The activated surface of the sensor chip was blocked injecting 85 μL of 1 M ethanolamine and the chip was left to equilibrate over night at a constant flow of 5 μL/min of HBS-EP.
Binding kinetics of the bispecific constructs were measured injecting 10 μL of protein solution at concentrations ranging from 4 μM-0.07 μM and monitoring the dissociation for 100 sec. Protein was buffered in HBS-EP. The data were fitted using BIAevalutionTM software determining the rate constant for dissociation and association kinetics with a 1:1 Langmuir binding equation (1, 2). Where A is the concentration of injected analyte and B[0] is Rmax.

dB/dt=−(ka*[A]*[B]−kd*[AB])  (1)

dAB/dt=−(ka*[A]*[B]−kd*[AB])  (2)

Kinetic binding curves were determined in four concentrations of each bispecific construct analysed. The independent fitting of the raw data resulted in dissociation and association rate constants that were used to calculate the equilibrium dissociation constant (KD). The calculated KD values were unbiased for concentration indicating reliable data analysis. The average of the independently determined dissociation constants as well as the standard deviation are summarized in table 3.
The analysed bispecific constructs bind to the Ep-CAM antigen immobilized on the chip surface within a well defined affinity range. The standard deviation for the calculated average dissociation constant is as expected.







TABLE 3







Dissociation constants for the bispecific


constructs binding to EpCAM.









KD (M)














M79 x anti-CD3 (control)
4.0 × 10−6



4-1 x anti-CD3 (SEQ ID
2.5 × 10−7



NO.: 39)



3-5 x anti-CD3 (SEQ ID
2.3 × 10−7



NO.: 30)










The prior art anti-EpCAM x anti-CD3 construct M79xCD3 had a KD of 4.0×10−6 M while surprisingly the constructs of the invention have a KD in the range of 2.3×10−7-2.5×10−7 M. Thus, the constructs of the invention have more than 15 times stronger binding affinity than the prior art construct.
EXAMPLE 5
Comparison of the Cytotoxic Activity of the Constructs of the Invention with Prior Art Constructs
In order to compare the bioactivity of constructs having the NXD motif with conventional M79xCD3 and HD70xCD3 constructs the following cytotoxic assay was carried out.
KatoIII cells (ATCC HTB-103) were used as target cells and grown in RPMI supplemented with 10% fetal calf serum at 37° C. in a 5% CO2 humidified incubator. Subconfluent cultures were treated with 0.25% trypsin, counted in a Neubauer chamber slide and checked for vitality by trypan-blue exclusion. Only cultures with >95% vitality were used for cytotoxicity assays. Target cells were stained with PKH26 fluorescent membrane dye according to the manufacturers manual (Sigma-Aldrich GmbH, Germany, PKH26-GL). Cell number was adjusted to 8×105 cells/ml in RPMI complete medium.
Human peripheral blood mononuclear cells (PBMCs) were used as effector cells and isolated from healthy donors using ficoll density gradient centrifugation with subsequent 100×g centrifugation to remove thrombocytes. The pellet was resuspended in 10 vol. erythrocyte lysing buffer and incubated at room temperature for 10 min. Lysing reaction was stopped by addition PBS. PBMCs were resuspended in RPMI 1640 complete medium and cell number adjusted to 8×106 cells/ml.
Equal volumes of target and effector cell suspension were mixed and 50 μl of this suspension transferred to each well of a 96 well round bottom plate, 50 μl of EpCAM bispecific antibody serial dilution or RPMI complete medium as a negative control was added. Plates were incubated for 16 to 20 hrs at 37° C., 5% CO2 in a humidified incubator. 50 μl propidium iodide was added to a final concentration of 1 μg/ml and incubated 15 min at room temperature. Samples were analysed by flow cytometry (FACSCalibur, Becton Dickinson). 2×104 events were counted.
Target cells were identified by their PKH26 fluorescent label and cytotoxicity within this population was subsequently determined. Viable cells were separated from dead cells by propidium iodide staining and the percentage of dead target cells was used as a measure for cytotoxicity. Mean values were plotted against the concentration of the bispecific antibody on a logarithmic scale, resulting in a dose response curve (FIG. 11B). The corresponding EC50 values were obtained after nonlinear fitting of data with the GraphPad Prism software.
The cytotoxic activity of constructs having the NXD motif (SEQ ID NO.:36, 44, 2 and 18) was compared with conventional constructs M79xanti-CD3 and HD70-xanti-CD3 (FIG. 11B). A sequence alignment of the CDR3 regions of the VH chains of 3-1, 5-10, 4-7, 3-5 and 4-1 with M79, HD70 and 3B10 is shown in FIG. 11A. Only 3-1, 5-10, 4-7, 3-5 and 4-1 have the NXD motif and furthermore, the lengths of the CDR3 regions differ. As can be seen from FIG. 11A, 3-1, 4-1 and 5-10 have a CDR-H3 region of 10 amino acids, 3-5 and 4-7 have 14 amino acids whereas the prior art M79 has 8 amino acids, 3B10 has 6 amino acids and HD70 has 18 amino acids.
SEQ ID NO.: 36, 44, 2 and 18 showed a clearly better bioactivity compared to the conventional M79 and HD70 constructs (2250 pg/ml and less compared to 71460 and 11327 pg/ml of the prior art constructs, respectively) demonstrating the advantageous effects of the constructs of the invention.

## Claims

1. A bispecific single chain antibody construct, whereby said construct comprises at least two domains, whereby one of said domains binds to human EpCAM antigen and a second domain binds to human CD3 antigen, wherein said binding domain specific for EpCAM comprises at least one CDR-H3 region comprising the amino acid sequence NXD preferably in position 102 to 104 of SEQ ID NOs: 80, 88 and 96, or preferably in position 106 to 108 of SEQ ID NOS: 84 and 92, wherein X is an aromatic amino acid and
wherein the VH chain domain specific for human EpCAM antigen is selected from the group consisting of:
(a) an amino acid sequence as shown in any of SEQ ID NO: 80, SEQ ID NO: 84,
SEQ ID NO: 88, SEQ ID NO: 92 and SEQ ID NO: 96;
(b) an amino acid sequence encoded by a nucleic acid sequence as shown in SEQ ID NO: 79, SEQ ID NO: 83, SEQ ID NO: 87, SEQ ID NO: 91 and SEQ ID NO: 95; and
(c) an amino acid sequence encoded by a nucleic acid sequence which is degenerate as a result of the genetic code to a nucleotide sequence of (b); and
wherein the VL chain domain specific for human EpCAM antigen is selected from the group consisting of:
(a) an amino acid sequence as shown in any of SEQ ID NO: 82, SEQ ID NO: 86, SEQ ID NO: 90, SEQ ID NO: 94 and SEQ ID NO: 98;
(b) an amino acid sequence encoded by a nucleic acid sequence as shown in SEQ ID NO: 81, SEQ ID NO: 85, SEQ ID NO: 89, SEQ ID NO: 93 and SEQ ID NO: 97; and
(c) an amino acid sequence encoded by a nucleic acid sequence which is degenerate as a result of the genetic code to a nucleotide sequence of (b).

2. The bispecific single chain antibody construct of claim 1, wherein X is W or Y.

3. The bispecific single chain antibody construct of claim 1, wherein the CDR-H3 comprises at least 9 amino acid residues.

4. The bispecific single chain antibody construct of claim 1, wherein said binding domain specific for EpCAM has a KD value of more than 5×10−9 M.

5. The bispecific single chain antibody construct of claim 1, wherein said binding domain specific for EpCAM has a KD value in a range between I×10−7 and 5×10−9 M and said binding domain specific for CD3 has a KD value in a range between 1×10−6 and 5×10−9 M.

6. The bispecific single chain antibody construct of claim 1, wherein said binding domain specific for CD3 has a KD value of more than 10−7 M.

7. The bispecific single chain antibody construct of claim 1, wherein the CDR-H3 region comprises at least 14 amino acids.

8. The bispecific single chain antibody construct of claim 1, wherein the binding domain specific for the CD3 antigen is derived from the OKT3D antibody.

9. The bispecific single chain antibody construct of claim 1, wherein said bispecific single chain antibody construct comprises an amino add sequence selected from the group consisting of
(a) an amino acid sequence as shown in any of SEQ ID NOs: 2,4, 8,10, 12,14, 16,18, 20,30, 36, 39, 42, 46, 48, 50,52, 54,56, 58 and 60:
(b) an amino acid sequence encoded by a nucleic acid sequence as shown in any of SEQ ID NOs: 1,3, 7,9, 11,13, 15,17, 19,29, 35, 38,41, 43, 45, 47,49, 51,53, 55,57 and 59; and
(c) an amino acid sequence encoded by a nucleic acid sequence which is degenerate as a result of the genetic code to a nucleotide sequence of (b).

10. A pharmaceutical composition comprising the bispecific single chain antibody construct of claim 1.

11. A pharmaceutical composition of claim 10, further comprising a proteinaceous compound capable of providing an activation signal for immune effector cells.

12. The pharmaceutical composition of claim 11, wherein the pharmaceutical composition is thermostable at 237° C.

13. A kit comprising a bispecific single chain antibody construct of claim 1.